Yannis Schumann
| Snapshot Date: 2026-04-29 13:40 -0400 (Wed, 29 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_23 |
| git_last_commit: 0c9135c |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-30 11:35 -0400 (Thu, 30 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4718 |
| 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 172/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.8.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2026-04-29 21:49:48 -0400 (Wed, 29 Apr 2026) |
| EndedAt: 2026-04-29 21:51:25 -0400 (Wed, 29 Apr 2026) |
| EllapsedTime: 97.1 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-30 01:49:48 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.8.0’
* 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 26.936 1.281 20.436
* 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 ‘1.8.0’ ** 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 version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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")
2026-04-29 21:50:43.410978 INFO::Formatting Data.
2026-04-29 21:50:43.41228 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:43.423555 INFO::Removing potential empty rows and columns
2026-04-29 21:50:43.658524 INFO::Found 0 missing values.
2026-04-29 21:50:43.66209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:43.662817 INFO::Done
2026-04-29 21:50:43.663424 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:43.676656 INFO::Starting hierarchical adjustment
2026-04-29 21:50:43.677607 INFO::Found 3 batches.
2026-04-29 21:50:43.678249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:43.679402 INFO::Using default BPPARAM
2026-04-29 21:50:43.680014 INFO::Processing subtree level 1
2026-04-29 21:50:43.796776 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:50:43.799688 INFO::Done
2026-04-29 21:50:43.800715 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:43.804151 INFO::ASW Batch was -0.108746795613149 prior to batch effect correction and is now -0.108746795613149 .
2026-04-29 21:50:43.805482 INFO::Total function execution time is 0.395032644271851 s and adjustment time is 0.122193098068237 s ( 30.93 )
2026-04-29 21:50:43.821771 INFO::Formatting Data.
2026-04-29 21:50:43.822688 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:43.823783 INFO::Removing potential empty rows and columns
2026-04-29 21:50:43.825151 INFO::Found 0 missing values.
2026-04-29 21:50:43.826283 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.
2026-04-29 21:50:43.838925 INFO::Formatting Data.
2026-04-29 21:50:43.839969 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:43.841133 INFO::Removing potential empty rows and columns
2026-04-29 21:50:43.842469 INFO::Found 0 missing values.
2026-04-29 21:50:43.843586 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.
2026-04-29 21:50:43.86278 INFO::Formatting Data.
2026-04-29 21:50:43.863742 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:43.864818 INFO::Removing potential empty rows and columns
2026-04-29 21:50:43.865962 INFO::Found 0 missing values.
2026-04-29 21:50:43.867001 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.
2026-04-29 21:50:43.871856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:43.87252 INFO::Done
2026-04-29 21:50:43.873117 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:43.875517 INFO::Starting hierarchical adjustment
2026-04-29 21:50:43.876345 INFO::Found 2 batches.
2026-04-29 21:50:43.876989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:43.877712 INFO::Using default BPPARAM
2026-04-29 21:50:43.878395 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:43.879531 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:50:43.905049 INFO::Done
2026-04-29 21:50:43.9059 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:43.908135 INFO::ASW Batch was 0.0187006517780474 prior to batch effect correction and is now -0.115250760386629 .
2026-04-29 21:50:43.908989 INFO::Total function execution time is 0.0463411808013916 s and adjustment time is 0.0288019180297852 s ( 62.15 )
2026-04-29 21:50:43.912109 INFO::Formatting Data.
2026-04-29 21:50:43.912786 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:43.922018 INFO::Formatting Data.
2026-04-29 21:50:43.9228 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:43.923766 INFO::Removing potential empty rows and columns
2026-04-29 21:50:43.924937 INFO::Found 0 missing values.
2026-04-29 21:50:43.927994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:43.928574 INFO::Done
2026-04-29 21:50:43.929146 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:43.9313 INFO::Starting hierarchical adjustment
2026-04-29 21:50:43.932063 INFO::Found 2 batches.
2026-04-29 21:50:43.932638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:43.933329 INFO::Using default BPPARAM
2026-04-29 21:50:43.933921 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:43.934954 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:50:43.953295 INFO::Done
2026-04-29 21:50:43.954246 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:43.956699 INFO::ASW Batch was 0.000853194108005433 prior to batch effect correction and is now -0.0948871914376216 .
2026-04-29 21:50:43.957721 INFO::Total function execution time is 0.0357115268707275 s and adjustment time is 0.0213382244110107 s ( 59.75 )
2026-04-29 21:50:43.958978 INFO::Formatting Data.
2026-04-29 21:50:43.959706 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:43.960726 INFO::Removing potential empty rows and columns
2026-04-29 21:50:43.961918 INFO::Found 0 missing values.
2026-04-29 21:50:43.965135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:43.965775 INFO::Done
2026-04-29 21:50:43.966381 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:43.968712 INFO::Starting hierarchical adjustment
2026-04-29 21:50:43.969545 INFO::Found 2 batches.
2026-04-29 21:50:43.970184 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:43.970901 INFO::Using default BPPARAM
2026-04-29 21:50:43.971529 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:43.97257 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:50:43.989176 INFO::Done
2026-04-29 21:50:43.990024 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:43.992295 INFO::ASW Batch was 0.000853194108005433 prior to batch effect correction and is now -0.0948871914376216 .
2026-04-29 21:50:43.993168 INFO::Total function execution time is 0.034198522567749 s and adjustment time is 0.0197579860687256 s ( 57.77 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-29 21:50:47.362336 INFO::Formatting Data.
2026-04-29 21:50:47.363425 INFO::Recognized SummarizedExperiment
2026-04-29 21:50:47.364076 INFO::Typecasting input to dataframe.
2026-04-29 21:50:47.398432 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:47.399736 INFO::Removing potential empty rows and columns
2026-04-29 21:50:47.403124 INFO::Found 0 missing values.
2026-04-29 21:50:47.409522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:47.410172 INFO::Done
2026-04-29 21:50:47.410723 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:47.414104 INFO::Starting hierarchical adjustment
2026-04-29 21:50:47.41488 INFO::Found 2 batches.
2026-04-29 21:50:47.415413 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:47.416579 INFO::Using default BPPARAM
2026-04-29 21:50:47.417137 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:47.418122 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:50:47.469983 INFO::Done
2026-04-29 21:50:47.47078 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:47.474162 INFO::ASW Batch was 0.0102723530182928 prior to batch effect correction and is now -0.089268034334275 .
2026-04-29 21:50:47.475076 INFO::Total function execution time is 0.113123893737793 s and adjustment time is 0.055239200592041 s ( 48.83 )
Warning: stack imbalance in '{', 73 then 75
2026-04-29 21:50:47.492633 INFO::Formatting Data.
2026-04-29 21:50:47.493517 INFO::Recognized SummarizedExperiment
2026-04-29 21:50:47.494099 INFO::Typecasting input to dataframe.
2026-04-29 21:50:47.502941 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:47.504156 INFO::Removing potential empty rows and columns
2026-04-29 21:50:47.507463 INFO::Found 0 missing values.
2026-04-29 21:50:47.514024 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:47.514727 INFO::Done
2026-04-29 21:50:47.515295 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:47.518995 INFO::Starting hierarchical adjustment
2026-04-29 21:50:47.519781 INFO::Found 2 batches.
2026-04-29 21:50:47.520333 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:47.520977 INFO::Using default BPPARAM
2026-04-29 21:50:47.521576 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:47.522648 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:50:47.549353 INFO::Done
2026-04-29 21:50:47.550355 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:47.554503 INFO::ASW Batch was 0.00559297170279605 prior to batch effect correction and is now 0.00559297170279605 .
2026-04-29 21:50:47.555559 INFO::Total function execution time is 0.0628838539123535 s and adjustment time is 0.0296988487243652 s ( 47.23 )
2026-04-29 21:50:47.576354 INFO::Formatting Data.
2026-04-29 21:50:47.57732 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:47.578347 INFO::Removing potential empty rows and columns
2026-04-29 21:50:47.57946 INFO::Found 0 missing values.
2026-04-29 21:50:47.58266 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:47.583286 INFO::Done
2026-04-29 21:50:47.583869 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:47.586225 INFO::Starting hierarchical adjustment
2026-04-29 21:50:47.587025 INFO::Found 3 batches.
2026-04-29 21:50:47.587605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:47.588291 INFO::Using default BPPARAM
2026-04-29 21:50:47.58888 INFO::Processing subtree level 1
2026-04-29 21:50:47.744826 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:50:47.747244 INFO::Done
2026-04-29 21:50:47.74818 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:47.751317 INFO::ASW Batch was -0.109219647024199 prior to batch effect correction and is now -0.158447377635047 .
2026-04-29 21:50:47.75247 INFO::Total function execution time is 0.176167249679565 s and adjustment time is 0.16031551361084 s ( 91 )
2026-04-29 21:50:47.771432 INFO::Skipping initial DF formatting
2026-04-29 21:50:47.772471 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:47.777152 INFO::Starting hierarchical adjustment
2026-04-29 21:50:47.778083 INFO::Found 5 batches.
2026-04-29 21:50:47.778713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:47.779412 INFO::Using default BPPARAM
2026-04-29 21:50:47.78003 INFO::Processing subtree level 1
2026-04-29 21:50:47.917365 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:47.919274 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:50:47.939909 INFO::Done
2026-04-29 21:50:47.940696 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:47.94523 INFO::ASW Batch was 0.510869536848565 prior to batch effect correction and is now 0.510869536848565 .
2026-04-29 21:50:47.945917 INFO::ASW Label was 0.387560997663607 prior to batch effect correction and is now 0.387560997663607 .
2026-04-29 21:50:47.946885 INFO::Total function execution time is 0.175638198852539 s and adjustment time is 0.162018537521362 s ( 92.25 )
2026-04-29 21:50:47.966122 INFO::Formatting Data.
2026-04-29 21:50:47.967165 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:47.96826 INFO::Removing potential empty rows and columns
2026-04-29 21:50:47.969408 INFO::Found 0 missing values.
2026-04-29 21:50:47.97395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:47.974541 INFO::Done
2026-04-29 21:50:47.975124 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:47.978326 INFO::Starting hierarchical adjustment
2026-04-29 21:50:47.9791 INFO::Found 5 batches.
2026-04-29 21:50:47.979698 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:47.980357 INFO::Using default BPPARAM
2026-04-29 21:50:47.980963 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.
2026-04-29 21:50:48.108849 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.110921 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:50:48.130302 INFO::Done
2026-04-29 21:50:48.131435 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.135438 INFO::ASW Batch was 0.510829253861984 prior to batch effect correction and is now -0.0798855851706743 .
2026-04-29 21:50:48.136212 INFO::ASW Label was 0.22907146638776 prior to batch effect correction and is now 0.81782619507654 .
2026-04-29 21:50:48.137193 INFO::Total function execution time is 0.171186923980713 s and adjustment time is 0.151244640350342 s ( 88.35 )
2026-04-29 21:50:48.138138 INFO::Formatting Data.
2026-04-29 21:50:48.138865 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:48.139836 INFO::Removing potential empty rows and columns
2026-04-29 21:50:48.141053 INFO::Found 0 missing values.
2026-04-29 21:50:48.145735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:48.146384 INFO::Done
2026-04-29 21:50:48.147007 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:48.150814 INFO::Starting hierarchical adjustment
2026-04-29 21:50:48.151834 INFO::Found 5 batches.
2026-04-29 21:50:48.152421 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:48.153165 INFO::Using default BPPARAM
2026-04-29 21:50:48.15377 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.
2026-04-29 21:50:48.274991 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.276799 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:50:48.293519 INFO::Done
2026-04-29 21:50:48.294352 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.297845 INFO::ASW Batch was 0.510829253861984 prior to batch effect correction and is now -0.0798855851706743 .
2026-04-29 21:50:48.2985 INFO::ASW Label was 0.22907146638776 prior to batch effect correction and is now 0.81782619507654 .
2026-04-29 21:50:48.299423 INFO::Total function execution time is 0.161301374435425 s and adjustment time is 0.142026901245117 s ( 88.05 )
2026-04-29 21:50:48.314877 INFO::Formatting Data.
2026-04-29 21:50:48.315939 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:48.317045 INFO::Removing potential empty rows and columns
2026-04-29 21:50:48.318203 INFO::Found 0 missing values.
2026-04-29 21:50:48.322748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:48.3235 INFO::Done
2026-04-29 21:50:48.324147 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:48.327661 INFO::Starting hierarchical adjustment
2026-04-29 21:50:48.328492 INFO::Found 5 batches.
2026-04-29 21:50:48.329103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:48.329829 INFO::Using default BPPARAM
2026-04-29 21:50:48.330415 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.
2026-04-29 21:50:48.445878 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.44757 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:50:48.463773 INFO::Done
2026-04-29 21:50:48.464575 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.467996 INFO::ASW Batch was 0.546289348339744 prior to batch effect correction and is now -0.0667653529013952 .
2026-04-29 21:50:48.468648 INFO::ASW Label was 0.190146230232421 prior to batch effect correction and is now 0.79998532687535 .
2026-04-29 21:50:48.469523 INFO::Total function execution time is 0.154829025268555 s and adjustment time is 0.135419607162476 s ( 87.46 )
2026-04-29 21:50:48.47042 INFO::Formatting Data.
2026-04-29 21:50:48.471107 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:48.472068 INFO::Removing potential empty rows and columns
2026-04-29 21:50:48.473112 INFO::Found 0 missing values.
2026-04-29 21:50:48.477305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:48.477905 INFO::Done
2026-04-29 21:50:48.478467 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:48.481492 INFO::Starting hierarchical adjustment
2026-04-29 21:50:48.482257 INFO::Found 5 batches.
2026-04-29 21:50:48.482877 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:48.483545 INFO::Using default BPPARAM
2026-04-29 21:50:48.484254 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.
2026-04-29 21:50:48.601694 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.603532 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:50:48.620543 INFO::Done
2026-04-29 21:50:48.621424 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.625014 INFO::ASW Batch was 0.546289348339744 prior to batch effect correction and is now -0.0667653529013952 .
2026-04-29 21:50:48.625662 INFO::ASW Label was 0.190146230232421 prior to batch effect correction and is now 0.79998532687535 .
2026-04-29 21:50:48.626606 INFO::Total function execution time is 0.156169414520264 s and adjustment time is 0.138374805450439 s ( 88.61 )
2026-04-29 21:50:48.641662 INFO::Formatting Data.
2026-04-29 21:50:48.656053 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:48.657579 INFO::Removing potential empty rows and columns
2026-04-29 21:50:48.658894 INFO::Found 0 missing values.
2026-04-29 21:50:48.662091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:48.662723 INFO::Done
2026-04-29 21:50:48.663311 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:48.667022 INFO::Starting hierarchical adjustment
2026-04-29 21:50:48.667834 INFO::Found 2 batches.
2026-04-29 21:50:48.668411 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:48.669152 INFO::Using default BPPARAM
2026-04-29 21:50:48.669795 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.670829 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:50:48.68902 INFO::Done
2026-04-29 21:50:48.689837 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.692958 INFO::ASW Batch was 0.512626151841839 prior to batch effect correction and is now 0.114271759611675 .
2026-04-29 21:50:48.693588 INFO::ASW Label was 0.633000697756081 prior to batch effect correction and is now 0.85017521989795 .
2026-04-29 21:50:48.694472 INFO::Total function execution time is 0.0529329776763916 s and adjustment time is 0.0213468074798584 s ( 40.33 )
2026-04-29 21:50:48.695359 INFO::Formatting Data.
2026-04-29 21:50:48.696058 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:48.696979 INFO::Removing potential empty rows and columns
2026-04-29 21:50:48.698016 INFO::Found 0 missing values.
2026-04-29 21:50:48.701086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:48.701703 INFO::Done
2026-04-29 21:50:48.702276 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:48.70535 INFO::Starting hierarchical adjustment
2026-04-29 21:50:48.706127 INFO::Found 2 batches.
2026-04-29 21:50:48.706726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:48.707396 INFO::Using default BPPARAM
2026-04-29 21:50:48.708015 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.70905 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:50:48.724309 INFO::Done
2026-04-29 21:50:48.725064 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.728106 INFO::ASW Batch was 0.512626151841839 prior to batch effect correction and is now 0.114271759611675 .
2026-04-29 21:50:48.72875 INFO::ASW Label was 0.633000697756081 prior to batch effect correction and is now 0.85017521989795 .
2026-04-29 21:50:48.729614 INFO::Total function execution time is 0.0342659950256348 s and adjustment time is 0.0183112621307373 s ( 53.44 )
2026-04-29 21:50:48.744508 INFO::Formatting Data.
2026-04-29 21:50:48.745451 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:48.74654 INFO::Removing potential empty rows and columns
2026-04-29 21:50:48.747584 INFO::Found 0 missing values.
2026-04-29 21:50:48.750009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:48.750627 INFO::Done
2026-04-29 21:50:48.751247 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:48.753398 INFO::Starting hierarchical adjustment
2026-04-29 21:50:48.75417 INFO::Found 2 batches.
2026-04-29 21:50:48.754772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:48.755431 INFO::Using default BPPARAM
2026-04-29 21:50:48.75606 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.757055 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:50:48.792638 INFO::Done
2026-04-29 21:50:48.793481 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.795801 INFO::ASW Batch was 0.0941885485464803 prior to batch effect correction and is now -0.129166464535204 .
2026-04-29 21:50:48.796709 INFO::Total function execution time is 0.052293062210083 s and adjustment time is 0.0385861396789551 s ( 73.79 )
2026-04-29 21:50:48.810293 INFO::Formatting Data.
2026-04-29 21:50:48.811204 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:48.812268 INFO::Removing potential empty rows and columns
2026-04-29 21:50:48.813432 INFO::Found 0 missing values.
2026-04-29 21:50:48.8148 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.
2026-04-29 21:50:48.819845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:48.820554 INFO::Done
2026-04-29 21:50:48.821177 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:48.824449 INFO::Starting hierarchical adjustment
2026-04-29 21:50:48.825265 INFO::Found 2 batches.
2026-04-29 21:50:48.825873 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:48.826524 INFO::Using default BPPARAM
2026-04-29 21:50:48.827158 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.828171 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:50:48.845407 INFO::Done
2026-04-29 21:50:48.846261 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.849533 INFO::ASW Batch was 0.672237011892667 prior to batch effect correction and is now -0.0123460636698448 .
2026-04-29 21:50:48.850219 INFO::ASW Label was 0.399602495022584 prior to batch effect correction and is now 0.901359737409857 .
2026-04-29 21:50:48.851118 INFO::Total function execution time is 0.0409364700317383 s and adjustment time is 0.020275354385376 s ( 49.53 )
2026-04-29 21:50:48.852015 INFO::Formatting Data.
2026-04-29 21:50:48.852724 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:48.853738 INFO::Removing potential empty rows and columns
2026-04-29 21:50:48.854823 INFO::Found 0 missing values.
2026-04-29 21:50:48.855807 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.
2026-04-29 21:50:48.860669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:48.861293 INFO::Done
2026-04-29 21:50:48.861871 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:48.864999 INFO::Starting hierarchical adjustment
2026-04-29 21:50:48.865767 INFO::Found 2 batches.
2026-04-29 21:50:48.866365 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:48.867048 INFO::Using default BPPARAM
2026-04-29 21:50:48.86762 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:48.868632 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:50:48.886364 INFO::Done
2026-04-29 21:50:48.887207 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:48.890291 INFO::ASW Batch was 0.672237011892667 prior to batch effect correction and is now -0.0123460636698448 .
2026-04-29 21:50:48.890964 INFO::ASW Label was 0.399602495022584 prior to batch effect correction and is now 0.901359737409857 .
2026-04-29 21:50:48.891832 INFO::Total function execution time is 0.0398433208465576 s and adjustment time is 0.0207223892211914 s ( 52.01 )
2026-04-29 21:50:49.114765 INFO::Formatting Data.
2026-04-29 21:50:49.115702 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:49.116706 INFO::Removing potential empty rows and columns
2026-04-29 21:50:49.117841 INFO::Found 0 missing values.
2026-04-29 21:50:49.121007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:49.121891 INFO::Done
2026-04-29 21:50:49.12248 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:49.124669 INFO::Starting hierarchical adjustment
2026-04-29 21:50:49.12547 INFO::Found 3 batches.
2026-04-29 21:50:49.126065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:49.126793 INFO::Using default BPPARAM
2026-04-29 21:50:49.12737 INFO::Processing subtree level 1
2026-04-29 21:50:49.224779 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:50:49.226915 INFO::Done
2026-04-29 21:50:49.227706 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:49.230507 INFO::ASW Batch was -0.0634240369246391 prior to batch effect correction and is now -0.0634240369246391 .
2026-04-29 21:50:49.23164 INFO::Total function execution time is 0.116939067840576 s and adjustment time is 0.101583242416382 s ( 86.87 )
2026-04-29 21:50:49.232842 INFO::Formatting Data.
2026-04-29 21:50:49.233546 INFO::Typecasting input to dataframe.
2026-04-29 21:50:49.234379 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:49.235384 INFO::Removing potential empty rows and columns
2026-04-29 21:50:49.236546 INFO::Found 0 missing values.
2026-04-29 21:50:49.239766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:49.240396 INFO::Done
2026-04-29 21:50:49.240994 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:49.243172 INFO::Starting hierarchical adjustment
2026-04-29 21:50:49.243968 INFO::Found 3 batches.
2026-04-29 21:50:49.244556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:49.245243 INFO::Using default BPPARAM
2026-04-29 21:50:49.245844 INFO::Processing subtree level 1
2026-04-29 21:50:49.338634 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:50:49.34075 INFO::Done
2026-04-29 21:50:49.341502 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:49.34427 INFO::ASW Batch was -0.0634240369246391 prior to batch effect correction and is now -0.0634240369246391 .
2026-04-29 21:50:49.345347 INFO::Total function execution time is 0.112491607666016 s and adjustment time is 0.0969033241271973 s ( 86.14 )
2026-04-29 21:50:49.359434 INFO::Formatting Data.
2026-04-29 21:50:49.360373 INFO::Typecasting input to dataframe.
2026-04-29 21:50:49.36134 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:49.362365 INFO::Removing potential empty rows and columns
2026-04-29 21:50:49.363528 INFO::Found 0 missing values.
2026-04-29 21:50:49.366647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:49.367269 INFO::Done
2026-04-29 21:50:49.367985 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:49.370301 INFO::Starting hierarchical adjustment
2026-04-29 21:50:49.371085 INFO::Found 3 batches.
2026-04-29 21:50:49.371665 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:49.372366 INFO::Using default BPPARAM
2026-04-29 21:50:49.372974 INFO::Processing subtree level 1
2026-04-29 21:50:49.485027 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:50:49.487601 INFO::Done
2026-04-29 21:50:49.488616 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:49.492096 INFO::ASW Batch was -0.0213036577775025 prior to batch effect correction and is now -0.0213036577775025 .
2026-04-29 21:50:49.493406 INFO::Total function execution time is 0.133970737457275 s and adjustment time is 0.116602420806885 s ( 87.04 )
2026-04-29 21:50:49.646344 INFO::Formatting Data.
2026-04-29 21:50:49.64733 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:49.64856 INFO::Removing potential empty rows and columns
2026-04-29 21:50:49.651793 INFO::Found 1000 missing values.
2026-04-29 21:50:49.672261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:49.673126 INFO::Done
2026-04-29 21:50:49.673762 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:49.679773 INFO::Starting hierarchical adjustment
2026-04-29 21:50:49.680615 INFO::Found 10 batches.
2026-04-29 21:50:49.681216 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:49.681962 INFO::Using default BPPARAM
2026-04-29 21:50:49.682561 INFO::Processing subtree level 1
2026-04-29 21:50:49.847361 INFO::Processing subtree level 2
2026-04-29 21:50:50.00088 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:50:50.003267 INFO::Done
2026-04-29 21:50:50.004134 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:50.010266 INFO::ASW Batch was 0.491087534891451 prior to batch effect correction and is now 0.491087534891451 .
2026-04-29 21:50:50.011123 INFO::ASW Label was 0.321105543049 prior to batch effect correction and is now 0.321105543049 .
2026-04-29 21:50:50.012219 INFO::Total function execution time is 0.365920066833496 s and adjustment time is 0.322780132293701 s ( 88.21 )
2026-04-29 21:50:50.013214 INFO::Formatting Data.
2026-04-29 21:50:50.013959 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:50.015409 INFO::Removing potential empty rows and columns
2026-04-29 21:50:50.018559 INFO::Found 1000 missing values.
2026-04-29 21:50:50.039539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:50.040539 INFO::Done
2026-04-29 21:50:50.041215 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:50.047116 INFO::Starting hierarchical adjustment
2026-04-29 21:50:50.047976 INFO::Found 10 batches.
2026-04-29 21:50:51.630963 INFO::Set up parallel execution backend with 2 workers
2026-04-29 21:50:51.634351 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-29 21:50:53.202007 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:50:53.207011 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:50:53.225624 INFO::Done
2026-04-29 21:50:53.226572 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:53.232074 INFO::ASW Batch was 0.491087534891451 prior to batch effect correction and is now 0.491087534891451 .
2026-04-29 21:50:53.23288 INFO::ASW Label was 0.321105543049 prior to batch effect correction and is now 0.321105543049 .
2026-04-29 21:50:53.233827 INFO::Total function execution time is 3.22064137458801 s and adjustment time is 3.17775988578796 s ( 98.67 )
2026-04-29 21:50:53.400118 INFO::Formatting Data.
2026-04-29 21:50:53.401117 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:53.402184 INFO::Removing potential empty rows and columns
2026-04-29 21:50:53.403521 INFO::Found 0 missing values.
2026-04-29 21:50:53.407458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:53.40812 INFO::Done
2026-04-29 21:50:53.408721 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:50:53.411714 INFO::Starting hierarchical adjustment
2026-04-29 21:50:53.412484 INFO::Found 3 batches.
2026-04-29 21:50:53.413102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:50:53.413799 INFO::Using default BPPARAM
2026-04-29 21:50:53.414413 INFO::Processing subtree level 1
2026-04-29 21:50:53.534753 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:50:53.536798 INFO::Done
2026-04-29 21:50:53.537559 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:50:53.541077 INFO::ASW Batch was 0.129192038862011 prior to batch effect correction and is now -0.12302657153243 .
2026-04-29 21:50:53.541785 INFO::ASW Label was -0.168571521600576 prior to batch effect correction and is now -0.0499595708824698 .
2026-04-29 21:50:53.542841 INFO::Total function execution time is 0.142769575119019 s and adjustment time is 0.124419689178467 s ( 87.15 )
2026-04-29 21:50:53.683837 INFO::Formatting Data.
2026-04-29 21:50:53.684868 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:53.685967 INFO::Removing potential empty rows and columns
2026-04-29 21:50:53.687152 INFO::Found 2 missing values.
2026-04-29 21:50:53.690357 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:53.69106 INFO::Done
2026-04-29 21:50:53.722586 INFO::Found NA in Reference column
2026-04-29 21:50:53.733211 INFO::Require at least two references per batch.
2026-04-29 21:50:53.77267 INFO::Formatting Data.
2026-04-29 21:50:53.773828 INFO::Recognized SummarizedExperiment
2026-04-29 21:50:53.774449 INFO::Typecasting input to dataframe.
2026-04-29 21:50:53.788305 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:53.789907 INFO::Removing potential empty rows and columns
2026-04-29 21:50:53.793818 INFO::Found 0 missing values.
2026-04-29 21:50:53.800991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:53.801761 INFO::Done
2026-04-29 21:50:53.818486 INFO::Formatting Data.
2026-04-29 21:50:53.819402 INFO::Recognized SummarizedExperiment
2026-04-29 21:50:53.820023 INFO::Typecasting input to dataframe.
2026-04-29 21:50:53.838502 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:53.839979 INFO::Removing potential empty rows and columns
2026-04-29 21:50:53.84386 INFO::Found 0 missing values.
2026-04-29 21:50:53.855428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:53.85637 INFO::Done
2026-04-29 21:50:53.873036 INFO::Formatting Data.
2026-04-29 21:50:53.874003 INFO::Recognized SummarizedExperiment
2026-04-29 21:50:53.874595 INFO::Typecasting input to dataframe.
2026-04-29 21:50:53.891713 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:53.892968 INFO::Removing potential empty rows and columns
2026-04-29 21:50:53.894248 INFO::Found 0 missing values.
2026-04-29 21:50:53.895289 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.
2026-04-29 21:50:53.900013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:53.900629 INFO::Done
2026-04-29 21:50:53.911809 INFO::Formatting Data.
2026-04-29 21:50:53.912729 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:53.913822 INFO::Removing potential empty rows and columns
2026-04-29 21:50:53.914942 INFO::Found 0 missing values.
2026-04-29 21:50:53.91807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:53.918733 INFO::Done
2026-04-29 21:50:53.932161 INFO::Formatting Data.
2026-04-29 21:50:53.933136 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:53.934158 INFO::Removing potential empty rows and columns
2026-04-29 21:50:53.935285 INFO::Found 0 missing values.
2026-04-29 21:50:53.938481 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:53.939088 INFO::Done
2026-04-29 21:50:53.977011 INFO::Formatting Data.
2026-04-29 21:50:53.978177 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:53.979453 INFO::Removing potential empty rows and columns
2026-04-29 21:50:53.980878 INFO::Found 1 missing values.
2026-04-29 21:50:53.984088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:53.984814 INFO::Done
2026-04-29 21:50:54.008355 INFO::Formatting Data.
2026-04-29 21:50:54.009586 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:54.010743 INFO::Removing potential empty rows and columns
2026-04-29 21:50:54.011935 INFO::Found 2 missing values.
2026-04-29 21:50:54.013123 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.
2026-04-29 21:50:54.015905 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:54.016546 INFO::Done
2026-04-29 21:50:54.028305 INFO::Formatting Data.
2026-04-29 21:50:54.02925 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:54.030262 INFO::Removing potential empty rows and columns
2026-04-29 21:50:54.031333 INFO::Found 2 missing values.
2026-04-29 21:50:54.033221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:54.033948 INFO::Done
2026-04-29 21:50:54.048968 INFO::Formatting Data.
2026-04-29 21:50:54.050238 INFO::Typecasting input to dataframe.
2026-04-29 21:50:54.051354 INFO::Replacing NaNs with NAs.
2026-04-29 21:50:54.05255 INFO::Removing potential empty rows and columns
2026-04-29 21:50:54.05389 INFO::Found 0 missing values.
2026-04-29 21:50:54.057489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:50:54.058152 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.986 4.313 22.993
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.936 | 1.281 | 20.436 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.012 | 0.002 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |