Yannis Schumann
| Snapshot Date: 2026-02-19 13:45 -0500 (Thu, 19 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 2026-02-20 11:57 -0500 (Fri, 20 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" | 4890 |
| 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: 2026-02-19 21:39:24 -0500 (Thu, 19 Feb 2026) |
| EndedAt: 2026-02-19 21:40:54 -0500 (Thu, 19 Feb 2026) |
| EllapsedTime: 90.1 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 24.688 1.17 17.458
* 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")
2026-02-19 21:40:16.761981 INFO::Formatting Data.
2026-02-19 21:40:16.763483 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:16.776969 INFO::Removing potential empty rows and columns
2026-02-19 21:40:17.061595 INFO::Found 0 missing values.
2026-02-19 21:40:17.065628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:17.066377 INFO::Done
2026-02-19 21:40:17.067021 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:17.079941 INFO::Starting hierarchical adjustment
2026-02-19 21:40:17.080923 INFO::Found 3 batches.
2026-02-19 21:40:17.081543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:17.082863 INFO::Using default BPPARAM
2026-02-19 21:40:17.083475 INFO::Processing subtree level 1
2026-02-19 21:40:17.204466 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:40:17.206717 INFO::Done
2026-02-19 21:40:17.20755 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:17.21066 INFO::ASW Batch was 0.0552985511615864 prior to batch effect correction and is now 0.0552985511615864 .
2026-02-19 21:40:17.211924 INFO::Total function execution time is 0.450644731521606 s and adjustment time is 0.125967741012573 s ( 27.95 )
2026-02-19 21:40:17.228826 INFO::Formatting Data.
2026-02-19 21:40:17.229813 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:17.230988 INFO::Removing potential empty rows and columns
2026-02-19 21:40:17.232337 INFO::Found 0 missing values.
2026-02-19 21:40:17.233443 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.
2026-02-19 21:40:17.245988 INFO::Formatting Data.
2026-02-19 21:40:17.246843 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:17.247864 INFO::Removing potential empty rows and columns
2026-02-19 21:40:17.249082 INFO::Found 0 missing values.
2026-02-19 21:40:17.250166 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.
2026-02-19 21:40:17.270767 INFO::Formatting Data.
2026-02-19 21:40:17.271817 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:17.272951 INFO::Removing potential empty rows and columns
2026-02-19 21:40:17.274301 INFO::Found 0 missing values.
2026-02-19 21:40:17.275493 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.
2026-02-19 21:40:17.280975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:17.28161 INFO::Done
2026-02-19 21:40:17.282189 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:17.284698 INFO::Starting hierarchical adjustment
2026-02-19 21:40:17.285541 INFO::Found 2 batches.
2026-02-19 21:40:17.28612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:17.286807 INFO::Using default BPPARAM
2026-02-19 21:40:17.287388 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:17.288437 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:40:17.313262 INFO::Done
2026-02-19 21:40:17.314068 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:17.316616 INFO::ASW Batch was 0.00909503231902706 prior to batch effect correction and is now -0.0762579909916466 .
2026-02-19 21:40:17.31799 INFO::Total function execution time is 0.0473508834838867 s and adjustment time is 0.0278794765472412 s ( 58.88 )
2026-02-19 21:40:17.321116 INFO::Formatting Data.
2026-02-19 21:40:17.321809 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:17.3313 INFO::Formatting Data.
2026-02-19 21:40:17.332124 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:17.333085 INFO::Removing potential empty rows and columns
2026-02-19 21:40:17.334168 INFO::Found 0 missing values.
2026-02-19 21:40:17.337305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:17.33788 INFO::Done
2026-02-19 21:40:17.338424 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:17.366034 INFO::Starting hierarchical adjustment
2026-02-19 21:40:17.368803 INFO::Found 2 batches.
2026-02-19 21:40:17.369383 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:17.369983 INFO::Using default BPPARAM
2026-02-19 21:40:17.370481 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:17.371437 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:40:17.387009 INFO::Done
2026-02-19 21:40:17.387725 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:17.389885 INFO::ASW Batch was -0.0207724010530613 prior to batch effect correction and is now -0.0934415700800897 .
2026-02-19 21:40:17.390717 INFO::Total function execution time is 0.0594725608825684 s and adjustment time is 0.0183811187744141 s ( 30.91 )
2026-02-19 21:40:17.391795 INFO::Formatting Data.
2026-02-19 21:40:17.39241 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:17.393292 INFO::Removing potential empty rows and columns
2026-02-19 21:40:17.394287 INFO::Found 0 missing values.
2026-02-19 21:40:17.397092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:17.397634 INFO::Done
2026-02-19 21:40:17.398136 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:17.400292 INFO::Starting hierarchical adjustment
2026-02-19 21:40:17.401007 INFO::Found 2 batches.
2026-02-19 21:40:17.401541 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:17.402149 INFO::Using default BPPARAM
2026-02-19 21:40:17.402687 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:17.403585 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:40:17.418839 INFO::Done
2026-02-19 21:40:17.419554 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:17.421708 INFO::ASW Batch was -0.0207724010530613 prior to batch effect correction and is now -0.0934415700800897 .
2026-02-19 21:40:17.422523 INFO::Total function execution time is 0.0307109355926514 s and adjustment time is 0.0179426670074463 s ( 58.42 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-19 21:40:20.574006 INFO::Formatting Data.
2026-02-19 21:40:20.574788 INFO::Recognized SummarizedExperiment
2026-02-19 21:40:20.575311 INFO::Typecasting input to dataframe.
2026-02-19 21:40:20.605973 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:20.607307 INFO::Removing potential empty rows and columns
2026-02-19 21:40:20.611253 INFO::Found 0 missing values.
2026-02-19 21:40:20.618654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:20.619309 INFO::Done
2026-02-19 21:40:20.619855 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:20.623538 INFO::Starting hierarchical adjustment
2026-02-19 21:40:20.624275 INFO::Found 2 batches.
2026-02-19 21:40:20.624835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:20.62594 INFO::Using default BPPARAM
2026-02-19 21:40:20.626474 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:20.627481 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:40:20.685861 INFO::Done
2026-02-19 21:40:20.68668 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:20.690563 INFO::ASW Batch was -0.0207108972588165 prior to batch effect correction and is now -0.0885048683477578 .
2026-02-19 21:40:20.691469 INFO::Total function execution time is 0.117725610733032 s and adjustment time is 0.061692476272583 s ( 52.4 )
Warning: stack imbalance in '{', 73 then 75
2026-02-19 21:40:20.711743 INFO::Formatting Data.
2026-02-19 21:40:20.712598 INFO::Recognized SummarizedExperiment
2026-02-19 21:40:20.713163 INFO::Typecasting input to dataframe.
2026-02-19 21:40:20.722986 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:20.724219 INFO::Removing potential empty rows and columns
2026-02-19 21:40:20.728128 INFO::Found 0 missing values.
2026-02-19 21:40:20.735465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:20.73613 INFO::Done
2026-02-19 21:40:20.736684 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:20.740388 INFO::Starting hierarchical adjustment
2026-02-19 21:40:20.741163 INFO::Found 2 batches.
2026-02-19 21:40:20.741721 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:20.742332 INFO::Using default BPPARAM
2026-02-19 21:40:20.742882 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:20.743903 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:40:20.770075 INFO::Done
2026-02-19 21:40:20.770885 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:20.774771 INFO::ASW Batch was -0.00427993384337221 prior to batch effect correction and is now -0.00427993384337221 .
2026-02-19 21:40:20.775659 INFO::Total function execution time is 0.0639064311981201 s and adjustment time is 0.02901291847229 s ( 45.4 )
2026-02-19 21:40:20.794837 INFO::Formatting Data.
2026-02-19 21:40:20.795628 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:20.796515 INFO::Removing potential empty rows and columns
2026-02-19 21:40:20.797572 INFO::Found 0 missing values.
2026-02-19 21:40:20.800628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:20.80117 INFO::Done
2026-02-19 21:40:20.801699 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:20.803731 INFO::Starting hierarchical adjustment
2026-02-19 21:40:20.804422 INFO::Found 3 batches.
2026-02-19 21:40:20.805072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:20.805685 INFO::Using default BPPARAM
2026-02-19 21:40:20.806197 INFO::Processing subtree level 1
2026-02-19 21:40:20.950862 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:40:20.952956 INFO::Done
2026-02-19 21:40:20.953763 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:20.956682 INFO::ASW Batch was -0.0727003745457416 prior to batch effect correction and is now -0.163841298363551 .
2026-02-19 21:40:20.957836 INFO::Total function execution time is 0.163078308105469 s and adjustment time is 0.148623466491699 s ( 91.14 )
2026-02-19 21:40:20.97452 INFO::Skipping initial DF formatting
2026-02-19 21:40:20.975414 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:20.98014 INFO::Starting hierarchical adjustment
2026-02-19 21:40:20.981205 INFO::Found 5 batches.
2026-02-19 21:40:20.981874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:20.982561 INFO::Using default BPPARAM
2026-02-19 21:40:20.983124 INFO::Processing subtree level 1
2026-02-19 21:40:21.228281 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:21.230166 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:40:21.251044 INFO::Done
2026-02-19 21:40:21.251931 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:21.256702 INFO::ASW Batch was 0.511612103973757 prior to batch effect correction and is now 0.511612103973757 .
2026-02-19 21:40:21.25747 INFO::ASW Label was 0.377193799184627 prior to batch effect correction and is now 0.377193799184627 .
2026-02-19 21:40:21.2584 INFO::Total function execution time is 0.284021854400635 s and adjustment time is 0.270006656646729 s ( 95.07 )
2026-02-19 21:40:21.375806 INFO::Formatting Data.
2026-02-19 21:40:21.377267 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:21.378648 INFO::Removing potential empty rows and columns
2026-02-19 21:40:21.380063 INFO::Found 0 missing values.
2026-02-19 21:40:21.384782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:21.385463 INFO::Done
2026-02-19 21:40:21.386051 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:21.390535 INFO::Starting hierarchical adjustment
2026-02-19 21:40:21.391462 INFO::Found 5 batches.
2026-02-19 21:40:21.392071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:21.392858 INFO::Using default BPPARAM
2026-02-19 21:40:21.393399 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.
2026-02-19 21:40:21.561962 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:21.564655 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:40:21.593892 INFO::Done
2026-02-19 21:40:21.595226 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:21.601453 INFO::ASW Batch was 0.411230812235987 prior to batch effect correction and is now -0.0807358216199632 .
2026-02-19 21:40:21.602599 INFO::ASW Label was 0.313298352333727 prior to batch effect correction and is now 0.878091294721439 .
2026-02-19 21:40:21.604052 INFO::Total function execution time is 0.229055643081665 s and adjustment time is 0.202509641647339 s ( 88.41 )
2026-02-19 21:40:21.60547 INFO::Formatting Data.
2026-02-19 21:40:21.6066 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:21.608098 INFO::Removing potential empty rows and columns
2026-02-19 21:40:21.609823 INFO::Found 0 missing values.
2026-02-19 21:40:21.616863 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:21.617944 INFO::Done
2026-02-19 21:40:21.618891 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:21.624004 INFO::Starting hierarchical adjustment
2026-02-19 21:40:21.625206 INFO::Found 5 batches.
2026-02-19 21:40:21.626004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:21.62692 INFO::Using default BPPARAM
2026-02-19 21:40:21.627702 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.
2026-02-19 21:40:21.781896 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:21.783585 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:40:21.800704 INFO::Done
2026-02-19 21:40:21.801431 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:21.804961 INFO::ASW Batch was 0.411230812235987 prior to batch effect correction and is now -0.0807358216199632 .
2026-02-19 21:40:21.805634 INFO::ASW Label was 0.313298352333727 prior to batch effect correction and is now 0.878091294721439 .
2026-02-19 21:40:21.806485 INFO::Total function execution time is 0.201155185699463 s and adjustment time is 0.175748586654663 s ( 87.37 )
2026-02-19 21:40:21.821495 INFO::Formatting Data.
2026-02-19 21:40:21.822371 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:21.823357 INFO::Removing potential empty rows and columns
2026-02-19 21:40:21.82441 INFO::Found 0 missing values.
2026-02-19 21:40:21.828647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:21.829226 INFO::Done
2026-02-19 21:40:21.829745 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:21.832856 INFO::Starting hierarchical adjustment
2026-02-19 21:40:21.833604 INFO::Found 5 batches.
2026-02-19 21:40:21.834119 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:21.834714 INFO::Using default BPPARAM
2026-02-19 21:40:21.835238 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.
