Yannis Schumann
| Snapshot Date: 2026-04-15 13:40 -0400 (Wed, 15 Apr 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-16 11:35 -0400 (Thu, 16 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4928 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4659 |
| 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 170/2394 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| 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: 2026-04-15 21:42:20 -0400 (Wed, 15 Apr 2026) |
| EndedAt: 2026-04-15 21:43:48 -0400 (Wed, 15 Apr 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 version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-16 01:42:21 UTC
* 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 23.615 1.377 17.088
* 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 version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-04-15 21:43:11.474228 INFO::Formatting Data.
2026-04-15 21:43:11.475593 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:11.486503 INFO::Removing potential empty rows and columns
2026-04-15 21:43:11.717964 INFO::Found 0 missing values.
2026-04-15 21:43:11.721214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:11.721884 INFO::Done
2026-04-15 21:43:11.722466 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:11.734668 INFO::Starting hierarchical adjustment
2026-04-15 21:43:11.735543 INFO::Found 3 batches.
2026-04-15 21:43:11.736117 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:11.73722 INFO::Using default BPPARAM
2026-04-15 21:43:11.737794 INFO::Processing subtree level 1
2026-04-15 21:43:11.837022 INFO::Adjusting the last 1 batches sequentially
2026-04-15 21:43:11.838892 INFO::Done
2026-04-15 21:43:11.83958 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:11.842195 INFO::ASW Batch was 0.00291056763732792 prior to batch effect correction and is now 0.00291056763732792 .
2026-04-15 21:43:11.843325 INFO::Total function execution time is 0.369703769683838 s and adjustment time is 0.103507995605469 s ( 28 )
2026-04-15 21:43:11.857178 INFO::Formatting Data.
2026-04-15 21:43:11.857979 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:11.858926 INFO::Removing potential empty rows and columns
2026-04-15 21:43:11.86007 INFO::Found 0 missing values.
2026-04-15 21:43:11.861037 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-15 21:43:11.871892 INFO::Formatting Data.
2026-04-15 21:43:11.872665 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:11.873616 INFO::Removing potential empty rows and columns
2026-04-15 21:43:11.874815 INFO::Found 0 missing values.
2026-04-15 21:43:11.875773 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-15 21:43:11.891746 INFO::Formatting Data.
2026-04-15 21:43:11.892564 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:11.893475 INFO::Removing potential empty rows and columns
2026-04-15 21:43:11.894512 INFO::Found 0 missing values.
2026-04-15 21:43:11.895448 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-15 21:43:11.899778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:11.900356 INFO::Done
2026-04-15 21:43:11.900896 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:11.902937 INFO::Starting hierarchical adjustment
2026-04-15 21:43:11.90367 INFO::Found 2 batches.
2026-04-15 21:43:11.904229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:11.904905 INFO::Using default BPPARAM
2026-04-15 21:43:11.905472 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:11.906459 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-15 21:43:11.926998 INFO::Done
2026-04-15 21:43:11.927731 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:11.929716 INFO::ASW Batch was -0.0312157902559822 prior to batch effect correction and is now -0.118341381953365 .
2026-04-15 21:43:11.930532 INFO::Total function execution time is 0.0388517379760742 s and adjustment time is 0.0234453678131104 s ( 60.35 )
2026-04-15 21:43:11.933352 INFO::Formatting Data.
2026-04-15 21:43:11.934029 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:11.942694 INFO::Formatting Data.
2026-04-15 21:43:11.943418 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:11.944317 INFO::Removing potential empty rows and columns
2026-04-15 21:43:11.945399 INFO::Found 0 missing values.
2026-04-15 21:43:11.948375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:11.948945 INFO::Done
2026-04-15 21:43:11.949501 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:11.951534 INFO::Starting hierarchical adjustment
2026-04-15 21:43:11.952265 INFO::Found 2 batches.
2026-04-15 21:43:11.952835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:11.953478 INFO::Using default BPPARAM
2026-04-15 21:43:11.954062 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:11.954995 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:11.9705 INFO::Done
2026-04-15 21:43:11.971231 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:11.973348 INFO::ASW Batch was 0.0457246496486866 prior to batch effect correction and is now -0.104545457586153 .
2026-04-15 21:43:11.974219 INFO::Total function execution time is 0.031541109085083 s and adjustment time is 0.0183577537536621 s ( 58.2 )
2026-04-15 21:43:11.975326 INFO::Formatting Data.
2026-04-15 21:43:11.975975 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:11.976899 INFO::Removing potential empty rows and columns
2026-04-15 21:43:11.977985 INFO::Found 0 missing values.
2026-04-15 21:43:11.980967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:11.981574 INFO::Done
2026-04-15 21:43:11.982145 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:11.984215 INFO::Starting hierarchical adjustment
2026-04-15 21:43:11.984978 INFO::Found 2 batches.
2026-04-15 21:43:11.985589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:11.986266 INFO::Using default BPPARAM
2026-04-15 21:43:11.986831 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:11.987775 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:12.002686 INFO::Done
2026-04-15 21:43:12.003415 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:12.005436 INFO::ASW Batch was 0.0457246496486866 prior to batch effect correction and is now -0.104545457586153 .
2026-04-15 21:43:12.00624 INFO::Total function execution time is 0.0309300422668457 s and adjustment time is 0.017848014831543 s ( 57.7 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-15 21:43:14.996177 INFO::Formatting Data.
2026-04-15 21:43:14.996943 INFO::Recognized SummarizedExperiment
2026-04-15 21:43:14.997468 INFO::Typecasting input to dataframe.
2026-04-15 21:43:15.026471 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:15.027665 INFO::Removing potential empty rows and columns
2026-04-15 21:43:15.030879 INFO::Found 0 missing values.
2026-04-15 21:43:15.036925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:15.037501 INFO::Done
2026-04-15 21:43:15.038 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:15.041131 INFO::Starting hierarchical adjustment
2026-04-15 21:43:15.041804 INFO::Found 2 batches.
2026-04-15 21:43:15.042327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:15.043305 INFO::Using default BPPARAM
2026-04-15 21:43:15.043846 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:15.044753 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-15 21:43:15.093081 INFO::Done
2026-04-15 21:43:15.093863 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:15.097057 INFO::ASW Batch was -0.00777047299107102 prior to batch effect correction and is now -0.0901180366669048 .
2026-04-15 21:43:15.097873 INFO::Total function execution time is 0.101965427398682 s and adjustment time is 0.0513672828674316 s ( 50.38 )
Warning: stack imbalance in '{', 73 then 75
2026-04-15 21:43:15.114536 INFO::Formatting Data.
2026-04-15 21:43:15.115241 INFO::Recognized SummarizedExperiment
2026-04-15 21:43:15.115761 INFO::Typecasting input to dataframe.
2026-04-15 21:43:15.123816 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:15.124871 INFO::Removing potential empty rows and columns
2026-04-15 21:43:15.127984 INFO::Found 0 missing values.
2026-04-15 21:43:15.13402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:15.134592 INFO::Done
2026-04-15 21:43:15.135097 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:15.138196 INFO::Starting hierarchical adjustment
2026-04-15 21:43:15.138867 INFO::Found 2 batches.
2026-04-15 21:43:15.139384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:15.139944 INFO::Using default BPPARAM
2026-04-15 21:43:15.14048 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:15.14137 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-15 21:43:15.165137 INFO::Done
2026-04-15 21:43:15.165895 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:15.169415 INFO::ASW Batch was 0.00105724499267737 prior to batch effect correction and is now 0.00105724499267737 .
2026-04-15 21:43:15.170274 INFO::Total function execution time is 0.0557007789611816 s and adjustment time is 0.0263690948486328 s ( 47.34 )
2026-04-15 21:43:15.188094 INFO::Formatting Data.
2026-04-15 21:43:15.188889 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:15.189808 INFO::Removing potential empty rows and columns
2026-04-15 21:43:15.190848 INFO::Found 0 missing values.
2026-04-15 21:43:15.193779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:15.194354 INFO::Done
2026-04-15 21:43:15.1949 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:15.196896 INFO::Starting hierarchical adjustment
2026-04-15 21:43:15.197616 INFO::Found 3 batches.
2026-04-15 21:43:15.198167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:15.198812 INFO::Using default BPPARAM
2026-04-15 21:43:15.199371 INFO::Processing subtree level 1
2026-04-15 21:43:15.328752 INFO::Adjusting the last 1 batches sequentially
2026-04-15 21:43:15.330721 INFO::Done
2026-04-15 21:43:15.331483 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:15.334081 INFO::ASW Batch was -0.00331519769559528 prior to batch effect correction and is now -0.142202613561627 .
2026-04-15 21:43:15.335068 INFO::Total function execution time is 0.146993398666382 s and adjustment time is 0.133208274841309 s ( 90.62 )
2026-04-15 21:43:15.349598 INFO::Skipping initial DF formatting
2026-04-15 21:43:15.35038 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:15.354523 INFO::Starting hierarchical adjustment
2026-04-15 21:43:15.355335 INFO::Found 5 batches.
2026-04-15 21:43:15.355945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:15.356608 INFO::Using default BPPARAM
2026-04-15 21:43:15.357183 INFO::Processing subtree level 1
2026-04-15 21:43:15.47629 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:15.478102 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-15 21:43:15.498469 INFO::Done
2026-04-15 21:43:15.499553 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:15.503965 INFO::ASW Batch was 0.545787088971221 prior to batch effect correction and is now 0.545787088971221 .
2026-04-15 21:43:15.504643 INFO::ASW Label was 0.335595456012616 prior to batch effect correction and is now 0.335595456012616 .
2026-04-15 21:43:15.505544 INFO::Total function execution time is 0.156007766723633 s and adjustment time is 0.143254041671753 s ( 91.82 )
2026-04-15 21:43:15.52315 INFO::Formatting Data.
2026-04-15 21:43:15.523977 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:15.524922 INFO::Removing potential empty rows and columns
2026-04-15 21:43:15.525965 INFO::Found 0 missing values.
2026-04-15 21:43:15.530284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:15.530854 INFO::Done
2026-04-15 21:43:15.531428 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:15.534445 INFO::Starting hierarchical adjustment
2026-04-15 21:43:15.535175 INFO::Found 5 batches.
2026-04-15 21:43:15.535762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:15.536419 INFO::Using default BPPARAM
2026-04-15 21:43:15.536996 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:15.63908 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:15.640606 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:15.656029 INFO::Done
2026-04-15 21:43:15.656754 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:15.659895 INFO::ASW Batch was 0.441728025047811 prior to batch effect correction and is now -0.106045453541411 .
2026-04-15 21:43:15.660537 INFO::ASW Label was 0.261767523920883 prior to batch effect correction and is now 0.895342396665977 .
2026-04-15 21:43:15.66136 INFO::Total function execution time is 0.138263940811157 s and adjustment time is 0.120985269546509 s ( 87.5 )
2026-04-15 21:43:15.662202 INFO::Formatting Data.
2026-04-15 21:43:15.662873 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:15.663773 INFO::Removing potential empty rows and columns
2026-04-15 21:43:15.664806 INFO::Found 0 missing values.
2026-04-15 21:43:15.668889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:15.669484 INFO::Done
2026-04-15 21:43:15.670039 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:15.673193 INFO::Starting hierarchical adjustment
2026-04-15 21:43:15.673932 INFO::Found 5 batches.
2026-04-15 21:43:15.674507 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:15.67518 INFO::Using default BPPARAM
2026-04-15 21:43:15.675759 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:15.777306 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:15.778925 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:15.795648 INFO::Done
2026-04-15 21:43:15.796455 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:15.799823 INFO::ASW Batch was 0.441728025047811 prior to batch effect correction and is now -0.106045453541411 .
2026-04-15 21:43:15.800509 INFO::ASW Label was 0.261767523920883 prior to batch effect correction and is now 0.895342396665977 .
2026-04-15 21:43:15.801409 INFO::Total function execution time is 0.139179944992065 s and adjustment time is 0.121820449829102 s ( 87.53 )
2026-04-15 21:43:15.815943 INFO::Formatting Data.
2026-04-15 21:43:15.816841 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:15.818072 INFO::Removing potential empty rows and columns
2026-04-15 21:43:15.819121 INFO::Found 0 missing values.
2026-04-15 21:43:15.823287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:15.82388 INFO::Done
2026-04-15 21:43:15.824486 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:15.827497 INFO::Starting hierarchical adjustment
2026-04-15 21:43:15.828261 INFO::Found 5 batches.
2026-04-15 21:43:15.828821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:15.829491 INFO::Using default BPPARAM
2026-04-15 21:43:15.830067 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:15.93138 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:15.932934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:15.948301 INFO::Done
2026-04-15 21:43:15.949091 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:15.952349 INFO::ASW Batch was 0.353775275469479 prior to batch effect correction and is now -0.0685953828043074 .
2026-04-15 21:43:15.952987 INFO::ASW Label was 0.414725236491713 prior to batch effect correction and is now 0.857187359446465 .
2026-04-15 21:43:15.953853 INFO::Total function execution time is 0.137980461120605 s and adjustment time is 0.120168685913086 s ( 87.09 )
2026-04-15 21:43:15.954717 INFO::Formatting Data.
2026-04-15 21:43:15.955402 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:15.956354 INFO::Removing potential empty rows and columns
2026-04-15 21:43:15.957366 INFO::Found 0 missing values.
2026-04-15 21:43:15.961607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:15.962213 INFO::Done
2026-04-15 21:43:15.962779 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:15.965774 INFO::Starting hierarchical adjustment
2026-04-15 21:43:15.966521 INFO::Found 5 batches.
2026-04-15 21:43:15.967123 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:15.967798 INFO::Using default BPPARAM
2026-04-15 21:43:15.968394 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:16.069225 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:16.070932 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:16.087242 INFO::Done
2026-04-15 21:43:16.088039 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.09145 INFO::ASW Batch was 0.353775275469479 prior to batch effect correction and is now -0.0685953828043074 .
2026-04-15 21:43:16.092099 INFO::ASW Label was 0.414725236491713 prior to batch effect correction and is now 0.857187359446465 .
2026-04-15 21:43:16.093012 INFO::Total function execution time is 0.138284921646118 s and adjustment time is 0.120840311050415 s ( 87.39 )
2026-04-15 21:43:16.10711 INFO::Formatting Data.
2026-04-15 21:43:16.107934 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:16.108921 INFO::Removing potential empty rows and columns
2026-04-15 21:43:16.109967 INFO::Found 0 missing values.
2026-04-15 21:43:16.112708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:16.113303 INFO::Done
2026-04-15 21:43:16.113855 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:16.116783 INFO::Starting hierarchical adjustment
2026-04-15 21:43:16.117539 INFO::Found 2 batches.
2026-04-15 21:43:16.118095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:16.118763 INFO::Using default BPPARAM
2026-04-15 21:43:16.11933 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:16.120283 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:16.13473 INFO::Done
2026-04-15 21:43:16.135423 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.138328 INFO::ASW Batch was 0.808969299714859 prior to batch effect correction and is now -0.0245037437815332 .
2026-04-15 21:43:16.138929 INFO::ASW Label was 0.194086279373228 prior to batch effect correction and is now 0.802054950380838 .
2026-04-15 21:43:16.139752 INFO::Total function execution time is 0.032728910446167 s and adjustment time is 0.0173394680023193 s ( 52.98 )
2026-04-15 21:43:16.140588 INFO::Formatting Data.
2026-04-15 21:43:16.141243 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:16.142125 INFO::Removing potential empty rows and columns
2026-04-15 21:43:16.143121 INFO::Found 0 missing values.
2026-04-15 21:43:16.145833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:16.146429 INFO::Done
2026-04-15 21:43:16.146986 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:16.149862 INFO::Starting hierarchical adjustment
2026-04-15 21:43:16.150595 INFO::Found 2 batches.
2026-04-15 21:43:16.151149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:16.151787 INFO::Using default BPPARAM
2026-04-15 21:43:16.152372 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:16.15333 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-15 21:43:16.167735 INFO::Done
2026-04-15 21:43:16.168432 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.171319 INFO::ASW Batch was 0.808969299714859 prior to batch effect correction and is now -0.0245037437815332 .
2026-04-15 21:43:16.171918 INFO::ASW Label was 0.194086279373228 prior to batch effect correction and is now 0.802054950380838 .
2026-04-15 21:43:16.172756 INFO::Total function execution time is 0.0321784019470215 s and adjustment time is 0.0172760486602783 s ( 53.69 )
2026-04-15 21:43:16.183813 INFO::Formatting Data.
2026-04-15 21:43:16.184587 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:16.185484 INFO::Removing potential empty rows and columns
2026-04-15 21:43:16.186405 INFO::Found 0 missing values.
2026-04-15 21:43:16.188524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:16.189111 INFO::Done
2026-04-15 21:43:16.189684 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:16.191609 INFO::Starting hierarchical adjustment
2026-04-15 21:43:16.192326 INFO::Found 2 batches.
2026-04-15 21:43:16.192892 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:16.193612 INFO::Using default BPPARAM
2026-04-15 21:43:16.194196 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:16.195121 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-15 21:43:16.22569 INFO::Done
2026-04-15 21:43:16.226475 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.228465 INFO::ASW Batch was -0.00124293821212362 prior to batch effect correction and is now -0.164736201936785 .
2026-04-15 21:43:16.229294 INFO::Total function execution time is 0.0455431938171387 s and adjustment time is 0.0334916114807129 s ( 73.54 )
2026-04-15 21:43:16.240962 INFO::Formatting Data.
2026-04-15 21:43:16.241743 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:16.24264 INFO::Removing potential empty rows and columns
2026-04-15 21:43:16.243661 INFO::Found 0 missing values.
2026-04-15 21:43:16.244808 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-15 21:43:16.249377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:16.249991 INFO::Done
2026-04-15 21:43:16.250566 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:16.253585 INFO::Starting hierarchical adjustment
2026-04-15 21:43:16.254317 INFO::Found 2 batches.
2026-04-15 21:43:16.254883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:16.255524 INFO::Using default BPPARAM
2026-04-15 21:43:16.256105 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:16.25706 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-15 21:43:16.27316 INFO::Done
2026-04-15 21:43:16.273907 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.276801 INFO::ASW Batch was 0.734183289293707 prior to batch effect correction and is now 0.00399682075949325 .
2026-04-15 21:43:16.27742 INFO::ASW Label was 0.295665702780309 prior to batch effect correction and is now 0.879053990158075 .
2026-04-15 21:43:16.278234 INFO::Total function execution time is 0.0373425483703613 s and adjustment time is 0.0189807415008545 s ( 50.83 )
2026-04-15 21:43:16.279053 INFO::Formatting Data.
2026-04-15 21:43:16.279709 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:16.280648 INFO::Removing potential empty rows and columns
2026-04-15 21:43:16.281646 INFO::Found 0 missing values.
2026-04-15 21:43:16.282566 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-15 21:43:16.28721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:16.287812 INFO::Done
2026-04-15 21:43:16.288382 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:16.29129 INFO::Starting hierarchical adjustment
2026-04-15 21:43:16.292025 INFO::Found 2 batches.
2026-04-15 21:43:16.292588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:16.293252 INFO::Using default BPPARAM
2026-04-15 21:43:16.293824 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:16.294764 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-15 21:43:16.310907 INFO::Done
2026-04-15 21:43:16.311626 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.3146 INFO::ASW Batch was 0.734183289293707 prior to batch effect correction and is now 0.00399682075949325 .
2026-04-15 21:43:16.315215 INFO::ASW Label was 0.295665702780309 prior to batch effect correction and is now 0.879053990158075 .
2026-04-15 21:43:16.316028 INFO::Total function execution time is 0.0369932651519775 s and adjustment time is 0.019007682800293 s ( 51.38 )
2026-04-15 21:43:16.522462 INFO::Formatting Data.
2026-04-15 21:43:16.523333 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:16.524273 INFO::Removing potential empty rows and columns
2026-04-15 21:43:16.52534 INFO::Found 0 missing values.
2026-04-15 21:43:16.528392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:16.528967 INFO::Done
2026-04-15 21:43:16.529539 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:16.531598 INFO::Starting hierarchical adjustment
2026-04-15 21:43:16.532357 INFO::Found 3 batches.
2026-04-15 21:43:16.532912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:16.533587 INFO::Using default BPPARAM
2026-04-15 21:43:16.534144 INFO::Processing subtree level 1
2026-04-15 21:43:16.622815 INFO::Adjusting the last 1 batches sequentially
2026-04-15 21:43:16.624935 INFO::Done
2026-04-15 21:43:16.625751 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.628566 INFO::ASW Batch was -0.0695916849432811 prior to batch effect correction and is now -0.0695916849432811 .
2026-04-15 21:43:16.629719 INFO::Total function execution time is 0.107270956039429 s and adjustment time is 0.0926949977874756 s ( 86.41 )
2026-04-15 21:43:16.630937 INFO::Formatting Data.
2026-04-15 21:43:16.631668 INFO::Typecasting input to dataframe.
2026-04-15 21:43:16.632522 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:16.633558 INFO::Removing potential empty rows and columns
2026-04-15 21:43:16.634756 INFO::Found 0 missing values.
2026-04-15 21:43:16.638074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:16.638733 INFO::Done
2026-04-15 21:43:16.639337 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:16.641637 INFO::Starting hierarchical adjustment
2026-04-15 21:43:16.64243 INFO::Found 3 batches.
2026-04-15 21:43:16.643005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:16.643688 INFO::Using default BPPARAM
2026-04-15 21:43:16.644275 INFO::Processing subtree level 1
2026-04-15 21:43:16.738741 INFO::Adjusting the last 1 batches sequentially
2026-04-15 21:43:16.740672 INFO::Done
2026-04-15 21:43:16.741395 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.744063 INFO::ASW Batch was -0.0695916849432811 prior to batch effect correction and is now -0.0695916849432811 .
2026-04-15 21:43:16.745087 INFO::Total function execution time is 0.114142894744873 s and adjustment time is 0.0984020233154297 s ( 86.21 )
2026-04-15 21:43:16.758281 INFO::Formatting Data.
2026-04-15 21:43:16.759149 INFO::Typecasting input to dataframe.
2026-04-15 21:43:16.760051 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:16.76103 INFO::Removing potential empty rows and columns
2026-04-15 21:43:16.762148 INFO::Found 0 missing values.
2026-04-15 21:43:16.765193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:16.765794 INFO::Done
2026-04-15 21:43:16.7664 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:16.768478 INFO::Starting hierarchical adjustment
2026-04-15 21:43:16.769211 INFO::Found 3 batches.
2026-04-15 21:43:16.769804 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:16.770474 INFO::Using default BPPARAM
2026-04-15 21:43:16.771057 INFO::Processing subtree level 1
2026-04-15 21:43:16.859391 INFO::Adjusting the last 1 batches sequentially
2026-04-15 21:43:16.861539 INFO::Done
2026-04-15 21:43:16.86238 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:16.865251 INFO::ASW Batch was -0.109922337482791 prior to batch effect correction and is now -0.109922337482791 .
2026-04-15 21:43:16.866353 INFO::Total function execution time is 0.10811185836792 s and adjustment time is 0.092418909072876 s ( 85.48 )
2026-04-15 21:43:17.019639 INFO::Formatting Data.
2026-04-15 21:43:17.020722 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:17.022049 INFO::Removing potential empty rows and columns
2026-04-15 21:43:17.025093 INFO::Found 1000 missing values.
2026-04-15 21:43:17.045104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:17.046087 INFO::Done
2026-04-15 21:43:17.046769 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:17.052718 INFO::Starting hierarchical adjustment
2026-04-15 21:43:17.053655 INFO::Found 10 batches.
2026-04-15 21:43:17.054285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:17.055001 INFO::Using default BPPARAM
2026-04-15 21:43:17.055598 INFO::Processing subtree level 1
2026-04-15 21:43:17.220635 INFO::Processing subtree level 2
2026-04-15 21:43:17.368305 INFO::Adjusting the last 1 batches sequentially
2026-04-15 21:43:17.370647 INFO::Done
2026-04-15 21:43:17.37151 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:17.377788 INFO::ASW Batch was 0.488544328396685 prior to batch effect correction and is now 0.488544328396685 .
2026-04-15 21:43:17.378719 INFO::ASW Label was 0.327501930443787 prior to batch effect correction and is now 0.327501930443787 .
2026-04-15 21:43:17.379833 INFO::Total function execution time is 0.360343217849731 s and adjustment time is 0.317129135131836 s ( 88.01 )
2026-04-15 21:43:17.3808 INFO::Formatting Data.
2026-04-15 21:43:17.381526 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:17.382923 INFO::Removing potential empty rows and columns
2026-04-15 21:43:17.385959 INFO::Found 1000 missing values.
2026-04-15 21:43:17.40628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:17.407231 INFO::Done
2026-04-15 21:43:17.407913 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:17.413785 INFO::Starting hierarchical adjustment
2026-04-15 21:43:17.41478 INFO::Found 10 batches.
2026-04-15 21:43:18.8383 INFO::Set up parallel execution backend with 2 workers
2026-04-15 21:43:18.841397 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-15 21:43:20.479055 INFO::Adjusting the last 2 batches sequentially
2026-04-15 21:43:20.482592 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-15 21:43:20.500119 INFO::Done
2026-04-15 21:43:20.500847 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:20.505614 INFO::ASW Batch was 0.488544328396685 prior to batch effect correction and is now 0.488544328396685 .
2026-04-15 21:43:20.506235 INFO::ASW Label was 0.327501930443787 prior to batch effect correction and is now 0.327501930443787 .
2026-04-15 21:43:20.507081 INFO::Total function execution time is 3.12634325027466 s and adjustment time is 3.08552098274231 s ( 98.69 )
2026-04-15 21:43:20.653075 INFO::Formatting Data.
2026-04-15 21:43:20.653965 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:20.65495 INFO::Removing potential empty rows and columns
2026-04-15 21:43:20.65607 INFO::Found 0 missing values.
2026-04-15 21:43:20.659765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:20.660378 INFO::Done
2026-04-15 21:43:20.660926 INFO::Acquiring quality metrics before batch effect correction.
2026-04-15 21:43:20.663711 INFO::Starting hierarchical adjustment
2026-04-15 21:43:20.664446 INFO::Found 3 batches.
2026-04-15 21:43:20.665007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-15 21:43:20.665661 INFO::Using default BPPARAM
2026-04-15 21:43:20.666267 INFO::Processing subtree level 1
2026-04-15 21:43:20.769927 INFO::Adjusting the last 1 batches sequentially
2026-04-15 21:43:20.771744 INFO::Done
2026-04-15 21:43:20.772428 INFO::Acquiring quality metrics after batch effect correction.
2026-04-15 21:43:20.775586 INFO::ASW Batch was 0.180954627609672 prior to batch effect correction and is now -0.14487555628973 .
2026-04-15 21:43:20.776231 INFO::ASW Label was -0.184019354358348 prior to batch effect correction and is now 0.0387485039306353 .
2026-04-15 21:43:20.777159 INFO::Total function execution time is 0.124158382415771 s and adjustment time is 0.107434511184692 s ( 86.53 )
2026-04-15 21:43:20.896523 INFO::Formatting Data.
2026-04-15 21:43:20.897426 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:20.898399 INFO::Removing potential empty rows and columns
2026-04-15 21:43:20.899449 INFO::Found 2 missing values.
2026-04-15 21:43:20.90222 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:20.902809 INFO::Done
2026-04-15 21:43:20.930549 INFO::Found NA in Reference column
2026-04-15 21:43:20.9403 INFO::Require at least two references per batch.
2026-04-15 21:43:20.960636 INFO::Formatting Data.
2026-04-15 21:43:20.961462 INFO::Recognized SummarizedExperiment
2026-04-15 21:43:20.962026 INFO::Typecasting input to dataframe.
2026-04-15 21:43:20.971361 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:20.972631 INFO::Removing potential empty rows and columns
2026-04-15 21:43:20.976145 INFO::Found 0 missing values.
2026-04-15 21:43:20.98287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:20.983617 INFO::Done
2026-04-15 21:43:20.998627 INFO::Formatting Data.
2026-04-15 21:43:20.9995 INFO::Recognized SummarizedExperiment
2026-04-15 21:43:21.000067 INFO::Typecasting input to dataframe.
2026-04-15 21:43:21.02445 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:21.025932 INFO::Removing potential empty rows and columns
2026-04-15 21:43:21.029739 INFO::Found 0 missing values.
2026-04-15 21:43:21.040698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:21.041517 INFO::Done
2026-04-15 21:43:21.056993 INFO::Formatting Data.
2026-04-15 21:43:21.057843 INFO::Recognized SummarizedExperiment
2026-04-15 21:43:21.058411 INFO::Typecasting input to dataframe.
2026-04-15 21:43:21.074766 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:21.075922 INFO::Removing potential empty rows and columns
2026-04-15 21:43:21.077029 INFO::Found 0 missing values.
2026-04-15 21:43:21.077972 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-15 21:43:21.082386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:21.083054 INFO::Done
2026-04-15 21:43:21.093572 INFO::Formatting Data.
2026-04-15 21:43:21.09446 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:21.095436 INFO::Removing potential empty rows and columns
2026-04-15 21:43:21.096494 INFO::Found 0 missing values.
2026-04-15 21:43:21.09953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:21.100156 INFO::Done
2026-04-15 21:43:21.112267 INFO::Formatting Data.
2026-04-15 21:43:21.113165 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:21.114124 INFO::Removing potential empty rows and columns
2026-04-15 21:43:21.11517 INFO::Found 0 missing values.
2026-04-15 21:43:21.11833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:21.118959 INFO::Done
2026-04-15 21:43:21.151142 INFO::Formatting Data.
2026-04-15 21:43:21.152066 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:21.153236 INFO::Removing potential empty rows and columns
2026-04-15 21:43:21.154551 INFO::Found 1 missing values.
2026-04-15 21:43:21.157425 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:21.158095 INFO::Done
2026-04-15 21:43:21.179597 INFO::Formatting Data.
2026-04-15 21:43:21.1807 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:21.181705 INFO::Removing potential empty rows and columns
2026-04-15 21:43:21.182808 INFO::Found 2 missing values.
2026-04-15 21:43:21.183839 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-15 21:43:21.186322 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:21.18693 INFO::Done
2026-04-15 21:43:21.197661 INFO::Formatting Data.
2026-04-15 21:43:21.198539 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:21.199475 INFO::Removing potential empty rows and columns
2026-04-15 21:43:21.200449 INFO::Found 2 missing values.
2026-04-15 21:43:21.202145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:21.202799 INFO::Done
2026-04-15 21:43:21.214755 INFO::Formatting Data.
2026-04-15 21:43:21.215636 INFO::Typecasting input to dataframe.
2026-04-15 21:43:21.216528 INFO::Replacing NaNs with NAs.
2026-04-15 21:43:21.217467 INFO::Removing potential empty rows and columns
2026-04-15 21:43:21.218574 INFO::Found 0 missing values.
2026-04-15 21:43:21.22151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-15 21:43:21.222081 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.379 3.774 20.859
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.615 | 1.377 | 17.088 | |
| compute_asw | 0.023 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.000 | 0.013 | |
| generate_data_covariables | 0.010 | 0.002 | 0.012 | |
| generate_dataset | 0.010 | 0.002 | 0.012 | |