Yannis Schumann
| Snapshot Date: 2026-03-13 13:45 -0400 (Fri, 13 Mar 2026) |
| 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-14 11:57 -0400 (Sat, 14 Mar 2026).
| 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" | 4892 |
| 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 | | ||||||||
| 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-03-13 21:23:41 -0400 (Fri, 13 Mar 2026) |
| EndedAt: 2026-03-13 21:25:11 -0400 (Fri, 13 Mar 2026) |
| EllapsedTime: 90.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 24.623 1.313 17.758
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
2026-03-13 21:24:33.588306 INFO::Formatting Data.
2026-03-13 21:24:33.589644 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:33.600856 INFO::Removing potential empty rows and columns
2026-03-13 21:24:33.853345 INFO::Found 0 missing values.
2026-03-13 21:24:33.857046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:33.857805 INFO::Done
2026-03-13 21:24:33.858403 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:33.870579 INFO::Starting hierarchical adjustment
2026-03-13 21:24:33.871611 INFO::Found 3 batches.
2026-03-13 21:24:33.872229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:33.873592 INFO::Using default BPPARAM
2026-03-13 21:24:33.874199 INFO::Processing subtree level 1
2026-03-13 21:24:33.995939 INFO::Adjusting the last 1 batches sequentially
2026-03-13 21:24:33.997884 INFO::Done
2026-03-13 21:24:33.998599 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:34.00132 INFO::ASW Batch was -0.0824675781743733 prior to batch effect correction and is now -0.0824675781743733 .
2026-03-13 21:24:34.002491 INFO::Total function execution time is 0.414815187454224 s and adjustment time is 0.12651252746582 s ( 30.5 )
2026-03-13 21:24:34.017614 INFO::Formatting Data.
2026-03-13 21:24:34.018597 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:34.019676 INFO::Removing potential empty rows and columns
2026-03-13 21:24:34.020965 INFO::Found 0 missing values.
2026-03-13 21:24:34.022034 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.
2026-03-13 21:24:34.03392 INFO::Formatting Data.
2026-03-13 21:24:34.03484 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:34.035869 INFO::Removing potential empty rows and columns
2026-03-13 21:24:34.037009 INFO::Found 0 missing values.
2026-03-13 21:24:34.038031 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.
2026-03-13 21:24:34.055266 INFO::Formatting Data.
2026-03-13 21:24:34.056139 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:34.057252 INFO::Removing potential empty rows and columns
2026-03-13 21:24:34.058595 INFO::Found 0 missing values.
2026-03-13 21:24:34.059736 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.
2026-03-13 21:24:34.065464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:34.066171 INFO::Done
2026-03-13 21:24:34.066821 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:34.069173 INFO::Starting hierarchical adjustment
2026-03-13 21:24:34.070033 INFO::Found 2 batches.
2026-03-13 21:24:34.07068 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:34.07145 INFO::Using default BPPARAM
2026-03-13 21:24:34.072094 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:34.073251 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-13 21:24:34.097921 INFO::Done
2026-03-13 21:24:34.098721 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:34.101185 INFO::ASW Batch was -0.0375664723360277 prior to batch effect correction and is now -0.0984514172249298 .
2026-03-13 21:24:34.10209 INFO::Total function execution time is 0.046945333480835 s and adjustment time is 0.0280282497406006 s ( 59.7 )
2026-03-13 21:24:34.105283 INFO::Formatting Data.
2026-03-13 21:24:34.105984 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:34.115639 INFO::Formatting Data.
2026-03-13 21:24:34.11648 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:34.11748 INFO::Removing potential empty rows and columns
2026-03-13 21:24:34.118608 INFO::Found 0 missing values.
2026-03-13 21:24:34.121757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:34.122337 INFO::Done
2026-03-13 21:24:34.12289 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:34.152366 INFO::Starting hierarchical adjustment
2026-03-13 21:24:34.154059 INFO::Found 2 batches.
2026-03-13 21:24:34.154675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:34.155244 INFO::Using default BPPARAM
2026-03-13 21:24:34.155764 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:34.156742 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-13 21:24:34.172079 INFO::Done
2026-03-13 21:24:34.172858 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:34.174989 INFO::ASW Batch was 0.0150622263235749 prior to batch effect correction and is now -0.113169385980575 .
2026-03-13 21:24:34.175828 INFO::Total function execution time is 0.0602970123291016 s and adjustment time is 0.0182023048400879 s ( 30.19 )
2026-03-13 21:24:34.176879 INFO::Formatting Data.
2026-03-13 21:24:34.177467 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:34.178346 INFO::Removing potential empty rows and columns
2026-03-13 21:24:34.179363 INFO::Found 0 missing values.
2026-03-13 21:24:34.182133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:34.182678 INFO::Done
2026-03-13 21:24:34.183187 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:34.185376 INFO::Starting hierarchical adjustment
2026-03-13 21:24:34.186129 INFO::Found 2 batches.
2026-03-13 21:24:34.186642 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:34.187219 INFO::Using default BPPARAM
2026-03-13 21:24:34.187734 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:34.188646 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-13 21:24:34.204097 INFO::Done
2026-03-13 21:24:34.204839 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:34.20699 INFO::ASW Batch was 0.0150622263235749 prior to batch effect correction and is now -0.113169385980575 .
2026-03-13 21:24:34.207817 INFO::Total function execution time is 0.0309364795684814 s and adjustment time is 0.0180749893188477 s ( 58.43 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-13 21:24:37.579578 INFO::Formatting Data.
2026-03-13 21:24:37.580419 INFO::Recognized SummarizedExperiment
2026-03-13 21:24:37.580955 INFO::Typecasting input to dataframe.
2026-03-13 21:24:37.622494 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:37.623914 INFO::Removing potential empty rows and columns
2026-03-13 21:24:37.628306 INFO::Found 0 missing values.
2026-03-13 21:24:37.635851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:37.636527 INFO::Done
2026-03-13 21:24:37.637069 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:37.641159 INFO::Starting hierarchical adjustment
2026-03-13 21:24:37.641922 INFO::Found 2 batches.
2026-03-13 21:24:37.642445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:37.643796 INFO::Using default BPPARAM
2026-03-13 21:24:37.644346 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:37.645432 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-13 21:24:37.706555 INFO::Done
2026-03-13 21:24:37.707255 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:37.710889 INFO::ASW Batch was 0.0137818723082958 prior to batch effect correction and is now -0.0960099770779125 .
2026-03-13 21:24:37.711741 INFO::Total function execution time is 0.132546424865723 s and adjustment time is 0.0647618770599365 s ( 48.86 )
Warning: stack imbalance in '{', 73 then 75
2026-03-13 21:24:37.732587 INFO::Formatting Data.
2026-03-13 21:24:37.733453 INFO::Recognized SummarizedExperiment
2026-03-13 21:24:37.734023 INFO::Typecasting input to dataframe.
2026-03-13 21:24:37.743212 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:37.74432 INFO::Removing potential empty rows and columns
2026-03-13 21:24:37.748008 INFO::Found 0 missing values.
2026-03-13 21:24:37.755284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:37.755859 INFO::Done
2026-03-13 21:24:37.756362 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:37.7599 INFO::Starting hierarchical adjustment
2026-03-13 21:24:37.760607 INFO::Found 2 batches.
2026-03-13 21:24:37.761121 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:37.761719 INFO::Using default BPPARAM
2026-03-13 21:24:37.762236 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:37.763195 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-13 21:24:37.788437 INFO::Done
2026-03-13 21:24:37.789145 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:37.792699 INFO::ASW Batch was 0.003404509726015 prior to batch effect correction and is now 0.003404509726015 .
2026-03-13 21:24:37.793534 INFO::Total function execution time is 0.0609729290008545 s and adjustment time is 0.0279440879821777 s ( 45.83 )
2026-03-13 21:24:37.811841 INFO::Formatting Data.
2026-03-13 21:24:37.812608 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:37.813562 INFO::Removing potential empty rows and columns
2026-03-13 21:24:37.81457 INFO::Found 0 missing values.
2026-03-13 21:24:37.817594 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:37.818127 INFO::Done
2026-03-13 21:24:37.818648 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:37.820608 INFO::Starting hierarchical adjustment
2026-03-13 21:24:37.821294 INFO::Found 3 batches.
2026-03-13 21:24:37.821815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:37.822405 INFO::Using default BPPARAM
2026-03-13 21:24:37.822927 INFO::Processing subtree level 1
2026-03-13 21:24:37.955917 INFO::Adjusting the last 1 batches sequentially
2026-03-13 21:24:37.958017 INFO::Done
2026-03-13 21:24:37.958662 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:37.961157 INFO::ASW Batch was -0.0976136397671288 prior to batch effect correction and is now -0.169400608413749 .
2026-03-13 21:24:37.962087 INFO::Total function execution time is 0.150285005569458 s and adjustment time is 0.136834621429443 s ( 91.05 )
2026-03-13 21:24:37.97652 INFO::Skipping initial DF formatting
2026-03-13 21:24:37.977178 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:37.981111 INFO::Starting hierarchical adjustment
2026-03-13 21:24:37.981852 INFO::Found 5 batches.
2026-03-13 21:24:37.982383 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:37.983012 INFO::Using default BPPARAM
2026-03-13 21:24:37.98355 INFO::Processing subtree level 1
2026-03-13 21:24:38.200849 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:38.202428 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-13 21:24:38.22188 INFO::Done
2026-03-13 21:24:38.22259 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:38.226732 INFO::ASW Batch was 0.521824075778581 prior to batch effect correction and is now 0.521824075778581 .
2026-03-13 21:24:38.227298 INFO::ASW Label was 0.346405249288592 prior to batch effect correction and is now 0.346405249288592 .
2026-03-13 21:24:38.228127 INFO::Total function execution time is 0.251675367355347 s and adjustment time is 0.240165710449219 s ( 95.43 )
2026-03-13 21:24:38.288273 INFO::Formatting Data.
2026-03-13 21:24:38.289043 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:38.289936 INFO::Removing potential empty rows and columns
2026-03-13 21:24:38.290904 INFO::Found 0 missing values.
2026-03-13 21:24:38.294746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:38.295261 INFO::Done
2026-03-13 21:24:38.295782 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:38.298698 INFO::Starting hierarchical adjustment
2026-03-13 21:24:38.299381 INFO::Found 5 batches.
2026-03-13 21:24:38.29989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:38.300458 INFO::Using default BPPARAM
2026-03-13 21:24:38.300965 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.
2026-03-13 21:24:38.439026 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:38.440883 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-13 21:24:38.45939 INFO::Done
2026-03-13 21:24:38.460175 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:38.463835 INFO::ASW Batch was 0.342153319316147 prior to batch effect correction and is now -0.0985722030622897 .
2026-03-13 21:24:38.464452 INFO::ASW Label was 0.326647486184119 prior to batch effect correction and is now 0.877343488040061 .
2026-03-13 21:24:38.465287 INFO::Total function execution time is 0.177087545394897 s and adjustment time is 0.160099744796753 s ( 90.41 )
2026-03-13 21:24:38.466165 INFO::Formatting Data.
2026-03-13 21:24:38.466835 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:38.467748 INFO::Removing potential empty rows and columns
2026-03-13 21:24:38.468847 INFO::Found 0 missing values.
2026-03-13 21:24:38.473418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:38.473996 INFO::Done
2026-03-13 21:24:38.474524 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:38.477592 INFO::Starting hierarchical adjustment
2026-03-13 21:24:38.4783 INFO::Found 5 batches.
2026-03-13 21:24:38.478884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:38.479527 INFO::Using default BPPARAM
2026-03-13 21:24:38.480077 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.
2026-03-13 21:24:38.610576 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:38.612272 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-13 21:24:38.629029 INFO::Done
2026-03-13 21:24:38.629787 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:38.633404 INFO::ASW Batch was 0.342153319316147 prior to batch effect correction and is now -0.0985722030622897 .
2026-03-13 21:24:38.634073 INFO::ASW Label was 0.326647486184119 prior to batch effect correction and is now 0.877343488040061 .
2026-03-13 21:24:38.634891 INFO::Total function execution time is 0.168728351593018 s and adjustment time is 0.150841951370239 s ( 89.4 )
2026-03-13 21:24:38.648563 INFO::Formatting Data.
2026-03-13 21:24:38.649244 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:38.650209 INFO::Removing potential empty rows and columns
2026-03-13 21:24:38.65123 INFO::Found 0 missing values.
2026-03-13 21:24:38.663956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:38.66462 INFO::Done
2026-03-13 21:24:38.665187 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:38.668926 INFO::Starting hierarchical adjustment
2026-03-13 21:24:38.669725 INFO::Found 5 batches.
2026-03-13 21:24:38.670267 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:38.670947 INFO::Using default BPPARAM
2026-03-13 21:24:38.67148 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.
2026-03-13 21:24:38.811975 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:38.813917 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-13 21:24:38.832226 INFO::Done
2026-03-13 21:24:38.833054 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:38.836708 INFO::ASW Batch was 0.510658140073825 prior to batch effect correction and is now -0.0868924642203803 .
2026-03-13 21:24:38.837373 INFO::ASW Label was 0.166989791975741 prior to batch effect correction and is now 0.778806924935363 .
2026-03-13 21:24:38.83823 INFO::Total function execution time is 0.189688682556152 s and adjustment time is 0.162675857543945 s ( 85.76 )
2026-03-13 21:24:38.839142 INFO::Formatting Data.
2026-03-13 21:24:38.839832 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:38.840772 INFO::Removing potential empty rows and columns
2026-03-13 21:24:38.84188 INFO::Found 0 missing values.
2026-03-13 21:24:38.846278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:38.846879 INFO::Done
2026-03-13 21:24:38.847434 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:38.850534 INFO::Starting hierarchical adjustment
2026-03-13 21:24:38.851275 INFO::Found 5 batches.
2026-03-13 21:24:38.85182 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:38.85246 INFO::Using default BPPARAM
2026-03-13 21:24:38.853024 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.
2026-03-13 21:24:38.981027 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:38.982617 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-13 21:24:38.998942 INFO::Done
2026-03-13 21:24:38.999663 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.003307 INFO::ASW Batch was 0.510658140073825 prior to batch effect correction and is now -0.0868924642203803 .
2026-03-13 21:24:39.003925 INFO::ASW Label was 0.166989791975741 prior to batch effect correction and is now 0.778806924935363 .
2026-03-13 21:24:39.004716 INFO::Total function execution time is 0.165587425231934 s and adjustment time is 0.147788286209106 s ( 89.25 )
2026-03-13 21:24:39.017933 INFO::Formatting Data.
2026-03-13 21:24:39.01865 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.019545 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.020535 INFO::Found 0 missing values.
2026-03-13 21:24:39.023188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.023734 INFO::Done
2026-03-13 21:24:39.024236 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.027083 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.027786 INFO::Found 2 batches.
2026-03-13 21:24:39.028299 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.028914 INFO::Using default BPPARAM
2026-03-13 21:24:39.029433 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:39.030324 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-13 21:24:39.044341 INFO::Done
2026-03-13 21:24:39.04492 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.047671 INFO::ASW Batch was 0.547813709136669 prior to batch effect correction and is now 0.0367166489945609 .
2026-03-13 21:24:39.048217 INFO::ASW Label was 0.534679092266785 prior to batch effect correction and is now 0.905497642776715 .
2026-03-13 21:24:39.048944 INFO::Total function execution time is 0.0310702323913574 s and adjustment time is 0.0167007446289062 s ( 53.75 )
2026-03-13 21:24:39.049687 INFO::Formatting Data.
2026-03-13 21:24:39.050267 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.051082 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.052007 INFO::Found 0 missing values.
2026-03-13 21:24:39.05453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.055048 INFO::Done
2026-03-13 21:24:39.055557 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.058325 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.059086 INFO::Found 2 batches.
2026-03-13 21:24:39.059664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.060297 INFO::Using default BPPARAM
2026-03-13 21:24:39.060831 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:39.061696 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-13 21:24:39.075923 INFO::Done
2026-03-13 21:24:39.076547 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.079342 INFO::ASW Batch was 0.547813709136669 prior to batch effect correction and is now 0.0367166489945609 .
2026-03-13 21:24:39.079912 INFO::ASW Label was 0.534679092266785 prior to batch effect correction and is now 0.905497642776715 .
2026-03-13 21:24:39.08065 INFO::Total function execution time is 0.0309524536132812 s and adjustment time is 0.0169947147369385 s ( 54.91 )
2026-03-13 21:24:39.091289 INFO::Formatting Data.
2026-03-13 21:24:39.091996 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.092807 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.093666 INFO::Found 0 missing values.
2026-03-13 21:24:39.095628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.096136 INFO::Done
2026-03-13 21:24:39.096661 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.09839 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.099053 INFO::Found 2 batches.
2026-03-13 21:24:39.099557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.100127 INFO::Using default BPPARAM
2026-03-13 21:24:39.100651 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:39.101484 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-13 21:24:39.131444 INFO::Done
2026-03-13 21:24:39.132097 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.133938 INFO::ASW Batch was 0.0261122760470283 prior to batch effect correction and is now -0.138834923318267 .
2026-03-13 21:24:39.134709 INFO::Total function execution time is 0.0434505939483643 s and adjustment time is 0.0325019359588623 s ( 74.8 )
2026-03-13 21:24:39.14587 INFO::Formatting Data.
2026-03-13 21:24:39.146541 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.147345 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.14829 INFO::Found 0 missing values.
2026-03-13 21:24:39.149393 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.
2026-03-13 21:24:39.153661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.154169 INFO::Done
2026-03-13 21:24:39.154667 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.157404 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.158064 INFO::Found 2 batches.
2026-03-13 21:24:39.158569 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.159134 INFO::Using default BPPARAM
2026-03-13 21:24:39.159648 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:39.160499 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-13 21:24:39.175826 INFO::Done
2026-03-13 21:24:39.176395 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.179082 INFO::ASW Batch was 0.423366641213051 prior to batch effect correction and is now 0.294832138408662 .
2026-03-13 21:24:39.179626 INFO::ASW Label was 0.667463545504881 prior to batch effect correction and is now 0.733241432006898 .
2026-03-13 21:24:39.180339 INFO::Total function execution time is 0.0345149040222168 s and adjustment time is 0.0178921222686768 s ( 51.84 )
2026-03-13 21:24:39.181081 INFO::Formatting Data.
2026-03-13 21:24:39.181667 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.182517 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.183415 INFO::Found 0 missing values.
2026-03-13 21:24:39.184249 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.
2026-03-13 21:24:39.188373 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.188887 INFO::Done
2026-03-13 21:24:39.189358 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.192035 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.192695 INFO::Found 2 batches.
2026-03-13 21:24:39.193191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.193774 INFO::Using default BPPARAM
2026-03-13 21:24:39.194257 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:39.195129 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-13 21:24:39.210306 INFO::Done
2026-03-13 21:24:39.210888 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.213578 INFO::ASW Batch was 0.423366641213051 prior to batch effect correction and is now 0.294832138408662 .
2026-03-13 21:24:39.214104 INFO::ASW Label was 0.667463545504881 prior to batch effect correction and is now 0.733241432006898 .
2026-03-13 21:24:39.21485 INFO::Total function execution time is 0.0337800979614258 s and adjustment time is 0.0177454948425293 s ( 52.53 )
2026-03-13 21:24:39.407899 INFO::Formatting Data.
2026-03-13 21:24:39.408694 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.409582 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.410615 INFO::Found 0 missing values.
2026-03-13 21:24:39.413575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.414102 INFO::Done
2026-03-13 21:24:39.414628 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.416609 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.417302 INFO::Found 3 batches.
2026-03-13 21:24:39.417827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.418421 INFO::Using default BPPARAM
2026-03-13 21:24:39.418949 INFO::Processing subtree level 1
2026-03-13 21:24:39.505433 INFO::Adjusting the last 1 batches sequentially
2026-03-13 21:24:39.507146 INFO::Done
2026-03-13 21:24:39.507756 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.510114 INFO::ASW Batch was -0.0784547095614839 prior to batch effect correction and is now -0.0784547095614839 .
2026-03-13 21:24:39.511032 INFO::Total function execution time is 0.103185176849365 s and adjustment time is 0.0899710655212402 s ( 87.19 )
2026-03-13 21:24:39.512052 INFO::Formatting Data.
2026-03-13 21:24:39.512703 INFO::Typecasting input to dataframe.
2026-03-13 21:24:39.513438 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.514332 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.51541 INFO::Found 0 missing values.
2026-03-13 21:24:39.518456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.519002 INFO::Done
2026-03-13 21:24:39.519526 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.521521 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.52225 INFO::Found 3 batches.
2026-03-13 21:24:39.522801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.523402 INFO::Using default BPPARAM
2026-03-13 21:24:39.523943 INFO::Processing subtree level 1
2026-03-13 21:24:39.609112 INFO::Adjusting the last 1 batches sequentially
2026-03-13 21:24:39.610955 INFO::Done
2026-03-13 21:24:39.611624 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.61419 INFO::ASW Batch was -0.0784547095614839 prior to batch effect correction and is now -0.0784547095614839 .
2026-03-13 21:24:39.615192 INFO::Total function execution time is 0.10309624671936 s and adjustment time is 0.0888371467590332 s ( 86.17 )
2026-03-13 21:24:39.628311 INFO::Formatting Data.
2026-03-13 21:24:39.629127 INFO::Typecasting input to dataframe.
2026-03-13 21:24:39.629995 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.630897 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.631976 INFO::Found 0 missing values.
2026-03-13 21:24:39.634975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.635499 INFO::Done
2026-03-13 21:24:39.636029 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.638084 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.6388 INFO::Found 3 batches.
2026-03-13 21:24:39.639316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.63994 INFO::Using default BPPARAM
2026-03-13 21:24:39.640455 INFO::Processing subtree level 1
2026-03-13 21:24:39.725307 INFO::Adjusting the last 1 batches sequentially
2026-03-13 21:24:39.727137 INFO::Done
2026-03-13 21:24:39.727805 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:39.730264 INFO::ASW Batch was -0.0334322155048328 prior to batch effect correction and is now -0.0334322155048328 .
2026-03-13 21:24:39.731215 INFO::Total function execution time is 0.102929592132568 s and adjustment time is 0.0884497165679932 s ( 85.93 )
2026-03-13 21:24:39.86715 INFO::Formatting Data.
2026-03-13 21:24:39.867909 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:39.868992 INFO::Removing potential empty rows and columns
2026-03-13 21:24:39.872006 INFO::Found 1000 missing values.
2026-03-13 21:24:39.890911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:39.891634 INFO::Done
2026-03-13 21:24:39.89219 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:39.897591 INFO::Starting hierarchical adjustment
2026-03-13 21:24:39.898346 INFO::Found 10 batches.
2026-03-13 21:24:39.89889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:39.89952 INFO::Using default BPPARAM
2026-03-13 21:24:39.900047 INFO::Processing subtree level 1
2026-03-13 21:24:40.050556 INFO::Processing subtree level 2
2026-03-13 21:24:40.191591 INFO::Adjusting the last 1 batches sequentially
2026-03-13 21:24:40.193869 INFO::Done
2026-03-13 21:24:40.194614 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:40.200899 INFO::ASW Batch was 0.464005303979653 prior to batch effect correction and is now 0.464005303979653 .
2026-03-13 21:24:40.201797 INFO::ASW Label was 0.343691570250354 prior to batch effect correction and is now 0.343691570250354 .
2026-03-13 21:24:40.202849 INFO::Total function execution time is 0.335699558258057 s and adjustment time is 0.295648813247681 s ( 88.07 )
2026-03-13 21:24:40.203817 INFO::Formatting Data.
2026-03-13 21:24:40.204557 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:40.205973 INFO::Removing potential empty rows and columns
2026-03-13 21:24:40.2092 INFO::Found 1000 missing values.
2026-03-13 21:24:40.231346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:40.232174 INFO::Done
2026-03-13 21:24:40.232842 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:40.239053 INFO::Starting hierarchical adjustment
2026-03-13 21:24:40.239867 INFO::Found 10 batches.
2026-03-13 21:24:41.325669 INFO::Set up parallel execution backend with 2 workers
2026-03-13 21:24:41.32785 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-13 21:24:42.491428 INFO::Adjusting the last 2 batches sequentially
2026-03-13 21:24:42.493477 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-13 21:24:42.524244 INFO::Done
2026-03-13 21:24:42.524969 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:42.529996 INFO::ASW Batch was 0.464005303979653 prior to batch effect correction and is now 0.464005303979653 .
2026-03-13 21:24:42.530601 INFO::ASW Label was 0.343691570250354 prior to batch effect correction and is now 0.343691570250354 .
2026-03-13 21:24:42.531379 INFO::Total function execution time is 2.32760882377625 s and adjustment time is 2.284503698349 s ( 98.15 )
2026-03-13 21:24:42.707366 INFO::Formatting Data.
2026-03-13 21:24:42.708242 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:42.709226 INFO::Removing potential empty rows and columns
2026-03-13 21:24:42.710348 INFO::Found 0 missing values.
2026-03-13 21:24:42.714011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:42.714584 INFO::Done
2026-03-13 21:24:42.715095 INFO::Acquiring quality metrics before batch effect correction.
2026-03-13 21:24:42.717885 INFO::Starting hierarchical adjustment
2026-03-13 21:24:42.718611 INFO::Found 3 batches.
2026-03-13 21:24:42.719135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-13 21:24:42.719775 INFO::Using default BPPARAM
2026-03-13 21:24:42.720309 INFO::Processing subtree level 1
2026-03-13 21:24:42.866306 INFO::Adjusting the last 1 batches sequentially
2026-03-13 21:24:42.868457 INFO::Done
2026-03-13 21:24:42.869226 INFO::Acquiring quality metrics after batch effect correction.
2026-03-13 21:24:42.872791 INFO::ASW Batch was 0.281477383027276 prior to batch effect correction and is now -0.186946652642165 .
2026-03-13 21:24:42.873467 INFO::ASW Label was -0.180889759193805 prior to batch effect correction and is now 0.0192375934047977 .
2026-03-13 21:24:42.874459 INFO::Total function execution time is 0.167163133621216 s and adjustment time is 0.149955987930298 s ( 89.71 )
2026-03-13 21:24:43.030895 INFO::Formatting Data.
2026-03-13 21:24:43.031917 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.032953 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.034127 INFO::Found 2 missing values.
2026-03-13 21:24:43.037405 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.038006 INFO::Done
2026-03-13 21:24:43.069283 INFO::Found NA in Reference column
2026-03-13 21:24:43.080086 INFO::Require at least two references per batch.
2026-03-13 21:24:43.102572 INFO::Formatting Data.
2026-03-13 21:24:43.103402 INFO::Recognized SummarizedExperiment
2026-03-13 21:24:43.103979 INFO::Typecasting input to dataframe.
2026-03-13 21:24:43.114504 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.115756 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.119536 INFO::Found 0 missing values.
2026-03-13 21:24:43.126766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.127369 INFO::Done
2026-03-13 21:24:43.144674 INFO::Formatting Data.
2026-03-13 21:24:43.145501 INFO::Recognized SummarizedExperiment
2026-03-13 21:24:43.146123 INFO::Typecasting input to dataframe.
2026-03-13 21:24:43.165138 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.166492 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.170361 INFO::Found 0 missing values.
2026-03-13 21:24:43.182156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.1829 INFO::Done
2026-03-13 21:24:43.20054 INFO::Formatting Data.
2026-03-13 21:24:43.201355 INFO::Recognized SummarizedExperiment
2026-03-13 21:24:43.20193 INFO::Typecasting input to dataframe.
2026-03-13 21:24:43.220983 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.2222 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.223425 INFO::Found 0 missing values.
2026-03-13 21:24:43.224448 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.
2026-03-13 21:24:43.229201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.229813 INFO::Done
2026-03-13 21:24:43.241318 INFO::Formatting Data.
2026-03-13 21:24:43.242217 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.243165 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.244269 INFO::Found 0 missing values.
2026-03-13 21:24:43.247369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.247954 INFO::Done
2026-03-13 21:24:43.260668 INFO::Formatting Data.
2026-03-13 21:24:43.261595 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.262656 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.263733 INFO::Found 0 missing values.
2026-03-13 21:24:43.266681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.267232 INFO::Done
2026-03-13 21:24:43.302113 INFO::Formatting Data.
2026-03-13 21:24:43.303165 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.304343 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.305621 INFO::Found 1 missing values.
2026-03-13 21:24:43.308439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.309017 INFO::Done
2026-03-13 21:24:43.330204 INFO::Formatting Data.
2026-03-13 21:24:43.331096 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.332028 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.333028 INFO::Found 2 missing values.
2026-03-13 21:24:43.333973 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.
2026-03-13 21:24:43.336304 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.336862 INFO::Done
2026-03-13 21:24:43.347786 INFO::Formatting Data.
2026-03-13 21:24:43.348623 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.349562 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.350532 INFO::Found 2 missing values.
2026-03-13 21:24:43.352181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.352733 INFO::Done
2026-03-13 21:24:43.363898 INFO::Formatting Data.
2026-03-13 21:24:43.364843 INFO::Typecasting input to dataframe.
2026-03-13 21:24:43.365752 INFO::Replacing NaNs with NAs.
2026-03-13 21:24:43.366706 INFO::Removing potential empty rows and columns
2026-03-13 21:24:43.36777 INFO::Found 0 missing values.
2026-03-13 21:24:43.37091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-13 21:24:43.371483 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.978 3.962 21.593
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.623 | 1.313 | 17.758 | |
| compute_asw | 0.024 | 0.001 | 0.025 | |
| count_existing | 0.014 | 0.000 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.010 | 0.001 | 0.011 | |