Yannis Schumann
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-11 12:05 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-12-09 15:33:48 -0500 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 15:35:43 -0500 (Tue, 09 Dec 2025) |
| EllapsedTime: 114.9 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 Patched (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 ‘1.6.0’
* 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 29.976 1.125 30.993
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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")
2025-12-09 15:35:14.575263 INFO::Formatting Data.
2025-12-09 15:35:14.580734 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:14.594309 INFO::Removing potential empty rows and columns
2025-12-09 15:35:14.995772 INFO::Found 0 missing values.
2025-12-09 15:35:14.99997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:15.003675 INFO::Done
2025-12-09 15:35:15.004978 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:15.021348 INFO::Starting hierarchical adjustment
2025-12-09 15:35:15.022477 INFO::Found 3 batches.
2025-12-09 15:35:15.023102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:15.024512 INFO::Using default BPPARAM
2025-12-09 15:35:15.025075 INFO::Processing subtree level 1
2025-12-09 15:35:15.17272 INFO::Adjusting the last 1 batches sequentially
2025-12-09 15:35:15.186084 INFO::Done
2025-12-09 15:35:15.187254 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:15.191292 INFO::ASW Batch was -0.0417355976628596 prior to batch effect correction and is now -0.0417355976628596 .
2025-12-09 15:35:15.194262 INFO::Total function execution time is 0.619668006896973 s and adjustment time is 0.163722038269043 s ( 26.42 )
2025-12-09 15:35:15.219794 INFO::Formatting Data.
2025-12-09 15:35:15.220857 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:15.222034 INFO::Removing potential empty rows and columns
2025-12-09 15:35:15.225696 INFO::Found 0 missing values.
2025-12-09 15:35:15.230477 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.
2025-12-09 15:35:15.254385 INFO::Formatting Data.
2025-12-09 15:35:15.255395 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:15.256436 INFO::Removing potential empty rows and columns
2025-12-09 15:35:15.257774 INFO::Found 0 missing values.
2025-12-09 15:35:15.258887 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.
2025-12-09 15:35:15.278919 INFO::Formatting Data.
2025-12-09 15:35:15.279839 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:15.281911 INFO::Removing potential empty rows and columns
2025-12-09 15:35:15.283285 INFO::Found 0 missing values.
2025-12-09 15:35:15.284343 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.
2025-12-09 15:35:15.28962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:15.290346 INFO::Done
2025-12-09 15:35:15.290906 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:15.293364 INFO::Starting hierarchical adjustment
2025-12-09 15:35:15.29423 INFO::Found 2 batches.
2025-12-09 15:35:15.294828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:15.295586 INFO::Using default BPPARAM
2025-12-09 15:35:15.29614 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:15.297159 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 15:35:15.335516 INFO::Done
2025-12-09 15:35:15.33642 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:15.342983 INFO::ASW Batch was 0.0172077807232949 prior to batch effect correction and is now -0.124855523024778 .
2025-12-09 15:35:15.344279 INFO::Total function execution time is 0.0654618740081787 s and adjustment time is 0.0413789749145508 s ( 63.21 )
2025-12-09 15:35:15.347935 INFO::Formatting Data.
2025-12-09 15:35:15.348675 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:15.364524 INFO::Formatting Data.
2025-12-09 15:35:15.365557 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:15.366593 INFO::Removing potential empty rows and columns
2025-12-09 15:35:15.36772 INFO::Found 0 missing values.
2025-12-09 15:35:15.372972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:15.375428 INFO::Done
2025-12-09 15:35:15.376386 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:15.424787 INFO::Starting hierarchical adjustment
2025-12-09 15:35:15.425951 INFO::Found 2 batches.
2025-12-09 15:35:15.426492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:15.427077 INFO::Using default BPPARAM
2025-12-09 15:35:15.427537 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:15.428481 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 15:35:15.44334 INFO::Done
2025-12-09 15:35:15.448447 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:15.451055 INFO::ASW Batch was 0.0304476587998126 prior to batch effect correction and is now -0.118761862525116 .
2025-12-09 15:35:15.457929 INFO::Total function execution time is 0.0876190662384033 s and adjustment time is 0.0175611972808838 s ( 20.04 )
2025-12-09 15:35:15.46625 INFO::Formatting Data.
2025-12-09 15:35:15.46799 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:15.469021 INFO::Removing potential empty rows and columns
2025-12-09 15:35:15.47002 INFO::Found 0 missing values.
2025-12-09 15:35:15.472679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:15.47327 INFO::Done
2025-12-09 15:35:15.474457 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:15.478657 INFO::Starting hierarchical adjustment
2025-12-09 15:35:15.481269 INFO::Found 2 batches.
2025-12-09 15:35:15.482314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:15.482967 INFO::Using default BPPARAM
2025-12-09 15:35:15.483503 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:15.484831 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 15:35:15.500434 INFO::Done
2025-12-09 15:35:15.501219 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:15.503382 INFO::ASW Batch was 0.0304476587998126 prior to batch effect correction and is now -0.118761862525116 .
2025-12-09 15:35:15.504228 INFO::Total function execution time is 0.0382189750671387 s and adjustment time is 0.0194840431213379 s ( 50.98 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-09 15:35:20.572932 INFO::Formatting Data.
2025-12-09 15:35:20.573717 INFO::Recognized SummarizedExperiment
2025-12-09 15:35:20.574207 INFO::Typecasting input to dataframe.
2025-12-09 15:35:20.608786 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:20.619234 INFO::Removing potential empty rows and columns
2025-12-09 15:35:20.641835 INFO::Found 0 missing values.
2025-12-09 15:35:20.653357 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:20.654267 INFO::Done
2025-12-09 15:35:20.654782 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:20.687758 INFO::Starting hierarchical adjustment
2025-12-09 15:35:20.69896 INFO::Found 2 batches.
2025-12-09 15:35:20.69975 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:20.701033 INFO::Using default BPPARAM
2025-12-09 15:35:20.701555 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:20.702643 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 15:35:20.762021 INFO::Done
2025-12-09 15:35:20.762833 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:20.767509 INFO::ASW Batch was 0.0194865852454223 prior to batch effect correction and is now -0.0934675681826906 .
2025-12-09 15:35:20.7685 INFO::Total function execution time is 0.195883989334106 s and adjustment time is 0.0648138523101807 s ( 33.09 )
Warning: stack imbalance in '{', 73 then 75
2025-12-09 15:35:20.791685 INFO::Formatting Data.
2025-12-09 15:35:20.792588 INFO::Recognized SummarizedExperiment
2025-12-09 15:35:20.793141 INFO::Typecasting input to dataframe.
2025-12-09 15:35:20.90724 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:20.908683 INFO::Removing potential empty rows and columns
2025-12-09 15:35:20.912349 INFO::Found 0 missing values.
2025-12-09 15:35:20.919335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:20.920084 INFO::Done
2025-12-09 15:35:20.920588 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:20.924439 INFO::Starting hierarchical adjustment
2025-12-09 15:35:20.925252 INFO::Found 2 batches.
2025-12-09 15:35:20.925758 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:20.926332 INFO::Using default BPPARAM
2025-12-09 15:35:20.926864 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:20.927825 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 15:35:20.95314 INFO::Done
2025-12-09 15:35:20.953994 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:20.958095 INFO::ASW Batch was -0.0157174661334764 prior to batch effect correction and is now -0.0157174661334764 .
2025-12-09 15:35:20.959066 INFO::Total function execution time is 0.167449951171875 s and adjustment time is 0.0279459953308105 s ( 16.69 )
2025-12-09 15:35:21.007088 INFO::Formatting Data.
2025-12-09 15:35:21.008023 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:21.010421 INFO::Removing potential empty rows and columns
2025-12-09 15:35:21.014608 INFO::Found 0 missing values.
2025-12-09 15:35:21.019672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:21.020775 INFO::Done
2025-12-09 15:35:21.021456 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:21.023776 INFO::Starting hierarchical adjustment
2025-12-09 15:35:21.024588 INFO::Found 3 batches.
2025-12-09 15:35:21.025091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:21.025662 INFO::Using default BPPARAM
2025-12-09 15:35:21.026117 INFO::Processing subtree level 1
2025-12-09 15:35:21.216873 INFO::Adjusting the last 1 batches sequentially
2025-12-09 15:35:21.219947 INFO::Done
2025-12-09 15:35:21.220675 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:21.224301 INFO::ASW Batch was -0.0369689513253131 prior to batch effect correction and is now -0.167259048593459 .
2025-12-09 15:35:21.225494 INFO::Total function execution time is 0.218514919281006 s and adjustment time is 0.195497989654541 s ( 89.47 )
2025-12-09 15:35:21.24293 INFO::Skipping initial DF formatting
2025-12-09 15:35:21.243771 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:21.249639 INFO::Starting hierarchical adjustment
2025-12-09 15:35:21.250518 INFO::Found 5 batches.
2025-12-09 15:35:21.25104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:21.2517 INFO::Using default BPPARAM
2025-12-09 15:35:21.25219 INFO::Processing subtree level 1
2025-12-09 15:35:21.562673 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:21.566458 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 15:35:21.615649 INFO::Done
2025-12-09 15:35:21.617317 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:21.624603 INFO::ASW Batch was 0.518216510143569 prior to batch effect correction and is now 0.518216510143569 .
2025-12-09 15:35:21.627398 INFO::ASW Label was 0.443633690317876 prior to batch effect correction and is now 0.443633690317876 .
2025-12-09 15:35:21.629712 INFO::Total function execution time is 0.386378049850464 s and adjustment time is 0.365187883377075 s ( 94.52 )
2025-12-09 15:35:21.738071 INFO::Formatting Data.
2025-12-09 15:35:21.738925 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:21.739825 INFO::Removing potential empty rows and columns
2025-12-09 15:35:21.740819 INFO::Found 0 missing values.
2025-12-09 15:35:21.744496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:21.74511 INFO::Done
2025-12-09 15:35:21.74561 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:21.750123 INFO::Starting hierarchical adjustment
2025-12-09 15:35:21.751633 INFO::Found 5 batches.
2025-12-09 15:35:21.752396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:21.753363 INFO::Using default BPPARAM
2025-12-09 15:35:21.754053 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.
2025-12-09 15:35:21.95461 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:21.962202 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 15:35:21.99386 INFO::Done
2025-12-09 15:35:21.995286 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:22.000533 INFO::ASW Batch was 0.556013694464378 prior to batch effect correction and is now -0.0913725076996078 .
2025-12-09 15:35:22.001368 INFO::ASW Label was 0.22661153017674 prior to batch effect correction and is now 0.825233714237254 .
2025-12-09 15:35:22.002348 INFO::Total function execution time is 0.264309883117676 s and adjustment time is 0.242611885070801 s ( 91.79 )
2025-12-09 15:35:22.00335 INFO::Formatting Data.
2025-12-09 15:35:22.004002 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:22.00533 INFO::Removing potential empty rows and columns
2025-12-09 15:35:22.00645 INFO::Found 0 missing values.
2025-12-09 15:35:22.0112 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:22.012668 INFO::Done
2025-12-09 15:35:22.01359 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:22.017818 INFO::Starting hierarchical adjustment
2025-12-09 15:35:22.018824 INFO::Found 5 batches.
2025-12-09 15:35:22.019428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:22.020153 INFO::Using default BPPARAM
2025-12-09 15:35:22.020737 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.
2025-12-09 15:35:22.199773 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:22.208096 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 15:35:22.249011 INFO::Done
2025-12-09 15:35:22.25004 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:22.255791 INFO::ASW Batch was 0.556013694464378 prior to batch effect correction and is now -0.0913725076996078 .
2025-12-09 15:35:22.256708 INFO::ASW Label was 0.22661153017674 prior to batch effect correction and is now 0.825233714237254 .
2025-12-09 15:35:22.257926 INFO::Total function execution time is 0.25447416305542 s and adjustment time is 0.230324983596802 s ( 90.51 )
2025-12-09 15:35:22.278492 INFO::Formatting Data.
2025-12-09 15:35:22.279392 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:22.280372 INFO::Removing potential empty rows and columns
2025-12-09 15:35:22.282233 INFO::Found 0 missing values.
2025-12-09 15:35:22.287287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:22.288021 INFO::Done
2025-12-09 15:35:22.288593 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:22.300552 INFO::Starting hierarchical adjustment
2025-12-09 15:35:22.301713 INFO::Found 5 batches.
2025-12-09 15:35:22.302306 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:22.302967 INFO::Using default BPPARAM
2025-12-09 15:35:22.303502 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.
2025-12-09 15:35:22.4895 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:22.49716 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 15:35:22.526102 INFO::Done
2025-12-09 15:35:22.527475 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:22.531985 INFO::ASW Batch was 0.448880257385114 prior to batch effect correction and is now -0.0804779717015181 .
2025-12-09 15:35:22.532839 INFO::ASW Label was 0.243481830560915 prior to batch effect correction and is now 0.845532304553107 .
2025-12-09 15:35:22.533942 INFO::Total function execution time is 0.255546092987061 s and adjustment time is 0.224496126174927 s ( 87.85 )
2025-12-09 15:35:22.534928 INFO::Formatting Data.
2025-12-09 15:35:22.535569 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:22.540127 INFO::Removing potential empty rows and columns
2025-12-09 15:35:22.541938 INFO::Found 0 missing values.
2025-12-09 15:35:22.546253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:22.546943 INFO::Done
2025-12-09 15:35:22.547532 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:22.551137 INFO::Starting hierarchical adjustment
2025-12-09 15:35:22.552065 INFO::Found 5 batches.
2025-12-09 15:35:22.552632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:22.553369 INFO::Using default BPPARAM
2025-12-09 15:35:22.554159 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.
2025-12-09 15:35:22.735472 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:22.756106 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 15:35:22.80366 INFO::Done
2025-12-09 15:35:22.805027 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:22.811273 INFO::ASW Batch was 0.448880257385114 prior to batch effect correction and is now -0.0804779717015181 .
2025-12-09 15:35:22.812441 INFO::ASW Label was 0.243481830560915 prior to batch effect correction and is now 0.845532304553107 .
2025-12-09 15:35:22.814349 INFO::Total function execution time is 0.279160022735596 s and adjustment time is 0.251666069030762 s ( 90.15 )
2025-12-09 15:35:22.833853 INFO::Formatting Data.
2025-12-09 15:35:22.834756 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:22.835729 INFO::Removing potential empty rows and columns
2025-12-09 15:35:22.836846 INFO::Found 0 missing values.
2025-12-09 15:35:22.839801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:22.840552 INFO::Done
2025-12-09 15:35:22.841155 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:22.844524 INFO::Starting hierarchical adjustment
2025-12-09 15:35:22.845503 INFO::Found 2 batches.
2025-12-09 15:35:22.846094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:22.846825 INFO::Using default BPPARAM
2025-12-09 15:35:22.847357 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:22.848367 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 15:35:22.865484 INFO::Done
2025-12-09 15:35:22.866272 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:22.869214 INFO::ASW Batch was 0.549681601918589 prior to batch effect correction and is now -0.0370974136010614 .
2025-12-09 15:35:22.86984 INFO::ASW Label was 0.526969780409502 prior to batch effect correction and is now 0.950467518872715 .
2025-12-09 15:35:22.87306 INFO::Total function execution time is 0.039207935333252 s and adjustment time is 0.0201060771942139 s ( 51.28 )
2025-12-09 15:35:22.874481 INFO::Formatting Data.
2025-12-09 15:35:22.875253 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:22.876638 INFO::Removing potential empty rows and columns
2025-12-09 15:35:22.877975 INFO::Found 0 missing values.
2025-12-09 15:35:22.882734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:22.883842 INFO::Done
2025-12-09 15:35:22.884407 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:22.88765 INFO::Starting hierarchical adjustment
2025-12-09 15:35:22.888452 INFO::Found 2 batches.
2025-12-09 15:35:22.88897 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:22.889581 INFO::Using default BPPARAM
2025-12-09 15:35:22.89006 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:22.890931 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 15:35:22.908796 INFO::Done
2025-12-09 15:35:22.909609 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:22.912803 INFO::ASW Batch was 0.549681601918589 prior to batch effect correction and is now -0.0370974136010614 .
2025-12-09 15:35:22.913554 INFO::ASW Label was 0.526969780409502 prior to batch effect correction and is now 0.950467518872715 .
2025-12-09 15:35:22.914394 INFO::Total function execution time is 0.0399918556213379 s and adjustment time is 0.020449161529541 s ( 51.13 )
2025-12-09 15:35:22.938495 INFO::Formatting Data.
2025-12-09 15:35:22.93938 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:22.940266 INFO::Removing potential empty rows and columns
2025-12-09 15:35:22.941463 INFO::Found 0 missing values.
2025-12-09 15:35:22.943636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:22.944234 INFO::Done
2025-12-09 15:35:22.94918 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:22.953487 INFO::Starting hierarchical adjustment
2025-12-09 15:35:22.954449 INFO::Found 2 batches.
2025-12-09 15:35:22.954971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:22.955602 INFO::Using default BPPARAM
2025-12-09 15:35:22.956167 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:22.957044 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 15:35:22.995656 INFO::Done
2025-12-09 15:35:22.996534 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:22.998867 INFO::ASW Batch was 0.00608814851161995 prior to batch effect correction and is now -0.0924905317191383 .
2025-12-09 15:35:22.999752 INFO::Total function execution time is 0.0614089965820312 s and adjustment time is 0.0413219928741455 s ( 67.29 )
2025-12-09 15:35:23.0272 INFO::Formatting Data.
2025-12-09 15:35:23.028193 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:23.029141 INFO::Removing potential empty rows and columns
2025-12-09 15:35:23.03019 INFO::Found 0 missing values.
2025-12-09 15:35:23.031621 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.
2025-12-09 15:35:23.040753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:23.041558 INFO::Done
2025-12-09 15:35:23.042106 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:23.045188 INFO::Starting hierarchical adjustment
2025-12-09 15:35:23.045989 INFO::Found 2 batches.
2025-12-09 15:35:23.04648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:23.047107 INFO::Using default BPPARAM
2025-12-09 15:35:23.047613 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:23.048575 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 15:35:23.068444 INFO::Done
2025-12-09 15:35:23.069269 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:23.077536 INFO::ASW Batch was 0.426825657685165 prior to batch effect correction and is now -0.0251086620123734 .
2025-12-09 15:35:23.07869 INFO::ASW Label was 0.652162366125836 prior to batch effect correction and is now 0.93337518986668 .
2025-12-09 15:35:23.079877 INFO::Total function execution time is 0.0527060031890869 s and adjustment time is 0.0225071907043457 s ( 42.7 )
2025-12-09 15:35:23.081051 INFO::Formatting Data.
2025-12-09 15:35:23.081701 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:23.082744 INFO::Removing potential empty rows and columns
2025-12-09 15:35:23.088902 INFO::Found 0 missing values.
2025-12-09 15:35:23.090763 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.
2025-12-09 15:35:23.095956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:23.09675 INFO::Done
2025-12-09 15:35:23.097296 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:23.107665 INFO::Starting hierarchical adjustment
2025-12-09 15:35:23.109162 INFO::Found 2 batches.
2025-12-09 15:35:23.109675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:23.110342 INFO::Using default BPPARAM
2025-12-09 15:35:23.111149 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:23.112252 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 15:35:23.129948 INFO::Done
2025-12-09 15:35:23.130767 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:23.133745 INFO::ASW Batch was 0.426825657685165 prior to batch effect correction and is now -0.0251086620123734 .
2025-12-09 15:35:23.134381 INFO::ASW Label was 0.652162366125836 prior to batch effect correction and is now 0.93337518986668 .
2025-12-09 15:35:23.135148 INFO::Total function execution time is 0.0541260242462158 s and adjustment time is 0.0210490226745605 s ( 38.89 )
2025-12-09 15:35:23.428356 INFO::Formatting Data.
2025-12-09 15:35:23.429279 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:23.43023 INFO::Removing potential empty rows and columns
2025-12-09 15:35:23.431326 INFO::Found 0 missing values.
2025-12-09 15:35:23.434247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:23.434927 INFO::Done
2025-12-09 15:35:23.435416 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:23.437541 INFO::Starting hierarchical adjustment
2025-12-09 15:35:23.438238 INFO::Found 3 batches.
2025-12-09 15:35:23.438759 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:23.439336 INFO::Using default BPPARAM
2025-12-09 15:35:23.439788 INFO::Processing subtree level 1
2025-12-09 15:35:23.568837 INFO::Adjusting the last 1 batches sequentially
2025-12-09 15:35:23.573338 INFO::Done
2025-12-09 15:35:23.574844 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:23.580345 INFO::ASW Batch was -0.014138533687713 prior to batch effect correction and is now -0.014138533687713 .
2025-12-09 15:35:23.581948 INFO::Total function execution time is 0.153603076934814 s and adjustment time is 0.135135173797607 s ( 87.98 )
2025-12-09 15:35:23.58331 INFO::Formatting Data.
2025-12-09 15:35:23.584043 INFO::Typecasting input to dataframe.
2025-12-09 15:35:23.584953 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:23.587259 INFO::Removing potential empty rows and columns
2025-12-09 15:35:23.589356 INFO::Found 0 missing values.
2025-12-09 15:35:23.593576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:23.594584 INFO::Done
2025-12-09 15:35:23.595362 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:23.598218 INFO::Starting hierarchical adjustment
2025-12-09 15:35:23.599347 INFO::Found 3 batches.
2025-12-09 15:35:23.600235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:23.600973 INFO::Using default BPPARAM
2025-12-09 15:35:23.601475 INFO::Processing subtree level 1
2025-12-09 15:35:23.72989 INFO::Adjusting the last 1 batches sequentially
2025-12-09 15:35:23.73771 INFO::Done
2025-12-09 15:35:23.738714 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:23.749605 INFO::ASW Batch was -0.014138533687713 prior to batch effect correction and is now -0.014138533687713 .
2025-12-09 15:35:23.751918 INFO::Total function execution time is 0.1685631275177 s and adjustment time is 0.138549089431763 s ( 82.19 )
2025-12-09 15:35:23.770695 INFO::Formatting Data.
2025-12-09 15:35:23.771616 INFO::Typecasting input to dataframe.
2025-12-09 15:35:23.772486 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:23.77451 INFO::Removing potential empty rows and columns
2025-12-09 15:35:23.775788 INFO::Found 0 missing values.
2025-12-09 15:35:23.778594 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:23.779195 INFO::Done
2025-12-09 15:35:23.779677 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:23.781716 INFO::Starting hierarchical adjustment
2025-12-09 15:35:23.782434 INFO::Found 3 batches.
2025-12-09 15:35:23.782923 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:23.783864 INFO::Using default BPPARAM
2025-12-09 15:35:23.78436 INFO::Processing subtree level 1
2025-12-09 15:35:23.904222 INFO::Adjusting the last 1 batches sequentially
2025-12-09 15:35:23.908388 INFO::Done
2025-12-09 15:35:23.90938 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:23.91845 INFO::ASW Batch was -0.0737347612028755 prior to batch effect correction and is now -0.0737347612028755 .
2025-12-09 15:35:23.920146 INFO::Total function execution time is 0.14955997467041 s and adjustment time is 0.126059055328369 s ( 84.29 )
2025-12-09 15:35:24.103672 INFO::Formatting Data.
2025-12-09 15:35:24.104659 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:24.105828 INFO::Removing potential empty rows and columns
2025-12-09 15:35:24.112684 INFO::Found 1000 missing values.
2025-12-09 15:35:24.130698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:24.131555 INFO::Done
2025-12-09 15:35:24.132106 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:24.138403 INFO::Starting hierarchical adjustment
2025-12-09 15:35:24.139389 INFO::Found 10 batches.
2025-12-09 15:35:24.139966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:24.140643 INFO::Using default BPPARAM
2025-12-09 15:35:24.141157 INFO::Processing subtree level 1
2025-12-09 15:35:24.303658 INFO::Processing subtree level 2
2025-12-09 15:35:24.500465 INFO::Adjusting the last 1 batches sequentially
2025-12-09 15:35:24.507306 INFO::Done
2025-12-09 15:35:24.5085 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:24.516571 INFO::ASW Batch was 0.516783939727364 prior to batch effect correction and is now 0.516783939727364 .
2025-12-09 15:35:24.517513 INFO::ASW Label was 0.314976452461034 prior to batch effect correction and is now 0.314976452461034 .
2025-12-09 15:35:24.51927 INFO::Total function execution time is 0.415632963180542 s and adjustment time is 0.367989063262939 s ( 88.54 )
2025-12-09 15:35:24.520332 INFO::Formatting Data.
2025-12-09 15:35:24.521303 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:24.522969 INFO::Removing potential empty rows and columns
2025-12-09 15:35:24.525692 INFO::Found 1000 missing values.
2025-12-09 15:35:24.542894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:24.543749 INFO::Done
2025-12-09 15:35:24.54429 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:24.550909 INFO::Starting hierarchical adjustment
2025-12-09 15:35:24.551946 INFO::Found 10 batches.
2025-12-09 15:35:26.326589 INFO::Set up parallel execution backend with 2 workers
2025-12-09 15:35:26.327449 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-09 15:35:28.184131 INFO::Adjusting the last 2 batches sequentially
2025-12-09 15:35:28.188731 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 15:35:28.207351 INFO::Done
2025-12-09 15:35:28.208205 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:28.21404 INFO::ASW Batch was 0.516783939727364 prior to batch effect correction and is now 0.516783939727364 .
2025-12-09 15:35:28.214642 INFO::ASW Label was 0.314976452461034 prior to batch effect correction and is now 0.314976452461034 .
2025-12-09 15:35:28.215387 INFO::Total function execution time is 3.6950900554657 s and adjustment time is 3.65554308891296 s ( 98.93 )
2025-12-09 15:35:28.490388 INFO::Formatting Data.
2025-12-09 15:35:28.491925 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:28.493169 INFO::Removing potential empty rows and columns
2025-12-09 15:35:28.49443 INFO::Found 0 missing values.
2025-12-09 15:35:28.498591 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:28.499319 INFO::Done
2025-12-09 15:35:28.499928 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 15:35:28.504046 INFO::Starting hierarchical adjustment
2025-12-09 15:35:28.504972 INFO::Found 3 batches.
2025-12-09 15:35:28.506111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 15:35:28.507347 INFO::Using default BPPARAM
2025-12-09 15:35:28.507967 INFO::Processing subtree level 1
2025-12-09 15:35:28.65517 INFO::Adjusting the last 1 batches sequentially
2025-12-09 15:35:28.660493 INFO::Done
2025-12-09 15:35:28.66199 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 15:35:28.671453 INFO::ASW Batch was 0.238861602083349 prior to batch effect correction and is now -0.166512131309953 .
2025-12-09 15:35:28.672234 INFO::ASW Label was -0.154669912850994 prior to batch effect correction and is now 0.0797180733688237 .
2025-12-09 15:35:28.673617 INFO::Total function execution time is 0.183381080627441 s and adjustment time is 0.155659198760986 s ( 84.88 )
2025-12-09 15:35:28.86251 INFO::Formatting Data.
2025-12-09 15:35:28.863458 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:28.864469 INFO::Removing potential empty rows and columns
2025-12-09 15:35:28.865601 INFO::Found 2 missing values.
2025-12-09 15:35:28.868282 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:28.869827 INFO::Done
2025-12-09 15:35:28.907567 INFO::Found NA in Reference column
2025-12-09 15:35:28.923427 INFO::Require at least two references per batch.
2025-12-09 15:35:28.986458 INFO::Formatting Data.
2025-12-09 15:35:28.987465 INFO::Recognized SummarizedExperiment
2025-12-09 15:35:28.98805 INFO::Typecasting input to dataframe.
2025-12-09 15:35:29.002681 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.004294 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.008299 INFO::Found 0 missing values.
2025-12-09 15:35:29.015856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.01661 INFO::Done
2025-12-09 15:35:29.046259 INFO::Formatting Data.
2025-12-09 15:35:29.047129 INFO::Recognized SummarizedExperiment
2025-12-09 15:35:29.047632 INFO::Typecasting input to dataframe.
2025-12-09 15:35:29.073363 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.07486 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.078572 INFO::Found 0 missing values.
2025-12-09 15:35:29.089746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.090469 INFO::Done
2025-12-09 15:35:29.120644 INFO::Formatting Data.
2025-12-09 15:35:29.121754 INFO::Recognized SummarizedExperiment
2025-12-09 15:35:29.125815 INFO::Typecasting input to dataframe.
2025-12-09 15:35:29.149758 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.151105 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.152254 INFO::Found 0 missing values.
2025-12-09 15:35:29.153217 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.
2025-12-09 15:35:29.157463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.158181 INFO::Done
2025-12-09 15:35:29.170974 INFO::Formatting Data.
2025-12-09 15:35:29.171942 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.172901 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.173945 INFO::Found 0 missing values.
2025-12-09 15:35:29.176864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.177558 INFO::Done
2025-12-09 15:35:29.19182 INFO::Formatting Data.
2025-12-09 15:35:29.192936 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.194063 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.195723 INFO::Found 0 missing values.
2025-12-09 15:35:29.198661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.199284 INFO::Done
2025-12-09 15:35:29.30477 INFO::Formatting Data.
2025-12-09 15:35:29.305881 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.311514 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.314121 INFO::Found 1 missing values.
2025-12-09 15:35:29.323547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.324523 INFO::Done
2025-12-09 15:35:29.379362 INFO::Formatting Data.
2025-12-09 15:35:29.382289 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.383484 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.384541 INFO::Found 2 missing values.
2025-12-09 15:35:29.385562 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.
2025-12-09 15:35:29.387977 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.388625 INFO::Done
2025-12-09 15:35:29.402713 INFO::Formatting Data.
2025-12-09 15:35:29.403693 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.404651 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.405599 INFO::Found 2 missing values.
2025-12-09 15:35:29.407288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.407863 INFO::Done
2025-12-09 15:35:29.421018 INFO::Formatting Data.
2025-12-09 15:35:29.421862 INFO::Typecasting input to dataframe.
2025-12-09 15:35:29.422617 INFO::Replacing NaNs with NAs.
2025-12-09 15:35:29.423465 INFO::Removing potential empty rows and columns
2025-12-09 15:35:29.424415 INFO::Found 0 missing values.
2025-12-09 15:35:29.427099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 15:35:29.427658 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.471 4.048 34.380
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.976 | 1.125 | 30.993 | |
| compute_asw | 0.029 | 0.001 | 0.052 | |
| count_existing | 0.015 | 0.002 | 0.017 | |
| generate_data_covariables | 0.015 | 0.001 | 0.024 | |
| generate_dataset | 0.014 | 0.001 | 0.025 | |