Yannis Schumann
| Snapshot Date: 2026-02-09 13:45 -0500 (Mon, 09 Feb 2026) |
| 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 Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-12 11:57 -0500 (Thu, 12 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4889 |
| 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 | | ||||||||
| 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-02-09 21:50:17 -0500 (Mon, 09 Feb 2026) |
| EndedAt: 2026-02-09 21:51:46 -0500 (Mon, 09 Feb 2026) |
| EllapsedTime: 89.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* 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 23.491 1.184 17.154
* 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-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-09 21:51:08.652021 INFO::Formatting Data.
2026-02-09 21:51:08.653433 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:08.664551 INFO::Removing potential empty rows and columns
2026-02-09 21:51:08.910876 INFO::Found 0 missing values.
2026-02-09 21:51:08.914475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:08.915174 INFO::Done
2026-02-09 21:51:08.915739 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:08.927442 INFO::Starting hierarchical adjustment
2026-02-09 21:51:08.928348 INFO::Found 3 batches.
2026-02-09 21:51:08.928904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:08.930101 INFO::Using default BPPARAM
2026-02-09 21:51:08.93064 INFO::Processing subtree level 1
2026-02-09 21:51:09.037297 INFO::Adjusting the last 1 batches sequentially
2026-02-09 21:51:09.039275 INFO::Done
2026-02-09 21:51:09.040013 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:09.042918 INFO::ASW Batch was -0.0378733417354777 prior to batch effect correction and is now -0.0378733417354777 .
2026-02-09 21:51:09.044064 INFO::Total function execution time is 0.392684698104858 s and adjustment time is 0.111098527908325 s ( 28.29 )
2026-02-09 21:51:09.058545 INFO::Formatting Data.
2026-02-09 21:51:09.05936 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:09.060328 INFO::Removing potential empty rows and columns
2026-02-09 21:51:09.061637 INFO::Found 0 missing values.
2026-02-09 21:51:09.062628 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-09 21:51:09.07424 INFO::Formatting Data.
2026-02-09 21:51:09.075087 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:09.076013 INFO::Removing potential empty rows and columns
2026-02-09 21:51:09.077073 INFO::Found 0 missing values.
2026-02-09 21:51:09.078017 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-09 21:51:09.103278 INFO::Formatting Data.
2026-02-09 21:51:09.104214 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:09.105231 INFO::Removing potential empty rows and columns
2026-02-09 21:51:09.106458 INFO::Found 0 missing values.
2026-02-09 21:51:09.107481 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-09 21:51:09.112182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:09.112743 INFO::Done
2026-02-09 21:51:09.113287 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:09.115615 INFO::Starting hierarchical adjustment
2026-02-09 21:51:09.116351 INFO::Found 2 batches.
2026-02-09 21:51:09.116896 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:09.117578 INFO::Using default BPPARAM
2026-02-09 21:51:09.118123 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:09.119053 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-09 21:51:09.141276 INFO::Done
2026-02-09 21:51:09.141981 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:09.144267 INFO::ASW Batch was -0.0306923078559339 prior to batch effect correction and is now -0.128879028236452 .
2026-02-09 21:51:09.145191 INFO::Total function execution time is 0.0420455932617188 s and adjustment time is 0.0250604152679443 s ( 59.6 )
2026-02-09 21:51:09.148156 INFO::Formatting Data.
2026-02-09 21:51:09.148783 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:09.158053 INFO::Formatting Data.
2026-02-09 21:51:09.158771 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:09.159693 INFO::Removing potential empty rows and columns
2026-02-09 21:51:09.16077 INFO::Found 0 missing values.
2026-02-09 21:51:09.163819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:09.164395 INFO::Done
2026-02-09 21:51:09.164949 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:09.200245 INFO::Starting hierarchical adjustment
2026-02-09 21:51:09.201582 INFO::Found 2 batches.
2026-02-09 21:51:09.202126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:09.202686 INFO::Using default BPPARAM
2026-02-09 21:51:09.20323 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:09.204148 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:09.218482 INFO::Done
2026-02-09 21:51:09.219125 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:09.221095 INFO::ASW Batch was -0.0287424823572592 prior to batch effect correction and is now -0.108971836312025 .
2026-02-09 21:51:09.221867 INFO::Total function execution time is 0.0638599395751953 s and adjustment time is 0.0170900821685791 s ( 26.76 )
2026-02-09 21:51:09.222868 INFO::Formatting Data.
2026-02-09 21:51:09.223446 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:09.224312 INFO::Removing potential empty rows and columns
2026-02-09 21:51:09.225307 INFO::Found 0 missing values.
2026-02-09 21:51:09.228113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:09.228641 INFO::Done
2026-02-09 21:51:09.229149 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:09.231182 INFO::Starting hierarchical adjustment
2026-02-09 21:51:09.231881 INFO::Found 2 batches.
2026-02-09 21:51:09.232377 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:09.232995 INFO::Using default BPPARAM
2026-02-09 21:51:09.233524 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:09.234407 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:09.249376 INFO::Done
2026-02-09 21:51:09.250008 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:09.251977 INFO::ASW Batch was -0.0287424823572592 prior to batch effect correction and is now -0.108971836312025 .
2026-02-09 21:51:09.252751 INFO::Total function execution time is 0.0298712253570557 s and adjustment time is 0.0176258087158203 s ( 59.01 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-09 21:51:12.175101 INFO::Formatting Data.
2026-02-09 21:51:12.175818 INFO::Recognized SummarizedExperiment
2026-02-09 21:51:12.176282 INFO::Typecasting input to dataframe.
2026-02-09 21:51:12.210093 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:12.211532 INFO::Removing potential empty rows and columns
2026-02-09 21:51:12.215712 INFO::Found 0 missing values.
2026-02-09 21:51:12.223002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:12.223658 INFO::Done
2026-02-09 21:51:12.224202 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:12.227893 INFO::Starting hierarchical adjustment
2026-02-09 21:51:12.228625 INFO::Found 2 batches.
2026-02-09 21:51:12.22916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:12.23029 INFO::Using default BPPARAM
2026-02-09 21:51:12.230839 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:12.231829 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-09 21:51:12.289648 INFO::Done
2026-02-09 21:51:12.290376 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:12.294013 INFO::ASW Batch was -0.0130438752595921 prior to batch effect correction and is now -0.0910589477980126 .
2026-02-09 21:51:12.294904 INFO::Total function execution time is 0.120048522949219 s and adjustment time is 0.0611491203308105 s ( 50.94 )
Warning: stack imbalance in '{', 73 then 75
2026-02-09 21:51:12.314246 INFO::Formatting Data.
2026-02-09 21:51:12.315004 INFO::Recognized SummarizedExperiment
2026-02-09 21:51:12.315577 INFO::Typecasting input to dataframe.
2026-02-09 21:51:12.325403 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:12.326721 INFO::Removing potential empty rows and columns
2026-02-09 21:51:12.330602 INFO::Found 0 missing values.
2026-02-09 21:51:12.33813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:12.338825 INFO::Done
2026-02-09 21:51:12.339367 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:12.343068 INFO::Starting hierarchical adjustment
2026-02-09 21:51:12.343861 INFO::Found 2 batches.
2026-02-09 21:51:12.344398 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:12.345008 INFO::Using default BPPARAM
2026-02-09 21:51:12.34553 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:12.346542 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-09 21:51:12.372484 INFO::Done
2026-02-09 21:51:12.373278 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:12.376981 INFO::ASW Batch was -0.0234161838936328 prior to batch effect correction and is now -0.0234161838936328 .
2026-02-09 21:51:12.377883 INFO::Total function execution time is 0.0636241436004639 s and adjustment time is 0.0287339687347412 s ( 45.16 )
2026-02-09 21:51:12.39867 INFO::Formatting Data.
2026-02-09 21:51:12.399479 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:12.400401 INFO::Removing potential empty rows and columns
2026-02-09 21:51:12.401456 INFO::Found 0 missing values.
2026-02-09 21:51:12.404609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:12.40516 INFO::Done
2026-02-09 21:51:12.405679 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:12.407714 INFO::Starting hierarchical adjustment
2026-02-09 21:51:12.408411 INFO::Found 3 batches.
2026-02-09 21:51:12.408944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:12.409544 INFO::Using default BPPARAM
2026-02-09 21:51:12.410069 INFO::Processing subtree level 1
2026-02-09 21:51:12.555865 INFO::Adjusting the last 1 batches sequentially
2026-02-09 21:51:12.557805 INFO::Done
2026-02-09 21:51:12.558445 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:12.561088 INFO::ASW Batch was 0.0589534902276195 prior to batch effect correction and is now -0.144495359173417 .
2026-02-09 21:51:12.562054 INFO::Total function execution time is 0.163438081741333 s and adjustment time is 0.149520397186279 s ( 91.48 )
2026-02-09 21:51:12.577131 INFO::Skipping initial DF formatting
2026-02-09 21:51:12.577859 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:12.5821 INFO::Starting hierarchical adjustment
2026-02-09 21:51:12.582904 INFO::Found 5 batches.
2026-02-09 21:51:12.583452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:12.584089 INFO::Using default BPPARAM
2026-02-09 21:51:12.584631 INFO::Processing subtree level 1
2026-02-09 21:51:12.881029 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:12.883168 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-09 21:51:12.90514 INFO::Done
2026-02-09 21:51:12.906106 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:12.910996 INFO::ASW Batch was 0.52607987400752 prior to batch effect correction and is now 0.52607987400752 .
2026-02-09 21:51:12.911798 INFO::ASW Label was 0.349005084892518 prior to batch effect correction and is now 0.349005084892518 .
2026-02-09 21:51:12.912776 INFO::Total function execution time is 0.335696458816528 s and adjustment time is 0.322315216064453 s ( 96.01 )
2026-02-09 21:51:12.983482 INFO::Formatting Data.
2026-02-09 21:51:12.984859 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:12.986411 INFO::Removing potential empty rows and columns
2026-02-09 21:51:12.988038 INFO::Found 0 missing values.
2026-02-09 21:51:12.994752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:12.995676 INFO::Done
2026-02-09 21:51:12.996494 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.001213 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.002265 INFO::Found 5 batches.
2026-02-09 21:51:13.003077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.004015 INFO::Using default BPPARAM
2026-02-09 21:51:13.004815 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.159136 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.160875 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.178344 INFO::Done
2026-02-09 21:51:13.17906 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.182597 INFO::ASW Batch was 0.510638795817749 prior to batch effect correction and is now -0.0596890068994512 .
2026-02-09 21:51:13.183249 INFO::ASW Label was 0.207224284576792 prior to batch effect correction and is now 0.731775349992706 .
2026-02-09 21:51:13.184102 INFO::Total function execution time is 0.200861692428589 s and adjustment time is 0.176296949386597 s ( 87.77 )
2026-02-09 21:51:13.184979 INFO::Formatting Data.
2026-02-09 21:51:13.185604 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:13.186515 INFO::Removing potential empty rows and columns
2026-02-09 21:51:13.187649 INFO::Found 0 missing values.
2026-02-09 21:51:13.192184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:13.192745 INFO::Done
2026-02-09 21:51:13.193268 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.196391 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.197138 INFO::Found 5 batches.
2026-02-09 21:51:13.197705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.198344 INFO::Using default BPPARAM
2026-02-09 21:51:13.198901 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.322824 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.324369 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.340778 INFO::Done
2026-02-09 21:51:13.341502 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.344895 INFO::ASW Batch was 0.510638795817749 prior to batch effect correction and is now -0.0596890068994512 .
2026-02-09 21:51:13.345523 INFO::ASW Label was 0.207224284576792 prior to batch effect correction and is now 0.731775349992706 .
2026-02-09 21:51:13.346321 INFO::Total function execution time is 0.161354780197144 s and adjustment time is 0.143748044967651 s ( 89.09 )
2026-02-09 21:51:13.360499 INFO::Formatting Data.
2026-02-09 21:51:13.361354 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:13.36229 INFO::Removing potential empty rows and columns
2026-02-09 21:51:13.363309 INFO::Found 0 missing values.
2026-02-09 21:51:13.367364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:13.367921 INFO::Done
2026-02-09 21:51:13.368423 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.371473 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.37219 INFO::Found 5 batches.
2026-02-09 21:51:13.372726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.373325 INFO::Using default BPPARAM
2026-02-09 21:51:13.373875 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.497275 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.498946 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.514637 INFO::Done
2026-02-09 21:51:13.515385 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.518737 INFO::ASW Batch was 0.353410454751949 prior to batch effect correction and is now -0.0638616585863714 .
2026-02-09 21:51:13.519351 INFO::ASW Label was 0.478193912127871 prior to batch effect correction and is now 0.800090254159367 .
2026-02-09 21:51:13.520169 INFO::Total function execution time is 0.159746885299683 s and adjustment time is 0.142537117004395 s ( 89.23 )
2026-02-09 21:51:13.520982 INFO::Formatting Data.
2026-02-09 21:51:13.521608 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:13.522478 INFO::Removing potential empty rows and columns
2026-02-09 21:51:13.523484 INFO::Found 0 missing values.
2026-02-09 21:51:13.527476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:13.52803 INFO::Done
2026-02-09 21:51:13.528533 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.531486 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.53219 INFO::Found 5 batches.
2026-02-09 21:51:13.532723 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.533334 INFO::Using default BPPARAM
2026-02-09 21:51:13.533883 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.668704 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.67058 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.690022 INFO::Done
2026-02-09 21:51:13.690968 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.695425 INFO::ASW Batch was 0.353410454751949 prior to batch effect correction and is now -0.0638616585863714 .
2026-02-09 21:51:13.696184 INFO::ASW Label was 0.478193912127871 prior to batch effect correction and is now 0.800090254159367 .
2026-02-09 21:51:13.697147 INFO::Total function execution time is 0.176134586334229 s and adjustment time is 0.157901525497437 s ( 89.65 )
2026-02-09 21:51:13.712554 INFO::Formatting Data.
2026-02-09 21:51:13.713468 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:13.71455 INFO::Removing potential empty rows and columns
2026-02-09 21:51:13.715691 INFO::Found 0 missing values.
2026-02-09 21:51:13.718693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:13.719282 INFO::Done
2026-02-09 21:51:13.719852 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.723226 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.724041 INFO::Found 2 batches.
2026-02-09 21:51:13.724605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.725249 INFO::Using default BPPARAM
2026-02-09 21:51:13.725837 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.726833 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.742868 INFO::Done
2026-02-09 21:51:13.743658 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.747011 INFO::ASW Batch was 0.724046080836681 prior to batch effect correction and is now -0.0254945037231438 .
2026-02-09 21:51:13.747693 INFO::ASW Label was 0.301885172208061 prior to batch effect correction and is now 0.847976935172717 .
2026-02-09 21:51:13.748546 INFO::Total function execution time is 0.036135196685791 s and adjustment time is 0.0189435482025146 s ( 52.42 )
2026-02-09 21:51:13.749382 INFO::Formatting Data.
2026-02-09 21:51:13.750043 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:13.751006 INFO::Removing potential empty rows and columns
2026-02-09 21:51:13.752076 INFO::Found 0 missing values.
2026-02-09 21:51:13.754969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:13.755548 INFO::Done
2026-02-09 21:51:13.756092 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.759363 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.760146 INFO::Found 2 batches.
2026-02-09 21:51:13.760706 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.761336 INFO::Using default BPPARAM
2026-02-09 21:51:13.7619 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.762884 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-09 21:51:13.779499 INFO::Done
2026-02-09 21:51:13.78031 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.78372 INFO::ASW Batch was 0.724046080836681 prior to batch effect correction and is now -0.0254945037231438 .
2026-02-09 21:51:13.784395 INFO::ASW Label was 0.301885172208061 prior to batch effect correction and is now 0.847976935172717 .
2026-02-09 21:51:13.785288 INFO::Total function execution time is 0.0359199047088623 s and adjustment time is 0.0194633007049561 s ( 54.19 )
2026-02-09 21:51:13.797984 INFO::Formatting Data.
2026-02-09 21:51:13.798877 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:13.799865 INFO::Removing potential empty rows and columns
2026-02-09 21:51:13.80092 INFO::Found 0 missing values.
2026-02-09 21:51:13.80319 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:13.803769 INFO::Done
2026-02-09 21:51:13.804305 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.806459 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.807221 INFO::Found 2 batches.
2026-02-09 21:51:13.807775 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.808383 INFO::Using default BPPARAM
2026-02-09 21:51:13.80894 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.80992 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-09 21:51:13.844657 INFO::Done
2026-02-09 21:51:13.845478 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.847745 INFO::ASW Batch was -0.0622093224550598 prior to batch effect correction and is now -0.131085900702573 .
2026-02-09 21:51:13.848685 INFO::Total function execution time is 0.0508148670196533 s and adjustment time is 0.0375368595123291 s ( 73.87 )
2026-02-09 21:51:13.862259 INFO::Formatting Data.
2026-02-09 21:51:13.863269 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:13.864346 INFO::Removing potential empty rows and columns
2026-02-09 21:51:13.865452 INFO::Found 0 missing values.
2026-02-09 21:51:13.866761 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-09 21:51:13.871729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:13.872364 INFO::Done
2026-02-09 21:51:13.872923 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.876212 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.876997 INFO::Found 2 batches.
2026-02-09 21:51:13.877551 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.87817 INFO::Using default BPPARAM
2026-02-09 21:51:13.878726 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.879733 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-09 21:51:13.898429 INFO::Done
2026-02-09 21:51:13.89927 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.902714 INFO::ASW Batch was 0.501300009593686 prior to batch effect correction and is now -0.0345119066284577 .
2026-02-09 21:51:13.903393 INFO::ASW Label was 0.57049233456561 prior to batch effect correction and is now 0.927079476334604 .
2026-02-09 21:51:13.904269 INFO::Total function execution time is 0.0421390533447266 s and adjustment time is 0.0215413570404053 s ( 51.12 )
2026-02-09 21:51:13.905121 INFO::Formatting Data.
2026-02-09 21:51:13.905776 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:13.906783 INFO::Removing potential empty rows and columns
2026-02-09 21:51:13.907888 INFO::Found 0 missing values.
2026-02-09 21:51:13.908887 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-09 21:51:13.913755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:13.914379 INFO::Done
2026-02-09 21:51:13.914929 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:13.918211 INFO::Starting hierarchical adjustment
2026-02-09 21:51:13.91898 INFO::Found 2 batches.
2026-02-09 21:51:13.919542 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:13.920166 INFO::Using default BPPARAM
2026-02-09 21:51:13.920724 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:13.921736 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-09 21:51:13.939617 INFO::Done
2026-02-09 21:51:13.940409 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:13.9438 INFO::ASW Batch was 0.501300009593686 prior to batch effect correction and is now -0.0345119066284577 .
2026-02-09 21:51:13.944466 INFO::ASW Label was 0.57049233456561 prior to batch effect correction and is now 0.927079476334604 .
2026-02-09 21:51:13.945318 INFO::Total function execution time is 0.0402133464813232 s and adjustment time is 0.020723819732666 s ( 51.53 )
2026-02-09 21:51:14.208612 INFO::Formatting Data.
2026-02-09 21:51:14.209535 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:14.210595 INFO::Removing potential empty rows and columns
2026-02-09 21:51:14.211733 INFO::Found 0 missing values.
2026-02-09 21:51:14.214833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:14.215383 INFO::Done
2026-02-09 21:51:14.215929 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:14.218124 INFO::Starting hierarchical adjustment
2026-02-09 21:51:14.218851 INFO::Found 3 batches.
2026-02-09 21:51:14.219378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:14.220012 INFO::Using default BPPARAM
2026-02-09 21:51:14.220557 INFO::Processing subtree level 1
2026-02-09 21:51:14.313308 INFO::Adjusting the last 1 batches sequentially
2026-02-09 21:51:14.315304 INFO::Done
2026-02-09 21:51:14.316072 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:14.318904 INFO::ASW Batch was -0.055238266729604 prior to batch effect correction and is now -0.055238266729604 .
2026-02-09 21:51:14.319983 INFO::Total function execution time is 0.111458539962769 s and adjustment time is 0.0965657234191895 s ( 86.64 )
2026-02-09 21:51:14.321192 INFO::Formatting Data.
2026-02-09 21:51:14.321929 INFO::Typecasting input to dataframe.
2026-02-09 21:51:14.322755 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:14.323817 INFO::Removing potential empty rows and columns
2026-02-09 21:51:14.325023 INFO::Found 0 missing values.
2026-02-09 21:51:14.328274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:14.328882 INFO::Done
2026-02-09 21:51:14.329415 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:14.331644 INFO::Starting hierarchical adjustment
2026-02-09 21:51:14.332384 INFO::Found 3 batches.
2026-02-09 21:51:14.332948 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:14.333603 INFO::Using default BPPARAM
2026-02-09 21:51:14.33414 INFO::Processing subtree level 1
2026-02-09 21:51:14.431151 INFO::Adjusting the last 1 batches sequentially
2026-02-09 21:51:14.433218 INFO::Done
2026-02-09 21:51:14.43403 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:14.4369 INFO::ASW Batch was -0.055238266729604 prior to batch effect correction and is now -0.055238266729604 .
2026-02-09 21:51:14.438019 INFO::Total function execution time is 0.116789579391479 s and adjustment time is 0.100934267044067 s ( 86.42 )
2026-02-09 21:51:14.452611 INFO::Formatting Data.
2026-02-09 21:51:14.453502 INFO::Typecasting input to dataframe.
2026-02-09 21:51:14.454428 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:14.455424 INFO::Removing potential empty rows and columns
2026-02-09 21:51:14.456541 INFO::Found 0 missing values.
2026-02-09 21:51:14.459656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:14.460216 INFO::Done
2026-02-09 21:51:14.460755 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:14.462912 INFO::Starting hierarchical adjustment
2026-02-09 21:51:14.463643 INFO::Found 3 batches.
2026-02-09 21:51:14.464178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:14.464805 INFO::Using default BPPARAM
2026-02-09 21:51:14.465342 INFO::Processing subtree level 1
2026-02-09 21:51:14.556813 INFO::Adjusting the last 1 batches sequentially
2026-02-09 21:51:14.558843 INFO::Done
2026-02-09 21:51:14.559596 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:14.562406 INFO::ASW Batch was -0.0727411456482438 prior to batch effect correction and is now -0.0727411456482438 .
2026-02-09 21:51:14.563436 INFO::Total function execution time is 0.110904216766357 s and adjustment time is 0.0953238010406494 s ( 85.95 )
2026-02-09 21:51:14.719189 INFO::Formatting Data.
2026-02-09 21:51:14.720042 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:14.721224 INFO::Removing potential empty rows and columns
2026-02-09 21:51:14.724338 INFO::Found 1000 missing values.
2026-02-09 21:51:14.751153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:14.752431 INFO::Done
2026-02-09 21:51:14.753465 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:14.762674 INFO::Starting hierarchical adjustment
2026-02-09 21:51:14.763916 INFO::Found 10 batches.
2026-02-09 21:51:14.764812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:14.765896 INFO::Using default BPPARAM
2026-02-09 21:51:14.766806 INFO::Processing subtree level 1
2026-02-09 21:51:14.954044 INFO::Processing subtree level 2
2026-02-09 21:51:15.116704 INFO::Adjusting the last 1 batches sequentially
2026-02-09 21:51:15.120381 INFO::Done
2026-02-09 21:51:15.121393 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:15.128195 INFO::ASW Batch was 0.532699812259437 prior to batch effect correction and is now 0.532699812259437 .
2026-02-09 21:51:15.129122 INFO::ASW Label was 0.262849896051231 prior to batch effect correction and is now 0.262849896051231 .
2026-02-09 21:51:15.13035 INFO::Total function execution time is 0.411147832870483 s and adjustment time is 0.356667041778564 s ( 86.75 )
2026-02-09 21:51:15.131449 INFO::Formatting Data.
2026-02-09 21:51:15.132245 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:15.134353 INFO::Removing potential empty rows and columns
2026-02-09 21:51:15.138613 INFO::Found 1000 missing values.
2026-02-09 21:51:15.164916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:15.16588 INFO::Done
2026-02-09 21:51:15.166612 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:15.182985 INFO::Starting hierarchical adjustment
2026-02-09 21:51:15.184062 INFO::Found 10 batches.
2026-02-09 21:51:16.44521 INFO::Set up parallel execution backend with 2 workers
2026-02-09 21:51:16.447228 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-09 21:51:17.698748 INFO::Adjusting the last 2 batches sequentially
2026-02-09 21:51:17.700775 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-09 21:51:17.716439 INFO::Done
2026-02-09 21:51:17.717072 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:17.721576 INFO::ASW Batch was 0.532699812259437 prior to batch effect correction and is now 0.532699812259437 .
2026-02-09 21:51:17.722107 INFO::ASW Label was 0.262849896051231 prior to batch effect correction and is now 0.262849896051231 .
2026-02-09 21:51:17.722809 INFO::Total function execution time is 2.59144163131714 s and adjustment time is 2.53260397911072 s ( 97.73 )
2026-02-09 21:51:17.871954 INFO::Formatting Data.
2026-02-09 21:51:17.872932 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:17.873917 INFO::Removing potential empty rows and columns
2026-02-09 21:51:17.875028 INFO::Found 0 missing values.
2026-02-09 21:51:17.878618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:17.879152 INFO::Done
2026-02-09 21:51:17.879673 INFO::Acquiring quality metrics before batch effect correction.
2026-02-09 21:51:17.882542 INFO::Starting hierarchical adjustment
2026-02-09 21:51:17.883245 INFO::Found 3 batches.
2026-02-09 21:51:17.883771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-09 21:51:17.884385 INFO::Using default BPPARAM
2026-02-09 21:51:17.884926 INFO::Processing subtree level 1
2026-02-09 21:51:17.991191 INFO::Adjusting the last 1 batches sequentially
2026-02-09 21:51:17.993109 INFO::Done
2026-02-09 21:51:17.993805 INFO::Acquiring quality metrics after batch effect correction.
2026-02-09 21:51:17.997174 INFO::ASW Batch was 0.205024654471265 prior to batch effect correction and is now -0.144493526393862 .
2026-02-09 21:51:17.99782 INFO::ASW Label was -0.175236821573652 prior to batch effect correction and is now -0.105053482714094 .
2026-02-09 21:51:17.998806 INFO::Total function execution time is 0.126960277557373 s and adjustment time is 0.109978199005127 s ( 86.62 )
2026-02-09 21:51:18.118672 INFO::Formatting Data.
2026-02-09 21:51:18.119543 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.120431 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.121476 INFO::Found 2 missing values.
2026-02-09 21:51:18.12422 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.124738 INFO::Done
2026-02-09 21:51:18.150178 INFO::Found NA in Reference column
2026-02-09 21:51:18.159008 INFO::Require at least two references per batch.
2026-02-09 21:51:18.178463 INFO::Formatting Data.
2026-02-09 21:51:18.179239 INFO::Recognized SummarizedExperiment
2026-02-09 21:51:18.179767 INFO::Typecasting input to dataframe.
2026-02-09 21:51:18.189003 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.190117 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.194189 INFO::Found 0 missing values.
2026-02-09 21:51:18.200746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.201313 INFO::Done
2026-02-09 21:51:18.216221 INFO::Formatting Data.
2026-02-09 21:51:18.216941 INFO::Recognized SummarizedExperiment
2026-02-09 21:51:18.217443 INFO::Typecasting input to dataframe.
2026-02-09 21:51:18.233906 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.235089 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.238398 INFO::Found 0 missing values.
2026-02-09 21:51:18.248567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.249211 INFO::Done
2026-02-09 21:51:18.263909 INFO::Formatting Data.
2026-02-09 21:51:18.264625 INFO::Recognized SummarizedExperiment
2026-02-09 21:51:18.265125 INFO::Typecasting input to dataframe.
2026-02-09 21:51:18.280738 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.281732 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.28274 INFO::Found 0 missing values.
2026-02-09 21:51:18.283614 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-09 21:51:18.287657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.288186 INFO::Done
2026-02-09 21:51:18.29772 INFO::Formatting Data.
2026-02-09 21:51:18.29841 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.299213 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.300139 INFO::Found 0 missing values.
2026-02-09 21:51:18.302774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.303276 INFO::Done
2026-02-09 21:51:18.313972 INFO::Formatting Data.
2026-02-09 21:51:18.314759 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.31572 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.316707 INFO::Found 0 missing values.
2026-02-09 21:51:18.3194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.319929 INFO::Done
2026-02-09 21:51:18.349431 INFO::Formatting Data.
2026-02-09 21:51:18.350322 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.351315 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.352477 INFO::Found 1 missing values.
2026-02-09 21:51:18.35509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.355613 INFO::Done
2026-02-09 21:51:18.374289 INFO::Formatting Data.
2026-02-09 21:51:18.375084 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.375955 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.376924 INFO::Found 2 missing values.
2026-02-09 21:51:18.377894 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-09 21:51:18.380092 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.380641 INFO::Done
2026-02-09 21:51:18.390384 INFO::Formatting Data.
2026-02-09 21:51:18.3912 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.392061 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.392951 INFO::Found 2 missing values.
2026-02-09 21:51:18.394481 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.395007 INFO::Done
2026-02-09 21:51:18.405295 INFO::Formatting Data.
2026-02-09 21:51:18.406024 INFO::Typecasting input to dataframe.
2026-02-09 21:51:18.406863 INFO::Replacing NaNs with NAs.
2026-02-09 21:51:18.407695 INFO::Removing potential empty rows and columns
2026-02-09 21:51:18.408643 INFO::Found 0 missing values.
2026-02-09 21:51:18.411411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-09 21:51:18.411923 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.073 4.081 20.721
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.491 | 1.184 | 17.154 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.011 | 0.003 | 0.014 | |
| generate_data_covariables | 0.013 | 0.000 | 0.012 | |
| generate_dataset | 0.012 | 0.001 | 0.013 | |