Yannis Schumann
| Snapshot Date: 2026-03-11 13:40 -0400 (Wed, 11 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 2026-03-12 11:33 -0400 (Thu, 12 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" | 4806 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4049 |
| 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 | ERROR | ERROR | skipped | skipped | |||||||||
| 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-03-11 21:24:53 -0400 (Wed, 11 Mar 2026) |
| EndedAt: 2026-03-11 21:26:27 -0400 (Wed, 11 Mar 2026) |
| EllapsedTime: 94.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-12 01:24:53 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 28.29 1.176 19.56
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-03-11 21:25:49.531215 INFO::Formatting Data.
2026-03-11 21:25:49.532468 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:49.543325 INFO::Removing potential empty rows and columns
2026-03-11 21:25:49.774318 INFO::Found 0 missing values.
2026-03-11 21:25:49.777457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:49.778119 INFO::Done
2026-03-11 21:25:49.778683 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:49.790888 INFO::Starting hierarchical adjustment
2026-03-11 21:25:49.791798 INFO::Found 3 batches.
2026-03-11 21:25:49.792376 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:49.793431 INFO::Using default BPPARAM
2026-03-11 21:25:49.793992 INFO::Processing subtree level 1
2026-03-11 21:25:49.890111 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:25:49.891884 INFO::Done
2026-03-11 21:25:49.892534 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:49.895013 INFO::ASW Batch was -0.0977986133461772 prior to batch effect correction and is now -0.0977986133461772 .
2026-03-11 21:25:49.896079 INFO::Total function execution time is 0.365442514419556 s and adjustment time is 0.100254535675049 s ( 27.43 )
2026-03-11 21:25:49.908951 INFO::Formatting Data.
2026-03-11 21:25:49.90976 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:49.910701 INFO::Removing potential empty rows and columns
2026-03-11 21:25:49.911824 INFO::Found 0 missing values.
2026-03-11 21:25:49.91281 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.
2026-03-11 21:25:49.923184 INFO::Formatting Data.
2026-03-11 21:25:49.923958 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:49.924867 INFO::Removing potential empty rows and columns
2026-03-11 21:25:49.925964 INFO::Found 0 missing values.
2026-03-11 21:25:49.926886 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.
2026-03-11 21:25:49.942431 INFO::Formatting Data.
2026-03-11 21:25:49.943236 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:49.944143 INFO::Removing potential empty rows and columns
2026-03-11 21:25:49.945191 INFO::Found 0 missing values.
2026-03-11 21:25:49.946117 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.
2026-03-11 21:25:49.950556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:49.951151 INFO::Done
2026-03-11 21:25:49.95171 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:49.953736 INFO::Starting hierarchical adjustment
2026-03-11 21:25:49.954457 INFO::Found 2 batches.
2026-03-11 21:25:49.955044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:49.95572 INFO::Using default BPPARAM
2026-03-11 21:25:49.956283 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:49.957227 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:25:49.977317 INFO::Done
2026-03-11 21:25:49.978078 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:49.980181 INFO::ASW Batch was 0.00854372639501718 prior to batch effect correction and is now -0.0788258715552886 .
2026-03-11 21:25:49.981012 INFO::Total function execution time is 0.0386388301849365 s and adjustment time is 0.0229701995849609 s ( 59.45 )
2026-03-11 21:25:49.983789 INFO::Formatting Data.
2026-03-11 21:25:49.984437 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:49.993412 INFO::Formatting Data.
2026-03-11 21:25:49.994173 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:49.995081 INFO::Removing potential empty rows and columns
2026-03-11 21:25:49.996147 INFO::Found 0 missing values.
2026-03-11 21:25:49.99909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:49.999667 INFO::Done
2026-03-11 21:25:50.000224 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:50.002303 INFO::Starting hierarchical adjustment
2026-03-11 21:25:50.003053 INFO::Found 2 batches.
2026-03-11 21:25:50.00364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:50.004307 INFO::Using default BPPARAM
2026-03-11 21:25:50.004892 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:50.005834 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:25:50.042895 INFO::Done
2026-03-11 21:25:50.043609 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:50.045564 INFO::ASW Batch was -0.0383243527926895 prior to batch effect correction and is now -0.117029807039527 .
2026-03-11 21:25:50.046358 INFO::Total function execution time is 0.0530023574829102 s and adjustment time is 0.0399696826934814 s ( 75.41 )
2026-03-11 21:25:50.047369 INFO::Formatting Data.
2026-03-11 21:25:50.047979 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:50.048824 INFO::Removing potential empty rows and columns
2026-03-11 21:25:50.049822 INFO::Found 0 missing values.
2026-03-11 21:25:50.052536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:50.053104 INFO::Done
2026-03-11 21:25:50.05363 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:50.055527 INFO::Starting hierarchical adjustment
2026-03-11 21:25:50.056219 INFO::Found 2 batches.
2026-03-11 21:25:50.056746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:50.057338 INFO::Using default BPPARAM
2026-03-11 21:25:50.057863 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:50.058765 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:25:50.07279 INFO::Done
2026-03-11 21:25:50.073479 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:50.075496 INFO::ASW Batch was -0.0383243527926895 prior to batch effect correction and is now -0.117029807039527 .
2026-03-11 21:25:50.076287 INFO::Total function execution time is 0.0289130210876465 s and adjustment time is 0.0166780948638916 s ( 57.68 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-11 21:25:52.874375 INFO::Formatting Data.
2026-03-11 21:25:52.87523 INFO::Recognized SummarizedExperiment
2026-03-11 21:25:52.875839 INFO::Typecasting input to dataframe.
2026-03-11 21:25:52.907222 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:52.908506 INFO::Removing potential empty rows and columns
2026-03-11 21:25:52.912042 INFO::Found 0 missing values.
2026-03-11 21:25:52.918702 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:52.919347 INFO::Done
2026-03-11 21:25:52.919907 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:52.923376 INFO::Starting hierarchical adjustment
2026-03-11 21:25:52.924133 INFO::Found 2 batches.
2026-03-11 21:25:52.924685 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:52.925812 INFO::Using default BPPARAM
2026-03-11 21:25:52.926373 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:52.927358 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:25:52.977047 INFO::Done
2026-03-11 21:25:52.977805 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:52.980973 INFO::ASW Batch was 0.00117682722738368 prior to batch effect correction and is now -0.0916812015024639 .
2026-03-11 21:25:52.981804 INFO::Total function execution time is 0.107738494873047 s and adjustment time is 0.0530505180358887 s ( 49.24 )
Warning: stack imbalance in '{', 73 then 75
2026-03-11 21:25:52.998573 INFO::Formatting Data.
2026-03-11 21:25:52.999352 INFO::Recognized SummarizedExperiment
2026-03-11 21:25:52.999904 INFO::Typecasting input to dataframe.
2026-03-11 21:25:53.008085 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:53.00918 INFO::Removing potential empty rows and columns
2026-03-11 21:25:53.012369 INFO::Found 0 missing values.
2026-03-11 21:25:53.018701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:53.019315 INFO::Done
2026-03-11 21:25:53.019855 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:53.023116 INFO::Starting hierarchical adjustment
2026-03-11 21:25:53.023836 INFO::Found 2 batches.
2026-03-11 21:25:53.024353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:53.024986 INFO::Using default BPPARAM
2026-03-11 21:25:53.025508 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:53.02643 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:25:53.051886 INFO::Done
2026-03-11 21:25:53.052715 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:53.056606 INFO::ASW Batch was -0.00243318760158732 prior to batch effect correction and is now -0.00243318760158732 .
2026-03-11 21:25:53.057558 INFO::Total function execution time is 0.058941125869751 s and adjustment time is 0.0281479358673096 s ( 47.76 )
2026-03-11 21:25:53.077009 INFO::Formatting Data.
2026-03-11 21:25:53.077931 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:53.07889 INFO::Removing potential empty rows and columns
2026-03-11 21:25:53.079989 INFO::Found 0 missing values.
2026-03-11 21:25:53.083101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:53.08369 INFO::Done
2026-03-11 21:25:53.084294 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:53.086395 INFO::Starting hierarchical adjustment
2026-03-11 21:25:53.087156 INFO::Found 3 batches.
2026-03-11 21:25:53.087738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:53.088394 INFO::Using default BPPARAM
2026-03-11 21:25:53.088969 INFO::Processing subtree level 1
2026-03-11 21:25:53.229499 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:25:53.231557 INFO::Done
2026-03-11 21:25:53.232294 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:53.234996 INFO::ASW Batch was -0.0150534453328579 prior to batch effect correction and is now -0.170900286463275 .
2026-03-11 21:25:53.236021 INFO::Total function execution time is 0.159039497375488 s and adjustment time is 0.144521474838257 s ( 90.87 )
2026-03-11 21:25:53.251067 INFO::Skipping initial DF formatting
2026-03-11 21:25:53.251868 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:53.256036 INFO::Starting hierarchical adjustment
2026-03-11 21:25:53.256865 INFO::Found 5 batches.
2026-03-11 21:25:53.257473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:53.258284 INFO::Using default BPPARAM
2026-03-11 21:25:53.258884 INFO::Processing subtree level 1
2026-03-11 21:25:53.384366 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:53.386205 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:25:53.407376 INFO::Done
2026-03-11 21:25:53.408264 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:53.412899 INFO::ASW Batch was 0.485541938400434 prior to batch effect correction and is now 0.485541938400434 .
2026-03-11 21:25:53.413749 INFO::ASW Label was 0.390553539298823 prior to batch effect correction and is now 0.390553539298823 .
2026-03-11 21:25:53.414752 INFO::Total function execution time is 0.163737058639526 s and adjustment time is 0.15064811706543 s ( 92.01 )
2026-03-11 21:25:53.433808 INFO::Formatting Data.
2026-03-11 21:25:53.434747 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:53.435732 INFO::Removing potential empty rows and columns
2026-03-11 21:25:53.436805 INFO::Found 0 missing values.
2026-03-11 21:25:53.441152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:53.441786 INFO::Done
2026-03-11 21:25:53.442356 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:53.445521 INFO::Starting hierarchical adjustment
2026-03-11 21:25:53.446311 INFO::Found 5 batches.
2026-03-11 21:25:53.446903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:53.447591 INFO::Using default BPPARAM
2026-03-11 21:25:53.448178 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.
2026-03-11 21:25:53.597253 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:53.599931 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:25:53.623875 INFO::Done
2026-03-11 21:25:53.625184 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:53.630203 INFO::ASW Batch was 0.352316776952206 prior to batch effect correction and is now -0.0719966875754155 .
2026-03-11 21:25:53.631212 INFO::ASW Label was 0.322144446022225 prior to batch effect correction and is now 0.83612147626796 .
2026-03-11 21:25:53.632446 INFO::Total function execution time is 0.198656558990479 s and adjustment time is 0.177559375762939 s ( 89.38 )
2026-03-11 21:25:53.63364 INFO::Formatting Data.
2026-03-11 21:25:53.634503 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:53.635799 INFO::Removing potential empty rows and columns
2026-03-11 21:25:53.637236 INFO::Found 0 missing values.
2026-03-11 21:25:53.642729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:53.643635 INFO::Done
2026-03-11 21:25:53.644486 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:53.648249 INFO::Starting hierarchical adjustment
2026-03-11 21:25:53.649173 INFO::Found 5 batches.
2026-03-11 21:25:53.649829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:53.650613 INFO::Using default BPPARAM
2026-03-11 21:25:53.651212 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.
2026-03-11 21:25:53.78043 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:53.782326 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:25:53.798569 INFO::Done
2026-03-11 21:25:53.799387 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:53.802808 INFO::ASW Batch was 0.352316776952206 prior to batch effect correction and is now -0.0719966875754155 .
2026-03-11 21:25:53.803469 INFO::ASW Label was 0.322144446022225 prior to batch effect correction and is now 0.83612147626796 .
2026-03-11 21:25:53.804395 INFO::Total function execution time is 0.170809030532837 s and adjustment time is 0.149564027786255 s ( 87.56 )
2026-03-11 21:25:53.818366 INFO::Formatting Data.
2026-03-11 21:25:53.819261 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:53.820283 INFO::Removing potential empty rows and columns
2026-03-11 21:25:53.821374 INFO::Found 0 missing values.
2026-03-11 21:25:53.825688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:53.826347 INFO::Done
2026-03-11 21:25:53.826941 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:53.830127 INFO::Starting hierarchical adjustment
2026-03-11 21:25:53.830939 INFO::Found 5 batches.
2026-03-11 21:25:53.831537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:53.832239 INFO::Using default BPPARAM
2026-03-11 21:25:53.832828 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.
2026-03-11 21:25:53.942336 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:53.943997 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:25:53.960004 INFO::Done
2026-03-11 21:25:53.960787 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:53.964045 INFO::ASW Batch was 0.194998884477814 prior to batch effect correction and is now -0.106155556605601 .
2026-03-11 21:25:53.964733 INFO::ASW Label was 0.609924145507795 prior to batch effect correction and is now 0.832010027974607 .
2026-03-11 21:25:53.965583 INFO::Total function execution time is 0.147289752960205 s and adjustment time is 0.129190444946289 s ( 87.71 )
2026-03-11 21:25:53.96647 INFO::Formatting Data.
2026-03-11 21:25:53.967163 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:53.96812 INFO::Removing potential empty rows and columns
2026-03-11 21:25:53.969163 INFO::Found 0 missing values.
2026-03-11 21:25:53.973345 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:53.973989 INFO::Done
2026-03-11 21:25:53.974573 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:53.977677 INFO::Starting hierarchical adjustment
2026-03-11 21:25:53.978478 INFO::Found 5 batches.
2026-03-11 21:25:53.979082 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:53.979765 INFO::Using default BPPARAM
2026-03-11 21:25:53.980345 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.
2026-03-11 21:25:54.090175 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:54.091883 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:25:54.107798 INFO::Done
2026-03-11 21:25:54.108654 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.111889 INFO::ASW Batch was 0.194998884477814 prior to batch effect correction and is now -0.106155556605601 .
2026-03-11 21:25:54.11253 INFO::ASW Label was 0.609924145507795 prior to batch effect correction and is now 0.832010027974607 .
2026-03-11 21:25:54.113411 INFO::Total function execution time is 0.1469566822052 s and adjustment time is 0.129447460174561 s ( 88.09 )
2026-03-11 21:25:54.127136 INFO::Formatting Data.
2026-03-11 21:25:54.128042 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:54.129035 INFO::Removing potential empty rows and columns
2026-03-11 21:25:54.130097 INFO::Found 0 missing values.
2026-03-11 21:25:54.132873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:54.133485 INFO::Done
2026-03-11 21:25:54.134072 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:54.137043 INFO::Starting hierarchical adjustment
2026-03-11 21:25:54.13781 INFO::Found 2 batches.
2026-03-11 21:25:54.138391 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:54.139061 INFO::Using default BPPARAM
2026-03-11 21:25:54.139668 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:54.140629 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:25:54.155628 INFO::Done
2026-03-11 21:25:54.15636 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.159361 INFO::ASW Batch was 0.591534137046817 prior to batch effect correction and is now -0.00624419156032144 .
2026-03-11 21:25:54.16004 INFO::ASW Label was 0.431495578898423 prior to batch effect correction and is now 0.898062139785419 .
2026-03-11 21:25:54.160869 INFO::Total function execution time is 0.0338258743286133 s and adjustment time is 0.0179390907287598 s ( 53.03 )
2026-03-11 21:25:54.161697 INFO::Formatting Data.
2026-03-11 21:25:54.162358 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:54.163273 INFO::Removing potential empty rows and columns
2026-03-11 21:25:54.164291 INFO::Found 0 missing values.
2026-03-11 21:25:54.167092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:54.167686 INFO::Done
2026-03-11 21:25:54.168249 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:54.171198 INFO::Starting hierarchical adjustment
2026-03-11 21:25:54.171977 INFO::Found 2 batches.
2026-03-11 21:25:54.172557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:54.17321 INFO::Using default BPPARAM
2026-03-11 21:25:54.17381 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:54.174791 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:25:54.189641 INFO::Done
2026-03-11 21:25:54.190424 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.193495 INFO::ASW Batch was 0.591534137046817 prior to batch effect correction and is now -0.00624419156032144 .
2026-03-11 21:25:54.194227 INFO::ASW Label was 0.431495578898423 prior to batch effect correction and is now 0.898062139785419 .
2026-03-11 21:25:54.195073 INFO::Total function execution time is 0.0334079265594482 s and adjustment time is 0.0177788734436035 s ( 53.22 )
2026-03-11 21:25:54.206506 INFO::Formatting Data.
2026-03-11 21:25:54.207363 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:54.208318 INFO::Removing potential empty rows and columns
2026-03-11 21:25:54.209272 INFO::Found 0 missing values.
2026-03-11 21:25:54.211588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:54.21217 INFO::Done
2026-03-11 21:25:54.21274 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:54.214719 INFO::Starting hierarchical adjustment
2026-03-11 21:25:54.215456 INFO::Found 2 batches.
2026-03-11 21:25:54.216033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:54.216715 INFO::Using default BPPARAM
2026-03-11 21:25:54.217285 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:54.218234 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:25:54.249991 INFO::Done
2026-03-11 21:25:54.250819 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.252961 INFO::ASW Batch was 0.0827220857101909 prior to batch effect correction and is now -0.128749453527466 .
2026-03-11 21:25:54.253842 INFO::Total function execution time is 0.0474166870117188 s and adjustment time is 0.0346043109893799 s ( 72.98 )
2026-03-11 21:25:54.266276 INFO::Formatting Data.
2026-03-11 21:25:54.26722 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:54.268224 INFO::Removing potential empty rows and columns
2026-03-11 21:25:54.269278 INFO::Found 0 missing values.
2026-03-11 21:25:54.270452 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.
2026-03-11 21:25:54.275201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:54.275865 INFO::Done
2026-03-11 21:25:54.276441 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:54.279449 INFO::Starting hierarchical adjustment
2026-03-11 21:25:54.28022 INFO::Found 2 batches.
2026-03-11 21:25:54.280826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:54.281507 INFO::Using default BPPARAM
2026-03-11 21:25:54.282082 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:54.283077 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:25:54.299948 INFO::Done
2026-03-11 21:25:54.3007 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.303836 INFO::ASW Batch was 0.440269551127267 prior to batch effect correction and is now -0.0349965360126294 .
2026-03-11 21:25:54.30448 INFO::ASW Label was 0.589356850024846 prior to batch effect correction and is now 0.905920951700924 .
2026-03-11 21:25:54.305336 INFO::Total function execution time is 0.0391561985015869 s and adjustment time is 0.0198497772216797 s ( 50.69 )
2026-03-11 21:25:54.306185 INFO::Formatting Data.
2026-03-11 21:25:54.306864 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:54.307843 INFO::Removing potential empty rows and columns
2026-03-11 21:25:54.308871 INFO::Found 0 missing values.
2026-03-11 21:25:54.309851 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.
2026-03-11 21:25:54.314571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:54.315207 INFO::Done
2026-03-11 21:25:54.315786 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:54.318901 INFO::Starting hierarchical adjustment
2026-03-11 21:25:54.319683 INFO::Found 2 batches.
2026-03-11 21:25:54.320284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:54.320949 INFO::Using default BPPARAM
2026-03-11 21:25:54.321524 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:54.32258 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:25:54.339575 INFO::Done
2026-03-11 21:25:54.340334 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.343462 INFO::ASW Batch was 0.440269551127267 prior to batch effect correction and is now -0.0349965360126294 .
2026-03-11 21:25:54.344135 INFO::ASW Label was 0.589356850024846 prior to batch effect correction and is now 0.905920951700924 .
2026-03-11 21:25:54.344992 INFO::Total function execution time is 0.038818359375 s and adjustment time is 0.0200190544128418 s ( 51.57 )
2026-03-11 21:25:54.576692 INFO::Formatting Data.
2026-03-11 21:25:54.577716 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:54.57877 INFO::Removing potential empty rows and columns
2026-03-11 21:25:54.579936 INFO::Found 0 missing values.
2026-03-11 21:25:54.583165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:54.583832 INFO::Done
2026-03-11 21:25:54.58442 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:54.586576 INFO::Starting hierarchical adjustment
2026-03-11 21:25:54.587336 INFO::Found 3 batches.
2026-03-11 21:25:54.587939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:54.588626 INFO::Using default BPPARAM
2026-03-11 21:25:54.589206 INFO::Processing subtree level 1
2026-03-11 21:25:54.680995 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:25:54.68288 INFO::Done
2026-03-11 21:25:54.6836 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.686185 INFO::ASW Batch was -0.0299309976417441 prior to batch effect correction and is now -0.0299309976417441 .
2026-03-11 21:25:54.687224 INFO::Total function execution time is 0.110604524612427 s and adjustment time is 0.0956885814666748 s ( 86.51 )
2026-03-11 21:25:54.688341 INFO::Formatting Data.
2026-03-11 21:25:54.689074 INFO::Typecasting input to dataframe.
2026-03-11 21:25:54.689899 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:54.690892 INFO::Removing potential empty rows and columns
2026-03-11 21:25:54.692055 INFO::Found 0 missing values.
2026-03-11 21:25:54.695222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:54.695849 INFO::Done
2026-03-11 21:25:54.696442 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:54.698632 INFO::Starting hierarchical adjustment
2026-03-11 21:25:54.699413 INFO::Found 3 batches.
2026-03-11 21:25:54.700023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:54.700701 INFO::Using default BPPARAM
2026-03-11 21:25:54.701321 INFO::Processing subtree level 1
2026-03-11 21:25:54.841304 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:25:54.844007 INFO::Done
2026-03-11 21:25:54.84502 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.847811 INFO::ASW Batch was -0.0299309976417441 prior to batch effect correction and is now -0.0299309976417441 .
2026-03-11 21:25:54.84893 INFO::Total function execution time is 0.160553693771362 s and adjustment time is 0.144620418548584 s ( 90.08 )
2026-03-11 21:25:54.862652 INFO::Formatting Data.
2026-03-11 21:25:54.863563 INFO::Typecasting input to dataframe.
2026-03-11 21:25:54.864485 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:54.865476 INFO::Removing potential empty rows and columns
2026-03-11 21:25:54.866661 INFO::Found 0 missing values.
2026-03-11 21:25:54.869883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:54.870496 INFO::Done
2026-03-11 21:25:54.871118 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:54.873378 INFO::Starting hierarchical adjustment
2026-03-11 21:25:54.874206 INFO::Found 3 batches.
2026-03-11 21:25:54.874822 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:54.875518 INFO::Using default BPPARAM
2026-03-11 21:25:54.876139 INFO::Processing subtree level 1
2026-03-11 21:25:54.972316 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:25:54.974398 INFO::Done
2026-03-11 21:25:54.975154 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:54.977833 INFO::ASW Batch was -0.140074187270462 prior to batch effect correction and is now -0.140074187270462 .
2026-03-11 21:25:54.978856 INFO::Total function execution time is 0.116276264190674 s and adjustment time is 0.10034441947937 s ( 86.3 )
2026-03-11 21:25:55.124143 INFO::Formatting Data.
2026-03-11 21:25:55.125185 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:55.126489 INFO::Removing potential empty rows and columns
2026-03-11 21:25:55.129557 INFO::Found 1000 missing values.
2026-03-11 21:25:55.155047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:55.156027 INFO::Done
2026-03-11 21:25:55.156688 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:55.162482 INFO::Starting hierarchical adjustment
2026-03-11 21:25:55.163383 INFO::Found 10 batches.
2026-03-11 21:25:55.164028 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:55.16479 INFO::Using default BPPARAM
2026-03-11 21:25:55.165391 INFO::Processing subtree level 1
2026-03-11 21:25:55.344786 INFO::Processing subtree level 2
2026-03-11 21:25:55.627784 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:25:55.629916 INFO::Done
2026-03-11 21:25:55.630728 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:55.636888 INFO::ASW Batch was 0.562565874418089 prior to batch effect correction and is now 0.562565874418089 .
2026-03-11 21:25:55.63776 INFO::ASW Label was 0.268867220167119 prior to batch effect correction and is now 0.268867220167119 .
2026-03-11 21:25:55.638898 INFO::Total function execution time is 0.514768362045288 s and adjustment time is 0.466700315475464 s ( 90.66 )
2026-03-11 21:25:55.639883 INFO::Formatting Data.
2026-03-11 21:25:55.640656 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:55.642025 INFO::Removing potential empty rows and columns
2026-03-11 21:25:55.645268 INFO::Found 1000 missing values.
2026-03-11 21:25:55.722497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:55.723393 INFO::Done
2026-03-11 21:25:55.724057 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:55.729681 INFO::Starting hierarchical adjustment
2026-03-11 21:25:55.730579 INFO::Found 10 batches.
2026-03-11 21:25:56.92113 INFO::Set up parallel execution backend with 2 workers
2026-03-11 21:25:56.922475 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-11 21:25:58.133801 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:25:58.13684 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:25:58.152794 INFO::Done
2026-03-11 21:25:58.153494 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:58.157999 INFO::ASW Batch was 0.562565874418089 prior to batch effect correction and is now 0.562565874418089 .
2026-03-11 21:25:58.158638 INFO::ASW Label was 0.268867220167119 prior to batch effect correction and is now 0.268867220167119 .
2026-03-11 21:25:58.159399 INFO::Total function execution time is 2.51957154273987 s and adjustment time is 2.42238473892212 s ( 96.14 )
2026-03-11 21:25:58.334602 INFO::Formatting Data.
2026-03-11 21:25:58.335669 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.336806 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.338042 INFO::Found 0 missing values.
2026-03-11 21:25:58.342141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.342878 INFO::Done
2026-03-11 21:25:58.343493 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:25:58.346599 INFO::Starting hierarchical adjustment
2026-03-11 21:25:58.347431 INFO::Found 3 batches.
2026-03-11 21:25:58.348045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:25:58.348775 INFO::Using default BPPARAM
2026-03-11 21:25:58.349376 INFO::Processing subtree level 1
2026-03-11 21:25:58.478022 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:25:58.480318 INFO::Done
2026-03-11 21:25:58.4815 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:25:58.485759 INFO::ASW Batch was 0.169316060287217 prior to batch effect correction and is now -0.168618791010985 .
2026-03-11 21:25:58.486737 INFO::ASW Label was -0.146374168730615 prior to batch effect correction and is now 0.0621323718751362 .
2026-03-11 21:25:58.487938 INFO::Total function execution time is 0.153437852859497 s and adjustment time is 0.133003234863281 s ( 86.68 )
2026-03-11 21:25:58.617491 INFO::Formatting Data.
2026-03-11 21:25:58.618498 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.619439 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.620558 INFO::Found 2 missing values.
2026-03-11 21:25:58.62349 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.624124 INFO::Done
2026-03-11 21:25:58.651504 INFO::Found NA in Reference column
2026-03-11 21:25:58.660991 INFO::Require at least two references per batch.
2026-03-11 21:25:58.680726 INFO::Formatting Data.
2026-03-11 21:25:58.681619 INFO::Recognized SummarizedExperiment
2026-03-11 21:25:58.682253 INFO::Typecasting input to dataframe.
2026-03-11 21:25:58.691796 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.693034 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.696552 INFO::Found 0 missing values.
2026-03-11 21:25:58.703334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.703946 INFO::Done
2026-03-11 21:25:58.718653 INFO::Formatting Data.
2026-03-11 21:25:58.719345 INFO::Recognized SummarizedExperiment
2026-03-11 21:25:58.719914 INFO::Typecasting input to dataframe.
2026-03-11 21:25:58.736281 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.737473 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.740992 INFO::Found 0 missing values.
2026-03-11 21:25:58.761118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.76226 INFO::Done
2026-03-11 21:25:58.780936 INFO::Formatting Data.
2026-03-11 21:25:58.781791 INFO::Recognized SummarizedExperiment
2026-03-11 21:25:58.782381 INFO::Typecasting input to dataframe.
2026-03-11 21:25:58.800169 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.801532 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.802803 INFO::Found 0 missing values.
2026-03-11 21:25:58.80384 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.
2026-03-11 21:25:58.808727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.809354 INFO::Done
2026-03-11 21:25:58.820647 INFO::Formatting Data.
2026-03-11 21:25:58.821588 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.822531 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.823628 INFO::Found 0 missing values.
2026-03-11 21:25:58.826732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.827316 INFO::Done
2026-03-11 21:25:58.83979 INFO::Formatting Data.
2026-03-11 21:25:58.840672 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.841682 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.842861 INFO::Found 0 missing values.
2026-03-11 21:25:58.846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.846648 INFO::Done
2026-03-11 21:25:58.876164 INFO::Formatting Data.
2026-03-11 21:25:58.877038 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.878114 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.879366 INFO::Found 1 missing values.
2026-03-11 21:25:58.88207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.882697 INFO::Done
2026-03-11 21:25:58.90208 INFO::Formatting Data.
2026-03-11 21:25:58.903185 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.904484 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.905648 INFO::Found 2 missing values.
2026-03-11 21:25:58.906826 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.
2026-03-11 21:25:58.909505 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.910117 INFO::Done
2026-03-11 21:25:58.921558 INFO::Formatting Data.
2026-03-11 21:25:58.922561 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.923572 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.924557 INFO::Found 2 missing values.
2026-03-11 21:25:58.926238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.926847 INFO::Done
2026-03-11 21:25:58.937951 INFO::Formatting Data.
2026-03-11 21:25:58.939003 INFO::Typecasting input to dataframe.
2026-03-11 21:25:58.939951 INFO::Replacing NaNs with NAs.
2026-03-11 21:25:58.940936 INFO::Removing potential empty rows and columns
2026-03-11 21:25:58.942002 INFO::Found 0 missing values.
2026-03-11 21:25:58.944972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:25:58.945583 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.937 3.916 20.377
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.290 | 1.176 | 19.560 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |