Yannis Schumann
| Snapshot Date: 2025-12-22 13:45 -0500 (Mon, 22 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 2025-12-25 11:58 -0500 (Thu, 25 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 |
| 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 | | ||||||||
| 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: 2025-12-22 21:59:22 -0500 (Mon, 22 Dec 2025) |
| EndedAt: 2025-12-22 22:00:54 -0500 (Mon, 22 Dec 2025) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.983 1.507 18.335
* 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")
2025-12-22 22:00:15.838714 INFO::Formatting Data.
2025-12-22 22:00:15.839949 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:15.853049 INFO::Removing potential empty rows and columns
2025-12-22 22:00:16.10142 INFO::Found 0 missing values.
2025-12-22 22:00:16.105021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:16.105717 INFO::Done
2025-12-22 22:00:16.106258 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:16.116966 INFO::Starting hierarchical adjustment
2025-12-22 22:00:16.117788 INFO::Found 3 batches.
2025-12-22 22:00:16.118312 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:16.119377 INFO::Using default BPPARAM
2025-12-22 22:00:16.119907 INFO::Processing subtree level 1
2025-12-22 22:00:16.216802 INFO::Adjusting the last 1 batches sequentially
2025-12-22 22:00:16.21846 INFO::Done
2025-12-22 22:00:16.219127 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:16.221743 INFO::ASW Batch was -0.047683482569916 prior to batch effect correction and is now -0.047683482569916 .
2025-12-22 22:00:16.222819 INFO::Total function execution time is 0.384693384170532 s and adjustment time is 0.100855588912964 s ( 26.22 )
2025-12-22 22:00:16.236096 INFO::Formatting Data.
2025-12-22 22:00:16.236849 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:16.237759 INFO::Removing potential empty rows and columns
2025-12-22 22:00:16.238882 INFO::Found 0 missing values.
2025-12-22 22:00:16.239794 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.
2025-12-22 22:00:16.250306 INFO::Formatting Data.
2025-12-22 22:00:16.251019 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:16.251872 INFO::Removing potential empty rows and columns
2025-12-22 22:00:16.252884 INFO::Found 0 missing values.
2025-12-22 22:00:16.253788 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.
2025-12-22 22:00:16.269399 INFO::Formatting Data.
2025-12-22 22:00:16.270138 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:16.271016 INFO::Removing potential empty rows and columns
2025-12-22 22:00:16.272021 INFO::Found 0 missing values.
2025-12-22 22:00:16.27295 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.
2025-12-22 22:00:16.277377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:16.277945 INFO::Done
2025-12-22 22:00:16.278464 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:16.280452 INFO::Starting hierarchical adjustment
2025-12-22 22:00:16.281161 INFO::Found 2 batches.
2025-12-22 22:00:16.281683 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:16.282287 INFO::Using default BPPARAM
2025-12-22 22:00:16.282807 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:16.28372 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-22 22:00:16.30424 INFO::Done
2025-12-22 22:00:16.305055 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:16.307128 INFO::ASW Batch was -0.0441329573631442 prior to batch effect correction and is now -0.0752263229865972 .
2025-12-22 22:00:16.307916 INFO::Total function execution time is 0.0385830402374268 s and adjustment time is 0.023190975189209 s ( 60.11 )
2025-12-22 22:00:16.310689 INFO::Formatting Data.
2025-12-22 22:00:16.311315 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:16.320155 INFO::Formatting Data.
2025-12-22 22:00:16.320906 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:16.321803 INFO::Removing potential empty rows and columns
2025-12-22 22:00:16.323262 INFO::Found 0 missing values.
2025-12-22 22:00:16.326207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:16.326755 INFO::Done
2025-12-22 22:00:16.327272 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:16.329292 INFO::Starting hierarchical adjustment
2025-12-22 22:00:16.329998 INFO::Found 2 batches.
