Yannis Schumann
| Snapshot Date: 2026-05-20 13:45 -0400 (Wed, 20 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-21 11:33 -0400 (Thu, 21 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4936 |
| 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 174/2378 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | 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: 1.9.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz |
| StartedAt: 2026-05-20 21:41:32 -0400 (Wed, 20 May 2026) |
| EndedAt: 2026-05-20 21:43:05 -0400 (Wed, 20 May 2026) |
| EllapsedTime: 93.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-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: 2026-05-21 01:41:32 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 24.793 1.154 18.167
* 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-3.24-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.9.0’ ** 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")
2026-05-20 21:42:26.021472 INFO::Formatting Data.
2026-05-20 21:42:26.022884 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:26.034103 INFO::Removing potential empty rows and columns
2026-05-20 21:42:26.278782 INFO::Found 0 missing values.
2026-05-20 21:42:26.282196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:26.282902 INFO::Done
2026-05-20 21:42:26.283496 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:26.296459 INFO::Starting hierarchical adjustment
2026-05-20 21:42:26.297405 INFO::Found 3 batches.
2026-05-20 21:42:26.298005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:26.299145 INFO::Using default BPPARAM
2026-05-20 21:42:26.299753 INFO::Processing subtree level 1
2026-05-20 21:42:26.400473 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:42:26.402317 INFO::Done
2026-05-20 21:42:26.40303 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:26.40562 INFO::ASW Batch was -0.0143922348200179 prior to batch effect correction and is now -0.0143922348200179 .
2026-05-20 21:42:26.406705 INFO::Total function execution time is 0.385841846466064 s and adjustment time is 0.105099439620972 s ( 27.24 )
2026-05-20 21:42:26.430402 INFO::Formatting Data.
2026-05-20 21:42:26.431527 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:26.432753 INFO::Removing potential empty rows and columns
2026-05-20 21:42:26.434131 INFO::Found 0 missing values.
2026-05-20 21:42:26.435297 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.
2026-05-20 21:42:26.448689 INFO::Formatting Data.
2026-05-20 21:42:26.449696 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:26.450897 INFO::Removing potential empty rows and columns
2026-05-20 21:42:26.45227 INFO::Found 0 missing values.
2026-05-20 21:42:26.453497 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.
2026-05-20 21:42:26.472568 INFO::Formatting Data.
2026-05-20 21:42:26.473501 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:26.47455 INFO::Removing potential empty rows and columns
2026-05-20 21:42:26.475765 INFO::Found 0 missing values.
2026-05-20 21:42:26.476897 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.
2026-05-20 21:42:26.482124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:26.482925 INFO::Done
2026-05-20 21:42:26.483555 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:26.486062 INFO::Starting hierarchical adjustment
2026-05-20 21:42:26.486949 INFO::Found 2 batches.
2026-05-20 21:42:26.48761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:26.488333 INFO::Using default BPPARAM
2026-05-20 21:42:26.488955 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:26.490106 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:42:26.513574 INFO::Done
2026-05-20 21:42:26.514387 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:26.516619 INFO::ASW Batch was 0.0154475232226977 prior to batch effect correction and is now -0.116197895805683 .
2026-05-20 21:42:26.517513 INFO::Total function execution time is 0.0450410842895508 s and adjustment time is 0.0267701148986816 s ( 59.43 )
2026-05-20 21:42:26.520635 INFO::Formatting Data.
2026-05-20 21:42:26.521362 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:26.531043 INFO::Formatting Data.
2026-05-20 21:42:26.531961 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:26.53301 INFO::Removing potential empty rows and columns
2026-05-20 21:42:26.534194 INFO::Found 0 missing values.
2026-05-20 21:42:26.537545 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:26.538337 INFO::Done
2026-05-20 21:42:26.538996 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:26.541403 INFO::Starting hierarchical adjustment
2026-05-20 21:42:26.542452 INFO::Found 2 batches.
2026-05-20 21:42:26.543187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:26.543901 INFO::Using default BPPARAM
2026-05-20 21:42:26.544505 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:26.545581 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:42:26.594957 INFO::Done
2026-05-20 21:42:26.595709 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:26.597747 INFO::ASW Batch was -0.0692776471827933 prior to batch effect correction and is now -0.114368835557046 .
2026-05-20 21:42:26.598563 INFO::Total function execution time is 0.0676100254058838 s and adjustment time is 0.0527355670928955 s ( 78 )
2026-05-20 21:42:26.599623 INFO::Formatting Data.
2026-05-20 21:42:26.600241 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:26.601113 INFO::Removing potential empty rows and columns
2026-05-20 21:42:26.602126 INFO::Found 0 missing values.
2026-05-20 21:42:26.604907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:26.605475 INFO::Done
2026-05-20 21:42:26.605996 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:26.60801 INFO::Starting hierarchical adjustment
2026-05-20 21:42:26.608734 INFO::Found 2 batches.
2026-05-20 21:42:26.609264 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:26.609876 INFO::Using default BPPARAM
2026-05-20 21:42:26.610443 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:26.611347 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:42:26.626054 INFO::Done
2026-05-20 21:42:26.626778 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:26.628767 INFO::ASW Batch was -0.0692776471827933 prior to batch effect correction and is now -0.114368835557046 .
2026-05-20 21:42:26.629586 INFO::Total function execution time is 0.029963493347168 s and adjustment time is 0.0174417495727539 s ( 58.21 )
2026-05-20 21:42:29.695276 INFO::Formatting Data.
2026-05-20 21:42:29.696053 INFO::Recognized SummarizedExperiment
2026-05-20 21:42:29.69659 INFO::Typecasting input to dataframe.
2026-05-20 21:42:29.724791 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:29.725919 INFO::Removing potential empty rows and columns
2026-05-20 21:42:29.729038 INFO::Found 0 missing values.
2026-05-20 21:42:29.735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:29.735634 INFO::Done
2026-05-20 21:42:29.736135 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:29.739122 INFO::Starting hierarchical adjustment
2026-05-20 21:42:29.739795 INFO::Found 2 batches.
2026-05-20 21:42:29.740283 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:29.741252 INFO::Using default BPPARAM
2026-05-20 21:42:29.741777 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:29.742662 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:42:29.799779 INFO::Done
2026-05-20 21:42:29.800763 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:29.805069 INFO::ASW Batch was 0.00138602587680408 prior to batch effect correction and is now -0.10098506440966 .
2026-05-20 21:42:29.805943 INFO::Total function execution time is 0.110923528671265 s and adjustment time is 0.0599720478057861 s ( 54.07 )
2026-05-20 21:42:29.824181 INFO::Formatting Data.
2026-05-20 21:42:29.824936 INFO::Recognized SummarizedExperiment
2026-05-20 21:42:29.825466 INFO::Typecasting input to dataframe.
2026-05-20 21:42:29.834093 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:29.835207 INFO::Removing potential empty rows and columns
2026-05-20 21:42:29.838343 INFO::Found 0 missing values.
2026-05-20 21:42:29.844521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:29.845099 INFO::Done
2026-05-20 21:42:29.845614 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:29.848689 INFO::Starting hierarchical adjustment
2026-05-20 21:42:29.849345 INFO::Found 2 batches.
2026-05-20 21:42:29.849851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:29.850425 INFO::Using default BPPARAM
2026-05-20 21:42:29.850919 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:29.851819 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:42:29.87566 INFO::Done
2026-05-20 21:42:29.876532 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:29.880779 INFO::ASW Batch was 0.0018030992053058 prior to batch effect correction and is now 0.0018030992053058 .
2026-05-20 21:42:29.881823 INFO::Total function execution time is 0.0575814247131348 s and adjustment time is 0.0263876914978027 s ( 45.83 )
2026-05-20 21:42:29.90233 INFO::Formatting Data.
2026-05-20 21:42:29.903325 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:29.904305 INFO::Removing potential empty rows and columns
2026-05-20 21:42:29.905526 INFO::Found 0 missing values.
2026-05-20 21:42:29.908854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:29.909491 INFO::Done
2026-05-20 21:42:29.91007 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:29.91228 INFO::Starting hierarchical adjustment
2026-05-20 21:42:29.913276 INFO::Found 3 batches.
2026-05-20 21:42:29.913913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:29.914662 INFO::Using default BPPARAM
2026-05-20 21:42:29.915273 INFO::Processing subtree level 1
2026-05-20 21:42:30.061811 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:42:30.063924 INFO::Done
2026-05-20 21:42:30.064725 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:30.067578 INFO::ASW Batch was -0.0595801244377059 prior to batch effect correction and is now -0.161327120044858 .
2026-05-20 21:42:30.068746 INFO::Total function execution time is 0.16639232635498 s and adjustment time is 0.15095043182373 s ( 90.72 )
2026-05-20 21:42:30.084976 INFO::Skipping initial DF formatting
2026-05-20 21:42:30.085862 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:30.090353 INFO::Starting hierarchical adjustment
2026-05-20 21:42:30.091294 INFO::Found 5 batches.
2026-05-20 21:42:30.091977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:30.09271 INFO::Using default BPPARAM
2026-05-20 21:42:30.093307 INFO::Processing subtree level 1
2026-05-20 21:42:30.219665 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:30.22214 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:42:30.24565 INFO::Done
2026-05-20 21:42:30.246537 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:30.251226 INFO::ASW Batch was 0.489506484219 prior to batch effect correction and is now 0.489506484219 .
2026-05-20 21:42:30.251972 INFO::ASW Label was 0.398020124907114 prior to batch effect correction and is now 0.398020124907114 .
2026-05-20 21:42:30.253043 INFO::Total function execution time is 0.168158292770386 s and adjustment time is 0.154515504837036 s ( 91.89 )
2026-05-20 21:42:30.274297 INFO::Formatting Data.
2026-05-20 21:42:30.275298 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:30.276488 INFO::Removing potential empty rows and columns
2026-05-20 21:42:30.277701 INFO::Found 0 missing values.
2026-05-20 21:42:30.282567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:30.28327 INFO::Done
2026-05-20 21:42:30.283932 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:30.287523 INFO::Starting hierarchical adjustment
2026-05-20 21:42:30.288393 INFO::Found 5 batches.
2026-05-20 21:42:30.289055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:30.289805 INFO::Using default BPPARAM
2026-05-20 21:42:30.290456 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.
2026-05-20 21:42:30.427664 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:30.42944 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:42:30.446057 INFO::Done
2026-05-20 21:42:30.446901 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:30.450758 INFO::ASW Batch was 0.20498303229191 prior to batch effect correction and is now -0.109247723126909 .
2026-05-20 21:42:30.451551 INFO::ASW Label was 0.494942793072419 prior to batch effect correction and is now 0.81696585193314 .
2026-05-20 21:42:30.452538 INFO::Total function execution time is 0.178299903869629 s and adjustment time is 0.157819509506226 s ( 88.51 )
2026-05-20 21:42:30.453564 INFO::Formatting Data.
2026-05-20 21:42:30.454331 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:30.455414 INFO::Removing potential empty rows and columns
2026-05-20 21:42:30.456644 INFO::Found 0 missing values.
2026-05-20 21:42:30.461448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:30.462123 INFO::Done
2026-05-20 21:42:30.462781 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:30.466247 INFO::Starting hierarchical adjustment
2026-05-20 21:42:30.467119 INFO::Found 5 batches.
2026-05-20 21:42:30.467769 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:30.468527 INFO::Using default BPPARAM
2026-05-20 21:42:30.469734 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.
2026-05-20 21:42:30.587782 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:30.589772 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:42:30.611684 INFO::Done
2026-05-20 21:42:30.612764 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:30.617036 INFO::ASW Batch was 0.20498303229191 prior to batch effect correction and is now -0.109247723126909 .
2026-05-20 21:42:30.617934 INFO::ASW Label was 0.494942793072419 prior to batch effect correction and is now 0.81696585193314 .
2026-05-20 21:42:30.619049 INFO::Total function execution time is 0.165473937988281 s and adjustment time is 0.144687652587891 s ( 87.44 )
2026-05-20 21:42:30.637521 INFO::Formatting Data.
2026-05-20 21:42:30.638587 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:30.639748 INFO::Removing potential empty rows and columns
2026-05-20 21:42:30.640974 INFO::Found 0 missing values.
2026-05-20 21:42:30.646167 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:30.646977 INFO::Done
2026-05-20 21:42:30.647664 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:30.651397 INFO::Starting hierarchical adjustment
2026-05-20 21:42:30.652336 INFO::Found 5 batches.
2026-05-20 21:42:30.652993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:30.653793 INFO::Using default BPPARAM
2026-05-20 21:42:30.654471 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.
2026-05-20 21:42:30.77593 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:30.777806 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:42:30.795523 INFO::Done
2026-05-20 21:42:30.796417 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:30.800185 INFO::ASW Batch was 0.299083468206103 prior to batch effect correction and is now -0.0815422479472514 .
2026-05-20 21:42:30.801026 INFO::ASW Label was 0.456808435030632 prior to batch effect correction and is now 0.844884195148279 .
2026-05-20 21:42:30.802042 INFO::Total function execution time is 0.164634704589844 s and adjustment time is 0.143301248550415 s ( 87.04 )
2026-05-20 21:42:30.803061 INFO::Formatting Data.
2026-05-20 21:42:30.803817 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:30.804901 INFO::Removing potential empty rows and columns
2026-05-20 21:42:30.806147 INFO::Found 0 missing values.
2026-05-20 21:42:30.810696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:30.81144 INFO::Done
2026-05-20 21:42:30.812056 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:30.815472 INFO::Starting hierarchical adjustment
2026-05-20 21:42:30.81628 INFO::Found 5 batches.
2026-05-20 21:42:30.816886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:30.817577 INFO::Using default BPPARAM
2026-05-20 21:42:30.818148 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.
2026-05-20 21:42:30.934939 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:30.937001 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:42:30.954807 INFO::Done
2026-05-20 21:42:30.955828 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:30.959621 INFO::ASW Batch was 0.299083468206103 prior to batch effect correction and is now -0.0815422479472514 .
2026-05-20 21:42:30.960444 INFO::ASW Label was 0.456808435030632 prior to batch effect correction and is now 0.844884195148279 .
2026-05-20 21:42:30.961417 INFO::Total function execution time is 0.15833854675293 s and adjustment time is 0.13861870765686 s ( 87.55 )
2026-05-20 21:42:30.97682 INFO::Formatting Data.
2026-05-20 21:42:30.977856 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:30.978985 INFO::Removing potential empty rows and columns
2026-05-20 21:42:30.980188 INFO::Found 0 missing values.
2026-05-20 21:42:30.983284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:30.98394 INFO::Done
2026-05-20 21:42:30.984541 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:30.987872 INFO::Starting hierarchical adjustment
2026-05-20 21:42:30.988691 INFO::Found 2 batches.
2026-05-20 21:42:30.989271 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:30.989975 INFO::Using default BPPARAM
2026-05-20 21:42:30.990578 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:30.991636 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:42:31.008303 INFO::Done
2026-05-20 21:42:31.009248 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:31.01276 INFO::ASW Batch was 0.411312417091307 prior to batch effect correction and is now 0.0400364704744435 .
2026-05-20 21:42:31.013814 INFO::ASW Label was 0.680963002085764 prior to batch effect correction and is now 0.911584089383446 .
2026-05-20 21:42:31.01474 INFO::Total function execution time is 0.0380492210388184 s and adjustment time is 0.0197262763977051 s ( 51.84 )
2026-05-20 21:42:31.015676 INFO::Formatting Data.
2026-05-20 21:42:31.01634 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:31.017351 INFO::Removing potential empty rows and columns
2026-05-20 21:42:31.018476 INFO::Found 0 missing values.
2026-05-20 21:42:31.02144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:31.022047 INFO::Done
2026-05-20 21:42:31.022645 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:31.025919 INFO::Starting hierarchical adjustment
2026-05-20 21:42:31.026741 INFO::Found 2 batches.
2026-05-20 21:42:31.027309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:31.028022 INFO::Using default BPPARAM
2026-05-20 21:42:31.028614 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:31.029683 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:42:31.046338 INFO::Done
2026-05-20 21:42:31.047424 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:31.050897 INFO::ASW Batch was 0.411312417091307 prior to batch effect correction and is now 0.0400364704744435 .
2026-05-20 21:42:31.051581 INFO::ASW Label was 0.680963002085764 prior to batch effect correction and is now 0.911584089383446 .
2026-05-20 21:42:31.052479 INFO::Total function execution time is 0.0367846488952637 s and adjustment time is 0.0197110176086426 s ( 53.58 )
2026-05-20 21:42:31.065581 INFO::Formatting Data.
2026-05-20 21:42:31.066644 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:31.067931 INFO::Removing potential empty rows and columns
2026-05-20 21:42:31.069084 INFO::Found 0 missing values.
2026-05-20 21:42:31.071944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:31.072587 INFO::Done
2026-05-20 21:42:31.073172 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:31.075547 INFO::Starting hierarchical adjustment
2026-05-20 21:42:31.076316 INFO::Found 2 batches.
2026-05-20 21:42:31.076939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:31.07763 INFO::Using default BPPARAM
2026-05-20 21:42:31.078209 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:31.079253 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:42:31.117464 INFO::Done
2026-05-20 21:42:31.118874 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:31.121717 INFO::ASW Batch was -0.153454697591662 prior to batch effect correction and is now -0.193292011021628 .
2026-05-20 21:42:31.122811 INFO::Total function execution time is 0.0574631690979004 s and adjustment time is 0.0411887168884277 s ( 71.68 )
2026-05-20 21:42:31.147088 INFO::Formatting Data.
2026-05-20 21:42:31.148546 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:31.149889 INFO::Removing potential empty rows and columns
2026-05-20 21:42:31.151292 INFO::Found 0 missing values.
2026-05-20 21:42:31.153112 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.
2026-05-20 21:42:31.158646 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:31.159438 INFO::Done
2026-05-20 21:42:31.160071 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:31.163829 INFO::Starting hierarchical adjustment
2026-05-20 21:42:31.164671 INFO::Found 2 batches.
2026-05-20 21:42:31.165281 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:31.165993 INFO::Using default BPPARAM
2026-05-20 21:42:31.166643 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:31.167921 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:42:31.187547 INFO::Done
2026-05-20 21:42:31.188512 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:31.191967 INFO::ASW Batch was 0.634082083942842 prior to batch effect correction and is now 0.0212514869389206 .
2026-05-20 21:42:31.192712 INFO::ASW Label was 0.39632087863521 prior to batch effect correction and is now 0.895742835322898 .
2026-05-20 21:42:31.193655 INFO::Total function execution time is 0.0467889308929443 s and adjustment time is 0.0229697227478027 s ( 49.09 )
2026-05-20 21:42:31.194598 INFO::Formatting Data.
2026-05-20 21:42:31.195312 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:31.196394 INFO::Removing potential empty rows and columns
2026-05-20 21:42:31.197498 INFO::Found 0 missing values.
2026-05-20 21:42:31.198573 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.
2026-05-20 21:42:31.203539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:31.204188 INFO::Done
2026-05-20 21:42:31.204793 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:31.208273 INFO::Starting hierarchical adjustment
2026-05-20 21:42:31.209175 INFO::Found 2 batches.
2026-05-20 21:42:31.209817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:31.210601 INFO::Using default BPPARAM
2026-05-20 21:42:31.211187 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:31.212295 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:42:31.230829 INFO::Done
2026-05-20 21:42:31.231866 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:31.235328 INFO::ASW Batch was 0.634082083942842 prior to batch effect correction and is now 0.0212514869389206 .
2026-05-20 21:42:31.236117 INFO::ASW Label was 0.39632087863521 prior to batch effect correction and is now 0.895742835322898 .
2026-05-20 21:42:31.237061 INFO::Total function execution time is 0.0424785614013672 s and adjustment time is 0.0217733383178711 s ( 51.26 )
2026-05-20 21:42:31.476646 INFO::Formatting Data.
2026-05-20 21:42:31.477663 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:31.478756 INFO::Removing potential empty rows and columns
2026-05-20 21:42:31.479934 INFO::Found 0 missing values.
2026-05-20 21:42:31.48336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:31.484022 INFO::Done
2026-05-20 21:42:31.484648 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:31.487036 INFO::Starting hierarchical adjustment
2026-05-20 21:42:31.487859 INFO::Found 3 batches.
2026-05-20 21:42:31.488482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:31.489156 INFO::Using default BPPARAM
2026-05-20 21:42:31.489809 INFO::Processing subtree level 1
2026-05-20 21:42:31.587306 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:42:31.589464 INFO::Done
2026-05-20 21:42:31.590225 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:31.593053 INFO::ASW Batch was -0.0273853100185885 prior to batch effect correction and is now -0.0273853100185885 .
2026-05-20 21:42:31.594153 INFO::Total function execution time is 0.117638826370239 s and adjustment time is 0.101717948913574 s ( 86.47 )
2026-05-20 21:42:31.595365 INFO::Formatting Data.
2026-05-20 21:42:31.596102 INFO::Typecasting input to dataframe.
2026-05-20 21:42:31.596963 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:31.598042 INFO::Removing potential empty rows and columns
2026-05-20 21:42:31.599259 INFO::Found 0 missing values.
2026-05-20 21:42:31.602652 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:31.603263 INFO::Done
2026-05-20 21:42:31.603876 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:31.606173 INFO::Starting hierarchical adjustment
2026-05-20 21:42:31.607017 INFO::Found 3 batches.
2026-05-20 21:42:31.607634 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:31.608329 INFO::Using default BPPARAM
2026-05-20 21:42:31.608926 INFO::Processing subtree level 1
2026-05-20 21:42:31.700577 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:42:31.702773 INFO::Done
2026-05-20 21:42:31.703583 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:31.706396 INFO::ASW Batch was -0.0273853100185885 prior to batch effect correction and is now -0.0273853100185885 .
2026-05-20 21:42:31.707489 INFO::Total function execution time is 0.112097263336182 s and adjustment time is 0.0958852767944336 s ( 85.54 )
2026-05-20 21:42:31.722239 INFO::Formatting Data.
2026-05-20 21:42:31.723249 INFO::Typecasting input to dataframe.
2026-05-20 21:42:31.724239 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:31.72526 INFO::Removing potential empty rows and columns
2026-05-20 21:42:31.72649 INFO::Found 0 missing values.
2026-05-20 21:42:31.729806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:31.730581 INFO::Done
2026-05-20 21:42:31.731168 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:31.733527 INFO::Starting hierarchical adjustment
2026-05-20 21:42:31.734341 INFO::Found 3 batches.
2026-05-20 21:42:31.734957 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:31.735668 INFO::Using default BPPARAM
2026-05-20 21:42:31.736269 INFO::Processing subtree level 1
2026-05-20 21:42:31.830848 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:42:31.832875 INFO::Done
2026-05-20 21:42:31.833731 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:31.836667 INFO::ASW Batch was -0.120388207483241 prior to batch effect correction and is now -0.120388207483241 .
2026-05-20 21:42:31.837806 INFO::Total function execution time is 0.115623235702515 s and adjustment time is 0.0986692905426025 s ( 85.34 )
2026-05-20 21:42:31.989334 INFO::Formatting Data.
2026-05-20 21:42:31.990339 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:31.99162 INFO::Removing potential empty rows and columns
2026-05-20 21:42:31.994689 INFO::Found 1000 missing values.
2026-05-20 21:42:32.015514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:32.016543 INFO::Done
2026-05-20 21:42:32.017198 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:32.023261 INFO::Starting hierarchical adjustment
2026-05-20 21:42:32.024162 INFO::Found 10 batches.
2026-05-20 21:42:32.024754 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:32.025444 INFO::Using default BPPARAM
2026-05-20 21:42:32.026033 INFO::Processing subtree level 1
2026-05-20 21:42:32.180578 INFO::Processing subtree level 2
2026-05-20 21:42:32.516072 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:42:32.518622 INFO::Done
2026-05-20 21:42:32.519593 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:32.526639 INFO::ASW Batch was 0.496872539367251 prior to batch effect correction and is now 0.496872539367251 .
2026-05-20 21:42:32.527648 INFO::ASW Label was 0.309095063116777 prior to batch effect correction and is now 0.309095063116776 .
2026-05-20 21:42:32.528834 INFO::Total function execution time is 0.539584636688232 s and adjustment time is 0.494590520858765 s ( 91.66 )
2026-05-20 21:42:32.529944 INFO::Formatting Data.
2026-05-20 21:42:32.530786 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:32.532268 INFO::Removing potential empty rows and columns
2026-05-20 21:42:32.535967 INFO::Found 1000 missing values.
2026-05-20 21:42:32.560845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:32.56188 INFO::Done
2026-05-20 21:42:32.56265 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:32.569161 INFO::Starting hierarchical adjustment
2026-05-20 21:42:32.570133 INFO::Found 10 batches.
2026-05-20 21:42:33.81674 INFO::Set up parallel execution backend with 2 workers
2026-05-20 21:42:33.819705 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-20 21:42:35.227466 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:42:35.230573 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:42:35.24725 INFO::Done
2026-05-20 21:42:35.247986 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:35.252624 INFO::ASW Batch was 0.496872539367251 prior to batch effect correction and is now 0.496872539367251 .
2026-05-20 21:42:35.253211 INFO::ASW Label was 0.309095063116777 prior to batch effect correction and is now 0.309095063116776 .
2026-05-20 21:42:35.253979 INFO::Total function execution time is 2.72412276268005 s and adjustment time is 2.67729091644287 s ( 98.28 )
2026-05-20 21:42:35.40902 INFO::Formatting Data.
2026-05-20 21:42:35.410088 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.411238 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.412494 INFO::Found 0 missing values.
2026-05-20 21:42:35.416486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.417091 INFO::Done
2026-05-20 21:42:35.417686 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:42:35.420784 INFO::Starting hierarchical adjustment
2026-05-20 21:42:35.421569 INFO::Found 3 batches.
2026-05-20 21:42:35.422155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:42:35.422843 INFO::Using default BPPARAM
2026-05-20 21:42:35.423442 INFO::Processing subtree level 1
2026-05-20 21:42:35.543872 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:42:35.546013 INFO::Done
2026-05-20 21:42:35.546765 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:42:35.550245 INFO::ASW Batch was 0.219501851015734 prior to batch effect correction and is now -0.106527660547366 .
2026-05-20 21:42:35.55093 INFO::ASW Label was -0.182893865665323 prior to batch effect correction and is now -0.0758053985512194 .
2026-05-20 21:42:35.551903 INFO::Total function execution time is 0.14300274848938 s and adjustment time is 0.124584197998047 s ( 87.12 )
2026-05-20 21:42:35.691083 INFO::Formatting Data.
2026-05-20 21:42:35.69224 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.693246 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.694393 INFO::Found 2 missing values.
2026-05-20 21:42:35.69728 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.697828 INFO::Done
2026-05-20 21:42:35.724834 INFO::Found NA in Reference column
2026-05-20 21:42:35.734166 INFO::Require at least two references per batch.
2026-05-20 21:42:35.755676 INFO::Formatting Data.
2026-05-20 21:42:35.756579 INFO::Recognized SummarizedExperiment
2026-05-20 21:42:35.757162 INFO::Typecasting input to dataframe.
2026-05-20 21:42:35.767519 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.768762 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.772337 INFO::Found 0 missing values.
2026-05-20 21:42:35.779149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.779779 INFO::Done
2026-05-20 21:42:35.795257 INFO::Formatting Data.
2026-05-20 21:42:35.796031 INFO::Recognized SummarizedExperiment
2026-05-20 21:42:35.796593 INFO::Typecasting input to dataframe.
2026-05-20 21:42:35.813183 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.814532 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.818036 INFO::Found 0 missing values.
2026-05-20 21:42:35.82884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.829566 INFO::Done
2026-05-20 21:42:35.844656 INFO::Formatting Data.
2026-05-20 21:42:35.845476 INFO::Recognized SummarizedExperiment
2026-05-20 21:42:35.846038 INFO::Typecasting input to dataframe.
2026-05-20 21:42:35.861917 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.863037 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.86417 INFO::Found 0 missing values.
2026-05-20 21:42:35.86513 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.
2026-05-20 21:42:35.869625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.870209 INFO::Done
2026-05-20 21:42:35.880211 INFO::Formatting Data.
2026-05-20 21:42:35.881146 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.882104 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.883145 INFO::Found 0 missing values.
2026-05-20 21:42:35.885966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.886528 INFO::Done
2026-05-20 21:42:35.898116 INFO::Formatting Data.
2026-05-20 21:42:35.898998 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.899928 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.900965 INFO::Found 0 missing values.
2026-05-20 21:42:35.903793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.904351 INFO::Done
2026-05-20 21:42:35.933954 INFO::Formatting Data.
2026-05-20 21:42:35.934825 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.935931 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.937132 INFO::Found 1 missing values.
2026-05-20 21:42:35.93979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.940368 INFO::Done
2026-05-20 21:42:35.95976 INFO::Formatting Data.
2026-05-20 21:42:35.960745 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.961723 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.962704 INFO::Found 2 missing values.
2026-05-20 21:42:35.963656 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.
2026-05-20 21:42:35.965873 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.96648 INFO::Done
2026-05-20 21:42:35.975997 INFO::Formatting Data.
2026-05-20 21:42:35.976802 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.977766 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.978743 INFO::Found 2 missing values.
2026-05-20 21:42:35.980356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.980979 INFO::Done
2026-05-20 21:42:35.991179 INFO::Formatting Data.
2026-05-20 21:42:35.991961 INFO::Typecasting input to dataframe.
2026-05-20 21:42:35.992887 INFO::Replacing NaNs with NAs.
2026-05-20 21:42:35.993765 INFO::Removing potential empty rows and columns
2026-05-20 21:42:35.994802 INFO::Found 0 missing values.
2026-05-20 21:42:35.997652 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:42:35.998217 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.988 4.095 21.742
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.793 | 1.154 | 18.167 | |
| compute_asw | 0.026 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.011 | 0.000 | 0.012 | |