Yannis Schumann
| Snapshot Date: 2025-12-17 13:40 -0500 (Wed, 17 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-18 11:34 -0500 (Thu, 18 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 168/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-12-17 21:12:28 -0500 (Wed, 17 Dec 2025) |
| EndedAt: 2025-12-17 21:13:57 -0500 (Wed, 17 Dec 2025) |
| EllapsedTime: 89.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.137 1.073 17.24
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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")
2025-12-17 21:13:18.582662 INFO::Formatting Data.
2025-12-17 21:13:18.583937 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:18.594867 INFO::Removing potential empty rows and columns
2025-12-17 21:13:18.853487 INFO::Found 0 missing values.
2025-12-17 21:13:18.857068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:18.857717 INFO::Done
2025-12-17 21:13:18.858271 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:18.870995 INFO::Starting hierarchical adjustment
2025-12-17 21:13:18.871926 INFO::Found 3 batches.
2025-12-17 21:13:18.872517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:18.873675 INFO::Using default BPPARAM
2025-12-17 21:13:18.874246 INFO::Processing subtree level 1
2025-12-17 21:13:18.987979 INFO::Adjusting the last 1 batches sequentially
2025-12-17 21:13:18.9899 INFO::Done
2025-12-17 21:13:18.990595 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:18.993375 INFO::ASW Batch was -0.039931049793978 prior to batch effect correction and is now -0.039931049793978 .
2025-12-17 21:13:18.994532 INFO::Total function execution time is 0.412466049194336 s and adjustment time is 0.1181480884552 s ( 28.64 )
2025-12-17 21:13:19.010087 INFO::Formatting Data.
2025-12-17 21:13:19.010929 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:19.011939 INFO::Removing potential empty rows and columns
2025-12-17 21:13:19.013162 INFO::Found 0 missing values.
2025-12-17 21:13:19.014216 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.
2025-12-17 21:13:19.025902 INFO::Formatting Data.
2025-12-17 21:13:19.026701 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:19.027686 INFO::Removing potential empty rows and columns
2025-12-17 21:13:19.028921 INFO::Found 0 missing values.
2025-12-17 21:13:19.029964 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.
2025-12-17 21:13:19.047145 INFO::Formatting Data.
2025-12-17 21:13:19.047996 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:19.048961 INFO::Removing potential empty rows and columns
2025-12-17 21:13:19.050047 INFO::Found 0 missing values.
2025-12-17 21:13:19.051043 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.
2025-12-17 21:13:19.055734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:19.056312 INFO::Done
2025-12-17 21:13:19.05688 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:19.05899 INFO::Starting hierarchical adjustment
2025-12-17 21:13:19.059723 INFO::Found 2 batches.
2025-12-17 21:13:19.060286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:19.060965 INFO::Using default BPPARAM
2025-12-17 21:13:19.06152 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:19.062531 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-17 21:13:19.084922 INFO::Done
2025-12-17 21:13:19.085706 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:19.087902 INFO::ASW Batch was -0.011684245605237 prior to batch effect correction and is now -0.0694249680932106 .
2025-12-17 21:13:19.088802 INFO::Total function execution time is 0.0417332649230957 s and adjustment time is 0.0252907276153564 s ( 60.6 )
2025-12-17 21:13:19.0918 INFO::Formatting Data.
2025-12-17 21:13:19.092465 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:19.102007 INFO::Formatting Data.
2025-12-17 21:13:19.102728 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:19.103676 INFO::Removing potential empty rows and columns
2025-12-17 21:13:19.104766 INFO::Found 0 missing values.
2025-12-17 21:13:19.107812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:19.108385 INFO::Done
2025-12-17 21:13:19.108952 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:19.111167 INFO::Starting hierarchical adjustment
2025-12-17 21:13:19.11192 INFO::Found 2 batches.
2025-12-17 21:13:19.112485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:19.113168 INFO::Using default BPPARAM
2025-12-17 21:13:19.113729 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:19.114735 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-17 21:13:19.162987 INFO::Done
2025-12-17 21:13:19.163669 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:19.165625 INFO::ASW Batch was 0.103094509053415 prior to batch effect correction and is now -0.125842476895011 .
2025-12-17 21:13:19.166401 INFO::Total function execution time is 0.0644340515136719 s and adjustment time is 0.0512118339538574 s ( 79.48 )
2025-12-17 21:13:19.1674 INFO::Formatting Data.