2026-02-19 21:40:21.9666 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:21.968514 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:40:21.986059 INFO::Done
2026-02-19 21:40:21.986854 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:21.990596 INFO::ASW Batch was 0.47944300408521 prior to batch effect correction and is now 0.0164125761261708 .
2026-02-19 21:40:21.991346 INFO::ASW Label was 0.373704508238821 prior to batch effect correction and is now 0.720373805348962 .
2026-02-19 21:40:21.992237 INFO::Total function execution time is 0.17087197303772 s and adjustment time is 0.152559757232666 s ( 89.28 )
2026-02-19 21:40:21.993116 INFO::Formatting Data.
2026-02-19 21:40:21.993767 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:21.994739 INFO::Removing potential empty rows and columns
2026-02-19 21:40:21.995838 INFO::Found 0 missing values.
2026-02-19 21:40:22.000031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.000643 INFO::Done
2026-02-19 21:40:22.001148 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.004313 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.005079 INFO::Found 5 batches.
2026-02-19 21:40:22.005623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.006251 INFO::Using default BPPARAM
2026-02-19 21:40:22.006816 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.
2026-02-19 21:40:22.154809 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:22.156729 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:40:22.176213 INFO::Done
2026-02-19 21:40:22.177164 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.181123 INFO::ASW Batch was 0.47944300408521 prior to batch effect correction and is now 0.0164125761261708 .
2026-02-19 21:40:22.181992 INFO::ASW Label was 0.373704508238821 prior to batch effect correction and is now 0.720373805348962 .
2026-02-19 21:40:22.183047 INFO::Total function execution time is 0.189921617507935 s and adjustment time is 0.17122745513916 s ( 90.16 )
2026-02-19 21:40:22.200099 INFO::Formatting Data.
2026-02-19 21:40:22.201069 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:22.202161 INFO::Removing potential empty rows and columns
2026-02-19 21:40:22.203308 INFO::Found 0 missing values.
2026-02-19 21:40:22.206376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.206987 INFO::Done
2026-02-19 21:40:22.207551 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.210999 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.211801 INFO::Found 2 batches.
2026-02-19 21:40:22.212375 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.213052 INFO::Using default BPPARAM
2026-02-19 21:40:22.213625 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:22.214631 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:40:22.230842 INFO::Done
2026-02-19 21:40:22.231631 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.234806 INFO::ASW Batch was 0.710488432988455 prior to batch effect correction and is now -0.0267195700045979 .
2026-02-19 21:40:22.235414 INFO::ASW Label was 0.345157491392826 prior to batch effect correction and is now 0.885669563494833 .
2026-02-19 21:40:22.236242 INFO::Total function execution time is 0.0363190174102783 s and adjustment time is 0.0191857814788818 s ( 52.83 )
2026-02-19 21:40:22.237066 INFO::Formatting Data.
2026-02-19 21:40:22.237702 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:22.238618 INFO::Removing potential empty rows and columns
2026-02-19 21:40:22.239645 INFO::Found 0 missing values.
2026-02-19 21:40:22.242446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.242991 INFO::Done
2026-02-19 21:40:22.2435 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.246499 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.247221 INFO::Found 2 batches.
2026-02-19 21:40:22.247754 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.24835 INFO::Using default BPPARAM
2026-02-19 21:40:22.248873 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:22.249795 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:40:22.264859 INFO::Done
2026-02-19 21:40:22.265597 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.268634 INFO::ASW Batch was 0.710488432988455 prior to batch effect correction and is now -0.0267195700045979 .
2026-02-19 21:40:22.26923 INFO::ASW Label was 0.345157491392826 prior to batch effect correction and is now 0.885669563494833 .
2026-02-19 21:40:22.270015 INFO::Total function execution time is 0.0329761505126953 s and adjustment time is 0.0177412033081055 s ( 53.8 )
2026-02-19 21:40:22.281739 INFO::Formatting Data.
2026-02-19 21:40:22.28254 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:22.283446 INFO::Removing potential empty rows and columns
2026-02-19 21:40:22.284366 INFO::Found 0 missing values.
2026-02-19 21:40:22.286482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.287011 INFO::Done
2026-02-19 21:40:22.287522 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.289521 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.290216 INFO::Found 2 batches.
2026-02-19 21:40:22.290745 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.291327 INFO::Using default BPPARAM
2026-02-19 21:40:22.291877 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:22.292772 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:40:22.324451 INFO::Done
2026-02-19 21:40:22.325257 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.327415 INFO::ASW Batch was -0.017642671503592 prior to batch effect correction and is now -0.151073522073727 .
2026-02-19 21:40:22.328268 INFO::Total function execution time is 0.0467145442962646 s and adjustment time is 0.0343277454376221 s ( 73.48 )
2026-02-19 21:40:22.340654 INFO::Formatting Data.
2026-02-19 21:40:22.341475 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:22.342407 INFO::Removing potential empty rows and columns
2026-02-19 21:40:22.34341 INFO::Found 0 missing values.
2026-02-19 21:40:22.344605 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.
2026-02-19 21:40:22.357619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.358551 INFO::Done
2026-02-19 21:40:22.359135 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.362804 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.363561 INFO::Found 2 batches.
2026-02-19 21:40:22.364098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.364739 INFO::Using default BPPARAM
2026-02-19 21:40:22.365274 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:22.366241 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:40:22.383769 INFO::Done
2026-02-19 21:40:22.384496 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.38758 INFO::ASW Batch was 0.494818840976466 prior to batch effect correction and is now -0.0370550830956222 .
2026-02-19 21:40:22.388188 INFO::ASW Label was 0.578992481866003 prior to batch effect correction and is now 0.944242364526168 .
2026-02-19 21:40:22.389056 INFO::Total function execution time is 0.0485212802886963 s and adjustment time is 0.0203282833099365 s ( 41.9 )
2026-02-19 21:40:22.389905 INFO::Formatting Data.
2026-02-19 21:40:22.390501 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:22.39143 INFO::Removing potential empty rows and columns
2026-02-19 21:40:22.392425 INFO::Found 0 missing values.
2026-02-19 21:40:22.393326 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.
2026-02-19 21:40:22.397801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.398386 INFO::Done
2026-02-19 21:40:22.398946 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.401989 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.402737 INFO::Found 2 batches.
2026-02-19 21:40:22.403261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.403882 INFO::Using default BPPARAM
2026-02-19 21:40:22.404396 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:22.405365 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:40:22.423195 INFO::Done
2026-02-19 21:40:22.424 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.427112 INFO::ASW Batch was 0.494818840976466 prior to batch effect correction and is now -0.0370550830956222 .
2026-02-19 21:40:22.427789 INFO::ASW Label was 0.578992481866003 prior to batch effect correction and is now 0.944242364526168 .
2026-02-19 21:40:22.428646 INFO::Total function execution time is 0.0387380123138428 s and adjustment time is 0.0205543041229248 s ( 53.06 )
2026-02-19 21:40:22.649752 INFO::Formatting Data.
2026-02-19 21:40:22.650688 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:22.651731 INFO::Removing potential empty rows and columns
2026-02-19 21:40:22.652827 INFO::Found 0 missing values.
2026-02-19 21:40:22.655985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.656541 INFO::Done
2026-02-19 21:40:22.657072 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.659204 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.659925 INFO::Found 3 batches.
2026-02-19 21:40:22.660449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.661072 INFO::Using default BPPARAM
2026-02-19 21:40:22.661615 INFO::Processing subtree level 1
2026-02-19 21:40:22.755023 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:40:22.756983 INFO::Done
2026-02-19 21:40:22.75769 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.760335 INFO::ASW Batch was -0.0504520854882088 prior to batch effect correction and is now -0.0504520854882088 .
2026-02-19 21:40:22.761364 INFO::Total function execution time is 0.111706018447876 s and adjustment time is 0.0971739292144775 s ( 86.99 )
2026-02-19 21:40:22.762492 INFO::Formatting Data.
2026-02-19 21:40:22.763173 INFO::Typecasting input to dataframe.
2026-02-19 21:40:22.763996 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:22.764997 INFO::Removing potential empty rows and columns
2026-02-19 21:40:22.766127 INFO::Found 0 missing values.
2026-02-19 21:40:22.769347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.769931 INFO::Done
2026-02-19 21:40:22.77047 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.772634 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.773362 INFO::Found 3 batches.
2026-02-19 21:40:22.773934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.7746 INFO::Using default BPPARAM
2026-02-19 21:40:22.775151 INFO::Processing subtree level 1
2026-02-19 21:40:22.863789 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:40:22.865717 INFO::Done
2026-02-19 21:40:22.866415 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.869031 INFO::ASW Batch was -0.0504520854882088 prior to batch effect correction and is now -0.0504520854882088 .
2026-02-19 21:40:22.870023 INFO::Total function execution time is 0.107507944107056 s and adjustment time is 0.0924704074859619 s ( 86.01 )
2026-02-19 21:40:22.883784 INFO::Formatting Data.
2026-02-19 21:40:22.884691 INFO::Typecasting input to dataframe.
2026-02-19 21:40:22.885669 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:22.886705 INFO::Removing potential empty rows and columns
2026-02-19 21:40:22.887865 INFO::Found 0 missing values.
2026-02-19 21:40:22.891021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:22.8916 INFO::Done
2026-02-19 21:40:22.892137 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:22.894315 INFO::Starting hierarchical adjustment
2026-02-19 21:40:22.895057 INFO::Found 3 batches.
2026-02-19 21:40:22.895598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:22.896226 INFO::Using default BPPARAM
2026-02-19 21:40:22.896785 INFO::Processing subtree level 1
2026-02-19 21:40:22.987836 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:40:22.991044 INFO::Done
2026-02-19 21:40:22.991866 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:22.994686 INFO::ASW Batch was 0.036971794538486 prior to batch effect correction and is now 0.036971794538486 .
2026-02-19 21:40:22.995761 INFO::Total function execution time is 0.112028360366821 s and adjustment time is 0.0960581302642822 s ( 85.74 )
2026-02-19 21:40:23.13961 INFO::Formatting Data.
2026-02-19 21:40:23.140478 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:23.148961 INFO::Removing potential empty rows and columns
2026-02-19 21:40:23.152193 INFO::Found 1000 missing values.
2026-02-19 21:40:23.171451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:23.172329 INFO::Done
2026-02-19 21:40:23.172923 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:23.178584 INFO::Starting hierarchical adjustment
2026-02-19 21:40:23.179402 INFO::Found 10 batches.
2026-02-19 21:40:23.179985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:23.180614 INFO::Using default BPPARAM
2026-02-19 21:40:23.181144 INFO::Processing subtree level 1
2026-02-19 21:40:23.323737 INFO::Processing subtree level 2
2026-02-19 21:40:23.463825 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:40:23.465822 INFO::Done
2026-02-19 21:40:23.466501 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:23.472107 INFO::ASW Batch was 0.497855907787521 prior to batch effect correction and is now 0.497855907787521 .
2026-02-19 21:40:23.472817 INFO::ASW Label was 0.328338619111155 prior to batch effect correction and is now 0.328338619111155 .
2026-02-19 21:40:23.473766 INFO::Total function execution time is 0.334263324737549 s and adjustment time is 0.286571502685547 s ( 85.73 )
2026-02-19 21:40:23.474647 INFO::Formatting Data.
2026-02-19 21:40:23.475283 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:23.47658 INFO::Removing potential empty rows and columns
2026-02-19 21:40:23.479345 INFO::Found 1000 missing values.
2026-02-19 21:40:23.498583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:23.499364 INFO::Done
2026-02-19 21:40:23.499939 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:23.505569 INFO::Starting hierarchical adjustment
2026-02-19 21:40:23.506461 INFO::Found 10 batches.
2026-02-19 21:40:24.803894 INFO::Set up parallel execution backend with 2 workers
2026-02-19 21:40:24.805805 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-19 21:40:25.935636 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:40:25.937612 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:40:25.953599 INFO::Done
2026-02-19 21:40:25.954247 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:25.95871 INFO::ASW Batch was 0.497855907787521 prior to batch effect correction and is now 0.497855907787521 .
2026-02-19 21:40:25.959256 INFO::ASW Label was 0.328338619111155 prior to batch effect correction and is now 0.328338619111155 .
2026-02-19 21:40:25.95997 INFO::Total function execution time is 2.48538398742676 s and adjustment time is 2.44727802276611 s ( 98.47 )
2026-02-19 21:40:26.112909 INFO::Formatting Data.
2026-02-19 21:40:26.113788 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.114804 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.115949 INFO::Found 0 missing values.
2026-02-19 21:40:26.11982 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.120392 INFO::Done
2026-02-19 21:40:26.12095 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:40:26.124064 INFO::Starting hierarchical adjustment
2026-02-19 21:40:26.124811 INFO::Found 3 batches.
2026-02-19 21:40:26.125339 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:40:26.125987 INFO::Using default BPPARAM
2026-02-19 21:40:26.126534 INFO::Processing subtree level 1
2026-02-19 21:40:26.247301 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:40:26.249756 INFO::Done
2026-02-19 21:40:26.250657 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:40:26.254718 INFO::ASW Batch was 0.282325624292354 prior to batch effect correction and is now -0.145269511731358 .
2026-02-19 21:40:26.255581 INFO::ASW Label was -0.182100829500225 prior to batch effect correction and is now -0.00628633463905636 .
2026-02-19 21:40:26.256774 INFO::Total function execution time is 0.143892765045166 s and adjustment time is 0.124828100204468 s ( 86.75 )
2026-02-19 21:40:26.385138 INFO::Formatting Data.
2026-02-19 21:40:26.386081 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.387001 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.38805 INFO::Found 2 missing values.
2026-02-19 21:40:26.390836 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.391352 INFO::Done
2026-02-19 21:40:26.417338 INFO::Found NA in Reference column
2026-02-19 21:40:26.426612 INFO::Require at least two references per batch.
2026-02-19 21:40:26.446711 INFO::Formatting Data.
2026-02-19 21:40:26.447445 INFO::Recognized SummarizedExperiment
2026-02-19 21:40:26.447998 INFO::Typecasting input to dataframe.
2026-02-19 21:40:26.457457 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.458583 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.46194 INFO::Found 0 missing values.
2026-02-19 21:40:26.468392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.469041 INFO::Done
2026-02-19 21:40:26.484817 INFO::Formatting Data.
2026-02-19 21:40:26.485565 INFO::Recognized SummarizedExperiment
2026-02-19 21:40:26.486084 INFO::Typecasting input to dataframe.
2026-02-19 21:40:26.512616 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.514645 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.518278 INFO::Found 0 missing values.
2026-02-19 21:40:26.528917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.529517 INFO::Done
2026-02-19 21:40:26.54855 INFO::Formatting Data.
2026-02-19 21:40:26.549318 INFO::Recognized SummarizedExperiment
2026-02-19 21:40:26.549854 INFO::Typecasting input to dataframe.
2026-02-19 21:40:26.568083 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.569181 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.570276 INFO::Found 0 missing values.
2026-02-19 21:40:26.571194 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.
2026-02-19 21:40:26.575658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.576193 INFO::Done
2026-02-19 21:40:26.586975 INFO::Formatting Data.
2026-02-19 21:40:26.587798 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.588663 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.589637 INFO::Found 0 missing values.
2026-02-19 21:40:26.592384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.592907 INFO::Done
2026-02-19 21:40:26.604229 INFO::Formatting Data.
2026-02-19 21:40:26.605102 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.606101 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.607097 INFO::Found 0 missing values.
2026-02-19 21:40:26.609891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.610415 INFO::Done
2026-02-19 21:40:26.640424 INFO::Formatting Data.
2026-02-19 21:40:26.641531 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.642773 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.644084 INFO::Found 1 missing values.
2026-02-19 21:40:26.64693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.647529 INFO::Done
2026-02-19 21:40:26.66776 INFO::Formatting Data.
2026-02-19 21:40:26.668591 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.669448 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.670379 INFO::Found 2 missing values.
2026-02-19 21:40:26.671272 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.
2026-02-19 21:40:26.673501 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.674041 INFO::Done
2026-02-19 21:40:26.683806 INFO::Formatting Data.
2026-02-19 21:40:26.684559 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.685406 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.68633 INFO::Found 2 missing values.
2026-02-19 21:40:26.688234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.688802 INFO::Done
2026-02-19 21:40:26.699167 INFO::Formatting Data.
2026-02-19 21:40:26.699939 INFO::Typecasting input to dataframe.
2026-02-19 21:40:26.700727 INFO::Replacing NaNs with NAs.
2026-02-19 21:40:26.701569 INFO::Removing potential empty rows and columns
2026-02-19 21:40:26.702541 INFO::Found 0 missing values.
2026-02-19 21:40:26.705379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:40:26.705917 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.733 4.031 21.387
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.688 | 1.170 | 17.458 | |
| compute_asw | 0.023 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.000 | 0.011 | |