Yannis Schumann
| Snapshot Date: 2026-04-30 13:40 -0400 (Thu, 30 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_23 |
| git_last_commit: 0c9135c |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-01 11:35 -0400 (Fri, 01 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4718 |
| 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 172/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.8.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2026-04-30 21:43:38 -0400 (Thu, 30 Apr 2026) |
| EndedAt: 2026-04-30 21:45:10 -0400 (Thu, 30 Apr 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-01 01:43:38 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.8.0’
* 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 23.803 1.67 17.889
* 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 ‘1.8.0’ ** 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 version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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")
2026-04-30 21:44:30.057852 INFO::Formatting Data.
2026-04-30 21:44:30.059219 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:30.070501 INFO::Removing potential empty rows and columns
2026-04-30 21:44:30.316218 INFO::Found 0 missing values.
2026-04-30 21:44:30.320085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:30.320905 INFO::Done
2026-04-30 21:44:30.321541 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:30.335537 INFO::Starting hierarchical adjustment
2026-04-30 21:44:30.336468 INFO::Found 3 batches.
2026-04-30 21:44:30.337068 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:30.33826 INFO::Using default BPPARAM
2026-04-30 21:44:30.338886 INFO::Processing subtree level 1
2026-04-30 21:44:30.442574 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:44:30.444516 INFO::Done
2026-04-30 21:44:30.445254 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:30.447944 INFO::ASW Batch was -0.0367528453782524 prior to batch effect correction and is now -0.0367528453782524 .
2026-04-30 21:44:30.449074 INFO::Total function execution time is 0.391865730285645 s and adjustment time is 0.108208417892456 s ( 27.61 )
2026-04-30 21:44:30.463358 INFO::Formatting Data.
2026-04-30 21:44:30.464211 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:30.465178 INFO::Removing potential empty rows and columns
2026-04-30 21:44:30.466308 INFO::Found 0 missing values.
2026-04-30 21:44:30.467304 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.
2026-04-30 21:44:30.478274 INFO::Formatting Data.
2026-04-30 21:44:30.479117 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:30.48013 INFO::Removing potential empty rows and columns
2026-04-30 21:44:30.481325 INFO::Found 0 missing values.
2026-04-30 21:44:30.482311 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.
2026-04-30 21:44:30.498934 INFO::Formatting Data.
2026-04-30 21:44:30.499873 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:30.500821 INFO::Removing potential empty rows and columns
2026-04-30 21:44:30.501897 INFO::Found 0 missing values.
2026-04-30 21:44:30.502856 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.
2026-04-30 21:44:30.507353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:30.507954 INFO::Done
2026-04-30 21:44:30.508505 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:30.510598 INFO::Starting hierarchical adjustment
2026-04-30 21:44:30.511347 INFO::Found 2 batches.
2026-04-30 21:44:30.511939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:30.512646 INFO::Using default BPPARAM
2026-04-30 21:44:30.513245 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:30.514254 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:44:30.536002 INFO::Done
2026-04-30 21:44:30.536777 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:30.538904 INFO::ASW Batch was 0.0385854577780129 prior to batch effect correction and is now -0.112284605873688 .
2026-04-30 21:44:30.539774 INFO::Total function execution time is 0.0409464836120605 s and adjustment time is 0.024766206741333 s ( 60.48 )
2026-04-30 21:44:30.542767 INFO::Formatting Data.
2026-04-30 21:44:30.543474 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:30.552901 INFO::Formatting Data.
2026-04-30 21:44:30.553806 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:30.554823 INFO::Removing potential empty rows and columns
2026-04-30 21:44:30.555961 INFO::Found 0 missing values.
2026-04-30 21:44:30.559027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:30.559636 INFO::Done
2026-04-30 21:44:30.560201 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:30.562341 INFO::Starting hierarchical adjustment
2026-04-30 21:44:30.563103 INFO::Found 2 batches.
2026-04-30 21:44:30.563671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:30.564349 INFO::Using default BPPARAM
2026-04-30 21:44:30.564924 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:30.565892 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:44:30.582231 INFO::Done
2026-04-30 21:44:30.583039 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:30.585211 INFO::ASW Batch was -0.0282424124271366 prior to batch effect correction and is now -0.110607698138318 .
2026-04-30 21:44:30.586133 INFO::Total function execution time is 0.0333206653594971 s and adjustment time is 0.0192716121673584 s ( 57.84 )
2026-04-30 21:44:30.587279 INFO::Formatting Data.
2026-04-30 21:44:30.588181 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:30.589131 INFO::Removing potential empty rows and columns
2026-04-30 21:44:30.590286 INFO::Found 0 missing values.
2026-04-30 21:44:30.593287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:30.59391 INFO::Done
2026-04-30 21:44:30.594488 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:30.596662 INFO::Starting hierarchical adjustment
2026-04-30 21:44:30.59745 INFO::Found 2 batches.
2026-04-30 21:44:30.598048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:30.598746 INFO::Using default BPPARAM
2026-04-30 21:44:30.599341 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:30.600304 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:44:30.615581 INFO::Done
2026-04-30 21:44:30.616328 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:30.618364 INFO::ASW Batch was -0.0282424124271366 prior to batch effect correction and is now -0.110607698138318 .
2026-04-30 21:44:30.619172 INFO::Total function execution time is 0.0319011211395264 s and adjustment time is 0.018261194229126 s ( 57.24 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-30 21:44:33.907092 INFO::Formatting Data.
2026-04-30 21:44:33.907858 INFO::Recognized SummarizedExperiment
2026-04-30 21:44:33.908405 INFO::Typecasting input to dataframe.
2026-04-30 21:44:33.938874 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:33.940094 INFO::Removing potential empty rows and columns
2026-04-30 21:44:33.943509 INFO::Found 0 missing values.
2026-04-30 21:44:33.949957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:33.950622 INFO::Done
2026-04-30 21:44:33.951168 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:33.954458 INFO::Starting hierarchical adjustment
2026-04-30 21:44:33.955196 INFO::Found 2 batches.
2026-04-30 21:44:33.955746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:33.956855 INFO::Using default BPPARAM
2026-04-30 21:44:33.957411 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:33.958369 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:44:34.008803 INFO::Done
2026-04-30 21:44:34.009551 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:34.012753 INFO::ASW Batch was -0.00519195793975397 prior to batch effect correction and is now -0.100829128792311 .
2026-04-30 21:44:34.013549 INFO::Total function execution time is 0.106765747070312 s and adjustment time is 0.0537078380584717 s ( 50.3 )
Warning: stack imbalance in '{', 73 then 75
2026-04-30 21:44:34.029653 INFO::Formatting Data.
2026-04-30 21:44:34.030415 INFO::Recognized SummarizedExperiment
2026-04-30 21:44:34.030962 INFO::Typecasting input to dataframe.
2026-04-30 21:44:34.03918 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:34.040339 INFO::Removing potential empty rows and columns
2026-04-30 21:44:34.043573 INFO::Found 0 missing values.
2026-04-30 21:44:34.049845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:34.050505 INFO::Done
2026-04-30 21:44:34.051077 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:34.05451 INFO::Starting hierarchical adjustment
2026-04-30 21:44:34.055261 INFO::Found 2 batches.
2026-04-30 21:44:34.055828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:34.056495 INFO::Using default BPPARAM
2026-04-30 21:44:34.057039 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:34.058035 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:44:34.082788 INFO::Done
2026-04-30 21:44:34.083593 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:34.087287 INFO::ASW Batch was 0.0212829211521117 prior to batch effect correction and is now 0.0212829211521117 .
2026-04-30 21:44:34.088205 INFO::Total function execution time is 0.0585191249847412 s and adjustment time is 0.027611255645752 s ( 47.18 )
2026-04-30 21:44:34.106522 INFO::Formatting Data.
2026-04-30 21:44:34.107392 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:34.108332 INFO::Removing potential empty rows and columns
2026-04-30 21:44:34.109616 INFO::Found 0 missing values.
2026-04-30 21:44:34.112607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:34.113178 INFO::Done
2026-04-30 21:44:34.113744 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:34.115834 INFO::Starting hierarchical adjustment
2026-04-30 21:44:34.116565 INFO::Found 3 batches.
2026-04-30 21:44:34.117129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:34.117787 INFO::Using default BPPARAM
2026-04-30 21:44:34.118353 INFO::Processing subtree level 1
2026-04-30 21:44:34.254876 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:44:34.256875 INFO::Done
2026-04-30 21:44:34.257659 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:34.260381 INFO::ASW Batch was -0.0576975253211137 prior to batch effect correction and is now -0.174626581321327 .
2026-04-30 21:44:34.261374 INFO::Total function execution time is 0.154873371124268 s and adjustment time is 0.140433788299561 s ( 90.68 )
2026-04-30 21:44:34.276657 INFO::Skipping initial DF formatting
2026-04-30 21:44:34.277492 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:34.281839 INFO::Starting hierarchical adjustment
2026-04-30 21:44:34.282666 INFO::Found 5 batches.
2026-04-30 21:44:34.283261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:34.283952 INFO::Using default BPPARAM
2026-04-30 21:44:34.28453 INFO::Processing subtree level 1
2026-04-30 21:44:34.407789 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:34.409621 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:44:34.430116 INFO::Done
2026-04-30 21:44:34.43102 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:34.435469 INFO::ASW Batch was 0.583621807929632 prior to batch effect correction and is now 0.583621807929632 .
2026-04-30 21:44:34.436182 INFO::ASW Label was 0.382358665535099 prior to batch effect correction and is now 0.382358665535099 .
2026-04-30 21:44:34.437106 INFO::Total function execution time is 0.160556316375732 s and adjustment time is 0.147574424743652 s ( 91.91 )
2026-04-30 21:44:34.455633 INFO::Formatting Data.
2026-04-30 21:44:34.456552 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:34.457538 INFO::Removing potential empty rows and columns
2026-04-30 21:44:34.458608 INFO::Found 0 missing values.
2026-04-30 21:44:34.462821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:34.463417 INFO::Done
2026-04-30 21:44:34.464006 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:34.467157 INFO::Starting hierarchical adjustment
2026-04-30 21:44:34.467938 INFO::Found 5 batches.
2026-04-30 21:44:34.468516 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:34.469203 INFO::Using default BPPARAM
2026-04-30 21:44:34.469797 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.
2026-04-30 21:44:34.57495 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:34.576607 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:44:34.59291 INFO::Done
2026-04-30 21:44:34.593741 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:34.597094 INFO::ASW Batch was 0.442337459600401 prior to batch effect correction and is now -0.0997176388021855 .
2026-04-30 21:44:34.597796 INFO::ASW Label was 0.292462755975113 prior to batch effect correction and is now 0.861990191126562 .
2026-04-30 21:44:34.59869 INFO::Total function execution time is 0.143138885498047 s and adjustment time is 0.125106573104858 s ( 87.4 )
2026-04-30 21:44:34.599611 INFO::Formatting Data.
2026-04-30 21:44:34.600283 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:34.601223 INFO::Removing potential empty rows and columns
2026-04-30 21:44:34.602324 INFO::Found 0 missing values.
2026-04-30 21:44:34.606687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:34.607292 INFO::Done
2026-04-30 21:44:34.607862 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:34.610962 INFO::Starting hierarchical adjustment
2026-04-30 21:44:34.611726 INFO::Found 5 batches.
2026-04-30 21:44:34.612306 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:34.61302 INFO::Using default BPPARAM
2026-04-30 21:44:34.613601 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.
2026-04-30 21:44:34.722256 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:34.723954 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:44:34.740135 INFO::Done
2026-04-30 21:44:34.740986 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:34.744287 INFO::ASW Batch was 0.442337459600401 prior to batch effect correction and is now -0.0997176388021855 .
2026-04-30 21:44:34.744961 INFO::ASW Label was 0.292462755975113 prior to batch effect correction and is now 0.861990191126562 .
2026-04-30 21:44:34.745886 INFO::Total function execution time is 0.146274328231812 s and adjustment time is 0.128541469573975 s ( 87.88 )
2026-04-30 21:44:34.75966 INFO::Formatting Data.
2026-04-30 21:44:34.760535 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:34.761503 INFO::Removing potential empty rows and columns
2026-04-30 21:44:34.76257 INFO::Found 0 missing values.
2026-04-30 21:44:34.766734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:34.767341 INFO::Done
2026-04-30 21:44:34.767921 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:34.771075 INFO::Starting hierarchical adjustment
2026-04-30 21:44:34.771837 INFO::Found 5 batches.
2026-04-30 21:44:34.772414 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:34.773081 INFO::Using default BPPARAM
2026-04-30 21:44:34.773656 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.
2026-04-30 21:44:34.879245 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:34.880832 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:44:34.896613 INFO::Done
2026-04-30 21:44:34.897409 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:34.900724 INFO::ASW Batch was 0.341431190362331 prior to batch effect correction and is now -0.0934275272353318 .
2026-04-30 21:44:34.901369 INFO::ASW Label was 0.170261536356643 prior to batch effect correction and is now 0.82338252410062 .
2026-04-30 21:44:34.902218 INFO::Total function execution time is 0.142630338668823 s and adjustment time is 0.124916076660156 s ( 87.58 )
2026-04-30 21:44:34.903107 INFO::Formatting Data.
2026-04-30 21:44:34.903787 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:34.904744 INFO::Removing potential empty rows and columns
2026-04-30 21:44:34.905782 INFO::Found 0 missing values.
2026-04-30 21:44:34.909863 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:34.91044 INFO::Done
2026-04-30 21:44:34.911016 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:34.914008 INFO::Starting hierarchical adjustment
2026-04-30 21:44:34.914767 INFO::Found 5 batches.
2026-04-30 21:44:34.915352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:34.916044 INFO::Using default BPPARAM
2026-04-30 21:44:34.916617 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.
2026-04-30 21:44:35.022433 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:35.024242 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:44:35.040649 INFO::Done
2026-04-30 21:44:35.041544 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.044962 INFO::ASW Batch was 0.341431190362331 prior to batch effect correction and is now -0.0934275272353318 .
2026-04-30 21:44:35.045635 INFO::ASW Label was 0.170261536356643 prior to batch effect correction and is now 0.82338252410062 .
2026-04-30 21:44:35.046552 INFO::Total function execution time is 0.143435001373291 s and adjustment time is 0.125983715057373 s ( 87.83 )
2026-04-30 21:44:35.060489 INFO::Formatting Data.
2026-04-30 21:44:35.061382 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.062382 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.063457 INFO::Found 0 missing values.
2026-04-30 21:44:35.066305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.066916 INFO::Done
2026-04-30 21:44:35.06749 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.070498 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.071242 INFO::Found 2 batches.
2026-04-30 21:44:35.071825 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.072495 INFO::Using default BPPARAM
2026-04-30 21:44:35.073102 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:35.074065 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:44:35.088915 INFO::Done
2026-04-30 21:44:35.089663 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.092713 INFO::ASW Batch was 0.653336059743183 prior to batch effect correction and is now -0.0274047612464221 .
2026-04-30 21:44:35.093338 INFO::ASW Label was 0.419660935706394 prior to batch effect correction and is now 0.913884714747006 .
2026-04-30 21:44:35.094233 INFO::Total function execution time is 0.0338284969329834 s and adjustment time is 0.0177936553955078 s ( 52.6 )
2026-04-30 21:44:35.095091 INFO::Formatting Data.
2026-04-30 21:44:35.095763 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.096686 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.097732 INFO::Found 0 missing values.
2026-04-30 21:44:35.101258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.101894 INFO::Done
2026-04-30 21:44:35.102466 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.105559 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.106347 INFO::Found 2 batches.
2026-04-30 21:44:35.106936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.107597 INFO::Using default BPPARAM
2026-04-30 21:44:35.10821 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:35.109185 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:44:35.124638 INFO::Done
2026-04-30 21:44:35.125424 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.128527 INFO::ASW Batch was 0.653336059743183 prior to batch effect correction and is now -0.0274047612464221 .
2026-04-30 21:44:35.129252 INFO::ASW Label was 0.419660935706394 prior to batch effect correction and is now 0.913884714747006 .
2026-04-30 21:44:35.130091 INFO::Total function execution time is 0.0350162982940674 s and adjustment time is 0.0184257030487061 s ( 52.62 )
2026-04-30 21:44:35.141539 INFO::Formatting Data.
2026-04-30 21:44:35.14236 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.143296 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.144285 INFO::Found 0 missing values.
2026-04-30 21:44:35.146743 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.147529 INFO::Done
2026-04-30 21:44:35.14809 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.150061 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.150803 INFO::Found 2 batches.
2026-04-30 21:44:35.15136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.152009 INFO::Using default BPPARAM
2026-04-30 21:44:35.152606 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:35.153546 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:44:35.185319 INFO::Done
2026-04-30 21:44:35.18615 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.188224 INFO::ASW Batch was -0.0538808220747254 prior to batch effect correction and is now -0.106472221148264 .
2026-04-30 21:44:35.189084 INFO::Total function execution time is 0.0476114749908447 s and adjustment time is 0.0346453189849854 s ( 72.77 )
2026-04-30 21:44:35.201119 INFO::Formatting Data.
2026-04-30 21:44:35.201943 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.202872 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.203923 INFO::Found 0 missing values.
2026-04-30 21:44:35.205089 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.
2026-04-30 21:44:35.210027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.210611 INFO::Done
2026-04-30 21:44:35.211185 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.214211 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.214982 INFO::Found 2 batches.
2026-04-30 21:44:35.215543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.216248 INFO::Using default BPPARAM
2026-04-30 21:44:35.216827 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:35.217827 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:44:35.234796 INFO::Done
2026-04-30 21:44:35.235568 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.238621 INFO::ASW Batch was 0.47198267464844 prior to batch effect correction and is now -0.0361495712225254 .
2026-04-30 21:44:35.239261 INFO::ASW Label was 0.60939198180255 prior to batch effect correction and is now 0.92742189012557 .
2026-04-30 21:44:35.240104 INFO::Total function execution time is 0.0390512943267822 s and adjustment time is 0.0199346542358398 s ( 51.05 )
2026-04-30 21:44:35.241059 INFO::Formatting Data.
2026-04-30 21:44:35.241725 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.242671 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.243709 INFO::Found 0 missing values.
2026-04-30 21:44:35.244637 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.
2026-04-30 21:44:35.249213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.249816 INFO::Done
2026-04-30 21:44:35.250374 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.253314 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.254042 INFO::Found 2 batches.
2026-04-30 21:44:35.25463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.255291 INFO::Using default BPPARAM
2026-04-30 21:44:35.255868 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:35.256828 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:44:35.273436 INFO::Done
2026-04-30 21:44:35.274219 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.27722 INFO::ASW Batch was 0.47198267464844 prior to batch effect correction and is now -0.0361495712225254 .
2026-04-30 21:44:35.277895 INFO::ASW Label was 0.60939198180255 prior to batch effect correction and is now 0.92742189012557 .
2026-04-30 21:44:35.278725 INFO::Total function execution time is 0.0376672744750977 s and adjustment time is 0.0195121765136719 s ( 51.8 )
2026-04-30 21:44:35.488135 INFO::Formatting Data.
2026-04-30 21:44:35.489065 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.490028 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.491169 INFO::Found 0 missing values.
2026-04-30 21:44:35.494266 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.494867 INFO::Done
2026-04-30 21:44:35.49542 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.497535 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.498276 INFO::Found 3 batches.
2026-04-30 21:44:35.498871 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.499543 INFO::Using default BPPARAM
2026-04-30 21:44:35.500124 INFO::Processing subtree level 1
2026-04-30 21:44:35.590331 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:44:35.592287 INFO::Done
2026-04-30 21:44:35.593037 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.595633 INFO::ASW Batch was -0.0872662276752484 prior to batch effect correction and is now -0.0872662276752484 .
2026-04-30 21:44:35.596702 INFO::Total function execution time is 0.108579874038696 s and adjustment time is 0.0941245555877686 s ( 86.69 )
2026-04-30 21:44:35.597925 INFO::Formatting Data.
2026-04-30 21:44:35.598618 INFO::Typecasting input to dataframe.
2026-04-30 21:44:35.59943 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.600414 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.601587 INFO::Found 0 missing values.
2026-04-30 21:44:35.604746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.605357 INFO::Done
2026-04-30 21:44:35.605953 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.608103 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.608867 INFO::Found 3 batches.
2026-04-30 21:44:35.609443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.61014 INFO::Using default BPPARAM
2026-04-30 21:44:35.610804 INFO::Processing subtree level 1
2026-04-30 21:44:35.6975 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:44:35.699361 INFO::Done
2026-04-30 21:44:35.700068 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.702577 INFO::ASW Batch was -0.0872662276752484 prior to batch effect correction and is now -0.0872662276752484 .
2026-04-30 21:44:35.703553 INFO::Total function execution time is 0.105627059936523 s and adjustment time is 0.090634822845459 s ( 85.81 )
2026-04-30 21:44:35.71654 INFO::Formatting Data.
2026-04-30 21:44:35.717658 INFO::Typecasting input to dataframe.
2026-04-30 21:44:35.718591 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.719558 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.720702 INFO::Found 0 missing values.
2026-04-30 21:44:35.723769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.724342 INFO::Done
2026-04-30 21:44:35.724922 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.72709 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.727856 INFO::Found 3 batches.
2026-04-30 21:44:35.728424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.729101 INFO::Using default BPPARAM
2026-04-30 21:44:35.729685 INFO::Processing subtree level 1
2026-04-30 21:44:35.81581 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:44:35.817802 INFO::Done
2026-04-30 21:44:35.818571 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:35.821337 INFO::ASW Batch was 0.059736922313219 prior to batch effect correction and is now 0.059736922313219 .
2026-04-30 21:44:35.822309 INFO::Total function execution time is 0.10582160949707 s and adjustment time is 0.0900599956512451 s ( 85.11 )
2026-04-30 21:44:35.959565 INFO::Formatting Data.
2026-04-30 21:44:35.960495 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:35.961673 INFO::Removing potential empty rows and columns
2026-04-30 21:44:35.964599 INFO::Found 1000 missing values.
2026-04-30 21:44:35.984465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:35.985361 INFO::Done
2026-04-30 21:44:35.986006 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:35.991942 INFO::Starting hierarchical adjustment
2026-04-30 21:44:35.992759 INFO::Found 10 batches.
2026-04-30 21:44:35.993341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:35.99407 INFO::Using default BPPARAM
2026-04-30 21:44:35.994654 INFO::Processing subtree level 1
2026-04-30 21:44:36.143199 INFO::Processing subtree level 2
2026-04-30 21:44:36.29596 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:44:36.298125 INFO::Done
2026-04-30 21:44:36.298868 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:36.304517 INFO::ASW Batch was 0.46749094270732 prior to batch effect correction and is now 0.46749094270732 .
2026-04-30 21:44:36.30533 INFO::ASW Label was 0.351587331113109 prior to batch effect correction and is now 0.351587331113109 .
2026-04-30 21:44:36.306319 INFO::Total function execution time is 0.346831321716309 s and adjustment time is 0.305516958236694 s ( 88.09 )
2026-04-30 21:44:36.307233 INFO::Formatting Data.
2026-04-30 21:44:36.307951 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:36.309299 INFO::Removing potential empty rows and columns
2026-04-30 21:44:36.312315 INFO::Found 1000 missing values.
2026-04-30 21:44:36.332255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:36.333128 INFO::Done
2026-04-30 21:44:36.333759 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:36.339399 INFO::Starting hierarchical adjustment
2026-04-30 21:44:36.340223 INFO::Found 10 batches.
2026-04-30 21:44:37.315857 INFO::Set up parallel execution backend with 2 workers
2026-04-30 21:44:37.318687 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-30 21:44:38.665829 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:44:38.669071 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:44:38.686018 INFO::Done
2026-04-30 21:44:38.686769 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:38.691355 INFO::ASW Batch was 0.46749094270732 prior to batch effect correction and is now 0.46749094270732 .
2026-04-30 21:44:38.692008 INFO::ASW Label was 0.351587331113109 prior to batch effect correction and is now 0.351587331113109 .
2026-04-30 21:44:38.692782 INFO::Total function execution time is 2.38557600975037 s and adjustment time is 2.34593224525452 s ( 98.34 )
2026-04-30 21:44:38.844876 INFO::Formatting Data.
2026-04-30 21:44:38.845763 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:38.846778 INFO::Removing potential empty rows and columns
2026-04-30 21:44:38.847911 INFO::Found 0 missing values.
2026-04-30 21:44:38.851649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:38.852247 INFO::Done
2026-04-30 21:44:38.852823 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:44:38.855663 INFO::Starting hierarchical adjustment
2026-04-30 21:44:38.856422 INFO::Found 3 batches.
2026-04-30 21:44:38.856992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:44:38.857691 INFO::Using default BPPARAM
2026-04-30 21:44:38.858255 INFO::Processing subtree level 1
2026-04-30 21:44:38.974192 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:44:38.976334 INFO::Done
2026-04-30 21:44:38.977178 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:44:38.980834 INFO::ASW Batch was 0.239286506590293 prior to batch effect correction and is now -0.124745844175231 .
2026-04-30 21:44:38.981556 INFO::ASW Label was -0.20690811362458 prior to batch effect correction and is now -0.0215899945149995 .
2026-04-30 21:44:38.982635 INFO::Total function execution time is 0.137828588485718 s and adjustment time is 0.120008230209351 s ( 87.07 )
2026-04-30 21:44:39.111057 INFO::Formatting Data.
2026-04-30 21:44:39.112114 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.113135 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.11427 INFO::Found 2 missing values.
2026-04-30 21:44:39.117309 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.117954 INFO::Done
2026-04-30 21:44:39.146153 INFO::Found NA in Reference column
2026-04-30 21:44:39.155904 INFO::Require at least two references per batch.
2026-04-30 21:44:39.176332 INFO::Formatting Data.
2026-04-30 21:44:39.177273 INFO::Recognized SummarizedExperiment
2026-04-30 21:44:39.1779 INFO::Typecasting input to dataframe.
2026-04-30 21:44:39.187431 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.188687 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.192415 INFO::Found 0 missing values.
2026-04-30 21:44:39.199481 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.20016 INFO::Done
2026-04-30 21:44:39.21652 INFO::Formatting Data.
2026-04-30 21:44:39.21737 INFO::Recognized SummarizedExperiment
2026-04-30 21:44:39.217958 INFO::Typecasting input to dataframe.
2026-04-30 21:44:39.235358 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.236715 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.24054 INFO::Found 0 missing values.
2026-04-30 21:44:39.251816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.252584 INFO::Done
2026-04-30 21:44:39.268064 INFO::Formatting Data.
2026-04-30 21:44:39.268931 INFO::Recognized SummarizedExperiment
2026-04-30 21:44:39.269518 INFO::Typecasting input to dataframe.
2026-04-30 21:44:39.285595 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.286787 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.288015 INFO::Found 0 missing values.
2026-04-30 21:44:39.288992 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.
2026-04-30 21:44:39.29349 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.294102 INFO::Done
2026-04-30 21:44:39.304592 INFO::Formatting Data.
2026-04-30 21:44:39.305613 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.306614 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.307767 INFO::Found 0 missing values.
2026-04-30 21:44:39.310891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.311541 INFO::Done
2026-04-30 21:44:39.323978 INFO::Formatting Data.
2026-04-30 21:44:39.325 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.326046 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.32726 INFO::Found 0 missing values.
2026-04-30 21:44:39.330742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.331416 INFO::Done
2026-04-30 21:44:39.36413 INFO::Formatting Data.
2026-04-30 21:44:39.365173 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.36647 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.367884 INFO::Found 1 missing values.
2026-04-30 21:44:39.370898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.371598 INFO::Done
2026-04-30 21:44:39.392668 INFO::Formatting Data.
2026-04-30 21:44:39.393705 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.394717 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.395709 INFO::Found 2 missing values.
2026-04-30 21:44:39.39667 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.
2026-04-30 21:44:39.398981 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.399568 INFO::Done
2026-04-30 21:44:39.40995 INFO::Formatting Data.
2026-04-30 21:44:39.410861 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.411866 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.412906 INFO::Found 2 missing values.
2026-04-30 21:44:39.414658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.415338 INFO::Done
2026-04-30 21:44:39.426705 INFO::Formatting Data.
2026-04-30 21:44:39.427612 INFO::Typecasting input to dataframe.
2026-04-30 21:44:39.428549 INFO::Replacing NaNs with NAs.
2026-04-30 21:44:39.429545 INFO::Removing potential empty rows and columns
2026-04-30 21:44:39.430683 INFO::Found 0 missing values.
2026-04-30 21:44:39.433554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:44:39.434118 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.659 3.348 20.754
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.803 | 1.670 | 17.889 | |
| compute_asw | 0.028 | 0.003 | 0.031 | |
| count_existing | 0.013 | 0.005 | 0.020 | |
| generate_data_covariables | 0.014 | 0.004 | 0.017 | |
| generate_dataset | 0.008 | 0.008 | 0.017 | |