Yannis Schumann
| Snapshot Date: 2026-04-21 13:40 -0400 (Tue, 21 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-22 11:35 -0400 (Wed, 22 Apr 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" | 4738 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4701 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 170/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (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: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-04-21 18:36:11 -0400 (Tue, 21 Apr 2026) |
| EndedAt: 2026-04-21 18:36:44 -0400 (Tue, 21 Apr 2026) |
| EllapsedTime: 33.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-21 22:36:11 UTC
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.775 0.398 6.985
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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")
2026-04-21 18:36:36.589722 INFO::Formatting Data.
2026-04-21 18:36:36.591205 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:36.595264 INFO::Removing potential empty rows and columns
2026-04-21 18:36:36.70802 INFO::Found 0 missing values.
2026-04-21 18:36:36.7097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:36.710083 INFO::Done
2026-04-21 18:36:36.710471 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:36.717442 INFO::Starting hierarchical adjustment
2026-04-21 18:36:36.717997 INFO::Found 3 batches.
2026-04-21 18:36:36.718363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:36.718996 INFO::Using default BPPARAM
2026-04-21 18:36:36.719341 INFO::Processing subtree level 1
2026-04-21 18:36:36.820491 INFO::Adjusting the last 1 batches sequentially
2026-04-21 18:36:36.821842 INFO::Done
2026-04-21 18:36:36.822192 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:36.823353 INFO::ASW Batch was -0.116435685884242 prior to batch effect correction and is now -0.116435685884242 .
2026-04-21 18:36:36.823979 INFO::Total function execution time is 0.234694957733154 s and adjustment time is 0.103957891464233 s ( 44.29 )
2026-04-21 18:36:36.833372 INFO::Formatting Data.
2026-04-21 18:36:36.833837 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:36.834515 INFO::Removing potential empty rows and columns
2026-04-21 18:36:36.835407 INFO::Found 0 missing values.
2026-04-21 18:36:36.835976 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.
2026-04-21 18:36:36.842525 INFO::Formatting Data.
2026-04-21 18:36:36.843384 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:36.844231 INFO::Removing potential empty rows and columns
2026-04-21 18:36:36.844829 INFO::Found 0 missing values.
2026-04-21 18:36:36.845401 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.
2026-04-21 18:36:36.855349 INFO::Formatting Data.
2026-04-21 18:36:36.855803 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:36.856289 INFO::Removing potential empty rows and columns
2026-04-21 18:36:36.856808 INFO::Found 0 missing values.
2026-04-21 18:36:36.85722 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.
2026-04-21 18:36:36.858794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:36.859284 INFO::Done
2026-04-21 18:36:36.859873 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:36.861291 INFO::Starting hierarchical adjustment
2026-04-21 18:36:36.862032 INFO::Found 2 batches.
2026-04-21 18:36:36.86237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:36.862743 INFO::Using default BPPARAM
2026-04-21 18:36:36.863033 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:36.863511 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-21 18:36:36.874859 INFO::Done
2026-04-21 18:36:36.875265 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:36.876605 INFO::ASW Batch was -0.0920861655444739 prior to batch effect correction and is now -0.123497474742275 .
2026-04-21 18:36:36.877046 INFO::Total function execution time is 0.0217249393463135 s and adjustment time is 0.0129251480102539 s ( 59.49 )
2026-04-21 18:36:36.878369 INFO::Formatting Data.
2026-04-21 18:36:36.878732 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:36.882028 INFO::Formatting Data.
2026-04-21 18:36:36.88261 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:36.883296 INFO::Removing potential empty rows and columns
2026-04-21 18:36:36.883768 INFO::Found 0 missing values.
2026-04-21 18:36:36.885399 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:36.885721 INFO::Done
2026-04-21 18:36:36.886005 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:36.886916 INFO::Starting hierarchical adjustment
2026-04-21 18:36:36.887351 INFO::Found 2 batches.
2026-04-21 18:36:36.887826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:36.888177 INFO::Using default BPPARAM
2026-04-21 18:36:36.888883 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:36.889584 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-21 18:36:36.897954 INFO::Done
2026-04-21 18:36:36.89842 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:36.899254 INFO::ASW Batch was -0.00526489253334992 prior to batch effect correction and is now -0.132153785672456 .
2026-04-21 18:36:36.899689 INFO::Total function execution time is 0.0176739692687988 s and adjustment time is 0.0106589794158936 s ( 60.31 )
2026-04-21 18:36:36.900256 INFO::Formatting Data.
2026-04-21 18:36:36.900608 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:36.900976 INFO::Removing potential empty rows and columns
2026-04-21 18:36:36.90155 INFO::Found 0 missing values.
2026-04-21 18:36:36.903063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:36.90352 INFO::Done
2026-04-21 18:36:36.903826 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:36.904783 INFO::Starting hierarchical adjustment
2026-04-21 18:36:36.905163 INFO::Found 2 batches.
2026-04-21 18:36:36.905458 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:36.905772 INFO::Using default BPPARAM
2026-04-21 18:36:36.906051 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:36.906442 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-21 18:36:36.911135 INFO::Done
2026-04-21 18:36:36.911484 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:36.912186 INFO::ASW Batch was -0.00526489253334992 prior to batch effect correction and is now -0.132153785672456 .
2026-04-21 18:36:36.912573 INFO::Total function execution time is 0.0123140811920166 s and adjustment time is 0.00602412223815918 s ( 48.92 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-21 18:36:38.144404 INFO::Formatting Data.
2026-04-21 18:36:38.144854 INFO::Recognized SummarizedExperiment
2026-04-21 18:36:38.145181 INFO::Typecasting input to dataframe.
2026-04-21 18:36:38.156096 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.156734 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.158076 INFO::Found 0 missing values.
2026-04-21 18:36:38.160407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.160744 INFO::Done
2026-04-21 18:36:38.16107 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.162386 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.162754 INFO::Found 2 batches.
2026-04-21 18:36:38.163063 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.163581 INFO::Using default BPPARAM
2026-04-21 18:36:38.163829 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.164238 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-21 18:36:38.181362 INFO::Done
2026-04-21 18:36:38.181812 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.18309 INFO::ASW Batch was 0.0130376362168805 prior to batch effect correction and is now -0.102485363949968 .
2026-04-21 18:36:38.183472 INFO::Total function execution time is 0.0391829013824463 s and adjustment time is 0.0186431407928467 s ( 47.58 )
Warning: stack imbalance in '{', 73 then 75
2026-04-21 18:36:38.18966 INFO::Formatting Data.
2026-04-21 18:36:38.190051 INFO::Recognized SummarizedExperiment
2026-04-21 18:36:38.19033 INFO::Typecasting input to dataframe.
2026-04-21 18:36:38.193308 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.193835 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.19511 INFO::Found 0 missing values.
2026-04-21 18:36:38.197309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.197618 INFO::Done
2026-04-21 18:36:38.197866 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.199136 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.199454 INFO::Found 2 batches.
2026-04-21 18:36:38.199709 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.200005 INFO::Using default BPPARAM
2026-04-21 18:36:38.200246 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.200663 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-21 18:36:38.208982 INFO::Done
2026-04-21 18:36:38.209496 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.211028 INFO::ASW Batch was -0.0265115648218192 prior to batch effect correction and is now -0.0265115648218192 .
2026-04-21 18:36:38.211511 INFO::Total function execution time is 0.0218420028686523 s and adjustment time is 0.00953984260559082 s ( 43.68 )
2026-04-21 18:36:38.219152 INFO::Formatting Data.
2026-04-21 18:36:38.219548 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.219982 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.220415 INFO::Found 0 missing values.
2026-04-21 18:36:38.221477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.221813 INFO::Done
2026-04-21 18:36:38.222093 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.22285 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.223174 INFO::Found 3 batches.
2026-04-21 18:36:38.223472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.223764 INFO::Using default BPPARAM
2026-04-21 18:36:38.224034 INFO::Processing subtree level 1
2026-04-21 18:36:38.364115 INFO::Adjusting the last 1 batches sequentially
2026-04-21 18:36:38.365508 INFO::Done
2026-04-21 18:36:38.365874 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.367301 INFO::ASW Batch was -0.122814555996258 prior to batch effect correction and is now -0.157530766316835 .
2026-04-21 18:36:38.367975 INFO::Total function execution time is 0.148821115493774 s and adjustment time is 0.14235782623291 s ( 95.66 )
2026-04-21 18:36:38.374132 INFO::Skipping initial DF formatting
2026-04-21 18:36:38.374551 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.376085 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.37649 INFO::Found 5 batches.
2026-04-21 18:36:38.376798 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.377171 INFO::Using default BPPARAM
2026-04-21 18:36:38.377464 INFO::Processing subtree level 1
2026-04-21 18:36:38.433688 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.434802 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-21 18:36:38.442472 INFO::Done
2026-04-21 18:36:38.443069 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.444996 INFO::ASW Batch was 0.558710275607704 prior to batch effect correction and is now 0.558710275607704 .
2026-04-21 18:36:38.445554 INFO::ASW Label was 0.326683821987878 prior to batch effect correction and is now 0.326683821987878 .
2026-04-21 18:36:38.446234 INFO::Total function execution time is 0.0720059871673584 s and adjustment time is 0.06601881980896 s ( 91.69 )
2026-04-21 18:36:38.455072 INFO::Formatting Data.
2026-04-21 18:36:38.455652 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.456136 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.456601 INFO::Found 0 missing values.
2026-04-21 18:36:38.457911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.458222 INFO::Done
2026-04-21 18:36:38.458524 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.459594 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.459942 INFO::Found 5 batches.
2026-04-21 18:36:38.460236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.460589 INFO::Using default BPPARAM
2026-04-21 18:36:38.460904 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.
2026-04-21 18:36:38.515355 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.516622 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-21 18:36:38.522789 INFO::Done
2026-04-21 18:36:38.523207 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.524471 INFO::ASW Batch was 0.348615122313292 prior to batch effect correction and is now -0.0378728009197882 .
2026-04-21 18:36:38.524832 INFO::ASW Label was 0.31490511435716 prior to batch effect correction and is now 0.821197971385446 .
2026-04-21 18:36:38.525272 INFO::Total function execution time is 0.0702571868896484 s and adjustment time is 0.0628881454467773 s ( 89.51 )
2026-04-21 18:36:38.525674 INFO::Formatting Data.
2026-04-21 18:36:38.525976 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.526356 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.526811 INFO::Found 0 missing values.
2026-04-21 18:36:38.528103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.528388 INFO::Done
2026-04-21 18:36:38.52864 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.529634 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.529971 INFO::Found 5 batches.
2026-04-21 18:36:38.530236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.530551 INFO::Using default BPPARAM
2026-04-21 18:36:38.530812 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.
2026-04-21 18:36:38.581826 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.58297 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-21 18:36:38.590695 INFO::Done
2026-04-21 18:36:38.591117 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.592377 INFO::ASW Batch was 0.348615122313292 prior to batch effect correction and is now -0.0378728009197882 .
2026-04-21 18:36:38.592694 INFO::ASW Label was 0.31490511435716 prior to batch effect correction and is now 0.821197971385446 .
2026-04-21 18:36:38.593094 INFO::Total function execution time is 0.06740403175354 s and adjustment time is 0.0607681274414062 s ( 90.16 )
2026-04-21 18:36:38.598929 INFO::Formatting Data.
2026-04-21 18:36:38.599453 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.59992 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.600409 INFO::Found 0 missing values.
2026-04-21 18:36:38.601943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.602331 INFO::Done
2026-04-21 18:36:38.602648 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.603917 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.604328 INFO::Found 5 batches.
2026-04-21 18:36:38.604667 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.605037 INFO::Using default BPPARAM
2026-04-21 18:36:38.605387 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.
2026-04-21 18:36:38.661475 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.662727 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-21 18:36:38.66903 INFO::Done
2026-04-21 18:36:38.66945 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.670824 INFO::ASW Batch was 0.226769721976854 prior to batch effect correction and is now -0.0890347250347564 .
2026-04-21 18:36:38.671186 INFO::ASW Label was 0.525247077349955 prior to batch effect correction and is now 0.886628485966349 .
2026-04-21 18:36:38.671618 INFO::Total function execution time is 0.0726981163024902 s and adjustment time is 0.064763069152832 s ( 89.08 )
2026-04-21 18:36:38.672029 INFO::Formatting Data.
2026-04-21 18:36:38.67233 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.672717 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.673177 INFO::Found 0 missing values.
2026-04-21 18:36:38.674509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.674821 INFO::Done
2026-04-21 18:36:38.675118 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.676117 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.676539 INFO::Found 5 batches.
2026-04-21 18:36:38.67685 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.677204 INFO::Using default BPPARAM
2026-04-21 18:36:38.677531 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.
2026-04-21 18:36:38.738705 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.739851 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-21 18:36:38.745861 INFO::Done
2026-04-21 18:36:38.746245 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.747514 INFO::ASW Batch was 0.226769721976854 prior to batch effect correction and is now -0.0890347250347564 .
2026-04-21 18:36:38.747833 INFO::ASW Label was 0.525247077349955 prior to batch effect correction and is now 0.886628485966349 .
2026-04-21 18:36:38.748277 INFO::Total function execution time is 0.0762240886688232 s and adjustment time is 0.0693650245666504 s ( 91 )
2026-04-21 18:36:38.754211 INFO::Formatting Data.
2026-04-21 18:36:38.754602 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.755058 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.755527 INFO::Found 0 missing values.
2026-04-21 18:36:38.756502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.756808 INFO::Done
2026-04-21 18:36:38.757094 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.758214 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.758581 INFO::Found 2 batches.
2026-04-21 18:36:38.758878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.759205 INFO::Using default BPPARAM
2026-04-21 18:36:38.75947 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.75987 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-21 18:36:38.764709 INFO::Done
2026-04-21 18:36:38.765067 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.766132 INFO::ASW Batch was 0.323168660021199 prior to batch effect correction and is now -0.0251923747255444 .
2026-04-21 18:36:38.766486 INFO::ASW Label was 0.723458197305602 prior to batch effect correction and is now 0.937379422723416 .
2026-04-21 18:36:38.766852 INFO::Total function execution time is 0.0126709938049316 s and adjustment time is 0.00617504119873047 s ( 48.73 )
2026-04-21 18:36:38.76721 INFO::Formatting Data.
2026-04-21 18:36:38.767544 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.767928 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.768352 INFO::Found 0 missing values.
2026-04-21 18:36:38.769238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.769523 INFO::Done
2026-04-21 18:36:38.769818 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.770755 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.77108 INFO::Found 2 batches.
2026-04-21 18:36:38.771365 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.771678 INFO::Using default BPPARAM
2026-04-21 18:36:38.771931 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.77234 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-21 18:36:38.777205 INFO::Done
2026-04-21 18:36:38.777604 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.778622 INFO::ASW Batch was 0.323168660021199 prior to batch effect correction and is now -0.0251923747255444 .
2026-04-21 18:36:38.778952 INFO::ASW Label was 0.723458197305602 prior to batch effect correction and is now 0.937379422723416 .
2026-04-21 18:36:38.779329 INFO::Total function execution time is 0.012103796005249 s and adjustment time is 0.00616192817687988 s ( 50.91 )
2026-04-21 18:36:38.783869 INFO::Formatting Data.
2026-04-21 18:36:38.784242 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.784632 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.785042 INFO::Found 0 missing values.
2026-04-21 18:36:38.785773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.786109 INFO::Done
2026-04-21 18:36:38.786417 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.787122 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.787474 INFO::Found 2 batches.
2026-04-21 18:36:38.787737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.788053 INFO::Using default BPPARAM
2026-04-21 18:36:38.788341 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.788691 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-21 18:36:38.799305 INFO::Done
2026-04-21 18:36:38.799702 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.800455 INFO::ASW Batch was 1.72087106056831e-05 prior to batch effect correction and is now -0.162374746204808 .
2026-04-21 18:36:38.800819 INFO::Total function execution time is 0.0169610977172852 s and adjustment time is 0.0118589401245117 s ( 69.92 )
2026-04-21 18:36:38.805535 INFO::Formatting Data.
2026-04-21 18:36:38.805915 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.806363 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.806791 INFO::Found 0 missing values.
2026-04-21 18:36:38.807332 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.
2026-04-21 18:36:38.808817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.80912 INFO::Done
2026-04-21 18:36:38.80939 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.810473 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.810842 INFO::Found 2 batches.
2026-04-21 18:36:38.811119 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.81144 INFO::Using default BPPARAM
2026-04-21 18:36:38.811701 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.81209 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-21 18:36:38.818102 INFO::Done
2026-04-21 18:36:38.818528 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.819637 INFO::ASW Batch was 0.50615545345483 prior to batch effect correction and is now -0.0381790629188741 .
2026-04-21 18:36:38.81998 INFO::ASW Label was 0.552998132611574 prior to batch effect correction and is now 0.956882146318485 .
2026-04-21 18:36:38.820375 INFO::Total function execution time is 0.014847993850708 s and adjustment time is 0.00728392601013184 s ( 49.06 )
2026-04-21 18:36:38.820754 INFO::Formatting Data.
2026-04-21 18:36:38.821082 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.821495 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.821937 INFO::Found 0 missing values.
2026-04-21 18:36:38.82235 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.
2026-04-21 18:36:38.823831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.824192 INFO::Done
2026-04-21 18:36:38.824481 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.825473 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.825857 INFO::Found 2 batches.
2026-04-21 18:36:38.82619 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.826496 INFO::Using default BPPARAM
2026-04-21 18:36:38.826792 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:38.827201 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-21 18:36:38.832497 INFO::Done
2026-04-21 18:36:38.83288 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.833877 INFO::ASW Batch was 0.50615545345483 prior to batch effect correction and is now -0.0381790629188741 .
2026-04-21 18:36:38.834204 INFO::ASW Label was 0.552998132611574 prior to batch effect correction and is now 0.956882146318485 .
2026-04-21 18:36:38.834577 INFO::Total function execution time is 0.013808012008667 s and adjustment time is 0.00668096542358398 s ( 48.38 )
2026-04-21 18:36:38.902494 INFO::Formatting Data.
2026-04-21 18:36:38.903003 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.903435 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.903932 INFO::Found 0 missing values.
2026-04-21 18:36:38.905012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.905358 INFO::Done
2026-04-21 18:36:38.905687 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.906588 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.906949 INFO::Found 3 batches.
2026-04-21 18:36:38.907224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.907537 INFO::Using default BPPARAM
2026-04-21 18:36:38.907851 INFO::Processing subtree level 1
2026-04-21 18:36:38.966092 INFO::Adjusting the last 1 batches sequentially
2026-04-21 18:36:38.967569 INFO::Done
2026-04-21 18:36:38.967949 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:38.969288 INFO::ASW Batch was 0.0133625273511745 prior to batch effect correction and is now 0.0133625273511745 .
2026-04-21 18:36:38.969929 INFO::Total function execution time is 0.0674729347229004 s and adjustment time is 0.0606639385223389 s ( 89.91 )
2026-04-21 18:36:38.970472 INFO::Formatting Data.
2026-04-21 18:36:38.970831 INFO::Typecasting input to dataframe.
2026-04-21 18:36:38.971263 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:38.971828 INFO::Removing potential empty rows and columns
2026-04-21 18:36:38.972418 INFO::Found 0 missing values.
2026-04-21 18:36:38.973683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:38.974019 INFO::Done
2026-04-21 18:36:38.974337 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:38.975209 INFO::Starting hierarchical adjustment
2026-04-21 18:36:38.975629 INFO::Found 3 batches.
2026-04-21 18:36:38.975943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:38.976332 INFO::Using default BPPARAM
2026-04-21 18:36:38.976723 INFO::Processing subtree level 1
2026-04-21 18:36:39.028202 INFO::Adjusting the last 1 batches sequentially
2026-04-21 18:36:39.029419 INFO::Done
2026-04-21 18:36:39.029766 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:39.030979 INFO::ASW Batch was 0.0133625273511745 prior to batch effect correction and is now 0.0133625273511745 .
2026-04-21 18:36:39.031513 INFO::Total function execution time is 0.0610361099243164 s and adjustment time is 0.0538539886474609 s ( 88.23 )
2026-04-21 18:36:39.037773 INFO::Formatting Data.
2026-04-21 18:36:39.038148 INFO::Typecasting input to dataframe.
2026-04-21 18:36:39.038528 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:39.038961 INFO::Removing potential empty rows and columns
2026-04-21 18:36:39.03949 INFO::Found 0 missing values.
2026-04-21 18:36:39.040511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:39.040858 INFO::Done
2026-04-21 18:36:39.041168 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:39.041902 INFO::Starting hierarchical adjustment
2026-04-21 18:36:39.042229 INFO::Found 3 batches.
2026-04-21 18:36:39.042492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:39.04283 INFO::Using default BPPARAM
2026-04-21 18:36:39.04309 INFO::Processing subtree level 1
2026-04-21 18:36:39.091996 INFO::Adjusting the last 1 batches sequentially
2026-04-21 18:36:39.09349 INFO::Done
2026-04-21 18:36:39.093918 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:39.095323 INFO::ASW Batch was -0.102164182622326 prior to batch effect correction and is now -0.102164182622326 .
2026-04-21 18:36:39.09595 INFO::Total function execution time is 0.0581681728363037 s and adjustment time is 0.0512979030609131 s ( 88.19 )
2026-04-21 18:36:39.176151 INFO::Formatting Data.
2026-04-21 18:36:39.176609 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:39.177361 INFO::Removing potential empty rows and columns
2026-04-21 18:36:39.178654 INFO::Found 1000 missing values.
2026-04-21 18:36:39.185813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:39.186185 INFO::Done
2026-04-21 18:36:39.186485 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:39.188735 INFO::Starting hierarchical adjustment
2026-04-21 18:36:39.189141 INFO::Found 10 batches.
2026-04-21 18:36:39.189551 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:39.189952 INFO::Using default BPPARAM
2026-04-21 18:36:39.190263 INFO::Processing subtree level 1
2026-04-21 18:36:39.270222 INFO::Processing subtree level 2
2026-04-21 18:36:39.336512 INFO::Adjusting the last 1 batches sequentially
2026-04-21 18:36:39.337964 INFO::Done
2026-04-21 18:36:39.338346 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:39.341181 INFO::ASW Batch was 0.493225910512304 prior to batch effect correction and is now 0.493225910512304 .
2026-04-21 18:36:39.341599 INFO::ASW Label was 0.325375272214156 prior to batch effect correction and is now 0.325375272214156 .
2026-04-21 18:36:39.342176 INFO::Total function execution time is 0.165998935699463 s and adjustment time is 0.148880004882812 s ( 89.69 )
2026-04-21 18:36:39.342625 INFO::Formatting Data.
2026-04-21 18:36:39.342923 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:39.343498 INFO::Removing potential empty rows and columns
2026-04-21 18:36:39.344641 INFO::Found 1000 missing values.
2026-04-21 18:36:39.351505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:39.351917 INFO::Done
2026-04-21 18:36:39.352346 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:39.354524 INFO::Starting hierarchical adjustment
2026-04-21 18:36:39.35496 INFO::Found 10 batches.
2026-04-21 18:36:39.830673 INFO::Set up parallel execution backend with 2 workers
2026-04-21 18:36:39.831242 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-21 18:36:40.373075 INFO::Adjusting the last 2 batches sequentially
2026-04-21 18:36:40.373999 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-21 18:36:40.380171 INFO::Done
2026-04-21 18:36:40.380618 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:40.382661 INFO::ASW Batch was 0.493225910512304 prior to batch effect correction and is now 0.493225910512304 .
2026-04-21 18:36:40.382972 INFO::ASW Label was 0.325375272214156 prior to batch effect correction and is now 0.325375272214156 .
2026-04-21 18:36:40.383321 INFO::Total function execution time is 1.04071402549744 s and adjustment time is 1.0252730846405 s ( 98.52 )
2026-04-21 18:36:40.587158 INFO::Formatting Data.
2026-04-21 18:36:40.587635 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.588117 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.588695 INFO::Found 0 missing values.
2026-04-21 18:36:40.590287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.590647 INFO::Done
2026-04-21 18:36:40.590959 INFO::Acquiring quality metrics before batch effect correction.
2026-04-21 18:36:40.592074 INFO::Starting hierarchical adjustment
2026-04-21 18:36:40.592471 INFO::Found 3 batches.
2026-04-21 18:36:40.592826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-21 18:36:40.593224 INFO::Using default BPPARAM
2026-04-21 18:36:40.593523 INFO::Processing subtree level 1
2026-04-21 18:36:40.668316 INFO::Adjusting the last 1 batches sequentially
2026-04-21 18:36:40.670164 INFO::Done
2026-04-21 18:36:40.670578 INFO::Acquiring quality metrics after batch effect correction.
2026-04-21 18:36:40.672032 INFO::ASW Batch was 0.16457325109159 prior to batch effect correction and is now -0.188829774414079 .
2026-04-21 18:36:40.672397 INFO::ASW Label was -0.15490370445909 prior to batch effect correction and is now 0.0503180682679232 .
2026-04-21 18:36:40.673173 INFO::Total function execution time is 0.0858728885650635 s and adjustment time is 0.0777370929718018 s ( 90.53 )
2026-04-21 18:36:40.746405 INFO::Formatting Data.
2026-04-21 18:36:40.747078 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.747605 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.748143 INFO::Found 2 missing values.
2026-04-21 18:36:40.749592 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.75025 INFO::Done
2026-04-21 18:36:40.767154 INFO::Found NA in Reference column
2026-04-21 18:36:40.772345 INFO::Require at least two references per batch.
2026-04-21 18:36:40.78371 INFO::Formatting Data.
2026-04-21 18:36:40.78421 INFO::Recognized SummarizedExperiment
2026-04-21 18:36:40.784914 INFO::Typecasting input to dataframe.
2026-04-21 18:36:40.790923 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.791583 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.793578 INFO::Found 0 missing values.
2026-04-21 18:36:40.798433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.798961 INFO::Done
2026-04-21 18:36:40.80803 INFO::Formatting Data.
2026-04-21 18:36:40.808502 INFO::Recognized SummarizedExperiment
2026-04-21 18:36:40.809061 INFO::Typecasting input to dataframe.
2026-04-21 18:36:40.81853 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.819214 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.82238 INFO::Found 0 missing values.
2026-04-21 18:36:40.827981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.828431 INFO::Done
2026-04-21 18:36:40.838134 INFO::Formatting Data.
2026-04-21 18:36:40.838924 INFO::Recognized SummarizedExperiment
2026-04-21 18:36:40.839758 INFO::Typecasting input to dataframe.
2026-04-21 18:36:40.848613 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.849226 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.850164 INFO::Found 0 missing values.
2026-04-21 18:36:40.850704 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.
2026-04-21 18:36:40.853206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.853561 INFO::Done
2026-04-21 18:36:40.858512 INFO::Formatting Data.
2026-04-21 18:36:40.859152 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.859624 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.860198 INFO::Found 0 missing values.
2026-04-21 18:36:40.861232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.861718 INFO::Done
2026-04-21 18:36:40.868472 INFO::Formatting Data.
2026-04-21 18:36:40.868995 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.869469 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.869987 INFO::Found 0 missing values.
2026-04-21 18:36:40.87115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.871517 INFO::Done
2026-04-21 18:36:40.88361 INFO::Formatting Data.
2026-04-21 18:36:40.884055 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.884499 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.884996 INFO::Found 1 missing values.
2026-04-21 18:36:40.885933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.886243 INFO::Done
2026-04-21 18:36:40.893532 INFO::Formatting Data.
2026-04-21 18:36:40.89391 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.894335 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.894797 INFO::Found 2 missing values.
2026-04-21 18:36:40.895222 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.
2026-04-21 18:36:40.896122 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.896428 INFO::Done
2026-04-21 18:36:40.902016 INFO::Formatting Data.
2026-04-21 18:36:40.90251 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.902949 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.903397 INFO::Found 2 missing values.
2026-04-21 18:36:40.904098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.9044 INFO::Done
2026-04-21 18:36:40.909286 INFO::Formatting Data.
2026-04-21 18:36:40.909744 INFO::Typecasting input to dataframe.
2026-04-21 18:36:40.910145 INFO::Replacing NaNs with NAs.
2026-04-21 18:36:40.910555 INFO::Removing potential empty rows and columns
2026-04-21 18:36:40.911029 INFO::Found 0 missing values.
2026-04-21 18:36:40.912257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-21 18:36:40.912572 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.145 1.874 9.322
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.775 | 0.398 | 6.985 | |
| compute_asw | 0.01 | 0.00 | 0.01 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.004 | |