Yannis Schumann
| Snapshot Date: 2026-02-26 13:40 -0500 (Thu, 26 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 2026-02-27 11:32 -0500 (Fri, 27 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4877 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 169/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 2026-02-26 21:34:51 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 21:36:20 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 89.1 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 23.866 1.511 17.571
* 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")
2026-02-26 21:35:42.672884 INFO::Formatting Data.
2026-02-26 21:35:42.674431 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:42.685944 INFO::Removing potential empty rows and columns
2026-02-26 21:35:42.937419 INFO::Found 0 missing values.
2026-02-26 21:35:42.941066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:42.941821 INFO::Done
2026-02-26 21:35:42.942411 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:42.961597 INFO::Starting hierarchical adjustment
2026-02-26 21:35:42.962696 INFO::Found 3 batches.
2026-02-26 21:35:42.963325 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:42.964741 INFO::Using default BPPARAM
2026-02-26 21:35:42.965425 INFO::Processing subtree level 1
2026-02-26 21:35:43.070684 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:35:43.072539 INFO::Done
2026-02-26 21:35:43.073245 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:43.076046 INFO::ASW Batch was -0.0948603292669166 prior to batch effect correction and is now -0.0948603292669166 .
2026-02-26 21:35:43.077206 INFO::Total function execution time is 0.404969930648804 s and adjustment time is 0.110055923461914 s ( 27.18 )
2026-02-26 21:35:43.091976 INFO::Formatting Data.
2026-02-26 21:35:43.092837 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:43.093882 INFO::Removing potential empty rows and columns
2026-02-26 21:35:43.095218 INFO::Found 0 missing values.
2026-02-26 21:35:43.096278 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.
2026-02-26 21:35:43.108505 INFO::Formatting Data.
2026-02-26 21:35:43.109233 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:43.110181 INFO::Removing potential empty rows and columns
2026-02-26 21:35:43.111285 INFO::Found 0 missing values.
2026-02-26 21:35:43.112278 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.
2026-02-26 21:35:43.130556 INFO::Formatting Data.
2026-02-26 21:35:43.131403 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:43.132342 INFO::Removing potential empty rows and columns
2026-02-26 21:35:43.133566 INFO::Found 0 missing values.
2026-02-26 21:35:43.134592 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.
2026-02-26 21:35:43.139709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:43.14034 INFO::Done
2026-02-26 21:35:43.140957 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:43.14329 INFO::Starting hierarchical adjustment
2026-02-26 21:35:43.144056 INFO::Found 2 batches.
2026-02-26 21:35:43.14464 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:43.145322 INFO::Using default BPPARAM
2026-02-26 21:35:43.1459 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:43.14691 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:35:43.170077 INFO::Done
2026-02-26 21:35:43.170815 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:43.173336 INFO::ASW Batch was 0.0248790461437152 prior to batch effect correction and is now -0.126130212713715 .
2026-02-26 21:35:43.174222 INFO::Total function execution time is 0.0437602996826172 s and adjustment time is 0.0261530876159668 s ( 59.76 )
2026-02-26 21:35:43.177342 INFO::Formatting Data.
2026-02-26 21:35:43.178052 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:43.187329 INFO::Formatting Data.
2026-02-26 21:35:43.18805 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:43.189002 INFO::Removing potential empty rows and columns
2026-02-26 21:35:43.190081 INFO::Found 0 missing values.
2026-02-26 21:35:43.193155 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:43.193753 INFO::Done
2026-02-26 21:35:43.194301 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:43.196407 INFO::Starting hierarchical adjustment
2026-02-26 21:35:43.197139 INFO::Found 2 batches.
2026-02-26 21:35:43.19774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:43.19841 INFO::Using default BPPARAM
2026-02-26 21:35:43.198972 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:43.19996 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:35:43.252641 INFO::Done
2026-02-26 21:35:43.253397 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:43.255525 INFO::ASW Batch was 0.0458369206354793 prior to batch effect correction and is now -0.103223903793158 .
2026-02-26 21:35:43.256326 INFO::Total function execution time is 0.0690221786499023 s and adjustment time is 0.0556159019470215 s ( 80.58 )
2026-02-26 21:35:43.257437 INFO::Formatting Data.
2026-02-26 21:35:43.258044 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:43.258911 INFO::Removing potential empty rows and columns
2026-02-26 21:35:43.259955 INFO::Found 0 missing values.
2026-02-26 21:35:43.262773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:43.263304 INFO::Done
2026-02-26 21:35:43.26385 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:43.265865 INFO::Starting hierarchical adjustment
2026-02-26 21:35:43.2666 INFO::Found 2 batches.
2026-02-26 21:35:43.267127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:43.267741 INFO::Using default BPPARAM
2026-02-26 21:35:43.268237 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:43.269169 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:35:43.284664 INFO::Done
2026-02-26 21:35:43.285317 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:43.287557 INFO::ASW Batch was 0.0458369206354793 prior to batch effect correction and is now -0.103223903793158 .
2026-02-26 21:35:43.288404 INFO::Total function execution time is 0.0309658050537109 s and adjustment time is 0.0182211399078369 s ( 58.84 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-26 21:35:46.276017 INFO::Formatting Data.
2026-02-26 21:35:46.276726 INFO::Recognized SummarizedExperiment
2026-02-26 21:35:46.277221 INFO::Typecasting input to dataframe.
2026-02-26 21:35:46.30705 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:46.308313 INFO::Removing potential empty rows and columns
2026-02-26 21:35:46.312428 INFO::Found 0 missing values.
2026-02-26 21:35:46.320271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:46.320989 INFO::Done
2026-02-26 21:35:46.321572 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:46.325319 INFO::Starting hierarchical adjustment
2026-02-26 21:35:46.326089 INFO::Found 2 batches.
2026-02-26 21:35:46.326655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:46.327907 INFO::Using default BPPARAM
2026-02-26 21:35:46.328478 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:46.329515 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:35:46.387907 INFO::Done
2026-02-26 21:35:46.388661 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:46.392271 INFO::ASW Batch was -0.0105261497568761 prior to batch effect correction and is now -0.0900088040206394 .
2026-02-26 21:35:46.39315 INFO::Total function execution time is 0.117406368255615 s and adjustment time is 0.0619471073150635 s ( 52.76 )
Warning: stack imbalance in '{', 73 then 75
2026-02-26 21:35:46.412517 INFO::Formatting Data.
2026-02-26 21:35:46.413297 INFO::Recognized SummarizedExperiment
2026-02-26 21:35:46.413893 INFO::Typecasting input to dataframe.
2026-02-26 21:35:46.423573 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:46.424806 INFO::Removing potential empty rows and columns
2026-02-26 21:35:46.428802 INFO::Found 0 missing values.
2026-02-26 21:35:46.436604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:46.437271 INFO::Done
2026-02-26 21:35:46.437861 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:46.441522 INFO::Starting hierarchical adjustment
2026-02-26 21:35:46.442263 INFO::Found 2 batches.
2026-02-26 21:35:46.44281 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:46.443461 INFO::Using default BPPARAM
2026-02-26 21:35:46.443993 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:46.445013 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:35:46.471683 INFO::Done
2026-02-26 21:35:46.472489 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:46.476201 INFO::ASW Batch was 0.032412430071314 prior to batch effect correction and is now 0.032412430071314 .
2026-02-26 21:35:46.477101 INFO::Total function execution time is 0.064586877822876 s and adjustment time is 0.0295326709747314 s ( 45.73 )
2026-02-26 21:35:46.496332 INFO::Formatting Data.
2026-02-26 21:35:46.497178 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:46.498142 INFO::Removing potential empty rows and columns
2026-02-26 21:35:46.499237 INFO::Found 0 missing values.
2026-02-26 21:35:46.502418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:46.502973 INFO::Done
2026-02-26 21:35:46.503537 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:46.505643 INFO::Starting hierarchical adjustment
2026-02-26 21:35:46.506364 INFO::Found 3 batches.
2026-02-26 21:35:46.506914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:46.507556 INFO::Using default BPPARAM
2026-02-26 21:35:46.508092 INFO::Processing subtree level 1
2026-02-26 21:35:46.642997 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:35:46.644921 INFO::Done
2026-02-26 21:35:46.645636 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:46.648233 INFO::ASW Batch was 0.0141735828509601 prior to batch effect correction and is now -0.183206130405605 .
2026-02-26 21:35:46.649206 INFO::Total function execution time is 0.152894735336304 s and adjustment time is 0.138677597045898 s ( 90.7 )
2026-02-26 21:35:46.663708 INFO::Skipping initial DF formatting
2026-02-26 21:35:46.664426 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:46.668611 INFO::Starting hierarchical adjustment
2026-02-26 21:35:46.66941 INFO::Found 5 batches.
2026-02-26 21:35:46.669973 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:46.670633 INFO::Using default BPPARAM
2026-02-26 21:35:46.671172 INFO::Processing subtree level 1
2026-02-26 21:35:46.907096 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:46.909011 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:35:46.930642 INFO::Done
2026-02-26 21:35:46.931499 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:46.936066 INFO::ASW Batch was 0.532916709249605 prior to batch effect correction and is now 0.532916709249605 .
2026-02-26 21:35:46.936727 INFO::ASW Label was 0.394250964776468 prior to batch effect correction and is now 0.394250964776468 .
2026-02-26 21:35:46.937688 INFO::Total function execution time is 0.274042367935181 s and adjustment time is 0.261365413665771 s ( 95.37 )
2026-02-26 21:35:47.001536 INFO::Formatting Data.
2026-02-26 21:35:47.002318 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.003276 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.00423 INFO::Found 0 missing values.
2026-02-26 21:35:47.008427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.008979 INFO::Done
2026-02-26 21:35:47.009593 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.012744 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.013469 INFO::Found 5 batches.
2026-02-26 21:35:47.014018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.014683 INFO::Using default BPPARAM
2026-02-26 21:35:47.015224 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.
2026-02-26 21:35:47.154845 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.156628 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:35:47.174843 INFO::Done
2026-02-26 21:35:47.175613 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.179252 INFO::ASW Batch was 0.338920647419195 prior to batch effect correction and is now -0.0971711551129463 .
2026-02-26 21:35:47.179979 INFO::ASW Label was 0.300013233680889 prior to batch effect correction and is now 0.908619790801925 .
2026-02-26 21:35:47.18088 INFO::Total function execution time is 0.179426431655884 s and adjustment time is 0.161514282226562 s ( 90.02 )
2026-02-26 21:35:47.181807 INFO::Formatting Data.
2026-02-26 21:35:47.182494 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.183519 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.184727 INFO::Found 0 missing values.
2026-02-26 21:35:47.189353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.189987 INFO::Done
2026-02-26 21:35:47.190598 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.19399 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.194798 INFO::Found 5 batches.
2026-02-26 21:35:47.195376 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.196068 INFO::Using default BPPARAM
2026-02-26 21:35:47.196675 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.
2026-02-26 21:35:47.327176 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.329197 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:35:47.348716 INFO::Done
2026-02-26 21:35:47.349665 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.35365 INFO::ASW Batch was 0.338920647419195 prior to batch effect correction and is now -0.0971711551129463 .
2026-02-26 21:35:47.354398 INFO::ASW Label was 0.300013233680889 prior to batch effect correction and is now 0.908619790801925 .
2026-02-26 21:35:47.35545 INFO::Total function execution time is 0.173598289489746 s and adjustment time is 0.154023408889771 s ( 88.72 )
2026-02-26 21:35:47.38165 INFO::Formatting Data.
2026-02-26 21:35:47.382903 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.384054 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.385302 INFO::Found 0 missing values.
2026-02-26 21:35:47.389964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.390616 INFO::Done
2026-02-26 21:35:47.391198 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.394957 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.395773 INFO::Found 5 batches.
2026-02-26 21:35:47.396338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.397091 INFO::Using default BPPARAM
2026-02-26 21:35:47.397686 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.
2026-02-26 21:35:47.547663 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.54942 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:35:47.566817 INFO::Done
2026-02-26 21:35:47.567632 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.571212 INFO::ASW Batch was 0.315775306251447 prior to batch effect correction and is now -0.0464020902695472 .
2026-02-26 21:35:47.571922 INFO::ASW Label was 0.459161998150561 prior to batch effect correction and is now 0.819350395222037 .
2026-02-26 21:35:47.572835 INFO::Total function execution time is 0.191666841506958 s and adjustment time is 0.171194791793823 s ( 89.32 )
2026-02-26 21:35:47.573748 INFO::Formatting Data.
2026-02-26 21:35:47.574469 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.575441 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.576576 INFO::Found 0 missing values.
2026-02-26 21:35:47.581076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.581686 INFO::Done
2026-02-26 21:35:47.582278 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.585729 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.586511 INFO::Found 5 batches.
2026-02-26 21:35:47.587126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.58783 INFO::Using default BPPARAM
2026-02-26 21:35:47.588424 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.
2026-02-26 21:35:47.715648 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.717395 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:35:47.735139 INFO::Done
2026-02-26 21:35:47.735957 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.739587 INFO::ASW Batch was 0.315775306251447 prior to batch effect correction and is now -0.0464020902695472 .
2026-02-26 21:35:47.740285 INFO::ASW Label was 0.459161998150561 prior to batch effect correction and is now 0.819350395222037 .
2026-02-26 21:35:47.741314 INFO::Total function execution time is 0.167535066604614 s and adjustment time is 0.14875316619873 s ( 88.79 )
2026-02-26 21:35:47.756746 INFO::Formatting Data.
2026-02-26 21:35:47.757565 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.75849 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.759534 INFO::Found 0 missing values.
2026-02-26 21:35:47.762248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.762849 INFO::Done
2026-02-26 21:35:47.763399 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.766423 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.767144 INFO::Found 2 batches.
2026-02-26 21:35:47.767709 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.768342 INFO::Using default BPPARAM
2026-02-26 21:35:47.768936 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.769877 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:35:47.784705 INFO::Done
2026-02-26 21:35:47.785357 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.788354 INFO::ASW Batch was 0.51921686825991 prior to batch effect correction and is now 0.0573667440538974 .
2026-02-26 21:35:47.788937 INFO::ASW Label was 0.51597952944957 prior to batch effect correction and is now 0.877127974559901 .
2026-02-26 21:35:47.789753 INFO::Total function execution time is 0.0330941677093506 s and adjustment time is 0.0177047252655029 s ( 53.5 )
2026-02-26 21:35:47.790563 INFO::Formatting Data.
2026-02-26 21:35:47.791175 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.792062 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.793045 INFO::Found 0 missing values.
2026-02-26 21:35:47.795764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.796327 INFO::Done
2026-02-26 21:35:47.79687 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.799786 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.800503 INFO::Found 2 batches.
2026-02-26 21:35:47.80104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.801658 INFO::Using default BPPARAM
2026-02-26 21:35:47.802216 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.803159 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:35:47.818552 INFO::Done
2026-02-26 21:35:47.819239 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.822132 INFO::ASW Batch was 0.51921686825991 prior to batch effect correction and is now 0.0573667440538974 .
2026-02-26 21:35:47.822743 INFO::ASW Label was 0.51597952944957 prior to batch effect correction and is now 0.877127974559901 .
2026-02-26 21:35:47.82354 INFO::Total function execution time is 0.0329756736755371 s and adjustment time is 0.0181894302368164 s ( 55.16 )
2026-02-26 21:35:47.834841 INFO::Formatting Data.
2026-02-26 21:35:47.835603 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.836495 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.837416 INFO::Found 0 missing values.
2026-02-26 21:35:47.839596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.840151 INFO::Done
2026-02-26 21:35:47.840684 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.842672 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.843389 INFO::Found 2 batches.
2026-02-26 21:35:47.84391 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.844531 INFO::Using default BPPARAM
2026-02-26 21:35:47.845079 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.84598 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:35:47.877107 INFO::Done
2026-02-26 21:35:47.877813 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.879764 INFO::ASW Batch was 0.104568128741578 prior to batch effect correction and is now -0.103218205673522 .
2026-02-26 21:35:47.88061 INFO::Total function execution time is 0.0458197593688965 s and adjustment time is 0.0338501930236816 s ( 73.88 )
2026-02-26 21:35:47.892677 INFO::Formatting Data.
2026-02-26 21:35:47.893465 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.894352 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.895355 INFO::Found 0 missing values.
2026-02-26 21:35:47.896556 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.
2026-02-26 21:35:47.901028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.901588 INFO::Done
2026-02-26 21:35:47.902113 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.904999 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.905708 INFO::Found 2 batches.
2026-02-26 21:35:47.906224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.906876 INFO::Using default BPPARAM
2026-02-26 21:35:47.907437 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.908349 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:35:47.924552 INFO::Done
2026-02-26 21:35:47.92521 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.928045 INFO::ASW Batch was 0.636668123189679 prior to batch effect correction and is now 0.0129903911885616 .
2026-02-26 21:35:47.928674 INFO::ASW Label was 0.344027502237549 prior to batch effect correction and is now 0.871614513312966 .
2026-02-26 21:35:47.929467 INFO::Total function execution time is 0.0368680953979492 s and adjustment time is 0.0189595222473145 s ( 51.43 )
2026-02-26 21:35:47.930226 INFO::Formatting Data.
2026-02-26 21:35:47.930838 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:47.931746 INFO::Removing potential empty rows and columns
2026-02-26 21:35:47.932743 INFO::Found 0 missing values.
2026-02-26 21:35:47.933625 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.
2026-02-26 21:35:47.938111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:47.938675 INFO::Done
2026-02-26 21:35:47.939189 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:47.941998 INFO::Starting hierarchical adjustment
2026-02-26 21:35:47.942688 INFO::Found 2 batches.
2026-02-26 21:35:47.943227 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:47.943838 INFO::Using default BPPARAM
2026-02-26 21:35:47.944351 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:47.945283 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:35:47.961393 INFO::Done
2026-02-26 21:35:47.962055 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:47.964895 INFO::ASW Batch was 0.636668123189679 prior to batch effect correction and is now 0.0129903911885616 .
2026-02-26 21:35:47.965495 INFO::ASW Label was 0.344027502237549 prior to batch effect correction and is now 0.871614513312966 .
2026-02-26 21:35:47.966253 INFO::Total function execution time is 0.0360417366027832 s and adjustment time is 0.018808126449585 s ( 52.18 )
2026-02-26 21:35:48.17498 INFO::Formatting Data.
2026-02-26 21:35:48.175953 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:48.176952 INFO::Removing potential empty rows and columns
2026-02-26 21:35:48.178133 INFO::Found 0 missing values.
2026-02-26 21:35:48.181446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:48.182017 INFO::Done
2026-02-26 21:35:48.182581 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:48.185007 INFO::Starting hierarchical adjustment
2026-02-26 21:35:48.185765 INFO::Found 3 batches.
2026-02-26 21:35:48.186312 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:48.187035 INFO::Using default BPPARAM
2026-02-26 21:35:48.1876 INFO::Processing subtree level 1
2026-02-26 21:35:48.278545 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:35:48.280425 INFO::Done
2026-02-26 21:35:48.281131 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:48.283705 INFO::ASW Batch was -0.0504150101302241 prior to batch effect correction and is now -0.0504150101302241 .
2026-02-26 21:35:48.284752 INFO::Total function execution time is 0.109898567199707 s and adjustment time is 0.09478759765625 s ( 86.25 )
2026-02-26 21:35:48.285769 INFO::Formatting Data.
2026-02-26 21:35:48.286442 INFO::Typecasting input to dataframe.
2026-02-26 21:35:48.287203 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:48.288145 INFO::Removing potential empty rows and columns
2026-02-26 21:35:48.289251 INFO::Found 0 missing values.
2026-02-26 21:35:48.292405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:48.293002 INFO::Done
2026-02-26 21:35:48.29359 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:48.295621 INFO::Starting hierarchical adjustment
2026-02-26 21:35:48.296324 INFO::Found 3 batches.
2026-02-26 21:35:48.2969 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:48.297539 INFO::Using default BPPARAM
2026-02-26 21:35:48.298116 INFO::Processing subtree level 1
2026-02-26 21:35:48.381634 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:35:48.383415 INFO::Done
2026-02-26 21:35:48.384076 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:48.386584 INFO::ASW Batch was -0.0504150101302241 prior to batch effect correction and is now -0.0504150101302241 .
2026-02-26 21:35:48.387573 INFO::Total function execution time is 0.101733684539795 s and adjustment time is 0.0871813297271729 s ( 85.7 )
2026-02-26 21:35:48.401061 INFO::Formatting Data.
2026-02-26 21:35:48.401888 INFO::Typecasting input to dataframe.
2026-02-26 21:35:48.402769 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:48.403704 INFO::Removing potential empty rows and columns
2026-02-26 21:35:48.404835 INFO::Found 0 missing values.
2026-02-26 21:35:48.407888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:48.408462 INFO::Done
2026-02-26 21:35:48.409002 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:48.411193 INFO::Starting hierarchical adjustment
2026-02-26 21:35:48.411947 INFO::Found 3 batches.
2026-02-26 21:35:48.412522 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:48.413162 INFO::Using default BPPARAM
2026-02-26 21:35:48.41374 INFO::Processing subtree level 1
2026-02-26 21:35:48.498082 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:35:48.499999 INFO::Done
2026-02-26 21:35:48.50074 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:48.503383 INFO::ASW Batch was 0.0126063170554177 prior to batch effect correction and is now 0.0126063170554177 .
2026-02-26 21:35:48.504391 INFO::Total function execution time is 0.10336971282959 s and adjustment time is 0.0881743431091309 s ( 85.3 )
2026-02-26 21:35:48.642395 INFO::Formatting Data.
2026-02-26 21:35:48.643213 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:48.644355 INFO::Removing potential empty rows and columns
2026-02-26 21:35:48.647323 INFO::Found 1000 missing values.
2026-02-26 21:35:48.668235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:48.669026 INFO::Done
2026-02-26 21:35:48.669647 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:48.67526 INFO::Starting hierarchical adjustment
2026-02-26 21:35:48.676055 INFO::Found 10 batches.
2026-02-26 21:35:48.67664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:48.677322 INFO::Using default BPPARAM
2026-02-26 21:35:48.677925 INFO::Processing subtree level 1
2026-02-26 21:35:48.817976 INFO::Processing subtree level 2
2026-02-26 21:35:48.958814 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:35:48.961551 INFO::Done
2026-02-26 21:35:48.962508 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:48.970986 INFO::ASW Batch was 0.474239576164109 prior to batch effect correction and is now 0.474239576164109 .
2026-02-26 21:35:48.972013 INFO::ASW Label was 0.352570251344763 prior to batch effect correction and is now 0.352570251344763 .
2026-02-26 21:35:48.97339 INFO::Total function execution time is 0.330991983413696 s and adjustment time is 0.285595655441284 s ( 86.28 )
2026-02-26 21:35:48.974618 INFO::Formatting Data.
2026-02-26 21:35:48.975546 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:48.977205 INFO::Removing potential empty rows and columns
2026-02-26 21:35:48.981865 INFO::Found 1000 missing values.
2026-02-26 21:35:49.014376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:49.015468 INFO::Done
2026-02-26 21:35:49.016378 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:49.024701 INFO::Starting hierarchical adjustment
2026-02-26 21:35:49.025866 INFO::Found 10 batches.
2026-02-26 21:35:50.118718 INFO::Set up parallel execution backend with 2 workers
2026-02-26 21:35:50.120794 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-26 21:35:51.256529 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:35:51.258398 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:35:51.275665 INFO::Done
2026-02-26 21:35:51.276421 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:51.281077 INFO::ASW Batch was 0.474239576164109 prior to batch effect correction and is now 0.474239576164109 .
2026-02-26 21:35:51.281773 INFO::ASW Label was 0.352570251344763 prior to batch effect correction and is now 0.352570251344763 .
2026-02-26 21:35:51.282546 INFO::Total function execution time is 2.30804204940796 s and adjustment time is 2.25005173683167 s ( 97.49 )
2026-02-26 21:35:51.428307 INFO::Formatting Data.
2026-02-26 21:35:51.429168 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.430107 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.431198 INFO::Found 0 missing values.
2026-02-26 21:35:51.434953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.435545 INFO::Done
2026-02-26 21:35:51.436056 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:35:51.43879 INFO::Starting hierarchical adjustment
2026-02-26 21:35:51.439522 INFO::Found 3 batches.
2026-02-26 21:35:51.440041 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:35:51.440705 INFO::Using default BPPARAM
2026-02-26 21:35:51.441231 INFO::Processing subtree level 1
2026-02-26 21:35:51.546911 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:35:51.548882 INFO::Done
2026-02-26 21:35:51.549638 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:35:51.55305 INFO::ASW Batch was 0.103517058761385 prior to batch effect correction and is now -0.128079515337842 .
2026-02-26 21:35:51.553795 INFO::ASW Label was -0.146665743457274 prior to batch effect correction and is now 0.0143021801347709 .
2026-02-26 21:35:51.55478 INFO::Total function execution time is 0.126545429229736 s and adjustment time is 0.109475374221802 s ( 86.51 )
2026-02-26 21:35:51.685188 INFO::Formatting Data.
2026-02-26 21:35:51.686084 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.687056 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.688146 INFO::Found 2 missing values.
2026-02-26 21:35:51.691035 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.691655 INFO::Done
2026-02-26 21:35:51.721006 INFO::Found NA in Reference column
2026-02-26 21:35:51.731412 INFO::Require at least two references per batch.
2026-02-26 21:35:51.751376 INFO::Formatting Data.
2026-02-26 21:35:51.752171 INFO::Recognized SummarizedExperiment
2026-02-26 21:35:51.752722 INFO::Typecasting input to dataframe.
2026-02-26 21:35:51.762259 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.763513 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.767202 INFO::Found 0 missing values.
2026-02-26 21:35:51.774147 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.774844 INFO::Done
2026-02-26 21:35:51.790416 INFO::Formatting Data.
2026-02-26 21:35:51.791191 INFO::Recognized SummarizedExperiment
2026-02-26 21:35:51.791726 INFO::Typecasting input to dataframe.
2026-02-26 21:35:51.809325 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.810617 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.814289 INFO::Found 0 missing values.
2026-02-26 21:35:51.825556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.826317 INFO::Done
2026-02-26 21:35:51.843135 INFO::Formatting Data.
2026-02-26 21:35:51.844033 INFO::Recognized SummarizedExperiment
2026-02-26 21:35:51.844636 INFO::Typecasting input to dataframe.
2026-02-26 21:35:51.861228 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.862287 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.863422 INFO::Found 0 missing values.
2026-02-26 21:35:51.864313 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.
2026-02-26 21:35:51.868539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.86914 INFO::Done
2026-02-26 21:35:51.879847 INFO::Formatting Data.
2026-02-26 21:35:51.880775 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.881787 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.882869 INFO::Found 0 missing values.
2026-02-26 21:35:51.885917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.886494 INFO::Done
2026-02-26 21:35:51.89892 INFO::Formatting Data.
2026-02-26 21:35:51.899785 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.900702 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.901792 INFO::Found 0 missing values.
2026-02-26 21:35:51.904812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.905376 INFO::Done
2026-02-26 21:35:51.948889 INFO::Formatting Data.
2026-02-26 21:35:51.950099 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.951248 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.952486 INFO::Found 1 missing values.
2026-02-26 21:35:51.955116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.955694 INFO::Done
2026-02-26 21:35:51.975377 INFO::Formatting Data.
2026-02-26 21:35:51.976228 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.977113 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.978079 INFO::Found 2 missing values.
2026-02-26 21:35:51.978976 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.
2026-02-26 21:35:51.981418 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.981937 INFO::Done
2026-02-26 21:35:51.992021 INFO::Formatting Data.
2026-02-26 21:35:51.992821 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:51.993711 INFO::Removing potential empty rows and columns
2026-02-26 21:35:51.994625 INFO::Found 2 missing values.
2026-02-26 21:35:51.996158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:51.996705 INFO::Done
2026-02-26 21:35:52.00707 INFO::Formatting Data.
2026-02-26 21:35:52.007876 INFO::Typecasting input to dataframe.
2026-02-26 21:35:52.008687 INFO::Replacing NaNs with NAs.
2026-02-26 21:35:52.00953 INFO::Removing potential empty rows and columns
2026-02-26 21:35:52.010508 INFO::Found 0 missing values.
2026-02-26 21:35:52.013314 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:35:52.013867 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.170 3.668 20.600
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.866 | 1.511 | 17.571 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.013 | |
| generate_dataset | 0.011 | 0.000 | 0.012 | |