2025-12-17 21:13:19.167997 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:19.16883 INFO::Removing potential empty rows and columns
2025-12-17 21:13:19.169802 INFO::Found 0 missing values.
2025-12-17 21:13:19.172429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:19.172986 INFO::Done
2025-12-17 21:13:19.173491 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:19.175405 INFO::Starting hierarchical adjustment
2025-12-17 21:13:19.176086 INFO::Found 2 batches.
2025-12-17 21:13:19.176607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:19.177207 INFO::Using default BPPARAM
2025-12-17 21:13:19.177701 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:19.17859 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-17 21:13:19.192944 INFO::Done
2025-12-17 21:13:19.193569 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:19.195531 INFO::ASW Batch was 0.103094509053415 prior to batch effect correction and is now -0.125842476895011 .
2025-12-17 21:13:19.1963 INFO::Total function execution time is 0.0288894176483154 s and adjustment time is 0.0169844627380371 s ( 58.79 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-17 21:13:22.463161 INFO::Formatting Data.
2025-12-17 21:13:22.464101 INFO::Recognized SummarizedExperiment
2025-12-17 21:13:22.464649 INFO::Typecasting input to dataframe.
2025-12-17 21:13:22.49687 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:22.498362 INFO::Removing potential empty rows and columns
2025-12-17 21:13:22.501953 INFO::Found 0 missing values.
2025-12-17 21:13:22.50863 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:22.50929 INFO::Done
2025-12-17 21:13:22.50983 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:22.513469 INFO::Starting hierarchical adjustment
2025-12-17 21:13:22.514233 INFO::Found 2 batches.
2025-12-17 21:13:22.514758 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:22.515997 INFO::Using default BPPARAM
2025-12-17 21:13:22.516532 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:22.517581 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-17 21:13:22.573831 INFO::Done
2025-12-17 21:13:22.574727 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:22.578591 INFO::ASW Batch was 0.0107035471077291 prior to batch effect correction and is now -0.0907713637881516 .
2025-12-17 21:13:22.579576 INFO::Total function execution time is 0.116754770278931 s and adjustment time is 0.0596816539764404 s ( 51.12 )
Warning: stack imbalance in '{', 73 then 75
2025-12-17 21:13:22.598475 INFO::Formatting Data.
2025-12-17 21:13:22.599266 INFO::Recognized SummarizedExperiment
2025-12-17 21:13:22.599813 INFO::Typecasting input to dataframe.
2025-12-17 21:13:22.60907 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:22.610247 INFO::Removing potential empty rows and columns
2025-12-17 21:13:22.613526 INFO::Found 0 missing values.
2025-12-17 21:13:22.620135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:22.620695 INFO::Done
2025-12-17 21:13:22.6212 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:22.624776 INFO::Starting hierarchical adjustment
2025-12-17 21:13:22.625548 INFO::Found 2 batches.
2025-12-17 21:13:22.626142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:22.626796 INFO::Using default BPPARAM
2025-12-17 21:13:22.627368 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:22.628399 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-17 21:13:22.655098 INFO::Done
2025-12-17 21:13:22.65601 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:22.659934 INFO::ASW Batch was -0.0255437693962506 prior to batch effect correction and is now -0.0255437693962506 .
2025-12-17 21:13:22.660936 INFO::Total function execution time is 0.062408447265625 s and adjustment time is 0.0296530723571777 s ( 47.51 )
2025-12-17 21:13:22.682253 INFO::Formatting Data.
2025-12-17 21:13:22.683259 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:22.684317 INFO::Removing potential empty rows and columns
2025-12-17 21:13:22.685496 INFO::Found 0 missing values.
2025-12-17 21:13:22.68874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:22.689326 INFO::Done
2025-12-17 21:13:22.689875 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:22.692209 INFO::Starting hierarchical adjustment
2025-12-17 21:13:22.692963 INFO::Found 3 batches.
2025-12-17 21:13:22.693516 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:22.694173 INFO::Using default BPPARAM
2025-12-17 21:13:22.694721 INFO::Processing subtree level 1
2025-12-17 21:13:22.851662 INFO::Adjusting the last 1 batches sequentially
2025-12-17 21:13:22.853888 INFO::Done
2025-12-17 21:13:22.85464 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:22.857529 INFO::ASW Batch was 0.103762801047058 prior to batch effect correction and is now -0.181324557084731 .
2025-12-17 21:13:22.858646 INFO::Total function execution time is 0.176433324813843 s and adjustment time is 0.161027669906616 s ( 91.27 )
2025-12-17 21:13:22.875442 INFO::Skipping initial DF formatting
2025-12-17 21:13:22.876532 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:22.881858 INFO::Starting hierarchical adjustment
2025-12-17 21:13:22.882844 INFO::Found 5 batches.
2025-12-17 21:13:22.88345 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:22.884166 INFO::Using default BPPARAM
2025-12-17 21:13:22.88477 INFO::Processing subtree level 1
2025-12-17 21:13:23.04434 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.047316 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-17 21:13:23.085904 INFO::Done
2025-12-17 21:13:23.087181 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.092335 INFO::ASW Batch was 0.603184101783526 prior to batch effect correction and is now 0.603184101783526 .
2025-12-17 21:13:23.093084 INFO::ASW Label was 0.342775174312065 prior to batch effect correction and is now 0.342775174312065 .
2025-12-17 21:13:23.094285 INFO::Total function execution time is 0.219021797180176 s and adjustment time is 0.203205585479736 s ( 92.78 )
2025-12-17 21:13:23.115976 INFO::Formatting Data.
2025-12-17 21:13:23.116942 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.118002 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.119119 INFO::Found 0 missing values.
2025-12-17 21:13:23.123499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.124125 INFO::Done
2025-12-17 21:13:23.124686 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.128058 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.128857 INFO::Found 5 batches.
2025-12-17 21:13:23.129428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.130161 INFO::Using default BPPARAM
2025-12-17 21:13:23.130745 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.
2025-12-17 21:13:23.249464 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.251193 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-17 21:13:23.267797 INFO::Done
2025-12-17 21:13:23.26857 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.271848 INFO::ASW Batch was 0.381115798931652 prior to batch effect correction and is now -0.0472869991715772 .
2025-12-17 21:13:23.272537 INFO::ASW Label was 0.464758535711998 prior to batch effect correction and is now 0.781553365404983 .
2025-12-17 21:13:23.273401 INFO::Total function execution time is 0.157553911209106 s and adjustment time is 0.139080047607422 s ( 88.27 )
2025-12-17 21:13:23.274266 INFO::Formatting Data.
2025-12-17 21:13:23.274916 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.275845 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.276893 INFO::Found 0 missing values.
2025-12-17 21:13:23.281115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.281698 INFO::Done
2025-12-17 21:13:23.282264 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.285287 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.286091 INFO::Found 5 batches.
2025-12-17 21:13:23.286646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.287325 INFO::Using default BPPARAM
2025-12-17 21:13:23.287899 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.
2025-12-17 21:13:23.400055 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.401706 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-17 21:13:23.418654 INFO::Done
2025-12-17 21:13:23.419466 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.422926 INFO::ASW Batch was 0.381115798931652 prior to batch effect correction and is now -0.0472869991715772 .
2025-12-17 21:13:23.423606 INFO::ASW Label was 0.464758535711998 prior to batch effect correction and is now 0.781553365404983 .
2025-12-17 21:13:23.424521 INFO::Total function execution time is 0.150238752365112 s and adjustment time is 0.132684230804443 s ( 88.32 )
2025-12-17 21:13:23.439247 INFO::Formatting Data.
2025-12-17 21:13:23.440174 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.441185 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.442251 INFO::Found 0 missing values.
2025-12-17 21:13:23.446606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.447227 INFO::Done
2025-12-17 21:13:23.447823 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.451042 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.451815 INFO::Found 5 batches.
2025-12-17 21:13:23.452377 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.453048 INFO::Using default BPPARAM
2025-12-17 21:13:23.453608 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.
2025-12-17 21:13:23.573906 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.575572 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-17 21:13:23.592366 INFO::Done
2025-12-17 21:13:23.59322 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.596758 INFO::ASW Batch was 0.569889635173843 prior to batch effect correction and is now -0.0738585908684281 .
2025-12-17 21:13:23.597448 INFO::ASW Label was 0.284240826546949 prior to batch effect correction and is now 0.712776627548585 .
2025-12-17 21:13:23.59834 INFO::Total function execution time is 0.159198045730591 s and adjustment time is 0.140674114227295 s ( 88.36 )
2025-12-17 21:13:23.599208 INFO::Formatting Data.
2025-12-17 21:13:23.599859 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.600857 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.601899 INFO::Found 0 missing values.
2025-12-17 21:13:23.606184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.606779 INFO::Done
2025-12-17 21:13:23.607337 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.610503 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.611264 INFO::Found 5 batches.
2025-12-17 21:13:23.611863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.612521 INFO::Using default BPPARAM
2025-12-17 21:13:23.613148 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.
2025-12-17 21:13:23.732839 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.734661 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-17 21:13:23.751695 INFO::Done
2025-12-17 21:13:23.752548 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.756159 INFO::ASW Batch was 0.569889635173843 prior to batch effect correction and is now -0.0738585908684281 .
2025-12-17 21:13:23.756846 INFO::ASW Label was 0.284240826546949 prior to batch effect correction and is now 0.712776627548585 .
2025-12-17 21:13:23.757816 INFO::Total function execution time is 0.158576726913452 s and adjustment time is 0.140532493591309 s ( 88.62 )
2025-12-17 21:13:23.773076 INFO::Formatting Data.
2025-12-17 21:13:23.773979 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.775007 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.776125 INFO::Found 0 missing values.
2025-12-17 21:13:23.779111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.779717 INFO::Done
2025-12-17 21:13:23.780304 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.783515 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.784282 INFO::Found 2 batches.
2025-12-17 21:13:23.784861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.785511 INFO::Using default BPPARAM
2025-12-17 21:13:23.786109 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.787127 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-17 21:13:23.803422 INFO::Done
2025-12-17 21:13:23.804199 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.807475 INFO::ASW Batch was 0.452591234765052 prior to batch effect correction and is now -0.0203172830829914 .
2025-12-17 21:13:23.808155 INFO::ASW Label was 0.649995311238208 prior to batch effect correction and is now 0.950407347963085 .
2025-12-17 21:13:23.809066 INFO::Total function execution time is 0.0361261367797852 s and adjustment time is 0.0192642211914062 s ( 53.32 )
2025-12-17 21:13:23.809936 INFO::Formatting Data.
2025-12-17 21:13:23.81058 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.811507 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.812555 INFO::Found 0 missing values.
2025-12-17 21:13:23.815433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.816055 INFO::Done
2025-12-17 21:13:23.816605 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.819719 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.82048 INFO::Found 2 batches.
2025-12-17 21:13:23.821054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.821699 INFO::Using default BPPARAM
2025-12-17 21:13:23.822298 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.823278 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-17 21:13:23.838995 INFO::Done
2025-12-17 21:13:23.83973 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.842861 INFO::ASW Batch was 0.452591234765052 prior to batch effect correction and is now -0.0203172830829914 .
2025-12-17 21:13:23.843534 INFO::ASW Label was 0.649995311238208 prior to batch effect correction and is now 0.950407347963085 .
2025-12-17 21:13:23.84438 INFO::Total function execution time is 0.0344831943511963 s and adjustment time is 0.0186471939086914 s ( 54.08 )
2025-12-17 21:13:23.856426 INFO::Formatting Data.
2025-12-17 21:13:23.857295 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.858252 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.859233 INFO::Found 0 missing values.
2025-12-17 21:13:23.861531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.862113 INFO::Done
2025-12-17 21:13:23.862654 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.864751 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.865501 INFO::Found 2 batches.
2025-12-17 21:13:23.866073 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.866706 INFO::Using default BPPARAM
2025-12-17 21:13:23.867303 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.868286 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-17 21:13:23.90433 INFO::Done
2025-12-17 21:13:23.90525 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.907723 INFO::ASW Batch was -0.0237825728054286 prior to batch effect correction and is now -0.0918340669324244 .
2025-12-17 21:13:23.908682 INFO::Total function execution time is 0.0523293018341064 s and adjustment time is 0.0389142036437988 s ( 74.36 )
2025-12-17 21:13:23.922317 INFO::Formatting Data.
2025-12-17 21:13:23.923317 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.92433 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.925408 INFO::Found 0 missing values.
2025-12-17 21:13:23.926671 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.
2025-12-17 21:13:23.931776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.932414 INFO::Done
2025-12-17 21:13:23.932988 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.936257 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.937027 INFO::Found 2 batches.
2025-12-17 21:13:23.937905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.938607 INFO::Using default BPPARAM
2025-12-17 21:13:23.939176 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.94018 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-17 21:13:23.958333 INFO::Done
2025-12-17 21:13:23.959169 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:23.962439 INFO::ASW Batch was 0.318653995165843 prior to batch effect correction and is now -0.024399232072769 .
2025-12-17 21:13:23.96311 INFO::ASW Label was 0.745117596413465 prior to batch effect correction and is now 0.953780802017712 .
2025-12-17 21:13:23.964 INFO::Total function execution time is 0.0417995452880859 s and adjustment time is 0.0214419364929199 s ( 51.3 )
2025-12-17 21:13:23.964867 INFO::Formatting Data.
2025-12-17 21:13:23.965534 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:23.966542 INFO::Removing potential empty rows and columns
2025-12-17 21:13:23.967605 INFO::Found 0 missing values.
2025-12-17 21:13:23.968593 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.
2025-12-17 21:13:23.973723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:23.974325 INFO::Done
2025-12-17 21:13:23.974878 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:23.978081 INFO::Starting hierarchical adjustment
2025-12-17 21:13:23.978836 INFO::Found 2 batches.
2025-12-17 21:13:23.979433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:23.980088 INFO::Using default BPPARAM
2025-12-17 21:13:23.980646 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:23.981661 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-17 21:13:24.001832 INFO::Done
2025-12-17 21:13:24.002711 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:24.006572 INFO::ASW Batch was 0.318653995165843 prior to batch effect correction and is now -0.024399232072769 .
2025-12-17 21:13:24.007312 INFO::ASW Label was 0.745117596413465 prior to batch effect correction and is now 0.953780802017712 .
2025-12-17 21:13:24.008198 INFO::Total function execution time is 0.0433585643768311 s and adjustment time is 0.0231180191040039 s ( 53.32 )
2025-12-17 21:13:24.251475 INFO::Formatting Data.
2025-12-17 21:13:24.252647 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:24.253752 INFO::Removing potential empty rows and columns
2025-12-17 21:13:24.254968 INFO::Found 0 missing values.
2025-12-17 21:13:24.258283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:24.258883 INFO::Done
2025-12-17 21:13:24.259444 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:24.261921 INFO::Starting hierarchical adjustment
2025-12-17 21:13:24.262701 INFO::Found 3 batches.
2025-12-17 21:13:24.263273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:24.263989 INFO::Using default BPPARAM
2025-12-17 21:13:24.264552 INFO::Processing subtree level 1
2025-12-17 21:13:24.365891 INFO::Adjusting the last 1 batches sequentially
2025-12-17 21:13:24.368286 INFO::Done
2025-12-17 21:13:24.369132 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:24.372207 INFO::ASW Batch was -0.102847401924336 prior to batch effect correction and is now -0.102847401924336 .
2025-12-17 21:13:24.373412 INFO::Total function execution time is 0.122106552124023 s and adjustment time is 0.105702877044678 s ( 86.57 )
2025-12-17 21:13:24.374577 INFO::Formatting Data.
2025-12-17 21:13:24.375289 INFO::Typecasting input to dataframe.
2025-12-17 21:13:24.376124 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:24.377266 INFO::Removing potential empty rows and columns
2025-12-17 21:13:24.378501 INFO::Found 0 missing values.
2025-12-17 21:13:24.381836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:24.382452 INFO::Done
2025-12-17 21:13:24.383045 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:24.385303 INFO::Starting hierarchical adjustment
2025-12-17 21:13:24.386086 INFO::Found 3 batches.
2025-12-17 21:13:24.386666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:24.387361 INFO::Using default BPPARAM
2025-12-17 21:13:24.38797 INFO::Processing subtree level 1
2025-12-17 21:13:24.488514 INFO::Adjusting the last 1 batches sequentially
2025-12-17 21:13:24.4907 INFO::Done
2025-12-17 21:13:24.491561 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:24.494463 INFO::ASW Batch was -0.102847401924336 prior to batch effect correction and is now -0.102847401924336 .
2025-12-17 21:13:24.495526 INFO::Total function execution time is 0.120913982391357 s and adjustment time is 0.104697227478027 s ( 86.59 )
2025-12-17 21:13:24.513268 INFO::Formatting Data.
2025-12-17 21:13:24.514468 INFO::Typecasting input to dataframe.
2025-12-17 21:13:24.515609 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:24.516833 INFO::Removing potential empty rows and columns
2025-12-17 21:13:24.51818 INFO::Found 0 missing values.
2025-12-17 21:13:24.521626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:24.522268 INFO::Done
2025-12-17 21:13:24.522867 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:24.525407 INFO::Starting hierarchical adjustment
2025-12-17 21:13:24.526236 INFO::Found 3 batches.
2025-12-17 21:13:24.526829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:24.527501 INFO::Using default BPPARAM
2025-12-17 21:13:24.528109 INFO::Processing subtree level 1
2025-12-17 21:13:24.6241 INFO::Adjusting the last 1 batches sequentially
2025-12-17 21:13:24.626126 INFO::Done
2025-12-17 21:13:24.626944 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:24.629864 INFO::ASW Batch was -0.00467815628475226 prior to batch effect correction and is now -0.00467815628475226 .
2025-12-17 21:13:24.630968 INFO::Total function execution time is 0.117929220199585 s and adjustment time is 0.100031852722168 s ( 84.82 )
2025-12-17 21:13:24.774307 INFO::Formatting Data.
2025-12-17 21:13:24.775267 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:24.776521 INFO::Removing potential empty rows and columns
2025-12-17 21:13:24.779492 INFO::Found 1000 missing values.
2025-12-17 21:13:24.799411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:24.800273 INFO::Done
2025-12-17 21:13:24.800892 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:24.806645 INFO::Starting hierarchical adjustment
2025-12-17 21:13:24.807568 INFO::Found 10 batches.
2025-12-17 21:13:24.808178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:24.808995 INFO::Using default BPPARAM
2025-12-17 21:13:24.809573 INFO::Processing subtree level 1
2025-12-17 21:13:24.955502 INFO::Processing subtree level 2
2025-12-17 21:13:25.235897 INFO::Adjusting the last 1 batches sequentially
2025-12-17 21:13:25.23848 INFO::Done
2025-12-17 21:13:25.239353 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:25.245864 INFO::ASW Batch was 0.489996529146474 prior to batch effect correction and is now 0.489996529146474 .
2025-12-17 21:13:25.246711 INFO::ASW Label was 0.318383459942623 prior to batch effect correction and is now 0.318383459942623 .
2025-12-17 21:13:25.247806 INFO::Total function execution time is 0.473571062088013 s and adjustment time is 0.431047677993774 s ( 91.02 )
2025-12-17 21:13:25.248874 INFO::Formatting Data.
2025-12-17 21:13:25.249613 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:25.250947 INFO::Removing potential empty rows and columns
2025-12-17 21:13:25.316089 INFO::Found 1000 missing values.
2025-12-17 21:13:25.336337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:25.337173 INFO::Done
2025-12-17 21:13:25.337824 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:25.343445 INFO::Starting hierarchical adjustment
2025-12-17 21:13:25.344266 INFO::Found 10 batches.
2025-12-17 21:13:26.688943 INFO::Set up parallel execution backend with 2 workers
2025-12-17 21:13:26.690548 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-17 21:13:28.012664 INFO::Adjusting the last 2 batches sequentially
2025-12-17 21:13:28.01615 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-17 21:13:28.034593 INFO::Done
2025-12-17 21:13:28.035431 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:28.040552 INFO::ASW Batch was 0.489996529146474 prior to batch effect correction and is now 0.489996529146474 .
2025-12-17 21:13:28.041296 INFO::ASW Label was 0.318383459942623 prior to batch effect correction and is now 0.318383459942623 .
2025-12-17 21:13:28.042178 INFO::Total function execution time is 2.79337167739868 s and adjustment time is 2.69043469429016 s ( 96.31 )
2025-12-17 21:13:28.227155 INFO::Formatting Data.
2025-12-17 21:13:28.228234 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.229372 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.230617 INFO::Found 0 missing values.
2025-12-17 21:13:28.234693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.235337 INFO::Done
2025-12-17 21:13:28.235943 INFO::Acquiring quality metrics before batch effect correction.
2025-12-17 21:13:28.23926 INFO::Starting hierarchical adjustment
2025-12-17 21:13:28.240071 INFO::Found 3 batches.
2025-12-17 21:13:28.240666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-17 21:13:28.241389 INFO::Using default BPPARAM
2025-12-17 21:13:28.241989 INFO::Processing subtree level 1
2025-12-17 21:13:28.363201 INFO::Adjusting the last 1 batches sequentially
2025-12-17 21:13:28.365745 INFO::Done
2025-12-17 21:13:28.366613 INFO::Acquiring quality metrics after batch effect correction.
2025-12-17 21:13:28.370842 INFO::ASW Batch was 0.166085005905314 prior to batch effect correction and is now -0.163478081023211 .
2025-12-17 21:13:28.371643 INFO::ASW Label was -0.205562267345967 prior to batch effect correction and is now 0.00911686429427106 .
2025-12-17 21:13:28.372843 INFO::Total function execution time is 0.145804882049561 s and adjustment time is 0.125781059265137 s ( 86.27 )
2025-12-17 21:13:28.532243 INFO::Formatting Data.
2025-12-17 21:13:28.533644 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.53474 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.535928 INFO::Found 2 missing values.
2025-12-17 21:13:28.539013 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.539623 INFO::Done
2025-12-17 21:13:28.568404 INFO::Found NA in Reference column
2025-12-17 21:13:28.578938 INFO::Require at least two references per batch.
2025-12-17 21:13:28.601727 INFO::Formatting Data.
2025-12-17 21:13:28.602593 INFO::Recognized SummarizedExperiment
2025-12-17 21:13:28.603181 INFO::Typecasting input to dataframe.
2025-12-17 21:13:28.614295 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.615591 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.619127 INFO::Found 0 missing values.
2025-12-17 21:13:28.625767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.626434 INFO::Done
2025-12-17 21:13:28.641992 INFO::Formatting Data.
2025-12-17 21:13:28.642804 INFO::Recognized SummarizedExperiment
2025-12-17 21:13:28.643354 INFO::Typecasting input to dataframe.
2025-12-17 21:13:28.660516 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.661818 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.665339 INFO::Found 0 missing values.
2025-12-17 21:13:28.676053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.676847 INFO::Done
2025-12-17 21:13:28.692453 INFO::Formatting Data.
2025-12-17 21:13:28.693262 INFO::Recognized SummarizedExperiment
2025-12-17 21:13:28.693825 INFO::Typecasting input to dataframe.
2025-12-17 21:13:28.711326 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.712489 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.713644 INFO::Found 0 missing values.
2025-12-17 21:13:28.714612 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.
2025-12-17 21:13:28.719062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.719634 INFO::Done
2025-12-17 21:13:28.730272 INFO::Formatting Data.
2025-12-17 21:13:28.731221 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.732162 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.733196 INFO::Found 0 missing values.
2025-12-17 21:13:28.736056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.736609 INFO::Done
2025-12-17 21:13:28.748235 INFO::Formatting Data.
2025-12-17 21:13:28.749101 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.750057 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.751191 INFO::Found 0 missing values.
2025-12-17 21:13:28.754101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.754651 INFO::Done
2025-12-17 21:13:28.784267 INFO::Formatting Data.
2025-12-17 21:13:28.785181 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.786258 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.787417 INFO::Found 1 missing values.
2025-12-17 21:13:28.789881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.79046 INFO::Done
2025-12-17 21:13:28.810181 INFO::Formatting Data.
2025-12-17 21:13:28.811133 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.812091 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.813099 INFO::Found 2 missing values.
2025-12-17 21:13:28.814053 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.
2025-12-17 21:13:28.816396 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.816972 INFO::Done
2025-12-17 21:13:28.828119 INFO::Formatting Data.
2025-12-17 21:13:28.829131 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.830205 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.831211 INFO::Found 2 missing values.
2025-12-17 21:13:28.83287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.833464 INFO::Done
2025-12-17 21:13:28.844062 INFO::Formatting Data.
2025-12-17 21:13:28.844913 INFO::Typecasting input to dataframe.
2025-12-17 21:13:28.845722 INFO::Replacing NaNs with NAs.
2025-12-17 21:13:28.8466 INFO::Removing potential empty rows and columns
2025-12-17 21:13:28.847609 INFO::Found 0 missing values.
2025-12-17 21:13:28.850337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-17 21:13:28.850896 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.923 4.037 21.543
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.137 | 1.073 | 17.240 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |