Yannis Schumann
| Snapshot Date: 2026-03-05 13:45 -0500 (Thu, 05 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-06 11:57 -0500 (Fri, 06 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4894 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-03-05 21:39:24 -0500 (Thu, 05 Mar 2026) |
| EndedAt: 2026-03-05 21:40:56 -0500 (Thu, 05 Mar 2026) |
| EllapsedTime: 91.1 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 24.491 1.498 18.133
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-03-05 21:40:16.508869 INFO::Formatting Data.
2026-03-05 21:40:16.51042 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:16.522772 INFO::Removing potential empty rows and columns
2026-03-05 21:40:16.762039 INFO::Found 0 missing values.
2026-03-05 21:40:16.765297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:16.765949 INFO::Done
2026-03-05 21:40:16.766486 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:16.777683 INFO::Starting hierarchical adjustment
2026-03-05 21:40:16.77858 INFO::Found 3 batches.
2026-03-05 21:40:16.779151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:16.780272 INFO::Using default BPPARAM
2026-03-05 21:40:16.780842 INFO::Processing subtree level 1
2026-03-05 21:40:16.880145 INFO::Adjusting the last 1 batches sequentially
2026-03-05 21:40:16.881874 INFO::Done
2026-03-05 21:40:16.882535 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:16.885099 INFO::ASW Batch was 0.0416973251769459 prior to batch effect correction and is now 0.0416973251769459 .
2026-03-05 21:40:16.886126 INFO::Total function execution time is 0.378080368041992 s and adjustment time is 0.103487253189087 s ( 27.37 )
2026-03-05 21:40:16.899456 INFO::Formatting Data.
2026-03-05 21:40:16.90034 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:16.901294 INFO::Removing potential empty rows and columns
2026-03-05 21:40:16.902461 INFO::Found 0 missing values.
2026-03-05 21:40:16.903422 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-05 21:40:16.914047 INFO::Formatting Data.
2026-03-05 21:40:16.914763 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:16.915648 INFO::Removing potential empty rows and columns
2026-03-05 21:40:16.916724 INFO::Found 0 missing values.
2026-03-05 21:40:16.917667 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-05 21:40:16.933664 INFO::Formatting Data.
2026-03-05 21:40:16.934442 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:16.935349 INFO::Removing potential empty rows and columns
2026-03-05 21:40:16.936392 INFO::Found 0 missing values.
2026-03-05 21:40:16.937298 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-05 21:40:16.941719 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:16.94226 INFO::Done
2026-03-05 21:40:16.94279 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:16.944747 INFO::Starting hierarchical adjustment
2026-03-05 21:40:16.945435 INFO::Found 2 batches.
2026-03-05 21:40:16.945958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:16.946589 INFO::Using default BPPARAM
2026-03-05 21:40:16.947108 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:16.948023 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 21:40:16.969028 INFO::Done
2026-03-05 21:40:16.969744 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:16.971997 INFO::ASW Batch was -0.052328431398704 prior to batch effect correction and is now -0.116497713254784 .
2026-03-05 21:40:16.972857 INFO::Total function execution time is 0.0392656326293945 s and adjustment time is 0.0237052440643311 s ( 60.37 )
2026-03-05 21:40:16.975745 INFO::Formatting Data.
2026-03-05 21:40:16.976409 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:16.985337 INFO::Formatting Data.
2026-03-05 21:40:16.986045 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:16.98693 INFO::Removing potential empty rows and columns
2026-03-05 21:40:16.987995 INFO::Found 0 missing values.
2026-03-05 21:40:16.991004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:16.991566 INFO::Done
2026-03-05 21:40:16.992101 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:17.01708 INFO::Starting hierarchical adjustment
2026-03-05 21:40:17.018623 INFO::Found 2 batches.
2026-03-05 21:40:17.019198 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:17.019777 INFO::Using default BPPARAM
2026-03-05 21:40:17.02028 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:17.021192 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:17.035312 INFO::Done
2026-03-05 21:40:17.035969 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:17.037917 INFO::ASW Batch was -0.0322320639522355 prior to batch effect correction and is now -0.118248369276856 .
2026-03-05 21:40:17.03871 INFO::Total function execution time is 0.0534060001373291 s and adjustment time is 0.0168936252593994 s ( 31.63 )
2026-03-05 21:40:17.039742 INFO::Formatting Data.
2026-03-05 21:40:17.04032 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:17.041138 INFO::Removing potential empty rows and columns
2026-03-05 21:40:17.042097 INFO::Found 0 missing values.
2026-03-05 21:40:17.04476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:17.045281 INFO::Done
2026-03-05 21:40:17.045783 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:17.047747 INFO::Starting hierarchical adjustment
2026-03-05 21:40:17.048426 INFO::Found 2 batches.
2026-03-05 21:40:17.048927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:17.049491 INFO::Using default BPPARAM
2026-03-05 21:40:17.050005 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:17.050875 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:17.065247 INFO::Done
2026-03-05 21:40:17.06594 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:17.067945 INFO::ASW Batch was -0.0322320639522355 prior to batch effect correction and is now -0.118248369276856 .
2026-03-05 21:40:17.068732 INFO::Total function execution time is 0.0289921760559082 s and adjustment time is 0.0169296264648438 s ( 58.39 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-05 21:40:19.963884 INFO::Formatting Data.
2026-03-05 21:40:19.964674 INFO::Recognized SummarizedExperiment
2026-03-05 21:40:19.965199 INFO::Typecasting input to dataframe.
2026-03-05 21:40:19.997309 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:19.998722 INFO::Removing potential empty rows and columns
2026-03-05 21:40:20.002723 INFO::Found 0 missing values.
2026-03-05 21:40:20.010402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:20.011158 INFO::Done
2026-03-05 21:40:20.011713 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:20.015438 INFO::Starting hierarchical adjustment
2026-03-05 21:40:20.016208 INFO::Found 2 batches.
2026-03-05 21:40:20.016761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:20.017883 INFO::Using default BPPARAM
2026-03-05 21:40:20.018441 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:20.019467 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 21:40:20.077388 INFO::Done
2026-03-05 21:40:20.078183 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:20.081991 INFO::ASW Batch was 0.0111082257903289 prior to batch effect correction and is now -0.0939524970421163 .
2026-03-05 21:40:20.082885 INFO::Total function execution time is 0.119324684143066 s and adjustment time is 0.0612907409667969 s ( 51.36 )
Warning: stack imbalance in '{', 73 then 75
2026-03-05 21:40:20.102984 INFO::Formatting Data.
2026-03-05 21:40:20.10382 INFO::Recognized SummarizedExperiment
2026-03-05 21:40:20.104387 INFO::Typecasting input to dataframe.
2026-03-05 21:40:20.114337 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:20.115579 INFO::Removing potential empty rows and columns
2026-03-05 21:40:20.11939 INFO::Found 0 missing values.
2026-03-05 21:40:20.126731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:20.127376 INFO::Done
2026-03-05 21:40:20.127934 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:20.131613 INFO::Starting hierarchical adjustment
2026-03-05 21:40:20.132365 INFO::Found 2 batches.
2026-03-05 21:40:20.132908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:20.133504 INFO::Using default BPPARAM
2026-03-05 21:40:20.134052 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:20.135049 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 21:40:20.160782 INFO::Done
2026-03-05 21:40:20.161573 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:20.165391 INFO::ASW Batch was -0.00153720800547048 prior to batch effect correction and is now -0.00153720800547048 .
2026-03-05 21:40:20.166301 INFO::Total function execution time is 0.0633246898651123 s and adjustment time is 0.0285146236419678 s ( 45.03 )
2026-03-05 21:40:20.185955 INFO::Formatting Data.
