Yannis Schumann
| Snapshot Date: 2026-03-02 13:45 -0500 (Mon, 02 Mar 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 2026-03-03 11:57 -0500 (Tue, 03 Mar 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" | 4892 |
| 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: 2026-03-02 21:27:37 -0500 (Mon, 02 Mar 2026) |
| EndedAt: 2026-03-02 21:29:06 -0500 (Mon, 02 Mar 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 24.122 1.249 17.146
* 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")
2026-03-02 21:28:29.827947 INFO::Formatting Data.
2026-03-02 21:28:29.829232 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:29.84006 INFO::Removing potential empty rows and columns
2026-03-02 21:28:30.083595 INFO::Found 0 missing values.
2026-03-02 21:28:30.087096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:30.087772 INFO::Done
2026-03-02 21:28:30.088309 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:30.099846 INFO::Starting hierarchical adjustment
2026-03-02 21:28:30.100691 INFO::Found 3 batches.
2026-03-02 21:28:30.101231 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:30.102347 INFO::Using default BPPARAM
2026-03-02 21:28:30.102904 INFO::Processing subtree level 1
2026-03-02 21:28:30.200795 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:28:30.202516 INFO::Done
2026-03-02 21:28:30.203148 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:30.205655 INFO::ASW Batch was -0.0462743390102466 prior to batch effect correction and is now -0.0462743390102466 .
2026-03-02 21:28:30.206723 INFO::Total function execution time is 0.379402637481689 s and adjustment time is 0.101989507675171 s ( 26.88 )
2026-03-02 21:28:30.220222 INFO::Formatting Data.
2026-03-02 21:28:30.221011 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:30.221946 INFO::Removing potential empty rows and columns
2026-03-02 21:28:30.223089 INFO::Found 0 missing values.
2026-03-02 21:28:30.224047 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.
2026-03-02 21:28:30.234958 INFO::Formatting Data.
2026-03-02 21:28:30.235767 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:30.23667 INFO::Removing potential empty rows and columns
2026-03-02 21:28:30.237722 INFO::Found 0 missing values.
2026-03-02 21:28:30.238634 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.
2026-03-02 21:28:30.25447 INFO::Formatting Data.
2026-03-02 21:28:30.255197 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:30.25606 INFO::Removing potential empty rows and columns
2026-03-02 21:28:30.257067 INFO::Found 0 missing values.
2026-03-02 21:28:30.257956 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.
2026-03-02 21:28:30.262248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:30.262793 INFO::Done
2026-03-02 21:28:30.263293 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:30.265217 INFO::Starting hierarchical adjustment
2026-03-02 21:28:30.265904 INFO::Found 2 batches.
2026-03-02 21:28:30.26641 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:30.267033 INFO::Using default BPPARAM
2026-03-02 21:28:30.267551 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:30.268452 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:28:30.289948 INFO::Done
2026-03-02 21:28:30.290675 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:30.293086 INFO::ASW Batch was 0.136211089545734 prior to batch effect correction and is now -0.118784709985139 .
2026-03-02 21:28:30.293993 INFO::Total function execution time is 0.0395643711090088 s and adjustment time is 0.0241551399230957 s ( 61.05 )
2026-03-02 21:28:30.297051 INFO::Formatting Data.
2026-03-02 21:28:30.297758 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:30.307644 INFO::Formatting Data.
2026-03-02 21:28:30.308417 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:30.30945 INFO::Removing potential empty rows and columns
2026-03-02 21:28:30.310618 INFO::Found 0 missing values.
2026-03-02 21:28:30.314059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:30.314664 INFO::Done
2026-03-02 21:28:30.315241 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:30.339993 INFO::Starting hierarchical adjustment
2026-03-02 21:28:30.341336 INFO::Found 2 batches.
2026-03-02 21:28:30.341894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:30.342448 INFO::Using default BPPARAM
2026-03-02 21:28:30.342951 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:30.343831 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:28:30.3571 INFO::Done
2026-03-02 21:28:30.357681 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:30.359504 INFO::ASW Batch was -0.0300640036591907 prior to batch effect correction and is now -0.124080145374655 .
2026-03-02 21:28:30.36021 INFO::Total function execution time is 0.0526456832885742 s and adjustment time is 0.0159525871276855 s ( 30.3 )
2026-03-02 21:28:30.361162 INFO::Formatting Data.
2026-03-02 21:28:30.36172 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:30.362486 INFO::Removing potential empty rows and columns
2026-03-02 21:28:30.363395 INFO::Found 0 missing values.
2026-03-02 21:28:30.365905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:30.366399 INFO::Done
2026-03-02 21:28:30.366872 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:30.368667 INFO::Starting hierarchical adjustment
2026-03-02 21:28:30.369303 INFO::Found 2 batches.
2026-03-02 21:28:30.369782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:30.370327 INFO::Using default BPPARAM
2026-03-02 21:28:30.37081 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:30.371619 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:28:30.384952 INFO::Done
2026-03-02 21:28:30.385552 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:30.387357 INFO::ASW Batch was -0.0300640036591907 prior to batch effect correction and is now -0.124080145374655 .
2026-03-02 21:28:30.388079 INFO::Total function execution time is 0.026909351348877 s and adjustment time is 0.0157685279846191 s ( 58.6 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-02 21:28:33.227893 INFO::Formatting Data.
2026-03-02 21:28:33.228581 INFO::Recognized SummarizedExperiment
2026-03-02 21:28:33.22906 INFO::Typecasting input to dataframe.
2026-03-02 21:28:33.259602 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:33.260878 INFO::Removing potential empty rows and columns
2026-03-02 21:28:33.264874 INFO::Found 0 missing values.
2026-03-02 21:28:33.272064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:33.272736 INFO::Done
2026-03-02 21:28:33.273292 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:33.276911 INFO::Starting hierarchical adjustment
2026-03-02 21:28:33.277651 INFO::Found 2 batches.
2026-03-02 21:28:33.278187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:33.279286 INFO::Using default BPPARAM
2026-03-02 21:28:33.279846 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:33.28085 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:28:33.339209 INFO::Done
2026-03-02 21:28:33.339944 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:33.34365 INFO::ASW Batch was -0.00407681438296261 prior to batch effect correction and is now -0.094975963133967 .
2026-03-02 21:28:33.34455 INFO::Total function execution time is 0.116919755935669 s and adjustment time is 0.0616817474365234 s ( 52.76 )
Warning: stack imbalance in '{', 73 then 75
2026-03-02 21:28:33.363953 INFO::Formatting Data.
2026-03-02 21:28:33.364728 INFO::Recognized SummarizedExperiment
2026-03-02 21:28:33.365292 INFO::Typecasting input to dataframe.
2026-03-02 21:28:33.374973 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:33.376189 INFO::Removing potential empty rows and columns
2026-03-02 21:28:33.380037 INFO::Found 0 missing values.
2026-03-02 21:28:33.387679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:33.38842 INFO::Done
2026-03-02 21:28:33.38901 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:33.392768 INFO::Starting hierarchical adjustment
2026-03-02 21:28:33.393535 INFO::Found 2 batches.
2026-03-02 21:28:33.394075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:33.394686 INFO::Using default BPPARAM
2026-03-02 21:28:33.395223 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:33.396255 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:28:33.422349 INFO::Done
2026-03-02 21:28:33.423257 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:33.427294 INFO::ASW Batch was -0.00990265408137366 prior to batch effect correction and is now -0.00990265408137366 .
2026-03-02 21:28:33.4282 INFO::Total function execution time is 0.0642163753509521 s and adjustment time is 0.0289256572723389 s ( 45.04 )
2026-03-02 21:28:33.44724 INFO::Formatting Data.
