Yannis Schumann
| Snapshot Date: 2026-03-04 13:40 -0500 (Wed, 04 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-05 11:34 -0500 (Thu, 05 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4891 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4583 |
| 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 169/2357 | 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: /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: 2026-03-04 21:38:24 -0500 (Wed, 04 Mar 2026) |
| EndedAt: 2026-03-04 21:39:56 -0500 (Wed, 04 Mar 2026) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.716 1.423 17.538
* 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) (2026-01-15 r89304) -- "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")
2026-03-04 21:39:16.074144 INFO::Formatting Data.
2026-03-04 21:39:16.075718 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:16.087767 INFO::Removing potential empty rows and columns
2026-03-04 21:39:16.344689 INFO::Found 0 missing values.
2026-03-04 21:39:16.348516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:16.349258 INFO::Done
2026-03-04 21:39:16.349839 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:16.363533 INFO::Starting hierarchical adjustment
2026-03-04 21:39:16.364531 INFO::Found 3 batches.
2026-03-04 21:39:16.365124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:16.366318 INFO::Using default BPPARAM
2026-03-04 21:39:16.366896 INFO::Processing subtree level 1
2026-03-04 21:39:16.493492 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:39:16.495771 INFO::Done
2026-03-04 21:39:16.496573 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:16.499812 INFO::ASW Batch was -0.0672265154416488 prior to batch effect correction and is now -0.0672265154416488 .
2026-03-04 21:39:16.501093 INFO::Total function execution time is 0.427662372589111 s and adjustment time is 0.131402015686035 s ( 30.73 )
2026-03-04 21:39:16.516913 INFO::Formatting Data.
2026-03-04 21:39:16.517864 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:16.518932 INFO::Removing potential empty rows and columns
2026-03-04 21:39:16.520261 INFO::Found 0 missing values.
2026-03-04 21:39:16.521393 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.
2026-03-04 21:39:16.533684 INFO::Formatting Data.
2026-03-04 21:39:16.534688 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:16.535769 INFO::Removing potential empty rows and columns
2026-03-04 21:39:16.53694 INFO::Found 0 missing values.
2026-03-04 21:39:16.537987 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.
2026-03-04 21:39:16.55597 INFO::Formatting Data.
2026-03-04 21:39:16.556951 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:16.558197 INFO::Removing potential empty rows and columns
2026-03-04 21:39:16.559799 INFO::Found 0 missing values.
2026-03-04 21:39:16.560978 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.
2026-03-04 21:39:16.567236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:16.568099 INFO::Done
2026-03-04 21:39:16.568807 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:16.57163 INFO::Starting hierarchical adjustment
2026-03-04 21:39:16.572589 INFO::Found 2 batches.
2026-03-04 21:39:16.573268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:16.574091 INFO::Using default BPPARAM
2026-03-04 21:39:16.574771 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:16.576004 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:39:16.60226 INFO::Done
2026-03-04 21:39:16.603179 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:16.605865 INFO::ASW Batch was -0.0898500648190971 prior to batch effect correction and is now -0.119410177778317 .
2026-03-04 21:39:16.606835 INFO::Total function execution time is 0.0509824752807617 s and adjustment time is 0.0298523902893066 s ( 58.55 )
2026-03-04 21:39:16.61011 INFO::Formatting Data.
2026-03-04 21:39:16.610836 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:16.620527 INFO::Formatting Data.
2026-03-04 21:39:16.621413 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:16.622404 INFO::Removing potential empty rows and columns
2026-03-04 21:39:16.623751 INFO::Found 0 missing values.
2026-03-04 21:39:16.62692 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:16.627515 INFO::Done
2026-03-04 21:39:16.62806 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:16.630301 INFO::Starting hierarchical adjustment
2026-03-04 21:39:16.631073 INFO::Found 2 batches.
2026-03-04 21:39:16.631638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:16.632305 INFO::Using default BPPARAM
2026-03-04 21:39:16.632874 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:16.633882 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:39:16.678638 INFO::Done
2026-03-04 21:39:16.679451 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:16.681695 INFO::ASW Batch was 0.0525305823965424 prior to batch effect correction and is now -0.0937368912324434 .
2026-03-04 21:39:16.68258 INFO::Total function execution time is 0.0621635913848877 s and adjustment time is 0.047675609588623 s ( 76.69 )
2026-03-04 21:39:16.683723 INFO::Formatting Data.
2026-03-04 21:39:16.684345 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:16.685267 INFO::Removing potential empty rows and columns
2026-03-04 21:39:16.686364 INFO::Found 0 missing values.
2026-03-04 21:39:16.68947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:16.690073 INFO::Done
2026-03-04 21:39:16.690602 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:16.692842 INFO::Starting hierarchical adjustment
2026-03-04 21:39:16.693562 INFO::Found 2 batches.
2026-03-04 21:39:16.694094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:16.69471 INFO::Using default BPPARAM
2026-03-04 21:39:16.695229 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:16.696181 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:39:16.711581 INFO::Done
2026-03-04 21:39:16.712314 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:16.71447 INFO::ASW Batch was 0.0525305823965424 prior to batch effect correction and is now -0.0937368912324434 .
2026-03-04 21:39:16.715294 INFO::Total function execution time is 0.0315663814544678 s and adjustment time is 0.018146276473999 s ( 57.49 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-04 21:39:20.422097 INFO::Formatting Data.
2026-03-04 21:39:20.42308 INFO::Recognized SummarizedExperiment
2026-03-04 21:39:20.423781 INFO::Typecasting input to dataframe.
2026-03-04 21:39:20.457156 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:20.458521 INFO::Removing potential empty rows and columns
2026-03-04 21:39:20.462739 INFO::Found 0 missing values.
2026-03-04 21:39:20.470442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:20.471138 INFO::Done
2026-03-04 21:39:20.471707 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:20.475651 INFO::Starting hierarchical adjustment
2026-03-04 21:39:20.476419 INFO::Found 2 batches.
2026-03-04 21:39:20.476956 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:20.478136 INFO::Using default BPPARAM
2026-03-04 21:39:20.478691 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:20.4797 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:39:20.539244 INFO::Done
2026-03-04 21:39:20.539982 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:20.543603 INFO::ASW Batch was -0.00142805910798994 prior to batch effect correction and is now -0.0919066683579122 .
2026-03-04 21:39:20.544479 INFO::Total function execution time is 0.122738361358643 s and adjustment time is 0.0629820823669434 s ( 51.31 )
Warning: stack imbalance in '{', 73 then 75
2026-03-04 21:39:20.563915 INFO::Formatting Data.
2026-03-04 21:39:20.564705 INFO::Recognized SummarizedExperiment
2026-03-04 21:39:20.565266 INFO::Typecasting input to dataframe.
2026-03-04 21:39:20.574787 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:20.576073 INFO::Removing potential empty rows and columns
2026-03-04 21:39:20.580041 INFO::Found 0 missing values.
2026-03-04 21:39:20.58762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:20.588211 INFO::Done
2026-03-04 21:39:20.588756 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:20.592363 INFO::Starting hierarchical adjustment
2026-03-04 21:39:20.593101 INFO::Found 2 batches.
2026-03-04 21:39:20.593632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:20.594258 INFO::Using default BPPARAM
2026-03-04 21:39:20.594809 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:20.5958 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:39:20.621753 INFO::Done
2026-03-04 21:39:20.622487 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:20.626026 INFO::ASW Batch was -0.0157752036618299 prior to batch effect correction and is now -0.0157752036618299 .
2026-03-04 21:39:20.626894 INFO::Total function execution time is 0.0629668235778809 s and adjustment time is 0.0287680625915527 s ( 45.69 )
2026-03-04 21:39:20.645241 INFO::Formatting Data.
2026-03-04 21:39:20.646051 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:20.646973 INFO::Removing potential empty rows and columns
2026-03-04 21:39:20.648002 INFO::Found 0 missing values.
2026-03-04 21:39:20.650987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:20.651543 INFO::Done
2026-03-04 21:39:20.65206 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:20.654277 INFO::Starting hierarchical adjustment
2026-03-04 21:39:20.654988 INFO::Found 3 batches.
2026-03-04 21:39:20.655522 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:20.656125 INFO::Using default BPPARAM
2026-03-04 21:39:20.65667 INFO::Processing subtree level 1
2026-03-04 21:39:20.800111 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:39:20.8021 INFO::Done
2026-03-04 21:39:20.802763 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:20.805423 INFO::ASW Batch was 0.0544684742904709 prior to batch effect correction and is now -0.197682480715771 .
2026-03-04 21:39:20.806397 INFO::Total function execution time is 0.161163568496704 s and adjustment time is 0.147231340408325 s ( 91.36 )
2026-03-04 21:39:20.821338 INFO::Skipping initial DF formatting
2026-03-04 21:39:20.822064 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:20.826192 INFO::Starting hierarchical adjustment
2026-03-04 21:39:20.82699 INFO::Found 5 batches.
2026-03-04 21:39:20.82755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:20.82819 INFO::Using default BPPARAM
2026-03-04 21:39:20.828745 INFO::Processing subtree level 1
2026-03-04 21:39:21.070142 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:21.071778 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:39:21.092017 INFO::Done
2026-03-04 21:39:21.092776 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:21.148195 INFO::ASW Batch was 0.53138038822247 prior to batch effect correction and is now 0.53138038822247 .
2026-03-04 21:39:21.149537 INFO::ASW Label was 0.355983486417546 prior to batch effect correction and is now 0.355983486417546 .
2026-03-04 21:39:21.150458 INFO::Total function execution time is 0.3292236328125 s and adjustment time is 0.26516318321228 s ( 80.54 )
2026-03-04 21:39:21.169363 INFO::Formatting Data.
2026-03-04 21:39:21.170167 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:21.171126 INFO::Removing potential empty rows and columns
2026-03-04 21:39:21.172247 INFO::Found 0 missing values.
2026-03-04 21:39:21.176805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:21.177389 INFO::Done
2026-03-04 21:39:21.178024 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:21.181247 INFO::Starting hierarchical adjustment
2026-03-04 21:39:21.182003 INFO::Found 5 batches.
2026-03-04 21:39:21.182567 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:21.18321 INFO::Using default BPPARAM
2026-03-04 21:39:21.183799 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.
2026-03-04 21:39:21.333086 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:21.33477 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:39:21.352541 INFO::Done
2026-03-04 21:39:21.353438 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:21.357003 INFO::ASW Batch was 0.313873241870538 prior to batch effect correction and is now -0.068599006930536 .
2026-03-04 21:39:21.357686 INFO::ASW Label was 0.276877394026276 prior to batch effect correction and is now 0.800201842577878 .
2026-03-04 21:39:21.35857 INFO::Total function execution time is 0.189261674880981 s and adjustment time is 0.170655250549316 s ( 90.17 )
2026-03-04 21:39:21.359478 INFO::Formatting Data.
2026-03-04 21:39:21.360158 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:21.361179 INFO::Removing potential empty rows and columns
2026-03-04 21:39:21.36242 INFO::Found 0 missing values.
2026-03-04 21:39:21.366941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:21.36755 INFO::Done
2026-03-04 21:39:21.368098 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:21.371322 INFO::Starting hierarchical adjustment
2026-03-04 21:39:21.372092 INFO::Found 5 batches.
2026-03-04 21:39:21.372653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:21.373298 INFO::Using default BPPARAM
2026-03-04 21:39:21.373875 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.
2026-03-04 21:39:21.508967 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:21.511059 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:39:21.530138 INFO::Done
2026-03-04 21:39:21.531096 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:21.535285 INFO::ASW Batch was 0.313873241870538 prior to batch effect correction and is now -0.068599006930536 .
2026-03-04 21:39:21.536054 INFO::ASW Label was 0.276877394026276 prior to batch effect correction and is now 0.800201842577878 .
2026-03-04 21:39:21.537078 INFO::Total function execution time is 0.17759370803833 s and adjustment time is 0.158124685287476 s ( 89.04 )
2026-03-04 21:39:21.553558 INFO::Formatting Data.
2026-03-04 21:39:21.554503 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:21.555535 INFO::Removing potential empty rows and columns
2026-03-04 21:39:21.556659 INFO::Found 0 missing values.
2026-03-04 21:39:21.561183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:21.561833 INFO::Done
2026-03-04 21:39:21.562427 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:21.565767 INFO::Starting hierarchical adjustment
2026-03-04 21:39:21.566551 INFO::Found 5 batches.
2026-03-04 21:39:21.567102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:21.567784 INFO::Using default BPPARAM
2026-03-04 21:39:21.568356 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.
2026-03-04 21:39:21.694103 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:21.695662 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:39:21.711016 INFO::Done
2026-03-04 21:39:21.711728 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:21.723707 INFO::ASW Batch was 0.385512151974333 prior to batch effect correction and is now -0.110645901168008 .
2026-03-04 21:39:21.724674 INFO::ASW Label was 0.365499092440314 prior to batch effect correction and is now 0.87228937331685 .
2026-03-04 21:39:21.72572 INFO::Total function execution time is 0.172305583953857 s and adjustment time is 0.144634246826172 s ( 83.94 )
2026-03-04 21:39:21.726565 INFO::Formatting Data.
2026-03-04 21:39:21.727198 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:21.728297 INFO::Removing potential empty rows and columns
2026-03-04 21:39:21.72945 INFO::Found 0 missing values.
2026-03-04 21:39:21.733769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:21.734364 INFO::Done
2026-03-04 21:39:21.73496 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:21.738229 INFO::Starting hierarchical adjustment
2026-03-04 21:39:21.738968 INFO::Found 5 batches.
2026-03-04 21:39:21.739527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:21.740182 INFO::Using default BPPARAM
2026-03-04 21:39:21.740715 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.
2026-03-04 21:39:21.866462 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:21.868096 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:39:21.886632 INFO::Done
2026-03-04 21:39:21.887499 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:21.891666 INFO::ASW Batch was 0.385512151974333 prior to batch effect correction and is now -0.110645901168008 .
2026-03-04 21:39:21.89231 INFO::ASW Label was 0.365499092440314 prior to batch effect correction and is now 0.87228937331685 .
2026-03-04 21:39:21.893179 INFO::Total function execution time is 0.166599035263062 s and adjustment time is 0.147798776626587 s ( 88.72 )
2026-03-04 21:39:21.907834 INFO::Formatting Data.
2026-03-04 21:39:21.908599 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:21.909497 INFO::Removing potential empty rows and columns
2026-03-04 21:39:21.9105 INFO::Found 0 missing values.
2026-03-04 21:39:21.913145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:21.913726 INFO::Done
2026-03-04 21:39:21.914245 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:21.917141 INFO::Starting hierarchical adjustment
2026-03-04 21:39:21.917864 INFO::Found 2 batches.
2026-03-04 21:39:21.918396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:21.919013 INFO::Using default BPPARAM
2026-03-04 21:39:21.919571 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:21.92046 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:39:21.934347 INFO::Done
2026-03-04 21:39:21.934936 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:21.93769 INFO::ASW Batch was 0.365681389226823 prior to batch effect correction and is now 0.0361496962588355 .
2026-03-04 21:39:21.938252 INFO::ASW Label was 0.649013809092276 prior to batch effect correction and is now 0.902444052925623 .
2026-03-04 21:39:21.939041 INFO::Total function execution time is 0.0312700271606445 s and adjustment time is 0.0166327953338623 s ( 53.19 )
2026-03-04 21:39:21.939825 INFO::Formatting Data.
2026-03-04 21:39:21.940426 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:21.94125 INFO::Removing potential empty rows and columns
2026-03-04 21:39:21.942187 INFO::Found 0 missing values.
2026-03-04 21:39:21.944755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:21.945295 INFO::Done
2026-03-04 21:39:21.945812 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:21.948537 INFO::Starting hierarchical adjustment
2026-03-04 21:39:21.949215 INFO::Found 2 batches.
2026-03-04 21:39:21.949739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:21.950327 INFO::Using default BPPARAM
2026-03-04 21:39:21.951031 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:21.95193 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:39:21.965793 INFO::Done
2026-03-04 21:39:21.966402 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:21.969137 INFO::ASW Batch was 0.365681389226823 prior to batch effect correction and is now 0.0361496962588355 .
2026-03-04 21:39:21.969697 INFO::ASW Label was 0.649013809092276 prior to batch effect correction and is now 0.902444052925623 .
2026-03-04 21:39:21.970476 INFO::Total function execution time is 0.0306551456451416 s and adjustment time is 0.0167117118835449 s ( 54.52 )
2026-03-04 21:39:21.981337 INFO::Formatting Data.
2026-03-04 21:39:21.982054 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:21.9829 INFO::Removing potential empty rows and columns
2026-03-04 21:39:21.983782 INFO::Found 0 missing values.
2026-03-04 21:39:21.985799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:21.986346 INFO::Done
2026-03-04 21:39:21.986874 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:21.988678 INFO::Starting hierarchical adjustment
2026-03-04 21:39:21.989338 INFO::Found 2 batches.
2026-03-04 21:39:21.989865 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:21.990457 INFO::Using default BPPARAM
2026-03-04 21:39:21.990991 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:21.99185 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:39:22.021963 INFO::Done
2026-03-04 21:39:22.022687 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:22.024605 INFO::ASW Batch was -0.117064936453135 prior to batch effect correction and is now -0.166806233271677 .
2026-03-04 21:39:22.025398 INFO::Total function execution time is 0.0441014766693115 s and adjustment time is 0.0327284336090088 s ( 74.21 )
2026-03-04 21:39:22.036875 INFO::Formatting Data.
2026-03-04 21:39:22.037611 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:22.038473 INFO::Removing potential empty rows and columns
2026-03-04 21:39:22.03944 INFO::Found 0 missing values.
2026-03-04 21:39:22.040579 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.
2026-03-04 21:39:22.045065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:22.045625 INFO::Done
2026-03-04 21:39:22.046151 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:22.049176 INFO::Starting hierarchical adjustment
2026-03-04 21:39:22.049901 INFO::Found 2 batches.
2026-03-04 21:39:22.050447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:22.051058 INFO::Using default BPPARAM
2026-03-04 21:39:22.051653 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:22.052589 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:39:22.068407 INFO::Done
2026-03-04 21:39:22.069067 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:22.072157 INFO::ASW Batch was 0.483245047741984 prior to batch effect correction and is now 0.0052133491189854 .
2026-03-04 21:39:22.072791 INFO::ASW Label was 0.496600247350911 prior to batch effect correction and is now 0.930223173373794 .
2026-03-04 21:39:22.073584 INFO::Total function execution time is 0.0367858409881592 s and adjustment time is 0.0186269283294678 s ( 50.64 )
2026-03-04 21:39:22.074358 INFO::Formatting Data.
2026-03-04 21:39:22.07499 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:22.075881 INFO::Removing potential empty rows and columns
2026-03-04 21:39:22.076821 INFO::Found 0 missing values.
2026-03-04 21:39:22.077696 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.
2026-03-04 21:39:22.082111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:22.08266 INFO::Done
2026-03-04 21:39:22.083172 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:22.085964 INFO::Starting hierarchical adjustment
2026-03-04 21:39:22.08668 INFO::Found 2 batches.
2026-03-04 21:39:22.087233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:22.087849 INFO::Using default BPPARAM
2026-03-04 21:39:22.088381 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:22.089307 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:39:22.105427 INFO::Done
2026-03-04 21:39:22.106136 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:22.109051 INFO::ASW Batch was 0.483245047741984 prior to batch effect correction and is now 0.0052133491189854 .
2026-03-04 21:39:22.109683 INFO::ASW Label was 0.496600247350911 prior to batch effect correction and is now 0.930223173373794 .
2026-03-04 21:39:22.110504 INFO::Total function execution time is 0.036149263381958 s and adjustment time is 0.018867015838623 s ( 52.19 )
2026-03-04 21:39:22.316271 INFO::Formatting Data.
2026-03-04 21:39:22.317153 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:22.318116 INFO::Removing potential empty rows and columns
2026-03-04 21:39:22.319227 INFO::Found 0 missing values.
2026-03-04 21:39:22.322346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:22.322918 INFO::Done
2026-03-04 21:39:22.323456 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:22.32552 INFO::Starting hierarchical adjustment
2026-03-04 21:39:22.326236 INFO::Found 3 batches.
2026-03-04 21:39:22.326785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:22.327445 INFO::Using default BPPARAM
2026-03-04 21:39:22.327979 INFO::Processing subtree level 1
2026-03-04 21:39:22.413887 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:39:22.415661 INFO::Done
2026-03-04 21:39:22.416304 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:22.418773 INFO::ASW Batch was -0.0611885759941571 prior to batch effect correction and is now -0.0611885759941571 .
2026-03-04 21:39:22.419785 INFO::Total function execution time is 0.103569507598877 s and adjustment time is 0.0895593166351318 s ( 86.47 )
2026-03-04 21:39:22.420855 INFO::Formatting Data.
2026-03-04 21:39:22.421535 INFO::Typecasting input to dataframe.
2026-03-04 21:39:22.422294 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:22.423219 INFO::Removing potential empty rows and columns
2026-03-04 21:39:22.424304 INFO::Found 0 missing values.
2026-03-04 21:39:22.427377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:22.427959 INFO::Done
2026-03-04 21:39:22.428525 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:22.430537 INFO::Starting hierarchical adjustment
2026-03-04 21:39:22.431285 INFO::Found 3 batches.
2026-03-04 21:39:22.431837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:22.432466 INFO::Using default BPPARAM
2026-03-04 21:39:22.433008 INFO::Processing subtree level 1
2026-03-04 21:39:22.515682 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:39:22.517508 INFO::Done
2026-03-04 21:39:22.51816 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:22.520615 INFO::ASW Batch was -0.0611885759941571 prior to batch effect correction and is now -0.0611885759941571 .
2026-03-04 21:39:22.521578 INFO::Total function execution time is 0.100687503814697 s and adjustment time is 0.0863461494445801 s ( 85.76 )
2026-03-04 21:39:22.53811 INFO::Formatting Data.
2026-03-04 21:39:22.539031 INFO::Typecasting input to dataframe.
2026-03-04 21:39:22.539921 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:22.540887 INFO::Removing potential empty rows and columns
2026-03-04 21:39:22.542035 INFO::Found 0 missing values.
2026-03-04 21:39:22.545099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:22.545668 INFO::Done
2026-03-04 21:39:22.546211 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:22.548577 INFO::Starting hierarchical adjustment
2026-03-04 21:39:22.54932 INFO::Found 3 batches.
2026-03-04 21:39:22.549867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:22.55055 INFO::Using default BPPARAM
2026-03-04 21:39:22.551099 INFO::Processing subtree level 1
2026-03-04 21:39:22.636246 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:39:22.638283 INFO::Done
2026-03-04 21:39:22.639038 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:22.641646 INFO::ASW Batch was 0.0196472197410069 prior to batch effect correction and is now 0.0196472197410069 .
2026-03-04 21:39:22.642634 INFO::Total function execution time is 0.104619026184082 s and adjustment time is 0.0890967845916748 s ( 85.16 )
2026-03-04 21:39:22.776129 INFO::Formatting Data.
2026-03-04 21:39:22.776937 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:22.778049 INFO::Removing potential empty rows and columns
2026-03-04 21:39:22.78094 INFO::Found 1000 missing values.
2026-03-04 21:39:22.800775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:22.801508 INFO::Done
2026-03-04 21:39:22.802081 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:22.807489 INFO::Starting hierarchical adjustment
2026-03-04 21:39:22.80825 INFO::Found 10 batches.
2026-03-04 21:39:22.808809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:22.809472 INFO::Using default BPPARAM
2026-03-04 21:39:22.810023 INFO::Processing subtree level 1
2026-03-04 21:39:22.948716 INFO::Processing subtree level 2
2026-03-04 21:39:23.0927 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:39:23.095009 INFO::Done
2026-03-04 21:39:23.095821 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:23.102349 INFO::ASW Batch was 0.511355301309789 prior to batch effect correction and is now 0.511355301309789 .
2026-03-04 21:39:23.103138 INFO::ASW Label was 0.3030679807068 prior to batch effect correction and is now 0.3030679807068 .
2026-03-04 21:39:23.104194 INFO::Total function execution time is 0.328096389770508 s and adjustment time is 0.286880016326904 s ( 87.44 )
2026-03-04 21:39:23.10513 INFO::Formatting Data.
2026-03-04 21:39:23.105868 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:23.107241 INFO::Removing potential empty rows and columns
2026-03-04 21:39:23.110487 INFO::Found 1000 missing values.
2026-03-04 21:39:23.132924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:23.133788 INFO::Done
2026-03-04 21:39:23.134439 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:23.140648 INFO::Starting hierarchical adjustment
2026-03-04 21:39:23.141521 INFO::Found 10 batches.
2026-03-04 21:39:24.28013 INFO::Set up parallel execution backend with 2 workers
2026-03-04 21:39:24.282112 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-04 21:39:25.414567 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:39:25.417045 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:39:25.435387 INFO::Done
2026-03-04 21:39:25.436108 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:25.440987 INFO::ASW Batch was 0.511355301309789 prior to batch effect correction and is now 0.511355301309789 .
2026-03-04 21:39:25.441659 INFO::ASW Label was 0.3030679807068 prior to batch effect correction and is now 0.3030679807068 .
2026-03-04 21:39:25.442429 INFO::Total function execution time is 2.33734130859375 s and adjustment time is 2.29402589797974 s ( 98.15 )
2026-03-04 21:39:25.610688 INFO::Formatting Data.
2026-03-04 21:39:25.611538 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:25.612492 INFO::Removing potential empty rows and columns
2026-03-04 21:39:25.613632 INFO::Found 0 missing values.
2026-03-04 21:39:25.617529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:25.618097 INFO::Done
2026-03-04 21:39:25.618647 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:39:25.621607 INFO::Starting hierarchical adjustment
2026-03-04 21:39:25.622358 INFO::Found 3 batches.
2026-03-04 21:39:25.62294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:39:25.623599 INFO::Using default BPPARAM
2026-03-04 21:39:25.624184 INFO::Processing subtree level 1
2026-03-04 21:39:25.74861 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:39:25.750724 INFO::Done
2026-03-04 21:39:25.751492 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:39:25.755055 INFO::ASW Batch was 0.194328281061801 prior to batch effect correction and is now -0.164685732894047 .
2026-03-04 21:39:25.755803 INFO::ASW Label was -0.182171306352094 prior to batch effect correction and is now 0.0483131533239689 .
2026-03-04 21:39:25.756868 INFO::Total function execution time is 0.146213054656982 s and adjustment time is 0.128482103347778 s ( 87.87 )
2026-03-04 21:39:25.884506 INFO::Formatting Data.
2026-03-04 21:39:25.88547 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:25.886449 INFO::Removing potential empty rows and columns
2026-03-04 21:39:25.887566 INFO::Found 2 missing values.
2026-03-04 21:39:25.890592 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:25.891176 INFO::Done
2026-03-04 21:39:25.920156 INFO::Found NA in Reference column
2026-03-04 21:39:25.930246 INFO::Require at least two references per batch.
2026-03-04 21:39:25.951476 INFO::Formatting Data.
2026-03-04 21:39:25.952274 INFO::Recognized SummarizedExperiment
2026-03-04 21:39:25.952858 INFO::Typecasting input to dataframe.
2026-03-04 21:39:25.962651 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:25.96388 INFO::Removing potential empty rows and columns
2026-03-04 21:39:25.967704 INFO::Found 0 missing values.
2026-03-04 21:39:25.974979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:25.975672 INFO::Done
2026-03-04 21:39:25.992746 INFO::Formatting Data.
2026-03-04 21:39:25.993639 INFO::Recognized SummarizedExperiment
2026-03-04 21:39:25.994205 INFO::Typecasting input to dataframe.
2026-03-04 21:39:26.011642 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:26.012907 INFO::Removing potential empty rows and columns
2026-03-04 21:39:26.016709 INFO::Found 0 missing values.
2026-03-04 21:39:26.028338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:26.029098 INFO::Done
2026-03-04 21:39:26.044666 INFO::Formatting Data.
2026-03-04 21:39:26.045471 INFO::Recognized SummarizedExperiment
2026-03-04 21:39:26.046031 INFO::Typecasting input to dataframe.
2026-03-04 21:39:26.062885 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:26.063989 INFO::Removing potential empty rows and columns
2026-03-04 21:39:26.065163 INFO::Found 0 missing values.
2026-03-04 21:39:26.0661 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.
2026-03-04 21:39:26.070637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:26.071206 INFO::Done
2026-03-04 21:39:26.081676 INFO::Formatting Data.
2026-03-04 21:39:26.082519 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:26.08345 INFO::Removing potential empty rows and columns
2026-03-04 21:39:26.084472 INFO::Found 0 missing values.
2026-03-04 21:39:26.087423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:26.087988 INFO::Done
2026-03-04 21:39:26.099849 INFO::Formatting Data.
2026-03-04 21:39:26.100704 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:26.101589 INFO::Removing potential empty rows and columns
2026-03-04 21:39:26.102645 INFO::Found 0 missing values.
2026-03-04 21:39:26.105546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:26.106078 INFO::Done
2026-03-04 21:39:26.135491 INFO::Formatting Data.
2026-03-04 21:39:26.136336 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:26.13741 INFO::Removing potential empty rows and columns
2026-03-04 21:39:26.138558 INFO::Found 1 missing values.
2026-03-04 21:39:26.141143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:26.141711 INFO::Done
2026-03-04 21:39:26.160556 INFO::Formatting Data.
2026-03-04 21:39:26.161404 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:26.162282 INFO::Removing potential empty rows and columns
2026-03-04 21:39:26.163275 INFO::Found 2 missing values.
2026-03-04 21:39:26.164198 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.
2026-03-04 21:39:26.166561 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:26.167087 INFO::Done
2026-03-04 21:39:26.176945 INFO::Formatting Data.
2026-03-04 21:39:26.177748 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:26.178621 INFO::Removing potential empty rows and columns
2026-03-04 21:39:26.179547 INFO::Found 2 missing values.
2026-03-04 21:39:26.181089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:26.181639 INFO::Done
2026-03-04 21:39:26.191803 INFO::Formatting Data.
2026-03-04 21:39:26.192575 INFO::Typecasting input to dataframe.
2026-03-04 21:39:26.193374 INFO::Replacing NaNs with NAs.
2026-03-04 21:39:26.194211 INFO::Removing potential empty rows and columns
2026-03-04 21:39:26.195191 INFO::Found 0 missing values.
2026-03-04 21:39:26.198032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:39:26.198591 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.766 4.332 20.827
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.716 | 1.423 | 17.538 | |
| compute_asw | 0.027 | 0.000 | 0.027 | |
| count_existing | 0.015 | 0.001 | 0.016 | |
| generate_data_covariables | 0.010 | 0.003 | 0.014 | |
| generate_dataset | 0.010 | 0.003 | 0.013 | |