Yannis Schumann
| Snapshot Date: 2026-03-02 13:40 -0500 (Mon, 02 Mar 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 2026-03-03 11:34 -0500 (Tue, 03 Mar 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: 2026-03-02 21:36:53 -0500 (Mon, 02 Mar 2026) |
| EndedAt: 2026-03-02 21:38:25 -0500 (Mon, 02 Mar 2026) |
| EllapsedTime: 92.1 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 26.489 1.658 19.302
* 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")
2026-03-02 21:37:46.770125 INFO::Formatting Data.
2026-03-02 21:37:46.771328 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:46.782006 INFO::Removing potential empty rows and columns
2026-03-02 21:37:47.011862 INFO::Found 0 missing values.
2026-03-02 21:37:47.015105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:47.015741 INFO::Done
2026-03-02 21:37:47.016268 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:47.027161 INFO::Starting hierarchical adjustment
2026-03-02 21:37:47.028062 INFO::Found 3 batches.
2026-03-02 21:37:47.028632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:47.029711 INFO::Using default BPPARAM
2026-03-02 21:37:47.03024 INFO::Processing subtree level 1
2026-03-02 21:37:47.124614 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:37:47.126445 INFO::Done
2026-03-02 21:37:47.127085 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:47.129529 INFO::ASW Batch was -0.0845954244814825 prior to batch effect correction and is now -0.0845954244814825 .
2026-03-02 21:37:47.130549 INFO::Total function execution time is 0.36100959777832 s and adjustment time is 0.0985367298126221 s ( 27.29 )
2026-03-02 21:37:47.144404 INFO::Formatting Data.
2026-03-02 21:37:47.145184 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:47.146129 INFO::Removing potential empty rows and columns
2026-03-02 21:37:47.147302 INFO::Found 0 missing values.
2026-03-02 21:37:47.148279 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.
2026-03-02 21:37:47.15905 INFO::Formatting Data.
2026-03-02 21:37:47.159826 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:47.160742 INFO::Removing potential empty rows and columns
2026-03-02 21:37:47.161804 INFO::Found 0 missing values.
2026-03-02 21:37:47.162714 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.
2026-03-02 21:37:47.178338 INFO::Formatting Data.
2026-03-02 21:37:47.179095 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:47.179949 INFO::Removing potential empty rows and columns
2026-03-02 21:37:47.180974 INFO::Found 0 missing values.
2026-03-02 21:37:47.181859 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.
2026-03-02 21:37:47.186261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:47.186815 INFO::Done
2026-03-02 21:37:47.18734 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:47.189382 INFO::Starting hierarchical adjustment
2026-03-02 21:37:47.190069 INFO::Found 2 batches.
2026-03-02 21:37:47.190606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:47.19122 INFO::Using default BPPARAM
2026-03-02 21:37:47.191748 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:47.192653 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:37:47.213054 INFO::Done
2026-03-02 21:37:47.213758 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:47.215968 INFO::ASW Batch was 0.0350487928460242 prior to batch effect correction and is now -0.0709973134023385 .
2026-03-02 21:37:47.216788 INFO::Total function execution time is 0.0385065078735352 s and adjustment time is 0.0230937004089355 s ( 59.97 )
2026-03-02 21:37:47.219585 INFO::Formatting Data.
2026-03-02 21:37:47.220224 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:47.22909 INFO::Formatting Data.
2026-03-02 21:37:47.229808 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:47.230731 INFO::Removing potential empty rows and columns
2026-03-02 21:37:47.231816 INFO::Found 0 missing values.
2026-03-02 21:37:47.234765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:47.235319 INFO::Done
2026-03-02 21:37:47.235862 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:47.237878 INFO::Starting hierarchical adjustment
2026-03-02 21:37:47.238601 INFO::Found 2 batches.
2026-03-02 21:37:47.239137 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:47.239786 INFO::Using default BPPARAM
2026-03-02 21:37:47.24032 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:47.241247 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:37:47.275943 INFO::Done
2026-03-02 21:37:47.276587 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:47.278438 INFO::ASW Batch was -0.00431077767630881 prior to batch effect correction and is now -0.11374460542451 .
2026-03-02 21:37:47.27919 INFO::Total function execution time is 0.0501515865325928 s and adjustment time is 0.0374829769134521 s ( 74.74 )
2026-03-02 21:37:47.280135 INFO::Formatting Data.
2026-03-02 21:37:47.280699 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:47.281483 INFO::Removing potential empty rows and columns
2026-03-02 21:37:47.282414 INFO::Found 0 missing values.
2026-03-02 21:37:47.284962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:47.285485 INFO::Done
2026-03-02 21:37:47.285971 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:47.287782 INFO::Starting hierarchical adjustment
2026-03-02 21:37:47.288436 INFO::Found 2 batches.
2026-03-02 21:37:47.288925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:47.289486 INFO::Using default BPPARAM
2026-03-02 21:37:47.289969 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:47.2908 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:37:47.30452 INFO::Done
2026-03-02 21:37:47.305164 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:47.307075 INFO::ASW Batch was -0.00431077767630881 prior to batch effect correction and is now -0.11374460542451 .
2026-03-02 21:37:47.307821 INFO::Total function execution time is 0.0276763439178467 s and adjustment time is 0.0162022113800049 s ( 58.54 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-02 21:37:50.005023 INFO::Formatting Data.
2026-03-02 21:37:50.005686 INFO::Recognized SummarizedExperiment
2026-03-02 21:37:50.006164 INFO::Typecasting input to dataframe.
2026-03-02 21:37:50.03513 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:50.036451 INFO::Removing potential empty rows and columns
2026-03-02 21:37:50.040813 INFO::Found 0 missing values.
2026-03-02 21:37:50.048563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:50.049318 INFO::Done
2026-03-02 21:37:50.049905 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:50.053594 INFO::Starting hierarchical adjustment
2026-03-02 21:37:50.054358 INFO::Found 2 batches.
2026-03-02 21:37:50.054904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:50.056057 INFO::Using default BPPARAM
2026-03-02 21:37:50.056613 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:50.057632 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:37:50.115398 INFO::Done
2026-03-02 21:37:50.116108 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:50.119709 INFO::ASW Batch was -0.0106108570560585 prior to batch effect correction and is now -0.0929933902086752 .
2026-03-02 21:37:50.120569 INFO::Total function execution time is 0.115800380706787 s and adjustment time is 0.0611562728881836 s ( 52.81 )
Warning: stack imbalance in '{', 73 then 75
2026-03-02 21:37:50.13924 INFO::Formatting Data.
2026-03-02 21:37:50.139993 INFO::Recognized SummarizedExperiment
2026-03-02 21:37:50.140546 INFO::Typecasting input to dataframe.
2026-03-02 21:37:50.149669 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:50.150787 INFO::Removing potential empty rows and columns
2026-03-02 21:37:50.154653 INFO::Found 0 missing values.
2026-03-02 21:37:50.162056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:50.162648 INFO::Done
2026-03-02 21:37:50.163412 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:50.166952 INFO::Starting hierarchical adjustment
2026-03-02 21:37:50.167668 INFO::Found 2 batches.
2026-03-02 21:37:50.168199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:50.16883 INFO::Using default BPPARAM
2026-03-02 21:37:50.169351 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:50.170339 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:37:50.196825 INFO::Done
2026-03-02 21:37:50.19762 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:50.201315 INFO::ASW Batch was 0.027916215474163 prior to batch effect correction and is now 0.027916215474163 .
2026-03-02 21:37:50.202212 INFO::Total function execution time is 0.0629448890686035 s and adjustment time is 0.0292501449584961 s ( 46.47 )
2026-03-02 21:37:50.221196 INFO::Formatting Data.
2026-03-02 21:37:50.22199 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:50.222893 INFO::Removing potential empty rows and columns
2026-03-02 21:37:50.223926 INFO::Found 0 missing values.
2026-03-02 21:37:50.226918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:50.227454 INFO::Done
2026-03-02 21:37:50.227973 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:50.229974 INFO::Starting hierarchical adjustment
2026-03-02 21:37:50.230674 INFO::Found 3 batches.
2026-03-02 21:37:50.231196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:50.231811 INFO::Using default BPPARAM
2026-03-02 21:37:50.232334 INFO::Processing subtree level 1
2026-03-02 21:37:50.376114 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:37:50.379138 INFO::Done
2026-03-02 21:37:50.380296 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:50.383298 INFO::ASW Batch was -0.00594668281203602 prior to batch effect correction and is now -0.185274394492357 .
2026-03-02 21:37:50.38441 INFO::Total function execution time is 0.163203001022339 s and adjustment time is 0.148508310317993 s ( 91 )
2026-03-02 21:37:50.399976 INFO::Skipping initial DF formatting
2026-03-02 21:37:50.40082 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:50.405214 INFO::Starting hierarchical adjustment
2026-03-02 21:37:50.406112 INFO::Found 5 batches.
2026-03-02 21:37:50.406705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:50.407345 INFO::Using default BPPARAM
2026-03-02 21:37:50.407897 INFO::Processing subtree level 1
2026-03-02 21:37:50.645265 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:50.647062 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:37:50.667531 INFO::Done
2026-03-02 21:37:50.668312 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:50.719545 INFO::ASW Batch was 0.567205842489236 prior to batch effect correction and is now 0.567205842489236 .
2026-03-02 21:37:50.720272 INFO::ASW Label was 0.37375979934848 prior to batch effect correction and is now 0.37375979934848 .
2026-03-02 21:37:50.721177 INFO::Total function execution time is 0.321339845657349 s and adjustment time is 0.261587619781494 s ( 81.41 )
2026-03-02 21:37:50.739237 INFO::Formatting Data.
2026-03-02 21:37:50.740036 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:50.74097 INFO::Removing potential empty rows and columns
2026-03-02 21:37:50.742052 INFO::Found 0 missing values.
2026-03-02 21:37:50.746438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:50.747014 INFO::Done
2026-03-02 21:37:50.747585 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:50.750711 INFO::Starting hierarchical adjustment
2026-03-02 21:37:50.751481 INFO::Found 5 batches.
2026-03-02 21:37:50.752019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:50.752661 INFO::Using default BPPARAM
2026-03-02 21:37:50.753215 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.
2026-03-02 21:37:50.892262 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:50.894011 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:37:50.912058 INFO::Done
2026-03-02 21:37:50.912823 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:50.916264 INFO::ASW Batch was 0.35942929557272 prior to batch effect correction and is now -0.0972622367127346 .
2026-03-02 21:37:50.916934 INFO::ASW Label was 0.296114164774244 prior to batch effect correction and is now 0.88389046363135 .
2026-03-02 21:37:50.917801 INFO::Total function execution time is 0.178644418716431 s and adjustment time is 0.16071343421936 s ( 89.96 )
2026-03-02 21:37:50.918669 INFO::Formatting Data.
2026-03-02 21:37:50.919354 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:50.920291 INFO::Removing potential empty rows and columns
2026-03-02 21:37:50.9214 INFO::Found 0 missing values.
2026-03-02 21:37:50.925606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:50.926168 INFO::Done
2026-03-02 21:37:50.926747 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:50.92981 INFO::Starting hierarchical adjustment
2026-03-02 21:37:50.93055 INFO::Found 5 batches.
2026-03-02 21:37:50.931075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:50.931734 INFO::Using default BPPARAM
2026-03-02 21:37:50.932261 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.
2026-03-02 21:37:51.061797 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:51.063426 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:37:51.079847 INFO::Done
2026-03-02 21:37:51.08057 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:51.083789 INFO::ASW Batch was 0.35942929557272 prior to batch effect correction and is now -0.0972622367127346 .
2026-03-02 21:37:51.08441 INFO::ASW Label was 0.296114164774244 prior to batch effect correction and is now 0.88389046363135 .
2026-03-02 21:37:51.085249 INFO::Total function execution time is 0.166576862335205 s and adjustment time is 0.149399042129517 s ( 89.69 )
2026-03-02 21:37:51.098588 INFO::Formatting Data.
2026-03-02 21:37:51.099352 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:51.100255 INFO::Removing potential empty rows and columns
2026-03-02 21:37:51.101273 INFO::Found 0 missing values.
2026-03-02 21:37:51.105337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:51.105926 INFO::Done
2026-03-02 21:37:51.106457 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:51.10942 INFO::Starting hierarchical adjustment
2026-03-02 21:37:51.110126 INFO::Found 5 batches.
2026-03-02 21:37:51.110662 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:51.111272 INFO::Using default BPPARAM
2026-03-02 21:37:51.11182 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.
2026-03-02 21:37:51.238766 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:51.24065 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:37:51.258651 INFO::Done
2026-03-02 21:37:51.259524 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:51.263247 INFO::ASW Batch was 0.439908205035919 prior to batch effect correction and is now 0.000953134607574777 .
2026-03-02 21:37:51.263969 INFO::ASW Label was 0.366700448475773 prior to batch effect correction and is now 0.769533785837201 .
2026-03-02 21:37:51.264962 INFO::Total function execution time is 0.166429996490479 s and adjustment time is 0.148585557937622 s ( 89.28 )
2026-03-02 21:37:51.265897 INFO::Formatting Data.
2026-03-02 21:37:51.266616 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:51.26767 INFO::Removing potential empty rows and columns
2026-03-02 21:37:51.268837 INFO::Found 0 missing values.
2026-03-02 21:37:51.273428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:51.274082 INFO::Done
2026-03-02 21:37:51.274789 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:51.278212 INFO::Starting hierarchical adjustment
2026-03-02 21:37:51.278992 INFO::Found 5 batches.
2026-03-02 21:37:51.279591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:51.28025 INFO::Using default BPPARAM
2026-03-02 21:37:51.280828 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.
2026-03-02 21:37:51.418657 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:51.420559 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:37:51.43939 INFO::Done
2026-03-02 21:37:51.440336 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:51.444375 INFO::ASW Batch was 0.439908205035919 prior to batch effect correction and is now 0.000953134607574777 .
2026-03-02 21:37:51.445084 INFO::ASW Label was 0.366700448475773 prior to batch effect correction and is now 0.769533785837201 .
2026-03-02 21:37:51.446012 INFO::Total function execution time is 0.180129289627075 s and adjustment time is 0.160468339920044 s ( 89.09 )
2026-03-02 21:37:51.461049 INFO::Formatting Data.
2026-03-02 21:37:51.461964 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:51.46301 INFO::Removing potential empty rows and columns
2026-03-02 21:37:51.464163 INFO::Found 0 missing values.
2026-03-02 21:37:51.467228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:51.467863 INFO::Done
2026-03-02 21:37:51.468468 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:51.471839 INFO::Starting hierarchical adjustment
2026-03-02 21:37:51.472658 INFO::Found 2 batches.
2026-03-02 21:37:51.473248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:51.473948 INFO::Using default BPPARAM
2026-03-02 21:37:51.474559 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:51.475573 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:37:51.492548 INFO::Done
2026-03-02 21:37:51.493452 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:51.496851 INFO::ASW Batch was 0.719007422509245 prior to batch effect correction and is now -0.0264360820018494 .
2026-03-02 21:37:51.497551 INFO::ASW Label was 0.33232811469998 prior to batch effect correction and is now 0.902939729364824 .
2026-03-02 21:37:51.498463 INFO::Total function execution time is 0.0375330448150635 s and adjustment time is 0.0199809074401855 s ( 53.24 )
2026-03-02 21:37:51.49938 INFO::Formatting Data.
2026-03-02 21:37:51.500065 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:51.501044 INFO::Removing potential empty rows and columns
2026-03-02 21:37:51.502148 INFO::Found 0 missing values.
2026-03-02 21:37:51.505128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:51.50575 INFO::Done
2026-03-02 21:37:51.506318 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:51.509659 INFO::Starting hierarchical adjustment
2026-03-02 21:37:51.51044 INFO::Found 2 batches.
2026-03-02 21:37:51.511006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:51.511679 INFO::Using default BPPARAM
2026-03-02 21:37:51.512266 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:51.513258 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:37:51.529607 INFO::Done
2026-03-02 21:37:51.53034 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:51.533588 INFO::ASW Batch was 0.719007422509245 prior to batch effect correction and is now -0.0264360820018494 .
2026-03-02 21:37:51.53426 INFO::ASW Label was 0.33232811469998 prior to batch effect correction and is now 0.902939729364824 .
2026-03-02 21:37:51.535122 INFO::Total function execution time is 0.0357863903045654 s and adjustment time is 0.019331693649292 s ( 54.02 )
2026-03-02 21:37:51.547961 INFO::Formatting Data.
2026-03-02 21:37:51.548896 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:51.550002 INFO::Removing potential empty rows and columns
2026-03-02 21:37:51.551061 INFO::Found 0 missing values.
2026-03-02 21:37:51.553524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:51.55411 INFO::Done
2026-03-02 21:37:51.554687 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:51.556937 INFO::Starting hierarchical adjustment
2026-03-02 21:37:51.557694 INFO::Found 2 batches.
2026-03-02 21:37:51.55827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:51.558929 INFO::Using default BPPARAM
2026-03-02 21:37:51.559533 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:51.560521 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:37:51.594917 INFO::Done
2026-03-02 21:37:51.595761 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:51.598049 INFO::ASW Batch was 0.0750989934821098 prior to batch effect correction and is now -0.151948684927303 .
2026-03-02 21:37:51.598978 INFO::Total function execution time is 0.0511436462402344 s and adjustment time is 0.0373291969299316 s ( 72.99 )
2026-03-02 21:37:51.612474 INFO::Formatting Data.
2026-03-02 21:37:51.613396 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:51.614405 INFO::Removing potential empty rows and columns
2026-03-02 21:37:51.615494 INFO::Found 0 missing values.
2026-03-02 21:37:51.616767 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.
2026-03-02 21:37:51.621729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:51.622325 INFO::Done
2026-03-02 21:37:51.622894 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:51.626103 INFO::Starting hierarchical adjustment
2026-03-02 21:37:51.62686 INFO::Found 2 batches.
2026-03-02 21:37:51.627445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:51.628128 INFO::Using default BPPARAM
2026-03-02 21:37:51.628713 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:51.629689 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:37:51.647669 INFO::Done
2026-03-02 21:37:51.648477 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:51.651739 INFO::ASW Batch was 0.466636694987068 prior to batch effect correction and is now 0.0951127449247836 .
2026-03-02 21:37:51.652411 INFO::ASW Label was 0.600844223789634 prior to batch effect correction and is now 0.888105644843234 .
2026-03-02 21:37:51.6533 INFO::Total function execution time is 0.0409634113311768 s and adjustment time is 0.0209226608276367 s ( 51.08 )
2026-03-02 21:37:51.654258 INFO::Formatting Data.
2026-03-02 21:37:51.654993 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:51.656049 INFO::Removing potential empty rows and columns
2026-03-02 21:37:51.65723 INFO::Found 0 missing values.
2026-03-02 21:37:51.65829 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.
2026-03-02 21:37:51.663637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:51.664258 INFO::Done
2026-03-02 21:37:51.664848 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:51.668213 INFO::Starting hierarchical adjustment
2026-03-02 21:37:51.669041 INFO::Found 2 batches.
2026-03-02 21:37:51.669684 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:51.670364 INFO::Using default BPPARAM
2026-03-02 21:37:51.670964 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:51.67205 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:37:51.690274 INFO::Done
2026-03-02 21:37:51.691108 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:51.694428 INFO::ASW Batch was 0.466636694987068 prior to batch effect correction and is now 0.0951127449247836 .
2026-03-02 21:37:51.69512 INFO::ASW Label was 0.600844223789634 prior to batch effect correction and is now 0.888105644843234 .
2026-03-02 21:37:51.696028 INFO::Total function execution time is 0.0418174266815186 s and adjustment time is 0.021373987197876 s ( 51.11 )
2026-03-02 21:37:51.916946 INFO::Formatting Data.
2026-03-02 21:37:51.91793 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:51.918934 INFO::Removing potential empty rows and columns
2026-03-02 21:37:51.920078 INFO::Found 0 missing values.
2026-03-02 21:37:51.923294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:51.923856 INFO::Done
2026-03-02 21:37:51.924389 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:51.92664 INFO::Starting hierarchical adjustment
2026-03-02 21:37:51.927375 INFO::Found 3 batches.
2026-03-02 21:37:51.927909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:51.928795 INFO::Using default BPPARAM
2026-03-02 21:37:51.929333 INFO::Processing subtree level 1
2026-03-02 21:37:52.0251 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:37:52.027185 INFO::Done
2026-03-02 21:37:52.027951 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:52.030761 INFO::ASW Batch was -0.0320458987949717 prior to batch effect correction and is now -0.0320458987949717 .
2026-03-02 21:37:52.031856 INFO::Total function execution time is 0.115027666091919 s and adjustment time is 0.0999236106872559 s ( 86.87 )
2026-03-02 21:37:52.033033 INFO::Formatting Data.
2026-03-02 21:37:52.033752 INFO::Typecasting input to dataframe.
2026-03-02 21:37:52.034561 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:52.035564 INFO::Removing potential empty rows and columns
2026-03-02 21:37:52.036769 INFO::Found 0 missing values.
2026-03-02 21:37:52.040082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:52.040726 INFO::Done
2026-03-02 21:37:52.041281 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:52.043543 INFO::Starting hierarchical adjustment
2026-03-02 21:37:52.044351 INFO::Found 3 batches.
2026-03-02 21:37:52.044917 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:52.045594 INFO::Using default BPPARAM
2026-03-02 21:37:52.04615 INFO::Processing subtree level 1
2026-03-02 21:37:52.142157 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:37:52.144233 INFO::Done
2026-03-02 21:37:52.144996 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:52.147794 INFO::ASW Batch was -0.0320458987949717 prior to batch effect correction and is now -0.0320458987949717 .
2026-03-02 21:37:52.148872 INFO::Total function execution time is 0.115822553634644 s and adjustment time is 0.100008487701416 s ( 86.35 )
2026-03-02 21:37:52.163633 INFO::Formatting Data.
2026-03-02 21:37:52.16464 INFO::Typecasting input to dataframe.
2026-03-02 21:37:52.165597 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:52.166592 INFO::Removing potential empty rows and columns
2026-03-02 21:37:52.167743 INFO::Found 0 missing values.
2026-03-02 21:37:52.17096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:52.171512 INFO::Done
2026-03-02 21:37:52.172045 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:52.174318 INFO::Starting hierarchical adjustment
2026-03-02 21:37:52.175055 INFO::Found 3 batches.
2026-03-02 21:37:52.175609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:52.176252 INFO::Using default BPPARAM
2026-03-02 21:37:52.176819 INFO::Processing subtree level 1
2026-03-02 21:37:52.270814 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:37:52.272899 INFO::Done
2026-03-02 21:37:52.273663 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:52.276423 INFO::ASW Batch was -0.0144317942821864 prior to batch effect correction and is now -0.0144317942821864 .
2026-03-02 21:37:52.277409 INFO::Total function execution time is 0.113904237747192 s and adjustment time is 0.0979480743408203 s ( 85.99 )
2026-03-02 21:37:52.425559 INFO::Formatting Data.
2026-03-02 21:37:52.426458 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:52.427641 INFO::Removing potential empty rows and columns
2026-03-02 21:37:52.430621 INFO::Found 1000 missing values.
2026-03-02 21:37:52.45078 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:52.451594 INFO::Done
2026-03-02 21:37:52.452179 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:52.457763 INFO::Starting hierarchical adjustment
2026-03-02 21:37:52.45855 INFO::Found 10 batches.
2026-03-02 21:37:52.459102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:52.459797 INFO::Using default BPPARAM
2026-03-02 21:37:52.460342 INFO::Processing subtree level 1
2026-03-02 21:37:52.601816 INFO::Processing subtree level 2
2026-03-02 21:37:52.749156 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:37:52.751743 INFO::Done
2026-03-02 21:37:52.752609 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:52.759063 INFO::ASW Batch was 0.456499153011624 prior to batch effect correction and is now 0.456499153011624 .
2026-03-02 21:37:52.75989 INFO::ASW Label was 0.359994153142346 prior to batch effect correction and is now 0.359994153142346 .
2026-03-02 21:37:52.760959 INFO::Total function execution time is 0.335455417633057 s and adjustment time is 0.293294429779053 s ( 87.43 )
2026-03-02 21:37:52.761917 INFO::Formatting Data.
2026-03-02 21:37:52.76263 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:52.764174 INFO::Removing potential empty rows and columns
2026-03-02 21:37:52.767245 INFO::Found 1000 missing values.
2026-03-02 21:37:52.787792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:52.788751 INFO::Done
2026-03-02 21:37:52.789376 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:52.795288 INFO::Starting hierarchical adjustment
2026-03-02 21:37:52.796217 INFO::Found 10 batches.
2026-03-02 21:37:54.213954 INFO::Set up parallel execution backend with 2 workers
2026-03-02 21:37:54.220377 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-02 21:37:55.663702 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:37:55.665599 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:37:55.682009 INFO::Done
2026-03-02 21:37:55.682686 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:55.687169 INFO::ASW Batch was 0.456499153011624 prior to batch effect correction and is now 0.456499153011624 .
2026-03-02 21:37:55.687786 INFO::ASW Label was 0.359994153142346 prior to batch effect correction and is now 0.359994153142346 .
2026-03-02 21:37:55.688541 INFO::Total function execution time is 2.92670941352844 s and adjustment time is 2.88596773147583 s ( 98.61 )
2026-03-02 21:37:55.834987 INFO::Formatting Data.
2026-03-02 21:37:55.835744 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:55.83663 INFO::Removing potential empty rows and columns
2026-03-02 21:37:55.837672 INFO::Found 0 missing values.
2026-03-02 21:37:55.841275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:55.841801 INFO::Done
2026-03-02 21:37:55.8423 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:37:55.844936 INFO::Starting hierarchical adjustment
2026-03-02 21:37:55.845623 INFO::Found 3 batches.
2026-03-02 21:37:55.846133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:37:55.846756 INFO::Using default BPPARAM
2026-03-02 21:37:55.847274 INFO::Processing subtree level 1
2026-03-02 21:37:55.949479 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:37:55.951198 INFO::Done
2026-03-02 21:37:55.951823 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:37:55.954929 INFO::ASW Batch was 0.138737829884664 prior to batch effect correction and is now -0.150266216325009 .
2026-03-02 21:37:55.955559 INFO::ASW Label was -0.204884898993941 prior to batch effect correction and is now -0.0490668627503063 .
2026-03-02 21:37:55.956468 INFO::Total function execution time is 0.121513605117798 s and adjustment time is 0.105692625045776 s ( 86.98 )
2026-03-02 21:37:56.092427 INFO::Formatting Data.
2026-03-02 21:37:56.093307 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.094295 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.095502 INFO::Found 2 missing values.
2026-03-02 21:37:56.098907 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.099504 INFO::Done
2026-03-02 21:37:56.129056 INFO::Found NA in Reference column
2026-03-02 21:37:56.139168 INFO::Require at least two references per batch.
2026-03-02 21:37:56.161691 INFO::Formatting Data.
2026-03-02 21:37:56.162479 INFO::Recognized SummarizedExperiment
2026-03-02 21:37:56.163057 INFO::Typecasting input to dataframe.
2026-03-02 21:37:56.173739 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.175053 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.179093 INFO::Found 0 missing values.
2026-03-02 21:37:56.186826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.187497 INFO::Done
2026-03-02 21:37:56.203896 INFO::Formatting Data.
2026-03-02 21:37:56.204666 INFO::Recognized SummarizedExperiment
2026-03-02 21:37:56.205216 INFO::Typecasting input to dataframe.
2026-03-02 21:37:56.222997 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.224248 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.228289 INFO::Found 0 missing values.
2026-03-02 21:37:56.24082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.241546 INFO::Done
2026-03-02 21:37:56.257775 INFO::Formatting Data.
2026-03-02 21:37:56.258529 INFO::Recognized SummarizedExperiment
2026-03-02 21:37:56.259074 INFO::Typecasting input to dataframe.
2026-03-02 21:37:56.276026 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.277069 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.27818 INFO::Found 0 missing values.
2026-03-02 21:37:56.279114 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.
2026-03-02 21:37:56.283587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.284177 INFO::Done
2026-03-02 21:37:56.294643 INFO::Formatting Data.
2026-03-02 21:37:56.295425 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.296304 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.297316 INFO::Found 0 missing values.
2026-03-02 21:37:56.300201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.300729 INFO::Done
2026-03-02 21:37:56.312238 INFO::Formatting Data.
2026-03-02 21:37:56.312995 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.313869 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.314956 INFO::Found 0 missing values.
2026-03-02 21:37:56.317998 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.318558 INFO::Done
2026-03-02 21:37:56.348155 INFO::Formatting Data.
2026-03-02 21:37:56.348946 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.349975 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.351122 INFO::Found 1 missing values.
2026-03-02 21:37:56.353744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.354291 INFO::Done
2026-03-02 21:37:56.372526 INFO::Formatting Data.
2026-03-02 21:37:56.37331 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.374168 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.375099 INFO::Found 2 missing values.
2026-03-02 21:37:56.375984 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.
2026-03-02 21:37:56.378361 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.378887 INFO::Done
2026-03-02 21:37:56.388435 INFO::Formatting Data.
2026-03-02 21:37:56.389164 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.390007 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.390911 INFO::Found 2 missing values.
2026-03-02 21:37:56.392436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.392959 INFO::Done
2026-03-02 21:37:56.402959 INFO::Formatting Data.
2026-03-02 21:37:56.4037 INFO::Typecasting input to dataframe.
2026-03-02 21:37:56.404522 INFO::Replacing NaNs with NAs.
2026-03-02 21:37:56.405373 INFO::Removing potential empty rows and columns
2026-03-02 21:37:56.40633 INFO::Found 0 missing values.
2026-03-02 21:37:56.409191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:37:56.409711 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.345 3.968 21.030
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.489 | 1.658 | 19.302 | |
| compute_asw | 0.022 | 0.003 | 0.025 | |
| count_existing | 0.012 | 0.002 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |