Yannis Schumann
| Snapshot Date: 2026-04-03 13:40 -0400 (Fri, 03 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-04 11:35 -0400 (Sat, 04 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4900 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4634 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 170/2381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-04-03 18:35:07 -0400 (Fri, 03 Apr 2026) |
| EndedAt: 2026-04-03 18:35:41 -0400 (Fri, 03 Apr 2026) |
| EllapsedTime: 33.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-03 22:35:07 UTC
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.563 0.346 6.831
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-03-28 r89739)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-04-03 18:35:32.460357 INFO::Formatting Data.
2026-04-03 18:35:32.462 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:32.466329 INFO::Removing potential empty rows and columns
2026-04-03 18:35:32.576374 INFO::Found 0 missing values.
2026-04-03 18:35:32.577755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:32.578121 INFO::Done
2026-04-03 18:35:32.578424 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:32.585326 INFO::Starting hierarchical adjustment
2026-04-03 18:35:32.585882 INFO::Found 3 batches.
2026-04-03 18:35:32.586177 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:32.58669 INFO::Using default BPPARAM
2026-04-03 18:35:32.586962 INFO::Processing subtree level 1
2026-04-03 18:35:32.649711 INFO::Adjusting the last 1 batches sequentially
2026-04-03 18:35:32.651283 INFO::Done
2026-04-03 18:35:32.651683 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:32.652951 INFO::ASW Batch was -0.0953165771584012 prior to batch effect correction and is now -0.0953165771584012 .
2026-04-03 18:35:32.653518 INFO::Total function execution time is 0.193526983261108 s and adjustment time is 0.0654580593109131 s ( 33.82 )
2026-04-03 18:35:32.66223 INFO::Formatting Data.
2026-04-03 18:35:32.663058 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:32.663607 INFO::Removing potential empty rows and columns
2026-04-03 18:35:32.664246 INFO::Found 0 missing values.
2026-04-03 18:35:32.664771 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-03 18:35:32.671828 INFO::Formatting Data.
2026-04-03 18:35:32.672253 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:32.67267 INFO::Removing potential empty rows and columns
2026-04-03 18:35:32.673146 INFO::Found 0 missing values.
2026-04-03 18:35:32.673569 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-03 18:35:32.681192 INFO::Formatting Data.
2026-04-03 18:35:32.681975 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:32.682807 INFO::Removing potential empty rows and columns
2026-04-03 18:35:32.68347 INFO::Found 0 missing values.
2026-04-03 18:35:32.683925 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-03 18:35:32.685536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:32.685878 INFO::Done
2026-04-03 18:35:32.686283 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:32.68722 INFO::Starting hierarchical adjustment
2026-04-03 18:35:32.687615 INFO::Found 2 batches.
2026-04-03 18:35:32.688109 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:32.688488 INFO::Using default BPPARAM
2026-04-03 18:35:32.688783 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:32.689243 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 18:35:32.700798 INFO::Done
2026-04-03 18:35:32.701248 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:32.70225 INFO::ASW Batch was -0.0574897857473471 prior to batch effect correction and is now -0.129978854002066 .
2026-04-03 18:35:32.702827 INFO::Total function execution time is 0.0218169689178467 s and adjustment time is 0.0131759643554688 s ( 60.39 )
2026-04-03 18:35:32.704496 INFO::Formatting Data.
2026-04-03 18:35:32.70487 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:32.710045 INFO::Formatting Data.
2026-04-03 18:35:32.710432 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:32.710866 INFO::Removing potential empty rows and columns
2026-04-03 18:35:32.711345 INFO::Found 0 missing values.
2026-04-03 18:35:32.71275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:32.713197 INFO::Done
2026-04-03 18:35:32.713481 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:32.715151 INFO::Starting hierarchical adjustment
2026-04-03 18:35:32.715734 INFO::Found 2 batches.
2026-04-03 18:35:32.716361 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:32.716756 INFO::Using default BPPARAM
2026-04-03 18:35:32.717118 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:32.717573 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:32.726126 INFO::Done
2026-04-03 18:35:32.727182 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:32.728662 INFO::ASW Batch was -0.0503050534234554 prior to batch effect correction and is now -0.122345685683606 .
2026-04-03 18:35:32.729437 INFO::Total function execution time is 0.0194010734558105 s and adjustment time is 0.0105199813842773 s ( 54.22 )
2026-04-03 18:35:32.730358 INFO::Formatting Data.
2026-04-03 18:35:32.730739 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:32.731218 INFO::Removing potential empty rows and columns
2026-04-03 18:35:32.731747 INFO::Found 0 missing values.
2026-04-03 18:35:32.733388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:32.733791 INFO::Done
2026-04-03 18:35:32.73419 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:32.735136 INFO::Starting hierarchical adjustment
2026-04-03 18:35:32.735712 INFO::Found 2 batches.
2026-04-03 18:35:32.73619 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:32.736585 INFO::Using default BPPARAM
2026-04-03 18:35:32.736946 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:32.737346 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:32.742432 INFO::Done
2026-04-03 18:35:32.743074 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:32.744503 INFO::ASW Batch was -0.0503050534234554 prior to batch effect correction and is now -0.122345685683606 .
2026-04-03 18:35:32.744982 INFO::Total function execution time is 0.0146448612213135 s and adjustment time is 0.00691509246826172 s ( 47.22 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-03 18:35:34.022729 INFO::Formatting Data.
2026-04-03 18:35:34.023248 INFO::Recognized SummarizedExperiment
2026-04-03 18:35:34.02422 INFO::Typecasting input to dataframe.
2026-04-03 18:35:34.041115 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.041918 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.043367 INFO::Found 0 missing values.
2026-04-03 18:35:34.045825 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.046217 INFO::Done
2026-04-03 18:35:34.04683 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.048759 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.049186 INFO::Found 2 batches.
2026-04-03 18:35:34.049517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.050052 INFO::Using default BPPARAM
2026-04-03 18:35:34.050431 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.051271 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 18:35:34.078551 INFO::Done
2026-04-03 18:35:34.078965 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.081021 INFO::ASW Batch was 0.0321177364413356 prior to batch effect correction and is now -0.0948796533249141 .
2026-04-03 18:35:34.081954 INFO::Total function execution time is 0.0592999458312988 s and adjustment time is 0.0294020175933838 s ( 49.58 )
Warning: stack imbalance in '{', 73 then 75
2026-04-03 18:35:34.089798 INFO::Formatting Data.
2026-04-03 18:35:34.09026 INFO::Recognized SummarizedExperiment
2026-04-03 18:35:34.09057 INFO::Typecasting input to dataframe.
2026-04-03 18:35:34.093708 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.094244 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.09554 INFO::Found 0 missing values.
2026-04-03 18:35:34.097841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.098242 INFO::Done
2026-04-03 18:35:34.098518 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.099859 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.100206 INFO::Found 2 batches.
2026-04-03 18:35:34.100463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.100753 INFO::Using default BPPARAM
2026-04-03 18:35:34.101016 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.101414 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 18:35:34.109659 INFO::Done
2026-04-03 18:35:34.110072 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.111407 INFO::ASW Batch was -0.0104154766961437 prior to batch effect correction and is now -0.0104154766961437 .
2026-04-03 18:35:34.11185 INFO::Total function execution time is 0.0220630168914795 s and adjustment time is 0.00948905944824219 s ( 43.01 )
2026-04-03 18:35:34.118624 INFO::Formatting Data.
2026-04-03 18:35:34.119005 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.119397 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.119828 INFO::Found 0 missing values.
2026-04-03 18:35:34.120806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.121095 INFO::Done
2026-04-03 18:35:34.121361 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.122096 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.12241 INFO::Found 3 batches.
2026-04-03 18:35:34.122683 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.122973 INFO::Using default BPPARAM
2026-04-03 18:35:34.123223 INFO::Processing subtree level 1
2026-04-03 18:35:34.284462 INFO::Adjusting the last 1 batches sequentially
2026-04-03 18:35:34.285874 INFO::Done
2026-04-03 18:35:34.286475 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.287923 INFO::ASW Batch was 0.0465277553903175 prior to batch effect correction and is now -0.15748638320109 .
2026-04-03 18:35:34.288487 INFO::Total function execution time is 0.169825077056885 s and adjustment time is 0.163492918014526 s ( 96.27 )
2026-04-03 18:35:34.296477 INFO::Skipping initial DF formatting
2026-04-03 18:35:34.296934 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.298809 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.299321 INFO::Found 5 batches.
2026-04-03 18:35:34.299709 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.300104 INFO::Using default BPPARAM
2026-04-03 18:35:34.300484 INFO::Processing subtree level 1
2026-04-03 18:35:34.367389 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.369683 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 18:35:34.381435 INFO::Done
2026-04-03 18:35:34.38204 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.384665 INFO::ASW Batch was 0.457109701131372 prior to batch effect correction and is now 0.457109701131372 .
2026-04-03 18:35:34.38522 INFO::ASW Label was 0.41717835935962 prior to batch effect correction and is now 0.41717835935962 .
2026-04-03 18:35:34.3859 INFO::Total function execution time is 0.0894081592559814 s and adjustment time is 0.0820779800415039 s ( 91.8 )
2026-04-03 18:35:34.394292 INFO::Formatting Data.
2026-04-03 18:35:34.394984 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.395763 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.39637 INFO::Found 0 missing values.
2026-04-03 18:35:34.39782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.398184 INFO::Done
2026-04-03 18:35:34.398524 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.399679 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.400075 INFO::Found 5 batches.
2026-04-03 18:35:34.400396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.400774 INFO::Using default BPPARAM
2026-04-03 18:35:34.401129 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.466881 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.468384 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.477423 INFO::Done
2026-04-03 18:35:34.477944 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.479719 INFO::ASW Batch was 0.34562296929564 prior to batch effect correction and is now 0.0517993277332739 .
2026-04-03 18:35:34.480155 INFO::ASW Label was 0.320692215947793 prior to batch effect correction and is now 0.666823896908004 .
2026-04-03 18:35:34.480717 INFO::Total function execution time is 0.086406946182251 s and adjustment time is 0.0773758888244629 s ( 89.55 )
2026-04-03 18:35:34.481271 INFO::Formatting Data.
2026-04-03 18:35:34.481641 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.482152 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.482686 INFO::Found 0 missing values.
2026-04-03 18:35:34.484115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.484483 INFO::Done
2026-04-03 18:35:34.484829 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.485978 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.48638 INFO::Found 5 batches.
2026-04-03 18:35:34.486687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.48708 INFO::Using default BPPARAM
2026-04-03 18:35:34.487389 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.549827 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.551421 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.560273 INFO::Done
2026-04-03 18:35:34.560901 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.562964 INFO::ASW Batch was 0.34562296929564 prior to batch effect correction and is now 0.0517993277332739 .
2026-04-03 18:35:34.563398 INFO::ASW Label was 0.320692215947793 prior to batch effect correction and is now 0.666823896908004 .
2026-04-03 18:35:34.563972 INFO::Total function execution time is 0.0826249122619629 s and adjustment time is 0.073936939239502 s ( 89.49 )
2026-04-03 18:35:34.572183 INFO::Formatting Data.
2026-04-03 18:35:34.572844 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.573481 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.5741 INFO::Found 0 missing values.
2026-04-03 18:35:34.575511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.575876 INFO::Done
2026-04-03 18:35:34.576249 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.577413 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.577845 INFO::Found 5 batches.
2026-04-03 18:35:34.57819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.578611 INFO::Using default BPPARAM
2026-04-03 18:35:34.578939 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.636419 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.637633 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.644492 INFO::Done
2026-04-03 18:35:34.644933 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.646429 INFO::ASW Batch was 0.432178989435156 prior to batch effect correction and is now -0.0575630832294986 .
2026-04-03 18:35:34.646821 INFO::ASW Label was 0.310451157241553 prior to batch effect correction and is now 0.858274422737733 .
2026-04-03 18:35:34.647339 INFO::Total function execution time is 0.0752050876617432 s and adjustment time is 0.0666921138763428 s ( 88.68 )
2026-04-03 18:35:34.647827 INFO::Formatting Data.
2026-04-03 18:35:34.64845 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.648955 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.649468 INFO::Found 0 missing values.
2026-04-03 18:35:34.650814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.651138 INFO::Done
2026-04-03 18:35:34.651423 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.652521 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.652892 INFO::Found 5 batches.
2026-04-03 18:35:34.653191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.653557 INFO::Using default BPPARAM
2026-04-03 18:35:34.653909 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.710055 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.711736 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.719466 INFO::Done
2026-04-03 18:35:34.719922 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.721521 INFO::ASW Batch was 0.432178989435156 prior to batch effect correction and is now -0.0575630832294986 .
2026-04-03 18:35:34.721889 INFO::ASW Label was 0.310451157241553 prior to batch effect correction and is now 0.858274422737733 .
2026-04-03 18:35:34.722541 INFO::Total function execution time is 0.0746660232543945 s and adjustment time is 0.0666160583496094 s ( 89.22 )
2026-04-03 18:35:34.730153 INFO::Formatting Data.
2026-04-03 18:35:34.730625 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.731138 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.731728 INFO::Found 0 missing values.
2026-04-03 18:35:34.73275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.733085 INFO::Done
2026-04-03 18:35:34.733418 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.734486 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.734916 INFO::Found 2 batches.
2026-04-03 18:35:34.73573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.736232 INFO::Using default BPPARAM
2026-04-03 18:35:34.736583 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.737093 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.742382 INFO::Done
2026-04-03 18:35:34.742765 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.743897 INFO::ASW Batch was 0.534947552638281 prior to batch effect correction and is now 0.106949352648692 .
2026-04-03 18:35:34.744242 INFO::ASW Label was 0.598784789935349 prior to batch effect correction and is now 0.857147966039806 .
2026-04-03 18:35:34.744629 INFO::Total function execution time is 0.0145280361175537 s and adjustment time is 0.00750899314880371 s ( 51.69 )
2026-04-03 18:35:34.745181 INFO::Formatting Data.
2026-04-03 18:35:34.745542 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.745993 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.746462 INFO::Found 0 missing values.
2026-04-03 18:35:34.74744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.748076 INFO::Done
2026-04-03 18:35:34.748461 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.749702 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.750151 INFO::Found 2 batches.
2026-04-03 18:35:34.750486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.750861 INFO::Using default BPPARAM
2026-04-03 18:35:34.751193 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.751622 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 18:35:34.756449 INFO::Done
2026-04-03 18:35:34.75687 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.757918 INFO::ASW Batch was 0.534947552638281 prior to batch effect correction and is now 0.106949352648692 .
2026-04-03 18:35:34.758277 INFO::ASW Label was 0.598784789935349 prior to batch effect correction and is now 0.857147966039806 .
2026-04-03 18:35:34.758682 INFO::Total function execution time is 0.0135021209716797 s and adjustment time is 0.00635409355163574 s ( 47.06 )
2026-04-03 18:35:34.763383 INFO::Formatting Data.
2026-04-03 18:35:34.763791 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.764224 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.76467 INFO::Found 0 missing values.
2026-04-03 18:35:34.765682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.766042 INFO::Done
2026-04-03 18:35:34.76638 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.76717 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.767542 INFO::Found 2 batches.
2026-04-03 18:35:34.767873 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.768203 INFO::Using default BPPARAM
2026-04-03 18:35:34.768543 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.768946 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 18:35:34.780688 INFO::Done
2026-04-03 18:35:34.781112 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.78188 INFO::ASW Batch was 0.112890511183955 prior to batch effect correction and is now -0.0971021991060648 .
2026-04-03 18:35:34.78231 INFO::Total function execution time is 0.0189330577850342 s and adjustment time is 0.0131728649139404 s ( 69.58 )
2026-04-03 18:35:34.787326 INFO::Formatting Data.
2026-04-03 18:35:34.787731 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.788153 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.788626 INFO::Found 0 missing values.
2026-04-03 18:35:34.789303 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-03 18:35:34.790843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.79119 INFO::Done
2026-04-03 18:35:34.791538 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.792654 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.79308 INFO::Found 2 batches.
2026-04-03 18:35:34.793697 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.794203 INFO::Using default BPPARAM
2026-04-03 18:35:34.794534 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.79505 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 18:35:34.80052 INFO::Done
2026-04-03 18:35:34.80096 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.80205 INFO::ASW Batch was 0.628169344971189 prior to batch effect correction and is now -0.0339453593790872 .
2026-04-03 18:35:34.802391 INFO::ASW Label was 0.448172434409692 prior to batch effect correction and is now 0.914983969781796 .
2026-04-03 18:35:34.802809 INFO::Total function execution time is 0.0154948234558105 s and adjustment time is 0.00747394561767578 s ( 48.24 )
2026-04-03 18:35:34.803223 INFO::Formatting Data.
2026-04-03 18:35:34.803549 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.804004 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.804455 INFO::Found 0 missing values.
2026-04-03 18:35:34.804891 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-03 18:35:34.806393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.806741 INFO::Done
2026-04-03 18:35:34.807052 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.808123 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.808516 INFO::Found 2 batches.
2026-04-03 18:35:34.808826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.809193 INFO::Using default BPPARAM
2026-04-03 18:35:34.809506 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:34.809924 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 18:35:34.815014 INFO::Done
2026-04-03 18:35:34.815429 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.816493 INFO::ASW Batch was 0.628169344971189 prior to batch effect correction and is now -0.0339453593790872 .
2026-04-03 18:35:34.816879 INFO::ASW Label was 0.448172434409692 prior to batch effect correction and is now 0.914983969781796 .
2026-04-03 18:35:34.817284 INFO::Total function execution time is 0.0140540599822998 s and adjustment time is 0.00654006004333496 s ( 46.54 )
2026-04-03 18:35:34.920464 INFO::Formatting Data.
2026-04-03 18:35:34.920975 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.921523 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.92209 INFO::Found 0 missing values.
2026-04-03 18:35:34.923289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:34.923657 INFO::Done
2026-04-03 18:35:34.923982 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:34.925292 INFO::Starting hierarchical adjustment
2026-04-03 18:35:34.925792 INFO::Found 3 batches.
2026-04-03 18:35:34.926264 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:34.926705 INFO::Using default BPPARAM
2026-04-03 18:35:34.927148 INFO::Processing subtree level 1
2026-04-03 18:35:34.989771 INFO::Adjusting the last 1 batches sequentially
2026-04-03 18:35:34.991362 INFO::Done
2026-04-03 18:35:34.991897 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:34.994051 INFO::ASW Batch was -0.0335204714301559 prior to batch effect correction and is now -0.0335204714301559 .
2026-04-03 18:35:34.99477 INFO::Total function execution time is 0.0742921829223633 s and adjustment time is 0.0656900405883789 s ( 88.42 )
2026-04-03 18:35:34.995423 INFO::Formatting Data.
2026-04-03 18:35:34.995847 INFO::Typecasting input to dataframe.
2026-04-03 18:35:34.996326 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:34.997106 INFO::Removing potential empty rows and columns
2026-04-03 18:35:34.997904 INFO::Found 0 missing values.
2026-04-03 18:35:34.999852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:35.000279 INFO::Done
2026-04-03 18:35:35.000685 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:35.00191 INFO::Starting hierarchical adjustment
2026-04-03 18:35:35.00241 INFO::Found 3 batches.
2026-04-03 18:35:35.00279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:35.003219 INFO::Using default BPPARAM
2026-04-03 18:35:35.003608 INFO::Processing subtree level 1
2026-04-03 18:35:35.056064 INFO::Adjusting the last 1 batches sequentially
2026-04-03 18:35:35.057693 INFO::Done
2026-04-03 18:35:35.058118 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:35.059842 INFO::ASW Batch was -0.0335204714301559 prior to batch effect correction and is now -0.0335204714301559 .
2026-04-03 18:35:35.060616 INFO::Total function execution time is 0.0651290416717529 s and adjustment time is 0.0553600788116455 s ( 85 )
2026-04-03 18:35:35.06914 INFO::Formatting Data.
2026-04-03 18:35:35.069672 INFO::Typecasting input to dataframe.
2026-04-03 18:35:35.070168 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:35.071013 INFO::Removing potential empty rows and columns
2026-04-03 18:35:35.071859 INFO::Found 0 missing values.
2026-04-03 18:35:35.07346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:35.073842 INFO::Done
2026-04-03 18:35:35.074218 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:35.075296 INFO::Starting hierarchical adjustment
2026-04-03 18:35:35.075753 INFO::Found 3 batches.
2026-04-03 18:35:35.07612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:35.076568 INFO::Using default BPPARAM
2026-04-03 18:35:35.076949 INFO::Processing subtree level 1
2026-04-03 18:35:35.134433 INFO::Adjusting the last 1 batches sequentially
2026-04-03 18:35:35.136628 INFO::Done
2026-04-03 18:35:35.137273 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:35.139362 INFO::ASW Batch was -0.0122088498840494 prior to batch effect correction and is now -0.0122088498840494 .
2026-04-03 18:35:35.140527 INFO::Total function execution time is 0.0710511207580566 s and adjustment time is 0.0609121322631836 s ( 85.73 )
2026-04-03 18:35:35.225242 INFO::Formatting Data.
2026-04-03 18:35:35.225773 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:35.226414 INFO::Removing potential empty rows and columns
2026-04-03 18:35:35.22805 INFO::Found 1000 missing values.
2026-04-03 18:35:35.237933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:35.238385 INFO::Done
2026-04-03 18:35:35.238753 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:35.241244 INFO::Starting hierarchical adjustment
2026-04-03 18:35:35.241677 INFO::Found 10 batches.
2026-04-03 18:35:35.242018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:35.242429 INFO::Using default BPPARAM
2026-04-03 18:35:35.242773 INFO::Processing subtree level 1
2026-04-03 18:35:35.326154 INFO::Processing subtree level 2
2026-04-03 18:35:35.413771 INFO::Adjusting the last 1 batches sequentially
2026-04-03 18:35:35.41587 INFO::Done
2026-04-03 18:35:35.416359 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:35.420554 INFO::ASW Batch was 0.484036671701126 prior to batch effect correction and is now 0.484036671701126 .
2026-04-03 18:35:35.421176 INFO::ASW Label was 0.343777569837801 prior to batch effect correction and is now 0.343777569837801 .
2026-04-03 18:35:35.422136 INFO::Total function execution time is 0.196879148483276 s and adjustment time is 0.174227952957153 s ( 88.49 )
2026-04-03 18:35:35.422822 INFO::Formatting Data.
2026-04-03 18:35:35.423191 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:35.423997 INFO::Removing potential empty rows and columns
2026-04-03 18:35:35.426494 INFO::Found 1000 missing values.
2026-04-03 18:35:35.438157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:35.438655 INFO::Done
2026-04-03 18:35:35.438989 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:35.44155 INFO::Starting hierarchical adjustment
2026-04-03 18:35:35.442053 INFO::Found 10 batches.
2026-04-03 18:35:36.009641 INFO::Set up parallel execution backend with 2 workers
2026-04-03 18:35:36.010207 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-03 18:35:36.638646 INFO::Adjusting the last 2 batches sequentially
2026-04-03 18:35:36.639592 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 18:35:36.645739 INFO::Done
2026-04-03 18:35:36.646166 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:36.648192 INFO::ASW Batch was 0.484036671701126 prior to batch effect correction and is now 0.484036671701126 .
2026-04-03 18:35:36.648555 INFO::ASW Label was 0.343777569837801 prior to batch effect correction and is now 0.343777569837801 .
2026-04-03 18:35:36.648943 INFO::Total function execution time is 1.22616386413574 s and adjustment time is 1.20375800132751 s ( 98.17 )
2026-04-03 18:35:36.813718 INFO::Formatting Data.
2026-04-03 18:35:36.81414 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:36.814598 INFO::Removing potential empty rows and columns
2026-04-03 18:35:36.815155 INFO::Found 0 missing values.
2026-04-03 18:35:36.816537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:36.816848 INFO::Done
2026-04-03 18:35:36.817164 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 18:35:36.818505 INFO::Starting hierarchical adjustment
2026-04-03 18:35:36.819051 INFO::Found 3 batches.
2026-04-03 18:35:36.819423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 18:35:36.819866 INFO::Using default BPPARAM
2026-04-03 18:35:36.820236 INFO::Processing subtree level 1
2026-04-03 18:35:36.882351 INFO::Adjusting the last 1 batches sequentially
2026-04-03 18:35:36.884049 INFO::Done
2026-04-03 18:35:36.88452 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 18:35:36.886061 INFO::ASW Batch was 0.312669482648567 prior to batch effect correction and is now -0.146406043848835 .
2026-04-03 18:35:36.886464 INFO::ASW Label was -0.211776545026199 prior to batch effect correction and is now -0.0745633646855037 .
2026-04-03 18:35:36.887089 INFO::Total function execution time is 0.0733790397644043 s and adjustment time is 0.0650830268859863 s ( 88.69 )
2026-04-03 18:35:36.942452 INFO::Formatting Data.
2026-04-03 18:35:36.942948 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:36.943425 INFO::Removing potential empty rows and columns
2026-04-03 18:35:36.943947 INFO::Found 2 missing values.
2026-04-03 18:35:36.945055 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:36.945382 INFO::Done
2026-04-03 18:35:36.959161 INFO::Found NA in Reference column
2026-04-03 18:35:36.964257 INFO::Require at least two references per batch.
2026-04-03 18:35:36.97378 INFO::Formatting Data.
2026-04-03 18:35:36.974222 INFO::Recognized SummarizedExperiment
2026-04-03 18:35:36.974527 INFO::Typecasting input to dataframe.
2026-04-03 18:35:36.979372 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:36.979967 INFO::Removing potential empty rows and columns
2026-04-03 18:35:36.981599 INFO::Found 0 missing values.
2026-04-03 18:35:36.984435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:36.984767 INFO::Done
2026-04-03 18:35:36.990958 INFO::Formatting Data.
2026-04-03 18:35:36.991374 INFO::Recognized SummarizedExperiment
2026-04-03 18:35:36.99167 INFO::Typecasting input to dataframe.
2026-04-03 18:35:36.998168 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:36.998736 INFO::Removing potential empty rows and columns
2026-04-03 18:35:37.000336 INFO::Found 0 missing values.
2026-04-03 18:35:37.004769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:37.005093 INFO::Done
2026-04-03 18:35:37.010791 INFO::Formatting Data.
2026-04-03 18:35:37.011228 INFO::Recognized SummarizedExperiment
2026-04-03 18:35:37.011522 INFO::Typecasting input to dataframe.
2026-04-03 18:35:37.01743 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:37.017912 INFO::Removing potential empty rows and columns
2026-04-03 18:35:37.018421 INFO::Found 0 missing values.
2026-04-03 18:35:37.018957 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-03 18:35:37.020837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:37.021323 INFO::Done
2026-04-03 18:35:37.02572 INFO::Formatting Data.
2026-04-03 18:35:37.026109 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:37.026532 INFO::Removing potential empty rows and columns
2026-04-03 18:35:37.026991 INFO::Found 0 missing values.
2026-04-03 18:35:37.028181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:37.028485 INFO::Done
2026-04-03 18:35:37.033542 INFO::Formatting Data.
2026-04-03 18:35:37.033957 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:37.034351 INFO::Removing potential empty rows and columns
2026-04-03 18:35:37.034805 INFO::Found 0 missing values.
2026-04-03 18:35:37.035793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:37.036077 INFO::Done
2026-04-03 18:35:37.048347 INFO::Formatting Data.
2026-04-03 18:35:37.048817 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:37.049286 INFO::Removing potential empty rows and columns
2026-04-03 18:35:37.049794 INFO::Found 1 missing values.
2026-04-03 18:35:37.050797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:37.05107 INFO::Done
2026-04-03 18:35:37.059317 INFO::Formatting Data.
2026-04-03 18:35:37.059764 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:37.060152 INFO::Removing potential empty rows and columns
2026-04-03 18:35:37.060594 INFO::Found 2 missing values.
2026-04-03 18:35:37.060996 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-03 18:35:37.061982 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:37.062277 INFO::Done
2026-04-03 18:35:37.06665 INFO::Formatting Data.
2026-04-03 18:35:37.067057 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:37.067469 INFO::Removing potential empty rows and columns
2026-04-03 18:35:37.067894 INFO::Found 2 missing values.
2026-04-03 18:35:37.068592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:37.0689 INFO::Done
2026-04-03 18:35:37.073938 INFO::Formatting Data.
2026-04-03 18:35:37.074327 INFO::Typecasting input to dataframe.
2026-04-03 18:35:37.074712 INFO::Replacing NaNs with NAs.
2026-04-03 18:35:37.075173 INFO::Removing potential empty rows and columns
2026-04-03 18:35:37.075724 INFO::Found 0 missing values.
2026-04-03 18:35:37.076761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 18:35:37.077043 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.139 2.174 9.876
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.563 | 0.346 | 6.831 | |
| compute_asw | 0.010 | 0.000 | 0.009 | |
| count_existing | 0.005 | 0.001 | 0.006 | |
| generate_data_covariables | 0.005 | 0.001 | 0.017 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |