Yannis Schumann
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 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 2025-11-14 11:36 -0500 (Fri, 14 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" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 166/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2025-11-13 18:41:58 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-13 18:42:35 -0500 (Thu, 13 Nov 2025) |
| EllapsedTime: 37.5 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 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 10.372 0.429 7.994
* 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")
2025-11-13 18:42:25.840098 INFO::Formatting Data.
2025-11-13 18:42:25.841853 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:25.846353 INFO::Removing potential empty rows and columns
2025-11-13 18:42:25.960217 INFO::Found 0 missing values.
2025-11-13 18:42:25.961484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:25.961793 INFO::Done
2025-11-13 18:42:25.961969 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:25.971019 INFO::Starting hierarchical adjustment
2025-11-13 18:42:25.971414 INFO::Found 3 batches.
2025-11-13 18:42:25.97163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:25.972142 INFO::Using default BPPARAM
2025-11-13 18:42:25.972335 INFO::Processing subtree level 1
2025-11-13 18:42:26.025786 INFO::Adjusting the last 1 batches sequentially
2025-11-13 18:42:26.027113 INFO::Done
2025-11-13 18:42:26.027383 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:26.029073 INFO::ASW Batch was -0.0196362768585561 prior to batch effect correction and is now -0.0196362768585561 .
2025-11-13 18:42:26.029943 INFO::Total function execution time is 0.190145969390869 s and adjustment time is 0.0557730197906494 s ( 29.33 )
2025-11-13 18:42:26.038072 INFO::Formatting Data.
2025-11-13 18:42:26.038392 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:26.038806 INFO::Removing potential empty rows and columns
2025-11-13 18:42:26.039403 INFO::Found 0 missing values.
2025-11-13 18:42:26.039959 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.
2025-11-13 18:42:26.044735 INFO::Formatting Data.
2025-11-13 18:42:26.045019 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:26.045402 INFO::Removing potential empty rows and columns
2025-11-13 18:42:26.046186 INFO::Found 0 missing values.
2025-11-13 18:42:26.04658 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.
2025-11-13 18:42:26.056516 INFO::Formatting Data.
2025-11-13 18:42:26.056914 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:26.057385 INFO::Removing potential empty rows and columns
2025-11-13 18:42:26.057779 INFO::Found 0 missing values.
2025-11-13 18:42:26.058119 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.
2025-11-13 18:42:26.059814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:26.060055 INFO::Done
2025-11-13 18:42:26.060279 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:26.061288 INFO::Starting hierarchical adjustment
2025-11-13 18:42:26.061571 INFO::Found 2 batches.
2025-11-13 18:42:26.061784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:26.062053 INFO::Using default BPPARAM
2025-11-13 18:42:26.06227 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:26.062646 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-13 18:42:26.073545 INFO::Done
2025-11-13 18:42:26.073859 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:26.074722 INFO::ASW Batch was -0.00559406852054472 prior to batch effect correction and is now -0.0914007467897279 .
2025-11-13 18:42:26.075242 INFO::Total function execution time is 0.0185930728912354 s and adjustment time is 0.0120091438293457 s ( 64.59 )
2025-11-13 18:42:26.076521 INFO::Formatting Data.
2025-11-13 18:42:26.076763 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:26.080633 INFO::Formatting Data.
2025-11-13 18:42:26.080909 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:26.081245 INFO::Removing potential empty rows and columns
2025-11-13 18:42:26.081644 INFO::Found 0 missing values.
2025-11-13 18:42:26.082759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:26.082995 INFO::Done
2025-11-13 18:42:26.083178 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:26.083896 INFO::Starting hierarchical adjustment
2025-11-13 18:42:26.084126 INFO::Found 2 batches.
2025-11-13 18:42:26.084307 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:26.08451 INFO::Using default BPPARAM
2025-11-13 18:42:26.08468 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:26.084978 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-13 18:42:26.113462 INFO::Done
2025-11-13 18:42:26.113724 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:26.114393 INFO::ASW Batch was -0.0457528152088291 prior to batch effect correction and is now -0.11918324827172 .
2025-11-13 18:42:26.114641 INFO::Total function execution time is 0.0340240001678467 s and adjustment time is 0.029371976852417 s ( 86.33 )
2025-11-13 18:42:26.11496 INFO::Formatting Data.
2025-11-13 18:42:26.115147 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:26.115414 INFO::Removing potential empty rows and columns
2025-11-13 18:42:26.115728 INFO::Found 0 missing values.
2025-11-13 18:42:26.116619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:26.116814 INFO::Done
2025-11-13 18:42:26.117 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:26.117632 INFO::Starting hierarchical adjustment
2025-11-13 18:42:26.117877 INFO::Found 2 batches.
2025-11-13 18:42:26.118061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:26.118273 INFO::Using default BPPARAM
2025-11-13 18:42:26.118427 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:26.118728 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-13 18:42:26.124225 INFO::Done
2025-11-13 18:42:26.124464 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:26.125112 INFO::ASW Batch was -0.0457528152088291 prior to batch effect correction and is now -0.11918324827172 .
2025-11-13 18:42:26.125361 INFO::Total function execution time is 0.0103878974914551 s and adjustment time is 0.00639605522155762 s ( 61.57 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-13 18:42:27.468282 INFO::Formatting Data.
2025-11-13 18:42:27.468543 INFO::Recognized SummarizedExperiment
2025-11-13 18:42:27.468702 INFO::Typecasting input to dataframe.
2025-11-13 18:42:27.478707 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:27.479092 INFO::Removing potential empty rows and columns
2025-11-13 18:42:27.48013 INFO::Found 0 missing values.
2025-11-13 18:42:27.482047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:27.48221 INFO::Done
2025-11-13 18:42:27.482352 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:27.483433 INFO::Starting hierarchical adjustment
2025-11-13 18:42:27.483631 INFO::Found 2 batches.
2025-11-13 18:42:27.483906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:27.484272 INFO::Using default BPPARAM
2025-11-13 18:42:27.484441 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:27.484739 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-13 18:42:27.504327 INFO::Done
2025-11-13 18:42:27.504634 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:27.506035 INFO::ASW Batch was -0.00661974939590601 prior to batch effect correction and is now -0.0891564983676682 .
2025-11-13 18:42:27.506365 INFO::Total function execution time is 0.0381820201873779 s and adjustment time is 0.02071213722229 s ( 54.25 )
Warning: stack imbalance in '{', 73 then 74
2025-11-13 18:42:27.513498 INFO::Formatting Data.
2025-11-13 18:42:27.513814 INFO::Recognized SummarizedExperiment
2025-11-13 18:42:27.514036 INFO::Typecasting input to dataframe.
2025-11-13 18:42:27.517851 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:27.518305 INFO::Removing potential empty rows and columns
2025-11-13 18:42:27.519817 INFO::Found 0 missing values.
2025-11-13 18:42:27.522696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:27.522932 INFO::Done
2025-11-13 18:42:27.523146 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:27.524842 INFO::Starting hierarchical adjustment
2025-11-13 18:42:27.525284 INFO::Found 2 batches.
2025-11-13 18:42:27.525501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:27.52574 INFO::Using default BPPARAM
2025-11-13 18:42:27.525938 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:27.526336 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-13 18:42:27.536225 INFO::Done
2025-11-13 18:42:27.536477 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:27.537936 INFO::ASW Batch was 0.00215024509925991 prior to batch effect correction and is now 0.00215024509925991 .
2025-11-13 18:42:27.538271 INFO::Total function execution time is 0.0247561931610107 s and adjustment time is 0.0109949111938477 s ( 44.41 )
2025-11-13 18:42:27.545945 INFO::Formatting Data.
2025-11-13 18:42:27.546216 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:27.546504 INFO::Removing potential empty rows and columns
2025-11-13 18:42:27.546833 INFO::Found 0 missing values.
2025-11-13 18:42:27.547699 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:27.547866 INFO::Done
2025-11-13 18:42:27.548025 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:27.548672 INFO::Starting hierarchical adjustment
2025-11-13 18:42:27.548945 INFO::Found 3 batches.
2025-11-13 18:42:27.549145 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:27.549345 INFO::Using default BPPARAM
2025-11-13 18:42:27.549504 INFO::Processing subtree level 1
2025-11-13 18:42:27.608144 INFO::Adjusting the last 1 batches sequentially
2025-11-13 18:42:27.609663 INFO::Done
2025-11-13 18:42:27.610157 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:27.611627 INFO::ASW Batch was 0.0503013632517618 prior to batch effect correction and is now -0.152769786837418 .
2025-11-13 18:42:27.612057 INFO::Total function execution time is 0.0661129951477051 s and adjustment time is 0.0607759952545166 s ( 91.93 )
2025-11-13 18:42:27.619689 INFO::Skipping initial DF formatting
2025-11-13 18:42:27.619985 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:27.62169 INFO::Starting hierarchical adjustment
2025-11-13 18:42:27.621993 INFO::Found 5 batches.
2025-11-13 18:42:27.622216 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:27.622495 INFO::Using default BPPARAM
2025-11-13 18:42:27.622716 INFO::Processing subtree level 1
2025-11-13 18:42:27.682541 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:27.686787 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-13 18:42:27.69687 INFO::Done
2025-11-13 18:42:27.697622 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:27.700001 INFO::ASW Batch was 0.54406731090067 prior to batch effect correction and is now 0.54406731090067 .
2025-11-13 18:42:27.700271 INFO::ASW Label was 0.346540856913841 prior to batch effect correction and is now 0.346540856913841 .
2025-11-13 18:42:27.700772 INFO::Total function execution time is 0.0810859203338623 s and adjustment time is 0.074941873550415 s ( 92.42 )
2025-11-13 18:42:27.709169 INFO::Formatting Data.
2025-11-13 18:42:27.709442 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:27.709754 INFO::Removing potential empty rows and columns
2025-11-13 18:42:27.710111 INFO::Found 0 missing values.
2025-11-13 18:42:27.711338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:27.711517 INFO::Done
2025-11-13 18:42:27.711685 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:27.712906 INFO::Starting hierarchical adjustment
2025-11-13 18:42:27.713209 INFO::Found 5 batches.
2025-11-13 18:42:27.713385 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:27.713615 INFO::Using default BPPARAM
2025-11-13 18:42:27.713783 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.
2025-11-13 18:42:27.761052 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:27.763879 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-13 18:42:27.772754 INFO::Done
2025-11-13 18:42:27.773286 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:27.774658 INFO::ASW Batch was 0.491130572095027 prior to batch effect correction and is now -0.0871216282801536 .
2025-11-13 18:42:27.774871 INFO::ASW Label was 0.230705696549575 prior to batch effect correction and is now 0.826814027795182 .
2025-11-13 18:42:27.775235 INFO::Total function execution time is 0.066032886505127 s and adjustment time is 0.0595991611480713 s ( 90.26 )
2025-11-13 18:42:27.775527 INFO::Formatting Data.
2025-11-13 18:42:27.775712 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:27.776025 INFO::Removing potential empty rows and columns
2025-11-13 18:42:27.776364 INFO::Found 0 missing values.
2025-11-13 18:42:27.777612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:27.777795 INFO::Done
2025-11-13 18:42:27.777955 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:27.778866 INFO::Starting hierarchical adjustment
2025-11-13 18:42:27.779234 INFO::Found 5 batches.
2025-11-13 18:42:27.779412 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:27.779641 INFO::Using default BPPARAM
2025-11-13 18:42:27.779796 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.
2025-11-13 18:42:27.842111 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:27.848306 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-13 18:42:27.8578 INFO::Done
2025-11-13 18:42:27.858319 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:27.860021 INFO::ASW Batch was 0.491130572095027 prior to batch effect correction and is now -0.0871216282801536 .
2025-11-13 18:42:27.860242 INFO::ASW Label was 0.230705696549575 prior to batch effect correction and is now 0.826814027795182 .
2025-11-13 18:42:27.860598 INFO::Total function execution time is 0.0850119590759277 s and adjustment time is 0.078718900680542 s ( 92.6 )
2025-11-13 18:42:27.868487 INFO::Formatting Data.
2025-11-13 18:42:27.868762 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:27.869077 INFO::Removing potential empty rows and columns
2025-11-13 18:42:27.869422 INFO::Found 0 missing values.
2025-11-13 18:42:27.870664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:27.870858 INFO::Done
2025-11-13 18:42:27.871035 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:27.872067 INFO::Starting hierarchical adjustment
2025-11-13 18:42:27.872302 INFO::Found 5 batches.
2025-11-13 18:42:27.87247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:27.872701 INFO::Using default BPPARAM
2025-11-13 18:42:27.872871 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.
2025-11-13 18:42:27.929541 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:27.937329 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-13 18:42:27.947892 INFO::Done
2025-11-13 18:42:27.948863 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:27.950946 INFO::ASW Batch was 0.487448611013735 prior to batch effect correction and is now -0.0399806225923328 .
2025-11-13 18:42:27.951201 INFO::ASW Label was 0.278238256649562 prior to batch effect correction and is now 0.807465121497198 .
2025-11-13 18:42:27.952434 INFO::Total function execution time is 0.0837149620056152 s and adjustment time is 0.0756299495697021 s ( 90.34 )
2025-11-13 18:42:27.952795 INFO::Formatting Data.
2025-11-13 18:42:27.953001 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:27.953336 INFO::Removing potential empty rows and columns
2025-11-13 18:42:27.953735 INFO::Found 0 missing values.
2025-11-13 18:42:27.955109 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:27.955309 INFO::Done
2025-11-13 18:42:27.955518 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:27.956489 INFO::Starting hierarchical adjustment
2025-11-13 18:42:27.956776 INFO::Found 5 batches.
2025-11-13 18:42:27.956959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:27.957214 INFO::Using default BPPARAM
2025-11-13 18:42:27.957406 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.
2025-11-13 18:42:28.022115 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:28.029269 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-13 18:42:28.038607 INFO::Done
2025-11-13 18:42:28.039144 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.04049 INFO::ASW Batch was 0.487448611013735 prior to batch effect correction and is now -0.0399806225923328 .
2025-11-13 18:42:28.040982 INFO::ASW Label was 0.278238256649562 prior to batch effect correction and is now 0.807465121497198 .
2025-11-13 18:42:28.04174 INFO::Total function execution time is 0.0885779857635498 s and adjustment time is 0.0818750858306885 s ( 92.43 )
2025-11-13 18:42:28.049049 INFO::Formatting Data.
2025-11-13 18:42:28.049304 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.049616 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.050007 INFO::Found 0 missing values.
2025-11-13 18:42:28.050901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.051061 INFO::Done
2025-11-13 18:42:28.051224 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.052274 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.052505 INFO::Found 2 batches.
2025-11-13 18:42:28.052668 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.05289 INFO::Using default BPPARAM
2025-11-13 18:42:28.053044 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:28.053303 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-13 18:42:28.058104 INFO::Done
2025-11-13 18:42:28.0583 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.059167 INFO::ASW Batch was 0.563748576480994 prior to batch effect correction and is now -0.0256652450564392 .
2025-11-13 18:42:28.059347 INFO::ASW Label was 0.526835894165428 prior to batch effect correction and is now 0.933699507169625 .
2025-11-13 18:42:28.05958 INFO::Total function execution time is 0.0105700492858887 s and adjustment time is 0.00564289093017578 s ( 53.39 )
2025-11-13 18:42:28.0598 INFO::Formatting Data.
2025-11-13 18:42:28.059988 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.060249 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.060525 INFO::Found 0 missing values.
2025-11-13 18:42:28.061277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.061436 INFO::Done
2025-11-13 18:42:28.061584 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.062413 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.062627 INFO::Found 2 batches.
2025-11-13 18:42:28.062782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.062955 INFO::Using default BPPARAM
2025-11-13 18:42:28.063102 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:28.06336 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-13 18:42:28.068069 INFO::Done
2025-11-13 18:42:28.068288 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.06923 INFO::ASW Batch was 0.563748576480994 prior to batch effect correction and is now -0.0256652450564392 .
2025-11-13 18:42:28.069412 INFO::ASW Label was 0.526835894165428 prior to batch effect correction and is now 0.933699507169625 .
2025-11-13 18:42:28.069659 INFO::Total function execution time is 0.00984597206115723 s and adjustment time is 0.00547599792480469 s ( 55.62 )
2025-11-13 18:42:28.080314 INFO::Formatting Data.
2025-11-13 18:42:28.080649 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.080965 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.08128 INFO::Found 0 missing values.
2025-11-13 18:42:28.081963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.082139 INFO::Done
2025-11-13 18:42:28.082299 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.082955 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.083181 INFO::Found 2 batches.
2025-11-13 18:42:28.083342 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.083593 INFO::Using default BPPARAM
2025-11-13 18:42:28.083792 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:28.084126 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-13 18:42:28.096753 INFO::Done
2025-11-13 18:42:28.097057 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.097808 INFO::ASW Batch was -0.119150972109081 prior to batch effect correction and is now -0.193395677751135 .
2025-11-13 18:42:28.098125 INFO::Total function execution time is 0.0178849697113037 s and adjustment time is 0.0136039257049561 s ( 76.06 )
2025-11-13 18:42:28.103499 INFO::Formatting Data.
2025-11-13 18:42:28.103801 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.104113 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.104469 INFO::Found 0 missing values.
2025-11-13 18:42:28.104936 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.
2025-11-13 18:42:28.106462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.106667 INFO::Done
2025-11-13 18:42:28.106841 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.110598 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.11087 INFO::Found 2 batches.
2025-11-13 18:42:28.111046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.111238 INFO::Using default BPPARAM
2025-11-13 18:42:28.111385 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:28.11167 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-13 18:42:28.116953 INFO::Done
2025-11-13 18:42:28.117149 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.118016 INFO::ASW Batch was 0.200011235213947 prior to batch effect correction and is now 0.049121893633137 .
2025-11-13 18:42:28.118205 INFO::ASW Label was 0.784276969929318 prior to batch effect correction and is now 0.882202690760298 .
2025-11-13 18:42:28.11844 INFO::Total function execution time is 0.014962911605835 s and adjustment time is 0.00612807273864746 s ( 40.96 )
2025-11-13 18:42:28.118664 INFO::Formatting Data.
2025-11-13 18:42:28.118841 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.119118 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.11941 INFO::Found 0 missing values.
2025-11-13 18:42:28.119664 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.
2025-11-13 18:42:28.120948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.121109 INFO::Done
2025-11-13 18:42:28.121267 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.122095 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.122305 INFO::Found 2 batches.
2025-11-13 18:42:28.122468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.122652 INFO::Using default BPPARAM
2025-11-13 18:42:28.122802 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:28.123061 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-13 18:42:28.128045 INFO::Done
2025-11-13 18:42:28.128245 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.129112 INFO::ASW Batch was 0.200011235213947 prior to batch effect correction and is now 0.049121893633137 .
2025-11-13 18:42:28.129292 INFO::ASW Label was 0.784276969929318 prior to batch effect correction and is now 0.882202690760298 .
2025-11-13 18:42:28.129528 INFO::Total function execution time is 0.0108599662780762 s and adjustment time is 0.00577592849731445 s ( 53.19 )
2025-11-13 18:42:28.19556 INFO::Formatting Data.
2025-11-13 18:42:28.195848 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.196154 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.196483 INFO::Found 0 missing values.
2025-11-13 18:42:28.197366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.197537 INFO::Done
2025-11-13 18:42:28.197695 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.198384 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.19861 INFO::Found 3 batches.
2025-11-13 18:42:28.198774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.198953 INFO::Using default BPPARAM
2025-11-13 18:42:28.199102 INFO::Processing subtree level 1
2025-11-13 18:42:28.237467 INFO::Adjusting the last 1 batches sequentially
2025-11-13 18:42:28.23963 INFO::Done
2025-11-13 18:42:28.240087 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.241971 INFO::ASW Batch was -0.0087842086932899 prior to batch effect correction and is now -0.0087842086932899 .
2025-11-13 18:42:28.242705 INFO::Total function execution time is 0.0470521450042725 s and adjustment time is 0.0410580635070801 s ( 87.26 )
2025-11-13 18:42:28.243022 INFO::Formatting Data.
2025-11-13 18:42:28.2432 INFO::Typecasting input to dataframe.
2025-11-13 18:42:28.243413 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.243684 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.244147 INFO::Found 0 missing values.
2025-11-13 18:42:28.245009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.245167 INFO::Done
2025-11-13 18:42:28.245319 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.245908 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.246125 INFO::Found 3 batches.
2025-11-13 18:42:28.246275 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.246589 INFO::Using default BPPARAM
2025-11-13 18:42:28.246881 INFO::Processing subtree level 1
2025-11-13 18:42:28.290589 INFO::Adjusting the last 1 batches sequentially
2025-11-13 18:42:28.292981 INFO::Done
2025-11-13 18:42:28.294237 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.297046 INFO::ASW Batch was -0.0087842086932899 prior to batch effect correction and is now -0.0087842086932899 .
2025-11-13 18:42:28.297761 INFO::Total function execution time is 0.0547158718109131 s and adjustment time is 0.0468878746032715 s ( 85.69 )
2025-11-13 18:42:28.304465 INFO::Formatting Data.
2025-11-13 18:42:28.304727 INFO::Typecasting input to dataframe.
2025-11-13 18:42:28.305013 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.305338 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.305822 INFO::Found 0 missing values.
2025-11-13 18:42:28.30677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.306953 INFO::Done
2025-11-13 18:42:28.307129 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.307784 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.308016 INFO::Found 3 batches.
2025-11-13 18:42:28.308171 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.308478 INFO::Using default BPPARAM
2025-11-13 18:42:28.308633 INFO::Processing subtree level 1
2025-11-13 18:42:28.356981 INFO::Adjusting the last 1 batches sequentially
2025-11-13 18:42:28.359271 INFO::Done
2025-11-13 18:42:28.359807 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:28.361715 INFO::ASW Batch was -0.0491098977610289 prior to batch effect correction and is now -0.0491098977610289 .
2025-11-13 18:42:28.362501 INFO::Total function execution time is 0.0580480098724365 s and adjustment time is 0.0512838363647461 s ( 88.35 )
2025-11-13 18:42:28.442693 INFO::Formatting Data.
2025-11-13 18:42:28.443036 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:28.443487 INFO::Removing potential empty rows and columns
2025-11-13 18:42:28.444483 INFO::Found 1000 missing values.
2025-11-13 18:42:28.450426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:28.450668 INFO::Done
2025-11-13 18:42:28.450852 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:28.452849 INFO::Starting hierarchical adjustment
2025-11-13 18:42:28.453109 INFO::Found 10 batches.
2025-11-13 18:42:28.453288 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:28.453512 INFO::Using default BPPARAM
2025-11-13 18:42:28.453694 INFO::Processing subtree level 1
2025-11-13 18:42:28.523081 INFO::Processing subtree level 2
2025-11-13 18:42:29.267542 INFO::Adjusting the last 1 batches sequentially
2025-11-13 18:42:29.269008 INFO::Done
2025-11-13 18:42:29.269242 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:29.281207 INFO::ASW Batch was 0.464157646337917 prior to batch effect correction and is now 0.464157646337917 .
2025-11-13 18:42:29.283095 INFO::ASW Label was 0.362696839021002 prior to batch effect correction and is now 0.362696839021002 .
2025-11-13 18:42:29.284749 INFO::Total function execution time is 0.841804027557373 s and adjustment time is 0.815951824188232 s ( 96.93 )
2025-11-13 18:42:29.285397 INFO::Formatting Data.
2025-11-13 18:42:29.285696 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:29.286427 INFO::Removing potential empty rows and columns
2025-11-13 18:42:29.287813 INFO::Found 1000 missing values.
2025-11-13 18:42:29.330487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:29.330862 INFO::Done
2025-11-13 18:42:29.331246 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:29.334875 INFO::Starting hierarchical adjustment
2025-11-13 18:42:29.335267 INFO::Found 10 batches.
2025-11-13 18:42:29.876087 INFO::Set up parallel execution backend with 2 workers
2025-11-13 18:42:29.876397 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-13 18:42:30.496009 INFO::Adjusting the last 2 batches sequentially
2025-11-13 18:42:30.496587 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-13 18:42:30.502234 INFO::Done
2025-11-13 18:42:30.502451 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:30.504528 INFO::ASW Batch was 0.464157646337917 prior to batch effect correction and is now 0.464157646337917 .
2025-11-13 18:42:30.504708 INFO::ASW Label was 0.362696839021002 prior to batch effect correction and is now 0.362696839021002 .
2025-11-13 18:42:30.504961 INFO::Total function execution time is 1.21975708007812 s and adjustment time is 1.16704201698303 s ( 95.68 )
2025-11-13 18:42:30.582828 INFO::Formatting Data.
2025-11-13 18:42:30.58316 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.583673 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.584172 INFO::Found 0 missing values.
2025-11-13 18:42:30.586026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.586674 INFO::Done
2025-11-13 18:42:30.586938 INFO::Acquiring quality metrics before batch effect correction.
2025-11-13 18:42:30.588153 INFO::Starting hierarchical adjustment
2025-11-13 18:42:30.588471 INFO::Found 3 batches.