2025-12-22 22:00:16.330539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:16.351776 INFO::Using default BPPARAM
2025-12-22 22:00:16.354084 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:16.355052 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-22 22:00:16.368583 INFO::Done
2025-12-22 22:00:16.369159 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:16.371037 INFO::ASW Batch was 0.21256047732382 prior to batch effect correction and is now -0.0406314709561126 .
2025-12-22 22:00:16.371774 INFO::Total function execution time is 0.0516705513000488 s and adjustment time is 0.0387160778045654 s ( 74.93 )
2025-12-22 22:00:16.372775 INFO::Formatting Data.
2025-12-22 22:00:16.373338 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:16.374125 INFO::Removing potential empty rows and columns
2025-12-22 22:00:16.375038 INFO::Found 0 missing values.
2025-12-22 22:00:16.377651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:16.378142 INFO::Done
2025-12-22 22:00:16.378631 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:16.380541 INFO::Starting hierarchical adjustment
2025-12-22 22:00:16.381202 INFO::Found 2 batches.
2025-12-22 22:00:16.3817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:16.382251 INFO::Using default BPPARAM
2025-12-22 22:00:16.382744 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:16.383602 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-22 22:00:16.397644 INFO::Done
2025-12-22 22:00:16.398253 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:16.400157 INFO::ASW Batch was 0.21256047732382 prior to batch effect correction and is now -0.0406314709561126 .
2025-12-22 22:00:16.400899 INFO::Total function execution time is 0.0281276702880859 s and adjustment time is 0.0165600776672363 s ( 58.87 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-22 22:00:19.416994 INFO::Formatting Data.
2025-12-22 22:00:19.417788 INFO::Recognized SummarizedExperiment
2025-12-22 22:00:19.418276 INFO::Typecasting input to dataframe.
2025-12-22 22:00:19.450475 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:19.451981 INFO::Removing potential empty rows and columns
2025-12-22 22:00:19.456084 INFO::Found 0 missing values.
2025-12-22 22:00:19.463844 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:19.464597 INFO::Done
2025-12-22 22:00:19.465169 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:19.469163 INFO::Starting hierarchical adjustment
2025-12-22 22:00:19.469981 INFO::Found 2 batches.
2025-12-22 22:00:19.470524 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:19.471798 INFO::Using default BPPARAM
2025-12-22 22:00:19.472348 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:19.473413 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-22 22:00:19.532076 INFO::Done
2025-12-22 22:00:19.532843 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:19.53646 INFO::ASW Batch was 0.0181853392711902 prior to batch effect correction and is now -0.093857413043672 .
2025-12-22 22:00:19.537369 INFO::Total function execution time is 0.120725870132446 s and adjustment time is 0.0622410774230957 s ( 51.56 )
Warning: stack imbalance in '{', 73 then 75
2025-12-22 22:00:19.556934 INFO::Formatting Data.
2025-12-22 22:00:19.557769 INFO::Recognized SummarizedExperiment
2025-12-22 22:00:19.558321 INFO::Typecasting input to dataframe.
2025-12-22 22:00:19.568351 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:19.569655 INFO::Removing potential empty rows and columns
2025-12-22 22:00:19.57345 INFO::Found 0 missing values.
2025-12-22 22:00:19.580773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:19.581431 INFO::Done
2025-12-22 22:00:19.582012 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:19.58566 INFO::Starting hierarchical adjustment
2025-12-22 22:00:19.586383 INFO::Found 2 batches.
2025-12-22 22:00:19.586917 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:19.587524 INFO::Using default BPPARAM
2025-12-22 22:00:19.588039 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:19.589035 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-22 22:00:19.615113 INFO::Done
2025-12-22 22:00:19.615914 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:19.619714 INFO::ASW Batch was -0.0068437402957504 prior to batch effect correction and is now -0.0068437402957504 .
2025-12-22 22:00:19.62068 INFO::Total function execution time is 0.0637266635894775 s and adjustment time is 0.0288190841674805 s ( 45.22 )
2025-12-22 22:00:19.640843 INFO::Formatting Data.
2025-12-22 22:00:19.641737 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:19.642729 INFO::Removing potential empty rows and columns
2025-12-22 22:00:19.643842 INFO::Found 0 missing values.
2025-12-22 22:00:19.646897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:19.647442 INFO::Done
2025-12-22 22:00:19.648003 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:19.650026 INFO::Starting hierarchical adjustment
2025-12-22 22:00:19.65074 INFO::Found 3 batches.
2025-12-22 22:00:19.651252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:19.651864 INFO::Using default BPPARAM
2025-12-22 22:00:19.652373 INFO::Processing subtree level 1
2025-12-22 22:00:19.799796 INFO::Adjusting the last 1 batches sequentially
2025-12-22 22:00:19.801734 INFO::Done
2025-12-22 22:00:19.802387 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:19.804959 INFO::ASW Batch was -0.0605616511218456 prior to batch effect correction and is now -0.155847316414801 .
2025-12-22 22:00:19.805927 INFO::Total function execution time is 0.165244340896606 s and adjustment time is 0.151131153106689 s ( 91.46 )
2025-12-22 22:00:19.820351 INFO::Skipping initial DF formatting
2025-12-22 22:00:19.821052 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:19.825103 INFO::Starting hierarchical adjustment
2025-12-22 22:00:19.825894 INFO::Found 5 batches.
2025-12-22 22:00:19.826432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:19.827082 INFO::Using default BPPARAM
2025-12-22 22:00:19.827634 INFO::Processing subtree level 1
2025-12-22 22:00:20.065915 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:20.067689 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-22 22:00:20.087618 INFO::Done
2025-12-22 22:00:20.088408 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:20.092774 INFO::ASW Batch was 0.51297971870839 prior to batch effect correction and is now 0.51297971870839 .
2025-12-22 22:00:20.093384 INFO::ASW Label was 0.356887408675967 prior to batch effect correction and is now 0.356887408675967 .
2025-12-22 22:00:20.09423 INFO::Total function execution time is 0.27394700050354 s and adjustment time is 0.261789798736572 s ( 95.56 )
2025-12-22 22:00:20.159353 INFO::Formatting Data.
2025-12-22 22:00:20.16016 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:20.161131 INFO::Removing potential empty rows and columns
2025-12-22 22:00:20.162104 INFO::Found 0 missing values.
2025-12-22 22:00:20.166032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:20.166577 INFO::Done
2025-12-22 22:00:20.167078 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:20.170018 INFO::Starting hierarchical adjustment
2025-12-22 22:00:20.170716 INFO::Found 5 batches.
2025-12-22 22:00:20.171233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:20.171849 INFO::Using default BPPARAM
2025-12-22 22:00:20.172406 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.
2025-12-22 22:00:20.350453 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:20.352358 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-22 22:00:20.372406 INFO::Done
2025-12-22 22:00:20.373383 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:20.377617 INFO::ASW Batch was 0.267750607291151 prior to batch effect correction and is now -0.00885203920157261 .
2025-12-22 22:00:20.378338 INFO::ASW Label was 0.508486089516372 prior to batch effect correction and is now 0.761066652013434 .
2025-12-22 22:00:20.379352 INFO::Total function execution time is 0.220031976699829 s and adjustment time is 0.201773166656494 s ( 91.7 )
2025-12-22 22:00:20.380347 INFO::Formatting Data.
2025-12-22 22:00:20.381093 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:20.382158 INFO::Removing potential empty rows and columns
2025-12-22 22:00:20.383415 INFO::Found 0 missing values.
2025-12-22 22:00:20.388366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:20.388991 INFO::Done
2025-12-22 22:00:20.389531 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:20.392968 INFO::Starting hierarchical adjustment
2025-12-22 22:00:20.393741 INFO::Found 5 batches.
2025-12-22 22:00:20.394334 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:20.394994 INFO::Using default BPPARAM
2025-12-22 22:00:20.395582 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.
2025-12-22 22:00:20.583074 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:20.585087 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-22 22:00:20.60417 INFO::Done
2025-12-22 22:00:20.605069 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:20.609151 INFO::ASW Batch was 0.267750607291151 prior to batch effect correction and is now -0.00885203920157261 .
2025-12-22 22:00:20.609943 INFO::ASW Label was 0.508486089516372 prior to batch effect correction and is now 0.761066652013434 .
2025-12-22 22:00:20.610945 INFO::Total function execution time is 0.230577230453491 s and adjustment time is 0.210536479949951 s ( 91.31 )
2025-12-22 22:00:20.626891 INFO::Formatting Data.
2025-12-22 22:00:20.627821 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:20.628889 INFO::Removing potential empty rows and columns
2025-12-22 22:00:20.630047 INFO::Found 0 missing values.
2025-12-22 22:00:20.634698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:20.635319 INFO::Done
2025-12-22 22:00:20.635886 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:20.639612 INFO::Starting hierarchical adjustment
2025-12-22 22:00:20.640384 INFO::Found 5 batches.
2025-12-22 22:00:20.650048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:20.651052 INFO::Using default BPPARAM
2025-12-22 22:00:20.651727 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.
2025-12-22 22:00:20.802218 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:20.804461 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-22 22:00:20.824913 INFO::Done
2025-12-22 22:00:20.825889 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:20.830142 INFO::ASW Batch was 0.378841033629208 prior to batch effect correction and is now -0.102535525261875 .
2025-12-22 22:00:20.830898 INFO::ASW Label was 0.376389068409751 prior to batch effect correction and is now 0.762388305301049 .
2025-12-22 22:00:20.831919 INFO::Total function execution time is 0.205114603042603 s and adjustment time is 0.184625387191772 s ( 90.01 )
2025-12-22 22:00:20.832909 INFO::Formatting Data.
2025-12-22 22:00:20.833628 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:20.834666 INFO::Removing potential empty rows and columns
2025-12-22 22:00:20.835866 INFO::Found 0 missing values.
2025-12-22 22:00:20.840566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:20.841158 INFO::Done
2025-12-22 22:00:20.841748 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:20.845245 INFO::Starting hierarchical adjustment
2025-12-22 22:00:20.846057 INFO::Found 5 batches.
2025-12-22 22:00:20.846643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:20.847351 INFO::Using default BPPARAM
2025-12-22 22:00:20.847936 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.
2025-12-22 22:00:20.987749 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:20.989744 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-22 22:00:21.008267 INFO::Done
2025-12-22 22:00:21.009063 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.012773 INFO::ASW Batch was 0.378841033629208 prior to batch effect correction and is now -0.102535525261875 .
2025-12-22 22:00:21.013489 INFO::ASW Label was 0.376389068409751 prior to batch effect correction and is now 0.762388305301049 .
2025-12-22 22:00:21.014371 INFO::Total function execution time is 0.181495189666748 s and adjustment time is 0.162358522415161 s ( 89.46 )
2025-12-22 22:00:21.029364 INFO::Formatting Data.
2025-12-22 22:00:21.030196 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.031185 INFO::Removing potential empty rows and columns
2025-12-22 22:00:21.032298 INFO::Found 0 missing values.
2025-12-22 22:00:21.035366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:21.035975 INFO::Done
2025-12-22 22:00:21.036541 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:21.039867 INFO::Starting hierarchical adjustment
2025-12-22 22:00:21.040661 INFO::Found 2 batches.
2025-12-22 22:00:21.041214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:21.041899 INFO::Using default BPPARAM
2025-12-22 22:00:21.042464 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:21.043435 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-22 22:00:21.05987 INFO::Done
2025-12-22 22:00:21.060637 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.06395 INFO::ASW Batch was 0.601873693184827 prior to batch effect correction and is now 0.00384459094488494 .
2025-12-22 22:00:21.064619 INFO::ASW Label was 0.497968903827962 prior to batch effect correction and is now 0.922767564599448 .
2025-12-22 22:00:21.065429 INFO::Total function execution time is 0.0361630916595459 s and adjustment time is 0.0193641185760498 s ( 53.55 )
2025-12-22 22:00:21.066279 INFO::Formatting Data.
2025-12-22 22:00:21.066945 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.067873 INFO::Removing potential empty rows and columns
2025-12-22 22:00:21.068945 INFO::Found 0 missing values.
2025-12-22 22:00:21.071757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:21.072321 INFO::Done
2025-12-22 22:00:21.072894 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:21.076015 INFO::Starting hierarchical adjustment
2025-12-22 22:00:21.076817 INFO::Found 2 batches.
2025-12-22 22:00:21.077384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:21.078043 INFO::Using default BPPARAM
2025-12-22 22:00:21.07861 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:21.079603 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-22 22:00:21.095934 INFO::Done
2025-12-22 22:00:21.096703 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.100065 INFO::ASW Batch was 0.601873693184827 prior to batch effect correction and is now 0.00384459094488494 .
2025-12-22 22:00:21.100782 INFO::ASW Label was 0.497968903827962 prior to batch effect correction and is now 0.922767564599448 .
2025-12-22 22:00:21.101661 INFO::Total function execution time is 0.0353670120239258 s and adjustment time is 0.0192515850067139 s ( 54.43 )
2025-12-22 22:00:21.114426 INFO::Formatting Data.
2025-12-22 22:00:21.115287 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.11627 INFO::Removing potential empty rows and columns
2025-12-22 22:00:21.117265 INFO::Found 0 missing values.
2025-12-22 22:00:21.11961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:21.12018 INFO::Done
2025-12-22 22:00:21.120749 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:21.122913 INFO::Starting hierarchical adjustment
2025-12-22 22:00:21.123683 INFO::Found 2 batches.
2025-12-22 22:00:21.124256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:21.124926 INFO::Using default BPPARAM
2025-12-22 22:00:21.125489 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:21.126493 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-22 22:00:21.161357 INFO::Done
2025-12-22 22:00:21.1622 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.164546 INFO::ASW Batch was 0.017047593850995 prior to batch effect correction and is now -0.0841247522519177 .
2025-12-22 22:00:21.1655 INFO::Total function execution time is 0.0511651039123535 s and adjustment time is 0.0378043651580811 s ( 73.89 )
2025-12-22 22:00:21.178897 INFO::Formatting Data.
2025-12-22 22:00:21.17981 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.180797 INFO::Removing potential empty rows and columns
2025-12-22 22:00:21.181934 INFO::Found 0 missing values.
2025-12-22 22:00:21.183192 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.
2025-12-22 22:00:21.18845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:21.189095 INFO::Done
2025-12-22 22:00:21.189674 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:21.193041 INFO::Starting hierarchical adjustment
2025-12-22 22:00:21.19386 INFO::Found 2 batches.
2025-12-22 22:00:21.194428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:21.195123 INFO::Using default BPPARAM
2025-12-22 22:00:21.195717 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:21.196801 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-22 22:00:21.215677 INFO::Done
2025-12-22 22:00:21.216494 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.21995 INFO::ASW Batch was 0.331590038172629 prior to batch effect correction and is now 0.157178760304502 .
2025-12-22 22:00:21.220655 INFO::ASW Label was 0.760674484988632 prior to batch effect correction and is now 0.843166410182554 .
2025-12-22 22:00:21.221484 INFO::Total function execution time is 0.0427026748657227 s and adjustment time is 0.0219285488128662 s ( 51.35 )
2025-12-22 22:00:21.222391 INFO::Formatting Data.
2025-12-22 22:00:21.223116 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.22416 INFO::Removing potential empty rows and columns
2025-12-22 22:00:21.225261 INFO::Found 0 missing values.
2025-12-22 22:00:21.226277 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.
2025-12-22 22:00:21.231483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:21.232079 INFO::Done
2025-12-22 22:00:21.232655 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:21.23601 INFO::Starting hierarchical adjustment
2025-12-22 22:00:21.236772 INFO::Found 2 batches.
2025-12-22 22:00:21.23734 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:21.237994 INFO::Using default BPPARAM
2025-12-22 22:00:21.238584 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:21.239593 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-22 22:00:21.257947 INFO::Done
2025-12-22 22:00:21.258718 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.262449 INFO::ASW Batch was 0.331590038172629 prior to batch effect correction and is now 0.157178760304502 .
2025-12-22 22:00:21.263223 INFO::ASW Label was 0.760674484988632 prior to batch effect correction and is now 0.843166410182554 .
2025-12-22 22:00:21.264211 INFO::Total function execution time is 0.0418267250061035 s and adjustment time is 0.0213363170623779 s ( 51.01 )
2025-12-22 22:00:21.501717 INFO::Formatting Data.
2025-12-22 22:00:21.5027 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.5038 INFO::Removing potential empty rows and columns
2025-12-22 22:00:21.504999 INFO::Found 0 missing values.
2025-12-22 22:00:21.508342 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:21.508935 INFO::Done
2025-12-22 22:00:21.509472 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:21.511734 INFO::Starting hierarchical adjustment
2025-12-22 22:00:21.512475 INFO::Found 3 batches.
2025-12-22 22:00:21.513029 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:21.513676 INFO::Using default BPPARAM
2025-12-22 22:00:21.514203 INFO::Processing subtree level 1
2025-12-22 22:00:21.605736 INFO::Adjusting the last 1 batches sequentially
2025-12-22 22:00:21.60776 INFO::Done
2025-12-22 22:00:21.608433 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.61107 INFO::ASW Batch was -0.180406238965994 prior to batch effect correction and is now -0.180406238965994 .
2025-12-22 22:00:21.612118 INFO::Total function execution time is 0.110562562942505 s and adjustment time is 0.0954241752624512 s ( 86.31 )
2025-12-22 22:00:21.613272 INFO::Formatting Data.
2025-12-22 22:00:21.61396 INFO::Typecasting input to dataframe.
2025-12-22 22:00:21.614754 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.615734 INFO::Removing potential empty rows and columns
2025-12-22 22:00:21.616884 INFO::Found 0 missing values.
2025-12-22 22:00:21.620103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:21.620704 INFO::Done
2025-12-22 22:00:21.621246 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:21.623352 INFO::Starting hierarchical adjustment
2025-12-22 22:00:21.624118 INFO::Found 3 batches.
2025-12-22 22:00:21.624705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:21.625325 INFO::Using default BPPARAM
2025-12-22 22:00:21.625894 INFO::Processing subtree level 1
2025-12-22 22:00:21.718122 INFO::Adjusting the last 1 batches sequentially
2025-12-22 22:00:21.720091 INFO::Done
2025-12-22 22:00:21.720862 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.723612 INFO::ASW Batch was -0.180406238965994 prior to batch effect correction and is now -0.180406238965994 .
2025-12-22 22:00:21.724632 INFO::Total function execution time is 0.111313104629517 s and adjustment time is 0.0960838794708252 s ( 86.32 )
2025-12-22 22:00:21.73922 INFO::Formatting Data.
2025-12-22 22:00:21.740213 INFO::Typecasting input to dataframe.
2025-12-22 22:00:21.741189 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.74218 INFO::Removing potential empty rows and columns
2025-12-22 22:00:21.743309 INFO::Found 0 missing values.
2025-12-22 22:00:21.746537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:21.747106 INFO::Done
2025-12-22 22:00:21.747643 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:21.74984 INFO::Starting hierarchical adjustment
2025-12-22 22:00:21.750583 INFO::Found 3 batches.
2025-12-22 22:00:21.751112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:21.75175 INFO::Using default BPPARAM
2025-12-22 22:00:21.752275 INFO::Processing subtree level 1
2025-12-22 22:00:21.84694 INFO::Adjusting the last 1 batches sequentially
2025-12-22 22:00:21.84895 INFO::Done
2025-12-22 22:00:21.849684 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:21.852516 INFO::ASW Batch was -0.0846510249142055 prior to batch effect correction and is now -0.0846510249142055 .
2025-12-22 22:00:21.853558 INFO::Total function execution time is 0.114444732666016 s and adjustment time is 0.0984961986541748 s ( 86.06 )
2025-12-22 22:00:21.996468 INFO::Formatting Data.
2025-12-22 22:00:21.997325 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:21.998453 INFO::Removing potential empty rows and columns
2025-12-22 22:00:22.001262 INFO::Found 1000 missing values.
2025-12-22 22:00:22.020279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:22.021064 INFO::Done
2025-12-22 22:00:22.021653 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:22.02712 INFO::Starting hierarchical adjustment
2025-12-22 22:00:22.027924 INFO::Found 10 batches.
2025-12-22 22:00:22.028467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:22.029099 INFO::Using default BPPARAM
2025-12-22 22:00:22.02965 INFO::Processing subtree level 1
2025-12-22 22:00:22.16816 INFO::Processing subtree level 2
2025-12-22 22:00:22.316131 INFO::Adjusting the last 1 batches sequentially
2025-12-22 22:00:22.318178 INFO::Done
2025-12-22 22:00:22.318874 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:22.324771 INFO::ASW Batch was 0.512355589236308 prior to batch effect correction and is now 0.512355589236308 .
2025-12-22 22:00:22.325487 INFO::ASW Label was 0.329816056352705 prior to batch effect correction and is now 0.329816056352705 .
2025-12-22 22:00:22.326487 INFO::Total function execution time is 0.330074071884155 s and adjustment time is 0.290399074554443 s ( 87.98 )
2025-12-22 22:00:22.327371 INFO::Formatting Data.
2025-12-22 22:00:22.328052 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:22.329554 INFO::Removing potential empty rows and columns
2025-12-22 22:00:22.332549 INFO::Found 1000 missing values.
2025-12-22 22:00:22.353578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:22.354422 INFO::Done
2025-12-22 22:00:22.355046 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:22.36102 INFO::Starting hierarchical adjustment
2025-12-22 22:00:22.361913 INFO::Found 10 batches.
2025-12-22 22:00:23.468335 INFO::Set up parallel execution backend with 2 workers
2025-12-22 22:00:23.470237 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-22 22:00:24.670935 INFO::Adjusting the last 2 batches sequentially
2025-12-22 22:00:24.672756 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-22 22:00:24.689911 INFO::Done
2025-12-22 22:00:24.690806 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:24.695721 INFO::ASW Batch was 0.512355589236308 prior to batch effect correction and is now 0.512355589236308 .
2025-12-22 22:00:24.696339 INFO::ASW Label was 0.329816056352705 prior to batch effect correction and is now 0.329816056352705 .
2025-12-22 22:00:24.697117 INFO::Total function execution time is 2.36978554725647 s and adjustment time is 2.32812833786011 s ( 98.24 )
2025-12-22 22:00:24.908904 INFO::Formatting Data.
2025-12-22 22:00:24.909916 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:24.911222 INFO::Removing potential empty rows and columns
2025-12-22 22:00:24.91257 INFO::Found 0 missing values.
2025-12-22 22:00:24.91724 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:24.91808 INFO::Done
2025-12-22 22:00:24.918715 INFO::Acquiring quality metrics before batch effect correction.
2025-12-22 22:00:24.92187 INFO::Starting hierarchical adjustment
2025-12-22 22:00:24.922687 INFO::Found 3 batches.
2025-12-22 22:00:24.923226 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-22 22:00:24.923877 INFO::Using default BPPARAM
2025-12-22 22:00:24.924414 INFO::Processing subtree level 1
2025-12-22 22:00:25.05764 INFO::Adjusting the last 1 batches sequentially
2025-12-22 22:00:25.059723 INFO::Done
2025-12-22 22:00:25.060483 INFO::Acquiring quality metrics after batch effect correction.
2025-12-22 22:00:25.064035 INFO::ASW Batch was 0.196410208052772 prior to batch effect correction and is now -0.149236648243158 .
2025-12-22 22:00:25.064712 INFO::ASW Label was -0.186979904823417 prior to batch effect correction and is now -0.040568365006847 .
2025-12-22 22:00:25.065682 INFO::Total function execution time is 0.156961679458618 s and adjustment time is 0.137182235717773 s ( 87.4 )
2025-12-22 22:00:25.196818 INFO::Formatting Data.
2025-12-22 22:00:25.197667 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.198625 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.199792 INFO::Found 2 missing values.
2025-12-22 22:00:25.202732 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.203281 INFO::Done
2025-12-22 22:00:25.231799 INFO::Found NA in Reference column
2025-12-22 22:00:25.242321 INFO::Require at least two references per batch.
2025-12-22 22:00:25.263763 INFO::Formatting Data.
2025-12-22 22:00:25.264637 INFO::Recognized SummarizedExperiment
2025-12-22 22:00:25.2652 INFO::Typecasting input to dataframe.
2025-12-22 22:00:25.275458 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.276773 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.28024 INFO::Found 0 missing values.
2025-12-22 22:00:25.28685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.287449 INFO::Done
2025-12-22 22:00:25.304073 INFO::Formatting Data.
2025-12-22 22:00:25.304868 INFO::Recognized SummarizedExperiment
2025-12-22 22:00:25.305383 INFO::Typecasting input to dataframe.
2025-12-22 22:00:25.324349 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.325717 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.329143 INFO::Found 0 missing values.
2025-12-22 22:00:25.339741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.340439 INFO::Done
2025-12-22 22:00:25.357411 INFO::Formatting Data.
2025-12-22 22:00:25.358298 INFO::Recognized SummarizedExperiment
2025-12-22 22:00:25.358875 INFO::Typecasting input to dataframe.
2025-12-22 22:00:25.377204 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.378337 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.379445 INFO::Found 0 missing values.
2025-12-22 22:00:25.380398 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.
2025-12-22 22:00:25.384701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.385222 INFO::Done
2025-12-22 22:00:25.408174 INFO::Formatting Data.
2025-12-22 22:00:25.409145 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.410198 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.411365 INFO::Found 0 missing values.
2025-12-22 22:00:25.414612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.415222 INFO::Done
2025-12-22 22:00:25.428747 INFO::Formatting Data.
2025-12-22 22:00:25.429687 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.430628 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.431683 INFO::Found 0 missing values.
2025-12-22 22:00:25.434653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.435206 INFO::Done
2025-12-22 22:00:25.46804 INFO::Formatting Data.
2025-12-22 22:00:25.469055 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.470328 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.471713 INFO::Found 1 missing values.
2025-12-22 22:00:25.475133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.475779 INFO::Done
2025-12-22 22:00:25.497983 INFO::Formatting Data.
2025-12-22 22:00:25.499053 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.500149 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.501244 INFO::Found 2 missing values.
2025-12-22 22:00:25.502264 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.
2025-12-22 22:00:25.504707 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.505264 INFO::Done
2025-12-22 22:00:25.517088 INFO::Formatting Data.
2025-12-22 22:00:25.517999 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.518961 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.519941 INFO::Found 2 missing values.
2025-12-22 22:00:25.521687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.522267 INFO::Done
2025-12-22 22:00:25.534473 INFO::Formatting Data.
2025-12-22 22:00:25.535422 INFO::Typecasting input to dataframe.
2025-12-22 22:00:25.536291 INFO::Replacing NaNs with NAs.
2025-12-22 22:00:25.537219 INFO::Removing potential empty rows and columns
2025-12-22 22:00:25.538227 INFO::Found 0 missing values.
2025-12-22 22:00:25.541144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-22 22:00:25.541705 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.501 3.857 20.948
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.983 | 1.507 | 18.335 | |
| compute_asw | 0.024 | 0.001 | 0.025 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.009 | 0.003 | 0.012 | |