2026-03-05 21:40:20.186913 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:20.187922 INFO::Removing potential empty rows and columns
2026-03-05 21:40:20.189037 INFO::Found 0 missing values.
2026-03-05 21:40:20.192294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:20.192872 INFO::Done
2026-03-05 21:40:20.193403 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:20.195681 INFO::Starting hierarchical adjustment
2026-03-05 21:40:20.196404 INFO::Found 3 batches.
2026-03-05 21:40:20.196958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:20.197583 INFO::Using default BPPARAM
2026-03-05 21:40:20.19811 INFO::Processing subtree level 1
2026-03-05 21:40:20.343075 INFO::Adjusting the last 1 batches sequentially
2026-03-05 21:40:20.345311 INFO::Done
2026-03-05 21:40:20.346023 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:20.34879 INFO::ASW Batch was -0.135836640758538 prior to batch effect correction and is now -0.17062898088073 .
2026-03-05 21:40:20.349777 INFO::Total function execution time is 0.163897037506104 s and adjustment time is 0.149023294448853 s ( 90.92 )
2026-03-05 21:40:20.365206 INFO::Skipping initial DF formatting
2026-03-05 21:40:20.36604 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:20.370366 INFO::Starting hierarchical adjustment
2026-03-05 21:40:20.371187 INFO::Found 5 batches.
2026-03-05 21:40:20.371759 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:20.372388 INFO::Using default BPPARAM
2026-03-05 21:40:20.372932 INFO::Processing subtree level 1
2026-03-05 21:40:20.619098 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:20.620867 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 21:40:20.641132 INFO::Done
2026-03-05 21:40:20.641919 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:20.646404 INFO::ASW Batch was 0.533288436567017 prior to batch effect correction and is now 0.533288436567017 .
2026-03-05 21:40:20.647068 INFO::ASW Label was 0.411573096854757 prior to batch effect correction and is now 0.411573096854757 .
2026-03-05 21:40:20.647984 INFO::Total function execution time is 0.282902479171753 s and adjustment time is 0.27008318901062 s ( 95.47 )
2026-03-05 21:40:20.716238 INFO::Formatting Data.
2026-03-05 21:40:20.717156 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:20.718183 INFO::Removing potential empty rows and columns
2026-03-05 21:40:20.719281 INFO::Found 0 missing values.
2026-03-05 21:40:20.723574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:20.724137 INFO::Done
2026-03-05 21:40:20.724672 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:20.72785 INFO::Starting hierarchical adjustment
2026-03-05 21:40:20.728618 INFO::Found 5 batches.
2026-03-05 21:40:20.729152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:20.729806 INFO::Using default BPPARAM
2026-03-05 21:40:20.730344 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:20.884562 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:20.88647 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:20.904895 INFO::Done
2026-03-05 21:40:20.90574 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:20.909845 INFO::ASW Batch was 0.31547894201836 prior to batch effect correction and is now -0.0389356071451842 .
2026-03-05 21:40:20.91058 INFO::ASW Label was 0.346339395907752 prior to batch effect correction and is now 0.82095076378866 .
2026-03-05 21:40:20.911471 INFO::Total function execution time is 0.195345878601074 s and adjustment time is 0.176392555236816 s ( 90.3 )
2026-03-05 21:40:20.912362 INFO::Formatting Data.
2026-03-05 21:40:20.913041 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:20.913998 INFO::Removing potential empty rows and columns
2026-03-05 21:40:20.915117 INFO::Found 0 missing values.
2026-03-05 21:40:20.920002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:20.920615 INFO::Done
2026-03-05 21:40:20.921176 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:20.924549 INFO::Starting hierarchical adjustment
2026-03-05 21:40:20.925323 INFO::Found 5 batches.
2026-03-05 21:40:20.925888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:20.92655 INFO::Using default BPPARAM
2026-03-05 21:40:20.927105 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:21.062239 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:21.064893 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:21.093991 INFO::Done
2026-03-05 21:40:21.095421 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:21.101401 INFO::ASW Batch was 0.31547894201836 prior to batch effect correction and is now -0.0389356071451842 .