2025-11-13 18:42:30.588705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-13 18:42:30.588977 INFO::Using default BPPARAM
2025-11-13 18:42:30.589203 INFO::Processing subtree level 1
2025-11-13 18:42:30.644041 INFO::Adjusting the last 1 batches sequentially
2025-11-13 18:42:30.64845 INFO::Done
2025-11-13 18:42:30.648765 INFO::Acquiring quality metrics after batch effect correction.
2025-11-13 18:42:30.652958 INFO::ASW Batch was 0.182986205194754 prior to batch effect correction and is now -0.151710818282472 .
2025-11-13 18:42:30.653195 INFO::ASW Label was -0.162375085415612 prior to batch effect correction and is now 0.111826819774607 .
2025-11-13 18:42:30.654064 INFO::Total function execution time is 0.0710508823394775 s and adjustment time is 0.060028076171875 s ( 84.49 )
2025-11-13 18:42:30.713432 INFO::Formatting Data.
2025-11-13 18:42:30.713827 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.714198 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.714626 INFO::Found 2 missing values.
2025-11-13 18:42:30.71764 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.717927 INFO::Done
2025-11-13 18:42:30.731708 INFO::Found NA in Reference column
2025-11-13 18:42:30.735977 INFO::Require at least two references per batch.
2025-11-13 18:42:30.744987 INFO::Formatting Data.
2025-11-13 18:42:30.745254 INFO::Recognized SummarizedExperiment
2025-11-13 18:42:30.745435 INFO::Typecasting input to dataframe.
2025-11-13 18:42:30.750865 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.751641 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.753514 INFO::Found 0 missing values.
2025-11-13 18:42:30.756382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.756611 INFO::Done
2025-11-13 18:42:30.763115 INFO::Formatting Data.
2025-11-13 18:42:30.763398 INFO::Recognized SummarizedExperiment
2025-11-13 18:42:30.763618 INFO::Typecasting input to dataframe.
2025-11-13 18:42:30.77007 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.770598 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.772204 INFO::Found 0 missing values.
2025-11-13 18:42:30.777065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.777388 INFO::Done
2025-11-13 18:42:30.788299 INFO::Formatting Data.
2025-11-13 18:42:30.78864 INFO::Recognized SummarizedExperiment
2025-11-13 18:42:30.788889 INFO::Typecasting input to dataframe.
2025-11-13 18:42:30.797526 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.798047 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.798606 INFO::Found 0 missing values.
2025-11-13 18:42:30.799084 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.
2025-11-13 18:42:30.801443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.801739 INFO::Done
2025-11-13 18:42:30.808569 INFO::Formatting Data.
2025-11-13 18:42:30.808968 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.809344 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.809814 INFO::Found 0 missing values.
2025-11-13 18:42:30.811165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.811399 INFO::Done
2025-11-13 18:42:30.825216 INFO::Formatting Data.
2025-11-13 18:42:30.825621 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.826119 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.826548 INFO::Found 0 missing values.
2025-11-13 18:42:30.827639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.827833 INFO::Done
2025-11-13 18:42:30.842099 INFO::Formatting Data.
2025-11-13 18:42:30.84251 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.842954 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.843824 INFO::Found 1 missing values.
2025-11-13 18:42:30.844843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.845029 INFO::Done
2025-11-13 18:42:30.853638 INFO::Formatting Data.
2025-11-13 18:42:30.853952 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.854292 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.854664 INFO::Found 2 missing values.
2025-11-13 18:42:30.855014 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.
2025-11-13 18:42:30.855927 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.85613 INFO::Done
2025-11-13 18:42:30.860662 INFO::Formatting Data.
2025-11-13 18:42:30.861212 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.862253 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.862777 INFO::Found 2 missing values.
2025-11-13 18:42:30.863665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.863903 INFO::Done
2025-11-13 18:42:30.869699 INFO::Formatting Data.
2025-11-13 18:42:30.870039 INFO::Typecasting input to dataframe.
2025-11-13 18:42:30.870374 INFO::Replacing NaNs with NAs.
2025-11-13 18:42:30.870723 INFO::Removing potential empty rows and columns
2025-11-13 18:42:30.871098 INFO::Found 0 missing values.
2025-11-13 18:42:30.872135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-13 18:42:30.872323 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.693 1.951 10.394
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.372 | 0.429 | 7.994 | |
| compute_asw | 0.010 | 0.001 | 0.011 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |