Yannis Schumann
| Snapshot Date: 2026-04-24 13:40 -0400 (Fri, 24 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 2026-04-25 11:35 -0400 (Sat, 25 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4978 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4722 |
| 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 172/2415 | 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: 2026-04-24 21:41:56 -0400 (Fri, 24 Apr 2026) |
| EndedAt: 2026-04-24 21:43:31 -0400 (Fri, 24 Apr 2026) |
| EllapsedTime: 95.1 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 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-25 01:41:56 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 24.944 1.278 18.664
* 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 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-04-24 21:42:49.555389 INFO::Formatting Data.
2026-04-24 21:42:49.556901 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:49.56826 INFO::Removing potential empty rows and columns
2026-04-24 21:42:49.843929 INFO::Found 0 missing values.
2026-04-24 21:42:49.847658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:49.84842 INFO::Done
2026-04-24 21:42:49.849068 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:49.86361 INFO::Starting hierarchical adjustment
2026-04-24 21:42:49.864713 INFO::Found 3 batches.
2026-04-24 21:42:49.865388 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:49.866701 INFO::Using default BPPARAM
2026-04-24 21:42:49.867358 INFO::Processing subtree level 1
2026-04-24 21:42:49.978673 INFO::Adjusting the last 1 batches sequentially
2026-04-24 21:42:49.980768 INFO::Done
2026-04-24 21:42:49.981544 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:49.984456 INFO::ASW Batch was -0.0396760346077035 prior to batch effect correction and is now -0.0396760346077035 .
2026-04-24 21:42:49.985689 INFO::Total function execution time is 0.430951118469238 s and adjustment time is 0.116284847259521 s ( 26.98 )
2026-04-24 21:42:50.001667 INFO::Formatting Data.
2026-04-24 21:42:50.002574 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:50.003654 INFO::Removing potential empty rows and columns
2026-04-24 21:42:50.004922 INFO::Found 0 missing values.
2026-04-24 21:42:50.006052 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.
2026-04-24 21:42:50.018789 INFO::Formatting Data.
2026-04-24 21:42:50.019701 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:50.020799 INFO::Removing potential empty rows and columns
2026-04-24 21:42:50.022173 INFO::Found 0 missing values.
2026-04-24 21:42:50.023289 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.
2026-04-24 21:42:50.041822 INFO::Formatting Data.
2026-04-24 21:42:50.042767 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:50.043834 INFO::Removing potential empty rows and columns
2026-04-24 21:42:50.045012 INFO::Found 0 missing values.
2026-04-24 21:42:50.046045 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.
2026-04-24 21:42:50.051141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:50.051819 INFO::Done
2026-04-24 21:42:50.052428 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:50.054734 INFO::Starting hierarchical adjustment
2026-04-24 21:42:50.055558 INFO::Found 2 batches.
2026-04-24 21:42:50.056208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:50.057005 INFO::Using default BPPARAM
2026-04-24 21:42:50.057653 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:50.058788 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-24 21:42:50.083193 INFO::Done
2026-04-24 21:42:50.084184 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:50.086779 INFO::ASW Batch was -0.0640304136670582 prior to batch effect correction and is now -0.0985544355525634 .
2026-04-24 21:42:50.087812 INFO::Total function execution time is 0.0460600852966309 s and adjustment time is 0.0277519226074219 s ( 60.25 )
2026-04-24 21:42:50.091372 INFO::Formatting Data.
2026-04-24 21:42:50.092159 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:50.101878 INFO::Formatting Data.
2026-04-24 21:42:50.102781 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:50.103799 INFO::Removing potential empty rows and columns
2026-04-24 21:42:50.104994 INFO::Found 0 missing values.
2026-04-24 21:42:50.108207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:50.108822 INFO::Done
2026-04-24 21:42:50.10943 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:50.111645 INFO::Starting hierarchical adjustment
2026-04-24 21:42:50.112442 INFO::Found 2 batches.
2026-04-24 21:42:50.113062 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:50.113765 INFO::Using default BPPARAM
2026-04-24 21:42:50.114368 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:50.115447 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-24 21:42:50.133961 INFO::Done
2026-04-24 21:42:50.134918 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:50.137424 INFO::ASW Batch was -0.0506785614509691 prior to batch effect correction and is now -0.115398509922385 .
2026-04-24 21:42:50.138485 INFO::Total function execution time is 0.0366644859313965 s and adjustment time is 0.0216248035430908 s ( 58.98 )
2026-04-24 21:42:50.139791 INFO::Formatting Data.
2026-04-24 21:42:50.140526 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:50.14158 INFO::Removing potential empty rows and columns
2026-04-24 21:42:50.142816 INFO::Found 0 missing values.
2026-04-24 21:42:50.146192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:50.147058 INFO::Done
2026-04-24 21:42:50.147709 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:50.150153 INFO::Starting hierarchical adjustment
2026-04-24 21:42:50.151051 INFO::Found 2 batches.
2026-04-24 21:42:50.151726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:50.152463 INFO::Using default BPPARAM
2026-04-24 21:42:50.153144 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:50.154246 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-24 21:42:50.171275 INFO::Done
2026-04-24 21:42:50.172108 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:50.174317 INFO::ASW Batch was -0.0506785614509691 prior to batch effect correction and is now -0.115398509922385 .
2026-04-24 21:42:50.17519 INFO::Total function execution time is 0.0354220867156982 s and adjustment time is 0.0203621387481689 s ( 57.48 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-24 21:42:53.570096 INFO::Formatting Data.
2026-04-24 21:42:53.570882 INFO::Recognized SummarizedExperiment
2026-04-24 21:42:53.571438 INFO::Typecasting input to dataframe.
2026-04-24 21:42:53.601332 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:53.602583 INFO::Removing potential empty rows and columns
2026-04-24 21:42:53.606038 INFO::Found 0 missing values.
2026-04-24 21:42:53.612628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:53.613374 INFO::Done
2026-04-24 21:42:53.613972 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:53.617324 INFO::Starting hierarchical adjustment
2026-04-24 21:42:53.618097 INFO::Found 2 batches.
2026-04-24 21:42:53.618638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:53.619757 INFO::Using default BPPARAM
2026-04-24 21:42:53.620307 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:53.621296 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-24 21:42:53.671317 INFO::Done
2026-04-24 21:42:53.672095 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:53.675506 INFO::ASW Batch was 0.024061521596088 prior to batch effect correction and is now -0.0950208287239088 .
2026-04-24 21:42:53.676423 INFO::Total function execution time is 0.106606483459473 s and adjustment time is 0.0533547401428223 s ( 50.05 )
Warning: stack imbalance in '{', 73 then 75
2026-04-24 21:42:53.693136 INFO::Formatting Data.
2026-04-24 21:42:53.69396 INFO::Recognized SummarizedExperiment
2026-04-24 21:42:53.694516 INFO::Typecasting input to dataframe.
2026-04-24 21:42:53.702885 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:53.704063 INFO::Removing potential empty rows and columns
2026-04-24 21:42:53.707405 INFO::Found 0 missing values.
2026-04-24 21:42:53.714108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:53.714819 INFO::Done
2026-04-24 21:42:53.715384 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:53.718782 INFO::Starting hierarchical adjustment
2026-04-24 21:42:53.719507 INFO::Found 2 batches.
2026-04-24 21:42:53.720072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:53.720712 INFO::Using default BPPARAM
2026-04-24 21:42:53.721262 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:53.722239 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-24 21:42:53.748094 INFO::Done
2026-04-24 21:42:53.748968 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:53.753019 INFO::ASW Batch was 0.0083148665257133 prior to batch effect correction and is now 0.0083148665257133 .
2026-04-24 21:42:53.754011 INFO::Total function execution time is 0.0608348846435547 s and adjustment time is 0.0286731719970703 s ( 47.13 )
2026-04-24 21:42:53.774151 INFO::Formatting Data.
2026-04-24 21:42:53.775103 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:53.776127 INFO::Removing potential empty rows and columns
2026-04-24 21:42:53.777297 INFO::Found 0 missing values.
2026-04-24 21:42:53.780519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:53.78115 INFO::Done
2026-04-24 21:42:53.781748 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:53.783966 INFO::Starting hierarchical adjustment
2026-04-24 21:42:53.784765 INFO::Found 3 batches.
2026-04-24 21:42:53.785359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:53.786037 INFO::Using default BPPARAM
2026-04-24 21:42:53.786626 INFO::Processing subtree level 1
2026-04-24 21:42:53.923769 INFO::Adjusting the last 1 batches sequentially
2026-04-24 21:42:53.925671 INFO::Done
2026-04-24 21:42:53.92645 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:53.929063 INFO::ASW Batch was -0.098478635386385 prior to batch effect correction and is now -0.158445978264875 .
2026-04-24 21:42:53.930071 INFO::Total function execution time is 0.155967235565186 s and adjustment time is 0.141070365905762 s ( 90.45 )
2026-04-24 21:42:53.944804 INFO::Skipping initial DF formatting
2026-04-24 21:42:53.945584 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:53.949917 INFO::Starting hierarchical adjustment
2026-04-24 21:42:53.95084 INFO::Found 5 batches.
2026-04-24 21:42:53.951468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:53.952184 INFO::Using default BPPARAM
2026-04-24 21:42:53.952805 INFO::Processing subtree level 1
2026-04-24 21:42:54.076433 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.078488 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-24 21:42:54.099903 INFO::Done
2026-04-24 21:42:54.100838 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:54.105657 INFO::ASW Batch was 0.4697269710825 prior to batch effect correction and is now 0.4697269710825 .
2026-04-24 21:42:54.106495 INFO::ASW Label was 0.370205967883894 prior to batch effect correction and is now 0.370205967883894 .
2026-04-24 21:42:54.107527 INFO::Total function execution time is 0.162782669067383 s and adjustment time is 0.149187803268433 s ( 91.65 )
2026-04-24 21:42:54.127756 INFO::Formatting Data.
2026-04-24 21:42:54.128795 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:54.129945 INFO::Removing potential empty rows and columns
2026-04-24 21:42:54.131118 INFO::Found 0 missing values.
2026-04-24 21:42:54.135522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:54.136173 INFO::Done
2026-04-24 21:42:54.136786 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:54.140219 INFO::Starting hierarchical adjustment
2026-04-24 21:42:54.14105 INFO::Found 5 batches.
2026-04-24 21:42:54.141647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:54.142356 INFO::Using default BPPARAM
2026-04-24 21:42:54.142978 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.
2026-04-24 21:42:54.265513 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.267535 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-24 21:42:54.285832 INFO::Done
2026-04-24 21:42:54.28679 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:54.290601 INFO::ASW Batch was 0.486672347723014 prior to batch effect correction and is now -0.0763852357111266 .
2026-04-24 21:42:54.291451 INFO::ASW Label was 0.296460733601101 prior to batch effect correction and is now 0.834521403700852 .
2026-04-24 21:42:54.292398 INFO::Total function execution time is 0.164798974990845 s and adjustment time is 0.144865989685059 s ( 87.9 )
2026-04-24 21:42:54.293342 INFO::Formatting Data.
2026-04-24 21:42:54.294054 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:54.295074 INFO::Removing potential empty rows and columns
2026-04-24 21:42:54.296197 INFO::Found 0 missing values.
2026-04-24 21:42:54.300612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:54.301345 INFO::Done
2026-04-24 21:42:54.301954 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:54.305341 INFO::Starting hierarchical adjustment
2026-04-24 21:42:54.306206 INFO::Found 5 batches.
2026-04-24 21:42:54.306803 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:54.307517 INFO::Using default BPPARAM
2026-04-24 21:42:54.308109 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.
2026-04-24 21:42:54.435082 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.437047 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-24 21:42:54.454351 INFO::Done
2026-04-24 21:42:54.455298 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:54.458982 INFO::ASW Batch was 0.486672347723014 prior to batch effect correction and is now -0.0763852357111266 .
2026-04-24 21:42:54.459738 INFO::ASW Label was 0.296460733601101 prior to batch effect correction and is now 0.834521403700852 .
2026-04-24 21:42:54.460724 INFO::Total function execution time is 0.167366981506348 s and adjustment time is 0.148279905319214 s ( 88.6 )
2026-04-24 21:42:54.475737 INFO::Formatting Data.
2026-04-24 21:42:54.476713 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:54.47783 INFO::Removing potential empty rows and columns
2026-04-24 21:42:54.479026 INFO::Found 0 missing values.
2026-04-24 21:42:54.483615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:54.484422 INFO::Done
2026-04-24 21:42:54.485072 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:54.488595 INFO::Starting hierarchical adjustment
2026-04-24 21:42:54.489539 INFO::Found 5 batches.
2026-04-24 21:42:54.490186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:54.490917 INFO::Using default BPPARAM
2026-04-24 21:42:54.491522 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.
2026-04-24 21:42:54.610887 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.612931 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-24 21:42:54.631125 INFO::Done
2026-04-24 21:42:54.632184 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:54.63611 INFO::ASW Batch was 0.515572923301326 prior to batch effect correction and is now -0.0423482672352841 .
2026-04-24 21:42:54.636972 INFO::ASW Label was 0.203126028299231 prior to batch effect correction and is now 0.727210991203759 .
2026-04-24 21:42:54.637979 INFO::Total function execution time is 0.162307024002075 s and adjustment time is 0.141710758209229 s ( 87.31 )
2026-04-24 21:42:54.638937 INFO::Formatting Data.
2026-04-24 21:42:54.63964 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:54.64072 INFO::Removing potential empty rows and columns
2026-04-24 21:42:54.64184 INFO::Found 0 missing values.
2026-04-24 21:42:54.646421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:54.647246 INFO::Done
2026-04-24 21:42:54.647892 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:54.651392 INFO::Starting hierarchical adjustment
2026-04-24 21:42:54.652302 INFO::Found 5 batches.
2026-04-24 21:42:54.65295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:54.653649 INFO::Using default BPPARAM
2026-04-24 21:42:54.654268 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.
2026-04-24 21:42:54.784573 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.786634 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-24 21:42:54.804224 INFO::Done
2026-04-24 21:42:54.80516 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:54.808971 INFO::ASW Batch was 0.515572923301326 prior to batch effect correction and is now -0.0423482672352841 .
2026-04-24 21:42:54.809721 INFO::ASW Label was 0.203126028299231 prior to batch effect correction and is now 0.727210991203759 .
2026-04-24 21:42:54.810709 INFO::Total function execution time is 0.171772003173828 s and adjustment time is 0.152061462402344 s ( 88.53 )
2026-04-24 21:42:54.825166 INFO::Formatting Data.
2026-04-24 21:42:54.826096 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:54.827154 INFO::Removing potential empty rows and columns
2026-04-24 21:42:54.828279 INFO::Found 0 missing values.
2026-04-24 21:42:54.831273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:54.831921 INFO::Done
2026-04-24 21:42:54.832495 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:54.835708 INFO::Starting hierarchical adjustment
2026-04-24 21:42:54.836494 INFO::Found 2 batches.
2026-04-24 21:42:54.837102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:54.837801 INFO::Using default BPPARAM
2026-04-24 21:42:54.838419 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.839461 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-24 21:42:54.854975 INFO::Done
2026-04-24 21:42:54.855795 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:54.858976 INFO::ASW Batch was 0.427578326881332 prior to batch effect correction and is now 0.0888333211508165 .
2026-04-24 21:42:54.859654 INFO::ASW Label was 0.445923604317492 prior to batch effect correction and is now 0.856474754934965 .
2026-04-24 21:42:54.860548 INFO::Total function execution time is 0.0354883670806885 s and adjustment time is 0.0186023712158203 s ( 52.42 )
2026-04-24 21:42:54.861416 INFO::Formatting Data.
2026-04-24 21:42:54.862124 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:54.863075 INFO::Removing potential empty rows and columns
2026-04-24 21:42:54.864132 INFO::Found 0 missing values.
2026-04-24 21:42:54.867192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:54.867817 INFO::Done
2026-04-24 21:42:54.868406 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:54.871544 INFO::Starting hierarchical adjustment
2026-04-24 21:42:54.87233 INFO::Found 2 batches.
2026-04-24 21:42:54.872915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:54.87357 INFO::Using default BPPARAM
2026-04-24 21:42:54.87418 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.875198 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-24 21:42:54.89077 INFO::Done
2026-04-24 21:42:54.891649 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:54.89495 INFO::ASW Batch was 0.427578326881332 prior to batch effect correction and is now 0.0888333211508165 .
2026-04-24 21:42:54.895657 INFO::ASW Label was 0.445923604317492 prior to batch effect correction and is now 0.856474754934965 .
2026-04-24 21:42:54.896585 INFO::Total function execution time is 0.0351772308349609 s and adjustment time is 0.0185341835021973 s ( 52.69 )
2026-04-24 21:42:54.90911 INFO::Formatting Data.
2026-04-24 21:42:54.910125 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:54.91116 INFO::Removing potential empty rows and columns
2026-04-24 21:42:54.912182 INFO::Found 0 missing values.
2026-04-24 21:42:54.914536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:54.915174 INFO::Done
2026-04-24 21:42:54.915778 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:54.917946 INFO::Starting hierarchical adjustment
2026-04-24 21:42:54.918733 INFO::Found 2 batches.
2026-04-24 21:42:54.919317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:54.919999 INFO::Using default BPPARAM
2026-04-24 21:42:54.920597 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.921604 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-24 21:42:54.955609 INFO::Done
2026-04-24 21:42:54.956517 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:54.958843 INFO::ASW Batch was 0.0198234868276834 prior to batch effect correction and is now -0.174355397161385 .
2026-04-24 21:42:54.959822 INFO::Total function execution time is 0.0508170127868652 s and adjustment time is 0.0369958877563477 s ( 72.8 )
2026-04-24 21:42:54.973089 INFO::Formatting Data.
2026-04-24 21:42:54.974069 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:54.975092 INFO::Removing potential empty rows and columns
2026-04-24 21:42:54.976197 INFO::Found 0 missing values.
2026-04-24 21:42:54.977448 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.
2026-04-24 21:42:54.982431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:54.983136 INFO::Done
2026-04-24 21:42:54.983752 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:54.986965 INFO::Starting hierarchical adjustment
2026-04-24 21:42:54.987756 INFO::Found 2 batches.
2026-04-24 21:42:54.988334 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:54.989027 INFO::Using default BPPARAM
2026-04-24 21:42:54.989618 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:54.990609 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-24 21:42:55.007636 INFO::Done
2026-04-24 21:42:55.008443 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:55.011584 INFO::ASW Batch was 0.797884427549455 prior to batch effect correction and is now 0.0549239948773419 .
2026-04-24 21:42:55.012276 INFO::ASW Label was 0.165941514726901 prior to batch effect correction and is now 0.725416211842554 .
2026-04-24 21:42:55.013157 INFO::Total function execution time is 0.0401954650878906 s and adjustment time is 0.0200159549713135 s ( 49.8 )
2026-04-24 21:42:55.014019 INFO::Formatting Data.
2026-04-24 21:42:55.014703 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:55.015707 INFO::Removing potential empty rows and columns
2026-04-24 21:42:55.016775 INFO::Found 0 missing values.
2026-04-24 21:42:55.017761 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.
2026-04-24 21:42:55.022564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:55.023223 INFO::Done
2026-04-24 21:42:55.023824 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:55.026879 INFO::Starting hierarchical adjustment
2026-04-24 21:42:55.027653 INFO::Found 2 batches.
2026-04-24 21:42:55.028277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:55.028945 INFO::Using default BPPARAM
2026-04-24 21:42:55.029518 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:55.030526 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-24 21:42:55.047537 INFO::Done
2026-04-24 21:42:55.048351 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:55.051438 INFO::ASW Batch was 0.797884427549455 prior to batch effect correction and is now 0.0549239948773419 .
2026-04-24 21:42:55.052143 INFO::ASW Label was 0.165941514726901 prior to batch effect correction and is now 0.725416211842554 .
2026-04-24 21:42:55.053022 INFO::Total function execution time is 0.0390331745147705 s and adjustment time is 0.0200071334838867 s ( 51.26 )
2026-04-24 21:42:55.275009 INFO::Formatting Data.
2026-04-24 21:42:55.275983 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:55.277003 INFO::Removing potential empty rows and columns
2026-04-24 21:42:55.278166 INFO::Found 0 missing values.
2026-04-24 21:42:55.283062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:55.283928 INFO::Done
2026-04-24 21:42:55.284539 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:55.286765 INFO::Starting hierarchical adjustment
2026-04-24 21:42:55.287552 INFO::Found 3 batches.
2026-04-24 21:42:55.288156 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:55.289006 INFO::Using default BPPARAM
2026-04-24 21:42:55.289848 INFO::Processing subtree level 1
2026-04-24 21:42:55.396857 INFO::Adjusting the last 1 batches sequentially
2026-04-24 21:42:55.399484 INFO::Done
2026-04-24 21:42:55.400446 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:55.403306 INFO::ASW Batch was -0.0624656046027939 prior to batch effect correction and is now -0.0624656046027939 .
2026-04-24 21:42:55.404437 INFO::Total function execution time is 0.129454851150513 s and adjustment time is 0.111987829208374 s ( 86.51 )
2026-04-24 21:42:55.405639 INFO::Formatting Data.
2026-04-24 21:42:55.406409 INFO::Typecasting input to dataframe.
2026-04-24 21:42:55.407284 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:55.408381 INFO::Removing potential empty rows and columns
2026-04-24 21:42:55.409646 INFO::Found 0 missing values.
2026-04-24 21:42:55.413092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:55.413758 INFO::Done
2026-04-24 21:42:55.41437 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:55.416602 INFO::Starting hierarchical adjustment
2026-04-24 21:42:55.417398 INFO::Found 3 batches.
2026-04-24 21:42:55.418 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:55.418705 INFO::Using default BPPARAM
2026-04-24 21:42:55.419329 INFO::Processing subtree level 1
2026-04-24 21:42:55.512577 INFO::Adjusting the last 1 batches sequentially
2026-04-24 21:42:55.514823 INFO::Done
2026-04-24 21:42:55.515707 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:55.518698 INFO::ASW Batch was -0.0624656046027939 prior to batch effect correction and is now -0.0624656046027939 .
2026-04-24 21:42:55.519904 INFO::Total function execution time is 0.114220857620239 s and adjustment time is 0.097524881362915 s ( 85.38 )
2026-04-24 21:42:55.535273 INFO::Formatting Data.
2026-04-24 21:42:55.536363 INFO::Typecasting input to dataframe.
2026-04-24 21:42:55.537436 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:55.538545 INFO::Removing potential empty rows and columns
2026-04-24 21:42:55.539801 INFO::Found 0 missing values.
2026-04-24 21:42:55.543188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:55.543821 INFO::Done
2026-04-24 21:42:55.544441 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:55.546867 INFO::Starting hierarchical adjustment
2026-04-24 21:42:55.547666 INFO::Found 3 batches.
2026-04-24 21:42:55.548278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:55.548986 INFO::Using default BPPARAM
2026-04-24 21:42:55.54958 INFO::Processing subtree level 1
2026-04-24 21:42:55.652045 INFO::Adjusting the last 1 batches sequentially
2026-04-24 21:42:55.654281 INFO::Done
2026-04-24 21:42:55.65515 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:55.658144 INFO::ASW Batch was 0.00763729740805334 prior to batch effect correction and is now 0.00763729740805334 .
2026-04-24 21:42:55.659251 INFO::Total function execution time is 0.124095439910889 s and adjustment time is 0.106736183166504 s ( 86.01 )
2026-04-24 21:42:55.80842 INFO::Formatting Data.
2026-04-24 21:42:55.809578 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:55.811069 INFO::Removing potential empty rows and columns
2026-04-24 21:42:55.814332 INFO::Found 1000 missing values.
2026-04-24 21:42:55.83531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:55.836181 INFO::Done
2026-04-24 21:42:55.83686 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:55.842883 INFO::Starting hierarchical adjustment
2026-04-24 21:42:55.843828 INFO::Found 10 batches.
2026-04-24 21:42:55.844472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:55.845225 INFO::Using default BPPARAM
2026-04-24 21:42:55.845857 INFO::Processing subtree level 1
2026-04-24 21:42:55.994769 INFO::Processing subtree level 2
2026-04-24 21:42:56.160243 INFO::Adjusting the last 1 batches sequentially
2026-04-24 21:42:56.162401 INFO::Done
2026-04-24 21:42:56.163152 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:56.168915 INFO::ASW Batch was 0.486550575025667 prior to batch effect correction and is now 0.486550575025667 .
2026-04-24 21:42:56.169697 INFO::ASW Label was 0.321434776441584 prior to batch effect correction and is now 0.321434776441584 .
2026-04-24 21:42:56.170702 INFO::Total function execution time is 0.36243748664856 s and adjustment time is 0.318768262863159 s ( 87.95 )
2026-04-24 21:42:56.171582 INFO::Formatting Data.
2026-04-24 21:42:56.172314 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:56.173743 INFO::Removing potential empty rows and columns
2026-04-24 21:42:56.176771 INFO::Found 1000 missing values.
2026-04-24 21:42:56.197194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:56.198096 INFO::Done
2026-04-24 21:42:56.198751 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:56.204489 INFO::Starting hierarchical adjustment
2026-04-24 21:42:56.205408 INFO::Found 10 batches.
2026-04-24 21:42:57.472161 INFO::Set up parallel execution backend with 2 workers
2026-04-24 21:42:57.481423 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-24 21:42:58.955331 INFO::Adjusting the last 2 batches sequentially
2026-04-24 21:42:58.958548 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-24 21:42:58.975377 INFO::Done
2026-04-24 21:42:58.976197 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:58.980977 INFO::ASW Batch was 0.486550575025667 prior to batch effect correction and is now 0.486550575025667 .
2026-04-24 21:42:58.981673 INFO::ASW Label was 0.321434776441584 prior to batch effect correction and is now 0.321434776441584 .
2026-04-24 21:42:58.982531 INFO::Total function execution time is 2.81094861030579 s and adjustment time is 2.77011728286743 s ( 98.55 )
2026-04-24 21:42:59.160384 INFO::Formatting Data.
2026-04-24 21:42:59.161929 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.164028 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.166398 INFO::Found 0 missing values.
2026-04-24 21:42:59.17348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.174628 INFO::Done
2026-04-24 21:42:59.175622 INFO::Acquiring quality metrics before batch effect correction.
2026-04-24 21:42:59.180215 INFO::Starting hierarchical adjustment
2026-04-24 21:42:59.181487 INFO::Found 3 batches.
2026-04-24 21:42:59.182347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-24 21:42:59.18345 INFO::Using default BPPARAM
2026-04-24 21:42:59.184281 INFO::Processing subtree level 1
2026-04-24 21:42:59.327785 INFO::Adjusting the last 1 batches sequentially
2026-04-24 21:42:59.330169 INFO::Done
2026-04-24 21:42:59.331071 INFO::Acquiring quality metrics after batch effect correction.
2026-04-24 21:42:59.334746 INFO::ASW Batch was 0.144256975689905 prior to batch effect correction and is now -0.147974003921191 .
2026-04-24 21:42:59.335465 INFO::ASW Label was -0.205026556761862 prior to batch effect correction and is now -0.0533895732987441 .
2026-04-24 21:42:59.336573 INFO::Total function execution time is 0.176410675048828 s and adjustment time is 0.148876428604126 s ( 84.39 )
2026-04-24 21:42:59.476192 INFO::Formatting Data.
2026-04-24 21:42:59.477278 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.478392 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.479598 INFO::Found 2 missing values.
2026-04-24 21:42:59.482821 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.48346 INFO::Done
2026-04-24 21:42:59.516758 INFO::Found NA in Reference column
2026-04-24 21:42:59.528214 INFO::Require at least two references per batch.
2026-04-24 21:42:59.551609 INFO::Formatting Data.
2026-04-24 21:42:59.55263 INFO::Recognized SummarizedExperiment
2026-04-24 21:42:59.553305 INFO::Typecasting input to dataframe.
2026-04-24 21:42:59.564252 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.573822 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.579413 INFO::Found 0 missing values.
2026-04-24 21:42:59.58856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.589589 INFO::Done
2026-04-24 21:42:59.61002 INFO::Formatting Data.
2026-04-24 21:42:59.61106 INFO::Recognized SummarizedExperiment
2026-04-24 21:42:59.611806 INFO::Typecasting input to dataframe.
2026-04-24 21:42:59.633209 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.634831 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.639288 INFO::Found 0 missing values.
2026-04-24 21:42:59.652789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.653841 INFO::Done
2026-04-24 21:42:59.673589 INFO::Formatting Data.
2026-04-24 21:42:59.674645 INFO::Recognized SummarizedExperiment
2026-04-24 21:42:59.675399 INFO::Typecasting input to dataframe.
2026-04-24 21:42:59.69603 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.69745 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.698883 INFO::Found 0 missing values.
2026-04-24 21:42:59.699986 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.
2026-04-24 21:42:59.704861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.705507 INFO::Done
2026-04-24 21:42:59.717478 INFO::Formatting Data.
2026-04-24 21:42:59.71862 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.719769 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.721019 INFO::Found 0 missing values.
2026-04-24 21:42:59.724332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.724976 INFO::Done
2026-04-24 21:42:59.738576 INFO::Formatting Data.
2026-04-24 21:42:59.739691 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.740771 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.742015 INFO::Found 0 missing values.
2026-04-24 21:42:59.745309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.745927 INFO::Done
2026-04-24 21:42:59.781173 INFO::Formatting Data.
2026-04-24 21:42:59.782255 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.783548 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.784936 INFO::Found 1 missing values.
2026-04-24 21:42:59.787993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.788672 INFO::Done
2026-04-24 21:42:59.812246 INFO::Formatting Data.
2026-04-24 21:42:59.813359 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.814436 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.815586 INFO::Found 2 missing values.
2026-04-24 21:42:59.816642 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.
2026-04-24 21:42:59.81925 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.81991 INFO::Done
2026-04-24 21:42:59.83182 INFO::Formatting Data.
2026-04-24 21:42:59.832894 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.833981 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.835115 INFO::Found 2 missing values.
2026-04-24 21:42:59.837059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.837823 INFO::Done
2026-04-24 21:42:59.851191 INFO::Formatting Data.
2026-04-24 21:42:59.852285 INFO::Typecasting input to dataframe.
2026-04-24 21:42:59.853293 INFO::Replacing NaNs with NAs.
2026-04-24 21:42:59.854362 INFO::Removing potential empty rows and columns
2026-04-24 21:42:59.855582 INFO::Found 0 missing values.
2026-04-24 21:42:59.858801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-24 21:42:59.859411 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.989 4.231 22.877
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.944 | 1.278 | 18.664 | |
| compute_asw | 0.024 | 0.001 | 0.025 | |
| count_existing | 0.014 | 0.000 | 0.014 | |
| generate_data_covariables | 0.013 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.011 | |