Yannis Schumann
| Snapshot Date: 2026-01-12 13:45 -0500 (Mon, 12 Jan 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-15 11:59 -0500 (Thu, 15 Jan 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" | 4886 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4672 |
| 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-01-13 06:48:05 -0000 (Tue, 13 Jan 2026) |
| EndedAt: 2026-01-13 06:51:15 -0000 (Tue, 13 Jan 2026) |
| EllapsedTime: 189.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 28.351 1.669 20.767
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2026-01-13 06:50:59.025666 INFO::Formatting Data.
2026-01-13 06:50:59.027958 INFO::Replacing NaNs with NAs.
2026-01-13 06:50:59.045621 INFO::Removing potential empty rows and columns
2026-01-13 06:50:59.688735 INFO::Found 0 missing values.
2026-01-13 06:50:59.693518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:50:59.694355 INFO::Done
2026-01-13 06:50:59.695119 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:50:59.711435 INFO::Starting hierarchical adjustment
2026-01-13 06:50:59.712584 INFO::Found 3 batches.
2026-01-13 06:50:59.713406 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:50:59.714966 INFO::Using default BPPARAM
2026-01-13 06:50:59.715737 INFO::Processing subtree level 1
2026-01-13 06:50:59.842897 INFO::Adjusting the last 1 batches sequentially
2026-01-13 06:50:59.845432 INFO::Done
2026-01-13 06:50:59.846426 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:50:59.85026 INFO::ASW Batch was -0.0745328496114926 prior to batch effect correction and is now -0.0745328496114926 .
2026-01-13 06:50:59.851994 INFO::Total function execution time is 0.82733941078186 s and adjustment time is 0.132993698120117 s ( 16.07 )
2026-01-13 06:50:59.873115 INFO::Formatting Data.
2026-01-13 06:50:59.874227 INFO::Replacing NaNs with NAs.
2026-01-13 06:50:59.875525 INFO::Removing potential empty rows and columns
2026-01-13 06:50:59.87713 INFO::Found 0 missing values.
2026-01-13 06:50:59.878528 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.
2026-01-13 06:50:59.895128 INFO::Formatting Data.
2026-01-13 06:50:59.896115 INFO::Replacing NaNs with NAs.
2026-01-13 06:50:59.897384 INFO::Removing potential empty rows and columns
2026-01-13 06:50:59.898827 INFO::Found 0 missing values.
2026-01-13 06:50:59.900072 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.
2026-01-13 06:50:59.922956 INFO::Formatting Data.
2026-01-13 06:50:59.923962 INFO::Replacing NaNs with NAs.
2026-01-13 06:50:59.925212 INFO::Removing potential empty rows and columns
2026-01-13 06:50:59.926823 INFO::Found 0 missing values.
2026-01-13 06:50:59.92814 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.
2026-01-13 06:50:59.934638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:50:59.935526 INFO::Done
2026-01-13 06:50:59.936269 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:50:59.939054 INFO::Starting hierarchical adjustment
2026-01-13 06:50:59.940107 INFO::Found 2 batches.
2026-01-13 06:50:59.940892 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:50:59.941884 INFO::Using default BPPARAM
2026-01-13 06:50:59.942661 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:50:59.944045 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-13 06:50:59.97611 INFO::Done
2026-01-13 06:50:59.97708 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:50:59.98005 INFO::ASW Batch was -0.0567195292423977 prior to batch effect correction and is now -0.117039677503324 .
2026-01-13 06:50:59.981221 INFO::Total function execution time is 0.0583267211914062 s and adjustment time is 0.0361828804016113 s ( 62.03 )
2026-01-13 06:50:59.985063 INFO::Formatting Data.
2026-01-13 06:50:59.986056 INFO::Replacing NaNs with NAs.
2026-01-13 06:50:59.998694 INFO::Formatting Data.
2026-01-13 06:50:59.999749 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:00.001098 INFO::Removing potential empty rows and columns
2026-01-13 06:51:00.002677 INFO::Found 0 missing values.
2026-01-13 06:51:00.006981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:00.007965 INFO::Done
2026-01-13 06:51:00.008774 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:00.01169 INFO::Starting hierarchical adjustment
2026-01-13 06:51:00.012808 INFO::Found 2 batches.
2026-01-13 06:51:00.01362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:00.014596 INFO::Using default BPPARAM
2026-01-13 06:51:00.015637 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:00.017283 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-13 06:51:00.091609 INFO::Done
2026-01-13 06:51:00.092517 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:00.095546 INFO::ASW Batch was 0.0394019105766164 prior to batch effect correction and is now -0.0909613829387245 .
2026-01-13 06:51:00.096781 INFO::Total function execution time is 0.0981318950653076 s and adjustment time is 0.0790107250213623 s ( 80.51 )
2026-01-13 06:51:00.098441 INFO::Formatting Data.
2026-01-13 06:51:00.099346 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:00.100599 INFO::Removing potential empty rows and columns
2026-01-13 06:51:00.102122 INFO::Found 0 missing values.
2026-01-13 06:51:00.106579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:00.107517 INFO::Done
2026-01-13 06:51:00.108294 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:00.1114 INFO::Starting hierarchical adjustment
2026-01-13 06:51:00.112571 INFO::Found 2 batches.
2026-01-13 06:51:00.113417 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:00.114287 INFO::Using default BPPARAM
2026-01-13 06:51:00.115039 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:00.116369 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-13 06:51:00.140069 INFO::Done
2026-01-13 06:51:00.141071 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:00.143907 INFO::ASW Batch was 0.0394019105766164 prior to batch effect correction and is now -0.0909613829387245 .
2026-01-13 06:51:00.145035 INFO::Total function execution time is 0.0465805530548096 s and adjustment time is 0.0276961326599121 s ( 59.46 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-13 06:51:04.052325 INFO::Formatting Data.
2026-01-13 06:51:04.053331 INFO::Recognized SummarizedExperiment
2026-01-13 06:51:04.054017 INFO::Typecasting input to dataframe.
2026-01-13 06:51:04.097229 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:04.098898 INFO::Removing potential empty rows and columns
2026-01-13 06:51:04.104367 INFO::Found 0 missing values.
2026-01-13 06:51:04.115171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:04.116075 INFO::Done
2026-01-13 06:51:04.116827 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:04.122082 INFO::Starting hierarchical adjustment
2026-01-13 06:51:04.12322 INFO::Found 2 batches.
2026-01-13 06:51:04.123973 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:04.125488 INFO::Using default BPPARAM
2026-01-13 06:51:04.126279 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:04.127652 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-13 06:51:04.20834 INFO::Done
2026-01-13 06:51:04.20926 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:04.214276 INFO::ASW Batch was -0.0120404288398931 prior to batch effect correction and is now -0.0967344654027216 .
2026-01-13 06:51:04.215525 INFO::Total function execution time is 0.163726806640625 s and adjustment time is 0.0853314399719238 s ( 52.12 )
Warning: stack imbalance in '{', 73 then 75
2026-01-13 06:51:04.242928 INFO::Formatting Data.
2026-01-13 06:51:04.243902 INFO::Recognized SummarizedExperiment
2026-01-13 06:51:04.244692 INFO::Typecasting input to dataframe.
2026-01-13 06:51:04.258661 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:04.260286 INFO::Removing potential empty rows and columns
2026-01-13 06:51:04.265644 INFO::Found 0 missing values.
2026-01-13 06:51:04.276466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:04.277474 INFO::Done
2026-01-13 06:51:04.278289 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:04.283296 INFO::Starting hierarchical adjustment
2026-01-13 06:51:04.284435 INFO::Found 2 batches.
2026-01-13 06:51:04.285224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:04.286091 INFO::Using default BPPARAM
2026-01-13 06:51:04.286823 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:04.288219 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-13 06:51:04.323857 INFO::Done
2026-01-13 06:51:04.324729 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:04.329657 INFO::ASW Batch was -0.0129077263115926 prior to batch effect correction and is now -0.0129077263115926 .
2026-01-13 06:51:04.330933 INFO::Total function execution time is 0.0879931449890137 s and adjustment time is 0.0396280288696289 s ( 45.04 )
2026-01-13 06:51:04.356049 INFO::Formatting Data.
2026-01-13 06:51:04.357113 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:04.358351 INFO::Removing potential empty rows and columns
2026-01-13 06:51:04.359741 INFO::Found 0 missing values.
2026-01-13 06:51:04.364065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:04.364983 INFO::Done
2026-01-13 06:51:04.365762 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:04.368418 INFO::Starting hierarchical adjustment
2026-01-13 06:51:04.369517 INFO::Found 3 batches.
2026-01-13 06:51:04.370249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:04.371069 INFO::Using default BPPARAM
2026-01-13 06:51:04.371803 INFO::Processing subtree level 1
2026-01-13 06:51:04.54228 INFO::Adjusting the last 1 batches sequentially
2026-01-13 06:51:04.544832 INFO::Done
2026-01-13 06:51:04.545721 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:04.549192 INFO::ASW Batch was -0.0922939426237172 prior to batch effect correction and is now -0.178843286827662 .
2026-01-13 06:51:04.550539 INFO::Total function execution time is 0.194517850875854 s and adjustment time is 0.175482749938965 s ( 90.21 )
2026-01-13 06:51:04.570595 INFO::Skipping initial DF formatting
2026-01-13 06:51:04.571619 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:04.577659 INFO::Starting hierarchical adjustment
2026-01-13 06:51:04.578874 INFO::Found 5 batches.
2026-01-13 06:51:04.579717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:04.580652 INFO::Using default BPPARAM
2026-01-13 06:51:04.581551 INFO::Processing subtree level 1
2026-01-13 06:51:04.844974 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:04.847199 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-13 06:51:04.875154 INFO::Done
2026-01-13 06:51:04.876055 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:04.881935 INFO::ASW Batch was 0.535638130478777 prior to batch effect correction and is now 0.535638130478777 .
2026-01-13 06:51:04.882842 INFO::ASW Label was 0.347635732091497 prior to batch effect correction and is now 0.347635732091497 .
2026-01-13 06:51:04.884022 INFO::Total function execution time is 0.313524007797241 s and adjustment time is 0.296512603759766 s ( 94.57 )
2026-01-13 06:51:04.977993 INFO::Formatting Data.
2026-01-13 06:51:04.979052 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:04.980419 INFO::Removing potential empty rows and columns
2026-01-13 06:51:04.981946 INFO::Found 0 missing values.
2026-01-13 06:51:04.988244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:04.989168 INFO::Done
2026-01-13 06:51:04.989988 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:04.994246 INFO::Starting hierarchical adjustment
2026-01-13 06:51:04.995375 INFO::Found 5 batches.
2026-01-13 06:51:04.996219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:04.997234 INFO::Using default BPPARAM
2026-01-13 06:51:04.998172 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.
2026-01-13 06:51:05.16498 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:05.167365 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-13 06:51:05.193617 INFO::Done
2026-01-13 06:51:05.19462 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:05.199552 INFO::ASW Batch was 0.41234966546551 prior to batch effect correction and is now -0.0394048477608079 .
2026-01-13 06:51:05.200566 INFO::ASW Label was 0.401856640689198 prior to batch effect correction and is now 0.786216618846017 .
2026-01-13 06:51:05.201863 INFO::Total function execution time is 0.223943710327148 s and adjustment time is 0.198437213897705 s ( 88.61 )
2026-01-13 06:51:05.20318 INFO::Formatting Data.
2026-01-13 06:51:05.204125 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:05.20555 INFO::Removing potential empty rows and columns
2026-01-13 06:51:05.207203 INFO::Found 0 missing values.
2026-01-13 06:51:05.214261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:05.215206 INFO::Done
2026-01-13 06:51:05.215994 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:05.220598 INFO::Starting hierarchical adjustment
2026-01-13 06:51:05.221847 INFO::Found 5 batches.
2026-01-13 06:51:05.222667 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:05.2236 INFO::Using default BPPARAM
2026-01-13 06:51:05.224416 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.
2026-01-13 06:51:05.381407 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:05.383474 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-13 06:51:05.407393 INFO::Done
2026-01-13 06:51:05.408316 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:05.413089 INFO::ASW Batch was 0.41234966546551 prior to batch effect correction and is now -0.0394048477608079 .
2026-01-13 06:51:05.414126 INFO::ASW Label was 0.401856640689198 prior to batch effect correction and is now 0.786216618846017 .
2026-01-13 06:51:05.415316 INFO::Total function execution time is 0.212156534194946 s and adjustment time is 0.185757398605347 s ( 87.56 )
2026-01-13 06:51:05.435479 INFO::Formatting Data.
2026-01-13 06:51:05.436521 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:05.437847 INFO::Removing potential empty rows and columns
2026-01-13 06:51:05.439291 INFO::Found 0 missing values.
2026-01-13 06:51:05.445802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:05.446728 INFO::Done
2026-01-13 06:51:05.447517 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:05.451934 INFO::Starting hierarchical adjustment
2026-01-13 06:51:05.45312 INFO::Found 5 batches.
2026-01-13 06:51:05.453983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:05.454891 INFO::Using default BPPARAM
2026-01-13 06:51:05.455709 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.
2026-01-13 06:51:05.61209 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:05.614448 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-13 06:51:05.638677 INFO::Done
2026-01-13 06:51:05.639691 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:05.644329 INFO::ASW Batch was 0.272946732185456 prior to batch effect correction and is now -0.0485653906474911 .
2026-01-13 06:51:05.645276 INFO::ASW Label was 0.478864601857508 prior to batch effect correction and is now 0.870680313966088 .
2026-01-13 06:51:05.646518 INFO::Total function execution time is 0.211317539215088 s and adjustment time is 0.185783386230469 s ( 87.92 )
2026-01-13 06:51:05.647736 INFO::Formatting Data.
2026-01-13 06:51:05.648703 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:05.650143 INFO::Removing potential empty rows and columns
2026-01-13 06:51:05.651661 INFO::Found 0 missing values.
2026-01-13 06:51:05.667358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:05.668465 INFO::Done
2026-01-13 06:51:05.669418 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:05.674868 INFO::Starting hierarchical adjustment
2026-01-13 06:51:05.676214 INFO::Found 5 batches.
2026-01-13 06:51:05.677114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:05.678213 INFO::Using default BPPARAM
2026-01-13 06:51:05.679051 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.
2026-01-13 06:51:05.834196 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:05.836307 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-13 06:51:05.861952 INFO::Done
2026-01-13 06:51:05.863046 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:05.868278 INFO::ASW Batch was 0.272946732185456 prior to batch effect correction and is now -0.0485653906474911 .
2026-01-13 06:51:05.869389 INFO::ASW Label was 0.478864601857508 prior to batch effect correction and is now 0.870680313966088 .
2026-01-13 06:51:05.871093 INFO::Total function execution time is 0.22325587272644 s and adjustment time is 0.185992240905762 s ( 83.31 )
2026-01-13 06:51:05.891194 INFO::Formatting Data.
2026-01-13 06:51:05.892261 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:05.893631 INFO::Removing potential empty rows and columns
2026-01-13 06:51:05.895174 INFO::Found 0 missing values.
2026-01-13 06:51:05.899402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:05.900365 INFO::Done
2026-01-13 06:51:05.901234 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:05.905604 INFO::Starting hierarchical adjustment
2026-01-13 06:51:05.906766 INFO::Found 2 batches.
2026-01-13 06:51:05.907563 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:05.908487 INFO::Using default BPPARAM
2026-01-13 06:51:05.909308 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:05.910714 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-13 06:51:05.931827 INFO::Done
2026-01-13 06:51:05.932774 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:05.936929 INFO::ASW Batch was 0.581770051527487 prior to batch effect correction and is now 0.105933853908136 .
2026-01-13 06:51:05.937827 INFO::ASW Label was 0.53580164512262 prior to batch effect correction and is now 0.820186414665497 .
2026-01-13 06:51:05.938949 INFO::Total function execution time is 0.0478363037109375 s and adjustment time is 0.0252771377563477 s ( 52.84 )
2026-01-13 06:51:05.94003 INFO::Formatting Data.
2026-01-13 06:51:05.940933 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:05.942232 INFO::Removing potential empty rows and columns
2026-01-13 06:51:05.943694 INFO::Found 0 missing values.
2026-01-13 06:51:05.947686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:05.948534 INFO::Done
2026-01-13 06:51:05.949324 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:05.953468 INFO::Starting hierarchical adjustment
2026-01-13 06:51:05.954585 INFO::Found 2 batches.
2026-01-13 06:51:05.955363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:05.956243 INFO::Using default BPPARAM
2026-01-13 06:51:05.957046 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:05.95842 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-13 06:51:05.979593 INFO::Done
2026-01-13 06:51:05.980512 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:05.984664 INFO::ASW Batch was 0.581770051527487 prior to batch effect correction and is now 0.105933853908136 .
2026-01-13 06:51:05.985589 INFO::ASW Label was 0.53580164512262 prior to batch effect correction and is now 0.820186414665497 .
2026-01-13 06:51:05.986707 INFO::Total function execution time is 0.0466740131378174 s and adjustment time is 0.0252082347869873 s ( 54.01 )
2026-01-13 06:51:06.002868 INFO::Formatting Data.
2026-01-13 06:51:06.003895 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:06.005141 INFO::Removing potential empty rows and columns
2026-01-13 06:51:06.006485 INFO::Found 0 missing values.
2026-01-13 06:51:06.009694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:06.010573 INFO::Done
2026-01-13 06:51:06.011357 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:06.014191 INFO::Starting hierarchical adjustment
2026-01-13 06:51:06.015291 INFO::Found 2 batches.
2026-01-13 06:51:06.016102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:06.01703 INFO::Using default BPPARAM
2026-01-13 06:51:06.017864 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:06.019225 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-13 06:51:06.066391 INFO::Done
2026-01-13 06:51:06.067337 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:06.070061 INFO::ASW Batch was 0.12812796232709 prior to batch effect correction and is now -0.152666330735698 .
2026-01-13 06:51:06.071223 INFO::Total function execution time is 0.0684349536895752 s and adjustment time is 0.0512919425964355 s ( 74.95 )
2026-01-13 06:51:06.088157 INFO::Formatting Data.
2026-01-13 06:51:06.089238 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:06.090534 INFO::Removing potential empty rows and columns
2026-01-13 06:51:06.092022 INFO::Found 0 missing values.
2026-01-13 06:51:06.093756 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.
2026-01-13 06:51:06.100916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:06.101909 INFO::Done
2026-01-13 06:51:06.102709 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:06.106958 INFO::Starting hierarchical adjustment
2026-01-13 06:51:06.108146 INFO::Found 2 batches.
2026-01-13 06:51:06.108983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:06.109914 INFO::Using default BPPARAM
2026-01-13 06:51:06.110678 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:06.112072 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-13 06:51:06.136167 INFO::Done
2026-01-13 06:51:06.137129 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:06.141377 INFO::ASW Batch was 0.473767614952733 prior to batch effect correction and is now 0.0723426716958006 .
2026-01-13 06:51:06.142323 INFO::ASW Label was 0.656692397020065 prior to batch effect correction and is now 0.903196385075488 .
2026-01-13 06:51:06.143465 INFO::Total function execution time is 0.0553758144378662 s and adjustment time is 0.0282368659973145 s ( 50.99 )
2026-01-13 06:51:06.144603 INFO::Formatting Data.
2026-01-13 06:51:06.145545 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:06.146907 INFO::Removing potential empty rows and columns
2026-01-13 06:51:06.148382 INFO::Found 0 missing values.
2026-01-13 06:51:06.149767 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.
2026-01-13 06:51:06.156476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:06.157413 INFO::Done
2026-01-13 06:51:06.158212 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:06.162593 INFO::Starting hierarchical adjustment
2026-01-13 06:51:06.163811 INFO::Found 2 batches.
2026-01-13 06:51:06.16468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:06.165714 INFO::Using default BPPARAM
2026-01-13 06:51:06.166559 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:06.168105 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-13 06:51:06.192648 INFO::Done
2026-01-13 06:51:06.19361 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:06.197809 INFO::ASW Batch was 0.473767614952733 prior to batch effect correction and is now 0.0723426716958006 .
2026-01-13 06:51:06.198715 INFO::ASW Label was 0.656692397020065 prior to batch effect correction and is now 0.903196385075488 .
2026-01-13 06:51:06.199813 INFO::Total function execution time is 0.0552229881286621 s and adjustment time is 0.0290827751159668 s ( 52.66 )
2026-01-13 06:51:06.513766 INFO::Formatting Data.
2026-01-13 06:51:06.514883 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:06.516205 INFO::Removing potential empty rows and columns
2026-01-13 06:51:06.517893 INFO::Found 0 missing values.
2026-01-13 06:51:06.522731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:06.523669 INFO::Done
2026-01-13 06:51:06.524499 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:06.527602 INFO::Starting hierarchical adjustment
2026-01-13 06:51:06.528842 INFO::Found 3 batches.
2026-01-13 06:51:06.529787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:06.530731 INFO::Using default BPPARAM
2026-01-13 06:51:06.531566 INFO::Processing subtree level 1
2026-01-13 06:51:06.645661 INFO::Adjusting the last 1 batches sequentially
2026-01-13 06:51:06.648226 INFO::Done
2026-01-13 06:51:06.649319 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:06.653111 INFO::ASW Batch was -0.108025179032067 prior to batch effect correction and is now -0.108025179032067 .
2026-01-13 06:51:06.654676 INFO::Total function execution time is 0.140950441360474 s and adjustment time is 0.11965799331665 s ( 84.89 )
2026-01-13 06:51:06.65633 INFO::Formatting Data.
2026-01-13 06:51:06.657462 INFO::Typecasting input to dataframe.
2026-01-13 06:51:06.658876 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:06.660352 INFO::Removing potential empty rows and columns
2026-01-13 06:51:06.662226 INFO::Found 0 missing values.
2026-01-13 06:51:06.667452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:06.66848 INFO::Done
2026-01-13 06:51:06.66942 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:06.672507 INFO::Starting hierarchical adjustment
2026-01-13 06:51:06.673776 INFO::Found 3 batches.
2026-01-13 06:51:06.674651 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:06.675697 INFO::Using default BPPARAM
2026-01-13 06:51:06.676603 INFO::Processing subtree level 1
2026-01-13 06:51:06.792515 INFO::Adjusting the last 1 batches sequentially
2026-01-13 06:51:06.795363 INFO::Done
2026-01-13 06:51:06.796371 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:06.800153 INFO::ASW Batch was -0.108025179032067 prior to batch effect correction and is now -0.108025179032067 .
2026-01-13 06:51:06.801742 INFO::Total function execution time is 0.145371675491333 s and adjustment time is 0.121817827224731 s ( 83.8 )
2026-01-13 06:51:06.82294 INFO::Formatting Data.
2026-01-13 06:51:06.824206 INFO::Typecasting input to dataframe.
2026-01-13 06:51:06.825821 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:06.82751 INFO::Removing potential empty rows and columns
2026-01-13 06:51:06.829406 INFO::Found 0 missing values.
2026-01-13 06:51:06.834685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:06.835755 INFO::Done
2026-01-13 06:51:06.83672 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:06.840252 INFO::Starting hierarchical adjustment
2026-01-13 06:51:06.841644 INFO::Found 3 batches.
2026-01-13 06:51:06.842625 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:06.8437 INFO::Using default BPPARAM
2026-01-13 06:51:06.844667 INFO::Processing subtree level 1
2026-01-13 06:51:06.957015 INFO::Adjusting the last 1 batches sequentially
2026-01-13 06:51:06.959397 INFO::Done
2026-01-13 06:51:06.960208 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:06.963719 INFO::ASW Batch was -0.0835445224951158 prior to batch effect correction and is now -0.0835445224951158 .
2026-01-13 06:51:06.96506 INFO::Total function execution time is 0.142218828201294 s and adjustment time is 0.118121862411499 s ( 83.06 )
2026-01-13 06:51:07.146484 INFO::Formatting Data.
2026-01-13 06:51:07.147567 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:07.149092 INFO::Removing potential empty rows and columns
2026-01-13 06:51:07.153122 INFO::Found 1000 missing values.
2026-01-13 06:51:07.181633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:07.182532 INFO::Done
2026-01-13 06:51:07.183297 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:07.190791 INFO::Starting hierarchical adjustment
2026-01-13 06:51:07.192232 INFO::Found 10 batches.
2026-01-13 06:51:07.19307 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:07.194009 INFO::Using default BPPARAM
2026-01-13 06:51:07.194767 INFO::Processing subtree level 1
2026-01-13 06:51:07.355939 INFO::Processing subtree level 2
2026-01-13 06:51:07.537439 INFO::Adjusting the last 1 batches sequentially
2026-01-13 06:51:07.540187 INFO::Done
2026-01-13 06:51:07.541154 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:07.549139 INFO::ASW Batch was 0.437893796530628 prior to batch effect correction and is now 0.437893796530628 .
2026-01-13 06:51:07.55018 INFO::ASW Label was 0.371703108438888 prior to batch effect correction and is now 0.371703108438888 .
2026-01-13 06:51:07.551498 INFO::Total function execution time is 0.405102252960205 s and adjustment time is 0.348248481750488 s ( 85.97 )
2026-01-13 06:51:07.552713 INFO::Formatting Data.
2026-01-13 06:51:07.553722 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:07.555462 INFO::Removing potential empty rows and columns
2026-01-13 06:51:07.559593 INFO::Found 1000 missing values.
2026-01-13 06:51:07.587187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:07.588205 INFO::Done
2026-01-13 06:51:07.58903 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:07.596536 INFO::Starting hierarchical adjustment
2026-01-13 06:51:07.597667 INFO::Found 10 batches.
2026-01-13 06:51:09.094711 INFO::Set up parallel execution backend with 2 workers
2026-01-13 06:51:09.097088 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-13 06:51:10.501235 INFO::Adjusting the last 2 batches sequentially
2026-01-13 06:51:10.503843 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-13 06:51:10.527581 INFO::Done
2026-01-13 06:51:10.528793 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:10.535195 INFO::ASW Batch was 0.437893796530628 prior to batch effect correction and is now 0.437893796530628 .
2026-01-13 06:51:10.53596 INFO::ASW Label was 0.371703108438888 prior to batch effect correction and is now 0.371703108438888 .
2026-01-13 06:51:10.536987 INFO::Total function execution time is 2.98429107666016 s and adjustment time is 2.93016958236694 s ( 98.19 )
2026-01-13 06:51:10.723547 INFO::Formatting Data.
2026-01-13 06:51:10.724771 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:10.726192 INFO::Removing potential empty rows and columns
2026-01-13 06:51:10.727883 INFO::Found 0 missing values.
2026-01-13 06:51:10.733841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:10.734816 INFO::Done
2026-01-13 06:51:10.735609 INFO::Acquiring quality metrics before batch effect correction.
2026-01-13 06:51:10.739733 INFO::Starting hierarchical adjustment
2026-01-13 06:51:10.740919 INFO::Found 3 batches.
2026-01-13 06:51:10.741789 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-13 06:51:10.742739 INFO::Using default BPPARAM
2026-01-13 06:51:10.743529 INFO::Processing subtree level 1
2026-01-13 06:51:10.879796 INFO::Adjusting the last 1 batches sequentially
2026-01-13 06:51:10.882331 INFO::Done
2026-01-13 06:51:10.883272 INFO::Acquiring quality metrics after batch effect correction.
2026-01-13 06:51:10.888133 INFO::ASW Batch was 0.129848641901447 prior to batch effect correction and is now -0.138513114598914 .
2026-01-13 06:51:10.889188 INFO::ASW Label was -0.199914378346962 prior to batch effect correction and is now -0.156192753137776 .
2026-01-13 06:51:10.890591 INFO::Total function execution time is 0.167112112045288 s and adjustment time is 0.14165186882019 s ( 84.76 )
2026-01-13 06:51:11.072464 INFO::Formatting Data.
2026-01-13 06:51:11.073617 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.074918 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.076489 INFO::Found 2 missing values.
2026-01-13 06:51:11.090351 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.091881 INFO::Done
2026-01-13 06:51:11.13584 INFO::Found NA in Reference column
2026-01-13 06:51:11.150324 INFO::Require at least two references per batch.
2026-01-13 06:51:11.183349 INFO::Formatting Data.
2026-01-13 06:51:11.184389 INFO::Recognized SummarizedExperiment
2026-01-13 06:51:11.185189 INFO::Typecasting input to dataframe.
2026-01-13 06:51:11.200272 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.201945 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.207294 INFO::Found 0 missing values.
2026-01-13 06:51:11.217688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.218565 INFO::Done
2026-01-13 06:51:11.241222 INFO::Formatting Data.
2026-01-13 06:51:11.242206 INFO::Recognized SummarizedExperiment
2026-01-13 06:51:11.242953 INFO::Typecasting input to dataframe.
2026-01-13 06:51:11.268079 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.269716 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.275034 INFO::Found 0 missing values.
2026-01-13 06:51:11.292367 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.293311 INFO::Done
2026-01-13 06:51:11.315814 INFO::Formatting Data.
2026-01-13 06:51:11.316762 INFO::Recognized SummarizedExperiment
2026-01-13 06:51:11.31754 INFO::Typecasting input to dataframe.
2026-01-13 06:51:11.340993 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.3424 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.34391 INFO::Found 0 missing values.
2026-01-13 06:51:11.345175 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.
2026-01-13 06:51:11.351689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.352562 INFO::Done
2026-01-13 06:51:11.366563 INFO::Formatting Data.
2026-01-13 06:51:11.367582 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.368805 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.370228 INFO::Found 0 missing values.
2026-01-13 06:51:11.374408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.375217 INFO::Done
2026-01-13 06:51:11.391397 INFO::Formatting Data.
2026-01-13 06:51:11.392448 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.393702 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.39521 INFO::Found 0 missing values.
2026-01-13 06:51:11.399676 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.400473 INFO::Done
2026-01-13 06:51:11.443593 INFO::Formatting Data.
2026-01-13 06:51:11.444704 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.446264 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.447974 INFO::Found 1 missing values.
2026-01-13 06:51:11.45207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.453043 INFO::Done
2026-01-13 06:51:11.481457 INFO::Formatting Data.
2026-01-13 06:51:11.482493 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.483671 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.485049 INFO::Found 2 missing values.
2026-01-13 06:51:11.486419 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.
2026-01-13 06:51:11.489717 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.490552 INFO::Done
2026-01-13 06:51:11.504827 INFO::Formatting Data.
2026-01-13 06:51:11.505904 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.507079 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.508366 INFO::Found 2 missing values.
2026-01-13 06:51:11.510644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.51141 INFO::Done
2026-01-13 06:51:11.526294 INFO::Formatting Data.
2026-01-13 06:51:11.527292 INFO::Typecasting input to dataframe.
2026-01-13 06:51:11.528347 INFO::Replacing NaNs with NAs.
2026-01-13 06:51:11.529602 INFO::Removing potential empty rows and columns
2026-01-13 06:51:11.531029 INFO::Found 0 missing values.
2026-01-13 06:51:11.535192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-13 06:51:11.535998 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.114 5.828 26.729
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.351 | 1.669 | 20.767 | |
| compute_asw | 0.033 | 0.000 | 0.034 | |
| count_existing | 0.017 | 0.000 | 0.017 | |
| generate_data_covariables | 0.015 | 0.000 | 0.016 | |
| generate_dataset | 0.007 | 0.008 | 0.014 | |