Yannis Schumann
| Snapshot Date: 2026-01-22 13:45 -0500 (Thu, 22 Jan 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 2026-01-26 11:57 -0500 (Mon, 26 Jan 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" | 4886 |
| 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 | | ||||||||
|
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: 2026-01-22 21:31:35 -0500 (Thu, 22 Jan 2026) |
| EndedAt: 2026-01-22 21:33:02 -0500 (Thu, 22 Jan 2026) |
| EllapsedTime: 87.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.065 1.137 16.436
* 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")
2026-01-22 21:32:24.434753 INFO::Formatting Data.
2026-01-22 21:32:24.435938 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:24.446357 INFO::Removing potential empty rows and columns
2026-01-22 21:32:24.681104 INFO::Found 0 missing values.
2026-01-22 21:32:24.684332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:24.684956 INFO::Done
2026-01-22 21:32:24.685479 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:24.69622 INFO::Starting hierarchical adjustment
2026-01-22 21:32:24.697026 INFO::Found 3 batches.
2026-01-22 21:32:24.697566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:24.69866 INFO::Using default BPPARAM
2026-01-22 21:32:24.699182 INFO::Processing subtree level 1
2026-01-22 21:32:24.799467 INFO::Adjusting the last 1 batches sequentially
2026-01-22 21:32:24.801384 INFO::Done
2026-01-22 21:32:24.802098 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:24.804738 INFO::ASW Batch was 0.1262547476884 prior to batch effect correction and is now 0.1262547476884 .
2026-01-22 21:32:24.805857 INFO::Total function execution time is 0.371644020080566 s and adjustment time is 0.104502439498901 s ( 28.12 )
2026-01-22 21:32:24.81968 INFO::Formatting Data.
2026-01-22 21:32:24.820486 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:24.821447 INFO::Removing potential empty rows and columns
2026-01-22 21:32:24.822614 INFO::Found 0 missing values.
2026-01-22 21:32:24.823585 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.
2026-01-22 21:32:24.834632 INFO::Formatting Data.
2026-01-22 21:32:24.835397 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:24.836314 INFO::Removing potential empty rows and columns
2026-01-22 21:32:24.837337 INFO::Found 0 missing values.
2026-01-22 21:32:24.838291 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.
2026-01-22 21:32:24.854599 INFO::Formatting Data.
2026-01-22 21:32:24.8554 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:24.856313 INFO::Removing potential empty rows and columns
2026-01-22 21:32:24.857405 INFO::Found 0 missing values.
2026-01-22 21:32:24.858351 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.
2026-01-22 21:32:24.862873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:24.863446 INFO::Done
2026-01-22 21:32:24.863981 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:24.866206 INFO::Starting hierarchical adjustment
2026-01-22 21:32:24.866952 INFO::Found 2 batches.
2026-01-22 21:32:24.867481 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:24.868243 INFO::Using default BPPARAM
2026-01-22 21:32:24.868793 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:24.869736 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-22 21:32:24.890993 INFO::Done
2026-01-22 21:32:24.891736 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:24.893903 INFO::ASW Batch was -0.0398177162049229 prior to batch effect correction and is now -0.118845452778188 .
2026-01-22 21:32:24.894811 INFO::Total function execution time is 0.0403110980987549 s and adjustment time is 0.0241653919219971 s ( 59.95 )
2026-01-22 21:32:24.89774 INFO::Formatting Data.
2026-01-22 21:32:24.898375 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:24.907372 INFO::Formatting Data.
2026-01-22 21:32:24.90813 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:24.90903 INFO::Removing potential empty rows and columns
2026-01-22 21:32:24.91008 INFO::Found 0 missing values.
2026-01-22 21:32:24.913064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:24.913629 INFO::Done
2026-01-22 21:32:24.914152 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:24.938441 INFO::Starting hierarchical adjustment
2026-01-22 21:32:24.94116 INFO::Found 2 batches.
2026-01-22 21:32:24.941755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:24.942307 INFO::Using default BPPARAM
2026-01-22 21:32:24.94281 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:24.943691 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-22 21:32:24.957842 INFO::Done
2026-01-22 21:32:24.958551 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:24.960581 INFO::ASW Batch was -0.0684504471684895 prior to batch effect correction and is now -0.120300227609833 .
2026-01-22 21:32:24.961354 INFO::Total function execution time is 0.0540375709533691 s and adjustment time is 0.0168561935424805 s ( 31.19 )
2026-01-22 21:32:24.962383 INFO::Formatting Data.
2026-01-22 21:32:24.962967 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:24.963806 INFO::Removing potential empty rows and columns
2026-01-22 21:32:24.964774 INFO::Found 0 missing values.
2026-01-22 21:32:24.967434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:24.967962 INFO::Done
2026-01-22 21:32:24.968445 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:24.970381 INFO::Starting hierarchical adjustment
2026-01-22 21:32:24.971068 INFO::Found 2 batches.
2026-01-22 21:32:24.971554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:24.972116 INFO::Using default BPPARAM
2026-01-22 21:32:24.972612 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:24.973455 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-22 21:32:24.98742 INFO::Done
2026-01-22 21:32:24.988093 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:24.990024 INFO::ASW Batch was -0.0684504471684895 prior to batch effect correction and is now -0.120300227609833 .
2026-01-22 21:32:24.990788 INFO::Total function execution time is 0.0284051895141602 s and adjustment time is 0.0164616107940674 s ( 57.95 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-22 21:32:27.828154 INFO::Formatting Data.
2026-01-22 21:32:27.828831 INFO::Recognized SummarizedExperiment
2026-01-22 21:32:27.8293 INFO::Typecasting input to dataframe.
2026-01-22 21:32:27.858611 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:27.859846 INFO::Removing potential empty rows and columns
2026-01-22 21:32:27.863668 INFO::Found 0 missing values.
2026-01-22 21:32:27.871248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:27.871982 INFO::Done
2026-01-22 21:32:27.872537 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:27.876218 INFO::Starting hierarchical adjustment
2026-01-22 21:32:27.876989 INFO::Found 2 batches.
2026-01-22 21:32:27.87752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:27.878602 INFO::Using default BPPARAM
2026-01-22 21:32:27.879136 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:27.880112 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-22 21:32:27.938301 INFO::Done
2026-01-22 21:32:27.939116 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:27.942952 INFO::ASW Batch was 0.0255930363232799 prior to batch effect correction and is now -0.0908650089819562 .
2026-01-22 21:32:27.943917 INFO::Total function execution time is 0.116006851196289 s and adjustment time is 0.0614080429077148 s ( 52.93 )
Warning: stack imbalance in '{', 73 then 75
2026-01-22 21:32:27.963551 INFO::Formatting Data.
2026-01-22 21:32:27.964348 INFO::Recognized SummarizedExperiment
2026-01-22 21:32:27.964928 INFO::Typecasting input to dataframe.
2026-01-22 21:32:27.975028 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:27.976381 INFO::Removing potential empty rows and columns
2026-01-22 21:32:27.980229 INFO::Found 0 missing values.
2026-01-22 21:32:27.987601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:27.988326 INFO::Done
2026-01-22 21:32:27.988878 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:27.992598 INFO::Starting hierarchical adjustment
2026-01-22 21:32:27.993425 INFO::Found 2 batches.
2026-01-22 21:32:27.993972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:27.994593 INFO::Using default BPPARAM
2026-01-22 21:32:27.995109 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:27.996154 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-22 21:32:28.021986 INFO::Done
2026-01-22 21:32:28.022749 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:28.026401 INFO::ASW Batch was -0.0237466180591873 prior to batch effect correction and is now -0.0237466180591873 .
2026-01-22 21:32:28.027306 INFO::Total function execution time is 0.0637664794921875 s and adjustment time is 0.0286972522735596 s ( 45 )
2026-01-22 21:32:28.047188 INFO::Formatting Data.
2026-01-22 21:32:28.048104 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:28.04918 INFO::Removing potential empty rows and columns
2026-01-22 21:32:28.050347 INFO::Found 0 missing values.
2026-01-22 21:32:28.053592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:28.054148 INFO::Done
2026-01-22 21:32:28.054693 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:28.05699 INFO::Starting hierarchical adjustment
2026-01-22 21:32:28.057813 INFO::Found 3 batches.
2026-01-22 21:32:28.058352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:28.058973 INFO::Using default BPPARAM
2026-01-22 21:32:28.05949 INFO::Processing subtree level 1
2026-01-22 21:32:28.204902 INFO::Adjusting the last 1 batches sequentially
2026-01-22 21:32:28.207373 INFO::Done
2026-01-22 21:32:28.20817 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:28.211266 INFO::ASW Batch was -0.0769738403729612 prior to batch effect correction and is now -0.155317918329684 .
2026-01-22 21:32:28.212325 INFO::Total function execution time is 0.165189981460571 s and adjustment time is 0.149689674377441 s ( 90.62 )
2026-01-22 21:32:28.22987 INFO::Skipping initial DF formatting
2026-01-22 21:32:28.230669 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:28.235081 INFO::Starting hierarchical adjustment
2026-01-22 21:32:28.235913 INFO::Found 5 batches.
2026-01-22 21:32:28.236468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:28.23712 INFO::Using default BPPARAM
2026-01-22 21:32:28.237844 INFO::Processing subtree level 1
2026-01-22 21:32:28.498357 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:28.500158 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-22 21:32:28.519852 INFO::Done
2026-01-22 21:32:28.52063 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:28.525136 INFO::ASW Batch was 0.561711776116095 prior to batch effect correction and is now 0.561711776116095 .
2026-01-22 21:32:28.525777 INFO::ASW Label was 0.40184182245479 prior to batch effect correction and is now 0.40184182245479 .
2026-01-22 21:32:28.526682 INFO::Total function execution time is 0.296925067901611 s and adjustment time is 0.284104824066162 s ( 95.68 )
2026-01-22 21:32:28.590425 INFO::Formatting Data.
2026-01-22 21:32:28.591323 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:28.592279 INFO::Removing potential empty rows and columns
2026-01-22 21:32:28.593332 INFO::Found 0 missing values.
2026-01-22 21:32:28.597461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:28.598026 INFO::Done
2026-01-22 21:32:28.59856 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:28.601916 INFO::Starting hierarchical adjustment
2026-01-22 21:32:28.60269 INFO::Found 5 batches.
2026-01-22 21:32:28.603223 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:28.603868 INFO::Using default BPPARAM
2026-01-22 21:32:28.604405 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.
2026-01-22 21:32:28.746663 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:28.74864 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-22 21:32:28.768303 INFO::Done
2026-01-22 21:32:28.769269 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:28.773421 INFO::ASW Batch was 0.479348527955517 prior to batch effect correction and is now -0.0805550854412914 .
2026-01-22 21:32:28.774145 INFO::ASW Label was 0.281520274433608 prior to batch effect correction and is now 0.788730174653364 .
2026-01-22 21:32:28.775099 INFO::Total function execution time is 0.184782743453979 s and adjustment time is 0.165707588195801 s ( 89.68 )
2026-01-22 21:32:28.776057 INFO::Formatting Data.
2026-01-22 21:32:28.776788 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:28.777845 INFO::Removing potential empty rows and columns
2026-01-22 21:32:28.779044 INFO::Found 0 missing values.
2026-01-22 21:32:28.783907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:28.784583 INFO::Done
2026-01-22 21:32:28.785185 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:28.788804 INFO::Starting hierarchical adjustment
2026-01-22 21:32:28.789632 INFO::Found 5 batches.
2026-01-22 21:32:28.790229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:28.790935 INFO::Using default BPPARAM
2026-01-22 21:32:28.791522 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.
2026-01-22 21:32:28.934753 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:28.936735 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-22 21:32:28.954984 INFO::Done
2026-01-22 21:32:28.955775 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:28.959541 INFO::ASW Batch was 0.479348527955517 prior to batch effect correction and is now -0.0805550854412914 .
2026-01-22 21:32:28.960211 INFO::ASW Label was 0.281520274433608 prior to batch effect correction and is now 0.788730174653364 .
2026-01-22 21:32:28.961118 INFO::Total function execution time is 0.185064315795898 s and adjustment time is 0.165513277053833 s ( 89.44 )
2026-01-22 21:32:28.976646 INFO::Formatting Data.
2026-01-22 21:32:28.977533 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:28.978608 INFO::Removing potential empty rows and columns
2026-01-22 21:32:28.979804 INFO::Found 0 missing values.
2026-01-22 21:32:28.984254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:28.984844 INFO::Done
2026-01-22 21:32:28.985378 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:28.988639 INFO::Starting hierarchical adjustment
2026-01-22 21:32:28.989365 INFO::Found 5 batches.
2026-01-22 21:32:28.989912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:28.990588 INFO::Using default BPPARAM
2026-01-22 21:32:28.991177 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.
2026-01-22 21:32:29.131978 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:29.133924 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-22 21:32:29.152397 INFO::Done
2026-01-22 21:32:29.153288 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:29.157127 INFO::ASW Batch was 0.460291018520645 prior to batch effect correction and is now -0.053237973962927 .
2026-01-22 21:32:29.157808 INFO::ASW Label was 0.234974346206549 prior to batch effect correction and is now 0.82547622212826 .
2026-01-22 21:32:29.158729 INFO::Total function execution time is 0.182162523269653 s and adjustment time is 0.163124561309814 s ( 89.55 )
2026-01-22 21:32:29.159687 INFO::Formatting Data.
2026-01-22 21:32:29.160385 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:29.161374 INFO::Removing potential empty rows and columns
2026-01-22 21:32:29.16261 INFO::Found 0 missing values.
2026-01-22 21:32:29.167549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:29.168235 INFO::Done
2026-01-22 21:32:29.168869 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:29.172639 INFO::Starting hierarchical adjustment
2026-01-22 21:32:29.173494 INFO::Found 5 batches.
2026-01-22 21:32:29.174108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:29.174862 INFO::Using default BPPARAM
2026-01-22 21:32:29.175487 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.
2026-01-22 21:32:29.320443 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:29.322297 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-22 21:32:29.339435 INFO::Done
2026-01-22 21:32:29.340209 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:29.344065 INFO::ASW Batch was 0.460291018520645 prior to batch effect correction and is now -0.053237973962927 .
2026-01-22 21:32:29.344682 INFO::ASW Label was 0.234974346206549 prior to batch effect correction and is now 0.82547622212826 .
2026-01-22 21:32:29.345469 INFO::Total function execution time is 0.18582010269165 s and adjustment time is 0.16612696647644 s ( 89.4 )
2026-01-22 21:32:29.359264 INFO::Formatting Data.
2026-01-22 21:32:29.360041 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:29.36096 INFO::Removing potential empty rows and columns
2026-01-22 21:32:29.362015 INFO::Found 0 missing values.
2026-01-22 21:32:29.364827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:29.365369 INFO::Done
2026-01-22 21:32:29.365901 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:29.36884 INFO::Starting hierarchical adjustment
2026-01-22 21:32:29.369551 INFO::Found 2 batches.
2026-01-22 21:32:29.370067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:29.370692 INFO::Using default BPPARAM
2026-01-22 21:32:29.3712 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:29.372092 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-22 21:32:29.386776 INFO::Done
2026-01-22 21:32:29.387424 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:29.390311 INFO::ASW Batch was 0.636677210392682 prior to batch effect correction and is now -0.00564158944731991 .
2026-01-22 21:32:29.390928 INFO::ASW Label was 0.38090308108501 prior to batch effect correction and is now 0.896853271923073 .
2026-01-22 21:32:29.391705 INFO::Total function execution time is 0.0325226783752441 s and adjustment time is 0.0173804759979248 s ( 53.44 )
2026-01-22 21:32:29.392503 INFO::Formatting Data.
2026-01-22 21:32:29.393151 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:29.394041 INFO::Removing potential empty rows and columns
2026-01-22 21:32:29.395075 INFO::Found 0 missing values.
2026-01-22 21:32:29.397846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:29.398382 INFO::Done
2026-01-22 21:32:29.398912 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:29.401925 INFO::Starting hierarchical adjustment
2026-01-22 21:32:29.40264 INFO::Found 2 batches.
2026-01-22 21:32:29.403178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:29.403801 INFO::Using default BPPARAM
2026-01-22 21:32:29.404317 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:29.405219 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-22 21:32:29.41991 INFO::Done
2026-01-22 21:32:29.420626 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:29.42368 INFO::ASW Batch was 0.636677210392682 prior to batch effect correction and is now -0.00564158944731991 .
2026-01-22 21:32:29.424301 INFO::ASW Label was 0.38090308108501 prior to batch effect correction and is now 0.896853271923073 .
2026-01-22 21:32:29.425129 INFO::Total function execution time is 0.0326309204101562 s and adjustment time is 0.0174098014831543 s ( 53.35 )
2026-01-22 21:32:29.436784 INFO::Formatting Data.
2026-01-22 21:32:29.43747 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:29.438309 INFO::Removing potential empty rows and columns
2026-01-22 21:32:29.439178 INFO::Found 0 missing values.
2026-01-22 21:32:29.441211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:29.441744 INFO::Done
2026-01-22 21:32:29.442247 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:29.444144 INFO::Starting hierarchical adjustment
2026-01-22 21:32:29.444834 INFO::Found 2 batches.
2026-01-22 21:32:29.445332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:29.445936 INFO::Using default BPPARAM
2026-01-22 21:32:29.446449 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:29.447316 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-22 21:32:29.477209 INFO::Done
2026-01-22 21:32:29.477897 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:29.479922 INFO::ASW Batch was -0.0892765510141641 prior to batch effect correction and is now -0.179494187571691 .
2026-01-22 21:32:29.48075 INFO::Total function execution time is 0.0440883636474609 s and adjustment time is 0.0324773788452148 s ( 73.66 )
2026-01-22 21:32:29.492563 INFO::Formatting Data.
2026-01-22 21:32:29.493258 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:29.494104 INFO::Removing potential empty rows and columns
2026-01-22 21:32:29.495067 INFO::Found 0 missing values.
2026-01-22 21:32:29.496141 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.
2026-01-22 21:32:29.500488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:29.501026 INFO::Done
2026-01-22 21:32:29.501537 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:29.504486 INFO::Starting hierarchical adjustment
2026-01-22 21:32:29.505195 INFO::Found 2 batches.
2026-01-22 21:32:29.505716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:29.506293 INFO::Using default BPPARAM
2026-01-22 21:32:29.506804 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:29.507711 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-22 21:32:29.523522 INFO::Done
2026-01-22 21:32:29.52417 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:29.527153 INFO::ASW Batch was 0.52423050132168 prior to batch effect correction and is now -0.0347146325606847 .
2026-01-22 21:32:29.527796 INFO::ASW Label was 0.522094088319457 prior to batch effect correction and is now 0.904365155351278 .
2026-01-22 21:32:29.528636 INFO::Total function execution time is 0.0361137390136719 s and adjustment time is 0.0184469223022461 s ( 51.08 )
2026-01-22 21:32:29.529488 INFO::Formatting Data.
2026-01-22 21:32:29.530123 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:29.531021 INFO::Removing potential empty rows and columns
2026-01-22 21:32:29.532029 INFO::Found 0 missing values.
2026-01-22 21:32:29.537497 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.
2026-01-22 21:32:29.542703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:29.543329 INFO::Done
2026-01-22 21:32:29.543928 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:29.54733 INFO::Starting hierarchical adjustment
2026-01-22 21:32:29.548119 INFO::Found 2 batches.
2026-01-22 21:32:29.548743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:29.54941 INFO::Using default BPPARAM
2026-01-22 21:32:29.55002 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:29.551026 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-22 21:32:29.569113 INFO::Done
2026-01-22 21:32:29.569828 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:29.572967 INFO::ASW Batch was 0.52423050132168 prior to batch effect correction and is now -0.0347146325606847 .
2026-01-22 21:32:29.573578 INFO::ASW Label was 0.522094088319457 prior to batch effect correction and is now 0.904365155351278 .
2026-01-22 21:32:29.574455 INFO::Total function execution time is 0.0449771881103516 s and adjustment time is 0.0211384296417236 s ( 47 )
2026-01-22 21:32:29.800611 INFO::Formatting Data.
2026-01-22 21:32:29.801464 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:29.802711 INFO::Removing potential empty rows and columns
2026-01-22 21:32:29.803811 INFO::Found 0 missing values.
2026-01-22 21:32:29.807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:29.80755 INFO::Done
2026-01-22 21:32:29.808076 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:29.810196 INFO::Starting hierarchical adjustment
2026-01-22 21:32:29.810941 INFO::Found 3 batches.
2026-01-22 21:32:29.811467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:29.812073 INFO::Using default BPPARAM
2026-01-22 21:32:29.81261 INFO::Processing subtree level 1
2026-01-22 21:32:29.899297 INFO::Adjusting the last 1 batches sequentially
2026-01-22 21:32:29.901054 INFO::Done
2026-01-22 21:32:29.901704 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:29.904277 INFO::ASW Batch was 0.0669082023393745 prior to batch effect correction and is now 0.0669082023393745 .
2026-01-22 21:32:29.905219 INFO::Total function execution time is 0.104729652404785 s and adjustment time is 0.090254545211792 s ( 86.18 )
2026-01-22 21:32:29.906282 INFO::Formatting Data.
2026-01-22 21:32:29.906935 INFO::Typecasting input to dataframe.
2026-01-22 21:32:29.907739 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:29.908656 INFO::Removing potential empty rows and columns
2026-01-22 21:32:29.909743 INFO::Found 0 missing values.
2026-01-22 21:32:29.912804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:29.913365 INFO::Done
2026-01-22 21:32:29.913908 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:29.916115 INFO::Starting hierarchical adjustment
2026-01-22 21:32:29.91685 INFO::Found 3 batches.
2026-01-22 21:32:29.917372 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:29.918002 INFO::Using default BPPARAM
2026-01-22 21:32:29.91853 INFO::Processing subtree level 1
2026-01-22 21:32:30.002792 INFO::Adjusting the last 1 batches sequentially
2026-01-22 21:32:30.004568 INFO::Done
2026-01-22 21:32:30.005223 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:30.007735 INFO::ASW Batch was 0.0669082023393745 prior to batch effect correction and is now 0.0669082023393745 .
2026-01-22 21:32:30.008691 INFO::Total function execution time is 0.102375984191895 s and adjustment time is 0.0878450870513916 s ( 85.81 )
2026-01-22 21:32:30.021947 INFO::Formatting Data.
2026-01-22 21:32:30.022826 INFO::Typecasting input to dataframe.
2026-01-22 21:32:30.023681 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:30.024591 INFO::Removing potential empty rows and columns
2026-01-22 21:32:30.025646 INFO::Found 0 missing values.
2026-01-22 21:32:30.028642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:30.029178 INFO::Done
2026-01-22 21:32:30.029707 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:30.031702 INFO::Starting hierarchical adjustment
2026-01-22 21:32:30.032393 INFO::Found 3 batches.
2026-01-22 21:32:30.032973 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:30.033576 INFO::Using default BPPARAM
2026-01-22 21:32:30.034125 INFO::Processing subtree level 1
2026-01-22 21:32:30.117666 INFO::Adjusting the last 1 batches sequentially
2026-01-22 21:32:30.119628 INFO::Done
2026-01-22 21:32:30.120325 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:30.1229 INFO::ASW Batch was -0.0891736343936828 prior to batch effect correction and is now -0.0891736343936828 .
2026-01-22 21:32:30.123911 INFO::Total function execution time is 0.102007150650024 s and adjustment time is 0.0873391628265381 s ( 85.62 )
2026-01-22 21:32:30.260074 INFO::Formatting Data.
2026-01-22 21:32:30.260857 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:30.261966 INFO::Removing potential empty rows and columns
2026-01-22 21:32:30.264727 INFO::Found 1000 missing values.
2026-01-22 21:32:30.283726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:30.284482 INFO::Done
2026-01-22 21:32:30.285038 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:30.290582 INFO::Starting hierarchical adjustment
2026-01-22 21:32:30.291389 INFO::Found 10 batches.
2026-01-22 21:32:30.291948 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:30.292562 INFO::Using default BPPARAM
2026-01-22 21:32:30.293093 INFO::Processing subtree level 1
2026-01-22 21:32:30.424248 INFO::Processing subtree level 2
2026-01-22 21:32:30.569305 INFO::Adjusting the last 1 batches sequentially
2026-01-22 21:32:30.571429 INFO::Done
2026-01-22 21:32:30.57217 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:30.577933 INFO::ASW Batch was 0.505330682236363 prior to batch effect correction and is now 0.505330682236363 .
2026-01-22 21:32:30.578681 INFO::ASW Label was 0.315721191369345 prior to batch effect correction and is now 0.315721191369345 .
2026-01-22 21:32:30.579623 INFO::Total function execution time is 0.319600105285645 s and adjustment time is 0.280182123184204 s ( 87.67 )
2026-01-22 21:32:30.580491 INFO::Formatting Data.
2026-01-22 21:32:30.581168 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:30.582429 INFO::Removing potential empty rows and columns
2026-01-22 21:32:30.585402 INFO::Found 1000 missing values.
2026-01-22 21:32:30.604618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:30.605373 INFO::Done
2026-01-22 21:32:30.605954 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:30.61144 INFO::Starting hierarchical adjustment
2026-01-22 21:32:30.612242 INFO::Found 10 batches.
2026-01-22 21:32:31.776096 INFO::Set up parallel execution backend with 2 workers
2026-01-22 21:32:31.783372 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-22 21:32:32.926377 INFO::Adjusting the last 2 batches sequentially
2026-01-22 21:32:32.92844 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-22 21:32:32.944907 INFO::Done
2026-01-22 21:32:32.94562 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:32.950196 INFO::ASW Batch was 0.505330682236363 prior to batch effect correction and is now 0.505330682236363 .
2026-01-22 21:32:32.950772 INFO::ASW Label was 0.315721191369345 prior to batch effect correction and is now 0.315721191369345 .
2026-01-22 21:32:32.951489 INFO::Total function execution time is 2.37103652954102 s and adjustment time is 2.33278656005859 s ( 98.39 )
2026-01-22 21:32:33.09909 INFO::Formatting Data.
2026-01-22 21:32:33.099974 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.100941 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.102065 INFO::Found 0 missing values.
2026-01-22 21:32:33.105717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.106246 INFO::Done
2026-01-22 21:32:33.106766 INFO::Acquiring quality metrics before batch effect correction.
2026-01-22 21:32:33.1098 INFO::Starting hierarchical adjustment
2026-01-22 21:32:33.110559 INFO::Found 3 batches.
2026-01-22 21:32:33.111099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-22 21:32:33.111726 INFO::Using default BPPARAM
2026-01-22 21:32:33.112236 INFO::Processing subtree level 1
2026-01-22 21:32:33.221848 INFO::Adjusting the last 1 batches sequentially
2026-01-22 21:32:33.22388 INFO::Done
2026-01-22 21:32:33.224627 INFO::Acquiring quality metrics after batch effect correction.
2026-01-22 21:32:33.228166 INFO::ASW Batch was 0.210833552826543 prior to batch effect correction and is now -0.1618109484132 .
2026-01-22 21:32:33.228843 INFO::ASW Label was -0.161962543988711 prior to batch effect correction and is now -0.012726747879455 .
2026-01-22 21:32:33.229793 INFO::Total function execution time is 0.130775213241577 s and adjustment time is 0.113454580307007 s ( 86.76 )
2026-01-22 21:32:33.346562 INFO::Formatting Data.
2026-01-22 21:32:33.347395 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.348344 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.349402 INFO::Found 2 missing values.
2026-01-22 21:32:33.352184 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.352729 INFO::Done
2026-01-22 21:32:33.37914 INFO::Found NA in Reference column
2026-01-22 21:32:33.388225 INFO::Require at least two references per batch.
2026-01-22 21:32:33.40806 INFO::Formatting Data.
2026-01-22 21:32:33.40879 INFO::Recognized SummarizedExperiment
2026-01-22 21:32:33.409288 INFO::Typecasting input to dataframe.
2026-01-22 21:32:33.418641 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.419778 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.423067 INFO::Found 0 missing values.
2026-01-22 21:32:33.429414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.42999 INFO::Done
2026-01-22 21:32:33.444973 INFO::Formatting Data.
2026-01-22 21:32:33.445702 INFO::Recognized SummarizedExperiment
2026-01-22 21:32:33.446198 INFO::Typecasting input to dataframe.
2026-01-22 21:32:33.462893 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.464087 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.467433 INFO::Found 0 missing values.
2026-01-22 21:32:33.477657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.478276 INFO::Done
2026-01-22 21:32:33.493709 INFO::Formatting Data.
2026-01-22 21:32:33.494408 INFO::Recognized SummarizedExperiment
2026-01-22 21:32:33.494927 INFO::Typecasting input to dataframe.
2026-01-22 21:32:33.510835 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.511815 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.512823 INFO::Found 0 missing values.
2026-01-22 21:32:33.513674 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.
2026-01-22 21:32:33.517786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.518291 INFO::Done
2026-01-22 21:32:33.52771 INFO::Formatting Data.
2026-01-22 21:32:33.528426 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.529345 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.530296 INFO::Found 0 missing values.
2026-01-22 21:32:33.532977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.533469 INFO::Done
2026-01-22 21:32:33.544169 INFO::Formatting Data.
2026-01-22 21:32:33.545017 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.545995 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.546971 INFO::Found 0 missing values.
2026-01-22 21:32:33.549684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.550199 INFO::Done
2026-01-22 21:32:33.579007 INFO::Formatting Data.
2026-01-22 21:32:33.579859 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.580915 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.582079 INFO::Found 1 missing values.
2026-01-22 21:32:33.584656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.585167 INFO::Done
2026-01-22 21:32:33.603387 INFO::Formatting Data.
2026-01-22 21:32:33.604189 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.605024 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.605967 INFO::Found 2 missing values.
2026-01-22 21:32:33.606882 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.
2026-01-22 21:32:33.609134 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.60968 INFO::Done
2026-01-22 21:32:33.619092 INFO::Formatting Data.
2026-01-22 21:32:33.619801 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.620683 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.621591 INFO::Found 2 missing values.
2026-01-22 21:32:33.623169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.623705 INFO::Done
2026-01-22 21:32:33.633322 INFO::Formatting Data.
2026-01-22 21:32:33.633986 INFO::Typecasting input to dataframe.
2026-01-22 21:32:33.634779 INFO::Replacing NaNs with NAs.
2026-01-22 21:32:33.635588 INFO::Removing potential empty rows and columns
2026-01-22 21:32:33.636503 INFO::Found 0 missing values.
2026-01-22 21:32:33.639268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-22 21:32:33.639784 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.122 3.350 20.125
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.065 | 1.137 | 16.436 | |
| compute_asw | 0.024 | 0.002 | 0.025 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.010 | 0.002 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |