Yannis Schumann
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 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 2025-12-22 12:05 -0500 (Mon, 22 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" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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: 2025-12-19 15:35:11 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 15:37:06 -0500 (Fri, 19 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 29.645 1.13 30.47
* 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")
2025-12-19 15:36:37.120917 INFO::Formatting Data.
2025-12-19 15:36:37.124779 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:37.136541 INFO::Removing potential empty rows and columns
2025-12-19 15:36:37.544484 INFO::Found 0 missing values.
2025-12-19 15:36:37.547828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:37.548454 INFO::Done
2025-12-19 15:36:37.549221 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:37.571905 INFO::Starting hierarchical adjustment
2025-12-19 15:36:37.572983 INFO::Found 3 batches.
2025-12-19 15:36:37.573571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:37.574897 INFO::Using default BPPARAM
2025-12-19 15:36:37.575455 INFO::Processing subtree level 1
2025-12-19 15:36:37.716958 INFO::Adjusting the last 1 batches sequentially
2025-12-19 15:36:37.725764 INFO::Done
2025-12-19 15:36:37.727123 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:37.732401 INFO::ASW Batch was -0.0918248674010342 prior to batch effect correction and is now -0.0918248674010342 .
2025-12-19 15:36:37.733844 INFO::Total function execution time is 0.61384105682373 s and adjustment time is 0.152774095535278 s ( 24.89 )
2025-12-19 15:36:37.752114 INFO::Formatting Data.
2025-12-19 15:36:37.752985 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:37.753987 INFO::Removing potential empty rows and columns
2025-12-19 15:36:37.755408 INFO::Found 0 missing values.
2025-12-19 15:36:37.756459 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.
2025-12-19 15:36:37.770239 INFO::Formatting Data.
2025-12-19 15:36:37.771058 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:37.772073 INFO::Removing potential empty rows and columns
2025-12-19 15:36:37.773751 INFO::Found 0 missing values.
2025-12-19 15:36:37.774799 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.
2025-12-19 15:36:37.794032 INFO::Formatting Data.
2025-12-19 15:36:37.794921 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:37.795913 INFO::Removing potential empty rows and columns
2025-12-19 15:36:37.797099 INFO::Found 0 missing values.
2025-12-19 15:36:37.798105 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.
2025-12-19 15:36:37.803481 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:37.804232 INFO::Done
2025-12-19 15:36:37.804833 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:37.807089 INFO::Starting hierarchical adjustment
2025-12-19 15:36:37.807838 INFO::Found 2 batches.
2025-12-19 15:36:37.808378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:37.809093 INFO::Using default BPPARAM
2025-12-19 15:36:37.809626 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:37.810634 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 15:36:37.912545 INFO::Done
2025-12-19 15:36:37.913828 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:37.917647 INFO::ASW Batch was -0.021300181815128 prior to batch effect correction and is now -0.112667576591485 .
2025-12-19 15:36:37.919766 INFO::Total function execution time is 0.125590801239014 s and adjustment time is 0.104225158691406 s ( 82.99 )
2025-12-19 15:36:37.926856 INFO::Formatting Data.
2025-12-19 15:36:37.927781 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:37.941958 INFO::Formatting Data.
2025-12-19 15:36:37.942989 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:37.944083 INFO::Removing potential empty rows and columns
2025-12-19 15:36:37.945294 INFO::Found 0 missing values.
2025-12-19 15:36:37.948622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:37.94938 INFO::Done
2025-12-19 15:36:37.949937 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:38.027867 INFO::Starting hierarchical adjustment
2025-12-19 15:36:38.029003 INFO::Found 2 batches.
2025-12-19 15:36:38.029573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:38.030129 INFO::Using default BPPARAM
2025-12-19 15:36:38.03062 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:38.031575 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 15:36:38.049914 INFO::Done
2025-12-19 15:36:38.050794 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:38.052942 INFO::ASW Batch was 0.0429721281901101 prior to batch effect correction and is now -0.134285036978142 .
2025-12-19 15:36:38.053739 INFO::Total function execution time is 0.111968994140625 s and adjustment time is 0.021061897277832 s ( 18.81 )
2025-12-19 15:36:38.054665 INFO::Formatting Data.
2025-12-19 15:36:38.055154 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:38.055947 INFO::Removing potential empty rows and columns
2025-12-19 15:36:38.056871 INFO::Found 0 missing values.
2025-12-19 15:36:38.05938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:38.059924 INFO::Done
2025-12-19 15:36:38.060383 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:38.062352 INFO::Starting hierarchical adjustment
2025-12-19 15:36:38.06311 INFO::Found 2 batches.
2025-12-19 15:36:38.063607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:38.064164 INFO::Using default BPPARAM
2025-12-19 15:36:38.064619 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:38.065461 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 15:36:38.095307 INFO::Done
2025-12-19 15:36:38.096112 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:38.098211 INFO::ASW Batch was 0.0429721281901101 prior to batch effect correction and is now -0.134285036978142 .
2025-12-19 15:36:38.098981 INFO::Total function execution time is 0.0442771911621094 s and adjustment time is 0.0322649478912354 s ( 72.87 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-19 15:36:43.082849 INFO::Formatting Data.
2025-12-19 15:36:43.08363 INFO::Recognized SummarizedExperiment
2025-12-19 15:36:43.084129 INFO::Typecasting input to dataframe.
2025-12-19 15:36:43.128597 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:43.130129 INFO::Removing potential empty rows and columns
2025-12-19 15:36:43.13388 INFO::Found 0 missing values.
2025-12-19 15:36:43.142904 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:43.143732 INFO::Done
2025-12-19 15:36:43.144267 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:43.148014 INFO::Starting hierarchical adjustment
2025-12-19 15:36:43.149857 INFO::Found 2 batches.
2025-12-19 15:36:43.150654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:43.152178 INFO::Using default BPPARAM
2025-12-19 15:36:43.153262 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:43.154672 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 15:36:43.276674 INFO::Done
2025-12-19 15:36:43.27772 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:43.281813 INFO::ASW Batch was -0.00801895263092404 prior to batch effect correction and is now -0.0856933144283782 .
2025-12-19 15:36:43.282813 INFO::Total function execution time is 0.20028018951416 s and adjustment time is 0.127161979675293 s ( 63.49 )
Warning: stack imbalance in '{', 73 then 75
2025-12-19 15:36:43.303391 INFO::Formatting Data.
2025-12-19 15:36:43.304307 INFO::Recognized SummarizedExperiment
2025-12-19 15:36:43.304819 INFO::Typecasting input to dataframe.
2025-12-19 15:36:43.314845 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:43.316213 INFO::Removing potential empty rows and columns
2025-12-19 15:36:43.319784 INFO::Found 0 missing values.
2025-12-19 15:36:43.32651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:43.32716 INFO::Done
2025-12-19 15:36:43.327636 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:43.331441 INFO::Starting hierarchical adjustment
2025-12-19 15:36:43.332188 INFO::Found 2 batches.
2025-12-19 15:36:43.332681 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:43.333241 INFO::Using default BPPARAM
2025-12-19 15:36:43.333699 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:43.334617 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 15:36:43.381672 INFO::Done
2025-12-19 15:36:43.382571 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:43.386583 INFO::ASW Batch was 0.0064385673582391 prior to batch effect correction and is now 0.0064385673582391 .
2025-12-19 15:36:43.390466 INFO::Total function execution time is 0.086353063583374 s and adjustment time is 0.049530029296875 s ( 57.36 )
2025-12-19 15:36:43.457383 INFO::Formatting Data.
2025-12-19 15:36:43.458219 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:43.459098 INFO::Removing potential empty rows and columns
2025-12-19 15:36:43.460188 INFO::Found 0 missing values.
2025-12-19 15:36:43.462889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:43.463469 INFO::Done
2025-12-19 15:36:43.46395 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:43.466006 INFO::Starting hierarchical adjustment
2025-12-19 15:36:43.466665 INFO::Found 3 batches.
2025-12-19 15:36:43.467141 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:43.467707 INFO::Using default BPPARAM
2025-12-19 15:36:43.468155 INFO::Processing subtree level 1
2025-12-19 15:36:43.652853 INFO::Adjusting the last 1 batches sequentially
2025-12-19 15:36:43.656772 INFO::Done
2025-12-19 15:36:43.657418 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:43.662564 INFO::ASW Batch was -0.129996860879277 prior to batch effect correction and is now -0.153235685218364 .
2025-12-19 15:36:43.664843 INFO::Total function execution time is 0.207433938980103 s and adjustment time is 0.19021487236023 s ( 91.7 )
2025-12-19 15:36:43.695539 INFO::Skipping initial DF formatting
2025-12-19 15:36:43.697618 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:43.702799 INFO::Starting hierarchical adjustment
2025-12-19 15:36:43.703774 INFO::Found 5 batches.
2025-12-19 15:36:43.704339 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:43.705018 INFO::Using default BPPARAM
2025-12-19 15:36:43.705911 INFO::Processing subtree level 1
2025-12-19 15:36:44.054005 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:44.0616 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 15:36:44.086984 INFO::Done
2025-12-19 15:36:44.08823 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:44.096201 INFO::ASW Batch was 0.502555519497954 prior to batch effect correction and is now 0.502555519497954 .
2025-12-19 15:36:44.097093 INFO::ASW Label was 0.397270720156329 prior to batch effect correction and is now 0.397270720156329 .
2025-12-19 15:36:44.098681 INFO::Total function execution time is 0.403527975082397 s and adjustment time is 0.383352041244507 s ( 95 )
2025-12-19 15:36:44.267141 INFO::Formatting Data.
2025-12-19 15:36:44.268112 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:44.269129 INFO::Removing potential empty rows and columns
2025-12-19 15:36:44.270227 INFO::Found 0 missing values.
2025-12-19 15:36:44.274335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:44.275004 INFO::Done
2025-12-19 15:36:44.275551 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:44.289596 INFO::Starting hierarchical adjustment
2025-12-19 15:36:44.290842 INFO::Found 5 batches.
2025-12-19 15:36:44.291471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:44.292182 INFO::Using default BPPARAM
2025-12-19 15:36:44.292706 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.
2025-12-19 15:36:44.488811 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:44.497997 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 15:36:44.534056 INFO::Done
2025-12-19 15:36:44.535058 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:44.542928 INFO::ASW Batch was 0.523868679026016 prior to batch effect correction and is now -0.0115238797641683 .
2025-12-19 15:36:44.547945 INFO::ASW Label was 0.329611142671672 prior to batch effect correction and is now 0.758856728821058 .
2025-12-19 15:36:44.549383 INFO::Total function execution time is 0.28226113319397 s and adjustment time is 0.243417978286743 s ( 86.24 )
2025-12-19 15:36:44.550359 INFO::Formatting Data.
2025-12-19 15:36:44.551061 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:44.558108 INFO::Removing potential empty rows and columns
2025-12-19 15:36:44.559781 INFO::Found 0 missing values.
2025-12-19 15:36:44.569788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:44.570866 INFO::Done
2025-12-19 15:36:44.57164 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:44.577295 INFO::Starting hierarchical adjustment
2025-12-19 15:36:44.578425 INFO::Found 5 batches.
2025-12-19 15:36:44.579025 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:44.579916 INFO::Using default BPPARAM
2025-12-19 15:36:44.58043 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.
2025-12-19 15:36:44.805141 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:44.814868 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 15:36:44.850103 INFO::Done
2025-12-19 15:36:44.851269 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:44.859131 INFO::ASW Batch was 0.523868679026016 prior to batch effect correction and is now -0.0115238797641683 .
2025-12-19 15:36:44.860028 INFO::ASW Label was 0.329611142671672 prior to batch effect correction and is now 0.758856728821058 .
2025-12-19 15:36:44.861086 INFO::Total function execution time is 0.310659885406494 s and adjustment time is 0.271784067153931 s ( 87.49 )
2025-12-19 15:36:44.882518 INFO::Formatting Data.
2025-12-19 15:36:44.883513 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:44.88472 INFO::Removing potential empty rows and columns
2025-12-19 15:36:44.885926 INFO::Found 0 missing values.
2025-12-19 15:36:44.890067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:44.890752 INFO::Done
2025-12-19 15:36:44.891299 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:44.894554 INFO::Starting hierarchical adjustment
2025-12-19 15:36:44.895338 INFO::Found 5 batches.
2025-12-19 15:36:44.895906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:44.896562 INFO::Using default BPPARAM
2025-12-19 15:36:44.897072 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.
2025-12-19 15:36:45.084516 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:45.096015 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 15:36:45.144377 INFO::Done
2025-12-19 15:36:45.14548 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:45.149905 INFO::ASW Batch was 0.508459369280949 prior to batch effect correction and is now 0.000823428303211511 .
2025-12-19 15:36:45.150664 INFO::ASW Label was 0.328039433101967 prior to batch effect correction and is now 0.793586506088928 .
2025-12-19 15:36:45.152002 INFO::Total function execution time is 0.269549131393433 s and adjustment time is 0.249114990234375 s ( 92.42 )
2025-12-19 15:36:45.152905 INFO::Formatting Data.
2025-12-19 15:36:45.153976 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:45.155574 INFO::Removing potential empty rows and columns
2025-12-19 15:36:45.157002 INFO::Found 0 missing values.
2025-12-19 15:36:45.161401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:45.162097 INFO::Done
2025-12-19 15:36:45.162658 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:45.166178 INFO::Starting hierarchical adjustment
2025-12-19 15:36:45.167121 INFO::Found 5 batches.
2025-12-19 15:36:45.167731 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:45.168496 INFO::Using default BPPARAM
2025-12-19 15:36:45.169132 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.
2025-12-19 15:36:45.337373 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:45.341386 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 15:36:45.37788 INFO::Done
2025-12-19 15:36:45.379057 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:45.39746 INFO::ASW Batch was 0.508459369280949 prior to batch effect correction and is now 0.000823428303211511 .
2025-12-19 15:36:45.399354 INFO::ASW Label was 0.328039433101967 prior to batch effect correction and is now 0.793586506088928 .
2025-12-19 15:36:45.400477 INFO::Total function execution time is 0.247503995895386 s and adjustment time is 0.210890054702759 s ( 85.21 )
2025-12-19 15:36:45.421076 INFO::Formatting Data.
2025-12-19 15:36:45.422058 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:45.423098 INFO::Removing potential empty rows and columns
2025-12-19 15:36:45.42572 INFO::Found 0 missing values.
2025-12-19 15:36:45.429758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:45.430474 INFO::Done
2025-12-19 15:36:45.430988 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:45.434261 INFO::Starting hierarchical adjustment
2025-12-19 15:36:45.435064 INFO::Found 2 batches.
2025-12-19 15:36:45.435551 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:45.436126 INFO::Using default BPPARAM
2025-12-19 15:36:45.436554 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:45.437319 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 15:36:45.456558 INFO::Done
2025-12-19 15:36:45.457407 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:45.461002 INFO::ASW Batch was 0.652286500807727 prior to batch effect correction and is now 0.0436871405382758 .
2025-12-19 15:36:45.461714 INFO::ASW Label was 0.390267990154575 prior to batch effect correction and is now 0.900520103823091 .
2025-12-19 15:36:45.462504 INFO::Total function execution time is 0.0415890216827393 s and adjustment time is 0.0216009616851807 s ( 51.94 )
2025-12-19 15:36:45.463272 INFO::Formatting Data.
2025-12-19 15:36:45.463846 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:45.464694 INFO::Removing potential empty rows and columns
2025-12-19 15:36:45.465722 INFO::Found 0 missing values.
2025-12-19 15:36:45.468341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:45.468931 INFO::Done
2025-12-19 15:36:45.469442 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:45.472585 INFO::Starting hierarchical adjustment
2025-12-19 15:36:45.473499 INFO::Found 2 batches.
2025-12-19 15:36:45.474057 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:45.474672 INFO::Using default BPPARAM
2025-12-19 15:36:45.475195 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:45.476111 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 15:36:45.497855 INFO::Done
2025-12-19 15:36:45.498651 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:45.50324 INFO::ASW Batch was 0.652286500807727 prior to batch effect correction and is now 0.0436871405382758 .
2025-12-19 15:36:45.504095 INFO::ASW Label was 0.390267990154575 prior to batch effect correction and is now 0.900520103823091 .
2025-12-19 15:36:45.510601 INFO::Total function execution time is 0.0468671321868896 s and adjustment time is 0.0244588851928711 s ( 52.19 )
2025-12-19 15:36:45.526285 INFO::Formatting Data.
2025-12-19 15:36:45.527211 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:45.528212 INFO::Removing potential empty rows and columns
2025-12-19 15:36:45.529192 INFO::Found 0 missing values.
2025-12-19 15:36:45.541137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:45.542325 INFO::Done
2025-12-19 15:36:45.543311 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:45.545741 INFO::Starting hierarchical adjustment
2025-12-19 15:36:45.546526 INFO::Found 2 batches.
2025-12-19 15:36:45.548661 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:45.549411 INFO::Using default BPPARAM
2025-12-19 15:36:45.550017 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:45.551028 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 15:36:45.592458 INFO::Done
2025-12-19 15:36:45.593316 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:45.595534 INFO::ASW Batch was -0.140050031433903 prior to batch effect correction and is now -0.128987827357036 .
2025-12-19 15:36:45.596525 INFO::Total function execution time is 0.0703580379486084 s and adjustment time is 0.0460419654846191 s ( 65.44 )
2025-12-19 15:36:45.618401 INFO::Formatting Data.
2025-12-19 15:36:45.619234 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:45.620084 INFO::Removing potential empty rows and columns
2025-12-19 15:36:45.63122 INFO::Found 0 missing values.
2025-12-19 15:36:45.633356 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.
2025-12-19 15:36:45.638755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:45.639614 INFO::Done
2025-12-19 15:36:45.640172 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:45.643573 INFO::Starting hierarchical adjustment
2025-12-19 15:36:45.648011 INFO::Found 2 batches.
2025-12-19 15:36:45.649068 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:45.649834 INFO::Using default BPPARAM
2025-12-19 15:36:45.650391 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:45.652306 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 15:36:45.686963 INFO::Done
2025-12-19 15:36:45.687922 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:45.691482 INFO::ASW Batch was 0.212351827267109 prior to batch effect correction and is now 0.0787731213862247 .
2025-12-19 15:36:45.692332 INFO::ASW Label was 0.81531559645757 prior to batch effect correction and is now 0.914182833411993 .
2025-12-19 15:36:45.693407 INFO::Total function execution time is 0.0750870704650879 s and adjustment time is 0.039902925491333 s ( 53.14 )
2025-12-19 15:36:45.694352 INFO::Formatting Data.
2025-12-19 15:36:45.695008 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:45.696007 INFO::Removing potential empty rows and columns
2025-12-19 15:36:45.697064 INFO::Found 0 missing values.
2025-12-19 15:36:45.698064 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.
2025-12-19 15:36:45.702491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:45.703211 INFO::Done
2025-12-19 15:36:45.703706 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:45.706725 INFO::Starting hierarchical adjustment
2025-12-19 15:36:45.707461 INFO::Found 2 batches.
2025-12-19 15:36:45.707943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:45.70852 INFO::Using default BPPARAM
2025-12-19 15:36:45.72195 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:45.723551 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 15:36:45.763351 INFO::Done
2025-12-19 15:36:45.764712 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:45.770664 INFO::ASW Batch was 0.212351827267109 prior to batch effect correction and is now 0.0787731213862247 .
2025-12-19 15:36:45.77161 INFO::ASW Label was 0.81531559645757 prior to batch effect correction and is now 0.914182833411993 .
2025-12-19 15:36:45.772711 INFO::Total function execution time is 0.0783360004425049 s and adjustment time is 0.0557570457458496 s ( 71.18 )
2025-12-19 15:36:46.224163 INFO::Formatting Data.
2025-12-19 15:36:46.225049 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:46.230882 INFO::Removing potential empty rows and columns
2025-12-19 15:36:46.232283 INFO::Found 0 missing values.
2025-12-19 15:36:46.235145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:46.235747 INFO::Done
2025-12-19 15:36:46.236247 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:46.238357 INFO::Starting hierarchical adjustment
2025-12-19 15:36:46.239055 INFO::Found 3 batches.
2025-12-19 15:36:46.239533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:46.240173 INFO::Using default BPPARAM
2025-12-19 15:36:46.240644 INFO::Processing subtree level 1
2025-12-19 15:36:46.344695 INFO::Adjusting the last 1 batches sequentially
2025-12-19 15:36:46.356406 INFO::Done
2025-12-19 15:36:46.357783 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:46.370577 INFO::ASW Batch was 0.0934301625369685 prior to batch effect correction and is now 0.0934301625369685 .
2025-12-19 15:36:46.37621 INFO::Total function execution time is 0.151964902877808 s and adjustment time is 0.117395162582397 s ( 77.25 )
2025-12-19 15:36:46.37966 INFO::Formatting Data.
2025-12-19 15:36:46.380726 INFO::Typecasting input to dataframe.
2025-12-19 15:36:46.38175 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:46.3833 INFO::Removing potential empty rows and columns
2025-12-19 15:36:46.384541 INFO::Found 0 missing values.
2025-12-19 15:36:46.387821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:46.388561 INFO::Done
2025-12-19 15:36:46.389084 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:46.391336 INFO::Starting hierarchical adjustment
2025-12-19 15:36:46.392139 INFO::Found 3 batches.
2025-12-19 15:36:46.39302 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:46.3937 INFO::Using default BPPARAM
2025-12-19 15:36:46.394193 INFO::Processing subtree level 1
2025-12-19 15:36:46.514276 INFO::Adjusting the last 1 batches sequentially
2025-12-19 15:36:46.517881 INFO::Done
2025-12-19 15:36:46.518527 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:46.522483 INFO::ASW Batch was 0.0934301625369685 prior to batch effect correction and is now 0.0934301625369685 .
2025-12-19 15:36:46.524062 INFO::Total function execution time is 0.144532918930054 s and adjustment time is 0.125885009765625 s ( 87.1 )
2025-12-19 15:36:46.551787 INFO::Formatting Data.
2025-12-19 15:36:46.552849 INFO::Typecasting input to dataframe.
2025-12-19 15:36:46.553748 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:46.554743 INFO::Removing potential empty rows and columns
2025-12-19 15:36:46.555905 INFO::Found 0 missing values.
2025-12-19 15:36:46.55884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:46.559499 INFO::Done
2025-12-19 15:36:46.560014 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:46.562196 INFO::Starting hierarchical adjustment
2025-12-19 15:36:46.562994 INFO::Found 3 batches.
2025-12-19 15:36:46.563502 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:46.564135 INFO::Using default BPPARAM
2025-12-19 15:36:46.564762 INFO::Processing subtree level 1
2025-12-19 15:36:46.687147 INFO::Adjusting the last 1 batches sequentially
2025-12-19 15:36:46.695127 INFO::Done
2025-12-19 15:36:46.698072 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:46.706627 INFO::ASW Batch was 0.00994409324946254 prior to batch effect correction and is now 0.00994409324946254 .
2025-12-19 15:36:46.710386 INFO::Total function execution time is 0.15725302696228 s and adjustment time is 0.132232904434204 s ( 84.09 )
2025-12-19 15:36:46.90737 INFO::Formatting Data.
2025-12-19 15:36:46.90835 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:46.90956 INFO::Removing potential empty rows and columns
2025-12-19 15:36:46.912451 INFO::Found 1000 missing values.
2025-12-19 15:36:46.939274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:46.940932 INFO::Done
2025-12-19 15:36:46.941895 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:46.950263 INFO::Starting hierarchical adjustment
2025-12-19 15:36:46.951406 INFO::Found 10 batches.
2025-12-19 15:36:46.951977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:46.952709 INFO::Using default BPPARAM
2025-12-19 15:36:46.953242 INFO::Processing subtree level 1
2025-12-19 15:36:47.135587 INFO::Processing subtree level 2
2025-12-19 15:36:47.334339 INFO::Adjusting the last 1 batches sequentially
2025-12-19 15:36:47.343447 INFO::Done
2025-12-19 15:36:47.345171 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:47.354928 INFO::ASW Batch was 0.47185700357224 prior to batch effect correction and is now 0.47185700357224 .
2025-12-19 15:36:47.357008 INFO::ASW Label was 0.354374337813902 prior to batch effect correction and is now 0.354374337813902 .
2025-12-19 15:36:47.361918 INFO::Total function execution time is 0.454195022583008 s and adjustment time is 0.392126083374023 s ( 86.33 )
2025-12-19 15:36:47.36352 INFO::Formatting Data.
2025-12-19 15:36:47.364237 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:47.366144 INFO::Removing potential empty rows and columns
2025-12-19 15:36:47.372133 INFO::Found 1000 missing values.
2025-12-19 15:36:47.405671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:47.406699 INFO::Done
2025-12-19 15:36:47.407276 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:47.41373 INFO::Starting hierarchical adjustment
2025-12-19 15:36:47.414844 INFO::Found 10 batches.
2025-12-19 15:36:49.170971 INFO::Set up parallel execution backend with 2 workers
2025-12-19 15:36:49.171808 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-19 15:36:51.050155 INFO::Adjusting the last 2 batches sequentially
2025-12-19 15:36:51.051669 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 15:36:51.074097 INFO::Done
2025-12-19 15:36:51.076118 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:51.084235 INFO::ASW Batch was 0.47185700357224 prior to batch effect correction and is now 0.47185700357224 .
2025-12-19 15:36:51.085042 INFO::ASW Label was 0.354374337813902 prior to batch effect correction and is now 0.354374337813902 .
2025-12-19 15:36:51.085893 INFO::Total function execution time is 3.72244501113892 s and adjustment time is 3.65941596031189 s ( 98.31 )
2025-12-19 15:36:51.283957 INFO::Formatting Data.
2025-12-19 15:36:51.285076 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:51.286193 INFO::Removing potential empty rows and columns
2025-12-19 15:36:51.28741 INFO::Found 0 missing values.
2025-12-19 15:36:51.291007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:51.291629 INFO::Done
2025-12-19 15:36:51.292126 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 15:36:51.295101 INFO::Starting hierarchical adjustment
2025-12-19 15:36:51.295847 INFO::Found 3 batches.
2025-12-19 15:36:51.296349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 15:36:51.297004 INFO::Using default BPPARAM
2025-12-19 15:36:51.297492 INFO::Processing subtree level 1
2025-12-19 15:36:51.46578 INFO::Adjusting the last 1 batches sequentially
2025-12-19 15:36:51.472834 INFO::Done
2025-12-19 15:36:51.47424 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 15:36:51.481134 INFO::ASW Batch was 0.162263553849638 prior to batch effect correction and is now -0.164593881970677 .
2025-12-19 15:36:51.482037 INFO::ASW Label was -0.159152101985438 prior to batch effect correction and is now -0.00466326025051651 .
2025-12-19 15:36:51.483756 INFO::Total function execution time is 0.199939966201782 s and adjustment time is 0.177093982696533 s ( 88.57 )
2025-12-19 15:36:51.682321 INFO::Formatting Data.
2025-12-19 15:36:51.684634 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:51.685746 INFO::Removing potential empty rows and columns
2025-12-19 15:36:51.690731 INFO::Found 2 missing values.
2025-12-19 15:36:51.694496 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:51.695168 INFO::Done
2025-12-19 15:36:51.752202 INFO::Found NA in Reference column
2025-12-19 15:36:51.798346 INFO::Require at least two references per batch.
2025-12-19 15:36:51.889345 INFO::Formatting Data.
2025-12-19 15:36:51.890272 INFO::Recognized SummarizedExperiment
2025-12-19 15:36:51.891418 INFO::Typecasting input to dataframe.
2025-12-19 15:36:51.918912 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:51.920468 INFO::Removing potential empty rows and columns
2025-12-19 15:36:51.92454 INFO::Found 0 missing values.
2025-12-19 15:36:51.940512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:51.944524 INFO::Done
2025-12-19 15:36:51.963399 INFO::Formatting Data.
2025-12-19 15:36:51.964247 INFO::Recognized SummarizedExperiment
2025-12-19 15:36:51.964764 INFO::Typecasting input to dataframe.
2025-12-19 15:36:51.987491 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:51.988957 INFO::Removing potential empty rows and columns
2025-12-19 15:36:51.995795 INFO::Found 0 missing values.
2025-12-19 15:36:52.015339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:52.016314 INFO::Done
2025-12-19 15:36:52.040241 INFO::Formatting Data.
2025-12-19 15:36:52.041156 INFO::Recognized SummarizedExperiment
2025-12-19 15:36:52.041668 INFO::Typecasting input to dataframe.
2025-12-19 15:36:52.058012 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:52.059243 INFO::Removing potential empty rows and columns
2025-12-19 15:36:52.060358 INFO::Found 0 missing values.
2025-12-19 15:36:52.061333 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.
2025-12-19 15:36:52.075955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:52.076856 INFO::Done
2025-12-19 15:36:52.092668 INFO::Formatting Data.
2025-12-19 15:36:52.093694 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:52.094665 INFO::Removing potential empty rows and columns
2025-12-19 15:36:52.095683 INFO::Found 0 missing values.
2025-12-19 15:36:52.098416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:52.099005 INFO::Done
2025-12-19 15:36:52.120165 INFO::Formatting Data.
2025-12-19 15:36:52.121297 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:52.122407 INFO::Removing potential empty rows and columns
2025-12-19 15:36:52.124021 INFO::Found 0 missing values.
2025-12-19 15:36:52.127058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:52.127733 INFO::Done
2025-12-19 15:36:52.186322 INFO::Formatting Data.
2025-12-19 15:36:52.189637 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:52.191062 INFO::Removing potential empty rows and columns
2025-12-19 15:36:52.192448 INFO::Found 1 missing values.
2025-12-19 15:36:52.195128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:52.195707 INFO::Done
2025-12-19 15:36:52.220371 INFO::Formatting Data.
2025-12-19 15:36:52.22133 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:52.222249 INFO::Removing potential empty rows and columns
2025-12-19 15:36:52.223204 INFO::Found 2 missing values.
2025-12-19 15:36:52.224136 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.
2025-12-19 15:36:52.226438 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:52.227031 INFO::Done
2025-12-19 15:36:52.261169 INFO::Formatting Data.
2025-12-19 15:36:52.262178 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:52.263144 INFO::Removing potential empty rows and columns
2025-12-19 15:36:52.264156 INFO::Found 2 missing values.
2025-12-19 15:36:52.265792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:52.266365 INFO::Done
2025-12-19 15:36:52.27965 INFO::Formatting Data.
2025-12-19 15:36:52.280598 INFO::Typecasting input to dataframe.
2025-12-19 15:36:52.291266 INFO::Replacing NaNs with NAs.
2025-12-19 15:36:52.292511 INFO::Removing potential empty rows and columns
2025-12-19 15:36:52.29367 INFO::Found 0 missing values.
2025-12-19 15:36:52.2978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 15:36:52.298442 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.302 3.944 34.880
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.645 | 1.130 | 30.470 | |
| compute_asw | 0.030 | 0.001 | 0.035 | |
| count_existing | 0.015 | 0.001 | 0.017 | |
| generate_data_covariables | 0.014 | 0.002 | 0.016 | |
| generate_dataset | 0.014 | 0.001 | 0.014 | |