2026-03-05 21:40:21.10248 INFO::ASW Label was 0.346339395907752 prior to batch effect correction and is now 0.82095076378866 .
2026-03-05 21:40:21.103932 INFO::Total function execution time is 0.191440582275391 s and adjustment time is 0.168639898300171 s ( 88.09 )
2026-03-05 21:40:21.129566 INFO::Formatting Data.
2026-03-05 21:40:21.131051 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:21.132783 INFO::Removing potential empty rows and columns
2026-03-05 21:40:21.13456 INFO::Found 0 missing values.
2026-03-05 21:40:21.141666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:21.14259 INFO::Done
2026-03-05 21:40:21.143458 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:21.148581 INFO::Starting hierarchical adjustment
2026-03-05 21:40:21.149742 INFO::Found 5 batches.
2026-03-05 21:40:21.150588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:21.151621 INFO::Using default BPPARAM
2026-03-05 21:40:21.152539 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:21.313308 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:21.315312 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:21.332274 INFO::Done
2026-03-05 21:40:21.333063 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:21.336733 INFO::ASW Batch was 0.579547079473883 prior to batch effect correction and is now -0.0251552062213297 .
2026-03-05 21:40:21.337371 INFO::ASW Label was 0.189912271804202 prior to batch effect correction and is now 0.752933826650242 .
2026-03-05 21:40:21.338208 INFO::Total function execution time is 0.209011077880859 s and adjustment time is 0.182806253433228 s ( 87.46 )
2026-03-05 21:40:21.339081 INFO::Formatting Data.
2026-03-05 21:40:21.339739 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:21.340673 INFO::Removing potential empty rows and columns
2026-03-05 21:40:21.341815 INFO::Found 0 missing values.
2026-03-05 21:40:21.346125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:21.346706 INFO::Done
2026-03-05 21:40:21.347271 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:21.350381 INFO::Starting hierarchical adjustment
2026-03-05 21:40:21.351178 INFO::Found 5 batches.
2026-03-05 21:40:21.35174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:21.352379 INFO::Using default BPPARAM
2026-03-05 21:40:21.352928 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:21.485917 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:21.48796 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:21.507182 INFO::Done
2026-03-05 21:40:21.50815 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:21.512631 INFO::ASW Batch was 0.579547079473883 prior to batch effect correction and is now -0.0251552062213297 .
2026-03-05 21:40:21.513311 INFO::ASW Label was 0.189912271804202 prior to batch effect correction and is now 0.752933826650242 .
2026-03-05 21:40:21.514269 INFO::Total function execution time is 0.175176620483398 s and adjustment time is 0.156073093414307 s ( 89.09 )
2026-03-05 21:40:21.529863 INFO::Formatting Data.
2026-03-05 21:40:21.530769 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:21.531837 INFO::Removing potential empty rows and columns
2026-03-05 21:40:21.53297 INFO::Found 0 missing values.
2026-03-05 21:40:21.535946 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:21.536524 INFO::Done
2026-03-05 21:40:21.537079 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:21.540332 INFO::Starting hierarchical adjustment
2026-03-05 21:40:21.541107 INFO::Found 2 batches.
2026-03-05 21:40:21.541684 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:21.542341 INFO::Using default BPPARAM
2026-03-05 21:40:21.542909 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:21.54388 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:21.560531 INFO::Done
2026-03-05 21:40:21.561288 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:21.564838 INFO::ASW Batch was 0.680861797616679 prior to batch effect correction and is now 0.136265075507366 .
2026-03-05 21:40:21.565543 INFO::ASW Label was 0.398287223155671 prior to batch effect correction and is now 0.822232861474221 .
2026-03-05 21:40:21.566443 INFO::Total function execution time is 0.0367045402526855 s and adjustment time is 0.0195491313934326 s ( 53.26 )
2026-03-05 21:40:21.567378 INFO::Formatting Data.
2026-03-05 21:40:21.568063 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:21.569044 INFO::Removing potential empty rows and columns
2026-03-05 21:40:21.570201 INFO::Found 0 missing values.
2026-03-05 21:40:21.573298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:21.573922 INFO::Done
2026-03-05 21:40:21.574514 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:21.578079 INFO::Starting hierarchical adjustment
2026-03-05 21:40:21.578876 INFO::Found 2 batches.
2026-03-05 21:40:21.579459 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:21.591946 INFO::Using default BPPARAM
2026-03-05 21:40:21.592867 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:21.594491 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 21:40:21.617831 INFO::Done
2026-03-05 21:40:21.618892 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:21.6238 INFO::ASW Batch was 0.680861797616679 prior to batch effect correction and is now 0.136265075507366 .
2026-03-05 21:40:21.624713 INFO::ASW Label was 0.398287223155671 prior to batch effect correction and is now 0.822232861474221 .
2026-03-05 21:40:21.625859 INFO::Total function execution time is 0.0584433078765869 s and adjustment time is 0.0390362739562988 s ( 66.79 )
2026-03-05 21:40:21.644525 INFO::Formatting Data.
2026-03-05 21:40:21.64563 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:21.646876 INFO::Removing potential empty rows and columns
2026-03-05 21:40:21.64817 INFO::Found 0 missing values.
2026-03-05 21:40:21.651235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:21.65201 INFO::Done
2026-03-05 21:40:21.652755 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:21.65557 INFO::Starting hierarchical adjustment
2026-03-05 21:40:21.65656 INFO::Found 2 batches.
2026-03-05 21:40:21.657259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:21.658089 INFO::Using default BPPARAM
2026-03-05 21:40:21.658803 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:21.660049 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 21:40:21.704399 INFO::Done
2026-03-05 21:40:21.705905 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:21.708824 INFO::ASW Batch was -0.0975686394909658 prior to batch effect correction and is now -0.135926682709383 .
2026-03-05 21:40:21.709995 INFO::Total function execution time is 0.0656380653381348 s and adjustment time is 0.0479896068572998 s ( 73.11 )
2026-03-05 21:40:21.728626 INFO::Formatting Data.
2026-03-05 21:40:21.729713 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:21.73094 INFO::Removing potential empty rows and columns
2026-03-05 21:40:21.732401 INFO::Found 0 missing values.
2026-03-05 21:40:21.734191 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-05 21:40:21.741554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:21.742298 INFO::Done
2026-03-05 21:40:21.742963 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:21.746991 INFO::Starting hierarchical adjustment
2026-03-05 21:40:21.74791 INFO::Found 2 batches.
2026-03-05 21:40:21.748606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:21.749383 INFO::Using default BPPARAM
2026-03-05 21:40:21.750098 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:21.75126 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 21:40:21.775246 INFO::Done
2026-03-05 21:40:21.776235 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:21.780853 INFO::ASW Batch was 0.42810849482301 prior to batch effect correction and is now 0.190577909780928 .
2026-03-05 21:40:21.781655 INFO::ASW Label was 0.567232262012353 prior to batch effect correction and is now 0.731698037987458 .
2026-03-05 21:40:21.782684 INFO::Total function execution time is 0.054243803024292 s and adjustment time is 0.0275003910064697 s ( 50.7 )
2026-03-05 21:40:21.783736 INFO::Formatting Data.
2026-03-05 21:40:21.784549 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:21.785734 INFO::Removing potential empty rows and columns
2026-03-05 21:40:21.786988 INFO::Found 0 missing values.
2026-03-05 21:40:21.788153 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-05 21:40:21.794081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:21.794784 INFO::Done
2026-03-05 21:40:21.795443 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:21.799525 INFO::Starting hierarchical adjustment
2026-03-05 21:40:21.800386 INFO::Found 2 batches.
2026-03-05 21:40:21.801049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:21.801854 INFO::Using default BPPARAM
2026-03-05 21:40:21.802483 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:21.803678 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 21:40:21.825239 INFO::Done
2026-03-05 21:40:21.826111 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:21.830242 INFO::ASW Batch was 0.42810849482301 prior to batch effect correction and is now 0.190577909780928 .
2026-03-05 21:40:21.830985 INFO::ASW Label was 0.567232262012353 prior to batch effect correction and is now 0.731698037987458 .
2026-03-05 21:40:21.831984 INFO::Total function execution time is 0.0483038425445557 s and adjustment time is 0.0249755382537842 s ( 51.71 )
2026-03-05 21:40:22.100166 INFO::Formatting Data.
2026-03-05 21:40:22.101145 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:22.102182 INFO::Removing potential empty rows and columns
2026-03-05 21:40:22.103304 INFO::Found 0 missing values.
2026-03-05 21:40:22.106554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:22.107104 INFO::Done
2026-03-05 21:40:22.10766 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:22.109927 INFO::Starting hierarchical adjustment
2026-03-05 21:40:22.110682 INFO::Found 3 batches.
2026-03-05 21:40:22.111205 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:22.111846 INFO::Using default BPPARAM
2026-03-05 21:40:22.112415 INFO::Processing subtree level 1
2026-03-05 21:40:22.210404 INFO::Adjusting the last 1 batches sequentially
2026-03-05 21:40:22.212356 INFO::Done
2026-03-05 21:40:22.213066 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:22.215787 INFO::ASW Batch was -0.0204415055098049 prior to batch effect correction and is now -0.0204415055098049 .
2026-03-05 21:40:22.216797 INFO::Total function execution time is 0.116770029067993 s and adjustment time is 0.101814746856689 s ( 87.19 )
2026-03-05 21:40:22.217931 INFO::Formatting Data.
2026-03-05 21:40:22.218613 INFO::Typecasting input to dataframe.
2026-03-05 21:40:22.219426 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:22.220421 INFO::Removing potential empty rows and columns
2026-03-05 21:40:22.221588 INFO::Found 0 missing values.
2026-03-05 21:40:22.224891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:22.225451 INFO::Done
2026-03-05 21:40:22.226 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:22.228274 INFO::Starting hierarchical adjustment
2026-03-05 21:40:22.229013 INFO::Found 3 batches.
2026-03-05 21:40:22.229606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:22.230245 INFO::Using default BPPARAM
2026-03-05 21:40:22.230807 INFO::Processing subtree level 1
2026-03-05 21:40:22.325466 INFO::Adjusting the last 1 batches sequentially
2026-03-05 21:40:22.327485 INFO::Done
2026-03-05 21:40:22.328262 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:22.33105 INFO::ASW Batch was -0.0204415055098049 prior to batch effect correction and is now -0.0204415055098049 .
2026-03-05 21:40:22.332095 INFO::Total function execution time is 0.114151239395142 s and adjustment time is 0.0985767841339111 s ( 86.36 )
2026-03-05 21:40:22.346897 INFO::Formatting Data.
2026-03-05 21:40:22.347948 INFO::Typecasting input to dataframe.
2026-03-05 21:40:22.348945 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:22.349991 INFO::Removing potential empty rows and columns
2026-03-05 21:40:22.35115 INFO::Found 0 missing values.
2026-03-05 21:40:22.354452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:22.355165 INFO::Done
2026-03-05 21:40:22.355711 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:22.357972 INFO::Starting hierarchical adjustment
2026-03-05 21:40:22.358709 INFO::Found 3 batches.
2026-03-05 21:40:22.359249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:22.359899 INFO::Using default BPPARAM
2026-03-05 21:40:22.360441 INFO::Processing subtree level 1
2026-03-05 21:40:22.455152 INFO::Adjusting the last 1 batches sequentially
2026-03-05 21:40:22.457253 INFO::Done
2026-03-05 21:40:22.457999 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:22.460864 INFO::ASW Batch was -0.0546679347280503 prior to batch effect correction and is now -0.0546679347280503 .
2026-03-05 21:40:22.461872 INFO::Total function execution time is 0.115098237991333 s and adjustment time is 0.0986640453338623 s ( 85.72 )
2026-03-05 21:40:22.619868 INFO::Formatting Data.
2026-03-05 21:40:22.620973 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:22.622352 INFO::Removing potential empty rows and columns
2026-03-05 21:40:22.625412 INFO::Found 1000 missing values.
2026-03-05 21:40:22.645794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:22.646734 INFO::Done
2026-03-05 21:40:22.647383 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:22.653561 INFO::Starting hierarchical adjustment
2026-03-05 21:40:22.654412 INFO::Found 10 batches.
2026-03-05 21:40:22.654992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:22.655672 INFO::Using default BPPARAM
2026-03-05 21:40:22.656239 INFO::Processing subtree level 1
2026-03-05 21:40:22.795755 INFO::Processing subtree level 2
2026-03-05 21:40:22.949902 INFO::Adjusting the last 1 batches sequentially
2026-03-05 21:40:22.952231 INFO::Done
2026-03-05 21:40:22.953008 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:22.959019 INFO::ASW Batch was 0.530739230178899 prior to batch effect correction and is now 0.530739230178899 .
2026-03-05 21:40:22.959832 INFO::ASW Label was 0.301890039010376 prior to batch effect correction and is now 0.301890039010376 .
2026-03-05 21:40:22.960844 INFO::Total function execution time is 0.341182470321655 s and adjustment time is 0.297950029373169 s ( 87.33 )
2026-03-05 21:40:22.961759 INFO::Formatting Data.
2026-03-05 21:40:22.962442 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:22.963806 INFO::Removing potential empty rows and columns
2026-03-05 21:40:22.966697 INFO::Found 1000 missing values.
2026-03-05 21:40:22.986496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:22.987372 INFO::Done
2026-03-05 21:40:22.987991 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:22.993811 INFO::Starting hierarchical adjustment
2026-03-05 21:40:22.994647 INFO::Found 10 batches.
2026-03-05 21:40:24.488731 INFO::Set up parallel execution backend with 2 workers
2026-03-05 21:40:24.4919 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-05 21:40:25.825576 INFO::Adjusting the last 2 batches sequentially
2026-03-05 21:40:25.827728 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 21:40:25.844938 INFO::Done
2026-03-05 21:40:25.845701 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:25.85066 INFO::ASW Batch was 0.530739230178899 prior to batch effect correction and is now 0.530739230178899 .
2026-03-05 21:40:25.851312 INFO::ASW Label was 0.301890039010376 prior to batch effect correction and is now 0.301890039010376 .
2026-03-05 21:40:25.852109 INFO::Total function execution time is 2.89039635658264 s and adjustment time is 2.850430727005 s ( 98.62 )
2026-03-05 21:40:26.014979 INFO::Formatting Data.
2026-03-05 21:40:26.015991 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.017029 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.018186 INFO::Found 0 missing values.
2026-03-05 21:40:26.021941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.022499 INFO::Done
2026-03-05 21:40:26.02304 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 21:40:26.026057 INFO::Starting hierarchical adjustment
2026-03-05 21:40:26.026798 INFO::Found 3 batches.
2026-03-05 21:40:26.027333 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 21:40:26.027975 INFO::Using default BPPARAM
2026-03-05 21:40:26.028519 INFO::Processing subtree level 1
2026-03-05 21:40:26.146983 INFO::Adjusting the last 1 batches sequentially
2026-03-05 21:40:26.149067 INFO::Done
2026-03-05 21:40:26.14982 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 21:40:26.153371 INFO::ASW Batch was 0.148652396352898 prior to batch effect correction and is now -0.173084579091194 .
2026-03-05 21:40:26.154047 INFO::ASW Label was -0.19518014973987 prior to batch effect correction and is now -0.0992803257359551 .
2026-03-05 21:40:26.155084 INFO::Total function execution time is 0.140233039855957 s and adjustment time is 0.122384548187256 s ( 87.27 )
2026-03-05 21:40:26.280635 INFO::Formatting Data.
2026-03-05 21:40:26.28159 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.2826 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.283726 INFO::Found 2 missing values.
2026-03-05 21:40:26.286723 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.287278 INFO::Done
2026-03-05 21:40:26.316993 INFO::Found NA in Reference column
2026-03-05 21:40:26.327115 INFO::Require at least two references per batch.
2026-03-05 21:40:26.348467 INFO::Formatting Data.
2026-03-05 21:40:26.349336 INFO::Recognized SummarizedExperiment
2026-03-05 21:40:26.349912 INFO::Typecasting input to dataframe.
2026-03-05 21:40:26.360155 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.361466 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.364928 INFO::Found 0 missing values.
2026-03-05 21:40:26.371476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.37217 INFO::Done
2026-03-05 21:40:26.388056 INFO::Formatting Data.
2026-03-05 21:40:26.388856 INFO::Recognized SummarizedExperiment
2026-03-05 21:40:26.389362 INFO::Typecasting input to dataframe.
2026-03-05 21:40:26.40743 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.408792 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.412277 INFO::Found 0 missing values.
2026-03-05 21:40:26.422802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.423574 INFO::Done
2026-03-05 21:40:26.43971 INFO::Formatting Data.
2026-03-05 21:40:26.440493 INFO::Recognized SummarizedExperiment
2026-03-05 21:40:26.441008 INFO::Typecasting input to dataframe.
2026-03-05 21:40:26.457535 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.458637 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.459714 INFO::Found 0 missing values.
2026-03-05 21:40:26.460626 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-05 21:40:26.464844 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.465371 INFO::Done
2026-03-05 21:40:26.475556 INFO::Formatting Data.
2026-03-05 21:40:26.476312 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.477233 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.478202 INFO::Found 0 missing values.
2026-03-05 21:40:26.480977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.481486 INFO::Done
2026-03-05 21:40:26.492872 INFO::Formatting Data.
2026-03-05 21:40:26.493749 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.494751 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.49578 INFO::Found 0 missing values.
2026-03-05 21:40:26.498636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.499157 INFO::Done
2026-03-05 21:40:26.531096 INFO::Formatting Data.
2026-03-05 21:40:26.532186 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.533381 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.534613 INFO::Found 1 missing values.
2026-03-05 21:40:26.537347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.537884 INFO::Done
2026-03-05 21:40:26.559056 INFO::Formatting Data.
2026-03-05 21:40:26.559988 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.560939 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.561957 INFO::Found 2 missing values.
2026-03-05 21:40:26.562903 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-05 21:40:26.56524 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.565785 INFO::Done
2026-03-05 21:40:26.576928 INFO::Formatting Data.
2026-03-05 21:40:26.577807 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.578749 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.579716 INFO::Found 2 missing values.
2026-03-05 21:40:26.581415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.581942 INFO::Done
2026-03-05 21:40:26.592951 INFO::Formatting Data.
2026-03-05 21:40:26.593783 INFO::Typecasting input to dataframe.
2026-03-05 21:40:26.594619 INFO::Replacing NaNs with NAs.
2026-03-05 21:40:26.595473 INFO::Removing potential empty rows and columns
2026-03-05 21:40:26.612708 INFO::Found 0 missing values.
2026-03-05 21:40:26.617404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 21:40:26.618074 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.697 3.972 21.278
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.491 | 1.498 | 18.133 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.003 | 0.015 | |
| generate_data_covariables | 0.011 | 0.002 | 0.013 | |
| generate_dataset | 0.010 | 0.003 | 0.013 | |