2026-03-02 21:28:33.448056 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:33.44898 INFO::Removing potential empty rows and columns
2026-03-02 21:28:33.450013 INFO::Found 0 missing values.
2026-03-02 21:28:33.452974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:33.453513 INFO::Done
2026-03-02 21:28:33.45402 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:33.456037 INFO::Starting hierarchical adjustment
2026-03-02 21:28:33.456754 INFO::Found 3 batches.
2026-03-02 21:28:33.457269 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:33.457882 INFO::Using default BPPARAM
2026-03-02 21:28:33.458398 INFO::Processing subtree level 1
2026-03-02 21:28:33.604102 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:28:33.606117 INFO::Done
2026-03-02 21:28:33.606804 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:33.609433 INFO::ASW Batch was -0.114635195812773 prior to batch effect correction and is now -0.163698932060482 .
2026-03-02 21:28:33.610385 INFO::Total function execution time is 0.163175821304321 s and adjustment time is 0.149493217468262 s ( 91.61 )
2026-03-02 21:28:33.626477 INFO::Skipping initial DF formatting
2026-03-02 21:28:33.627262 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:33.632345 INFO::Starting hierarchical adjustment
2026-03-02 21:28:33.633183 INFO::Found 5 batches.
2026-03-02 21:28:33.633749 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:33.63439 INFO::Using default BPPARAM
2026-03-02 21:28:33.634926 INFO::Processing subtree level 1
2026-03-02 21:28:33.876271 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:33.878108 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:28:33.899753 INFO::Done
2026-03-02 21:28:33.900608 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:33.905355 INFO::ASW Batch was 0.576832995875129 prior to batch effect correction and is now 0.576832995875129 .
2026-03-02 21:28:33.906049 INFO::ASW Label was 0.413472540360653 prior to batch effect correction and is now 0.413472540360653 .
2026-03-02 21:28:33.959233 INFO::Total function execution time is 0.332785367965698 s and adjustment time is 0.266687631607056 s ( 80.14 )
2026-03-02 21:28:33.978463 INFO::Formatting Data.
2026-03-02 21:28:33.979336 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:33.980304 INFO::Removing potential empty rows and columns
2026-03-02 21:28:33.981349 INFO::Found 0 missing values.
2026-03-02 21:28:33.985383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:33.985954 INFO::Done
2026-03-02 21:28:33.986447 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:33.989532 INFO::Starting hierarchical adjustment
2026-03-02 21:28:33.990231 INFO::Found 5 batches.
2026-03-02 21:28:33.990755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:33.991344 INFO::Using default BPPARAM
2026-03-02 21:28:33.991856 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.
2026-03-02 21:28:34.119251 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.120794 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:28:34.137498 INFO::Done
2026-03-02 21:28:34.138209 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.141539 INFO::ASW Batch was 0.604696003481626 prior to batch effect correction and is now -0.0573711500477864 .
2026-03-02 21:28:34.142145 INFO::ASW Label was 0.197576445844979 prior to batch effect correction and is now 0.69443810830891 .
2026-03-02 21:28:34.143006 INFO::Total function execution time is 0.164673805236816 s and adjustment time is 0.147379398345947 s ( 89.5 )
2026-03-02 21:28:34.143883 INFO::Formatting Data.
2026-03-02 21:28:34.144596 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:34.145492 INFO::Removing potential empty rows and columns
2026-03-02 21:28:34.146645 INFO::Found 0 missing values.
2026-03-02 21:28:34.150841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:34.151361 INFO::Done
2026-03-02 21:28:34.151903 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:34.154934 INFO::Starting hierarchical adjustment
2026-03-02 21:28:34.155647 INFO::Found 5 batches.
2026-03-02 21:28:34.156194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:34.156832 INFO::Using default BPPARAM
2026-03-02 21:28:34.157373 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.
2026-03-02 21:28:34.289536 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.291372 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:28:34.31303 INFO::Done
2026-03-02 21:28:34.314086 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.319035 INFO::ASW Batch was 0.604696003481626 prior to batch effect correction and is now -0.0573711500477864 .
2026-03-02 21:28:34.319994 INFO::ASW Label was 0.197576445844979 prior to batch effect correction and is now 0.69443810830891 .
2026-03-02 21:28:34.32112 INFO::Total function execution time is 0.177181959152222 s and adjustment time is 0.157429933547974 s ( 88.85 )
2026-03-02 21:28:34.338743 INFO::Formatting Data.
2026-03-02 21:28:34.339662 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:34.340704 INFO::Removing potential empty rows and columns
2026-03-02 21:28:34.341859 INFO::Found 0 missing values.
2026-03-02 21:28:34.346393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:34.347006 INFO::Done
2026-03-02 21:28:34.347543 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:34.351013 INFO::Starting hierarchical adjustment
2026-03-02 21:28:34.351853 INFO::Found 5 batches.
2026-03-02 21:28:34.352415 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:34.353038 INFO::Using default BPPARAM
2026-03-02 21:28:34.353572 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.
2026-03-02 21:28:34.49572 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.49745 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:28:34.514739 INFO::Done
2026-03-02 21:28:34.515595 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.519167 INFO::ASW Batch was 0.470431966652096 prior to batch effect correction and is now -0.0976557746818295 .
2026-03-02 21:28:34.519868 INFO::ASW Label was 0.195215536845297 prior to batch effect correction and is now 0.835799625236525 .
2026-03-02 21:28:34.52077 INFO::Total function execution time is 0.182173252105713 s and adjustment time is 0.163029432296753 s ( 89.49 )
2026-03-02 21:28:34.521679 INFO::Formatting Data.
2026-03-02 21:28:34.522343 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:34.523309 INFO::Removing potential empty rows and columns
2026-03-02 21:28:34.524393 INFO::Found 0 missing values.
2026-03-02 21:28:34.528656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:34.529249 INFO::Done
2026-03-02 21:28:34.529788 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:34.53308 INFO::Starting hierarchical adjustment
2026-03-02 21:28:34.533867 INFO::Found 5 batches.
2026-03-02 21:28:34.534432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:34.535096 INFO::Using default BPPARAM
2026-03-02 21:28:34.535651 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.
2026-03-02 21:28:34.67412 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.675902 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:28:34.693406 INFO::Done
2026-03-02 21:28:34.694124 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.69749 INFO::ASW Batch was 0.470431966652096 prior to batch effect correction and is now -0.0976557746818295 .
2026-03-02 21:28:34.69813 INFO::ASW Label was 0.195215536845297 prior to batch effect correction and is now 0.835799625236525 .
2026-03-02 21:28:34.698976 INFO::Total function execution time is 0.177326202392578 s and adjustment time is 0.159663677215576 s ( 90.04 )
2026-03-02 21:28:34.713079 INFO::Formatting Data.
2026-03-02 21:28:34.713947 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:34.714921 INFO::Removing potential empty rows and columns
2026-03-02 21:28:34.715947 INFO::Found 0 missing values.
2026-03-02 21:28:34.718653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:34.719192 INFO::Done
2026-03-02 21:28:34.719714 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:34.722648 INFO::Starting hierarchical adjustment
2026-03-02 21:28:34.72334 INFO::Found 2 batches.
2026-03-02 21:28:34.723875 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:34.724466 INFO::Using default BPPARAM
2026-03-02 21:28:34.724996 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.72589 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:28:34.740232 INFO::Done
2026-03-02 21:28:34.740924 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.743853 INFO::ASW Batch was 0.334322285017805 prior to batch effect correction and is now 0.0663177633169969 .
2026-03-02 21:28:34.744432 INFO::ASW Label was 0.734666966807953 prior to batch effect correction and is now 0.884979703310403 .
2026-03-02 21:28:34.745195 INFO::Total function execution time is 0.0322237014770508 s and adjustment time is 0.0170016288757324 s ( 52.76 )
2026-03-02 21:28:34.745966 INFO::Formatting Data.
2026-03-02 21:28:34.746575 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:34.747407 INFO::Removing potential empty rows and columns
2026-03-02 21:28:34.748365 INFO::Found 0 missing values.
2026-03-02 21:28:34.75098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:34.751514 INFO::Done
2026-03-02 21:28:34.752021 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:34.754942 INFO::Starting hierarchical adjustment
2026-03-02 21:28:34.755645 INFO::Found 2 batches.
2026-03-02 21:28:34.75616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:34.756755 INFO::Using default BPPARAM
2026-03-02 21:28:34.757265 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.758134 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-02 21:28:34.772332 INFO::Done
2026-03-02 21:28:34.773029 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.775976 INFO::ASW Batch was 0.334322285017805 prior to batch effect correction and is now 0.0663177633169969 .
2026-03-02 21:28:34.776615 INFO::ASW Label was 0.734666966807953 prior to batch effect correction and is now 0.884979703310403 .
2026-03-02 21:28:34.777425 INFO::Total function execution time is 0.0314655303955078 s and adjustment time is 0.016801118850708 s ( 53.4 )
2026-03-02 21:28:34.788604 INFO::Formatting Data.
2026-03-02 21:28:34.789401 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:34.790288 INFO::Removing potential empty rows and columns
2026-03-02 21:28:34.791223 INFO::Found 0 missing values.
2026-03-02 21:28:34.79325 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:34.793783 INFO::Done
2026-03-02 21:28:34.794279 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:34.796172 INFO::Starting hierarchical adjustment
2026-03-02 21:28:34.79687 INFO::Found 2 batches.
2026-03-02 21:28:34.797377 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:34.797975 INFO::Using default BPPARAM
2026-03-02 21:28:34.798481 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.799369 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:28:34.838857 INFO::Done
2026-03-02 21:28:34.839699 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.842208 INFO::ASW Batch was -0.08265796454988 prior to batch effect correction and is now -0.105192121153893 .
2026-03-02 21:28:34.843091 INFO::Total function execution time is 0.0546646118164062 s and adjustment time is 0.0420539379119873 s ( 76.93 )
2026-03-02 21:28:34.855525 INFO::Formatting Data.
2026-03-02 21:28:34.856314 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:34.857211 INFO::Removing potential empty rows and columns
2026-03-02 21:28:34.858258 INFO::Found 0 missing values.
2026-03-02 21:28:34.859422 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.
2026-03-02 21:28:34.863869 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:34.864433 INFO::Done
2026-03-02 21:28:34.864945 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:34.867776 INFO::Starting hierarchical adjustment
2026-03-02 21:28:34.868481 INFO::Found 2 batches.
2026-03-02 21:28:34.869001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:34.869597 INFO::Using default BPPARAM
2026-03-02 21:28:34.870098 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.871035 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:28:34.888275 INFO::Done
2026-03-02 21:28:34.889005 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.89207 INFO::ASW Batch was 0.756317790938518 prior to batch effect correction and is now 0.158587537093268 .
2026-03-02 21:28:34.892773 INFO::ASW Label was 0.322981301949028 prior to batch effect correction and is now 0.7770907706035 .
2026-03-02 21:28:34.893612 INFO::Total function execution time is 0.0381679534912109 s and adjustment time is 0.0198869705200195 s ( 52.1 )
2026-03-02 21:28:34.894429 INFO::Formatting Data.
2026-03-02 21:28:34.895062 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:34.896011 INFO::Removing potential empty rows and columns
2026-03-02 21:28:34.897024 INFO::Found 0 missing values.
2026-03-02 21:28:34.897983 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.
2026-03-02 21:28:34.902466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:34.903091 INFO::Done
2026-03-02 21:28:34.903637 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:34.906611 INFO::Starting hierarchical adjustment
2026-03-02 21:28:34.907341 INFO::Found 2 batches.
2026-03-02 21:28:34.9079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:34.908527 INFO::Using default BPPARAM
2026-03-02 21:28:34.909059 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:34.910048 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:28:34.926549 INFO::Done
2026-03-02 21:28:34.927256 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:34.93027 INFO::ASW Batch was 0.756317790938518 prior to batch effect correction and is now 0.158587537093268 .
2026-03-02 21:28:34.930897 INFO::ASW Label was 0.322981301949028 prior to batch effect correction and is now 0.7770907706035 .
2026-03-02 21:28:34.931703 INFO::Total function execution time is 0.0372881889343262 s and adjustment time is 0.0193166732788086 s ( 51.8 )
2026-03-02 21:28:35.153939 INFO::Formatting Data.
2026-03-02 21:28:35.154774 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:35.15578 INFO::Removing potential empty rows and columns
2026-03-02 21:28:35.156912 INFO::Found 0 missing values.
2026-03-02 21:28:35.160205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:35.160794 INFO::Done
2026-03-02 21:28:35.161355 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:35.163491 INFO::Starting hierarchical adjustment
2026-03-02 21:28:35.164452 INFO::Found 3 batches.
2026-03-02 21:28:35.165023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:35.165659 INFO::Using default BPPARAM
2026-03-02 21:28:35.166224 INFO::Processing subtree level 1
2026-03-02 21:28:35.261997 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:28:35.263725 INFO::Done
2026-03-02 21:28:35.264362 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:35.266883 INFO::ASW Batch was -0.100804190925944 prior to batch effect correction and is now -0.100804190925944 .
2026-03-02 21:28:35.267928 INFO::Total function execution time is 0.114047527313232 s and adjustment time is 0.0996229648590088 s ( 87.35 )
2026-03-02 21:28:35.269095 INFO::Formatting Data.
2026-03-02 21:28:35.269795 INFO::Typecasting input to dataframe.
2026-03-02 21:28:35.270644 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:35.27163 INFO::Removing potential empty rows and columns
2026-03-02 21:28:35.27279 INFO::Found 0 missing values.
2026-03-02 21:28:35.276115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:35.276732 INFO::Done
2026-03-02 21:28:35.277312 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:35.279477 INFO::Starting hierarchical adjustment
2026-03-02 21:28:35.280271 INFO::Found 3 batches.
2026-03-02 21:28:35.280853 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:35.281536 INFO::Using default BPPARAM
2026-03-02 21:28:35.282116 INFO::Processing subtree level 1
2026-03-02 21:28:35.376948 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:28:35.37887 INFO::Done
2026-03-02 21:28:35.37957 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:35.382288 INFO::ASW Batch was -0.100804190925944 prior to batch effect correction and is now -0.100804190925944 .
2026-03-02 21:28:35.383332 INFO::Total function execution time is 0.114203929901123 s and adjustment time is 0.0987479686737061 s ( 86.47 )
2026-03-02 21:28:35.397293 INFO::Formatting Data.
2026-03-02 21:28:35.398085 INFO::Typecasting input to dataframe.
2026-03-02 21:28:35.398919 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:35.399863 INFO::Removing potential empty rows and columns
2026-03-02 21:28:35.400936 INFO::Found 0 missing values.
2026-03-02 21:28:35.404108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:35.404697 INFO::Done
2026-03-02 21:28:35.405259 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:35.407524 INFO::Starting hierarchical adjustment
2026-03-02 21:28:35.408295 INFO::Found 3 batches.
2026-03-02 21:28:35.408878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:35.409575 INFO::Using default BPPARAM
2026-03-02 21:28:35.410148 INFO::Processing subtree level 1
2026-03-02 21:28:35.506204 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:28:35.508135 INFO::Done
2026-03-02 21:28:35.508823 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:35.511445 INFO::ASW Batch was 0.10093672080388 prior to batch effect correction and is now 0.10093672080388 .
2026-03-02 21:28:35.512403 INFO::Total function execution time is 0.115160703659058 s and adjustment time is 0.0999629497528076 s ( 86.8 )
2026-03-02 21:28:35.659379 INFO::Formatting Data.
2026-03-02 21:28:35.660174 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:35.661281 INFO::Removing potential empty rows and columns
2026-03-02 21:28:35.664121 INFO::Found 1000 missing values.
2026-03-02 21:28:35.683156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:35.683895 INFO::Done
2026-03-02 21:28:35.684455 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:35.689864 INFO::Starting hierarchical adjustment
2026-03-02 21:28:35.69062 INFO::Found 10 batches.
2026-03-02 21:28:35.691143 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:35.691774 INFO::Using default BPPARAM
2026-03-02 21:28:35.692302 INFO::Processing subtree level 1
2026-03-02 21:28:35.823558 INFO::Processing subtree level 2
2026-03-02 21:28:35.962779 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:28:35.964886 INFO::Done
2026-03-02 21:28:35.965574 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:35.971257 INFO::ASW Batch was 0.457857555704806 prior to batch effect correction and is now 0.457857555704806 .
2026-03-02 21:28:35.971934 INFO::ASW Label was 0.365450168547329 prior to batch effect correction and is now 0.365450168547329 .
2026-03-02 21:28:35.972873 INFO::Total function execution time is 0.313543558120728 s and adjustment time is 0.274378299713135 s ( 87.51 )
2026-03-02 21:28:35.973762 INFO::Formatting Data.
2026-03-02 21:28:35.974474 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:35.975789 INFO::Removing potential empty rows and columns
2026-03-02 21:28:35.978631 INFO::Found 1000 missing values.
2026-03-02 21:28:35.997917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:35.998688 INFO::Done
2026-03-02 21:28:35.999248 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:36.004659 INFO::Starting hierarchical adjustment
2026-03-02 21:28:36.005441 INFO::Found 10 batches.
2026-03-02 21:28:37.009687 INFO::Set up parallel execution backend with 2 workers
2026-03-02 21:28:37.011631 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-02 21:28:38.039094 INFO::Adjusting the last 2 batches sequentially
2026-03-02 21:28:38.040836 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-02 21:28:38.056917 INFO::Done
2026-03-02 21:28:38.057552 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:38.062062 INFO::ASW Batch was 0.457857555704806 prior to batch effect correction and is now 0.457857555704806 .
2026-03-02 21:28:38.062635 INFO::ASW Label was 0.365450168547329 prior to batch effect correction and is now 0.365450168547329 .
2026-03-02 21:28:38.063356 INFO::Total function execution time is 2.08964967727661 s and adjustment time is 2.05162143707275 s ( 98.18 )
2026-03-02 21:28:38.214845 INFO::Formatting Data.
2026-03-02 21:28:38.215802 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.216858 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.218076 INFO::Found 0 missing values.
2026-03-02 21:28:38.221887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.22243 INFO::Done
2026-03-02 21:28:38.222955 INFO::Acquiring quality metrics before batch effect correction.
2026-03-02 21:28:38.225873 INFO::Starting hierarchical adjustment
2026-03-02 21:28:38.226583 INFO::Found 3 batches.
2026-03-02 21:28:38.227101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-02 21:28:38.227724 INFO::Using default BPPARAM
2026-03-02 21:28:38.22824 INFO::Processing subtree level 1
2026-03-02 21:28:38.362431 INFO::Adjusting the last 1 batches sequentially
2026-03-02 21:28:38.364654 INFO::Done
2026-03-02 21:28:38.365346 INFO::Acquiring quality metrics after batch effect correction.
2026-03-02 21:28:38.368985 INFO::ASW Batch was 0.202799976041566 prior to batch effect correction and is now -0.153095140289659 .
2026-03-02 21:28:38.369642 INFO::ASW Label was -0.192774480857409 prior to batch effect correction and is now 0.0823506298249031 .
2026-03-02 21:28:38.370635 INFO::Total function execution time is 0.155862808227539 s and adjustment time is 0.138211727142334 s ( 88.68 )
2026-03-02 21:28:38.507006 INFO::Formatting Data.
2026-03-02 21:28:38.508066 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.509001 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.510089 INFO::Found 2 missing values.
2026-03-02 21:28:38.512905 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.513435 INFO::Done
2026-03-02 21:28:38.539724 INFO::Found NA in Reference column
2026-03-02 21:28:38.548998 INFO::Require at least two references per batch.
2026-03-02 21:28:38.570112 INFO::Formatting Data.
2026-03-02 21:28:38.570896 INFO::Recognized SummarizedExperiment
2026-03-02 21:28:38.571424 INFO::Typecasting input to dataframe.
2026-03-02 21:28:38.581602 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.582727 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.586046 INFO::Found 0 missing values.
2026-03-02 21:28:38.592431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.593012 INFO::Done
2026-03-02 21:28:38.607918 INFO::Formatting Data.
2026-03-02 21:28:38.608636 INFO::Recognized SummarizedExperiment
2026-03-02 21:28:38.609155 INFO::Typecasting input to dataframe.
2026-03-02 21:28:38.625639 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.626826 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.630107 INFO::Found 0 missing values.
2026-03-02 21:28:38.640094 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.640745 INFO::Done
2026-03-02 21:28:38.655686 INFO::Formatting Data.
2026-03-02 21:28:38.656399 INFO::Recognized SummarizedExperiment
2026-03-02 21:28:38.656927 INFO::Typecasting input to dataframe.
2026-03-02 21:28:38.672763 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.673767 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.674815 INFO::Found 0 missing values.
2026-03-02 21:28:38.675694 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.
2026-03-02 21:28:38.67979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.680314 INFO::Done
2026-03-02 21:28:38.690156 INFO::Formatting Data.
2026-03-02 21:28:38.690974 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.691871 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.692906 INFO::Found 0 missing values.
2026-03-02 21:28:38.695795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.696362 INFO::Done
2026-03-02 21:28:38.708771 INFO::Formatting Data.
2026-03-02 21:28:38.709688 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.710729 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.711773 INFO::Found 0 missing values.
2026-03-02 21:28:38.71464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.715156 INFO::Done
2026-03-02 21:28:38.743982 INFO::Formatting Data.
2026-03-02 21:28:38.74483 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.745884 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.747012 INFO::Found 1 missing values.
2026-03-02 21:28:38.749495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.750014 INFO::Done
2026-03-02 21:28:38.768191 INFO::Formatting Data.
2026-03-02 21:28:38.769037 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.769883 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.770826 INFO::Found 2 missing values.
2026-03-02 21:28:38.771706 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.
2026-03-02 21:28:38.773836 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.774341 INFO::Done
2026-03-02 21:28:38.783859 INFO::Formatting Data.
2026-03-02 21:28:38.78464 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.785467 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.786352 INFO::Found 2 missing values.
2026-03-02 21:28:38.787883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.788382 INFO::Done
2026-03-02 21:28:38.798071 INFO::Formatting Data.
2026-03-02 21:28:38.79881 INFO::Typecasting input to dataframe.
2026-03-02 21:28:38.79957 INFO::Replacing NaNs with NAs.
2026-03-02 21:28:38.800375 INFO::Removing potential empty rows and columns
2026-03-02 21:28:38.801306 INFO::Found 0 missing values.
2026-03-02 21:28:38.804052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-02 21:28:38.804572 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.286 3.693 20.677
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.122 | 1.249 | 17.146 | |
| compute_asw | 0.025 | 0.001 | 0.026 | |
| count_existing | 0.013 | 0.002 | 0.015 | |
| generate_data_covariables | 0.014 | 0.000 | 0.013 | |
| generate_dataset | 0.013 | 0.001 | 0.013 | |