Yannis Schumann
| Snapshot Date: 2025-11-14 13:45 -0500 (Fri, 14 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-15 11:58 -0500 (Sat, 15 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-11-14 07:04:09 -0000 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 07:05:29 -0000 (Fri, 14 Nov 2025) |
| EllapsedTime: 80.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* 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 27.546 1.626 20.552
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-11-14 07:05:13.326971 INFO::Formatting Data.
2025-11-14 07:05:13.328757 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:13.345487 INFO::Removing potential empty rows and columns
2025-11-14 07:05:13.726499 INFO::Found 0 missing values.
2025-11-14 07:05:13.731697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:13.732528 INFO::Done
2025-11-14 07:05:13.73331 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:13.749071 INFO::Starting hierarchical adjustment
2025-11-14 07:05:13.750234 INFO::Found 3 batches.
2025-11-14 07:05:13.751021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:13.752606 INFO::Using default BPPARAM
2025-11-14 07:05:13.753443 INFO::Processing subtree level 1
2025-11-14 07:05:13.881701 INFO::Adjusting the last 1 batches sequentially
2025-11-14 07:05:13.884283 INFO::Done
2025-11-14 07:05:13.885323 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:13.889343 INFO::ASW Batch was 0.00664515000921447 prior to batch effect correction and is now 0.00664515000921447 .
2025-11-14 07:05:13.891029 INFO::Total function execution time is 0.564850091934204 s and adjustment time is 0.134275197982788 s ( 23.77 )
2025-11-14 07:05:13.911836 INFO::Formatting Data.
2025-11-14 07:05:13.912862 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:13.914114 INFO::Removing potential empty rows and columns
2025-11-14 07:05:13.915737 INFO::Found 0 missing values.
2025-11-14 07:05:13.91706 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.
2025-11-14 07:05:13.932813 INFO::Formatting Data.
2025-11-14 07:05:13.933809 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:13.935023 INFO::Removing potential empty rows and columns
2025-11-14 07:05:13.936568 INFO::Found 0 missing values.
2025-11-14 07:05:13.93787 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.
2025-11-14 07:05:13.960389 INFO::Formatting Data.
2025-11-14 07:05:13.961379 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:13.962514 INFO::Removing potential empty rows and columns
2025-11-14 07:05:13.963963 INFO::Found 0 missing values.
2025-11-14 07:05:13.965191 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.
2025-11-14 07:05:13.971289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:13.972129 INFO::Done
2025-11-14 07:05:13.972888 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:13.975572 INFO::Starting hierarchical adjustment
2025-11-14 07:05:13.976542 INFO::Found 2 batches.
2025-11-14 07:05:13.977298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:13.978155 INFO::Using default BPPARAM
2025-11-14 07:05:13.978868 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:13.98016 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 07:05:14.010501 INFO::Done
2025-11-14 07:05:14.011583 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:14.014365 INFO::ASW Batch was 0.0568339935731599 prior to batch effect correction and is now -0.128925630664519 .
2025-11-14 07:05:14.015521 INFO::Total function execution time is 0.0551505088806152 s and adjustment time is 0.0341217517852783 s ( 61.87 )
2025-11-14 07:05:14.019038 INFO::Formatting Data.
2025-11-14 07:05:14.019986 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:14.031924 INFO::Formatting Data.
2025-11-14 07:05:14.032865 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:14.03407 INFO::Removing potential empty rows and columns
2025-11-14 07:05:14.036032 INFO::Found 0 missing values.
2025-11-14 07:05:14.040226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:14.041062 INFO::Done
2025-11-14 07:05:14.04183 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:14.044567 INFO::Starting hierarchical adjustment
2025-11-14 07:05:14.045625 INFO::Found 2 batches.
2025-11-14 07:05:14.046384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:14.047329 INFO::Using default BPPARAM
2025-11-14 07:05:14.048262 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:14.049733 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 07:05:14.107915 INFO::Done
2025-11-14 07:05:14.108768 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:14.111446 INFO::ASW Batch was -0.035834684200412 prior to batch effect correction and is now -0.121253959407795 .
2025-11-14 07:05:14.112501 INFO::Total function execution time is 0.0806300640106201 s and adjustment time is 0.0624830722808838 s ( 77.49 )
2025-11-14 07:05:14.113958 INFO::Formatting Data.
2025-11-14 07:05:14.114779 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:14.115981 INFO::Removing potential empty rows and columns
2025-11-14 07:05:14.11738 INFO::Found 0 missing values.
2025-11-14 07:05:14.121397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:14.122212 INFO::Done
2025-11-14 07:05:14.122936 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:14.125627 INFO::Starting hierarchical adjustment
2025-11-14 07:05:14.12662 INFO::Found 2 batches.
2025-11-14 07:05:14.127355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:14.128246 INFO::Using default BPPARAM
2025-11-14 07:05:14.129002 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:14.130255 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 07:05:14.150264 INFO::Done
2025-11-14 07:05:14.15111 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:14.15379 INFO::ASW Batch was -0.035834684200412 prior to batch effect correction and is now -0.121253959407795 .
2025-11-14 07:05:14.154924 INFO::Total function execution time is 0.0409038066864014 s and adjustment time is 0.0238213539123535 s ( 58.24 )
2025-11-14 07:05:17.816622 INFO::Formatting Data.
2025-11-14 07:05:17.817507 INFO::Recognized SummarizedExperiment
2025-11-14 07:05:17.818158 INFO::Typecasting input to dataframe.
2025-11-14 07:05:17.856635 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:17.858129 INFO::Removing potential empty rows and columns
2025-11-14 07:05:17.863098 INFO::Found 0 missing values.
2025-11-14 07:05:17.87294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:17.873803 INFO::Done
2025-11-14 07:05:17.874519 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:17.879203 INFO::Starting hierarchical adjustment
2025-11-14 07:05:17.880214 INFO::Found 2 batches.
2025-11-14 07:05:17.880972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:17.882337 INFO::Using default BPPARAM
2025-11-14 07:05:17.883071 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:17.884399 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 07:05:17.959962 INFO::Done
2025-11-14 07:05:17.96086 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:17.965518 INFO::ASW Batch was 0.0095275826569218 prior to batch effect correction and is now -0.0920153673226097 .
2025-11-14 07:05:17.96662 INFO::Total function execution time is 0.15036416053772 s and adjustment time is 0.0799355506896973 s ( 53.16 )
2025-11-14 07:05:17.99119 INFO::Formatting Data.
2025-11-14 07:05:17.992166 INFO::Recognized SummarizedExperiment
2025-11-14 07:05:17.992906 INFO::Typecasting input to dataframe.
2025-11-14 07:05:18.005223 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:18.006805 INFO::Removing potential empty rows and columns
2025-11-14 07:05:18.011964 INFO::Found 0 missing values.
2025-11-14 07:05:18.021721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:18.022575 INFO::Done
2025-11-14 07:05:18.023301 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:18.028066 INFO::Starting hierarchical adjustment
2025-11-14 07:05:18.029114 INFO::Found 2 batches.
2025-11-14 07:05:18.029851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:18.030658 INFO::Using default BPPARAM
2025-11-14 07:05:18.031366 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:18.032716 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 07:05:18.066742 INFO::Done
2025-11-14 07:05:18.067644 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:18.072435 INFO::ASW Batch was -0.0124663461322068 prior to batch effect correction and is now -0.0124663461322068 .
2025-11-14 07:05:18.073563 INFO::Total function execution time is 0.0823509693145752 s and adjustment time is 0.0378003120422363 s ( 45.9 )
2025-11-14 07:05:18.097024 INFO::Formatting Data.
2025-11-14 07:05:18.097955 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:18.099072 INFO::Removing potential empty rows and columns
2025-11-14 07:05:18.100438 INFO::Found 0 missing values.
2025-11-14 07:05:18.104452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:18.105213 INFO::Done
2025-11-14 07:05:18.105918 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:18.108494 INFO::Starting hierarchical adjustment
2025-11-14 07:05:18.109472 INFO::Found 3 batches.
2025-11-14 07:05:18.110176 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:18.110984 INFO::Using default BPPARAM
2025-11-14 07:05:18.111716 INFO::Processing subtree level 1
2025-11-14 07:05:18.282366 INFO::Adjusting the last 1 batches sequentially
2025-11-14 07:05:18.285012 INFO::Done
2025-11-14 07:05:18.285932 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:18.290119 INFO::ASW Batch was -0.0967717200219345 prior to batch effect correction and is now -0.174361850190047 .
2025-11-14 07:05:18.291687 INFO::Total function execution time is 0.19460391998291 s and adjustment time is 0.175716638565063 s ( 90.29 )
2025-11-14 07:05:18.312329 INFO::Skipping initial DF formatting
2025-11-14 07:05:18.313258 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:18.318751 INFO::Starting hierarchical adjustment
2025-11-14 07:05:18.319951 INFO::Found 5 batches.
2025-11-14 07:05:18.320779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:18.321716 INFO::Using default BPPARAM
2025-11-14 07:05:18.322586 INFO::Processing subtree level 1
2025-11-14 07:05:18.576283 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:18.578791 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 07:05:18.608198 INFO::Done
2025-11-14 07:05:18.609246 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:18.61551 INFO::ASW Batch was 0.573932501064976 prior to batch effect correction and is now 0.573932501064976 .
2025-11-14 07:05:18.616514 INFO::ASW Label was 0.352195788627816 prior to batch effect correction and is now 0.352195788627816 .
2025-11-14 07:05:18.617901 INFO::Total function execution time is 0.305568218231201 s and adjustment time is 0.28844952583313 s ( 94.4 )
2025-11-14 07:05:18.715 INFO::Formatting Data.
2025-11-14 07:05:18.716244 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:18.71783 INFO::Removing potential empty rows and columns
2025-11-14 07:05:18.719538 INFO::Found 0 missing values.
2025-11-14 07:05:18.72667 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:18.727746 INFO::Done
2025-11-14 07:05:18.728707 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:18.733659 INFO::Starting hierarchical adjustment
2025-11-14 07:05:18.735203 INFO::Found 5 batches.
2025-11-14 07:05:18.736294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:18.737511 INFO::Using default BPPARAM
2025-11-14 07:05:18.738533 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.
2025-11-14 07:05:18.909696 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:18.912255 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 07:05:18.938834 INFO::Done
2025-11-14 07:05:18.940093 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:18.945939 INFO::ASW Batch was 0.388802635365681 prior to batch effect correction and is now -0.0841343724283925 .
2025-11-14 07:05:18.947067 INFO::ASW Label was 0.344382907801142 prior to batch effect correction and is now 0.855807003011742 .
2025-11-14 07:05:18.948465 INFO::Total function execution time is 0.233525514602661 s and adjustment time is 0.203980922698975 s ( 87.35 )
2025-11-14 07:05:18.949917 INFO::Formatting Data.
2025-11-14 07:05:18.951016 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:18.952572 INFO::Removing potential empty rows and columns
2025-11-14 07:05:18.954478 INFO::Found 0 missing values.
2025-11-14 07:05:18.962285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:18.96328 INFO::Done
2025-11-14 07:05:18.964198 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:18.969081 INFO::Starting hierarchical adjustment
2025-11-14 07:05:18.970278 INFO::Found 5 batches.
2025-11-14 07:05:18.971114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:18.972135 INFO::Using default BPPARAM
2025-11-14 07:05:18.972981 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.
2025-11-14 07:05:19.129931 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:19.132287 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 07:05:19.177105 INFO::Done
2025-11-14 07:05:19.17932 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:19.185637 INFO::ASW Batch was 0.388802635365681 prior to batch effect correction and is now -0.0841343724283925 .
2025-11-14 07:05:19.186698 INFO::ASW Label was 0.344382907801142 prior to batch effect correction and is now 0.855807003011742 .
2025-11-14 07:05:19.188065 INFO::Total function execution time is 0.23809027671814 s and adjustment time is 0.206425189971924 s ( 86.7 )
2025-11-14 07:05:19.215125 INFO::Formatting Data.
2025-11-14 07:05:19.216254 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:19.217574 INFO::Removing potential empty rows and columns
2025-11-14 07:05:19.219035 INFO::Found 0 missing values.
2025-11-14 07:05:19.225389 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:19.226352 INFO::Done
2025-11-14 07:05:19.227202 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:19.231616 INFO::Starting hierarchical adjustment
2025-11-14 07:05:19.232719 INFO::Found 5 batches.
2025-11-14 07:05:19.233543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:19.234479 INFO::Using default BPPARAM
2025-11-14 07:05:19.235293 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.
2025-11-14 07:05:19.39932 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:19.401896 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 07:05:19.426378 INFO::Done
2025-11-14 07:05:19.427463 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:19.43267 INFO::ASW Batch was 0.408951845870628 prior to batch effect correction and is now 0.0274086825463252 .
2025-11-14 07:05:19.43381 INFO::ASW Label was 0.384044598406472 prior to batch effect correction and is now 0.763671929859335 .
2025-11-14 07:05:19.435018 INFO::Total function execution time is 0.219963550567627 s and adjustment time is 0.193862438201904 s ( 88.13 )
2025-11-14 07:05:19.436277 INFO::Formatting Data.
2025-11-14 07:05:19.437213 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:19.438522 INFO::Removing potential empty rows and columns
2025-11-14 07:05:19.440042 INFO::Found 0 missing values.
2025-11-14 07:05:19.446177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:19.447153 INFO::Done
2025-11-14 07:05:19.447935 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:19.452244 INFO::Starting hierarchical adjustment
2025-11-14 07:05:19.453458 INFO::Found 5 batches.
2025-11-14 07:05:19.45425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:19.455171 INFO::Using default BPPARAM
2025-11-14 07:05:19.455968 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.
2025-11-14 07:05:19.619679 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:19.622137 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 07:05:19.647733 INFO::Done
2025-11-14 07:05:19.648818 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:19.654056 INFO::ASW Batch was 0.408951845870628 prior to batch effect correction and is now 0.0274086825463252 .
2025-11-14 07:05:19.655068 INFO::ASW Label was 0.384044598406472 prior to batch effect correction and is now 0.763671929859335 .
2025-11-14 07:05:19.656421 INFO::Total function execution time is 0.220117807388306 s and adjustment time is 0.194466114044189 s ( 88.35 )
2025-11-14 07:05:19.678193 INFO::Formatting Data.
2025-11-14 07:05:19.679286 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:19.680661 INFO::Removing potential empty rows and columns
2025-11-14 07:05:19.682248 INFO::Found 0 missing values.
2025-11-14 07:05:19.686488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:19.687452 INFO::Done
2025-11-14 07:05:19.688255 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:19.692589 INFO::Starting hierarchical adjustment
2025-11-14 07:05:19.693759 INFO::Found 2 batches.
2025-11-14 07:05:19.694554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:19.695489 INFO::Using default BPPARAM
2025-11-14 07:05:19.696289 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:19.697722 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 07:05:19.721125 INFO::Done
2025-11-14 07:05:19.7221 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:19.72634 INFO::ASW Batch was 0.624510929696172 prior to batch effect correction and is now -0.0246278898124389 .
2025-11-14 07:05:19.727226 INFO::ASW Label was 0.410640299044961 prior to batch effect correction and is now 0.920947241454645 .
2025-11-14 07:05:19.728395 INFO::Total function execution time is 0.0502974987030029 s and adjustment time is 0.0275638103485107 s ( 54.8 )
2025-11-14 07:05:19.729547 INFO::Formatting Data.
2025-11-14 07:05:19.730436 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:19.731755 INFO::Removing potential empty rows and columns
2025-11-14 07:05:19.733245 INFO::Found 0 missing values.
2025-11-14 07:05:19.737373 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:19.73824 INFO::Done
2025-11-14 07:05:19.738999 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:19.743213 INFO::Starting hierarchical adjustment
2025-11-14 07:05:19.744403 INFO::Found 2 batches.
2025-11-14 07:05:19.745219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:19.7461 INFO::Using default BPPARAM
2025-11-14 07:05:19.746889 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:19.748303 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 07:05:19.769963 INFO::Done
2025-11-14 07:05:19.770881 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:19.775064 INFO::ASW Batch was 0.624510929696172 prior to batch effect correction and is now -0.0246278898124389 .
2025-11-14 07:05:19.776036 INFO::ASW Label was 0.410640299044961 prior to batch effect correction and is now 0.920947241454645 .
2025-11-14 07:05:19.777202 INFO::Total function execution time is 0.0476498603820801 s and adjustment time is 0.0257596969604492 s ( 54.06 )
2025-11-14 07:05:19.794791 INFO::Formatting Data.
2025-11-14 07:05:19.79602 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:19.797455 INFO::Removing potential empty rows and columns
2025-11-14 07:05:19.798954 INFO::Found 0 missing values.
2025-11-14 07:05:19.802458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:19.803476 INFO::Done
2025-11-14 07:05:19.804325 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:19.807347 INFO::Starting hierarchical adjustment
2025-11-14 07:05:19.808625 INFO::Found 2 batches.
2025-11-14 07:05:19.809567 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:19.810525 INFO::Using default BPPARAM
2025-11-14 07:05:19.811425 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:19.812964 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 07:05:19.861724 INFO::Done
2025-11-14 07:05:19.862756 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:19.865866 INFO::ASW Batch was -0.0103891233991037 prior to batch effect correction and is now -0.142792211959836 .
2025-11-14 07:05:19.867304 INFO::Total function execution time is 0.0725777149200439 s and adjustment time is 0.05332350730896 s ( 73.47 )
2025-11-14 07:05:19.885882 INFO::Formatting Data.
2025-11-14 07:05:19.887092 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:19.888562 INFO::Removing potential empty rows and columns
2025-11-14 07:05:19.890135 INFO::Found 0 missing values.
2025-11-14 07:05:19.891925 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.
2025-11-14 07:05:19.899144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:19.900133 INFO::Done
2025-11-14 07:05:19.900957 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:19.905354 INFO::Starting hierarchical adjustment
2025-11-14 07:05:19.906534 INFO::Found 2 batches.
2025-11-14 07:05:19.907377 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:19.90837 INFO::Using default BPPARAM
2025-11-14 07:05:19.909252 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:19.910787 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 07:05:19.936703 INFO::Done
2025-11-14 07:05:19.937733 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:19.942405 INFO::ASW Batch was 0.667231176518189 prior to batch effect correction and is now 0.155429293930673 .
2025-11-14 07:05:19.943475 INFO::ASW Label was 0.407900733139337 prior to batch effect correction and is now 0.747671367056765 .
2025-11-14 07:05:19.944712 INFO::Total function execution time is 0.0589005947113037 s and adjustment time is 0.0303611755371094 s ( 51.55 )
2025-11-14 07:05:19.945986 INFO::Formatting Data.
2025-11-14 07:05:19.946965 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:19.94845 INFO::Removing potential empty rows and columns
2025-11-14 07:05:19.950119 INFO::Found 0 missing values.
2025-11-14 07:05:19.951672 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.
2025-11-14 07:05:19.959266 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:19.960307 INFO::Done
2025-11-14 07:05:19.961186 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:19.972814 INFO::Starting hierarchical adjustment
2025-11-14 07:05:19.974229 INFO::Found 2 batches.
2025-11-14 07:05:19.9751 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:19.976126 INFO::Using default BPPARAM
2025-11-14 07:05:19.977021 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:19.978565 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 07:05:20.00508 INFO::Done
2025-11-14 07:05:20.006117 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:20.010835 INFO::ASW Batch was 0.667231176518189 prior to batch effect correction and is now 0.155429293930673 .
2025-11-14 07:05:20.011885 INFO::ASW Label was 0.407900733139337 prior to batch effect correction and is now 0.747671367056765 .
2025-11-14 07:05:20.013169 INFO::Total function execution time is 0.0671868324279785 s and adjustment time is 0.0311079025268555 s ( 46.3 )
2025-11-14 07:05:20.32733 INFO::Formatting Data.
2025-11-14 07:05:20.328431 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:20.329706 INFO::Removing potential empty rows and columns
2025-11-14 07:05:20.331175 INFO::Found 0 missing values.
2025-11-14 07:05:20.335628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:20.336545 INFO::Done
2025-11-14 07:05:20.337369 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:20.34025 INFO::Starting hierarchical adjustment
2025-11-14 07:05:20.341385 INFO::Found 3 batches.
2025-11-14 07:05:20.342137 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:20.342986 INFO::Using default BPPARAM
2025-11-14 07:05:20.343796 INFO::Processing subtree level 1
2025-11-14 07:05:20.457132 INFO::Adjusting the last 1 batches sequentially
2025-11-14 07:05:20.459594 INFO::Done
2025-11-14 07:05:20.4605 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:20.463988 INFO::ASW Batch was -0.095151780942901 prior to batch effect correction and is now -0.095151780942901 .
2025-11-14 07:05:20.46536 INFO::Total function execution time is 0.138043880462646 s and adjustment time is 0.118438005447388 s ( 85.8 )
2025-11-14 07:05:20.466804 INFO::Formatting Data.
2025-11-14 07:05:20.467709 INFO::Typecasting input to dataframe.
2025-11-14 07:05:20.468782 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:20.470214 INFO::Removing potential empty rows and columns
2025-11-14 07:05:20.471814 INFO::Found 0 missing values.
2025-11-14 07:05:20.476341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:20.477243 INFO::Done
2025-11-14 07:05:20.47802 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:20.480944 INFO::Starting hierarchical adjustment
2025-11-14 07:05:20.482031 INFO::Found 3 batches.
2025-11-14 07:05:20.48279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:20.483701 INFO::Using default BPPARAM
2025-11-14 07:05:20.484518 INFO::Processing subtree level 1
2025-11-14 07:05:20.598038 INFO::Adjusting the last 1 batches sequentially
2025-11-14 07:05:20.600541 INFO::Done
2025-11-14 07:05:20.601423 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:20.604899 INFO::ASW Batch was -0.095151780942901 prior to batch effect correction and is now -0.095151780942901 .
2025-11-14 07:05:20.606258 INFO::Total function execution time is 0.139417171478271 s and adjustment time is 0.118740081787109 s ( 85.17 )
2025-11-14 07:05:20.625449 INFO::Formatting Data.
2025-11-14 07:05:20.626611 INFO::Typecasting input to dataframe.
2025-11-14 07:05:20.627961 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:20.629544 INFO::Removing potential empty rows and columns
2025-11-14 07:05:20.631243 INFO::Found 0 missing values.
2025-11-14 07:05:20.63619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:20.637227 INFO::Done
2025-11-14 07:05:20.638072 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:20.641186 INFO::Starting hierarchical adjustment
2025-11-14 07:05:20.64242 INFO::Found 3 batches.
2025-11-14 07:05:20.643353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:20.644347 INFO::Using default BPPARAM
2025-11-14 07:05:20.645224 INFO::Processing subtree level 1
2025-11-14 07:05:20.765015 INFO::Adjusting the last 1 batches sequentially
2025-11-14 07:05:20.767807 INFO::Done
2025-11-14 07:05:20.768986 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:20.773292 INFO::ASW Batch was -0.0395631692487022 prior to batch effect correction and is now -0.0395631692487022 .
2025-11-14 07:05:20.774925 INFO::Total function execution time is 0.149476051330566 s and adjustment time is 0.125600099563599 s ( 84.03 )
2025-11-14 07:05:20.970059 INFO::Formatting Data.
2025-11-14 07:05:20.971277 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:20.973224 INFO::Removing potential empty rows and columns
2025-11-14 07:05:20.977831 INFO::Found 1000 missing values.
2025-11-14 07:05:21.009556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:21.010687 INFO::Done
2025-11-14 07:05:21.011776 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:21.020043 INFO::Starting hierarchical adjustment
2025-11-14 07:05:21.021302 INFO::Found 10 batches.
2025-11-14 07:05:21.022101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:21.022997 INFO::Using default BPPARAM
2025-11-14 07:05:21.02383 INFO::Processing subtree level 1
2025-11-14 07:05:21.206853 INFO::Processing subtree level 2
2025-11-14 07:05:21.425016 INFO::Adjusting the last 1 batches sequentially
2025-11-14 07:05:21.427656 INFO::Done
2025-11-14 07:05:21.433724 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:21.44565 INFO::ASW Batch was 0.486440041785682 prior to batch effect correction and is now 0.486440041785682 .
2025-11-14 07:05:21.446648 INFO::ASW Label was 0.336345191944813 prior to batch effect correction and is now 0.336345191944813 .
2025-11-14 07:05:21.44792 INFO::Total function execution time is 0.477936267852783 s and adjustment time is 0.40659236907959 s ( 85.07 )
2025-11-14 07:05:21.453256 INFO::Formatting Data.
2025-11-14 07:05:21.454389 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:21.456099 INFO::Removing potential empty rows and columns
2025-11-14 07:05:21.464266 INFO::Found 1000 missing values.
2025-11-14 07:05:21.525895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:21.526839 INFO::Done
2025-11-14 07:05:21.527612 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:21.547788 INFO::Starting hierarchical adjustment
2025-11-14 07:05:21.553225 INFO::Found 10 batches.
2025-11-14 07:05:22.872418 INFO::Set up parallel execution backend with 2 workers
2025-11-14 07:05:22.874626 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-14 07:05:24.182675 INFO::Adjusting the last 2 batches sequentially
2025-11-14 07:05:24.189154 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 07:05:24.238275 INFO::Done
2025-11-14 07:05:24.239116 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:24.253937 INFO::ASW Batch was 0.486440041785682 prior to batch effect correction and is now 0.486440041785682 .
2025-11-14 07:05:24.254788 INFO::ASW Label was 0.336345191944813 prior to batch effect correction and is now 0.336345191944813 .
2025-11-14 07:05:24.255827 INFO::Total function execution time is 2.80270338058472 s and adjustment time is 2.68950247764587 s ( 95.96 )
2025-11-14 07:05:24.442743 INFO::Formatting Data.
2025-11-14 07:05:24.443882 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:24.445143 INFO::Removing potential empty rows and columns
2025-11-14 07:05:24.446679 INFO::Found 0 missing values.
2025-11-14 07:05:24.452365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:24.453228 INFO::Done
2025-11-14 07:05:24.453984 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 07:05:24.457909 INFO::Starting hierarchical adjustment
2025-11-14 07:05:24.458949 INFO::Found 3 batches.
2025-11-14 07:05:24.459752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 07:05:24.460655 INFO::Using default BPPARAM
2025-11-14 07:05:24.461453 INFO::Processing subtree level 1
2025-11-14 07:05:24.595854 INFO::Adjusting the last 1 batches sequentially
2025-11-14 07:05:24.598295 INFO::Done
2025-11-14 07:05:24.599138 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 07:05:24.604044 INFO::ASW Batch was 0.220916827859798 prior to batch effect correction and is now -0.158222116608765 .
2025-11-14 07:05:24.605004 INFO::ASW Label was -0.203325354082882 prior to batch effect correction and is now 0.0257784282156749 .
2025-11-14 07:05:24.60627 INFO::Total function execution time is 0.163565158843994 s and adjustment time is 0.139558553695679 s ( 85.32 )
2025-11-14 07:05:24.778919 INFO::Formatting Data.
2025-11-14 07:05:24.780031 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:24.781277 INFO::Removing potential empty rows and columns
2025-11-14 07:05:24.782787 INFO::Found 2 missing values.
2025-11-14 07:05:24.786924 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:24.787735 INFO::Done
2025-11-14 07:05:24.82647 INFO::Found NA in Reference column
2025-11-14 07:05:24.83998 INFO::Require at least two references per batch.
2025-11-14 07:05:24.869556 INFO::Formatting Data.
2025-11-14 07:05:24.870496 INFO::Recognized SummarizedExperiment
2025-11-14 07:05:24.871229 INFO::Typecasting input to dataframe.
2025-11-14 07:05:24.885068 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:24.886553 INFO::Removing potential empty rows and columns
2025-11-14 07:05:24.891739 INFO::Found 0 missing values.
2025-11-14 07:05:24.901973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:24.902848 INFO::Done
2025-11-14 07:05:24.924714 INFO::Formatting Data.
2025-11-14 07:05:24.925701 INFO::Recognized SummarizedExperiment
2025-11-14 07:05:24.926424 INFO::Typecasting input to dataframe.
2025-11-14 07:05:24.950359 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:24.951869 INFO::Removing potential empty rows and columns
2025-11-14 07:05:24.957001 INFO::Found 0 missing values.
2025-11-14 07:05:24.973512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:24.974382 INFO::Done
2025-11-14 07:05:24.996121 INFO::Formatting Data.
2025-11-14 07:05:24.99708 INFO::Recognized SummarizedExperiment
2025-11-14 07:05:24.99781 INFO::Typecasting input to dataframe.
2025-11-14 07:05:25.020804 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:25.022109 INFO::Removing potential empty rows and columns
2025-11-14 07:05:25.023596 INFO::Found 0 missing values.
2025-11-14 07:05:25.024836 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.
2025-11-14 07:05:25.031045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:25.03185 INFO::Done
2025-11-14 07:05:25.045372 INFO::Formatting Data.
2025-11-14 07:05:25.046353 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:25.04753 INFO::Removing potential empty rows and columns
2025-11-14 07:05:25.048923 INFO::Found 0 missing values.
2025-11-14 07:05:25.053082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:25.05384 INFO::Done
2025-11-14 07:05:25.069421 INFO::Formatting Data.
2025-11-14 07:05:25.070382 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:25.071571 INFO::Removing potential empty rows and columns
2025-11-14 07:05:25.072981 INFO::Found 0 missing values.
2025-11-14 07:05:25.077434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:25.078213 INFO::Done
2025-11-14 07:05:25.121056 INFO::Formatting Data.
2025-11-14 07:05:25.12213 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:25.123572 INFO::Removing potential empty rows and columns
2025-11-14 07:05:25.125251 INFO::Found 1 missing values.
2025-11-14 07:05:25.129212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:25.130124 INFO::Done
2025-11-14 07:05:25.158185 INFO::Formatting Data.
2025-11-14 07:05:25.15921 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:25.160445 INFO::Removing potential empty rows and columns
2025-11-14 07:05:25.161802 INFO::Found 2 missing values.
2025-11-14 07:05:25.163081 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.
2025-11-14 07:05:25.16638 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:25.16717 INFO::Done
2025-11-14 07:05:25.181461 INFO::Formatting Data.
2025-11-14 07:05:25.182453 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:25.183669 INFO::Removing potential empty rows and columns
2025-11-14 07:05:25.185051 INFO::Found 2 missing values.
2025-11-14 07:05:25.187369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:25.188195 INFO::Done
2025-11-14 07:05:25.203378 INFO::Formatting Data.
2025-11-14 07:05:25.204439 INFO::Typecasting input to dataframe.
2025-11-14 07:05:25.205563 INFO::Replacing NaNs with NAs.
2025-11-14 07:05:25.206736 INFO::Removing potential empty rows and columns
2025-11-14 07:05:25.208282 INFO::Found 0 missing values.
2025-11-14 07:05:25.212568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 07:05:25.213346 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.315 5.183 25.572
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.546 | 1.626 | 20.552 | |
| compute_asw | 0.033 | 0.000 | 0.033 | |
| count_existing | 0.017 | 0.000 | 0.016 | |
| generate_data_covariables | 0.015 | 0.000 | 0.015 | |
| generate_dataset | 0.014 | 0.000 | 0.014 | |