Yannis Schumann
| Snapshot Date: 2026-05-24 13:40 -0400 (Sun, 24 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_23 |
| git_last_commit: 0c9135c |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-25 11:32 -0400 (Mon, 25 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 172/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.8.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.8.0.tar.gz |
| StartedAt: 2026-05-24 21:54:50 -0400 (Sun, 24 May 2026) |
| EndedAt: 2026-05-24 21:56:19 -0400 (Sun, 24 May 2026) |
| EllapsedTime: 89.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-25 01:54:50 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.52 1.152 16.729
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.8.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-05-24 21:55:40.405966 INFO::Formatting Data.
2026-05-24 21:55:40.407589 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:40.419837 INFO::Removing potential empty rows and columns
2026-05-24 21:55:40.657367 INFO::Found 0 missing values.
2026-05-24 21:55:40.660754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:40.661416 INFO::Done
2026-05-24 21:55:40.661992 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:40.674768 INFO::Starting hierarchical adjustment
2026-05-24 21:55:40.675731 INFO::Found 3 batches.
2026-05-24 21:55:40.676309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:40.677449 INFO::Using default BPPARAM
2026-05-24 21:55:40.678051 INFO::Processing subtree level 1
2026-05-24 21:55:40.777913 INFO::Adjusting the last 1 batches sequentially
2026-05-24 21:55:40.779802 INFO::Done
2026-05-24 21:55:40.780485 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:40.783009 INFO::ASW Batch was -0.0152806229355179 prior to batch effect correction and is now -0.0152806229355179 .
2026-05-24 21:55:40.784098 INFO::Total function execution time is 0.378928899765015 s and adjustment time is 0.104267597198486 s ( 27.52 )
2026-05-24 21:55:40.798017 INFO::Formatting Data.
2026-05-24 21:55:40.798812 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:40.799768 INFO::Removing potential empty rows and columns
2026-05-24 21:55:40.800907 INFO::Found 0 missing values.
2026-05-24 21:55:40.801888 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.
2026-05-24 21:55:40.812842 INFO::Formatting Data.
2026-05-24 21:55:40.813639 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:40.814638 INFO::Removing potential empty rows and columns
2026-05-24 21:55:40.815832 INFO::Found 0 missing values.
2026-05-24 21:55:40.816839 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.
2026-05-24 21:55:40.83329 INFO::Formatting Data.
2026-05-24 21:55:40.834176 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:40.835141 INFO::Removing potential empty rows and columns
2026-05-24 21:55:40.836233 INFO::Found 0 missing values.
2026-05-24 21:55:40.837192 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.
2026-05-24 21:55:40.841794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:40.842366 INFO::Done
2026-05-24 21:55:40.842935 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:40.844981 INFO::Starting hierarchical adjustment
2026-05-24 21:55:40.845726 INFO::Found 2 batches.
2026-05-24 21:55:40.846287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:40.846951 INFO::Using default BPPARAM
2026-05-24 21:55:40.847517 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:40.848495 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-24 21:55:40.869414 INFO::Done
2026-05-24 21:55:40.870225 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:40.872289 INFO::ASW Batch was 0.0790295584599488 prior to batch effect correction and is now -0.11394758543765 .
2026-05-24 21:55:40.873143 INFO::Total function execution time is 0.0399250984191895 s and adjustment time is 0.023808479309082 s ( 59.63 )
2026-05-24 21:55:40.876114 INFO::Formatting Data.
2026-05-24 21:55:40.876791 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:40.885999 INFO::Formatting Data.
2026-05-24 21:55:40.88683 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:40.887789 INFO::Removing potential empty rows and columns
2026-05-24 21:55:40.888897 INFO::Found 0 missing values.
2026-05-24 21:55:40.892019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:40.892591 INFO::Done
2026-05-24 21:55:40.893168 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:40.895351 INFO::Starting hierarchical adjustment
2026-05-24 21:55:40.896199 INFO::Found 2 batches.
2026-05-24 21:55:40.896873 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:40.897557 INFO::Using default BPPARAM
2026-05-24 21:55:40.898143 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:40.899134 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-24 21:55:40.941231 INFO::Done
2026-05-24 21:55:40.94205 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:40.944129 INFO::ASW Batch was -0.0236058651687063 prior to batch effect correction and is now -0.117341057953525 .
2026-05-24 21:55:40.945001 INFO::Total function execution time is 0.0590522289276123 s and adjustment time is 0.0451562404632568 s ( 76.47 )
2026-05-24 21:55:40.946094 INFO::Formatting Data.
2026-05-24 21:55:40.946719 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:40.947577 INFO::Removing potential empty rows and columns
2026-05-24 21:55:40.948647 INFO::Found 0 missing values.
2026-05-24 21:55:40.951421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:40.952036 INFO::Done
2026-05-24 21:55:40.952582 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:40.954761 INFO::Starting hierarchical adjustment
2026-05-24 21:55:40.955518 INFO::Found 2 batches.
2026-05-24 21:55:40.956105 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:40.95676 INFO::Using default BPPARAM
2026-05-24 21:55:40.957315 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:40.958304 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-24 21:55:40.973345 INFO::Done
2026-05-24 21:55:40.974168 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:40.976268 INFO::ASW Batch was -0.0236058651687063 prior to batch effect correction and is now -0.117341057953525 .
2026-05-24 21:55:40.977121 INFO::Total function execution time is 0.0310206413269043 s and adjustment time is 0.0179576873779297 s ( 57.89 )
2026-05-24 21:55:44.086866 INFO::Formatting Data.
2026-05-24 21:55:44.087636 INFO::Recognized SummarizedExperiment
2026-05-24 21:55:44.088168 INFO::Typecasting input to dataframe.
2026-05-24 21:55:44.116478 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:44.117736 INFO::Removing potential empty rows and columns
2026-05-24 21:55:44.120869 INFO::Found 0 missing values.
2026-05-24 21:55:44.126811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:44.127437 INFO::Done
2026-05-24 21:55:44.12796 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:44.131152 INFO::Starting hierarchical adjustment
2026-05-24 21:55:44.131912 INFO::Found 2 batches.
2026-05-24 21:55:44.132419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:44.13344 INFO::Using default BPPARAM
2026-05-24 21:55:44.133971 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:44.134933 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-24 21:55:44.182854 INFO::Done
2026-05-24 21:55:44.183638 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:44.186944 INFO::ASW Batch was 0.00629916168718191 prior to batch effect correction and is now -0.0943926945613166 .
2026-05-24 21:55:44.187777 INFO::Total function execution time is 0.101170778274536 s and adjustment time is 0.0510613918304443 s ( 50.47 )
2026-05-24 21:55:44.20433 INFO::Formatting Data.
2026-05-24 21:55:44.205084 INFO::Recognized SummarizedExperiment
2026-05-24 21:55:44.205616 INFO::Typecasting input to dataframe.
2026-05-24 21:55:44.218274 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:44.21971 INFO::Removing potential empty rows and columns
2026-05-24 21:55:44.223537 INFO::Found 0 missing values.
2026-05-24 21:55:44.230768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:44.23146 INFO::Done
2026-05-24 21:55:44.232041 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:44.235595 INFO::Starting hierarchical adjustment
2026-05-24 21:55:44.236353 INFO::Found 2 batches.
2026-05-24 21:55:44.236917 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:44.23753 INFO::Using default BPPARAM
2026-05-24 21:55:44.238088 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:44.239084 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-24 21:55:44.263752 INFO::Done
2026-05-24 21:55:44.264502 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:44.26813 INFO::ASW Batch was 0.0131513765125269 prior to batch effect correction and is now 0.0131513765125269 .
2026-05-24 21:55:44.269024 INFO::Total function execution time is 0.0646662712097168 s and adjustment time is 0.027493953704834 s ( 42.52 )
2026-05-24 21:55:44.287567 INFO::Formatting Data.
2026-05-24 21:55:44.288459 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:44.289412 INFO::Removing potential empty rows and columns
2026-05-24 21:55:44.290479 INFO::Found 0 missing values.
2026-05-24 21:55:44.29351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:44.294111 INFO::Done
2026-05-24 21:55:44.294667 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:44.296718 INFO::Starting hierarchical adjustment
2026-05-24 21:55:44.297472 INFO::Found 3 batches.
2026-05-24 21:55:44.298044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:44.298691 INFO::Using default BPPARAM
2026-05-24 21:55:44.299258 INFO::Processing subtree level 1
2026-05-24 21:55:44.430616 INFO::Adjusting the last 1 batches sequentially
2026-05-24 21:55:44.432486 INFO::Done
2026-05-24 21:55:44.433187 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:44.435733 INFO::ASW Batch was -0.00889844713549683 prior to batch effect correction and is now -0.144690775382993 .
2026-05-24 21:55:44.436738 INFO::Total function execution time is 0.149190902709961 s and adjustment time is 0.135148525238037 s ( 90.59 )
2026-05-24 21:55:44.451234 INFO::Skipping initial DF formatting
2026-05-24 21:55:44.451998 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:44.456296 INFO::Starting hierarchical adjustment
2026-05-24 21:55:44.457108 INFO::Found 5 batches.
2026-05-24 21:55:44.457734 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:44.45841 INFO::Using default BPPARAM
2026-05-24 21:55:44.459015 INFO::Processing subtree level 1
2026-05-24 21:55:44.575892 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:44.577643 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-24 21:55:44.598027 INFO::Done
2026-05-24 21:55:44.59884 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:44.603409 INFO::ASW Batch was 0.528858097335221 prior to batch effect correction and is now 0.528858097335221 .
2026-05-24 21:55:44.604084 INFO::ASW Label was 0.363436204470868 prior to batch effect correction and is now 0.363436204470868 .
2026-05-24 21:55:44.604998 INFO::Total function execution time is 0.153829336166382 s and adjustment time is 0.141054153442383 s ( 91.7 )
2026-05-24 21:55:44.622814 INFO::Formatting Data.
2026-05-24 21:55:44.623671 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:44.624671 INFO::Removing potential empty rows and columns
2026-05-24 21:55:44.625727 INFO::Found 0 missing values.
2026-05-24 21:55:44.63012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:44.630711 INFO::Done
2026-05-24 21:55:44.63128 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:44.634324 INFO::Starting hierarchical adjustment
2026-05-24 21:55:44.635085 INFO::Found 5 batches.
2026-05-24 21:55:44.635715 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:44.636374 INFO::Using default BPPARAM
2026-05-24 21:55:44.636975 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.
2026-05-24 21:55:44.747195 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:44.749233 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-24 21:55:44.766978 INFO::Done
2026-05-24 21:55:44.767943 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:44.77164 INFO::ASW Batch was 0.237970938343187 prior to batch effect correction and is now -0.0681403040666242 .
2026-05-24 21:55:44.772369 INFO::ASW Label was 0.487995532299585 prior to batch effect correction and is now 0.860288006784618 .
2026-05-24 21:55:44.773394 INFO::Total function execution time is 0.150636911392212 s and adjustment time is 0.131976842880249 s ( 87.61 )
2026-05-24 21:55:44.774355 INFO::Formatting Data.
2026-05-24 21:55:44.775074 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:44.776099 INFO::Removing potential empty rows and columns
2026-05-24 21:55:44.777204 INFO::Found 0 missing values.
2026-05-24 21:55:44.781591 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:44.782258 INFO::Done
2026-05-24 21:55:44.782839 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:44.78622 INFO::Starting hierarchical adjustment
2026-05-24 21:55:44.787027 INFO::Found 5 batches.
2026-05-24 21:55:44.787608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:44.788343 INFO::Using default BPPARAM
2026-05-24 21:55:44.788977 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.
2026-05-24 21:55:44.906052 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:44.907958 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-24 21:55:44.924255 INFO::Done
2026-05-24 21:55:44.925068 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:44.928518 INFO::ASW Batch was 0.237970938343187 prior to batch effect correction and is now -0.0681403040666242 .
2026-05-24 21:55:44.929209 INFO::ASW Label was 0.487995532299585 prior to batch effect correction and is now 0.860288006784618 .
2026-05-24 21:55:44.930102 INFO::Total function execution time is 0.15575647354126 s and adjustment time is 0.137370586395264 s ( 88.2 )
2026-05-24 21:55:44.944558 INFO::Formatting Data.
2026-05-24 21:55:44.945502 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:44.946562 INFO::Removing potential empty rows and columns
2026-05-24 21:55:44.947654 INFO::Found 0 missing values.
2026-05-24 21:55:44.952008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:44.952609 INFO::Done
2026-05-24 21:55:44.953207 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:44.956294 INFO::Starting hierarchical adjustment
2026-05-24 21:55:44.95709 INFO::Found 5 batches.
2026-05-24 21:55:44.957669 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:44.95834 INFO::Using default BPPARAM
2026-05-24 21:55:44.958942 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.
2026-05-24 21:55:45.074056 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:45.075949 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-24 21:55:45.093268 INFO::Done
2026-05-24 21:55:45.094553 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.098371 INFO::ASW Batch was 0.222909553462369 prior to batch effect correction and is now -0.0812647337636063 .
2026-05-24 21:55:45.099127 INFO::ASW Label was 0.574739096508181 prior to batch effect correction and is now 0.789628891687908 .
2026-05-24 21:55:45.100104 INFO::Total function execution time is 0.155638933181763 s and adjustment time is 0.136284112930298 s ( 87.56 )
2026-05-24 21:55:45.101057 INFO::Formatting Data.
2026-05-24 21:55:45.101759 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.102738 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.103808 INFO::Found 0 missing values.
2026-05-24 21:55:45.10808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.108765 INFO::Done
2026-05-24 21:55:45.109345 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.112402 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.113173 INFO::Found 5 batches.
2026-05-24 21:55:45.113761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.114451 INFO::Using default BPPARAM
2026-05-24 21:55:45.115045 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.
2026-05-24 21:55:45.220933 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:45.222671 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-24 21:55:45.238356 INFO::Done
2026-05-24 21:55:45.239108 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.242319 INFO::ASW Batch was 0.222909553462369 prior to batch effect correction and is now -0.0812647337636063 .
2026-05-24 21:55:45.242947 INFO::ASW Label was 0.574739096508181 prior to batch effect correction and is now 0.789628891687908 .
2026-05-24 21:55:45.243813 INFO::Total function execution time is 0.142762660980225 s and adjustment time is 0.125323057174683 s ( 87.78 )
2026-05-24 21:55:45.25734 INFO::Formatting Data.
2026-05-24 21:55:45.258144 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.259103 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.26016 INFO::Found 0 missing values.
2026-05-24 21:55:45.26291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.263494 INFO::Done
2026-05-24 21:55:45.264084 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.267112 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.267861 INFO::Found 2 batches.
2026-05-24 21:55:45.268434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.269314 INFO::Using default BPPARAM
2026-05-24 21:55:45.269901 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:45.270845 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-24 21:55:45.285369 INFO::Done
2026-05-24 21:55:45.28605 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.288976 INFO::ASW Batch was 0.538949776420943 prior to batch effect correction and is now -0.026120809312194 .
2026-05-24 21:55:45.289578 INFO::ASW Label was 0.535123981446793 prior to batch effect correction and is now 0.908358434358447 .
2026-05-24 21:55:45.290403 INFO::Total function execution time is 0.033118724822998 s and adjustment time is 0.0176727771759033 s ( 53.36 )
2026-05-24 21:55:45.291291 INFO::Formatting Data.
2026-05-24 21:55:45.291963 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.29286 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.293866 INFO::Found 0 missing values.
2026-05-24 21:55:45.296565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.297141 INFO::Done
2026-05-24 21:55:45.297733 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.300843 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.301576 INFO::Found 2 batches.
2026-05-24 21:55:45.302151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.3028 INFO::Using default BPPARAM
2026-05-24 21:55:45.303361 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:45.304295 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-24 21:55:45.319011 INFO::Done
2026-05-24 21:55:45.319752 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.322788 INFO::ASW Batch was 0.538949776420943 prior to batch effect correction and is now -0.026120809312194 .
2026-05-24 21:55:45.32342 INFO::ASW Label was 0.535123981446793 prior to batch effect correction and is now 0.908358434358447 .
2026-05-24 21:55:45.32424 INFO::Total function execution time is 0.032973051071167 s and adjustment time is 0.0175554752349854 s ( 53.24 )
2026-05-24 21:55:45.336058 INFO::Formatting Data.
2026-05-24 21:55:45.336866 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.337788 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.33874 INFO::Found 0 missing values.
2026-05-24 21:55:45.340928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.341509 INFO::Done
2026-05-24 21:55:45.342123 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.344202 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.344971 INFO::Found 2 batches.
2026-05-24 21:55:45.345527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.346202 INFO::Using default BPPARAM
2026-05-24 21:55:45.346795 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:45.347747 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-24 21:55:45.379179 INFO::Done
2026-05-24 21:55:45.379989 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.382053 INFO::ASW Batch was -0.0889521748663948 prior to batch effect correction and is now -0.163375299959829 .
2026-05-24 21:55:45.382917 INFO::Total function execution time is 0.0469393730163574 s and adjustment time is 0.0343341827392578 s ( 73.15 )
2026-05-24 21:55:45.395113 INFO::Formatting Data.
2026-05-24 21:55:45.395918 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.396883 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.397928 INFO::Found 0 missing values.
2026-05-24 21:55:45.399103 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.
2026-05-24 21:55:45.403766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.40434 INFO::Done
2026-05-24 21:55:45.40494 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.407934 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.40866 INFO::Found 2 batches.
2026-05-24 21:55:45.40924 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.409899 INFO::Using default BPPARAM
2026-05-24 21:55:45.41046 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:45.411417 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-24 21:55:45.42812 INFO::Done
2026-05-24 21:55:45.428877 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.431912 INFO::ASW Batch was 0.528742783800218 prior to batch effect correction and is now -0.0354271807627207 .
2026-05-24 21:55:45.43255 INFO::ASW Label was 0.53150703197505 prior to batch effect correction and is now 0.931278259861372 .
2026-05-24 21:55:45.433383 INFO::Total function execution time is 0.0383286476135254 s and adjustment time is 0.019575834274292 s ( 51.07 )
2026-05-24 21:55:45.434254 INFO::Formatting Data.
2026-05-24 21:55:45.434924 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.435862 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.436877 INFO::Found 0 missing values.
2026-05-24 21:55:45.437812 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.
2026-05-24 21:55:45.442413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.443019 INFO::Done
2026-05-24 21:55:45.443575 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.446511 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.447257 INFO::Found 2 batches.
2026-05-24 21:55:45.447839 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.448512 INFO::Using default BPPARAM
2026-05-24 21:55:45.44909 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:45.450046 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-24 21:55:45.466746 INFO::Done
2026-05-24 21:55:45.467512 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.470488 INFO::ASW Batch was 0.528742783800218 prior to batch effect correction and is now -0.0354271807627207 .
2026-05-24 21:55:45.471126 INFO::ASW Label was 0.53150703197505 prior to batch effect correction and is now 0.931278259861372 .
2026-05-24 21:55:45.471992 INFO::Total function execution time is 0.0377423763275146 s and adjustment time is 0.0195882320404053 s ( 51.9 )
2026-05-24 21:55:45.681229 INFO::Formatting Data.
2026-05-24 21:55:45.682096 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.683054 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.684123 INFO::Found 0 missing values.
2026-05-24 21:55:45.68722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.687873 INFO::Done
2026-05-24 21:55:45.688433 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.690516 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.691265 INFO::Found 3 batches.
2026-05-24 21:55:45.691856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.692612 INFO::Using default BPPARAM
2026-05-24 21:55:45.701019 INFO::Processing subtree level 1
2026-05-24 21:55:45.791282 INFO::Adjusting the last 1 batches sequentially
2026-05-24 21:55:45.793438 INFO::Done
2026-05-24 21:55:45.794233 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.797011 INFO::ASW Batch was -0.0891589120752641 prior to batch effect correction and is now -0.0891589120752641 .
2026-05-24 21:55:45.798079 INFO::Total function execution time is 0.116878747940063 s and adjustment time is 0.10228157043457 s ( 87.51 )
2026-05-24 21:55:45.799208 INFO::Formatting Data.
2026-05-24 21:55:45.799925 INFO::Typecasting input to dataframe.
2026-05-24 21:55:45.80075 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.801747 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.802912 INFO::Found 0 missing values.
2026-05-24 21:55:45.806246 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.80688 INFO::Done
2026-05-24 21:55:45.807476 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.809617 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.810426 INFO::Found 3 batches.
2026-05-24 21:55:45.81101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.811671 INFO::Using default BPPARAM
2026-05-24 21:55:45.812277 INFO::Processing subtree level 1
2026-05-24 21:55:45.89889 INFO::Adjusting the last 1 batches sequentially
2026-05-24 21:55:45.901479 INFO::Done
2026-05-24 21:55:45.902604 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:45.906273 INFO::ASW Batch was -0.0891589120752641 prior to batch effect correction and is now -0.0891589120752641 .
2026-05-24 21:55:45.90773 INFO::Total function execution time is 0.108412504196167 s and adjustment time is 0.0911774635314941 s ( 84.1 )
2026-05-24 21:55:45.929522 INFO::Formatting Data.
2026-05-24 21:55:45.930805 INFO::Typecasting input to dataframe.
2026-05-24 21:55:45.932212 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:45.933662 INFO::Removing potential empty rows and columns
2026-05-24 21:55:45.935359 INFO::Found 0 missing values.
2026-05-24 21:55:45.940241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:45.94116 INFO::Done
2026-05-24 21:55:45.942057 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:45.945112 INFO::Starting hierarchical adjustment
2026-05-24 21:55:45.946258 INFO::Found 3 batches.
2026-05-24 21:55:45.947157 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:45.948175 INFO::Using default BPPARAM
2026-05-24 21:55:45.949064 INFO::Processing subtree level 1
2026-05-24 21:55:46.050273 INFO::Adjusting the last 1 batches sequentially
2026-05-24 21:55:46.052147 INFO::Done
2026-05-24 21:55:46.052864 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:46.055463 INFO::ASW Batch was -0.00230793067634807 prior to batch effect correction and is now -0.00230793067634807 .
2026-05-24 21:55:46.056562 INFO::Total function execution time is 0.127168655395508 s and adjustment time is 0.106138229370117 s ( 83.46 )
2026-05-24 21:55:46.203029 INFO::Formatting Data.
2026-05-24 21:55:46.204111 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:46.205364 INFO::Removing potential empty rows and columns
2026-05-24 21:55:46.208282 INFO::Found 1000 missing values.
2026-05-24 21:55:46.228007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:46.228876 INFO::Done
2026-05-24 21:55:46.229522 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:46.235307 INFO::Starting hierarchical adjustment
2026-05-24 21:55:46.236207 INFO::Found 10 batches.
2026-05-24 21:55:46.236814 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:46.237484 INFO::Using default BPPARAM
2026-05-24 21:55:46.23811 INFO::Processing subtree level 1
2026-05-24 21:55:46.377403 INFO::Processing subtree level 2
2026-05-24 21:55:46.522992 INFO::Adjusting the last 1 batches sequentially
2026-05-24 21:55:46.525063 INFO::Done
2026-05-24 21:55:46.529078 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:46.534821 INFO::ASW Batch was 0.491166358016911 prior to batch effect correction and is now 0.491166358016911 .
2026-05-24 21:55:46.535561 INFO::ASW Label was 0.320335316377885 prior to batch effect correction and is now 0.320335316377885 .
2026-05-24 21:55:46.536576 INFO::Total function execution time is 0.333691120147705 s and adjustment time is 0.289021253585815 s ( 86.61 )
2026-05-24 21:55:46.537488 INFO::Formatting Data.
2026-05-24 21:55:46.538212 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:46.539487 INFO::Removing potential empty rows and columns
2026-05-24 21:55:46.542398 INFO::Found 1000 missing values.
2026-05-24 21:55:46.561995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:46.562886 INFO::Done
2026-05-24 21:55:46.563529 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:46.569138 INFO::Starting hierarchical adjustment
2026-05-24 21:55:46.570035 INFO::Found 10 batches.
2026-05-24 21:55:47.705782 INFO::Set up parallel execution backend with 2 workers
2026-05-24 21:55:47.708636 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-24 21:55:48.959636 INFO::Adjusting the last 2 batches sequentially
2026-05-24 21:55:48.962996 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-24 21:55:48.98038 INFO::Done
2026-05-24 21:55:48.981157 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:48.986109 INFO::ASW Batch was 0.491166358016911 prior to batch effect correction and is now 0.491166358016911 .
2026-05-24 21:55:48.986759 INFO::ASW Label was 0.320335316377885 prior to batch effect correction and is now 0.320335316377885 .
2026-05-24 21:55:48.987615 INFO::Total function execution time is 2.45014190673828 s and adjustment time is 2.41048622131348 s ( 98.38 )
2026-05-24 21:55:49.145471 INFO::Formatting Data.
2026-05-24 21:55:49.146422 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.147534 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.148809 INFO::Found 0 missing values.
2026-05-24 21:55:49.152841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.153493 INFO::Done
2026-05-24 21:55:49.154157 INFO::Acquiring quality metrics before batch effect correction.
2026-05-24 21:55:49.157328 INFO::Starting hierarchical adjustment
2026-05-24 21:55:49.158136 INFO::Found 3 batches.
2026-05-24 21:55:49.158756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-24 21:55:49.159448 INFO::Using default BPPARAM
2026-05-24 21:55:49.160069 INFO::Processing subtree level 1
2026-05-24 21:55:49.28291 INFO::Adjusting the last 1 batches sequentially
2026-05-24 21:55:49.285301 INFO::Done
2026-05-24 21:55:49.286135 INFO::Acquiring quality metrics after batch effect correction.
2026-05-24 21:55:49.29003 INFO::ASW Batch was 0.249912787828388 prior to batch effect correction and is now -0.1202234158896 .
2026-05-24 21:55:49.290796 INFO::ASW Label was -0.204356735083602 prior to batch effect correction and is now 0.0517229913916186 .
2026-05-24 21:55:49.2919 INFO::Total function execution time is 0.146452188491821 s and adjustment time is 0.127272367477417 s ( 86.9 )
2026-05-24 21:55:49.419842 INFO::Formatting Data.
2026-05-24 21:55:49.420798 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.421749 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.422841 INFO::Found 2 missing values.
2026-05-24 21:55:49.42564 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.42621 INFO::Done
2026-05-24 21:55:49.453237 INFO::Found NA in Reference column
2026-05-24 21:55:49.462646 INFO::Require at least two references per batch.
2026-05-24 21:55:49.48316 INFO::Formatting Data.
2026-05-24 21:55:49.483997 INFO::Recognized SummarizedExperiment
2026-05-24 21:55:49.484577 INFO::Typecasting input to dataframe.
2026-05-24 21:55:49.494119 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.495464 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.499027 INFO::Found 0 missing values.
2026-05-24 21:55:49.50579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.506567 INFO::Done
2026-05-24 21:55:49.530437 INFO::Formatting Data.
2026-05-24 21:55:49.531487 INFO::Recognized SummarizedExperiment
2026-05-24 21:55:49.532152 INFO::Typecasting input to dataframe.
2026-05-24 21:55:49.552271 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.553758 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.557795 INFO::Found 0 missing values.
2026-05-24 21:55:49.570255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.571191 INFO::Done
2026-05-24 21:55:49.588265 INFO::Formatting Data.
2026-05-24 21:55:49.589231 INFO::Recognized SummarizedExperiment
2026-05-24 21:55:49.589869 INFO::Typecasting input to dataframe.
2026-05-24 21:55:49.609369 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.610762 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.61222 INFO::Found 0 missing values.
2026-05-24 21:55:49.613397 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.
2026-05-24 21:55:49.619222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.620233 INFO::Done
2026-05-24 21:55:49.633217 INFO::Formatting Data.
2026-05-24 21:55:49.634276 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.635393 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.636578 INFO::Found 0 missing values.
2026-05-24 21:55:49.639937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.64057 INFO::Done
2026-05-24 21:55:49.653844 INFO::Formatting Data.
2026-05-24 21:55:49.654877 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.655951 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.657155 INFO::Found 0 missing values.
2026-05-24 21:55:49.660624 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.66132 INFO::Done
2026-05-24 21:55:49.697324 INFO::Formatting Data.
2026-05-24 21:55:49.698403 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.699749 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.701199 INFO::Found 1 missing values.
2026-05-24 21:55:49.704219 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.70489 INFO::Done
2026-05-24 21:55:49.727339 INFO::Formatting Data.
2026-05-24 21:55:49.728378 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.729383 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.730433 INFO::Found 2 missing values.
2026-05-24 21:55:49.731426 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.
2026-05-24 21:55:49.733812 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.734437 INFO::Done
2026-05-24 21:55:49.745211 INFO::Formatting Data.
2026-05-24 21:55:49.746152 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.74722 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.748361 INFO::Found 2 missing values.
2026-05-24 21:55:49.750421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.751092 INFO::Done
2026-05-24 21:55:49.763025 INFO::Formatting Data.
2026-05-24 21:55:49.764025 INFO::Typecasting input to dataframe.
2026-05-24 21:55:49.764994 INFO::Replacing NaNs with NAs.
2026-05-24 21:55:49.766012 INFO::Removing potential empty rows and columns
2026-05-24 21:55:49.767129 INFO::Found 0 missing values.
2026-05-24 21:55:49.770256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-24 21:55:49.770892 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.964 3.588 20.250
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.520 | 1.152 | 16.729 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.000 | 0.013 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.011 | |