Yannis Schumann
| Snapshot Date: 2026-03-08 13:40 -0400 (Sun, 08 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-09 11:33 -0400 (Mon, 09 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4508 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences" | 3381 |
| 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 170/2360 | 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 | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /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: 2026-03-08 16:35:48 -0400 (Sun, 08 Mar 2026) |
| EndedAt: 2026-03-08 16:36:19 -0400 (Sun, 08 Mar 2026) |
| EllapsedTime: 31.4 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) (2026-02-28 r89501)
* 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 Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-08 20:35:48 UTC
* 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 9.291 0.436 6.878
* 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) (2026-02-28 r89501) -- "Unsuffered Consequences"
Copyright (C) 2026 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")
2026-03-08 16:36:11.57903 INFO::Formatting Data.
2026-03-08 16:36:11.580431 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:11.584912 INFO::Removing potential empty rows and columns
2026-03-08 16:36:11.681875 INFO::Found 0 missing values.
2026-03-08 16:36:11.6831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:11.68332 INFO::Done
2026-03-08 16:36:11.683517 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:11.691213 INFO::Starting hierarchical adjustment
2026-03-08 16:36:11.691528 INFO::Found 3 batches.
2026-03-08 16:36:11.691738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:11.692151 INFO::Using default BPPARAM
2026-03-08 16:36:11.692353 INFO::Processing subtree level 1
2026-03-08 16:36:11.762669 INFO::Adjusting the last 1 batches sequentially
2026-03-08 16:36:11.763627 INFO::Done
2026-03-08 16:36:11.763851 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:11.764881 INFO::ASW Batch was -0.0991305283688797 prior to batch effect correction and is now -0.0991305283688797 .
2026-03-08 16:36:11.765323 INFO::Total function execution time is 0.186650991439819 s and adjustment time is 0.0721571445465088 s ( 38.66 )
2026-03-08 16:36:11.772283 INFO::Formatting Data.
2026-03-08 16:36:11.772935 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:11.773247 INFO::Removing potential empty rows and columns
2026-03-08 16:36:11.773661 INFO::Found 0 missing values.
2026-03-08 16:36:11.773998 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-08 16:36:11.778759 INFO::Formatting Data.
2026-03-08 16:36:11.779013 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:11.779348 INFO::Removing potential empty rows and columns
2026-03-08 16:36:11.779823 INFO::Found 0 missing values.
2026-03-08 16:36:11.780165 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-08 16:36:11.787918 INFO::Formatting Data.
2026-03-08 16:36:11.788187 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:11.788535 INFO::Removing potential empty rows and columns
2026-03-08 16:36:11.788935 INFO::Found 0 missing values.
2026-03-08 16:36:11.789272 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-08 16:36:11.790879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:11.79109 INFO::Done
2026-03-08 16:36:11.791283 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:11.792081 INFO::Starting hierarchical adjustment
2026-03-08 16:36:11.792335 INFO::Found 2 batches.
2026-03-08 16:36:11.792519 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:11.792784 INFO::Using default BPPARAM
2026-03-08 16:36:11.792966 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:11.793287 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-08 16:36:11.804112 INFO::Done
2026-03-08 16:36:11.804417 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:11.805354 INFO::ASW Batch was 0.00131347874322548 prior to batch effect correction and is now -0.115962632132718 .
2026-03-08 16:36:11.805635 INFO::Total function execution time is 0.0177531242370605 s and adjustment time is 0.0118038654327393 s ( 66.49 )
2026-03-08 16:36:11.806995 INFO::Formatting Data.
2026-03-08 16:36:11.807241 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:11.810592 INFO::Formatting Data.
2026-03-08 16:36:11.810835 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:11.811132 INFO::Removing potential empty rows and columns
2026-03-08 16:36:11.811503 INFO::Found 0 missing values.
2026-03-08 16:36:11.812436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:11.812655 INFO::Done
2026-03-08 16:36:11.812829 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:11.813493 INFO::Starting hierarchical adjustment
2026-03-08 16:36:11.813713 INFO::Found 2 batches.
2026-03-08 16:36:11.814241 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:11.814441 INFO::Using default BPPARAM
2026-03-08 16:36:11.814619 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:11.81492 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:11.820998 INFO::Done
2026-03-08 16:36:11.82124 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:11.821911 INFO::ASW Batch was 0.0387820793431815 prior to batch effect correction and is now -0.124289870732453 .
2026-03-08 16:36:11.822164 INFO::Total function execution time is 0.0115830898284912 s and adjustment time is 0.00732183456420898 s ( 63.21 )
2026-03-08 16:36:11.822511 INFO::Formatting Data.
2026-03-08 16:36:11.822704 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:11.823083 INFO::Removing potential empty rows and columns
2026-03-08 16:36:11.823549 INFO::Found 0 missing values.
2026-03-08 16:36:11.824859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:11.825078 INFO::Done
2026-03-08 16:36:11.825302 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:11.826048 INFO::Starting hierarchical adjustment
2026-03-08 16:36:11.826328 INFO::Found 2 batches.
2026-03-08 16:36:11.826533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:11.826733 INFO::Using default BPPARAM
2026-03-08 16:36:11.826912 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:11.827153 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:11.832219 INFO::Done
2026-03-08 16:36:11.832463 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:11.833153 INFO::ASW Batch was 0.0387820793431815 prior to batch effect correction and is now -0.124289870732453 .
2026-03-08 16:36:11.833406 INFO::Total function execution time is 0.0108799934387207 s and adjustment time is 0.0059208869934082 s ( 54.42 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-08 16:36:13.000451 INFO::Formatting Data.
2026-03-08 16:36:13.000695 INFO::Recognized SummarizedExperiment
2026-03-08 16:36:13.000852 INFO::Typecasting input to dataframe.
2026-03-08 16:36:13.01044 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.010805 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.011857 INFO::Found 0 missing values.
2026-03-08 16:36:13.013852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.014012 INFO::Done
2026-03-08 16:36:13.014157 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.015246 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.015437 INFO::Found 2 batches.
2026-03-08 16:36:13.015571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.015856 INFO::Using default BPPARAM
2026-03-08 16:36:13.015991 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.016246 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-08 16:36:13.033857 INFO::Done
2026-03-08 16:36:13.034121 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.035328 INFO::ASW Batch was -0.00179612624533465 prior to batch effect correction and is now -0.0891247418036357 .
2026-03-08 16:36:13.0356 INFO::Total function execution time is 0.0352411270141602 s and adjustment time is 0.0184459686279297 s ( 52.34 )
Warning: stack imbalance in '{', 73 then 75
2026-03-08 16:36:13.042554 INFO::Formatting Data.
2026-03-08 16:36:13.042806 INFO::Recognized SummarizedExperiment
2026-03-08 16:36:13.042975 INFO::Typecasting input to dataframe.
2026-03-08 16:36:13.046021 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.046402 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.047552 INFO::Found 0 missing values.
2026-03-08 16:36:13.050048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.050333 INFO::Done
2026-03-08 16:36:13.050515 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.051746 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.052006 INFO::Found 2 batches.
2026-03-08 16:36:13.05216 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.05234 INFO::Using default BPPARAM
2026-03-08 16:36:13.052482 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.052767 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-08 16:36:13.060728 INFO::Done
2026-03-08 16:36:13.060934 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.062044 INFO::ASW Batch was 0.000416331458518238 prior to batch effect correction and is now 0.000416331458518238 .
2026-03-08 16:36:13.062299 INFO::Total function execution time is 0.0197479724884033 s and adjustment time is 0.00876188278198242 s ( 44.37 )
2026-03-08 16:36:13.081001 INFO::Formatting Data.
2026-03-08 16:36:13.081243 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.081503 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.081789 INFO::Found 0 missing values.
2026-03-08 16:36:13.082551 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.082701 INFO::Done
2026-03-08 16:36:13.082835 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.083419 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.083598 INFO::Found 3 batches.
2026-03-08 16:36:13.083727 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.083882 INFO::Using default BPPARAM
2026-03-08 16:36:13.084007 INFO::Processing subtree level 1
2026-03-08 16:36:13.226608 INFO::Adjusting the last 1 batches sequentially
2026-03-08 16:36:13.227747 INFO::Done
2026-03-08 16:36:13.228068 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.229399 INFO::ASW Batch was -0.0826739527067834 prior to batch effect correction and is now -0.156983438477216 .
2026-03-08 16:36:13.229913 INFO::Total function execution time is 0.148907899856567 s and adjustment time is 0.144171953201294 s ( 96.82 )
2026-03-08 16:36:13.238206 INFO::Skipping initial DF formatting
2026-03-08 16:36:13.238559 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.240616 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.240991 INFO::Found 5 batches.
2026-03-08 16:36:13.24125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.241573 INFO::Using default BPPARAM
2026-03-08 16:36:13.241824 INFO::Processing subtree level 1
2026-03-08 16:36:13.329 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.329757 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-08 16:36:13.337786 INFO::Done
2026-03-08 16:36:13.338091 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.339754 INFO::ASW Batch was 0.521859897712673 prior to batch effect correction and is now 0.521859897712673 .
2026-03-08 16:36:13.339964 INFO::ASW Label was 0.362812877865959 prior to batch effect correction and is now 0.362812877865959 .
2026-03-08 16:36:13.34031 INFO::Total function execution time is 0.102115869522095 s and adjustment time is 0.0968689918518066 s ( 94.86 )
2026-03-08 16:36:13.34811 INFO::Formatting Data.
2026-03-08 16:36:13.348374 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.348699 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.349074 INFO::Found 0 missing values.
2026-03-08 16:36:13.350553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.350735 INFO::Done
2026-03-08 16:36:13.350911 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.351869 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.35211 INFO::Found 5 batches.
2026-03-08 16:36:13.352289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.352496 INFO::Using default BPPARAM
2026-03-08 16:36:13.352674 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.429392 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.430785 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.438282 INFO::Done
2026-03-08 16:36:13.438535 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.440006 INFO::ASW Batch was 0.585941054994118 prior to batch effect correction and is now -0.0773222245138409 .
2026-03-08 16:36:13.44023 INFO::ASW Label was 0.220356741540406 prior to batch effect correction and is now 0.76162358259809 .
2026-03-08 16:36:13.440612 INFO::Total function execution time is 0.0924849510192871 s and adjustment time is 0.0862131118774414 s ( 93.22 )
2026-03-08 16:36:13.440937 INFO::Formatting Data.
2026-03-08 16:36:13.441144 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.441481 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.441899 INFO::Found 0 missing values.
2026-03-08 16:36:13.443432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.443647 INFO::Done
2026-03-08 16:36:13.443839 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.444916 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.445189 INFO::Found 5 batches.
2026-03-08 16:36:13.445404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.445704 INFO::Using default BPPARAM
2026-03-08 16:36:13.445959 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.527876 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.528835 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.536943 INFO::Done
2026-03-08 16:36:13.537228 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.53874 INFO::ASW Batch was 0.585941054994118 prior to batch effect correction and is now -0.0773222245138409 .
2026-03-08 16:36:13.539001 INFO::ASW Label was 0.220356741540406 prior to batch effect correction and is now 0.76162358259809 .
2026-03-08 16:36:13.539358 INFO::Total function execution time is 0.0983779430389404 s and adjustment time is 0.0917949676513672 s ( 93.31 )
2026-03-08 16:36:13.546714 INFO::Formatting Data.
2026-03-08 16:36:13.547034 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.547444 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.547867 INFO::Found 0 missing values.
2026-03-08 16:36:13.549455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.549672 INFO::Done
2026-03-08 16:36:13.549862 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.551 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.551286 INFO::Found 5 batches.
2026-03-08 16:36:13.551482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.55174 INFO::Using default BPPARAM
2026-03-08 16:36:13.551965 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.641564 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.642345 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.649012 INFO::Done
2026-03-08 16:36:13.649307 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.65053 INFO::ASW Batch was 0.266225116756558 prior to batch effect correction and is now -0.0519200457859508 .
2026-03-08 16:36:13.650741 INFO::ASW Label was 0.523012900015634 prior to batch effect correction and is now 0.856376143318786 .
2026-03-08 16:36:13.651019 INFO::Total function execution time is 0.104331016540527 s and adjustment time is 0.0977709293365479 s ( 93.71 )
2026-03-08 16:36:13.651293 INFO::Formatting Data.
2026-03-08 16:36:13.651497 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.651805 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.652207 INFO::Found 0 missing values.
2026-03-08 16:36:13.653727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.654086 INFO::Done
2026-03-08 16:36:13.654348 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.655668 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.65601 INFO::Found 5 batches.
2026-03-08 16:36:13.656233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.65651 INFO::Using default BPPARAM
2026-03-08 16:36:13.656715 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.730399 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.73141 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.739525 INFO::Done
2026-03-08 16:36:13.739816 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.741019 INFO::ASW Batch was 0.266225116756558 prior to batch effect correction and is now -0.0519200457859508 .
2026-03-08 16:36:13.741214 INFO::ASW Label was 0.523012900015634 prior to batch effect correction and is now 0.856376143318786 .
2026-03-08 16:36:13.741526 INFO::Total function execution time is 0.0902090072631836 s and adjustment time is 0.0835919380187988 s ( 92.66 )
2026-03-08 16:36:13.747229 INFO::Formatting Data.
2026-03-08 16:36:13.747479 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.747806 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.748151 INFO::Found 0 missing values.
2026-03-08 16:36:13.749055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.749232 INFO::Done
2026-03-08 16:36:13.749395 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.750376 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.750611 INFO::Found 2 batches.
2026-03-08 16:36:13.750792 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.751027 INFO::Using default BPPARAM
2026-03-08 16:36:13.751196 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.751517 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.756873 INFO::Done
2026-03-08 16:36:13.757098 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.758067 INFO::ASW Batch was 0.771073806249737 prior to batch effect correction and is now 0.0318648713289612 .
2026-03-08 16:36:13.758264 INFO::ASW Label was 0.313076187960296 prior to batch effect correction and is now 0.894312915478667 .
2026-03-08 16:36:13.758518 INFO::Total function execution time is 0.0113110542297363 s and adjustment time is 0.00629782676696777 s ( 55.68 )
2026-03-08 16:36:13.758794 INFO::Formatting Data.
2026-03-08 16:36:13.758988 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.759276 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.75959 INFO::Found 0 missing values.
2026-03-08 16:36:13.760452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.760621 INFO::Done
2026-03-08 16:36:13.760783 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.761665 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.761895 INFO::Found 2 batches.
2026-03-08 16:36:13.762053 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.762261 INFO::Using default BPPARAM
2026-03-08 16:36:13.762418 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.762668 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-08 16:36:13.767555 INFO::Done
2026-03-08 16:36:13.767764 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.768709 INFO::ASW Batch was 0.771073806249737 prior to batch effect correction and is now 0.0318648713289612 .
2026-03-08 16:36:13.768913 INFO::ASW Label was 0.313076187960296 prior to batch effect correction and is now 0.894312915478667 .
2026-03-08 16:36:13.769194 INFO::Total function execution time is 0.0103859901428223 s and adjustment time is 0.00569987297058105 s ( 54.88 )
2026-03-08 16:36:13.774001 INFO::Formatting Data.
2026-03-08 16:36:13.774242 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.774515 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.774808 INFO::Found 0 missing values.
2026-03-08 16:36:13.775487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.775642 INFO::Done
2026-03-08 16:36:13.7758 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.776366 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.776572 INFO::Found 2 batches.
2026-03-08 16:36:13.776725 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.776911 INFO::Using default BPPARAM
2026-03-08 16:36:13.777056 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.777294 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-08 16:36:13.787708 INFO::Done
2026-03-08 16:36:13.787959 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.788666 INFO::ASW Batch was 0.0635988496128384 prior to batch effect correction and is now -0.0991417735614653 .
2026-03-08 16:36:13.788939 INFO::Total function execution time is 0.0149660110473633 s and adjustment time is 0.0111570358276367 s ( 74.55 )
2026-03-08 16:36:13.793598 INFO::Formatting Data.
2026-03-08 16:36:13.793829 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.794107 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.794441 INFO::Found 0 missing values.
2026-03-08 16:36:13.794845 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-08 16:36:13.796577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.796802 INFO::Done
2026-03-08 16:36:13.796978 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.798022 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.798266 INFO::Found 2 batches.
2026-03-08 16:36:13.798713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.798907 INFO::Using default BPPARAM
2026-03-08 16:36:13.799054 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.799366 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-08 16:36:13.804717 INFO::Done
2026-03-08 16:36:13.804916 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.805795 INFO::ASW Batch was 0.352538658849112 prior to batch effect correction and is now 0.000559669808065273 .
2026-03-08 16:36:13.805979 INFO::ASW Label was 0.711816045475817 prior to batch effect correction and is now 0.93002847683705 .
2026-03-08 16:36:13.806205 INFO::Total function execution time is 0.0126440525054932 s and adjustment time is 0.00649309158325195 s ( 51.35 )
2026-03-08 16:36:13.806459 INFO::Formatting Data.
2026-03-08 16:36:13.806627 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.806876 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.807158 INFO::Found 0 missing values.
2026-03-08 16:36:13.807401 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-08 16:36:13.808701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.808895 INFO::Done
2026-03-08 16:36:13.809051 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.809918 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.810142 INFO::Found 2 batches.
2026-03-08 16:36:13.810293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.810477 INFO::Using default BPPARAM
2026-03-08 16:36:13.810632 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:13.810921 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-08 16:36:13.816217 INFO::Done
2026-03-08 16:36:13.816448 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.817348 INFO::ASW Batch was 0.352538658849112 prior to batch effect correction and is now 0.000559669808065273 .
2026-03-08 16:36:13.817553 INFO::ASW Label was 0.711816045475817 prior to batch effect correction and is now 0.93002847683705 .
2026-03-08 16:36:13.817789 INFO::Total function execution time is 0.011340856552124 s and adjustment time is 0.00610089302062988 s ( 53.8 )
2026-03-08 16:36:13.883998 INFO::Formatting Data.
2026-03-08 16:36:13.884265 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.884556 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.884886 INFO::Found 0 missing values.
2026-03-08 16:36:13.885775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.88594 INFO::Done
2026-03-08 16:36:13.886113 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.886764 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.886977 INFO::Found 3 batches.
2026-03-08 16:36:13.887124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.887306 INFO::Using default BPPARAM
2026-03-08 16:36:13.887471 INFO::Processing subtree level 1
2026-03-08 16:36:13.9602 INFO::Adjusting the last 1 batches sequentially
2026-03-08 16:36:13.960994 INFO::Done
2026-03-08 16:36:13.961196 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:13.962103 INFO::ASW Batch was -0.089363429423104 prior to batch effect correction and is now -0.089363429423104 .
2026-03-08 16:36:13.962448 INFO::Total function execution time is 0.0784869194030762 s and adjustment time is 0.0740621089935303 s ( 94.36 )
2026-03-08 16:36:13.962761 INFO::Formatting Data.
2026-03-08 16:36:13.962939 INFO::Typecasting input to dataframe.
2026-03-08 16:36:13.963175 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:13.96345 INFO::Removing potential empty rows and columns
2026-03-08 16:36:13.963789 INFO::Found 0 missing values.
2026-03-08 16:36:13.964729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:13.964908 INFO::Done
2026-03-08 16:36:13.965074 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:13.965677 INFO::Starting hierarchical adjustment
2026-03-08 16:36:13.965884 INFO::Found 3 batches.
2026-03-08 16:36:13.966032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:13.966227 INFO::Using default BPPARAM
2026-03-08 16:36:13.966393 INFO::Processing subtree level 1
2026-03-08 16:36:14.022459 INFO::Adjusting the last 1 batches sequentially
2026-03-08 16:36:14.023398 INFO::Done
2026-03-08 16:36:14.023604 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:14.024586 INFO::ASW Batch was -0.089363429423104 prior to batch effect correction and is now -0.089363429423104 .
2026-03-08 16:36:14.024955 INFO::Total function execution time is 0.0621559619903564 s and adjustment time is 0.0575480461120605 s ( 92.59 )
2026-03-08 16:36:14.030449 INFO::Formatting Data.
2026-03-08 16:36:14.030684 INFO::Typecasting input to dataframe.
2026-03-08 16:36:14.030949 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:14.031248 INFO::Removing potential empty rows and columns
2026-03-08 16:36:14.031634 INFO::Found 0 missing values.
2026-03-08 16:36:14.032517 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:14.032686 INFO::Done
2026-03-08 16:36:14.032842 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:14.033455 INFO::Starting hierarchical adjustment
2026-03-08 16:36:14.033663 INFO::Found 3 batches.
2026-03-08 16:36:14.033823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:14.034032 INFO::Using default BPPARAM
2026-03-08 16:36:14.034188 INFO::Processing subtree level 1
2026-03-08 16:36:14.092633 INFO::Adjusting the last 1 batches sequentially
2026-03-08 16:36:14.09377 INFO::Done
2026-03-08 16:36:14.093977 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:14.095277 INFO::ASW Batch was -0.0606670506443415 prior to batch effect correction and is now -0.0606670506443415 .
2026-03-08 16:36:14.095755 INFO::Total function execution time is 0.065310001373291 s and adjustment time is 0.0601449012756348 s ( 92.09 )
2026-03-08 16:36:14.178817 INFO::Formatting Data.
2026-03-08 16:36:14.179097 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:14.179519 INFO::Removing potential empty rows and columns
2026-03-08 16:36:14.180457 INFO::Found 1000 missing values.
2026-03-08 16:36:14.186296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:14.186557 INFO::Done
2026-03-08 16:36:14.186738 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:14.188756 INFO::Starting hierarchical adjustment
2026-03-08 16:36:14.189026 INFO::Found 10 batches.
2026-03-08 16:36:14.1892 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:14.189445 INFO::Using default BPPARAM
2026-03-08 16:36:14.189613 INFO::Processing subtree level 1
2026-03-08 16:36:14.271546 INFO::Processing subtree level 2
2026-03-08 16:36:14.348638 INFO::Adjusting the last 1 batches sequentially
2026-03-08 16:36:14.349707 INFO::Done
2026-03-08 16:36:14.349948 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:14.35248 INFO::ASW Batch was 0.494231080290104 prior to batch effect correction and is now 0.494231080290104 .
2026-03-08 16:36:14.352724 INFO::ASW Label was 0.343541544819002 prior to batch effect correction and is now 0.343541544819002 .
2026-03-08 16:36:14.353134 INFO::Total function execution time is 0.174345016479492 s and adjustment time is 0.160732984542847 s ( 92.19 )
2026-03-08 16:36:14.353438 INFO::Formatting Data.
2026-03-08 16:36:14.353637 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:14.354091 INFO::Removing potential empty rows and columns
2026-03-08 16:36:14.355258 INFO::Found 1000 missing values.
2026-03-08 16:36:14.361654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:14.361859 INFO::Done
2026-03-08 16:36:14.362026 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:14.363913 INFO::Starting hierarchical adjustment
2026-03-08 16:36:14.364156 INFO::Found 10 batches.
2026-03-08 16:36:14.7733 INFO::Set up parallel execution backend with 2 workers
2026-03-08 16:36:14.773602 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-08 16:36:15.368791 INFO::Adjusting the last 2 batches sequentially
2026-03-08 16:36:15.369311 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-08 16:36:15.374978 INFO::Done
2026-03-08 16:36:15.375182 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:15.377042 INFO::ASW Batch was 0.494231080290104 prior to batch effect correction and is now 0.494231080290104 .
2026-03-08 16:36:15.377218 INFO::ASW Label was 0.343541544819002 prior to batch effect correction and is now 0.343541544819002 .
2026-03-08 16:36:15.37745 INFO::Total function execution time is 1.02401685714722 s and adjustment time is 1.01087117195129 s ( 98.72 )
2026-03-08 16:36:15.509762 INFO::Formatting Data.
2026-03-08 16:36:15.510037 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.510363 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.510816 INFO::Found 0 missing values.
2026-03-08 16:36:15.512192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.512394 INFO::Done
2026-03-08 16:36:15.512575 INFO::Acquiring quality metrics before batch effect correction.
2026-03-08 16:36:15.513565 INFO::Starting hierarchical adjustment
2026-03-08 16:36:15.513829 INFO::Found 3 batches.
2026-03-08 16:36:15.514024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-08 16:36:15.514264 INFO::Using default BPPARAM
2026-03-08 16:36:15.514453 INFO::Processing subtree level 1
2026-03-08 16:36:15.590652 INFO::Adjusting the last 1 batches sequentially
2026-03-08 16:36:15.591872 INFO::Done
2026-03-08 16:36:15.592118 INFO::Acquiring quality metrics after batch effect correction.
2026-03-08 16:36:15.593556 INFO::ASW Batch was 0.208503297057673 prior to batch effect correction and is now -0.169058140517282 .
2026-03-08 16:36:15.593801 INFO::ASW Label was -0.144859419015057 prior to batch effect correction and is now 0.0520152736705159 .
2026-03-08 16:36:15.59424 INFO::Total function execution time is 0.0844821929931641 s and adjustment time is 0.0780899524688721 s ( 92.43 )
2026-03-08 16:36:15.650161 INFO::Formatting Data.
2026-03-08 16:36:15.650512 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.650839 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.651244 INFO::Found 2 missing values.
2026-03-08 16:36:15.652221 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.652395 INFO::Done
2026-03-08 16:36:15.663718 INFO::Found NA in Reference column
2026-03-08 16:36:15.667651 INFO::Require at least two references per batch.
2026-03-08 16:36:15.67603 INFO::Formatting Data.
2026-03-08 16:36:15.676275 INFO::Recognized SummarizedExperiment
2026-03-08 16:36:15.676454 INFO::Typecasting input to dataframe.
2026-03-08 16:36:15.68009 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.680465 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.681734 INFO::Found 0 missing values.
2026-03-08 16:36:15.68416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.68433 INFO::Done
2026-03-08 16:36:15.689553 INFO::Formatting Data.
2026-03-08 16:36:15.689761 INFO::Recognized SummarizedExperiment
2026-03-08 16:36:15.689927 INFO::Typecasting input to dataframe.
2026-03-08 16:36:15.69572 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.696177 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.697401 INFO::Found 0 missing values.
2026-03-08 16:36:15.701104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.701291 INFO::Done
2026-03-08 16:36:15.706348 INFO::Formatting Data.
2026-03-08 16:36:15.706547 INFO::Recognized SummarizedExperiment
2026-03-08 16:36:15.706706 INFO::Typecasting input to dataframe.
2026-03-08 16:36:15.711964 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.712284 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.712622 INFO::Found 0 missing values.
2026-03-08 16:36:15.712932 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-08 16:36:15.714298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.714466 INFO::Done
2026-03-08 16:36:15.718684 INFO::Formatting Data.
2026-03-08 16:36:15.718952 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.71923 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.719537 INFO::Found 0 missing values.
2026-03-08 16:36:15.72042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.72059 INFO::Done
2026-03-08 16:36:15.72483 INFO::Formatting Data.
2026-03-08 16:36:15.725092 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.725361 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.725696 INFO::Found 0 missing values.
2026-03-08 16:36:15.726654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.726843 INFO::Done
2026-03-08 16:36:15.739051 INFO::Formatting Data.
2026-03-08 16:36:15.739356 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.739702 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.740093 INFO::Found 1 missing values.
2026-03-08 16:36:15.740949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.741126 INFO::Done
2026-03-08 16:36:15.748874 INFO::Formatting Data.
2026-03-08 16:36:15.74919 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.7498 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.750269 INFO::Found 2 missing values.
2026-03-08 16:36:15.750621 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-08 16:36:15.751417 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.751593 INFO::Done
2026-03-08 16:36:15.756256 INFO::Formatting Data.
2026-03-08 16:36:15.756564 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.756871 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.757194 INFO::Found 2 missing values.
2026-03-08 16:36:15.757747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.757917 INFO::Done
2026-03-08 16:36:15.762266 INFO::Formatting Data.
2026-03-08 16:36:15.762524 INFO::Typecasting input to dataframe.
2026-03-08 16:36:15.76281 INFO::Replacing NaNs with NAs.
2026-03-08 16:36:15.763099 INFO::Removing potential empty rows and columns
2026-03-08 16:36:15.763441 INFO::Found 0 missing values.
2026-03-08 16:36:15.764371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-08 16:36:15.764564 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.705 2.040 8.872
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.291 | 0.436 | 6.878 | |
| compute_asw | 0.009 | 0.001 | 0.013 | |
| count_existing | 0.005 | 0.000 | 0.006 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |