Yannis Schumann
| Snapshot Date: 2025-11-26 13:40 -0500 (Wed, 26 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-27 11:39 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4865 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| 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 167/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2025-11-26 18:39:05 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 18:39:42 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 36.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* 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 10.352 0.441 7.795
* 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-arm64/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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")
2025-11-26 18:39:32.925603 INFO::Formatting Data.
2025-11-26 18:39:32.930084 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:32.934579 INFO::Removing potential empty rows and columns
2025-11-26 18:39:33.052189 INFO::Found 0 missing values.
2025-11-26 18:39:33.053548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:33.053789 INFO::Done
2025-11-26 18:39:33.053999 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:33.05998 INFO::Starting hierarchical adjustment
2025-11-26 18:39:33.060271 INFO::Found 3 batches.
2025-11-26 18:39:33.060465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:33.060897 INFO::Using default BPPARAM
2025-11-26 18:39:33.061088 INFO::Processing subtree level 1
2025-11-26 18:39:33.125954 INFO::Adjusting the last 1 batches sequentially
2025-11-26 18:39:33.127852 INFO::Done
2025-11-26 18:39:33.128938 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:33.130915 INFO::ASW Batch was -0.00715674606964146 prior to batch effect correction and is now -0.00715674606964146 .
2025-11-26 18:39:33.131539 INFO::Total function execution time is 0.206117153167725 s and adjustment time is 0.0676159858703613 s ( 32.8 )
2025-11-26 18:39:33.140089 INFO::Formatting Data.
2025-11-26 18:39:33.140392 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:33.14078 INFO::Removing potential empty rows and columns
2025-11-26 18:39:33.141304 INFO::Found 0 missing values.
2025-11-26 18:39:33.142131 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.
2025-11-26 18:39:33.147523 INFO::Formatting Data.
2025-11-26 18:39:33.147835 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:33.148619 INFO::Removing potential empty rows and columns
2025-11-26 18:39:33.149329 INFO::Found 0 missing values.
2025-11-26 18:39:33.149737 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.
2025-11-26 18:39:33.156697 INFO::Formatting Data.
2025-11-26 18:39:33.157004 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:33.157441 INFO::Removing potential empty rows and columns
2025-11-26 18:39:33.157885 INFO::Found 0 missing values.
2025-11-26 18:39:33.158229 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.
2025-11-26 18:39:33.160704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:33.160934 INFO::Done
2025-11-26 18:39:33.161133 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:33.162077 INFO::Starting hierarchical adjustment
2025-11-26 18:39:33.162369 INFO::Found 2 batches.
2025-11-26 18:39:33.162592 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:33.162972 INFO::Using default BPPARAM
2025-11-26 18:39:33.163253 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:33.163773 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 18:39:33.1749 INFO::Done
2025-11-26 18:39:33.175167 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:33.176295 INFO::ASW Batch was -0.0105275753720302 prior to batch effect correction and is now -0.124946982069219 .
2025-11-26 18:39:33.176628 INFO::Total function execution time is 0.0199339389801025 s and adjustment time is 0.0125861167907715 s ( 63.14 )
2025-11-26 18:39:33.178207 INFO::Formatting Data.
2025-11-26 18:39:33.178778 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:33.183183 INFO::Formatting Data.
2025-11-26 18:39:33.183487 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:33.183874 INFO::Removing potential empty rows and columns
2025-11-26 18:39:33.18436 INFO::Found 0 missing values.
2025-11-26 18:39:33.185781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:33.186076 INFO::Done
2025-11-26 18:39:33.18631 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:33.187154 INFO::Starting hierarchical adjustment
2025-11-26 18:39:33.187449 INFO::Found 2 batches.
2025-11-26 18:39:33.187702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:33.187987 INFO::Using default BPPARAM
2025-11-26 18:39:33.188235 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:33.18869 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 18:39:33.223824 INFO::Done
2025-11-26 18:39:33.224174 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:33.22487 INFO::ASW Batch was -0.067797030024895 prior to batch effect correction and is now -0.12749800789444 .
2025-11-26 18:39:33.225136 INFO::Total function execution time is 0.041985034942627 s and adjustment time is 0.0364270210266113 s ( 86.76 )
2025-11-26 18:39:33.225489 INFO::Formatting Data.
2025-11-26 18:39:33.225692 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:33.225968 INFO::Removing potential empty rows and columns
2025-11-26 18:39:33.226311 INFO::Found 0 missing values.
2025-11-26 18:39:33.227275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:33.22746 INFO::Done
2025-11-26 18:39:33.227622 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:33.228246 INFO::Starting hierarchical adjustment
2025-11-26 18:39:33.228494 INFO::Found 2 batches.
2025-11-26 18:39:33.228675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:33.228894 INFO::Using default BPPARAM
2025-11-26 18:39:33.229062 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:33.229342 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 18:39:33.235122 INFO::Done
2025-11-26 18:39:33.235365 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:33.23607 INFO::ASW Batch was -0.067797030024895 prior to batch effect correction and is now -0.12749800789444 .
2025-11-26 18:39:33.236344 INFO::Total function execution time is 0.0108392238616943 s and adjustment time is 0.00665712356567383 s ( 61.42 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-26 18:39:34.591641 INFO::Formatting Data.
2025-11-26 18:39:34.59189 INFO::Recognized SummarizedExperiment
2025-11-26 18:39:34.592046 INFO::Typecasting input to dataframe.
2025-11-26 18:39:34.602354 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:34.602796 INFO::Removing potential empty rows and columns
2025-11-26 18:39:34.604015 INFO::Found 0 missing values.
2025-11-26 18:39:34.606308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:34.606541 INFO::Done
2025-11-26 18:39:34.606712 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:34.608069 INFO::Starting hierarchical adjustment
2025-11-26 18:39:34.608314 INFO::Found 2 batches.
2025-11-26 18:39:34.608473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:34.608876 INFO::Using default BPPARAM
2025-11-26 18:39:34.609031 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:34.609332 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 18:39:34.628667 INFO::Done
2025-11-26 18:39:34.628942 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:34.630228 INFO::ASW Batch was 0.0150510024979106 prior to batch effect correction and is now -0.0899575928033259 .
2025-11-26 18:39:34.630508 INFO::Total function execution time is 0.0389599800109863 s and adjustment time is 0.0203919410705566 s ( 52.34 )
Warning: stack imbalance in '{', 73 then 75
2025-11-26 18:39:34.638387 INFO::Formatting Data.
2025-11-26 18:39:34.638736 INFO::Recognized SummarizedExperiment
2025-11-26 18:39:34.638942 INFO::Typecasting input to dataframe.
2025-11-26 18:39:34.642419 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:34.642834 INFO::Removing potential empty rows and columns
2025-11-26 18:39:34.644024 INFO::Found 0 missing values.
2025-11-26 18:39:34.646222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:34.646394 INFO::Done
2025-11-26 18:39:34.646549 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:34.647772 INFO::Starting hierarchical adjustment
2025-11-26 18:39:34.64799 INFO::Found 2 batches.
2025-11-26 18:39:34.648166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:34.648347 INFO::Using default BPPARAM
2025-11-26 18:39:34.648494 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:34.648773 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 18:39:34.656669 INFO::Done
2025-11-26 18:39:34.656872 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:34.65817 INFO::ASW Batch was -0.00190883422486942 prior to batch effect correction and is now -0.00190883422486942 .
2025-11-26 18:39:34.658468 INFO::Total function execution time is 0.0201067924499512 s and adjustment time is 0.00871992111206055 s ( 43.37 )
2025-11-26 18:39:34.665481 INFO::Formatting Data.
2025-11-26 18:39:34.66573 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:34.666016 INFO::Removing potential empty rows and columns
2025-11-26 18:39:34.666331 INFO::Found 0 missing values.
2025-11-26 18:39:34.667188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:34.66736 INFO::Done
2025-11-26 18:39:34.667512 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:34.668215 INFO::Starting hierarchical adjustment
2025-11-26 18:39:34.668433 INFO::Found 3 batches.
2025-11-26 18:39:34.668621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:34.668848 INFO::Using default BPPARAM
2025-11-26 18:39:34.66903 INFO::Processing subtree level 1
2025-11-26 18:39:34.731288 INFO::Adjusting the last 1 batches sequentially
2025-11-26 18:39:34.732479 INFO::Done
2025-11-26 18:39:34.732703 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:34.734044 INFO::ASW Batch was -0.0910575907031838 prior to batch effect correction and is now -0.156758747983155 .
2025-11-26 18:39:34.734622 INFO::Total function execution time is 0.068932056427002 s and adjustment time is 0.0640859603881836 s ( 92.97 )
2025-11-26 18:39:34.741617 INFO::Skipping initial DF formatting
2025-11-26 18:39:34.741845 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:34.743172 INFO::Starting hierarchical adjustment
2025-11-26 18:39:34.743419 INFO::Found 5 batches.
2025-11-26 18:39:34.743591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:34.743806 INFO::Using default BPPARAM
2025-11-26 18:39:34.743955 INFO::Processing subtree level 1
2025-11-26 18:39:34.806564 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:34.82219 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 18:39:34.830787 INFO::Done
2025-11-26 18:39:34.831064 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:34.833593 INFO::ASW Batch was 0.469637788564149 prior to batch effect correction and is now 0.469637788564149 .
2025-11-26 18:39:34.833847 INFO::ASW Label was 0.395642491446383 prior to batch effect correction and is now 0.395642491446383 .
2025-11-26 18:39:34.83431 INFO::Total function execution time is 0.0926141738891602 s and adjustment time is 0.0874049663543701 s ( 94.38 )
2025-11-26 18:39:34.842838 INFO::Formatting Data.
2025-11-26 18:39:34.843129 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:34.84346 INFO::Removing potential empty rows and columns
2025-11-26 18:39:34.843854 INFO::Found 0 missing values.
2025-11-26 18:39:34.845128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:34.845322 INFO::Done
2025-11-26 18:39:34.84549 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:34.846505 INFO::Starting hierarchical adjustment
2025-11-26 18:39:34.846742 INFO::Found 5 batches.
2025-11-26 18:39:34.846901 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:34.847132 INFO::Using default BPPARAM
2025-11-26 18:39:34.847296 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.
2025-11-26 18:39:34.926956 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:34.929946 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 18:39:34.94473 INFO::Done
2025-11-26 18:39:34.945062 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:34.948852 INFO::ASW Batch was 0.717710440228644 prior to batch effect correction and is now -0.0749044876434069 .
2025-11-26 18:39:34.949262 INFO::ASW Label was 0.114118819633787 prior to batch effect correction and is now 0.751098965005235 .
2025-11-26 18:39:34.950007 INFO::Total function execution time is 0.107006072998047 s and adjustment time is 0.098020076751709 s ( 91.6 )
2025-11-26 18:39:34.950869 INFO::Formatting Data.
2025-11-26 18:39:34.951277 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:34.951909 INFO::Removing potential empty rows and columns
2025-11-26 18:39:34.952574 INFO::Found 0 missing values.
2025-11-26 18:39:34.954098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:34.954275 INFO::Done
2025-11-26 18:39:34.954443 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:34.955452 INFO::Starting hierarchical adjustment
2025-11-26 18:39:34.955748 INFO::Found 5 batches.
2025-11-26 18:39:34.955982 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:34.95635 INFO::Using default BPPARAM
2025-11-26 18:39:34.956708 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.
2025-11-26 18:39:35.021572 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:35.023446 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 18:39:35.035668 INFO::Done
2025-11-26 18:39:35.035982 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.038516 INFO::ASW Batch was 0.717710440228644 prior to batch effect correction and is now -0.0749044876434069 .
2025-11-26 18:39:35.038746 INFO::ASW Label was 0.114118819633787 prior to batch effect correction and is now 0.751098965005235 .
2025-11-26 18:39:35.039278 INFO::Total function execution time is 0.0882518291473389 s and adjustment time is 0.0800108909606934 s ( 90.66 )
2025-11-26 18:39:35.04693 INFO::Formatting Data.
2025-11-26 18:39:35.047234 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.047609 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.048034 INFO::Found 0 missing values.
2025-11-26 18:39:35.049336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.049526 INFO::Done
2025-11-26 18:39:35.049704 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.050765 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.051024 INFO::Found 5 batches.
2025-11-26 18:39:35.051197 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.051444 INFO::Using default BPPARAM
2025-11-26 18:39:35.05162 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.
2025-11-26 18:39:35.114889 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:35.117498 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 18:39:35.13008 INFO::Done
2025-11-26 18:39:35.130397 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.13234 INFO::ASW Batch was 0.406941121979519 prior to batch effect correction and is now -0.0826280452226127 .
2025-11-26 18:39:35.132607 INFO::ASW Label was 0.323974268198011 prior to batch effect correction and is now 0.838628805771795 .
2025-11-26 18:39:35.1331 INFO::Total function execution time is 0.0860521793365479 s and adjustment time is 0.0790970325469971 s ( 91.92 )
2025-11-26 18:39:35.133547 INFO::Formatting Data.
2025-11-26 18:39:35.133776 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.134195 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.134584 INFO::Found 0 missing values.
2025-11-26 18:39:35.135901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.1361 INFO::Done
2025-11-26 18:39:35.13627 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.137334 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.137587 INFO::Found 5 batches.
2025-11-26 18:39:35.137772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.138008 INFO::Using default BPPARAM
2025-11-26 18:39:35.138632 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.
2025-11-26 18:39:35.199182 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:35.203711 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 18:39:35.217278 INFO::Done
2025-11-26 18:39:35.21765 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.219511 INFO::ASW Batch was 0.406941121979519 prior to batch effect correction and is now -0.0826280452226127 .
2025-11-26 18:39:35.21976 INFO::ASW Label was 0.323974268198011 prior to batch effect correction and is now 0.838628805771795 .
2025-11-26 18:39:35.220278 INFO::Total function execution time is 0.0865399837493896 s and adjustment time is 0.0797090530395508 s ( 92.11 )
2025-11-26 18:39:35.228014 INFO::Formatting Data.
2025-11-26 18:39:35.228304 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.228661 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.229046 INFO::Found 0 missing values.
2025-11-26 18:39:35.22989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.230057 INFO::Done
2025-11-26 18:39:35.230237 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.231209 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.231431 INFO::Found 2 batches.
2025-11-26 18:39:35.231596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.231806 INFO::Using default BPPARAM
2025-11-26 18:39:35.231964 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:35.23223 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 18:39:35.237351 INFO::Done
2025-11-26 18:39:35.237559 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.238461 INFO::ASW Batch was 0.146609101096337 prior to batch effect correction and is now -0.0170773015939746 .
2025-11-26 18:39:35.238649 INFO::ASW Label was 0.851024099405799 prior to batch effect correction and is now 0.961522384887838 .
2025-11-26 18:39:35.238901 INFO::Total function execution time is 0.010936975479126 s and adjustment time is 0.00596213340759277 s ( 54.51 )
2025-11-26 18:39:35.239141 INFO::Formatting Data.
2025-11-26 18:39:35.239316 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.239574 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.239861 INFO::Found 0 missing values.
2025-11-26 18:39:35.240661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.240819 INFO::Done
2025-11-26 18:39:35.240972 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.241819 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.242047 INFO::Found 2 batches.
2025-11-26 18:39:35.242215 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.24241 INFO::Using default BPPARAM
2025-11-26 18:39:35.242559 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:35.242818 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 18:39:35.247585 INFO::Done
2025-11-26 18:39:35.247789 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.248675 INFO::ASW Batch was 0.146609101096337 prior to batch effect correction and is now -0.0170773015939746 .
2025-11-26 18:39:35.248852 INFO::ASW Label was 0.851024099405799 prior to batch effect correction and is now 0.961522384887838 .
2025-11-26 18:39:35.249098 INFO::Total function execution time is 0.00993490219116211 s and adjustment time is 0.00558090209960938 s ( 56.17 )
2025-11-26 18:39:35.253701 INFO::Formatting Data.
2025-11-26 18:39:35.253948 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.254228 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.254522 INFO::Found 0 missing values.
2025-11-26 18:39:35.255215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.255383 INFO::Done
2025-11-26 18:39:35.255546 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.25643 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.256661 INFO::Found 2 batches.
2025-11-26 18:39:35.256817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.257014 INFO::Using default BPPARAM
2025-11-26 18:39:35.25717 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:35.257423 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 18:39:35.269965 INFO::Done
2025-11-26 18:39:35.270418 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.271339 INFO::ASW Batch was 0.308970116870264 prior to batch effect correction and is now -0.167897472615406 .
2025-11-26 18:39:35.271682 INFO::Total function execution time is 0.0179970264434814 s and adjustment time is 0.0129640102386475 s ( 72.03 )
2025-11-26 18:39:35.27683 INFO::Formatting Data.
2025-11-26 18:39:35.277094 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.277391 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.277724 INFO::Found 0 missing values.
2025-11-26 18:39:35.27816 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.
2025-11-26 18:39:35.279609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.279794 INFO::Done
2025-11-26 18:39:35.279964 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.280926 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.281209 INFO::Found 2 batches.
2025-11-26 18:39:35.281422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.281662 INFO::Using default BPPARAM
2025-11-26 18:39:35.281842 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:35.282196 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 18:39:35.289329 INFO::Done
2025-11-26 18:39:35.289615 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.290741 INFO::ASW Batch was 0.475606241661953 prior to batch effect correction and is now 0.209654917772778 .
2025-11-26 18:39:35.290962 INFO::ASW Label was 0.694007150302237 prior to batch effect correction and is now 0.597581638255911 .
2025-11-26 18:39:35.29126 INFO::Total function execution time is 0.0144650936126709 s and adjustment time is 0.0081629753112793 s ( 56.43 )
2025-11-26 18:39:35.29154 INFO::Formatting Data.
2025-11-26 18:39:35.29174 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.292066 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.292419 INFO::Found 0 missing values.
2025-11-26 18:39:35.292739 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.
2025-11-26 18:39:35.294255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.294457 INFO::Done
2025-11-26 18:39:35.294652 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.295692 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.295951 INFO::Found 2 batches.
2025-11-26 18:39:35.296126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.296347 INFO::Using default BPPARAM
2025-11-26 18:39:35.29653 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:35.296832 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 18:39:35.302724 INFO::Done
2025-11-26 18:39:35.302962 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.303895 INFO::ASW Batch was 0.475606241661953 prior to batch effect correction and is now 0.209654917772778 .
2025-11-26 18:39:35.304084 INFO::ASW Label was 0.694007150302237 prior to batch effect correction and is now 0.597581638255911 .
2025-11-26 18:39:35.304337 INFO::Total function execution time is 0.0127980709075928 s and adjustment time is 0.00681209564208984 s ( 53.23 )
2025-11-26 18:39:35.378681 INFO::Formatting Data.
2025-11-26 18:39:35.379031 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.379493 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.379962 INFO::Found 0 missing values.
2025-11-26 18:39:35.383292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.383605 INFO::Done
2025-11-26 18:39:35.383824 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.384761 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.385082 INFO::Found 3 batches.
2025-11-26 18:39:35.385302 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.385559 INFO::Using default BPPARAM
2025-11-26 18:39:35.385787 INFO::Processing subtree level 1
2025-11-26 18:39:35.433659 INFO::Adjusting the last 1 batches sequentially
2025-11-26 18:39:35.434855 INFO::Done
2025-11-26 18:39:35.43509 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.436511 INFO::ASW Batch was -0.102629456044133 prior to batch effect correction and is now -0.102629456044133 .
2025-11-26 18:39:35.437141 INFO::Total function execution time is 0.0583279132843018 s and adjustment time is 0.0498549938201904 s ( 85.47 )
2025-11-26 18:39:35.437527 INFO::Formatting Data.
2025-11-26 18:39:35.43772 INFO::Typecasting input to dataframe.
2025-11-26 18:39:35.437984 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.438305 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.438693 INFO::Found 0 missing values.
2025-11-26 18:39:35.439646 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.440012 INFO::Done
2025-11-26 18:39:35.440229 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.441236 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.441517 INFO::Found 3 batches.
2025-11-26 18:39:35.441687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.441897 INFO::Using default BPPARAM
2025-11-26 18:39:35.442074 INFO::Processing subtree level 1
2025-11-26 18:39:35.495525 INFO::Adjusting the last 1 batches sequentially
2025-11-26 18:39:35.497563 INFO::Done
2025-11-26 18:39:35.497977 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.500573 INFO::ASW Batch was -0.102629456044133 prior to batch effect correction and is now -0.102629456044133 .
2025-11-26 18:39:35.501498 INFO::Total function execution time is 0.0635919570922852 s and adjustment time is 0.0560941696166992 s ( 88.21 )
2025-11-26 18:39:35.509267 INFO::Formatting Data.
2025-11-26 18:39:35.509533 INFO::Typecasting input to dataframe.
2025-11-26 18:39:35.509824 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.510152 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.510544 INFO::Found 0 missing values.
2025-11-26 18:39:35.511417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.511585 INFO::Done
2025-11-26 18:39:35.511747 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.512343 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.512562 INFO::Found 3 batches.
2025-11-26 18:39:35.512716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.512908 INFO::Using default BPPARAM
2025-11-26 18:39:35.513067 INFO::Processing subtree level 1
2025-11-26 18:39:35.556417 INFO::Adjusting the last 1 batches sequentially
2025-11-26 18:39:35.557971 INFO::Done
2025-11-26 18:39:35.55824 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.559793 INFO::ASW Batch was -0.0773843103636058 prior to batch effect correction and is now -0.0773843103636058 .
2025-11-26 18:39:35.560414 INFO::Total function execution time is 0.0509538650512695 s and adjustment time is 0.0454471111297607 s ( 89.19 )
2025-11-26 18:39:35.635815 INFO::Formatting Data.
2025-11-26 18:39:35.63608 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.636564 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.637693 INFO::Found 1000 missing values.
2025-11-26 18:39:35.648802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.649148 INFO::Done
2025-11-26 18:39:35.649394 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.651883 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.652215 INFO::Found 10 batches.
2025-11-26 18:39:35.652414 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:35.652636 INFO::Using default BPPARAM
2025-11-26 18:39:35.652793 INFO::Processing subtree level 1
2025-11-26 18:39:35.716379 INFO::Processing subtree level 2
2025-11-26 18:39:35.885615 INFO::Adjusting the last 1 batches sequentially
2025-11-26 18:39:35.894344 INFO::Done
2025-11-26 18:39:35.895256 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:35.901315 INFO::ASW Batch was 0.511757603270002 prior to batch effect correction and is now 0.511757603270002 .
2025-11-26 18:39:35.901857 INFO::ASW Label was 0.320446619209892 prior to batch effect correction and is now 0.320446619209892 .
2025-11-26 18:39:35.902794 INFO::Total function execution time is 0.266590118408203 s and adjustment time is 0.242169141769409 s ( 90.84 )
2025-11-26 18:39:35.903262 INFO::Formatting Data.
2025-11-26 18:39:35.903467 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:35.903922 INFO::Removing potential empty rows and columns
2025-11-26 18:39:35.95714 INFO::Found 1000 missing values.
2025-11-26 18:39:35.965993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:35.966421 INFO::Done
2025-11-26 18:39:35.966802 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:35.969632 INFO::Starting hierarchical adjustment
2025-11-26 18:39:35.969996 INFO::Found 10 batches.
2025-11-26 18:39:36.529453 INFO::Set up parallel execution backend with 2 workers
2025-11-26 18:39:36.529809 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-26 18:39:37.19271 INFO::Adjusting the last 2 batches sequentially
2025-11-26 18:39:37.193232 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 18:39:37.198634 INFO::Done
2025-11-26 18:39:37.198832 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:37.200611 INFO::ASW Batch was 0.511757603270002 prior to batch effect correction and is now 0.511757603270002 .
2025-11-26 18:39:37.20078 INFO::ASW Label was 0.320446619209892 prior to batch effect correction and is now 0.320446619209892 .
2025-11-26 18:39:37.201011 INFO::Total function execution time is 1.29775714874268 s and adjustment time is 1.22870016098022 s ( 94.68 )
2025-11-26 18:39:37.271729 INFO::Formatting Data.
2025-11-26 18:39:37.272055 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.272417 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.272854 INFO::Found 0 missing values.
2025-11-26 18:39:37.274131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.274326 INFO::Done
2025-11-26 18:39:37.274508 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 18:39:37.275474 INFO::Starting hierarchical adjustment
2025-11-26 18:39:37.275714 INFO::Found 3 batches.
2025-11-26 18:39:37.275877 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 18:39:37.276094 INFO::Using default BPPARAM
2025-11-26 18:39:37.276265 INFO::Processing subtree level 1
2025-11-26 18:39:37.347746 INFO::Adjusting the last 1 batches sequentially
2025-11-26 18:39:37.350041 INFO::Done
2025-11-26 18:39:37.350295 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 18:39:37.354134 INFO::ASW Batch was 0.175557094214066 prior to batch effect correction and is now -0.143701945710356 .
2025-11-26 18:39:37.354928 INFO::ASW Label was -0.165080905979314 prior to batch effect correction and is now 0.023695394691239 .
2025-11-26 18:39:37.356028 INFO::Total function execution time is 0.0843110084533691 s and adjustment time is 0.07436203956604 s ( 88.2 )
2025-11-26 18:39:37.420275 INFO::Formatting Data.
2025-11-26 18:39:37.42068 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.421091 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.42158 INFO::Found 2 missing values.
2025-11-26 18:39:37.423248 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.42355 INFO::Done
2025-11-26 18:39:37.436982 INFO::Found NA in Reference column
2025-11-26 18:39:37.441536 INFO::Require at least two references per batch.
2025-11-26 18:39:37.451143 INFO::Formatting Data.
2025-11-26 18:39:37.451569 INFO::Recognized SummarizedExperiment
2025-11-26 18:39:37.451792 INFO::Typecasting input to dataframe.
2025-11-26 18:39:37.456826 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.457395 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.459018 INFO::Found 0 missing values.
2025-11-26 18:39:37.461991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.46224 INFO::Done
2025-11-26 18:39:37.473391 INFO::Formatting Data.
2025-11-26 18:39:37.473863 INFO::Recognized SummarizedExperiment
2025-11-26 18:39:37.474121 INFO::Typecasting input to dataframe.
2025-11-26 18:39:37.480818 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.481299 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.482838 INFO::Found 0 missing values.
2025-11-26 18:39:37.492066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.492371 INFO::Done
2025-11-26 18:39:37.499533 INFO::Formatting Data.
2025-11-26 18:39:37.499824 INFO::Recognized SummarizedExperiment
2025-11-26 18:39:37.500036 INFO::Typecasting input to dataframe.
2025-11-26 18:39:37.508863 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.509327 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.509892 INFO::Found 0 missing values.
2025-11-26 18:39:37.510324 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.
2025-11-26 18:39:37.512334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.512576 INFO::Done
2025-11-26 18:39:37.518331 INFO::Formatting Data.
2025-11-26 18:39:37.51909 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.519642 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.52008 INFO::Found 0 missing values.
2025-11-26 18:39:37.521309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.521546 INFO::Done
2025-11-26 18:39:37.527578 INFO::Formatting Data.
2025-11-26 18:39:37.527959 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.52828 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.528594 INFO::Found 0 missing values.
2025-11-26 18:39:37.529523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.5297 INFO::Done
2025-11-26 18:39:37.543201 INFO::Formatting Data.
2025-11-26 18:39:37.543547 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.543932 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.544363 INFO::Found 1 missing values.
2025-11-26 18:39:37.545205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.545391 INFO::Done
2025-11-26 18:39:37.553179 INFO::Formatting Data.
2025-11-26 18:39:37.553459 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.55374 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.554043 INFO::Found 2 missing values.
2025-11-26 18:39:37.554339 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.
2025-11-26 18:39:37.555139 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.555332 INFO::Done
2025-11-26 18:39:37.560902 INFO::Formatting Data.
2025-11-26 18:39:37.561235 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.561579 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.561893 INFO::Found 2 missing values.
2025-11-26 18:39:37.562404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.562574 INFO::Done
2025-11-26 18:39:37.566332 INFO::Formatting Data.
2025-11-26 18:39:37.566591 INFO::Typecasting input to dataframe.
2025-11-26 18:39:37.566909 INFO::Replacing NaNs with NAs.
2025-11-26 18:39:37.567241 INFO::Removing potential empty rows and columns
2025-11-26 18:39:37.568135 INFO::Found 0 missing values.
2025-11-26 18:39:37.569423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 18:39:37.569654 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.398 1.763 9.885
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.352 | 0.441 | 7.795 | |
| compute_asw | 0.012 | 0.001 | 0.012 | |
| count_existing | 0.006 | 0.001 | 0.006 | |
| generate_data_covariables | 0.005 | 0.000 | 0.006 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |