Yannis Schumann
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-22 12:03 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /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: 2025-12-18 21:24:30 -0500 (Thu, 18 Dec 2025) |
| EndedAt: 2025-12-18 21:25:58 -0500 (Thu, 18 Dec 2025) |
| EllapsedTime: 88.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 24.161 1.218 17.439
* 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")
2025-12-18 21:25:22.441651 INFO::Formatting Data.
2025-12-18 21:25:22.442941 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:22.453848 INFO::Removing potential empty rows and columns
2025-12-18 21:25:22.691079 INFO::Found 0 missing values.
2025-12-18 21:25:22.6943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:22.694922 INFO::Done
2025-12-18 21:25:22.695438 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:22.705936 INFO::Starting hierarchical adjustment
2025-12-18 21:25:22.706762 INFO::Found 3 batches.
2025-12-18 21:25:22.707284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:22.708351 INFO::Using default BPPARAM
2025-12-18 21:25:22.708884 INFO::Processing subtree level 1
2025-12-18 21:25:22.810686 INFO::Adjusting the last 1 batches sequentially
2025-12-18 21:25:22.812461 INFO::Done
2025-12-18 21:25:22.813118 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:22.815634 INFO::ASW Batch was -0.0999322015598307 prior to batch effect correction and is now -0.0999322015598307 .
2025-12-18 21:25:22.816713 INFO::Total function execution time is 0.375661373138428 s and adjustment time is 0.105851888656616 s ( 28.18 )
2025-12-18 21:25:22.830407 INFO::Formatting Data.
2025-12-18 21:25:22.831204 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:22.832147 INFO::Removing potential empty rows and columns
2025-12-18 21:25:22.833298 INFO::Found 0 missing values.
2025-12-18 21:25:22.834248 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-18 21:25:22.844773 INFO::Formatting Data.
2025-12-18 21:25:22.845549 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:22.84641 INFO::Removing potential empty rows and columns
2025-12-18 21:25:22.847435 INFO::Found 0 missing values.
2025-12-18 21:25:22.848385 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-18 21:25:22.864239 INFO::Formatting Data.
2025-12-18 21:25:22.865001 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:22.865875 INFO::Removing potential empty rows and columns
2025-12-18 21:25:22.866885 INFO::Found 0 missing values.
2025-12-18 21:25:22.867803 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-18 21:25:22.872385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:22.872977 INFO::Done
2025-12-18 21:25:22.873528 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:22.875609 INFO::Starting hierarchical adjustment
2025-12-18 21:25:22.876324 INFO::Found 2 batches.
2025-12-18 21:25:22.876867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:22.877499 INFO::Using default BPPARAM
2025-12-18 21:25:22.878028 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:22.878944 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-18 21:25:22.900151 INFO::Done
2025-12-18 21:25:22.900908 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:22.90299 INFO::ASW Batch was 0.0424046703802119 prior to batch effect correction and is now -0.106465661732165 .
2025-12-18 21:25:22.903802 INFO::Total function execution time is 0.039618968963623 s and adjustment time is 0.0239417552947998 s ( 60.43 )
2025-12-18 21:25:22.90671 INFO::Formatting Data.
2025-12-18 21:25:22.907348 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:22.916384 INFO::Formatting Data.
2025-12-18 21:25:22.91713 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:22.918034 INFO::Removing potential empty rows and columns
2025-12-18 21:25:22.919105 INFO::Found 0 missing values.
2025-12-18 21:25:22.92209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:22.922637 INFO::Done
2025-12-18 21:25:22.923162 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:22.925229 INFO::Starting hierarchical adjustment
2025-12-18 21:25:22.925955 INFO::Found 2 batches.
2025-12-18 21:25:22.926495 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:22.949264 INFO::Using default BPPARAM
2025-12-18 21:25:22.95192 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:22.952981 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:22.967121 INFO::Done
2025-12-18 21:25:22.967833 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:22.969818 INFO::ASW Batch was -0.0516147658699113 prior to batch effect correction and is now -0.129988032471459 .
2025-12-18 21:25:22.970591 INFO::Total function execution time is 0.0542349815368652 s and adjustment time is 0.0412991046905518 s ( 76.15 )
2025-12-18 21:25:22.971595 INFO::Formatting Data.
2025-12-18 21:25:22.972164 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:22.972992 INFO::Removing potential empty rows and columns
2025-12-18 21:25:22.973963 INFO::Found 0 missing values.
2025-12-18 21:25:22.976625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:22.977131 INFO::Done
2025-12-18 21:25:22.977627 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:22.97953 INFO::Starting hierarchical adjustment
2025-12-18 21:25:22.980193 INFO::Found 2 batches.
2025-12-18 21:25:22.980691 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:22.981251 INFO::Using default BPPARAM
2025-12-18 21:25:22.981761 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:22.982602 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:22.99655 INFO::Done
2025-12-18 21:25:22.997205 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:22.999118 INFO::ASW Batch was -0.0516147658699113 prior to batch effect correction and is now -0.129988032471459 .
2025-12-18 21:25:22.999878 INFO::Total function execution time is 0.0282950401306152 s and adjustment time is 0.0164589881896973 s ( 58.17 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-18 21:25:25.868221 INFO::Formatting Data.
2025-12-18 21:25:25.868986 INFO::Recognized SummarizedExperiment
2025-12-18 21:25:25.869476 INFO::Typecasting input to dataframe.
2025-12-18 21:25:25.899402 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:25.900744 INFO::Removing potential empty rows and columns
2025-12-18 21:25:25.904596 INFO::Found 0 missing values.
2025-12-18 21:25:25.911834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:25.912429 INFO::Done
2025-12-18 21:25:25.91315 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:25.916851 INFO::Starting hierarchical adjustment
2025-12-18 21:25:25.917575 INFO::Found 2 batches.
2025-12-18 21:25:25.91809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:25.919213 INFO::Using default BPPARAM
2025-12-18 21:25:25.919754 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:25.920746 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-18 21:25:25.977677 INFO::Done
2025-12-18 21:25:25.978432 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:25.982157 INFO::ASW Batch was -0.0054931566946405 prior to batch effect correction and is now -0.0963390201050421 .
2025-12-18 21:25:25.983051 INFO::Total function execution time is 0.115137815475464 s and adjustment time is 0.0602328777313232 s ( 52.31 )
Warning: stack imbalance in '{', 73 then 75
2025-12-18 21:25:26.0022 INFO::Formatting Data.
2025-12-18 21:25:26.002987 INFO::Recognized SummarizedExperiment
2025-12-18 21:25:26.003538 INFO::Typecasting input to dataframe.
2025-12-18 21:25:26.013204 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:26.014414 INFO::Removing potential empty rows and columns
2025-12-18 21:25:26.018329 INFO::Found 0 missing values.
2025-12-18 21:25:26.025663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:26.026359 INFO::Done
2025-12-18 21:25:26.026917 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:26.030596 INFO::Starting hierarchical adjustment
2025-12-18 21:25:26.031338 INFO::Found 2 batches.
2025-12-18 21:25:26.031879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:26.032467 INFO::Using default BPPARAM
2025-12-18 21:25:26.033005 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:26.033998 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-18 21:25:26.059935 INFO::Done
2025-12-18 21:25:26.060765 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:26.064605 INFO::ASW Batch was 0.0041826108743567 prior to batch effect correction and is now 0.0041826108743567 .
2025-12-18 21:25:26.065538 INFO::Total function execution time is 0.0633106231689453 s and adjustment time is 0.0286948680877686 s ( 45.32 )
2025-12-18 21:25:26.085074 INFO::Formatting Data.
2025-12-18 21:25:26.086071 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:26.08705 INFO::Removing potential empty rows and columns
2025-12-18 21:25:26.088127 INFO::Found 0 missing values.
2025-12-18 21:25:26.091226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:26.091794 INFO::Done
2025-12-18 21:25:26.092308 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:26.094578 INFO::Starting hierarchical adjustment
2025-12-18 21:25:26.09531 INFO::Found 3 batches.
2025-12-18 21:25:26.095855 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:26.096458 INFO::Using default BPPARAM
2025-12-18 21:25:26.096993 INFO::Processing subtree level 1
2025-12-18 21:25:26.247877 INFO::Adjusting the last 1 batches sequentially
2025-12-18 21:25:26.249992 INFO::Done
2025-12-18 21:25:26.250744 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:26.253287 INFO::ASW Batch was -0.07830105217865 prior to batch effect correction and is now -0.18466471646039 .
2025-12-18 21:25:26.254257 INFO::Total function execution time is 0.169256448745728 s and adjustment time is 0.154804944992065 s ( 91.46 )
2025-12-18 21:25:26.269116 INFO::Skipping initial DF formatting
2025-12-18 21:25:26.269868 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:26.27397 INFO::Starting hierarchical adjustment
2025-12-18 21:25:26.274773 INFO::Found 5 batches.
2025-12-18 21:25:26.275318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:26.275938 INFO::Using default BPPARAM
2025-12-18 21:25:26.27648 INFO::Processing subtree level 1
2025-12-18 21:25:26.521923 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:26.523834 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-18 21:25:26.54476 INFO::Done
2025-12-18 21:25:26.545715 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:26.550728 INFO::ASW Batch was 0.487991841006343 prior to batch effect correction and is now 0.487991841006343 .
2025-12-18 21:25:26.55146 INFO::ASW Label was 0.363899125717035 prior to batch effect correction and is now 0.363899125717035 .
2025-12-18 21:25:26.552424 INFO::Total function execution time is 0.283367156982422 s and adjustment time is 0.270049095153809 s ( 95.3 )
2025-12-18 21:25:26.635453 INFO::Formatting Data.
2025-12-18 21:25:26.636452 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:26.637589 INFO::Removing potential empty rows and columns
2025-12-18 21:25:26.638769 INFO::Found 0 missing values.
2025-12-18 21:25:26.643443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:26.644071 INFO::Done
2025-12-18 21:25:26.644642 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:26.648168 INFO::Starting hierarchical adjustment
2025-12-18 21:25:26.648984 INFO::Found 5 batches.
2025-12-18 21:25:26.649635 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:26.650413 INFO::Using default BPPARAM
2025-12-18 21:25:26.650978 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:26.810247 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:26.812105 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:26.830215 INFO::Done
2025-12-18 21:25:26.830999 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:26.834722 INFO::ASW Batch was 0.401102010334431 prior to batch effect correction and is now -0.0406361922740013 .
2025-12-18 21:25:26.835374 INFO::ASW Label was 0.288947314707971 prior to batch effect correction and is now 0.815891317589655 .
2025-12-18 21:25:26.836239 INFO::Total function execution time is 0.20098090171814 s and adjustment time is 0.181392192840576 s ( 90.25 )
2025-12-18 21:25:26.837163 INFO::Formatting Data.
2025-12-18 21:25:26.83783 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:26.838845 INFO::Removing potential empty rows and columns
2025-12-18 21:25:26.840017 INFO::Found 0 missing values.
2025-12-18 21:25:26.844558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:26.845134 INFO::Done
2025-12-18 21:25:26.84568 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:26.848907 INFO::Starting hierarchical adjustment
2025-12-18 21:25:26.849691 INFO::Found 5 batches.
2025-12-18 21:25:26.850222 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:26.850895 INFO::Using default BPPARAM
2025-12-18 21:25:26.851413 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:26.992568 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:26.994325 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:27.011067 INFO::Done
2025-12-18 21:25:27.01182 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.015202 INFO::ASW Batch was 0.401102010334431 prior to batch effect correction and is now -0.0406361922740013 .
2025-12-18 21:25:27.015819 INFO::ASW Label was 0.288947314707971 prior to batch effect correction and is now 0.815891317589655 .
2025-12-18 21:25:27.016667 INFO::Total function execution time is 0.17949652671814 s and adjustment time is 0.161523818969727 s ( 89.99 )
2025-12-18 21:25:27.030819 INFO::Formatting Data.
2025-12-18 21:25:27.031678 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.032596 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.033589 INFO::Found 0 missing values.
2025-12-18 21:25:27.037656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.038202 INFO::Done
2025-12-18 21:25:27.038721 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.041709 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.042396 INFO::Found 5 batches.
2025-12-18 21:25:27.042927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.043553 INFO::Using default BPPARAM
2025-12-18 21:25:27.04407 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:27.187841 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:27.18954 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:27.206593 INFO::Done
2025-12-18 21:25:27.207378 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.210904 INFO::ASW Batch was 0.607527543487879 prior to batch effect correction and is now -0.00784629212325577 .
2025-12-18 21:25:27.211587 INFO::ASW Label was 0.185723613311207 prior to batch effect correction and is now 0.739611396042153 .
2025-12-18 21:25:27.212417 INFO::Total function execution time is 0.181657552719116 s and adjustment time is 0.164268016815186 s ( 90.43 )
2025-12-18 21:25:27.213285 INFO::Formatting Data.
2025-12-18 21:25:27.213943 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.214965 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.216161 INFO::Found 0 missing values.
2025-12-18 21:25:27.220764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.22139 INFO::Done
2025-12-18 21:25:27.221943 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.225164 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.225922 INFO::Found 5 batches.
2025-12-18 21:25:27.226468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.227126 INFO::Using default BPPARAM
2025-12-18 21:25:27.227682 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:27.358525 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:27.360324 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:27.377903 INFO::Done
2025-12-18 21:25:27.378782 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.382615 INFO::ASW Batch was 0.607527543487879 prior to batch effect correction and is now -0.00784629212325577 .
2025-12-18 21:25:27.383278 INFO::ASW Label was 0.185723613311207 prior to batch effect correction and is now 0.739611396042153 .
2025-12-18 21:25:27.384221 INFO::Total function execution time is 0.170944929122925 s and adjustment time is 0.152096748352051 s ( 88.97 )
2025-12-18 21:25:27.399617 INFO::Formatting Data.
2025-12-18 21:25:27.400463 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.401539 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.402816 INFO::Found 0 missing values.
2025-12-18 21:25:27.405902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.406487 INFO::Done
2025-12-18 21:25:27.407056 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.410212 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.410959 INFO::Found 2 batches.
2025-12-18 21:25:27.411525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.412169 INFO::Using default BPPARAM
2025-12-18 21:25:27.412731 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:27.413671 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:27.428631 INFO::Done
2025-12-18 21:25:27.429277 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.43231 INFO::ASW Batch was 0.677170206475203 prior to batch effect correction and is now -0.0126691149255501 .
2025-12-18 21:25:27.432929 INFO::ASW Label was 0.381379087516525 prior to batch effect correction and is now 0.874173093898048 .
2025-12-18 21:25:27.433736 INFO::Total function execution time is 0.034252405166626 s and adjustment time is 0.0178284645080566 s ( 52.05 )
2025-12-18 21:25:27.434544 INFO::Formatting Data.
2025-12-18 21:25:27.435156 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.436016 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.436999 INFO::Found 0 missing values.
2025-12-18 21:25:27.43963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.440155 INFO::Done
2025-12-18 21:25:27.440679 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.443576 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.444324 INFO::Found 2 batches.
2025-12-18 21:25:27.44489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.445502 INFO::Using default BPPARAM
2025-12-18 21:25:27.446035 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:27.44692 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-18 21:25:27.460855 INFO::Done
2025-12-18 21:25:27.461474 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.46435 INFO::ASW Batch was 0.677170206475203 prior to batch effect correction and is now -0.0126691149255501 .
2025-12-18 21:25:27.464927 INFO::ASW Label was 0.381379087516525 prior to batch effect correction and is now 0.874173093898048 .
2025-12-18 21:25:27.465678 INFO::Total function execution time is 0.0311651229858398 s and adjustment time is 0.0166840553283691 s ( 53.53 )
2025-12-18 21:25:27.476403 INFO::Formatting Data.
2025-12-18 21:25:27.477187 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.47806 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.47893 INFO::Found 0 missing values.
2025-12-18 21:25:27.480969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.481516 INFO::Done
2025-12-18 21:25:27.482015 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.483833 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.484524 INFO::Found 2 batches.
2025-12-18 21:25:27.485039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.485619 INFO::Using default BPPARAM
2025-12-18 21:25:27.486125 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:27.486983 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-18 21:25:27.516627 INFO::Done
2025-12-18 21:25:27.517303 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.519199 INFO::ASW Batch was 0.0301334994150495 prior to batch effect correction and is now -0.175795024001185 .
2025-12-18 21:25:27.519983 INFO::Total function execution time is 0.0436296463012695 s and adjustment time is 0.0322158336639404 s ( 73.84 )
2025-12-18 21:25:27.531261 INFO::Formatting Data.
2025-12-18 21:25:27.532042 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.53291 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.533878 INFO::Found 0 missing values.
2025-12-18 21:25:27.534982 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-18 21:25:27.539456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.540001 INFO::Done
2025-12-18 21:25:27.540497 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.543393 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.544078 INFO::Found 2 batches.
2025-12-18 21:25:27.544613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.545204 INFO::Using default BPPARAM
2025-12-18 21:25:27.545717 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:27.546608 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-18 21:25:27.562595 INFO::Done
2025-12-18 21:25:27.563262 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.566127 INFO::ASW Batch was 0.604035839748047 prior to batch effect correction and is now 0.0416312421941424 .
2025-12-18 21:25:27.56672 INFO::ASW Label was 0.484242884972609 prior to batch effect correction and is now 0.897071886165321 .
2025-12-18 21:25:27.567449 INFO::Total function execution time is 0.036273717880249 s and adjustment time is 0.0186214447021484 s ( 51.34 )
2025-12-18 21:25:27.568212 INFO::Formatting Data.
2025-12-18 21:25:27.568835 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.569716 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.570651 INFO::Found 0 missing values.
2025-12-18 21:25:27.571515 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-18 21:25:27.575799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.576316 INFO::Done
2025-12-18 21:25:27.576825 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.579617 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.580276 INFO::Found 2 batches.
2025-12-18 21:25:27.580797 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.581379 INFO::Using default BPPARAM
2025-12-18 21:25:27.581903 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:27.582802 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-18 21:25:27.598577 INFO::Done
2025-12-18 21:25:27.599243 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.60211 INFO::ASW Batch was 0.604035839748047 prior to batch effect correction and is now 0.0416312421941424 .
2025-12-18 21:25:27.602703 INFO::ASW Label was 0.484242884972609 prior to batch effect correction and is now 0.897071886165321 .
2025-12-18 21:25:27.603464 INFO::Total function execution time is 0.0352625846862793 s and adjustment time is 0.0183873176574707 s ( 52.14 )
2025-12-18 21:25:27.804526 INFO::Formatting Data.
2025-12-18 21:25:27.805337 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.806322 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.807381 INFO::Found 0 missing values.
2025-12-18 21:25:27.810479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.811024 INFO::Done
2025-12-18 21:25:27.811549 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.813568 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.81433 INFO::Found 3 batches.
2025-12-18 21:25:27.814863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.815469 INFO::Using default BPPARAM
2025-12-18 21:25:27.815986 INFO::Processing subtree level 1
2025-12-18 21:25:27.904979 INFO::Adjusting the last 1 batches sequentially
2025-12-18 21:25:27.906826 INFO::Done
2025-12-18 21:25:27.907496 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:27.910285 INFO::ASW Batch was -0.0443599634955395 prior to batch effect correction and is now -0.0443599634955395 .
2025-12-18 21:25:27.911265 INFO::Total function execution time is 0.106799125671387 s and adjustment time is 0.0926213264465332 s ( 86.72 )
2025-12-18 21:25:27.912384 INFO::Formatting Data.
2025-12-18 21:25:27.913074 INFO::Typecasting input to dataframe.
2025-12-18 21:25:27.913862 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:27.914822 INFO::Removing potential empty rows and columns
2025-12-18 21:25:27.915962 INFO::Found 0 missing values.
2025-12-18 21:25:27.919153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:27.919734 INFO::Done
2025-12-18 21:25:27.920262 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:27.922332 INFO::Starting hierarchical adjustment
2025-12-18 21:25:27.92306 INFO::Found 3 batches.
2025-12-18 21:25:27.923629 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:27.924244 INFO::Using default BPPARAM
2025-12-18 21:25:27.924797 INFO::Processing subtree level 1
2025-12-18 21:25:28.01334 INFO::Adjusting the last 1 batches sequentially
2025-12-18 21:25:28.01536 INFO::Done
2025-12-18 21:25:28.016117 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:28.018884 INFO::ASW Batch was -0.0443599634955395 prior to batch effect correction and is now -0.0443599634955395 .
2025-12-18 21:25:28.01992 INFO::Total function execution time is 0.107506513595581 s and adjustment time is 0.0924105644226074 s ( 85.96 )
2025-12-18 21:25:28.034386 INFO::Formatting Data.
2025-12-18 21:25:28.035325 INFO::Typecasting input to dataframe.
2025-12-18 21:25:28.036261 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:28.037258 INFO::Removing potential empty rows and columns
2025-12-18 21:25:28.03843 INFO::Found 0 missing values.
2025-12-18 21:25:28.041677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:28.042231 INFO::Done
2025-12-18 21:25:28.042765 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:28.044964 INFO::Starting hierarchical adjustment
2025-12-18 21:25:28.045703 INFO::Found 3 batches.
2025-12-18 21:25:28.046251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:28.046904 INFO::Using default BPPARAM
2025-12-18 21:25:28.047445 INFO::Processing subtree level 1
2025-12-18 21:25:28.141759 INFO::Adjusting the last 1 batches sequentially
2025-12-18 21:25:28.14375 INFO::Done
2025-12-18 21:25:28.144412 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:28.14719 INFO::ASW Batch was -0.0324878200862162 prior to batch effect correction and is now -0.0324878200862162 .
2025-12-18 21:25:28.148235 INFO::Total function execution time is 0.113943099975586 s and adjustment time is 0.0981969833374023 s ( 86.18 )
2025-12-18 21:25:28.290523 INFO::Formatting Data.
2025-12-18 21:25:28.291373 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:28.292519 INFO::Removing potential empty rows and columns
2025-12-18 21:25:28.295315 INFO::Found 1000 missing values.
2025-12-18 21:25:28.314588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:28.315346 INFO::Done
2025-12-18 21:25:28.315926 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:28.321447 INFO::Starting hierarchical adjustment
2025-12-18 21:25:28.322285 INFO::Found 10 batches.
2025-12-18 21:25:28.322855 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:28.323472 INFO::Using default BPPARAM
2025-12-18 21:25:28.324021 INFO::Processing subtree level 1
2025-12-18 21:25:28.461572 INFO::Processing subtree level 2
2025-12-18 21:25:28.602779 INFO::Adjusting the last 1 batches sequentially
2025-12-18 21:25:28.604988 INFO::Done
2025-12-18 21:25:28.605699 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:28.61141 INFO::ASW Batch was 0.482061023689682 prior to batch effect correction and is now 0.482061023689682 .
2025-12-18 21:25:28.612155 INFO::ASW Label was 0.330147067229701 prior to batch effect correction and is now 0.330147067229701 .
2025-12-18 21:25:28.613121 INFO::Total function execution time is 0.322666168212891 s and adjustment time is 0.28284478187561 s ( 87.66 )
2025-12-18 21:25:28.613979 INFO::Formatting Data.
2025-12-18 21:25:28.61462 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:28.615936 INFO::Removing potential empty rows and columns
2025-12-18 21:25:28.618775 INFO::Found 1000 missing values.
2025-12-18 21:25:28.638124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:28.638869 INFO::Done
2025-12-18 21:25:28.639413 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:28.645114 INFO::Starting hierarchical adjustment
2025-12-18 21:25:28.645931 INFO::Found 10 batches.
2025-12-18 21:25:29.70155 INFO::Set up parallel execution backend with 2 workers
2025-12-18 21:25:29.70352 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-18 21:25:30.77259 INFO::Adjusting the last 2 batches sequentially
2025-12-18 21:25:30.774365 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-18 21:25:30.790268 INFO::Done
2025-12-18 21:25:30.79101 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:30.7957 INFO::ASW Batch was 0.482061023689682 prior to batch effect correction and is now 0.482061023689682 .
2025-12-18 21:25:30.796343 INFO::ASW Label was 0.330147067229701 prior to batch effect correction and is now 0.330147067229701 .
2025-12-18 21:25:30.797108 INFO::Total function execution time is 2.18314838409424 s and adjustment time is 2.14445686340332 s ( 98.23 )
2025-12-18 21:25:30.947916 INFO::Formatting Data.
2025-12-18 21:25:30.94875 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:30.949711 INFO::Removing potential empty rows and columns
2025-12-18 21:25:30.95077 INFO::Found 0 missing values.
2025-12-18 21:25:30.954358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:30.954909 INFO::Done
2025-12-18 21:25:30.955406 INFO::Acquiring quality metrics before batch effect correction.
2025-12-18 21:25:30.958135 INFO::Starting hierarchical adjustment
2025-12-18 21:25:30.958837 INFO::Found 3 batches.
2025-12-18 21:25:30.959333 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-18 21:25:30.95993 INFO::Using default BPPARAM
2025-12-18 21:25:30.960432 INFO::Processing subtree level 1
2025-12-18 21:25:31.071483 INFO::Adjusting the last 1 batches sequentially
2025-12-18 21:25:31.073265 INFO::Done
2025-12-18 21:25:31.07391 INFO::Acquiring quality metrics after batch effect correction.
2025-12-18 21:25:31.077006 INFO::ASW Batch was 0.142776614529329 prior to batch effect correction and is now -0.143485413505203 .
2025-12-18 21:25:31.077624 INFO::ASW Label was -0.203886254003734 prior to batch effect correction and is now -0.0742973641584563 .
2025-12-18 21:25:31.078532 INFO::Total function execution time is 0.130683183670044 s and adjustment time is 0.114542722702026 s ( 87.65 )
2025-12-18 21:25:31.197129 INFO::Formatting Data.
2025-12-18 21:25:31.197943 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.198815 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.199801 INFO::Found 2 missing values.
2025-12-18 21:25:31.202484 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.203003 INFO::Done
2025-12-18 21:25:31.229183 INFO::Found NA in Reference column
2025-12-18 21:25:31.238115 INFO::Require at least two references per batch.
2025-12-18 21:25:31.257243 INFO::Formatting Data.
2025-12-18 21:25:31.257956 INFO::Recognized SummarizedExperiment
2025-12-18 21:25:31.258463 INFO::Typecasting input to dataframe.
2025-12-18 21:25:31.267339 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.26841 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.27169 INFO::Found 0 missing values.
2025-12-18 21:25:31.277937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.278484 INFO::Done
2025-12-18 21:25:31.293193 INFO::Formatting Data.
2025-12-18 21:25:31.293906 INFO::Recognized SummarizedExperiment
2025-12-18 21:25:31.294407 INFO::Typecasting input to dataframe.
2025-12-18 21:25:31.310717 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.311885 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.315162 INFO::Found 0 missing values.
2025-12-18 21:25:31.325181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.325795 INFO::Done
2025-12-18 21:25:31.340438 INFO::Formatting Data.
2025-12-18 21:25:31.341124 INFO::Recognized SummarizedExperiment
2025-12-18 21:25:31.341648 INFO::Typecasting input to dataframe.
2025-12-18 21:25:31.35726 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.358235 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.359232 INFO::Found 0 missing values.
2025-12-18 21:25:31.360082 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-18 21:25:31.364218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.364759 INFO::Done
2025-12-18 21:25:31.374058 INFO::Formatting Data.
2025-12-18 21:25:31.374776 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.375622 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.37656 INFO::Found 0 missing values.
2025-12-18 21:25:31.379209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.379712 INFO::Done
2025-12-18 21:25:31.390387 INFO::Formatting Data.
2025-12-18 21:25:31.391276 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.392097 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.393049 INFO::Found 0 missing values.
2025-12-18 21:25:31.395768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.396271 INFO::Done
2025-12-18 21:25:31.425255 INFO::Formatting Data.
2025-12-18 21:25:31.426118 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.42714 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.428259 INFO::Found 1 missing values.
2025-12-18 21:25:31.431009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.431542 INFO::Done
2025-12-18 21:25:31.449984 INFO::Formatting Data.
2025-12-18 21:25:31.450767 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.451682 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.452589 INFO::Found 2 missing values.
2025-12-18 21:25:31.453437 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-18 21:25:31.455564 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.456076 INFO::Done
2025-12-18 21:25:31.465975 INFO::Formatting Data.
2025-12-18 21:25:31.46673 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.467563 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.468428 INFO::Found 2 missing values.
2025-12-18 21:25:31.469939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.470447 INFO::Done
2025-12-18 21:25:31.480317 INFO::Formatting Data.
2025-12-18 21:25:31.481134 INFO::Typecasting input to dataframe.
2025-12-18 21:25:31.481904 INFO::Replacing NaNs with NAs.
2025-12-18 21:25:31.482712 INFO::Removing potential empty rows and columns
2025-12-18 21:25:31.483631 INFO::Found 0 missing values.
2025-12-18 21:25:31.486274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-18 21:25:31.486785 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.388 3.329 20.345
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.161 | 1.218 | 17.439 | |
| compute_asw | 0.026 | 0.000 | 0.025 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.012 | 0.000 | 0.014 | |
| generate_dataset | 0.010 | 0.002 | 0.013 | |