Yannis Schumann
| Snapshot Date: 2026-02-27 13:40 -0500 (Fri, 27 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-28 11:34 -0500 (Sat, 28 Feb 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" | 4877 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4570 |
| 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 169/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.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: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-27 21:33:47 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 21:35:15 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.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 ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.417 1.562 16.835
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-27 21:34:38.150077 INFO::Formatting Data.
2026-02-27 21:34:38.15133 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:38.162059 INFO::Removing potential empty rows and columns
2026-02-27 21:34:38.402079 INFO::Found 0 missing values.
2026-02-27 21:34:38.405464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:38.406116 INFO::Done
2026-02-27 21:34:38.406687 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:38.417946 INFO::Starting hierarchical adjustment
2026-02-27 21:34:38.418814 INFO::Found 3 batches.
2026-02-27 21:34:38.419385 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:38.420487 INFO::Using default BPPARAM
2026-02-27 21:34:38.421028 INFO::Processing subtree level 1
2026-02-27 21:34:38.519454 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:34:38.521168 INFO::Done
2026-02-27 21:34:38.521842 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:38.524395 INFO::ASW Batch was 0.0258843362311531 prior to batch effect correction and is now 0.0258843362311531 .
2026-02-27 21:34:38.525463 INFO::Total function execution time is 0.375991821289062 s and adjustment time is 0.102516889572144 s ( 27.27 )
2026-02-27 21:34:38.539294 INFO::Formatting Data.
2026-02-27 21:34:38.540083 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:38.54102 INFO::Removing potential empty rows and columns
2026-02-27 21:34:38.542215 INFO::Found 0 missing values.
2026-02-27 21:34:38.543216 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-27 21:34:38.55438 INFO::Formatting Data.
2026-02-27 21:34:38.555169 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:38.556078 INFO::Removing potential empty rows and columns
2026-02-27 21:34:38.557163 INFO::Found 0 missing values.
2026-02-27 21:34:38.558108 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-27 21:34:38.574825 INFO::Formatting Data.
2026-02-27 21:34:38.575636 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:38.576535 INFO::Removing potential empty rows and columns
2026-02-27 21:34:38.577646 INFO::Found 0 missing values.
2026-02-27 21:34:38.578596 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-27 21:34:38.583229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:38.583827 INFO::Done
2026-02-27 21:34:38.584394 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:38.586516 INFO::Starting hierarchical adjustment
2026-02-27 21:34:38.587231 INFO::Found 2 batches.
2026-02-27 21:34:38.587785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:38.588448 INFO::Using default BPPARAM
2026-02-27 21:34:38.588968 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:38.589919 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:34:38.611259 INFO::Done
2026-02-27 21:34:38.61201 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:38.614323 INFO::ASW Batch was 0.0623919934324277 prior to batch effect correction and is now -0.122090574259933 .
2026-02-27 21:34:38.615165 INFO::Total function execution time is 0.0404086112976074 s and adjustment time is 0.0241320133209229 s ( 59.72 )
2026-02-27 21:34:38.618112 INFO::Formatting Data.
2026-02-27 21:34:38.618769 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:38.627752 INFO::Formatting Data.
2026-02-27 21:34:38.628572 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:38.629534 INFO::Removing potential empty rows and columns
2026-02-27 21:34:38.630624 INFO::Found 0 missing values.
2026-02-27 21:34:38.6337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:38.634264 INFO::Done
2026-02-27 21:34:38.634807 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:38.636934 INFO::Starting hierarchical adjustment
2026-02-27 21:34:38.637675 INFO::Found 2 batches.
2026-02-27 21:34:38.638219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:38.638866 INFO::Using default BPPARAM
2026-02-27 21:34:38.63941 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:38.640362 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:38.677822 INFO::Done
2026-02-27 21:34:38.678503 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:38.680422 INFO::ASW Batch was -0.0209864954719546 prior to batch effect correction and is now -0.126093278208551 .
2026-02-27 21:34:38.681199 INFO::Total function execution time is 0.0535008907318115 s and adjustment time is 0.0402758121490479 s ( 75.28 )
2026-02-27 21:34:38.682196 INFO::Formatting Data.
2026-02-27 21:34:38.682783 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:38.683596 INFO::Removing potential empty rows and columns
2026-02-27 21:34:38.684542 INFO::Found 0 missing values.
2026-02-27 21:34:38.6871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:38.687625 INFO::Done
2026-02-27 21:34:38.688104 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:38.689925 INFO::Starting hierarchical adjustment
2026-02-27 21:34:38.690583 INFO::Found 2 batches.
2026-02-27 21:34:38.691073 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:38.691665 INFO::Using default BPPARAM
2026-02-27 21:34:38.692164 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:38.693063 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:38.707337 INFO::Done
2026-02-27 21:34:38.707999 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:38.709937 INFO::ASW Batch was -0.0209864954719546 prior to batch effect correction and is now -0.126093278208551 .
2026-02-27 21:34:38.71071 INFO::Total function execution time is 0.0285155773162842 s and adjustment time is 0.0168807506561279 s ( 59.2 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-27 21:34:41.398714 INFO::Formatting Data.
2026-02-27 21:34:41.399381 INFO::Recognized SummarizedExperiment
2026-02-27 21:34:41.399859 INFO::Typecasting input to dataframe.
2026-02-27 21:34:41.427863 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:41.429017 INFO::Removing potential empty rows and columns
2026-02-27 21:34:41.432902 INFO::Found 0 missing values.
2026-02-27 21:34:41.440245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:41.440848 INFO::Done
2026-02-27 21:34:41.441365 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:41.444887 INFO::Starting hierarchical adjustment
2026-02-27 21:34:41.445605 INFO::Found 2 batches.
2026-02-27 21:34:41.446133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:41.447217 INFO::Using default BPPARAM
2026-02-27 21:34:41.447758 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:41.448727 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:34:41.504107 INFO::Done
2026-02-27 21:34:41.504819 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:41.508311 INFO::ASW Batch was 0.00369511142304629 prior to batch effect correction and is now -0.0858563566977344 .
2026-02-27 21:34:41.509145 INFO::Total function execution time is 0.110692977905273 s and adjustment time is 0.0586440563201904 s ( 52.98 )
Warning: stack imbalance in '{', 73 then 75
2026-02-27 21:34:41.527264 INFO::Formatting Data.
2026-02-27 21:34:41.527992 INFO::Recognized SummarizedExperiment
2026-02-27 21:34:41.528541 INFO::Typecasting input to dataframe.
2026-02-27 21:34:41.537579 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:41.538668 INFO::Removing potential empty rows and columns
2026-02-27 21:34:41.54252 INFO::Found 0 missing values.
2026-02-27 21:34:41.549881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:41.550458 INFO::Done
2026-02-27 21:34:41.550974 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:41.554447 INFO::Starting hierarchical adjustment
2026-02-27 21:34:41.555146 INFO::Found 2 batches.
2026-02-27 21:34:41.555672 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:41.556278 INFO::Using default BPPARAM
2026-02-27 21:34:41.556817 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:41.557775 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:34:41.583673 INFO::Done
2026-02-27 21:34:41.584417 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:41.588048 INFO::ASW Batch was -0.00444829377648 prior to batch effect correction and is now -0.00444829377648 .
2026-02-27 21:34:41.588923 INFO::Total function execution time is 0.0616400241851807 s and adjustment time is 0.0286228656768799 s ( 46.44 )
2026-02-27 21:34:41.607505 INFO::Formatting Data.
2026-02-27 21:34:41.608263 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:41.609192 INFO::Removing potential empty rows and columns
2026-02-27 21:34:41.610236 INFO::Found 0 missing values.
2026-02-27 21:34:41.613197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:41.613732 INFO::Done
2026-02-27 21:34:41.61425 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:41.616253 INFO::Starting hierarchical adjustment
2026-02-27 21:34:41.616953 INFO::Found 3 batches.
2026-02-27 21:34:41.617483 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:41.618082 INFO::Using default BPPARAM
2026-02-27 21:34:41.618619 INFO::Processing subtree level 1
2026-02-27 21:34:41.752629 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:34:41.75468 INFO::Done
2026-02-27 21:34:41.755409 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:41.758155 INFO::ASW Batch was -0.0439908805294612 prior to batch effect correction and is now -0.156466309383254 .
2026-02-27 21:34:41.759133 INFO::Total function execution time is 0.151633977890015 s and adjustment time is 0.137834310531616 s ( 90.9 )
2026-02-27 21:34:41.773843 INFO::Skipping initial DF formatting
2026-02-27 21:34:41.774582 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:41.778774 INFO::Starting hierarchical adjustment
2026-02-27 21:34:41.779591 INFO::Found 5 batches.
2026-02-27 21:34:41.780132 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:41.780779 INFO::Using default BPPARAM
2026-02-27 21:34:41.781319 INFO::Processing subtree level 1
2026-02-27 21:34:42.008345 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.009953 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:34:42.029901 INFO::Done
2026-02-27 21:34:42.030644 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.034889 INFO::ASW Batch was 0.526305461269977 prior to batch effect correction and is now 0.526305461269977 .
2026-02-27 21:34:42.035511 INFO::ASW Label was 0.362933239644155 prior to batch effect correction and is now 0.362933239644155 .
2026-02-27 21:34:42.036364 INFO::Total function execution time is 0.262603998184204 s and adjustment time is 0.250484466552734 s ( 95.38 )
2026-02-27 21:34:42.096113 INFO::Formatting Data.
2026-02-27 21:34:42.096928 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.097833 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.098782 INFO::Found 0 missing values.
2026-02-27 21:34:42.102757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.103281 INFO::Done
2026-02-27 21:34:42.103844 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.106861 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.10757 INFO::Found 5 batches.
2026-02-27 21:34:42.108086 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.108709 INFO::Using default BPPARAM
2026-02-27 21:34:42.109246 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.237918 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.239484 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.256135 INFO::Done
2026-02-27 21:34:42.256876 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.260355 INFO::ASW Batch was 0.359453900723199 prior to batch effect correction and is now -0.107811774897838 .
2026-02-27 21:34:42.261028 INFO::ASW Label was 0.366052317237441 prior to batch effect correction and is now 0.809432556831344 .
2026-02-27 21:34:42.261898 INFO::Total function execution time is 0.165865421295166 s and adjustment time is 0.148680925369263 s ( 89.64 )
2026-02-27 21:34:42.26278 INFO::Formatting Data.
2026-02-27 21:34:42.263453 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.264359 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.265438 INFO::Found 0 missing values.
2026-02-27 21:34:42.269643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.270179 INFO::Done
2026-02-27 21:34:42.270745 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.273789 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.274496 INFO::Found 5 batches.
2026-02-27 21:34:42.275043 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.275691 INFO::Using default BPPARAM
2026-02-27 21:34:42.276207 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.40697 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.409409 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.429938 INFO::Done
2026-02-27 21:34:42.430771 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.434303 INFO::ASW Batch was 0.359453900723199 prior to batch effect correction and is now -0.107811774897838 .
2026-02-27 21:34:42.434951 INFO::ASW Label was 0.366052317237441 prior to batch effect correction and is now 0.809432556831344 .
2026-02-27 21:34:42.435865 INFO::Total function execution time is 0.173067569732666 s and adjustment time is 0.155545234680176 s ( 89.88 )
2026-02-27 21:34:42.450328 INFO::Formatting Data.
2026-02-27 21:34:42.451113 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.452088 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.45316 INFO::Found 0 missing values.
2026-02-27 21:34:42.457587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.45818 INFO::Done
2026-02-27 21:34:42.45876 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.461911 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.462677 INFO::Found 5 batches.
2026-02-27 21:34:42.46324 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.463908 INFO::Using default BPPARAM
2026-02-27 21:34:42.464489 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.586321 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.588006 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.603644 INFO::Done
2026-02-27 21:34:42.604326 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.607547 INFO::ASW Batch was 0.613908022567363 prior to batch effect correction and is now -0.0274087650410216 .
2026-02-27 21:34:42.608135 INFO::ASW Label was 0.259744253775589 prior to batch effect correction and is now 0.741089408282934 .
2026-02-27 21:34:42.608939 INFO::Total function execution time is 0.158685207366943 s and adjustment time is 0.141113042831421 s ( 88.93 )
2026-02-27 21:34:42.609772 INFO::Formatting Data.
2026-02-27 21:34:42.610431 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.611288 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.612329 INFO::Found 0 missing values.
2026-02-27 21:34:42.61636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.616916 INFO::Done
2026-02-27 21:34:42.617443 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.62041 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.621193 INFO::Found 5 batches.
2026-02-27 21:34:42.621742 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.62235 INFO::Using default BPPARAM
2026-02-27 21:34:42.622887 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.749374 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.751249 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.780851 INFO::Done
2026-02-27 21:34:42.782191 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.786541 INFO::ASW Batch was 0.613908022567363 prior to batch effect correction and is now -0.0274087650410216 .
2026-02-27 21:34:42.787422 INFO::ASW Label was 0.259744253775589 prior to batch effect correction and is now 0.741089408282934 .
2026-02-27 21:34:42.788543 INFO::Total function execution time is 0.178704738616943 s and adjustment time is 0.159600496292114 s ( 89.31 )
2026-02-27 21:34:42.804336 INFO::Formatting Data.
2026-02-27 21:34:42.805233 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.80632 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.807532 INFO::Found 0 missing values.
2026-02-27 21:34:42.810542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.81115 INFO::Done
2026-02-27 21:34:42.811735 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.814855 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.815642 INFO::Found 2 batches.
2026-02-27 21:34:42.816207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.816896 INFO::Using default BPPARAM
2026-02-27 21:34:42.817521 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.818537 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.834847 INFO::Done
2026-02-27 21:34:42.835502 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.838363 INFO::ASW Batch was 0.537911717286987 prior to batch effect correction and is now 0.0889074887012072 .
2026-02-27 21:34:42.838946 INFO::ASW Label was 0.534558172970678 prior to batch effect correction and is now 0.857096361370367 .
2026-02-27 21:34:42.83975 INFO::Total function execution time is 0.0355222225189209 s and adjustment time is 0.0193729400634766 s ( 54.54 )
2026-02-27 21:34:42.840558 INFO::Formatting Data.
2026-02-27 21:34:42.841179 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.842028 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.843008 INFO::Found 0 missing values.
2026-02-27 21:34:42.845616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.846185 INFO::Done
2026-02-27 21:34:42.846723 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.849528 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.850221 INFO::Found 2 batches.
2026-02-27 21:34:42.850757 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.851346 INFO::Using default BPPARAM
2026-02-27 21:34:42.8519 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.852802 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:34:42.867155 INFO::Done
2026-02-27 21:34:42.867783 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.870646 INFO::ASW Batch was 0.537911717286987 prior to batch effect correction and is now 0.0889074887012072 .
2026-02-27 21:34:42.87124 INFO::ASW Label was 0.534558172970678 prior to batch effect correction and is now 0.857096361370367 .
2026-02-27 21:34:42.87203 INFO::Total function execution time is 0.0315060615539551 s and adjustment time is 0.017066478729248 s ( 54.17 )
2026-02-27 21:34:42.883364 INFO::Formatting Data.
2026-02-27 21:34:42.884141 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.885103 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.886085 INFO::Found 0 missing values.
2026-02-27 21:34:42.888341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.888907 INFO::Done
2026-02-27 21:34:42.88947 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.891564 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.89233 INFO::Found 2 batches.
2026-02-27 21:34:42.892904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.893552 INFO::Using default BPPARAM
2026-02-27 21:34:42.894132 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.895104 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:34:42.927391 INFO::Done
2026-02-27 21:34:42.928084 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.930032 INFO::ASW Batch was 0.0188505557415073 prior to batch effect correction and is now -0.111507968867257 .
2026-02-27 21:34:42.930838 INFO::Total function execution time is 0.0475480556488037 s and adjustment time is 0.0351955890655518 s ( 74.02 )
2026-02-27 21:34:42.942495 INFO::Formatting Data.
2026-02-27 21:34:42.943262 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.944165 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.945201 INFO::Found 0 missing values.
2026-02-27 21:34:42.946401 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-27 21:34:42.95103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.951583 INFO::Done
2026-02-27 21:34:42.952091 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.954986 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.955681 INFO::Found 2 batches.
2026-02-27 21:34:42.956199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.95683 INFO::Using default BPPARAM
2026-02-27 21:34:42.957342 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.958255 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:34:42.974144 INFO::Done
2026-02-27 21:34:42.974842 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:42.977751 INFO::ASW Batch was 0.781509867692609 prior to batch effect correction and is now 0.0491064448775536 .
2026-02-27 21:34:42.978352 INFO::ASW Label was 0.185015997990985 prior to batch effect correction and is now 0.83430520531811 .
2026-02-27 21:34:42.979178 INFO::Total function execution time is 0.0367734432220459 s and adjustment time is 0.0185847282409668 s ( 50.54 )
2026-02-27 21:34:42.97999 INFO::Formatting Data.
2026-02-27 21:34:42.980614 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:42.981523 INFO::Removing potential empty rows and columns
2026-02-27 21:34:42.982491 INFO::Found 0 missing values.
2026-02-27 21:34:42.983405 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-27 21:34:42.987905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:42.988484 INFO::Done
2026-02-27 21:34:42.989 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:42.991876 INFO::Starting hierarchical adjustment
2026-02-27 21:34:42.992574 INFO::Found 2 batches.
2026-02-27 21:34:42.993123 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:42.993736 INFO::Using default BPPARAM
2026-02-27 21:34:42.99425 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:42.995189 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:34:43.011307 INFO::Done
2026-02-27 21:34:43.012021 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:43.014963 INFO::ASW Batch was 0.781509867692609 prior to batch effect correction and is now 0.0491064448775536 .
2026-02-27 21:34:43.015601 INFO::ASW Label was 0.185015997990985 prior to batch effect correction and is now 0.83430520531811 .
2026-02-27 21:34:43.016401 INFO::Total function execution time is 0.0364196300506592 s and adjustment time is 0.0188584327697754 s ( 51.78 )
2026-02-27 21:34:43.229078 INFO::Formatting Data.
2026-02-27 21:34:43.229923 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:43.230882 INFO::Removing potential empty rows and columns
2026-02-27 21:34:43.231979 INFO::Found 0 missing values.
2026-02-27 21:34:43.235129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:43.235701 INFO::Done
2026-02-27 21:34:43.236234 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:43.238329 INFO::Starting hierarchical adjustment
2026-02-27 21:34:43.239046 INFO::Found 3 batches.
2026-02-27 21:34:43.239595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:43.240226 INFO::Using default BPPARAM
2026-02-27 21:34:43.240782 INFO::Processing subtree level 1
2026-02-27 21:34:43.339118 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:34:43.340992 INFO::Done
2026-02-27 21:34:43.341666 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:43.344167 INFO::ASW Batch was 0.0241844261413209 prior to batch effect correction and is now 0.0241844261413209 .
2026-02-27 21:34:43.34514 INFO::Total function execution time is 0.116117715835571 s and adjustment time is 0.102065324783325 s ( 87.9 )
2026-02-27 21:34:43.346229 INFO::Formatting Data.
2026-02-27 21:34:43.346911 INFO::Typecasting input to dataframe.
2026-02-27 21:34:43.347689 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:43.348625 INFO::Removing potential empty rows and columns
2026-02-27 21:34:43.349722 INFO::Found 0 missing values.
2026-02-27 21:34:43.352878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:43.353473 INFO::Done
2026-02-27 21:34:43.354021 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:43.356102 INFO::Starting hierarchical adjustment
2026-02-27 21:34:43.356833 INFO::Found 3 batches.
2026-02-27 21:34:43.357364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:43.357998 INFO::Using default BPPARAM
2026-02-27 21:34:43.358603 INFO::Processing subtree level 1
2026-02-27 21:34:43.442527 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:34:43.444339 INFO::Done
2026-02-27 21:34:43.445025 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:43.44749 INFO::ASW Batch was 0.0241844261413209 prior to batch effect correction and is now 0.0241844261413209 .
2026-02-27 21:34:43.448432 INFO::Total function execution time is 0.102174043655396 s and adjustment time is 0.0876297950744629 s ( 85.77 )
2026-02-27 21:34:43.461364 INFO::Formatting Data.
2026-02-27 21:34:43.462169 INFO::Typecasting input to dataframe.
2026-02-27 21:34:43.463051 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:43.463974 INFO::Removing potential empty rows and columns
2026-02-27 21:34:43.465079 INFO::Found 0 missing values.
2026-02-27 21:34:43.468116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:43.468668 INFO::Done
2026-02-27 21:34:43.469207 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:43.471242 INFO::Starting hierarchical adjustment
2026-02-27 21:34:43.471961 INFO::Found 3 batches.
2026-02-27 21:34:43.472502 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:43.473145 INFO::Using default BPPARAM
2026-02-27 21:34:43.473693 INFO::Processing subtree level 1
2026-02-27 21:34:43.557888 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:34:43.559766 INFO::Done
2026-02-27 21:34:43.560483 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:43.563042 INFO::ASW Batch was -0.0315698211932854 prior to batch effect correction and is now -0.0315698211932854 .
2026-02-27 21:34:43.564012 INFO::Total function execution time is 0.102702856063843 s and adjustment time is 0.0879356861114502 s ( 85.62 )
2026-02-27 21:34:43.70417 INFO::Formatting Data.
2026-02-27 21:34:43.70498 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:43.706118 INFO::Removing potential empty rows and columns
2026-02-27 21:34:43.709001 INFO::Found 1000 missing values.
2026-02-27 21:34:43.728734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:43.729498 INFO::Done
2026-02-27 21:34:43.730059 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:43.735518 INFO::Starting hierarchical adjustment
2026-02-27 21:34:43.73627 INFO::Found 10 batches.
2026-02-27 21:34:43.736838 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:43.737515 INFO::Using default BPPARAM
2026-02-27 21:34:43.738058 INFO::Processing subtree level 1
2026-02-27 21:34:43.871286 INFO::Processing subtree level 2
2026-02-27 21:34:44.010108 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:34:44.01212 INFO::Done
2026-02-27 21:34:44.012842 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:44.018614 INFO::ASW Batch was 0.482908607214868 prior to batch effect correction and is now 0.482908607214868 .
2026-02-27 21:34:44.01935 INFO::ASW Label was 0.336416348381229 prior to batch effect correction and is now 0.336416348381229 .
2026-02-27 21:34:44.020329 INFO::Total function execution time is 0.316202163696289 s and adjustment time is 0.275976896286011 s ( 87.28 )
2026-02-27 21:34:44.021234 INFO::Formatting Data.
2026-02-27 21:34:44.021931 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:44.023226 INFO::Removing potential empty rows and columns
2026-02-27 21:34:44.026292 INFO::Found 1000 missing values.
2026-02-27 21:34:44.04748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:44.048267 INFO::Done
2026-02-27 21:34:44.048881 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:44.054635 INFO::Starting hierarchical adjustment
2026-02-27 21:34:44.055444 INFO::Found 10 batches.
2026-02-27 21:34:45.050472 INFO::Set up parallel execution backend with 2 workers
2026-02-27 21:34:45.052649 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-27 21:34:46.134688 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:34:46.136728 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:34:46.153863 INFO::Done
2026-02-27 21:34:46.154538 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:46.158923 INFO::ASW Batch was 0.482908607214868 prior to batch effect correction and is now 0.482908607214868 .
2026-02-27 21:34:46.159524 INFO::ASW Label was 0.336416348381229 prior to batch effect correction and is now 0.336416348381229 .
2026-02-27 21:34:46.160231 INFO::Total function execution time is 2.13905096054077 s and adjustment time is 2.09856677055359 s ( 98.11 )
2026-02-27 21:34:46.325751 INFO::Formatting Data.
2026-02-27 21:34:46.326737 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.327809 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.329076 INFO::Found 0 missing values.
2026-02-27 21:34:46.333513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.334162 INFO::Done
2026-02-27 21:34:46.334777 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:34:46.338107 INFO::Starting hierarchical adjustment
2026-02-27 21:34:46.338926 INFO::Found 3 batches.
2026-02-27 21:34:46.339531 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:34:46.340259 INFO::Using default BPPARAM
2026-02-27 21:34:46.340862 INFO::Processing subtree level 1
2026-02-27 21:34:46.464235 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:34:46.466279 INFO::Done
2026-02-27 21:34:46.467084 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:34:46.470795 INFO::ASW Batch was 0.160817564889556 prior to batch effect correction and is now -0.142927319646841 .
2026-02-27 21:34:46.471495 INFO::ASW Label was -0.199066445624246 prior to batch effect correction and is now -0.0544981238333729 .
2026-02-27 21:34:46.472533 INFO::Total function execution time is 0.146848678588867 s and adjustment time is 0.127485990524292 s ( 86.81 )
2026-02-27 21:34:46.597642 INFO::Formatting Data.
2026-02-27 21:34:46.598537 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.599493 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.601608 INFO::Found 2 missing values.
2026-02-27 21:34:46.604782 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.605406 INFO::Done
2026-02-27 21:34:46.635001 INFO::Found NA in Reference column
2026-02-27 21:34:46.645273 INFO::Require at least two references per batch.
2026-02-27 21:34:46.667801 INFO::Formatting Data.
2026-02-27 21:34:46.668797 INFO::Recognized SummarizedExperiment
2026-02-27 21:34:46.669413 INFO::Typecasting input to dataframe.
2026-02-27 21:34:46.680337 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.681665 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.685463 INFO::Found 0 missing values.
2026-02-27 21:34:46.692628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.693271 INFO::Done
2026-02-27 21:34:46.710691 INFO::Formatting Data.
2026-02-27 21:34:46.711636 INFO::Recognized SummarizedExperiment
2026-02-27 21:34:46.712205 INFO::Typecasting input to dataframe.
2026-02-27 21:34:46.730189 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.731586 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.735442 INFO::Found 0 missing values.
2026-02-27 21:34:46.746909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.747673 INFO::Done
2026-02-27 21:34:46.764104 INFO::Formatting Data.
2026-02-27 21:34:46.764966 INFO::Recognized SummarizedExperiment
2026-02-27 21:34:46.765521 INFO::Typecasting input to dataframe.
2026-02-27 21:34:46.782028 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.783079 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.784184 INFO::Found 0 missing values.
2026-02-27 21:34:46.785082 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-27 21:34:46.789387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.789916 INFO::Done
2026-02-27 21:34:46.800673 INFO::Formatting Data.
2026-02-27 21:34:46.801452 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.802329 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.803384 INFO::Found 0 missing values.
2026-02-27 21:34:46.806271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.80683 INFO::Done
2026-02-27 21:34:46.819655 INFO::Formatting Data.
2026-02-27 21:34:46.820595 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.821558 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.822717 INFO::Found 0 missing values.
2026-02-27 21:34:46.825657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.826174 INFO::Done
2026-02-27 21:34:46.856467 INFO::Formatting Data.
2026-02-27 21:34:46.857326 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.858395 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.859567 INFO::Found 1 missing values.
2026-02-27 21:34:46.862138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.862701 INFO::Done
2026-02-27 21:34:46.881568 INFO::Formatting Data.
2026-02-27 21:34:46.88245 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.883335 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.884322 INFO::Found 2 missing values.
2026-02-27 21:34:46.885234 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-27 21:34:46.887719 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.888234 INFO::Done
2026-02-27 21:34:46.897951 INFO::Formatting Data.
2026-02-27 21:34:46.898689 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.899549 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.900491 INFO::Found 2 missing values.
2026-02-27 21:34:46.902046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.902619 INFO::Done
2026-02-27 21:34:46.91273 INFO::Formatting Data.
2026-02-27 21:34:46.913491 INFO::Typecasting input to dataframe.
2026-02-27 21:34:46.914268 INFO::Replacing NaNs with NAs.
2026-02-27 21:34:46.915116 INFO::Removing potential empty rows and columns
2026-02-27 21:34:46.916111 INFO::Found 0 missing values.
2026-02-27 21:34:46.919019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:34:46.919552 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.422 3.285 19.467
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.417 | 1.562 | 16.835 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.000 | 0.013 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.010 | 0.001 | 0.012 | |