Yannis Schumann
| Snapshot Date: 2026-02-13 13:40 -0500 (Fri, 13 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-14 11:32 -0500 (Sat, 14 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4864 |
| 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 169/2352 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-13 21:40:17 -0500 (Fri, 13 Feb 2026) |
| EndedAt: 2026-02-13 21:41:48 -0500 (Fri, 13 Feb 2026) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.646 1.522 18.289
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-13 21:41:10.741941 INFO::Formatting Data.
2026-02-13 21:41:10.743289 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:10.754013 INFO::Removing potential empty rows and columns
2026-02-13 21:41:10.987206 INFO::Found 0 missing values.
2026-02-13 21:41:10.99052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:10.991184 INFO::Done
2026-02-13 21:41:10.991749 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:11.002957 INFO::Starting hierarchical adjustment
2026-02-13 21:41:11.003845 INFO::Found 3 batches.
2026-02-13 21:41:11.004432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:11.005559 INFO::Using default BPPARAM
2026-02-13 21:41:11.006109 INFO::Processing subtree level 1
2026-02-13 21:41:11.100423 INFO::Adjusting the last 1 batches sequentially
2026-02-13 21:41:11.102231 INFO::Done
2026-02-13 21:41:11.102919 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:11.105451 INFO::ASW Batch was -0.0132448830466472 prior to batch effect correction and is now -0.0132448830466472 .
2026-02-13 21:41:11.106515 INFO::Total function execution time is 0.365209817886353 s and adjustment time is 0.098555326461792 s ( 26.99 )
2026-02-13 21:41:11.1199 INFO::Formatting Data.
2026-02-13 21:41:11.120683 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:11.121626 INFO::Removing potential empty rows and columns
2026-02-13 21:41:11.122766 INFO::Found 0 missing values.
2026-02-13 21:41:11.123725 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.
2026-02-13 21:41:11.134333 INFO::Formatting Data.
2026-02-13 21:41:11.135093 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:11.136001 INFO::Removing potential empty rows and columns
2026-02-13 21:41:11.137086 INFO::Found 0 missing values.
2026-02-13 21:41:11.137998 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.
2026-02-13 21:41:11.153902 INFO::Formatting Data.
2026-02-13 21:41:11.154688 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:11.155579 INFO::Removing potential empty rows and columns
2026-02-13 21:41:11.156609 INFO::Found 0 missing values.
2026-02-13 21:41:11.157531 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.
2026-02-13 21:41:11.161931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:11.162497 INFO::Done
2026-02-13 21:41:11.163034 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:11.165066 INFO::Starting hierarchical adjustment
2026-02-13 21:41:11.165803 INFO::Found 2 batches.
2026-02-13 21:41:11.16635 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:11.166998 INFO::Using default BPPARAM
2026-02-13 21:41:11.167539 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:11.168459 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-13 21:41:11.188904 INFO::Done
2026-02-13 21:41:11.189629 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:11.197801 INFO::ASW Batch was 0.0419069763033191 prior to batch effect correction and is now -0.115328284761239 .
2026-02-13 21:41:11.199546 INFO::Total function execution time is 0.0456511974334717 s and adjustment time is 0.0232150554656982 s ( 50.85 )
2026-02-13 21:41:11.203668 INFO::Formatting Data.
2026-02-13 21:41:11.204345 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:11.214203 INFO::Formatting Data.
2026-02-13 21:41:11.21499 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:11.215914 INFO::Removing potential empty rows and columns
2026-02-13 21:41:11.217046 INFO::Found 0 missing values.
2026-02-13 21:41:11.220148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:11.220725 INFO::Done
2026-02-13 21:41:11.221272 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:11.223582 INFO::Starting hierarchical adjustment
2026-02-13 21:41:11.224329 INFO::Found 2 batches.
2026-02-13 21:41:11.224885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:11.225606 INFO::Using default BPPARAM
2026-02-13 21:41:11.226168 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:11.227152 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-13 21:41:11.275934 INFO::Done
2026-02-13 21:41:11.276608 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:11.278531 INFO::ASW Batch was -0.0248443533602155 prior to batch effect correction and is now -0.118525718411278 .
2026-02-13 21:41:11.279297 INFO::Total function execution time is 0.0651471614837646 s and adjustment time is 0.0517368316650391 s ( 79.42 )
2026-02-13 21:41:11.280314 INFO::Formatting Data.
2026-02-13 21:41:11.280904 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:11.281721 INFO::Removing potential empty rows and columns
2026-02-13 21:41:11.282691 INFO::Found 0 missing values.
2026-02-13 21:41:11.285338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:11.285885 INFO::Done
2026-02-13 21:41:11.286396 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:11.288277 INFO::Starting hierarchical adjustment
2026-02-13 21:41:11.288965 INFO::Found 2 batches.
2026-02-13 21:41:11.289482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:11.290049 INFO::Using default BPPARAM
2026-02-13 21:41:11.290552 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:11.291442 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-13 21:41:11.305377 INFO::Done
2026-02-13 21:41:11.306056 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:11.307992 INFO::ASW Batch was -0.0248443533602155 prior to batch effect correction and is now -0.118525718411278 .
2026-02-13 21:41:11.308764 INFO::Total function execution time is 0.0284423828125 s and adjustment time is 0.016512393951416 s ( 58.06 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-13 21:41:14.183639 INFO::Formatting Data.
2026-02-13 21:41:14.184301 INFO::Recognized SummarizedExperiment
2026-02-13 21:41:14.18479 INFO::Typecasting input to dataframe.
2026-02-13 21:41:14.213202 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:14.21438 INFO::Removing potential empty rows and columns
2026-02-13 21:41:14.218348 INFO::Found 0 missing values.
2026-02-13 21:41:14.225951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:14.2266 INFO::Done
2026-02-13 21:41:14.227135 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:14.230714 INFO::Starting hierarchical adjustment
2026-02-13 21:41:14.23145 INFO::Found 2 batches.
2026-02-13 21:41:14.231977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:14.233098 INFO::Using default BPPARAM
2026-02-13 21:41:14.233664 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:14.23466 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-13 21:41:14.291594 INFO::Done
2026-02-13 21:41:14.292287 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:14.295888 INFO::ASW Batch was -0.0024768320549689 prior to batch effect correction and is now -0.0974487986386957 .
2026-02-13 21:41:14.296726 INFO::Total function execution time is 0.113374710083008 s and adjustment time is 0.0602827072143555 s ( 53.17 )
Warning: stack imbalance in '{', 73 then 75
2026-02-13 21:41:14.315155 INFO::Formatting Data.
2026-02-13 21:41:14.316012 INFO::Recognized SummarizedExperiment
2026-02-13 21:41:14.316594 INFO::Typecasting input to dataframe.
2026-02-13 21:41:14.333234 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:14.334682 INFO::Removing potential empty rows and columns
2026-02-13 21:41:14.338696 INFO::Found 0 missing values.
2026-02-13 21:41:14.346277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:14.346944 INFO::Done
2026-02-13 21:41:14.3475 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:14.351462 INFO::Starting hierarchical adjustment
2026-02-13 21:41:14.352223 INFO::Found 2 batches.
2026-02-13 21:41:14.352773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:14.353443 INFO::Using default BPPARAM
2026-02-13 21:41:14.353982 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:14.354997 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-13 21:41:14.381783 INFO::Done
2026-02-13 21:41:14.382524 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:14.386133 INFO::ASW Batch was 0.00390985710212832 prior to batch effect correction and is now 0.00390985710212832 .
2026-02-13 21:41:14.38703 INFO::Total function execution time is 0.0718648433685303 s and adjustment time is 0.029691219329834 s ( 41.32 )
2026-02-13 21:41:14.405496 INFO::Formatting Data.
2026-02-13 21:41:14.40625 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:14.407151 INFO::Removing potential empty rows and columns
2026-02-13 21:41:14.408196 INFO::Found 0 missing values.
2026-02-13 21:41:14.411351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:14.411912 INFO::Done
2026-02-13 21:41:14.412442 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:14.414497 INFO::Starting hierarchical adjustment
2026-02-13 21:41:14.415193 INFO::Found 3 batches.
2026-02-13 21:41:14.415747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:14.416364 INFO::Using default BPPARAM
2026-02-13 21:41:14.416904 INFO::Processing subtree level 1
2026-02-13 21:41:14.543276 INFO::Adjusting the last 1 batches sequentially
2026-02-13 21:41:14.545219 INFO::Done
2026-02-13 21:41:14.54592 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:14.548514 INFO::ASW Batch was -0.0251223837240538 prior to batch effect correction and is now -0.158773551379279 .
2026-02-13 21:41:14.549475 INFO::Total function execution time is 0.144010305404663 s and adjustment time is 0.130128145217896 s ( 90.36 )
2026-02-13 21:41:14.564059 INFO::Skipping initial DF formatting
2026-02-13 21:41:14.564804 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:14.568901 INFO::Starting hierarchical adjustment
2026-02-13 21:41:14.569695 INFO::Found 5 batches.
2026-02-13 21:41:14.570253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:14.570896 INFO::Using default BPPARAM
2026-02-13 21:41:14.571467 INFO::Processing subtree level 1
2026-02-13 21:41:14.80914 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:14.811002 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-13 21:41:14.831611 INFO::Done
2026-02-13 21:41:14.832399 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:14.891923 INFO::ASW Batch was 0.504613517717325 prior to batch effect correction and is now 0.504613517717325 .
2026-02-13 21:41:14.892641 INFO::ASW Label was 0.365621478362338 prior to batch effect correction and is now 0.365621478362338 .
2026-02-13 21:41:14.893506 INFO::Total function execution time is 0.329516410827637 s and adjustment time is 0.262044429779053 s ( 79.52 )
2026-02-13 21:41:14.911303 INFO::Formatting Data.
2026-02-13 21:41:14.912163 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:14.913184 INFO::Removing potential empty rows and columns
2026-02-13 21:41:14.914454 INFO::Found 0 missing values.
2026-02-13 21:41:14.918868 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:14.919465 INFO::Done
2026-02-13 21:41:14.920047 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:14.923246 INFO::Starting hierarchical adjustment
2026-02-13 21:41:14.923974 INFO::Found 5 batches.
2026-02-13 21:41:14.924525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:14.925143 INFO::Using default BPPARAM
2026-02-13 21:41:14.925686 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.
2026-02-13 21:41:15.050421 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.052178 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-13 21:41:15.070213 INFO::Done
2026-02-13 21:41:15.070998 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.074632 INFO::ASW Batch was 0.449981602266009 prior to batch effect correction and is now -0.0627269664187443 .
2026-02-13 21:41:15.075308 INFO::ASW Label was 0.422595276487763 prior to batch effect correction and is now 0.805535052621701 .
2026-02-13 21:41:15.076202 INFO::Total function execution time is 0.164952516555786 s and adjustment time is 0.146340608596802 s ( 88.72 )
2026-02-13 21:41:15.077113 INFO::Formatting Data.
2026-02-13 21:41:15.0778 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:15.078778 INFO::Removing potential empty rows and columns
2026-02-13 21:41:15.079921 INFO::Found 0 missing values.
2026-02-13 21:41:15.0847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:15.085327 INFO::Done
2026-02-13 21:41:15.085988 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:15.089378 INFO::Starting hierarchical adjustment
2026-02-13 21:41:15.090141 INFO::Found 5 batches.
2026-02-13 21:41:15.090721 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:15.091408 INFO::Using default BPPARAM
2026-02-13 21:41:15.091977 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.
2026-02-13 21:41:15.238148 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.240935 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-13 21:41:15.260533 INFO::Done
2026-02-13 21:41:15.26133 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.265149 INFO::ASW Batch was 0.449981602266009 prior to batch effect correction and is now -0.0627269664187443 .
2026-02-13 21:41:15.265888 INFO::ASW Label was 0.422595276487763 prior to batch effect correction and is now 0.805535052621701 .
2026-02-13 21:41:15.266878 INFO::Total function execution time is 0.189746379852295 s and adjustment time is 0.170517921447754 s ( 89.87 )
2026-02-13 21:41:15.282828 INFO::Formatting Data.
2026-02-13 21:41:15.283815 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:15.284875 INFO::Removing potential empty rows and columns
2026-02-13 21:41:15.286033 INFO::Found 0 missing values.
2026-02-13 21:41:15.290456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:15.291057 INFO::Done
2026-02-13 21:41:15.291645 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:15.294928 INFO::Starting hierarchical adjustment
2026-02-13 21:41:15.295789 INFO::Found 5 batches.
2026-02-13 21:41:15.296491 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:15.297208 INFO::Using default BPPARAM
2026-02-13 21:41:15.297869 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.
2026-02-13 21:41:15.439307 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.441409 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-13 21:41:15.461322 INFO::Done
2026-02-13 21:41:15.462265 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.46647 INFO::ASW Batch was 0.396526338709044 prior to batch effect correction and is now -0.0910410239161449 .
2026-02-13 21:41:15.467319 INFO::ASW Label was 0.336396928466692 prior to batch effect correction and is now 0.878783371795074 .
2026-02-13 21:41:15.468395 INFO::Total function execution time is 0.185620784759521 s and adjustment time is 0.165620803833008 s ( 89.23 )
2026-02-13 21:41:15.469457 INFO::Formatting Data.
2026-02-13 21:41:15.470294 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:15.471438 INFO::Removing potential empty rows and columns
2026-02-13 21:41:15.473168 INFO::Found 0 missing values.
2026-02-13 21:41:15.478722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:15.479523 INFO::Done
2026-02-13 21:41:15.480167 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:15.483918 INFO::Starting hierarchical adjustment
2026-02-13 21:41:15.484783 INFO::Found 5 batches.
2026-02-13 21:41:15.485428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:15.486186 INFO::Using default BPPARAM
2026-02-13 21:41:15.486802 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.
2026-02-13 21:41:15.611791 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.613495 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-13 21:41:15.630022 INFO::Done
2026-02-13 21:41:15.630868 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.634055 INFO::ASW Batch was 0.396526338709044 prior to batch effect correction and is now -0.0910410239161449 .
2026-02-13 21:41:15.634682 INFO::ASW Label was 0.336396928466692 prior to batch effect correction and is now 0.878783371795074 .
2026-02-13 21:41:15.635559 INFO::Total function execution time is 0.166149139404297 s and adjustment time is 0.145366430282593 s ( 87.49 )
2026-02-13 21:41:15.649033 INFO::Formatting Data.
2026-02-13 21:41:15.649828 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:15.650773 INFO::Removing potential empty rows and columns
2026-02-13 21:41:15.651815 INFO::Found 0 missing values.
2026-02-13 21:41:15.65451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:15.65508 INFO::Done
2026-02-13 21:41:15.655613 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:15.658519 INFO::Starting hierarchical adjustment
2026-02-13 21:41:15.659236 INFO::Found 2 batches.
2026-02-13 21:41:15.659791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:15.660411 INFO::Using default BPPARAM
2026-02-13 21:41:15.660972 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.661883 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-13 21:41:15.676111 INFO::Done
2026-02-13 21:41:15.676796 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.679706 INFO::ASW Batch was 0.410795861241716 prior to batch effect correction and is now 0.0495447594724816 .
2026-02-13 21:41:15.680298 INFO::ASW Label was 0.659271225236615 prior to batch effect correction and is now 0.863169936857859 .
2026-02-13 21:41:15.681114 INFO::Total function execution time is 0.0321667194366455 s and adjustment time is 0.0169909000396729 s ( 52.82 )
2026-02-13 21:41:15.681908 INFO::Formatting Data.
2026-02-13 21:41:15.682538 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:15.683397 INFO::Removing potential empty rows and columns
2026-02-13 21:41:15.684358 INFO::Found 0 missing values.
2026-02-13 21:41:15.687012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:15.687567 INFO::Done
2026-02-13 21:41:15.68808 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:15.69091 INFO::Starting hierarchical adjustment
2026-02-13 21:41:15.691614 INFO::Found 2 batches.
2026-02-13 21:41:15.69214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:15.692737 INFO::Using default BPPARAM
2026-02-13 21:41:15.693281 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.694175 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-13 21:41:15.708237 INFO::Done
2026-02-13 21:41:15.708927 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.711824 INFO::ASW Batch was 0.410795861241716 prior to batch effect correction and is now 0.0495447594724816 .
2026-02-13 21:41:15.712446 INFO::ASW Label was 0.659271225236615 prior to batch effect correction and is now 0.863169936857859 .
2026-02-13 21:41:15.713208 INFO::Total function execution time is 0.0313048362731934 s and adjustment time is 0.0167391300201416 s ( 53.47 )
2026-02-13 21:41:15.724168 INFO::Formatting Data.
2026-02-13 21:41:15.724952 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:15.725823 INFO::Removing potential empty rows and columns
2026-02-13 21:41:15.726722 INFO::Found 0 missing values.
2026-02-13 21:41:15.728775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:15.729297 INFO::Done
2026-02-13 21:41:15.729822 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:15.731685 INFO::Starting hierarchical adjustment
2026-02-13 21:41:15.732363 INFO::Found 2 batches.
2026-02-13 21:41:15.732907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:15.733531 INFO::Using default BPPARAM
2026-02-13 21:41:15.734068 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.734956 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-13 21:41:15.767125 INFO::Done
2026-02-13 21:41:15.767905 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.770043 INFO::ASW Batch was -0.0279877476398301 prior to batch effect correction and is now -0.1497932909573 .
2026-02-13 21:41:15.770911 INFO::Total function execution time is 0.0468184947967529 s and adjustment time is 0.0348539352416992 s ( 74.44 )
2026-02-13 21:41:15.782648 INFO::Formatting Data.
2026-02-13 21:41:15.783424 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:15.784297 INFO::Removing potential empty rows and columns
2026-02-13 21:41:15.785281 INFO::Found 0 missing values.
2026-02-13 21:41:15.786416 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.
2026-02-13 21:41:15.790991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:15.791606 INFO::Done
2026-02-13 21:41:15.792134 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:15.794978 INFO::Starting hierarchical adjustment
2026-02-13 21:41:15.795689 INFO::Found 2 batches.
2026-02-13 21:41:15.796206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:15.79683 INFO::Using default BPPARAM
2026-02-13 21:41:15.797347 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.798275 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-13 21:41:15.813908 INFO::Done
2026-02-13 21:41:15.814642 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.817513 INFO::ASW Batch was 0.575504960565309 prior to batch effect correction and is now 0.316694092933326 .
2026-02-13 21:41:15.818109 INFO::ASW Label was 0.592276549389517 prior to batch effect correction and is now 0.663903099664872 .
2026-02-13 21:41:15.818914 INFO::Total function execution time is 0.0363538265228271 s and adjustment time is 0.0183298587799072 s ( 50.42 )
2026-02-13 21:41:15.819697 INFO::Formatting Data.
2026-02-13 21:41:15.820309 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:15.821219 INFO::Removing potential empty rows and columns
2026-02-13 21:41:15.822181 INFO::Found 0 missing values.
2026-02-13 21:41:15.823095 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.
2026-02-13 21:41:15.827579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:15.828156 INFO::Done
2026-02-13 21:41:15.828672 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:15.831502 INFO::Starting hierarchical adjustment
2026-02-13 21:41:15.832191 INFO::Found 2 batches.
2026-02-13 21:41:15.83275 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:15.833352 INFO::Using default BPPARAM
2026-02-13 21:41:15.833885 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:15.834807 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-13 21:41:15.850396 INFO::Done
2026-02-13 21:41:15.851101 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:15.853941 INFO::ASW Batch was 0.575504960565309 prior to batch effect correction and is now 0.316694092933326 .
2026-02-13 21:41:15.854573 INFO::ASW Label was 0.592276549389517 prior to batch effect correction and is now 0.663903099664872 .
2026-02-13 21:41:15.855349 INFO::Total function execution time is 0.0356674194335938 s and adjustment time is 0.0183045864105225 s ( 51.32 )
2026-02-13 21:41:16.06227 INFO::Formatting Data.
2026-02-13 21:41:16.063076 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:16.064007 INFO::Removing potential empty rows and columns
2026-02-13 21:41:16.065078 INFO::Found 0 missing values.
2026-02-13 21:41:16.068146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:16.068722 INFO::Done
2026-02-13 21:41:16.069252 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:16.071351 INFO::Starting hierarchical adjustment
2026-02-13 21:41:16.072068 INFO::Found 3 batches.
2026-02-13 21:41:16.072609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:16.073246 INFO::Using default BPPARAM
2026-02-13 21:41:16.073788 INFO::Processing subtree level 1
2026-02-13 21:41:16.15813 INFO::Adjusting the last 1 batches sequentially
2026-02-13 21:41:16.160756 INFO::Done
2026-02-13 21:41:16.161749 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:16.165391 INFO::ASW Batch was 0.0508224439940921 prior to batch effect correction and is now 0.0508224439940921 .
2026-02-13 21:41:16.166968 INFO::Total function execution time is 0.104657649993896 s and adjustment time is 0.0887534618377686 s ( 84.8 )
2026-02-13 21:41:16.168618 INFO::Formatting Data.
2026-02-13 21:41:16.169622 INFO::Typecasting input to dataframe.
2026-02-13 21:41:16.170828 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:16.172205 INFO::Removing potential empty rows and columns
2026-02-13 21:41:16.173872 INFO::Found 0 missing values.
2026-02-13 21:41:16.178835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:16.179835 INFO::Done
2026-02-13 21:41:16.180707 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:16.183804 INFO::Starting hierarchical adjustment
2026-02-13 21:41:16.184933 INFO::Found 3 batches.
2026-02-13 21:41:16.185777 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:16.186754 INFO::Using default BPPARAM
2026-02-13 21:41:16.187625 INFO::Processing subtree level 1
2026-02-13 21:41:16.285592 INFO::Adjusting the last 1 batches sequentially
2026-02-13 21:41:16.287679 INFO::Done
2026-02-13 21:41:16.288475 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:16.291308 INFO::ASW Batch was 0.0508224439940921 prior to batch effect correction and is now 0.0508224439940921 .
2026-02-13 21:41:16.292378 INFO::Total function execution time is 0.123847484588623 s and adjustment time is 0.102981567382812 s ( 83.15 )
2026-02-13 21:41:16.308125 INFO::Formatting Data.
2026-02-13 21:41:16.309016 INFO::Typecasting input to dataframe.
2026-02-13 21:41:16.309899 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:16.310843 INFO::Removing potential empty rows and columns
2026-02-13 21:41:16.311962 INFO::Found 0 missing values.
2026-02-13 21:41:16.315049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:16.31563 INFO::Done
2026-02-13 21:41:16.316172 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:16.318416 INFO::Starting hierarchical adjustment
2026-02-13 21:41:16.319142 INFO::Found 3 batches.
2026-02-13 21:41:16.319696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:16.320338 INFO::Using default BPPARAM
2026-02-13 21:41:16.320915 INFO::Processing subtree level 1
2026-02-13 21:41:16.403867 INFO::Adjusting the last 1 batches sequentially
2026-02-13 21:41:16.405821 INFO::Done
2026-02-13 21:41:16.40654 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:16.409176 INFO::ASW Batch was -0.107652480242374 prior to batch effect correction and is now -0.107652480242374 .
2026-02-13 21:41:16.410196 INFO::Total function execution time is 0.102182626724243 s and adjustment time is 0.0868103504180908 s ( 84.96 )
2026-02-13 21:41:16.546285 INFO::Formatting Data.
2026-02-13 21:41:16.547171 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:16.548413 INFO::Removing potential empty rows and columns
2026-02-13 21:41:16.551807 INFO::Found 1000 missing values.
2026-02-13 21:41:16.573066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:16.573958 INFO::Done
2026-02-13 21:41:16.574566 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:16.580136 INFO::Starting hierarchical adjustment
2026-02-13 21:41:16.581013 INFO::Found 10 batches.
2026-02-13 21:41:16.581598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:16.582265 INFO::Using default BPPARAM
2026-02-13 21:41:16.582829 INFO::Processing subtree level 1
2026-02-13 21:41:16.717561 INFO::Processing subtree level 2
2026-02-13 21:41:16.861258 INFO::Adjusting the last 1 batches sequentially
2026-02-13 21:41:16.863419 INFO::Done
2026-02-13 21:41:16.864134 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:16.869767 INFO::ASW Batch was 0.480687687056505 prior to batch effect correction and is now 0.480687687056505 .
2026-02-13 21:41:16.870621 INFO::ASW Label was 0.35512291105125 prior to batch effect correction and is now 0.35512291105125 .
2026-02-13 21:41:16.871598 INFO::Total function execution time is 0.325404167175293 s and adjustment time is 0.282553672790527 s ( 86.83 )
2026-02-13 21:41:16.87248 INFO::Formatting Data.
2026-02-13 21:41:16.873143 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:16.874356 INFO::Removing potential empty rows and columns
2026-02-13 21:41:16.877354 INFO::Found 1000 missing values.
2026-02-13 21:41:16.898039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:16.898855 INFO::Done
2026-02-13 21:41:16.899464 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:16.905205 INFO::Starting hierarchical adjustment
2026-02-13 21:41:16.906131 INFO::Found 10 batches.
2026-02-13 21:41:17.99172 INFO::Set up parallel execution backend with 2 workers
2026-02-13 21:41:17.995238 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-13 21:41:19.147259 INFO::Adjusting the last 2 batches sequentially
2026-02-13 21:41:19.149222 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-13 21:41:19.166597 INFO::Done
2026-02-13 21:41:19.167461 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:19.172524 INFO::ASW Batch was 0.480687687056505 prior to batch effect correction and is now 0.480687687056505 .
2026-02-13 21:41:19.173202 INFO::ASW Label was 0.35512291105125 prior to batch effect correction and is now 0.35512291105125 .
2026-02-13 21:41:19.174046 INFO::Total function execution time is 2.30159568786621 s and adjustment time is 2.26060342788696 s ( 98.22 )
2026-02-13 21:41:19.312398 INFO::Formatting Data.
2026-02-13 21:41:19.313176 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.314072 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.315114 INFO::Found 0 missing values.
2026-02-13 21:41:19.318757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.3193 INFO::Done
2026-02-13 21:41:19.31982 INFO::Acquiring quality metrics before batch effect correction.
2026-02-13 21:41:19.322635 INFO::Starting hierarchical adjustment
2026-02-13 21:41:19.323351 INFO::Found 3 batches.
2026-02-13 21:41:19.323906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-13 21:41:19.324564 INFO::Using default BPPARAM
2026-02-13 21:41:19.325102 INFO::Processing subtree level 1
2026-02-13 21:41:19.423992 INFO::Adjusting the last 1 batches sequentially
2026-02-13 21:41:19.425718 INFO::Done
2026-02-13 21:41:19.426364 INFO::Acquiring quality metrics after batch effect correction.
2026-02-13 21:41:19.429433 INFO::ASW Batch was 0.243561742046064 prior to batch effect correction and is now -0.148610193818822 .
2026-02-13 21:41:19.430027 INFO::ASW Label was -0.188859221818975 prior to batch effect correction and is now -0.0308348335303641 .
2026-02-13 21:41:19.430939 INFO::Total function execution time is 0.118611812591553 s and adjustment time is 0.10249662399292 s ( 86.41 )
2026-02-13 21:41:19.553064 INFO::Formatting Data.
2026-02-13 21:41:19.553949 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.554851 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.555907 INFO::Found 2 missing values.
2026-02-13 21:41:19.558656 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.559211 INFO::Done
2026-02-13 21:41:19.585221 INFO::Found NA in Reference column
2026-02-13 21:41:19.594334 INFO::Require at least two references per batch.
2026-02-13 21:41:19.614382 INFO::Formatting Data.
2026-02-13 21:41:19.615149 INFO::Recognized SummarizedExperiment
2026-02-13 21:41:19.615704 INFO::Typecasting input to dataframe.
2026-02-13 21:41:19.625022 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.626149 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.629638 INFO::Found 0 missing values.
2026-02-13 21:41:19.636282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.636899 INFO::Done
2026-02-13 21:41:19.652144 INFO::Formatting Data.
2026-02-13 21:41:19.652886 INFO::Recognized SummarizedExperiment
2026-02-13 21:41:19.65342 INFO::Typecasting input to dataframe.
2026-02-13 21:41:19.669755 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.670996 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.674534 INFO::Found 0 missing values.
2026-02-13 21:41:19.685309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.685983 INFO::Done
2026-02-13 21:41:19.700953 INFO::Formatting Data.
2026-02-13 21:41:19.701779 INFO::Recognized SummarizedExperiment
2026-02-13 21:41:19.702312 INFO::Typecasting input to dataframe.
2026-02-13 21:41:19.718227 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.719265 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.720352 INFO::Found 0 missing values.
2026-02-13 21:41:19.721246 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.
2026-02-13 21:41:19.725482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.726028 INFO::Done
2026-02-13 21:41:19.73573 INFO::Formatting Data.
2026-02-13 21:41:19.736564 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.737508 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.738571 INFO::Found 0 missing values.
2026-02-13 21:41:19.741585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.742125 INFO::Done
2026-02-13 21:41:19.754213 INFO::Formatting Data.
2026-02-13 21:41:19.755028 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.755968 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.757004 INFO::Found 0 missing values.
2026-02-13 21:41:19.760012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.76056 INFO::Done
2026-02-13 21:41:19.791831 INFO::Formatting Data.
2026-02-13 21:41:19.792703 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.793798 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.79501 INFO::Found 1 missing values.
2026-02-13 21:41:19.797777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.798359 INFO::Done
2026-02-13 21:41:19.81814 INFO::Formatting Data.
2026-02-13 21:41:19.81896 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.819888 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.820864 INFO::Found 2 missing values.
2026-02-13 21:41:19.821795 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.
2026-02-13 21:41:19.824359 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.824909 INFO::Done
2026-02-13 21:41:19.834796 INFO::Formatting Data.
2026-02-13 21:41:19.835546 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.836443 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.837347 INFO::Found 2 missing values.
2026-02-13 21:41:19.838933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.839499 INFO::Done
2026-02-13 21:41:19.849704 INFO::Formatting Data.
2026-02-13 21:41:19.85046 INFO::Typecasting input to dataframe.
2026-02-13 21:41:19.851264 INFO::Replacing NaNs with NAs.
2026-02-13 21:41:19.85213 INFO::Removing potential empty rows and columns
2026-02-13 21:41:19.85313 INFO::Found 0 missing values.
2026-02-13 21:41:19.856092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-13 21:41:19.856647 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.459 3.418 20.648
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.646 | 1.522 | 18.289 | |
| compute_asw | 0.024 | 0.003 | 0.027 | |
| count_existing | 0.013 | 0.002 | 0.015 | |
| generate_data_covariables | 0.011 | 0.003 | 0.014 | |
| generate_dataset | 0.011 | 0.002 | 0.013 | |