Yannis Schumann
| Snapshot Date: 2025-12-21 13:40 -0500 (Sun, 21 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 2025-12-22 11:35 -0500 (Mon, 22 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" | 4878 |
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-12-21 18:34:00 -0500 (Sun, 21 Dec 2025) |
| EndedAt: 2025-12-21 18:34:37 -0500 (Sun, 21 Dec 2025) |
| EllapsedTime: 36.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 10.138 0.416 7.547
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")
2025-12-21 18:34:27.601033 INFO::Formatting Data.
2025-12-21 18:34:27.602466 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:27.606483 INFO::Removing potential empty rows and columns
2025-12-21 18:34:27.713598 INFO::Found 0 missing values.
2025-12-21 18:34:27.714983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:27.715232 INFO::Done
2025-12-21 18:34:27.715448 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:27.721402 INFO::Starting hierarchical adjustment
2025-12-21 18:34:27.721756 INFO::Found 3 batches.
2025-12-21 18:34:27.721981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:27.722508 INFO::Using default BPPARAM
2025-12-21 18:34:27.722683 INFO::Processing subtree level 1
2025-12-21 18:34:27.783924 INFO::Adjusting the last 1 batches sequentially
2025-12-21 18:34:27.785408 INFO::Done
2025-12-21 18:34:27.785636 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:27.787357 INFO::ASW Batch was -0.0640809016592392 prior to batch effect correction and is now -0.0640809016592392 .
2025-12-21 18:34:27.787882 INFO::Total function execution time is 0.187073945999146 s and adjustment time is 0.0637350082397461 s ( 34.07 )
2025-12-21 18:34:27.799091 INFO::Formatting Data.
2025-12-21 18:34:27.799457 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:27.799849 INFO::Removing potential empty rows and columns
2025-12-21 18:34:27.800326 INFO::Found 0 missing values.
2025-12-21 18:34:27.800686 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.
2025-12-21 18:34:27.805392 INFO::Formatting Data.
2025-12-21 18:34:27.80563 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:27.80596 INFO::Removing potential empty rows and columns
2025-12-21 18:34:27.806392 INFO::Found 0 missing values.
2025-12-21 18:34:27.806835 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.
2025-12-21 18:34:27.813528 INFO::Formatting Data.
2025-12-21 18:34:27.813779 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:27.814083 INFO::Removing potential empty rows and columns
2025-12-21 18:34:27.814426 INFO::Found 0 missing values.
2025-12-21 18:34:27.814711 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.
2025-12-21 18:34:27.816198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:27.816619 INFO::Done
2025-12-21 18:34:27.816788 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:27.817583 INFO::Starting hierarchical adjustment
2025-12-21 18:34:27.817852 INFO::Found 2 batches.
2025-12-21 18:34:27.818077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:27.818347 INFO::Using default BPPARAM
2025-12-21 18:34:27.818537 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:27.818886 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-21 18:34:27.827416 INFO::Done
2025-12-21 18:34:27.827675 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:27.828363 INFO::ASW Batch was 0.0167795220780961 prior to batch effect correction and is now -0.0983165919290908 .
2025-12-21 18:34:27.828801 INFO::Total function execution time is 0.0152878761291504 s and adjustment time is 0.00961494445800781 s ( 62.89 )
2025-12-21 18:34:27.830801 INFO::Formatting Data.
2025-12-21 18:34:27.831156 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:27.834525 INFO::Formatting Data.
2025-12-21 18:34:27.834767 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:27.835079 INFO::Removing potential empty rows and columns
2025-12-21 18:34:27.835447 INFO::Found 0 missing values.
2025-12-21 18:34:27.836496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:27.836686 INFO::Done
2025-12-21 18:34:27.836866 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:27.83757 INFO::Starting hierarchical adjustment
2025-12-21 18:34:27.837805 INFO::Found 2 batches.
2025-12-21 18:34:27.838002 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:27.838238 INFO::Using default BPPARAM
2025-12-21 18:34:27.838446 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:27.838759 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-21 18:34:27.860157 INFO::Done
2025-12-21 18:34:27.860402 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:27.861033 INFO::ASW Batch was 0.114600335002271 prior to batch effect correction and is now -0.132357290971702 .
2025-12-21 18:34:27.861278 INFO::Total function execution time is 0.0267560482025146 s and adjustment time is 0.0223870277404785 s ( 83.67 )
2025-12-21 18:34:27.861566 INFO::Formatting Data.
2025-12-21 18:34:27.861733 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:27.861975 INFO::Removing potential empty rows and columns
2025-12-21 18:34:27.862266 INFO::Found 0 missing values.
2025-12-21 18:34:27.863081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:27.863245 INFO::Done
2025-12-21 18:34:27.863388 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:27.863934 INFO::Starting hierarchical adjustment
2025-12-21 18:34:27.864142 INFO::Found 2 batches.
2025-12-21 18:34:27.864291 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:27.86447 INFO::Using default BPPARAM
2025-12-21 18:34:27.864612 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:27.864849 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-21 18:34:27.869353 INFO::Done
2025-12-21 18:34:27.869546 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:27.870097 INFO::ASW Batch was 0.114600335002271 prior to batch effect correction and is now -0.132357290971702 .
2025-12-21 18:34:27.870319 INFO::Total function execution time is 0.00874495506286621 s and adjustment time is 0.0052490234375 s ( 60.02 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-21 18:34:29.130417 INFO::Formatting Data.
2025-12-21 18:34:29.130667 INFO::Recognized SummarizedExperiment
2025-12-21 18:34:29.13082 INFO::Typecasting input to dataframe.
2025-12-21 18:34:29.141166 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.141603 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.142768 INFO::Found 0 missing values.
2025-12-21 18:34:29.144772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.144946 INFO::Done
2025-12-21 18:34:29.145089 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.146219 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.146433 INFO::Found 2 batches.
2025-12-21 18:34:29.146571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.146882 INFO::Using default BPPARAM
2025-12-21 18:34:29.147024 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.147326 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-21 18:34:29.169126 INFO::Done
2025-12-21 18:34:29.169411 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.170697 INFO::ASW Batch was 0.00866855417976057 prior to batch effect correction and is now -0.0933804448325298 .
2025-12-21 18:34:29.170979 INFO::Total function execution time is 0.0406551361083984 s and adjustment time is 0.0227138996124268 s ( 55.87 )
Warning: stack imbalance in '{', 73 then 75
2025-12-21 18:34:29.178434 INFO::Formatting Data.
2025-12-21 18:34:29.17873 INFO::Recognized SummarizedExperiment
2025-12-21 18:34:29.178935 INFO::Typecasting input to dataframe.
2025-12-21 18:34:29.182489 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.182937 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.184319 INFO::Found 0 missing values.
2025-12-21 18:34:29.186945 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.187145 INFO::Done
2025-12-21 18:34:29.187337 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.188785 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.189056 INFO::Found 2 batches.
2025-12-21 18:34:29.189245 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.189467 INFO::Using default BPPARAM
2025-12-21 18:34:29.189652 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.190011 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-21 18:34:29.199786 INFO::Done
2025-12-21 18:34:29.200057 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.201513 INFO::ASW Batch was 0.0100341783691181 prior to batch effect correction and is now 0.0100341783691181 .
2025-12-21 18:34:29.201787 INFO::Total function execution time is 0.0233700275421143 s and adjustment time is 0.0107779502868652 s ( 46.12 )
2025-12-21 18:34:29.209198 INFO::Formatting Data.
2025-12-21 18:34:29.209453 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.209759 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.210085 INFO::Found 0 missing values.
2025-12-21 18:34:29.211017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.211192 INFO::Done
2025-12-21 18:34:29.211356 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.212071 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.21233 INFO::Found 3 batches.
2025-12-21 18:34:29.212494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.212696 INFO::Using default BPPARAM
2025-12-21 18:34:29.212853 INFO::Processing subtree level 1
2025-12-21 18:34:29.292736 INFO::Adjusting the last 1 batches sequentially
2025-12-21 18:34:29.294625 INFO::Done
2025-12-21 18:34:29.295029 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.300217 INFO::ASW Batch was -0.107391578648916 prior to batch effect correction and is now -0.169371061732633 .
2025-12-21 18:34:29.30225 INFO::Total function execution time is 0.0926330089569092 s and adjustment time is 0.0823380947113037 s ( 88.89 )
2025-12-21 18:34:29.312465 INFO::Skipping initial DF formatting
2025-12-21 18:34:29.312945 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.315072 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.315374 INFO::Found 5 batches.
2025-12-21 18:34:29.315575 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.315831 INFO::Using default BPPARAM
2025-12-21 18:34:29.316149 INFO::Processing subtree level 1
2025-12-21 18:34:29.372658 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.374273 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-21 18:34:29.382556 INFO::Done
2025-12-21 18:34:29.382972 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.384982 INFO::ASW Batch was 0.49019727677666 prior to batch effect correction and is now 0.49019727677666 .
2025-12-21 18:34:29.385213 INFO::ASW Label was 0.401703437284989 prior to batch effect correction and is now 0.401703437284989 .
2025-12-21 18:34:29.385904 INFO::Total function execution time is 0.0733621120452881 s and adjustment time is 0.0672330856323242 s ( 91.65 )
2025-12-21 18:34:29.394462 INFO::Formatting Data.
2025-12-21 18:34:29.394817 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.395175 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.395569 INFO::Found 0 missing values.
2025-12-21 18:34:29.396841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.397208 INFO::Done
2025-12-21 18:34:29.397377 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.401791 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.402132 INFO::Found 5 batches.
2025-12-21 18:34:29.402743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.403148 INFO::Using default BPPARAM
2025-12-21 18:34:29.403659 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.
2025-12-21 18:34:29.461013 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.463543 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-21 18:34:29.472743 INFO::Done
2025-12-21 18:34:29.47316 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.474499 INFO::ASW Batch was 0.24650060337651 prior to batch effect correction and is now -0.0502133011616548 .
2025-12-21 18:34:29.474724 INFO::ASW Label was 0.527321311339015 prior to batch effect correction and is now 0.81097463407232 .
2025-12-21 18:34:29.475157 INFO::Total function execution time is 0.0806059837341309 s and adjustment time is 0.0706920623779297 s ( 87.7 )
2025-12-21 18:34:29.475547 INFO::Formatting Data.
2025-12-21 18:34:29.475765 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.476085 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.476546 INFO::Found 0 missing values.
2025-12-21 18:34:29.477731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.47789 INFO::Done
2025-12-21 18:34:29.478054 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.479005 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.479265 INFO::Found 5 batches.
2025-12-21 18:34:29.479426 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.479659 INFO::Using default BPPARAM
2025-12-21 18:34:29.47991 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.
2025-12-21 18:34:29.532264 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.534393 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-21 18:34:29.542202 INFO::Done
2025-12-21 18:34:29.542569 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.543881 INFO::ASW Batch was 0.24650060337651 prior to batch effect correction and is now -0.0502133011616548 .
2025-12-21 18:34:29.544082 INFO::ASW Label was 0.527321311339015 prior to batch effect correction and is now 0.81097463407232 .
2025-12-21 18:34:29.544534 INFO::Total function execution time is 0.068803071975708 s and adjustment time is 0.0629751682281494 s ( 91.53 )
2025-12-21 18:34:29.552629 INFO::Formatting Data.
2025-12-21 18:34:29.552879 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.553168 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.553486 INFO::Found 0 missing values.
2025-12-21 18:34:29.554651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.554819 INFO::Done
2025-12-21 18:34:29.554973 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.555866 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.556089 INFO::Found 5 batches.
2025-12-21 18:34:29.556245 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.556438 INFO::Using default BPPARAM
2025-12-21 18:34:29.556794 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.
2025-12-21 18:34:29.60864 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.6107 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-21 18:34:29.618359 INFO::Done
2025-12-21 18:34:29.618815 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.620266 INFO::ASW Batch was 0.315672052377599 prior to batch effect correction and is now -0.115326203765997 .
2025-12-21 18:34:29.620504 INFO::ASW Label was 0.441146376910123 prior to batch effect correction and is now 0.863660468202216 .
2025-12-21 18:34:29.621124 INFO::Total function execution time is 0.0683050155639648 s and adjustment time is 0.0622978210449219 s ( 91.21 )
2025-12-21 18:34:29.621419 INFO::Formatting Data.
2025-12-21 18:34:29.621593 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.62187 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.622188 INFO::Found 0 missing values.
2025-12-21 18:34:29.623332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.623504 INFO::Done
2025-12-21 18:34:29.623772 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.624637 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.624982 INFO::Found 5 batches.
2025-12-21 18:34:29.625143 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.625344 INFO::Using default BPPARAM
2025-12-21 18:34:29.625587 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.
2025-12-21 18:34:29.681775 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.686604 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-21 18:34:29.696484 INFO::Done
2025-12-21 18:34:29.69695 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.698788 INFO::ASW Batch was 0.315672052377599 prior to batch effect correction and is now -0.115326203765997 .
2025-12-21 18:34:29.699014 INFO::ASW Label was 0.441146376910123 prior to batch effect correction and is now 0.863660468202216 .
2025-12-21 18:34:29.699576 INFO::Total function execution time is 0.0778839588165283 s and adjustment time is 0.071530818939209 s ( 91.84 )
2025-12-21 18:34:29.70583 INFO::Formatting Data.
2025-12-21 18:34:29.706183 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.706472 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.706805 INFO::Found 0 missing values.
2025-12-21 18:34:29.707641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.707807 INFO::Done
2025-12-21 18:34:29.707969 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.708967 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.709201 INFO::Found 2 batches.
2025-12-21 18:34:29.709359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.709567 INFO::Using default BPPARAM
2025-12-21 18:34:29.709725 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.709989 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-21 18:34:29.715188 INFO::Done
2025-12-21 18:34:29.715421 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.716379 INFO::ASW Batch was 0.222745945436216 prior to batch effect correction and is now 0.0956984767423932 .
2025-12-21 18:34:29.716585 INFO::ASW Label was 0.838212423726782 prior to batch effect correction and is now 0.891126473321563 .
2025-12-21 18:34:29.716846 INFO::Total function execution time is 0.0110352039337158 s and adjustment time is 0.00602412223815918 s ( 54.59 )
2025-12-21 18:34:29.717082 INFO::Formatting Data.
2025-12-21 18:34:29.71728 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.717533 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.717824 INFO::Found 0 missing values.
2025-12-21 18:34:29.7186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.71876 INFO::Done
2025-12-21 18:34:29.718914 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.719749 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.719961 INFO::Found 2 batches.
2025-12-21 18:34:29.720118 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.720307 INFO::Using default BPPARAM
2025-12-21 18:34:29.720455 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.720709 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-21 18:34:29.725619 INFO::Done
2025-12-21 18:34:29.725832 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.726718 INFO::ASW Batch was 0.222745945436216 prior to batch effect correction and is now 0.0956984767423932 .
2025-12-21 18:34:29.726892 INFO::ASW Label was 0.838212423726782 prior to batch effect correction and is now 0.891126473321563 .
2025-12-21 18:34:29.727129 INFO::Total function execution time is 0.0100400447845459 s and adjustment time is 0.00569701194763184 s ( 56.74 )
2025-12-21 18:34:29.731653 INFO::Formatting Data.
2025-12-21 18:34:29.731931 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.732264 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.732628 INFO::Found 0 missing values.
2025-12-21 18:34:29.733367 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.733562 INFO::Done
2025-12-21 18:34:29.733759 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.734499 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.734753 INFO::Found 2 batches.
2025-12-21 18:34:29.734967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.735187 INFO::Using default BPPARAM
2025-12-21 18:34:29.735372 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.735684 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-21 18:34:29.747843 INFO::Done
2025-12-21 18:34:29.748087 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.7487 INFO::ASW Batch was -0.0110742871531921 prior to batch effect correction and is now -0.064464330242286 .
2025-12-21 18:34:29.748997 INFO::Total function execution time is 0.0173799991607666 s and adjustment time is 0.0131380558013916 s ( 75.59 )
2025-12-21 18:34:29.753511 INFO::Formatting Data.
2025-12-21 18:34:29.753744 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.754019 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.754336 INFO::Found 0 missing values.
2025-12-21 18:34:29.754748 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.
2025-12-21 18:34:29.756068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.756246 INFO::Done
2025-12-21 18:34:29.756408 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.75732 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.757542 INFO::Found 2 batches.
2025-12-21 18:34:29.757697 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.757871 INFO::Using default BPPARAM
2025-12-21 18:34:29.758024 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.758292 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-21 18:34:29.763515 INFO::Done
2025-12-21 18:34:29.763729 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.767244 INFO::ASW Batch was 0.386020466999861 prior to batch effect correction and is now -0.0201606362538501 .
2025-12-21 18:34:29.767555 INFO::ASW Label was 0.652549006771824 prior to batch effect correction and is now 0.917678446654685 .
2025-12-21 18:34:29.767825 INFO::Total function execution time is 0.0143239498138428 s and adjustment time is 0.00600814819335938 s ( 41.94 )
2025-12-21 18:34:29.76806 INFO::Formatting Data.
2025-12-21 18:34:29.768233 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.768512 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.768818 INFO::Found 0 missing values.
2025-12-21 18:34:29.769084 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.
2025-12-21 18:34:29.770376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.770563 INFO::Done
2025-12-21 18:34:29.770716 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.771595 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.771807 INFO::Found 2 batches.
2025-12-21 18:34:29.771966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.772153 INFO::Using default BPPARAM
2025-12-21 18:34:29.772313 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:29.77258 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-21 18:34:29.777733 INFO::Done
2025-12-21 18:34:29.777949 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.778828 INFO::ASW Batch was 0.386020466999861 prior to batch effect correction and is now -0.0201606362538501 .
2025-12-21 18:34:29.779015 INFO::ASW Label was 0.652549006771824 prior to batch effect correction and is now 0.917678446654685 .
2025-12-21 18:34:29.779265 INFO::Total function execution time is 0.0111958980560303 s and adjustment time is 0.00595903396606445 s ( 53.23 )
2025-12-21 18:34:29.852608 INFO::Formatting Data.
2025-12-21 18:34:29.852899 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.853208 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.853543 INFO::Found 0 missing values.
2025-12-21 18:34:29.854403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.854581 INFO::Done
2025-12-21 18:34:29.854743 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.855414 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.855745 INFO::Found 3 batches.
2025-12-21 18:34:29.855895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.856093 INFO::Using default BPPARAM
2025-12-21 18:34:29.856252 INFO::Processing subtree level 1
2025-12-21 18:34:29.902769 INFO::Adjusting the last 1 batches sequentially
2025-12-21 18:34:29.904895 INFO::Done
2025-12-21 18:34:29.905779 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.907954 INFO::ASW Batch was -0.0137918823627749 prior to batch effect correction and is now -0.0137918823627749 .
2025-12-21 18:34:29.908788 INFO::Total function execution time is 0.0560920238494873 s and adjustment time is 0.049271821975708 s ( 87.84 )
2025-12-21 18:34:29.90922 INFO::Formatting Data.
2025-12-21 18:34:29.909435 INFO::Typecasting input to dataframe.
2025-12-21 18:34:29.909814 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.910155 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.910579 INFO::Found 0 missing values.
2025-12-21 18:34:29.911688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.911881 INFO::Done
2025-12-21 18:34:29.912059 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.912779 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.913055 INFO::Found 3 batches.
2025-12-21 18:34:29.913217 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.913458 INFO::Using default BPPARAM
2025-12-21 18:34:29.913635 INFO::Processing subtree level 1
2025-12-21 18:34:29.975203 INFO::Adjusting the last 1 batches sequentially
2025-12-21 18:34:29.977346 INFO::Done
2025-12-21 18:34:29.977708 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:29.979812 INFO::ASW Batch was -0.0137918823627749 prior to batch effect correction and is now -0.0137918823627749 .
2025-12-21 18:34:29.980576 INFO::Total function execution time is 0.0712099075317383 s and adjustment time is 0.0643458366394043 s ( 90.36 )
2025-12-21 18:34:29.988479 INFO::Formatting Data.
2025-12-21 18:34:29.988766 INFO::Typecasting input to dataframe.
2025-12-21 18:34:29.98905 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:29.989389 INFO::Removing potential empty rows and columns
2025-12-21 18:34:29.989843 INFO::Found 0 missing values.
2025-12-21 18:34:29.990799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:29.990987 INFO::Done
2025-12-21 18:34:29.991147 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:29.991794 INFO::Starting hierarchical adjustment
2025-12-21 18:34:29.992054 INFO::Found 3 batches.
2025-12-21 18:34:29.99224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:29.992485 INFO::Using default BPPARAM
2025-12-21 18:34:29.992665 INFO::Processing subtree level 1
2025-12-21 18:34:30.047173 INFO::Adjusting the last 1 batches sequentially
2025-12-21 18:34:30.048989 INFO::Done
2025-12-21 18:34:30.049235 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:30.051827 INFO::ASW Batch was -0.0883560779409361 prior to batch effect correction and is now -0.0883560779409361 .
2025-12-21 18:34:30.052966 INFO::Total function execution time is 0.0643429756164551 s and adjustment time is 0.0569581985473633 s ( 88.52 )
2025-12-21 18:34:30.127772 INFO::Formatting Data.
2025-12-21 18:34:30.128089 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:30.129023 INFO::Removing potential empty rows and columns
2025-12-21 18:34:30.13004 INFO::Found 1000 missing values.
2025-12-21 18:34:30.137564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:30.137929 INFO::Done
2025-12-21 18:34:30.138167 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:30.140365 INFO::Starting hierarchical adjustment
2025-12-21 18:34:30.140629 INFO::Found 10 batches.
2025-12-21 18:34:30.140815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:30.141057 INFO::Using default BPPARAM
2025-12-21 18:34:30.141235 INFO::Processing subtree level 1
2025-12-21 18:34:30.212337 INFO::Processing subtree level 2
2025-12-21 18:34:30.373376 INFO::Adjusting the last 1 batches sequentially
2025-12-21 18:34:30.375006 INFO::Done
2025-12-21 18:34:30.375241 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:30.378061 INFO::ASW Batch was 0.484334123677433 prior to batch effect correction and is now 0.484334123677433 .
2025-12-21 18:34:30.379885 INFO::ASW Label was 0.347044933368416 prior to batch effect correction and is now 0.347044933368416 .
2025-12-21 18:34:30.423648 INFO::Total function execution time is 0.295639991760254 s and adjustment time is 0.234427928924561 s ( 79.3 )
2025-12-21 18:34:30.424144 INFO::Formatting Data.
2025-12-21 18:34:30.424416 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:30.424969 INFO::Removing potential empty rows and columns
2025-12-21 18:34:30.426173 INFO::Found 1000 missing values.
2025-12-21 18:34:30.434378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:30.43467 INFO::Done
2025-12-21 18:34:30.434871 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:30.43711 INFO::Starting hierarchical adjustment
2025-12-21 18:34:30.437432 INFO::Found 10 batches.
2025-12-21 18:34:30.949179 INFO::Set up parallel execution backend with 2 workers
2025-12-21 18:34:30.949529 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-21 18:34:31.527905 INFO::Adjusting the last 2 batches sequentially
2025-12-21 18:34:31.528588 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-21 18:34:31.535323 INFO::Done
2025-12-21 18:34:31.535564 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:31.537997 INFO::ASW Batch was 0.484334123677433 prior to batch effect correction and is now 0.484334123677433 .
2025-12-21 18:34:31.538227 INFO::ASW Label was 0.347044933368416 prior to batch effect correction and is now 0.347044933368416 .
2025-12-21 18:34:31.538496 INFO::Total function execution time is 1.1143970489502 s and adjustment time is 1.09794783592224 s ( 98.52 )
2025-12-21 18:34:31.615233 INFO::Formatting Data.
2025-12-21 18:34:31.615606 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.616057 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.616635 INFO::Found 0 missing values.
2025-12-21 18:34:31.618321 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.618591 INFO::Done
2025-12-21 18:34:31.618836 INFO::Acquiring quality metrics before batch effect correction.
2025-12-21 18:34:31.620069 INFO::Starting hierarchical adjustment
2025-12-21 18:34:31.620363 INFO::Found 3 batches.
2025-12-21 18:34:31.620565 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-21 18:34:31.620849 INFO::Using default BPPARAM
2025-12-21 18:34:31.621058 INFO::Processing subtree level 1
2025-12-21 18:34:31.684598 INFO::Adjusting the last 1 batches sequentially
2025-12-21 18:34:31.686376 INFO::Done
2025-12-21 18:34:31.686643 INFO::Acquiring quality metrics after batch effect correction.
2025-12-21 18:34:31.689103 INFO::ASW Batch was 0.175987271804689 prior to batch effect correction and is now -0.163071041548917 .
2025-12-21 18:34:31.689367 INFO::ASW Label was -0.125592862913203 prior to batch effect correction and is now 0.177355041742257 .
2025-12-21 18:34:31.689985 INFO::Total function execution time is 0.0747959613800049 s and adjustment time is 0.0660738945007324 s ( 88.34 )
2025-12-21 18:34:31.755194 INFO::Formatting Data.
2025-12-21 18:34:31.755556 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.755946 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.756427 INFO::Found 2 missing values.
2025-12-21 18:34:31.757506 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.757713 INFO::Done
2025-12-21 18:34:31.769348 INFO::Found NA in Reference column
2025-12-21 18:34:31.773972 INFO::Require at least two references per batch.
2025-12-21 18:34:31.784048 INFO::Formatting Data.
2025-12-21 18:34:31.784433 INFO::Recognized SummarizedExperiment
2025-12-21 18:34:31.784657 INFO::Typecasting input to dataframe.
2025-12-21 18:34:31.78977 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.790356 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.792153 INFO::Found 0 missing values.
2025-12-21 18:34:31.795151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.795383 INFO::Done
2025-12-21 18:34:31.802406 INFO::Formatting Data.
2025-12-21 18:34:31.802711 INFO::Recognized SummarizedExperiment
2025-12-21 18:34:31.802959 INFO::Typecasting input to dataframe.
2025-12-21 18:34:31.810638 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.811191 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.816907 INFO::Found 0 missing values.
2025-12-21 18:34:31.821418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.821677 INFO::Done
2025-12-21 18:34:31.829132 INFO::Formatting Data.
2025-12-21 18:34:31.829501 INFO::Recognized SummarizedExperiment
2025-12-21 18:34:31.829709 INFO::Typecasting input to dataframe.
2025-12-21 18:34:31.836523 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.836958 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.837444 INFO::Found 0 missing values.
2025-12-21 18:34:31.837778 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.
2025-12-21 18:34:31.839423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.839618 INFO::Done
2025-12-21 18:34:31.844562 INFO::Formatting Data.
2025-12-21 18:34:31.844894 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.845223 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.845591 INFO::Found 0 missing values.
2025-12-21 18:34:31.84664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.846834 INFO::Done
2025-12-21 18:34:31.852675 INFO::Formatting Data.
2025-12-21 18:34:31.85309 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.853459 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.853837 INFO::Found 0 missing values.
2025-12-21 18:34:31.854866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.855063 INFO::Done
2025-12-21 18:34:31.87021 INFO::Formatting Data.
2025-12-21 18:34:31.870555 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.870931 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.871309 INFO::Found 1 missing values.
2025-12-21 18:34:31.872132 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.872303 INFO::Done
2025-12-21 18:34:31.879974 INFO::Formatting Data.
2025-12-21 18:34:31.880232 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.880503 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.880796 INFO::Found 2 missing values.
2025-12-21 18:34:31.881082 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.
2025-12-21 18:34:31.881825 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.882008 INFO::Done
2025-12-21 18:34:31.886353 INFO::Formatting Data.
2025-12-21 18:34:31.886661 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.886948 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.887226 INFO::Found 2 missing values.
2025-12-21 18:34:31.887729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.887887 INFO::Done
2025-12-21 18:34:31.891749 INFO::Formatting Data.
2025-12-21 18:34:31.891991 INFO::Typecasting input to dataframe.
2025-12-21 18:34:31.892247 INFO::Replacing NaNs with NAs.
2025-12-21 18:34:31.892511 INFO::Removing potential empty rows and columns
2025-12-21 18:34:31.892831 INFO::Found 0 missing values.
2025-12-21 18:34:31.893734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-21 18:34:31.893899 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.323 1.653 9.582
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.138 | 0.416 | 7.547 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |