Yannis Schumann
| Snapshot Date: 2026-02-20 13:40 -0500 (Fri, 20 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-21 11:32 -0500 (Sat, 21 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4871 |
| 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 169/2354 | 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 | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-20 21:30:23 -0500 (Fri, 20 Feb 2026) |
| EndedAt: 2026-02-20 21:31:51 -0500 (Fri, 20 Feb 2026) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.341 1.127 16.549
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-20 21:31:13.908247 INFO::Formatting Data.
2026-02-20 21:31:13.909592 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:13.920731 INFO::Removing potential empty rows and columns
2026-02-20 21:31:14.158913 INFO::Found 0 missing values.
2026-02-20 21:31:14.16232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:14.163018 INFO::Done
2026-02-20 21:31:14.163595 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:14.175572 INFO::Starting hierarchical adjustment
2026-02-20 21:31:14.176501 INFO::Found 3 batches.
2026-02-20 21:31:14.177066 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:14.178198 INFO::Using default BPPARAM
2026-02-20 21:31:14.178773 INFO::Processing subtree level 1
2026-02-20 21:31:14.287323 INFO::Adjusting the last 1 batches sequentially
2026-02-20 21:31:14.289427 INFO::Done
2026-02-20 21:31:14.290235 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:14.293258 INFO::ASW Batch was 0.00227433631824035 prior to batch effect correction and is now 0.00227433631824035 .
2026-02-20 21:31:14.294547 INFO::Total function execution time is 0.386821508407593 s and adjustment time is 0.113089799880981 s ( 29.24 )
2026-02-20 21:31:14.309698 INFO::Formatting Data.
2026-02-20 21:31:14.31057 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:14.311603 INFO::Removing potential empty rows and columns
2026-02-20 21:31:14.312879 INFO::Found 0 missing values.
2026-02-20 21:31:14.313891 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-20 21:31:14.325061 INFO::Formatting Data.
2026-02-20 21:31:14.325875 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:14.326821 INFO::Removing potential empty rows and columns
2026-02-20 21:31:14.327925 INFO::Found 0 missing values.
2026-02-20 21:31:14.328866 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-20 21:31:14.344807 INFO::Formatting Data.
2026-02-20 21:31:14.345582 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:14.346465 INFO::Removing potential empty rows and columns
2026-02-20 21:31:14.347524 INFO::Found 0 missing values.
2026-02-20 21:31:14.348461 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-20 21:31:14.353013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:14.353638 INFO::Done
2026-02-20 21:31:14.354174 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:14.356222 INFO::Starting hierarchical adjustment
2026-02-20 21:31:14.356946 INFO::Found 2 batches.
2026-02-20 21:31:14.357498 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:14.358142 INFO::Using default BPPARAM
2026-02-20 21:31:14.358685 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:14.359607 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-20 21:31:14.379806 INFO::Done
2026-02-20 21:31:14.380499 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:14.382702 INFO::ASW Batch was -0.0487085950459482 prior to batch effect correction and is now -0.123507049769444 .
2026-02-20 21:31:14.383519 INFO::Total function execution time is 0.0387539863586426 s and adjustment time is 0.0229859352111816 s ( 59.31 )
2026-02-20 21:31:14.386297 INFO::Formatting Data.
2026-02-20 21:31:14.386935 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:14.395584 INFO::Formatting Data.
2026-02-20 21:31:14.396267 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:14.39714 INFO::Removing potential empty rows and columns
2026-02-20 21:31:14.398182 INFO::Found 0 missing values.
2026-02-20 21:31:14.401139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:14.401688 INFO::Done
2026-02-20 21:31:14.402214 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:14.404235 INFO::Starting hierarchical adjustment
2026-02-20 21:31:14.40495 INFO::Found 2 batches.
2026-02-20 21:31:14.405499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:14.406138 INFO::Using default BPPARAM
2026-02-20 21:31:14.406703 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:14.407648 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:14.442852 INFO::Done
2026-02-20 21:31:14.44352 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:14.44539 INFO::ASW Batch was -0.0627153243783966 prior to batch effect correction and is now -0.110850846546606 .
2026-02-20 21:31:14.446138 INFO::Total function execution time is 0.0505728721618652 s and adjustment time is 0.0380170345306396 s ( 75.17 )
2026-02-20 21:31:14.447105 INFO::Formatting Data.
2026-02-20 21:31:14.447664 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:14.448464 INFO::Removing potential empty rows and columns
2026-02-20 21:31:14.449402 INFO::Found 0 missing values.
2026-02-20 21:31:14.45196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:14.452479 INFO::Done
2026-02-20 21:31:14.452966 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:14.45477 INFO::Starting hierarchical adjustment
2026-02-20 21:31:14.455429 INFO::Found 2 batches.
2026-02-20 21:31:14.455919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:14.456489 INFO::Using default BPPARAM
2026-02-20 21:31:14.45697 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:14.457805 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:14.471145 INFO::Done
2026-02-20 21:31:14.471722 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:14.473532 INFO::ASW Batch was -0.0627153243783966 prior to batch effect correction and is now -0.110850846546606 .
2026-02-20 21:31:14.47424 INFO::Total function execution time is 0.0271289348602295 s and adjustment time is 0.0158615112304688 s ( 58.47 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-20 21:31:17.297564 INFO::Formatting Data.
2026-02-20 21:31:17.298289 INFO::Recognized SummarizedExperiment
2026-02-20 21:31:17.298823 INFO::Typecasting input to dataframe.
2026-02-20 21:31:17.328345 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:17.3296 INFO::Removing potential empty rows and columns
2026-02-20 21:31:17.333632 INFO::Found 0 missing values.
2026-02-20 21:31:17.341355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:17.342002 INFO::Done
2026-02-20 21:31:17.342558 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:17.346267 INFO::Starting hierarchical adjustment
2026-02-20 21:31:17.347007 INFO::Found 2 batches.
2026-02-20 21:31:17.347546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:17.348663 INFO::Using default BPPARAM
2026-02-20 21:31:17.349231 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:17.350236 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-20 21:31:17.408031 INFO::Done
2026-02-20 21:31:17.408819 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:17.412489 INFO::ASW Batch was -0.0181937757855967 prior to batch effect correction and is now -0.0928724312626435 .
2026-02-20 21:31:17.413344 INFO::Total function execution time is 0.116085290908813 s and adjustment time is 0.0611457824707031 s ( 52.67 )
Warning: stack imbalance in '{', 73 then 75
2026-02-20 21:31:17.432492 INFO::Formatting Data.
2026-02-20 21:31:17.433318 INFO::Recognized SummarizedExperiment
2026-02-20 21:31:17.433909 INFO::Typecasting input to dataframe.
2026-02-20 21:31:17.44347 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:17.44472 INFO::Removing potential empty rows and columns
2026-02-20 21:31:17.448756 INFO::Found 0 missing values.
2026-02-20 21:31:17.456415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:17.457051 INFO::Done
2026-02-20 21:31:17.457606 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:17.461246 INFO::Starting hierarchical adjustment
2026-02-20 21:31:17.461976 INFO::Found 2 batches.
2026-02-20 21:31:17.462514 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:17.463153 INFO::Using default BPPARAM
2026-02-20 21:31:17.4637 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:17.464699 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-20 21:31:17.490815 INFO::Done
2026-02-20 21:31:17.491569 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:17.495095 INFO::ASW Batch was 0.00834299371505098 prior to batch effect correction and is now 0.00834299371505098 .
2026-02-20 21:31:17.495998 INFO::Total function execution time is 0.0635371208190918 s and adjustment time is 0.0289590358734131 s ( 45.58 )
2026-02-20 21:31:17.514186 INFO::Formatting Data.
2026-02-20 21:31:17.514993 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:17.515911 INFO::Removing potential empty rows and columns
2026-02-20 21:31:17.516948 INFO::Found 0 missing values.
2026-02-20 21:31:17.51997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:17.520521 INFO::Done
2026-02-20 21:31:17.521041 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:17.523076 INFO::Starting hierarchical adjustment
2026-02-20 21:31:17.523808 INFO::Found 3 batches.
2026-02-20 21:31:17.524329 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:17.524943 INFO::Using default BPPARAM
2026-02-20 21:31:17.525484 INFO::Processing subtree level 1
2026-02-20 21:31:17.661719 INFO::Adjusting the last 1 batches sequentially
2026-02-20 21:31:17.663547 INFO::Done
2026-02-20 21:31:17.664196 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:17.666693 INFO::ASW Batch was -0.00413794034629968 prior to batch effect correction and is now -0.179714655734881 .
2026-02-20 21:31:17.667623 INFO::Total function execution time is 0.153478622436523 s and adjustment time is 0.139875411987305 s ( 91.14 )
2026-02-20 21:31:17.682118 INFO::Skipping initial DF formatting
2026-02-20 21:31:17.682852 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:17.686921 INFO::Starting hierarchical adjustment
2026-02-20 21:31:17.687733 INFO::Found 5 batches.
2026-02-20 21:31:17.688291 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:17.688935 INFO::Using default BPPARAM
2026-02-20 21:31:17.689493 INFO::Processing subtree level 1
2026-02-20 21:31:17.915575 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:17.91714 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-20 21:31:17.937274 INFO::Done
2026-02-20 21:31:17.938022 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:17.984251 INFO::ASW Batch was 0.528307932241638 prior to batch effect correction and is now 0.528307932241638 .
2026-02-20 21:31:17.984968 INFO::ASW Label was 0.332984539531673 prior to batch effect correction and is now 0.332984539531673 .
2026-02-20 21:31:17.985841 INFO::Total function execution time is 0.303812980651855 s and adjustment time is 0.249684572219849 s ( 82.18 )
2026-02-20 21:31:18.002736 INFO::Formatting Data.
2026-02-20 21:31:18.003533 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.004476 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.005496 INFO::Found 0 missing values.
2026-02-20 21:31:18.009732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.010277 INFO::Done
2026-02-20 21:31:18.010828 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.013834 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.014549 INFO::Found 5 batches.
2026-02-20 21:31:18.01509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.01578 INFO::Using default BPPARAM
2026-02-20 21:31:18.016332 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.143549 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.145256 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.162411 INFO::Done
2026-02-20 21:31:18.163102 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.166456 INFO::ASW Batch was 0.280096323942743 prior to batch effect correction and is now -0.0733127648231152 .
2026-02-20 21:31:18.167079 INFO::ASW Label was 0.430535339166406 prior to batch effect correction and is now 0.853511677991619 .
2026-02-20 21:31:18.167909 INFO::Total function execution time is 0.165230512619019 s and adjustment time is 0.147980928421021 s ( 89.56 )
2026-02-20 21:31:18.168826 INFO::Formatting Data.
2026-02-20 21:31:18.169482 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.17039 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.171423 INFO::Found 0 missing values.
2026-02-20 21:31:18.175737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.176284 INFO::Done
2026-02-20 21:31:18.176842 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.179942 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.180644 INFO::Found 5 batches.
2026-02-20 21:31:18.181178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.181801 INFO::Using default BPPARAM
2026-02-20 21:31:18.182346 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.301002 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.302834 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.318655 INFO::Done
2026-02-20 21:31:18.319342 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.322554 INFO::ASW Batch was 0.280096323942743 prior to batch effect correction and is now -0.0733127648231152 .
2026-02-20 21:31:18.323144 INFO::ASW Label was 0.430535339166406 prior to batch effect correction and is now 0.853511677991619 .
2026-02-20 21:31:18.323958 INFO::Total function execution time is 0.155136346817017 s and adjustment time is 0.138127088546753 s ( 89.04 )
2026-02-20 21:31:18.337442 INFO::Formatting Data.
2026-02-20 21:31:18.338241 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.339164 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.340261 INFO::Found 0 missing values.
2026-02-20 21:31:18.344316 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.344902 INFO::Done
2026-02-20 21:31:18.345443 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.348421 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.349129 INFO::Found 5 batches.
2026-02-20 21:31:18.349677 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.350302 INFO::Using default BPPARAM
2026-02-20 21:31:18.350899 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.482926 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.484788 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.502985 INFO::Done
2026-02-20 21:31:18.503722 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.507305 INFO::ASW Batch was 0.442084675675429 prior to batch effect correction and is now -0.0544559413530025 .
2026-02-20 21:31:18.50797 INFO::ASW Label was 0.412433737619124 prior to batch effect correction and is now 0.794529541753978 .
2026-02-20 21:31:18.508893 INFO::Total function execution time is 0.171515703201294 s and adjustment time is 0.153984308242798 s ( 89.78 )
2026-02-20 21:31:18.509859 INFO::Formatting Data.
2026-02-20 21:31:18.510591 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.511626 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.512799 INFO::Found 0 missing values.
2026-02-20 21:31:18.517669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.518425 INFO::Done
2026-02-20 21:31:18.519033 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.522343 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.523181 INFO::Found 5 batches.
2026-02-20 21:31:18.523757 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.524431 INFO::Using default BPPARAM
2026-02-20 21:31:18.525005 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.650202 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.652025 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.670053 INFO::Done
2026-02-20 21:31:18.670902 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.674721 INFO::ASW Batch was 0.442084675675429 prior to batch effect correction and is now -0.0544559413530025 .
2026-02-20 21:31:18.67535 INFO::ASW Label was 0.412433737619124 prior to batch effect correction and is now 0.794529541753978 .
2026-02-20 21:31:18.67625 INFO::Total function execution time is 0.166394233703613 s and adjustment time is 0.146997690200806 s ( 88.34 )
2026-02-20 21:31:18.690401 INFO::Formatting Data.
2026-02-20 21:31:18.691211 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.692153 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.693219 INFO::Found 0 missing values.
2026-02-20 21:31:18.695959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.696536 INFO::Done
2026-02-20 21:31:18.697063 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.700022 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.700759 INFO::Found 2 batches.
2026-02-20 21:31:18.701299 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.701934 INFO::Using default BPPARAM
2026-02-20 21:31:18.702515 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.703437 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.718569 INFO::Done
2026-02-20 21:31:18.719321 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.722326 INFO::ASW Batch was 0.725778793033613 prior to batch effect correction and is now 0.055872673604698 .
2026-02-20 21:31:18.722968 INFO::ASW Label was 0.360199622884094 prior to batch effect correction and is now 0.856292759650694 .
2026-02-20 21:31:18.723764 INFO::Total function execution time is 0.0334575176239014 s and adjustment time is 0.0179333686828613 s ( 53.6 )
2026-02-20 21:31:18.724567 INFO::Formatting Data.
2026-02-20 21:31:18.725196 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.726062 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.727061 INFO::Found 0 missing values.
2026-02-20 21:31:18.729849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.730402 INFO::Done
2026-02-20 21:31:18.73093 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.733785 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.734496 INFO::Found 2 batches.
2026-02-20 21:31:18.735019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.735627 INFO::Using default BPPARAM
2026-02-20 21:31:18.736158 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.73706 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-20 21:31:18.751081 INFO::Done
2026-02-20 21:31:18.751917 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.755048 INFO::ASW Batch was 0.725778793033613 prior to batch effect correction and is now 0.055872673604698 .
2026-02-20 21:31:18.755667 INFO::ASW Label was 0.360199622884094 prior to batch effect correction and is now 0.856292759650694 .
2026-02-20 21:31:18.756434 INFO::Total function execution time is 0.0318739414215088 s and adjustment time is 0.0167362689971924 s ( 52.51 )
2026-02-20 21:31:18.767652 INFO::Formatting Data.
2026-02-20 21:31:18.768379 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.769232 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.77011 INFO::Found 0 missing values.
2026-02-20 21:31:18.772173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.772701 INFO::Done
2026-02-20 21:31:18.773198 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.775014 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.775689 INFO::Found 2 batches.
2026-02-20 21:31:18.776194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.776809 INFO::Using default BPPARAM
2026-02-20 21:31:18.77732 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.778189 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-20 21:31:18.807577 INFO::Done
2026-02-20 21:31:18.808266 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.810148 INFO::ASW Batch was 0.0556274736098241 prior to batch effect correction and is now -0.104640999031893 .
2026-02-20 21:31:18.810941 INFO::Total function execution time is 0.0433597564697266 s and adjustment time is 0.0320003032684326 s ( 73.8 )
2026-02-20 21:31:18.82223 INFO::Formatting Data.
2026-02-20 21:31:18.822963 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.823801 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.824754 INFO::Found 0 missing values.
2026-02-20 21:31:18.825831 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-20 21:31:18.830209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.83075 INFO::Done
2026-02-20 21:31:18.831256 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.834033 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.834711 INFO::Found 2 batches.
2026-02-20 21:31:18.835225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.835848 INFO::Using default BPPARAM
2026-02-20 21:31:18.83636 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.837263 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-20 21:31:18.852805 INFO::Done
2026-02-20 21:31:18.853498 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.856324 INFO::ASW Batch was 0.573504863494262 prior to batch effect correction and is now 0.201988210169633 .
2026-02-20 21:31:18.856901 INFO::ASW Label was 0.432530173607048 prior to batch effect correction and is now 0.727594490955335 .
2026-02-20 21:31:18.857667 INFO::Total function execution time is 0.0355033874511719 s and adjustment time is 0.0182163715362549 s ( 51.31 )
2026-02-20 21:31:18.858422 INFO::Formatting Data.
2026-02-20 21:31:18.859009 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:18.859864 INFO::Removing potential empty rows and columns
2026-02-20 21:31:18.86079 INFO::Found 0 missing values.
2026-02-20 21:31:18.86164 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-20 21:31:18.865953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:18.866491 INFO::Done
2026-02-20 21:31:18.866995 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:18.869775 INFO::Starting hierarchical adjustment
2026-02-20 21:31:18.870447 INFO::Found 2 batches.
2026-02-20 21:31:18.87099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:18.871589 INFO::Using default BPPARAM
2026-02-20 21:31:18.872097 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:18.872971 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-20 21:31:18.888436 INFO::Done
2026-02-20 21:31:18.889112 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:18.891947 INFO::ASW Batch was 0.573504863494262 prior to batch effect correction and is now 0.201988210169633 .
2026-02-20 21:31:18.892566 INFO::ASW Label was 0.432530173607048 prior to batch effect correction and is now 0.727594490955335 .
2026-02-20 21:31:18.893342 INFO::Total function execution time is 0.0349435806274414 s and adjustment time is 0.0181043148040771 s ( 51.81 )
2026-02-20 21:31:19.097783 INFO::Formatting Data.
2026-02-20 21:31:19.098599 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:19.099534 INFO::Removing potential empty rows and columns
2026-02-20 21:31:19.100613 INFO::Found 0 missing values.
2026-02-20 21:31:19.103682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:19.10422 INFO::Done
2026-02-20 21:31:19.104758 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:19.106796 INFO::Starting hierarchical adjustment
2026-02-20 21:31:19.107517 INFO::Found 3 batches.
2026-02-20 21:31:19.108048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:19.1087 INFO::Using default BPPARAM
2026-02-20 21:31:19.10923 INFO::Processing subtree level 1
2026-02-20 21:31:19.195513 INFO::Adjusting the last 1 batches sequentially
2026-02-20 21:31:19.197356 INFO::Done
2026-02-20 21:31:19.198045 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:19.200742 INFO::ASW Batch was -0.0861126881172182 prior to batch effect correction and is now -0.0861126881172182 .
2026-02-20 21:31:19.201731 INFO::Total function execution time is 0.103995323181152 s and adjustment time is 0.0899736881256104 s ( 86.52 )
2026-02-20 21:31:19.202819 INFO::Formatting Data.
2026-02-20 21:31:19.203501 INFO::Typecasting input to dataframe.
2026-02-20 21:31:19.204295 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:19.205239 INFO::Removing potential empty rows and columns
2026-02-20 21:31:19.206346 INFO::Found 0 missing values.
2026-02-20 21:31:19.209549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:19.210147 INFO::Done
2026-02-20 21:31:19.2107 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:19.212787 INFO::Starting hierarchical adjustment
2026-02-20 21:31:19.21354 INFO::Found 3 batches.
2026-02-20 21:31:19.214083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:19.214738 INFO::Using default BPPARAM
2026-02-20 21:31:19.215302 INFO::Processing subtree level 1
2026-02-20 21:31:19.300897 INFO::Adjusting the last 1 batches sequentially
2026-02-20 21:31:19.302769 INFO::Done
2026-02-20 21:31:19.303487 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:19.306017 INFO::ASW Batch was -0.0861126881172182 prior to batch effect correction and is now -0.0861126881172182 .
2026-02-20 21:31:19.307 INFO::Total function execution time is 0.104146003723145 s and adjustment time is 0.089374303817749 s ( 85.82 )
2026-02-20 21:31:19.320417 INFO::Formatting Data.
2026-02-20 21:31:19.321258 INFO::Typecasting input to dataframe.
2026-02-20 21:31:19.322121 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:19.323044 INFO::Removing potential empty rows and columns
2026-02-20 21:31:19.324155 INFO::Found 0 missing values.
2026-02-20 21:31:19.32731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:19.327878 INFO::Done
2026-02-20 21:31:19.32843 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:19.330544 INFO::Starting hierarchical adjustment
2026-02-20 21:31:19.331261 INFO::Found 3 batches.
2026-02-20 21:31:19.331822 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:19.332465 INFO::Using default BPPARAM
2026-02-20 21:31:19.333009 INFO::Processing subtree level 1
2026-02-20 21:31:19.41992 INFO::Adjusting the last 1 batches sequentially
2026-02-20 21:31:19.421926 INFO::Done
2026-02-20 21:31:19.422653 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:19.425301 INFO::ASW Batch was -0.0599573534222104 prior to batch effect correction and is now -0.0599573534222104 .
2026-02-20 21:31:19.426317 INFO::Total function execution time is 0.105962038040161 s and adjustment time is 0.0907719135284424 s ( 85.66 )
2026-02-20 21:31:19.568968 INFO::Formatting Data.
2026-02-20 21:31:19.569842 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:19.571023 INFO::Removing potential empty rows and columns
2026-02-20 21:31:19.573969 INFO::Found 1000 missing values.
2026-02-20 21:31:19.594237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:19.59514 INFO::Done
2026-02-20 21:31:19.595798 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:19.601587 INFO::Starting hierarchical adjustment
2026-02-20 21:31:19.602457 INFO::Found 10 batches.
2026-02-20 21:31:19.603042 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:19.603746 INFO::Using default BPPARAM
2026-02-20 21:31:19.604297 INFO::Processing subtree level 1
2026-02-20 21:31:19.747313 INFO::Processing subtree level 2
2026-02-20 21:31:19.897925 INFO::Adjusting the last 1 batches sequentially
2026-02-20 21:31:19.900359 INFO::Done
2026-02-20 21:31:19.901196 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:19.90773 INFO::ASW Batch was 0.511758582078277 prior to batch effect correction and is now 0.511758582078277 .
2026-02-20 21:31:19.908573 INFO::ASW Label was 0.300754827041585 prior to batch effect correction and is now 0.300754827041585 .
2026-02-20 21:31:19.909696 INFO::Total function execution time is 0.340746402740479 s and adjustment time is 0.298061609268188 s ( 87.47 )
2026-02-20 21:31:19.910714 INFO::Formatting Data.
2026-02-20 21:31:19.911512 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:19.912983 INFO::Removing potential empty rows and columns
2026-02-20 21:31:19.91644 INFO::Found 1000 missing values.
2026-02-20 21:31:19.940144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:19.941104 INFO::Done
2026-02-20 21:31:19.941793 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:19.94786 INFO::Starting hierarchical adjustment
2026-02-20 21:31:19.948758 INFO::Found 10 batches.
2026-02-20 21:31:21.042635 INFO::Set up parallel execution backend with 2 workers
2026-02-20 21:31:21.045572 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-20 21:31:22.199888 INFO::Adjusting the last 2 batches sequentially
2026-02-20 21:31:22.201897 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-20 21:31:22.219242 INFO::Done
2026-02-20 21:31:22.220038 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:22.224918 INFO::ASW Batch was 0.511758582078277 prior to batch effect correction and is now 0.511758582078277 .
2026-02-20 21:31:22.2256 INFO::ASW Label was 0.300754827041585 prior to batch effect correction and is now 0.300754827041585 .
2026-02-20 21:31:22.226383 INFO::Total function execution time is 2.3157262802124 s and adjustment time is 2.27062749862671 s ( 98.05 )
2026-02-20 21:31:22.391028 INFO::Formatting Data.
2026-02-20 21:31:22.392385 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.39398 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.395883 INFO::Found 0 missing values.
2026-02-20 21:31:22.40277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:22.403809 INFO::Done
2026-02-20 21:31:22.404744 INFO::Acquiring quality metrics before batch effect correction.
2026-02-20 21:31:22.409359 INFO::Starting hierarchical adjustment
2026-02-20 21:31:22.410609 INFO::Found 3 batches.
2026-02-20 21:31:22.41153 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-20 21:31:22.412627 INFO::Using default BPPARAM
2026-02-20 21:31:22.413563 INFO::Processing subtree level 1
2026-02-20 21:31:22.559422 INFO::Adjusting the last 1 batches sequentially
2026-02-20 21:31:22.561722 INFO::Done
2026-02-20 21:31:22.562608 INFO::Acquiring quality metrics after batch effect correction.
2026-02-20 21:31:22.566514 INFO::ASW Batch was 0.1960354966432 prior to batch effect correction and is now -0.124212917372887 .
2026-02-20 21:31:22.567306 INFO::ASW Label was -0.204024484184098 prior to batch effect correction and is now -0.151363117908509 .
2026-02-20 21:31:22.568469 INFO::Total function execution time is 0.177567005157471 s and adjustment time is 0.151385545730591 s ( 85.26 )
2026-02-20 21:31:22.706978 INFO::Formatting Data.
2026-02-20 21:31:22.707922 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.708895 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.709978 INFO::Found 2 missing values.
2026-02-20 21:31:22.713012 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:22.713612 INFO::Done
2026-02-20 21:31:22.743793 INFO::Found NA in Reference column
2026-02-20 21:31:22.753887 INFO::Require at least two references per batch.
2026-02-20 21:31:22.774895 INFO::Formatting Data.
2026-02-20 21:31:22.775768 INFO::Recognized SummarizedExperiment
2026-02-20 21:31:22.776324 INFO::Typecasting input to dataframe.
2026-02-20 21:31:22.786473 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.787746 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.791538 INFO::Found 0 missing values.
2026-02-20 21:31:22.798861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:22.799661 INFO::Done
2026-02-20 21:31:22.816308 INFO::Formatting Data.
2026-02-20 21:31:22.817183 INFO::Recognized SummarizedExperiment
2026-02-20 21:31:22.817774 INFO::Typecasting input to dataframe.
2026-02-20 21:31:22.836575 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.838021 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.841809 INFO::Found 0 missing values.
2026-02-20 21:31:22.853445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:22.854256 INFO::Done
2026-02-20 21:31:22.870439 INFO::Formatting Data.
2026-02-20 21:31:22.871263 INFO::Recognized SummarizedExperiment
2026-02-20 21:31:22.871837 INFO::Typecasting input to dataframe.
2026-02-20 21:31:22.888932 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.890074 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.891227 INFO::Found 0 missing values.
2026-02-20 21:31:22.892159 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-20 21:31:22.896564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:22.897163 INFO::Done
2026-02-20 21:31:22.907535 INFO::Formatting Data.
2026-02-20 21:31:22.908424 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.909343 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.910392 INFO::Found 0 missing values.
2026-02-20 21:31:22.91331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:22.913872 INFO::Done
2026-02-20 21:31:22.926432 INFO::Formatting Data.
2026-02-20 21:31:22.927363 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.928359 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.929507 INFO::Found 0 missing values.
2026-02-20 21:31:22.932631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:22.933201 INFO::Done
2026-02-20 21:31:22.965667 INFO::Formatting Data.
2026-02-20 21:31:22.966626 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.967902 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.969131 INFO::Found 1 missing values.
2026-02-20 21:31:22.971938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:22.972544 INFO::Done
2026-02-20 21:31:22.993764 INFO::Formatting Data.
2026-02-20 21:31:22.994692 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:22.995771 INFO::Removing potential empty rows and columns
2026-02-20 21:31:22.996855 INFO::Found 2 missing values.
2026-02-20 21:31:22.997876 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-20 21:31:23.000725 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:23.001324 INFO::Done
2026-02-20 21:31:23.022099 INFO::Formatting Data.
2026-02-20 21:31:23.023128 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:23.024144 INFO::Removing potential empty rows and columns
2026-02-20 21:31:23.025166 INFO::Found 2 missing values.
2026-02-20 21:31:23.026862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:23.02747 INFO::Done
2026-02-20 21:31:23.039186 INFO::Formatting Data.
2026-02-20 21:31:23.040124 INFO::Typecasting input to dataframe.
2026-02-20 21:31:23.041239 INFO::Replacing NaNs with NAs.
2026-02-20 21:31:23.042185 INFO::Removing potential empty rows and columns
2026-02-20 21:31:23.04328 INFO::Found 0 missing values.
2026-02-20 21:31:23.046444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-20 21:31:23.047027 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.279 3.458 20.354
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.341 | 1.127 | 16.549 | |
| compute_asw | 0.025 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.010 | 0.001 | 0.012 | |