Yannis Schumann
| Snapshot Date: 2025-12-04 13:45 -0500 (Thu, 04 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 2025-12-08 12:02 -0500 (Mon, 08 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4668 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-12-05 07:32:13 -0000 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 07:34:51 -0000 (Fri, 05 Dec 2025) |
| EllapsedTime: 157.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 26.755 1.124 19.058
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-12-05 07:34:35.945353 INFO::Formatting Data.
2025-12-05 07:34:35.946992 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:35.964117 INFO::Removing potential empty rows and columns
2025-12-05 07:34:36.405325 INFO::Found 0 missing values.
2025-12-05 07:34:36.410094 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:36.411023 INFO::Done
2025-12-05 07:34:36.4118 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:36.426842 INFO::Starting hierarchical adjustment
2025-12-05 07:34:36.428004 INFO::Found 3 batches.
2025-12-05 07:34:36.428802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:36.430251 INFO::Using default BPPARAM
2025-12-05 07:34:36.43108 INFO::Processing subtree level 1
2025-12-05 07:34:36.55152 INFO::Adjusting the last 1 batches sequentially
2025-12-05 07:34:36.553902 INFO::Done
2025-12-05 07:34:36.554792 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:36.558441 INFO::ASW Batch was -0.0345817886075241 prior to batch effect correction and is now -0.0345817886075241 .
2025-12-05 07:34:36.559982 INFO::Total function execution time is 0.615407228469849 s and adjustment time is 0.126132249832153 s ( 20.5 )
2025-12-05 07:34:36.579028 INFO::Formatting Data.
2025-12-05 07:34:36.580014 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:36.581255 INFO::Removing potential empty rows and columns
2025-12-05 07:34:36.582799 INFO::Found 0 missing values.
2025-12-05 07:34:36.584095 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.
2025-12-05 07:34:36.599025 INFO::Formatting Data.
2025-12-05 07:34:36.599994 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:36.601218 INFO::Removing potential empty rows and columns
2025-12-05 07:34:36.602686 INFO::Found 0 missing values.
2025-12-05 07:34:36.603957 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.
2025-12-05 07:34:36.625846 INFO::Formatting Data.
2025-12-05 07:34:36.626857 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:36.628026 INFO::Removing potential empty rows and columns
2025-12-05 07:34:36.629462 INFO::Found 0 missing values.
2025-12-05 07:34:36.630686 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.
2025-12-05 07:34:36.63685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:36.63769 INFO::Done
2025-12-05 07:34:36.638448 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:36.641207 INFO::Starting hierarchical adjustment
2025-12-05 07:34:36.642218 INFO::Found 2 batches.
2025-12-05 07:34:36.642983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:36.643894 INFO::Using default BPPARAM
2025-12-05 07:34:36.644662 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:36.646038 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 07:34:36.675653 INFO::Done
2025-12-05 07:34:36.676563 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:36.679393 INFO::ASW Batch was 0.0179910771176073 prior to batch effect correction and is now -0.0548988422631566 .
2025-12-05 07:34:36.680474 INFO::Total function execution time is 0.0546822547912598 s and adjustment time is 0.0336182117462158 s ( 61.48 )
2025-12-05 07:34:36.684021 INFO::Formatting Data.
2025-12-05 07:34:36.684973 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:36.696951 INFO::Formatting Data.
2025-12-05 07:34:36.697915 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:36.699157 INFO::Removing potential empty rows and columns
2025-12-05 07:34:36.70067 INFO::Found 0 missing values.
2025-12-05 07:34:36.705084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:36.70602 INFO::Done
2025-12-05 07:34:36.706844 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:36.709648 INFO::Starting hierarchical adjustment
2025-12-05 07:34:36.710697 INFO::Found 2 batches.
2025-12-05 07:34:36.711505 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:36.712456 INFO::Using default BPPARAM
2025-12-05 07:34:36.713363 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:36.714837 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 07:34:36.767367 INFO::Done
2025-12-05 07:34:36.768257 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:36.771026 INFO::ASW Batch was -0.0389958440481065 prior to batch effect correction and is now -0.119078481789794 .
2025-12-05 07:34:36.77211 INFO::Total function execution time is 0.0752308368682861 s and adjustment time is 0.0568737983703613 s ( 75.6 )
2025-12-05 07:34:36.773602 INFO::Formatting Data.
2025-12-05 07:34:36.77446 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:36.77569 INFO::Removing potential empty rows and columns
2025-12-05 07:34:36.777124 INFO::Found 0 missing values.
2025-12-05 07:34:36.781121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:36.781907 INFO::Done
2025-12-05 07:34:36.782649 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:36.785357 INFO::Starting hierarchical adjustment
2025-12-05 07:34:36.786394 INFO::Found 2 batches.
2025-12-05 07:34:36.787187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:36.788038 INFO::Using default BPPARAM
2025-12-05 07:34:36.788806 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:36.790095 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 07:34:36.810664 INFO::Done
2025-12-05 07:34:36.811581 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:36.814325 INFO::ASW Batch was -0.0389958440481065 prior to batch effect correction and is now -0.119078481789794 .
2025-12-05 07:34:36.815466 INFO::Total function execution time is 0.0418543815612793 s and adjustment time is 0.0244624614715576 s ( 58.45 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-05 07:34:40.467826 INFO::Formatting Data.
2025-12-05 07:34:40.468839 INFO::Recognized SummarizedExperiment
2025-12-05 07:34:40.469537 INFO::Typecasting input to dataframe.
2025-12-05 07:34:40.511169 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:40.512718 INFO::Removing potential empty rows and columns
2025-12-05 07:34:40.517926 INFO::Found 0 missing values.
2025-12-05 07:34:40.528052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:40.528968 INFO::Done
2025-12-05 07:34:40.529693 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:40.534671 INFO::Starting hierarchical adjustment
2025-12-05 07:34:40.53584 INFO::Found 2 batches.
2025-12-05 07:34:40.536613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:40.538091 INFO::Using default BPPARAM
2025-12-05 07:34:40.539141 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:40.540501 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 07:34:40.623256 INFO::Done
2025-12-05 07:34:40.624196 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:40.629204 INFO::ASW Batch was 0.0078549807831757 prior to batch effect correction and is now -0.0911447632789939 .
2025-12-05 07:34:40.630461 INFO::Total function execution time is 0.163090229034424 s and adjustment time is 0.0876202583312988 s ( 53.73 )
Warning: stack imbalance in '{', 73 then 75
2025-12-05 07:34:40.657754 INFO::Formatting Data.
2025-12-05 07:34:40.658781 INFO::Recognized SummarizedExperiment
2025-12-05 07:34:40.659578 INFO::Typecasting input to dataframe.
2025-12-05 07:34:40.673241 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:40.674962 INFO::Removing potential empty rows and columns
2025-12-05 07:34:40.680304 INFO::Found 0 missing values.
2025-12-05 07:34:40.69136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:40.692342 INFO::Done
2025-12-05 07:34:40.693218 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:40.69838 INFO::Starting hierarchical adjustment
2025-12-05 07:34:40.699671 INFO::Found 2 batches.
2025-12-05 07:34:40.700518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:40.701491 INFO::Using default BPPARAM
2025-12-05 07:34:40.70233 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:40.703859 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 07:34:40.740195 INFO::Done
2025-12-05 07:34:40.741197 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:40.746308 INFO::ASW Batch was -0.00474753652981064 prior to batch effect correction and is now -0.00474753652981064 .
2025-12-05 07:34:40.747673 INFO::Total function execution time is 0.0898549556732178 s and adjustment time is 0.0407581329345703 s ( 45.36 )
2025-12-05 07:34:40.774934 INFO::Formatting Data.
2025-12-05 07:34:40.775914 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:40.777116 INFO::Removing potential empty rows and columns
2025-12-05 07:34:40.778525 INFO::Found 0 missing values.
2025-12-05 07:34:40.782747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:40.783583 INFO::Done
2025-12-05 07:34:40.784356 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:40.787146 INFO::Starting hierarchical adjustment
2025-12-05 07:34:40.788209 INFO::Found 3 batches.
2025-12-05 07:34:40.789024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:40.789905 INFO::Using default BPPARAM
2025-12-05 07:34:40.790689 INFO::Processing subtree level 1
2025-12-05 07:34:40.95488 INFO::Adjusting the last 1 batches sequentially
2025-12-05 07:34:40.957236 INFO::Done
2025-12-05 07:34:40.958062 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:40.961476 INFO::ASW Batch was -0.111798850530324 prior to batch effect correction and is now -0.170197087044526 .
2025-12-05 07:34:40.962828 INFO::Total function execution time is 0.187911987304688 s and adjustment time is 0.169230461120605 s ( 90.06 )
2025-12-05 07:34:40.982342 INFO::Skipping initial DF formatting
2025-12-05 07:34:40.983311 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:40.988695 INFO::Starting hierarchical adjustment
2025-12-05 07:34:40.989835 INFO::Found 5 batches.
2025-12-05 07:34:40.990604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:40.991533 INFO::Using default BPPARAM
2025-12-05 07:34:40.992358 INFO::Processing subtree level 1
2025-12-05 07:34:41.254839 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:41.256966 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 07:34:41.285314 INFO::Done
2025-12-05 07:34:41.28626 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:41.292225 INFO::ASW Batch was 0.514828307955176 prior to batch effect correction and is now 0.514828307955176 .
2025-12-05 07:34:41.293133 INFO::ASW Label was 0.373951096686282 prior to batch effect correction and is now 0.373951096686282 .
2025-12-05 07:34:41.294292 INFO::Total function execution time is 0.311979532241821 s and adjustment time is 0.295671463012695 s ( 94.77 )
2025-12-05 07:34:41.380798 INFO::Formatting Data.
2025-12-05 07:34:41.381828 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:41.383162 INFO::Removing potential empty rows and columns
2025-12-05 07:34:41.384572 INFO::Found 0 missing values.
2025-12-05 07:34:41.390874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:41.391806 INFO::Done
2025-12-05 07:34:41.392625 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:41.397051 INFO::Starting hierarchical adjustment
2025-12-05 07:34:41.398297 INFO::Found 5 batches.
2025-12-05 07:34:41.399135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:41.400058 INFO::Using default BPPARAM
2025-12-05 07:34:41.400946 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.
2025-12-05 07:34:41.559783 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:41.562032 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 07:34:41.587335 INFO::Done
2025-12-05 07:34:41.588347 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:41.593446 INFO::ASW Batch was 0.329312963819737 prior to batch effect correction and is now -0.0279663854674889 .
2025-12-05 07:34:41.594434 INFO::ASW Label was 0.478404648760472 prior to batch effect correction and is now 0.805251376411721 .
2025-12-05 07:34:41.595796 INFO::Total function execution time is 0.215019702911377 s and adjustment time is 0.189253568649292 s ( 88.02 )
2025-12-05 07:34:41.597096 INFO::Formatting Data.
2025-12-05 07:34:41.598014 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:41.599419 INFO::Removing potential empty rows and columns
2025-12-05 07:34:41.600988 INFO::Found 0 missing values.
2025-12-05 07:34:41.6075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:41.608403 INFO::Done
2025-12-05 07:34:41.609213 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:41.613694 INFO::Starting hierarchical adjustment
2025-12-05 07:34:41.614863 INFO::Found 5 batches.
2025-12-05 07:34:41.615623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:41.616511 INFO::Using default BPPARAM
2025-12-05 07:34:41.617332 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.
2025-12-05 07:34:41.771362 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:41.773386 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 07:34:41.796123 INFO::Done
2025-12-05 07:34:41.797096 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:41.801644 INFO::ASW Batch was 0.329312963819737 prior to batch effect correction and is now -0.0279663854674889 .
2025-12-05 07:34:41.802527 INFO::ASW Label was 0.478404648760472 prior to batch effect correction and is now 0.805251376411721 .
2025-12-05 07:34:41.803735 INFO::Total function execution time is 0.206632137298584 s and adjustment time is 0.181504726409912 s ( 87.84 )
2025-12-05 07:34:41.822931 INFO::Formatting Data.
2025-12-05 07:34:41.82395 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:41.825226 INFO::Removing potential empty rows and columns
2025-12-05 07:34:41.826809 INFO::Found 0 missing values.
2025-12-05 07:34:41.832927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:41.833779 INFO::Done
2025-12-05 07:34:41.834538 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:41.838804 INFO::Starting hierarchical adjustment
2025-12-05 07:34:41.839892 INFO::Found 5 batches.
2025-12-05 07:34:41.840674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:41.841614 INFO::Using default BPPARAM
2025-12-05 07:34:41.842393 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.
2025-12-05 07:34:41.990896 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:41.993205 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 07:34:42.027607 INFO::Done
2025-12-05 07:34:42.028964 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:42.034482 INFO::ASW Batch was 0.36303751795341 prior to batch effect correction and is now -0.0261268168442883 .
2025-12-05 07:34:42.035526 INFO::ASW Label was 0.399920494067098 prior to batch effect correction and is now 0.805452010930988 .
2025-12-05 07:34:42.036879 INFO::Total function execution time is 0.213942766189575 s and adjustment time is 0.187798500061035 s ( 87.78 )
2025-12-05 07:34:42.038284 INFO::Formatting Data.
2025-12-05 07:34:42.039305 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:42.040692 INFO::Removing potential empty rows and columns
2025-12-05 07:34:42.042335 INFO::Found 0 missing values.
2025-12-05 07:34:42.049149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:42.050126 INFO::Done
2025-12-05 07:34:42.051023 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:42.055579 INFO::Starting hierarchical adjustment
2025-12-05 07:34:42.056883 INFO::Found 5 batches.
2025-12-05 07:34:42.057798 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:42.058843 INFO::Using default BPPARAM
2025-12-05 07:34:42.059803 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.
2025-12-05 07:34:42.205502 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:42.207735 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 07:34:42.232133 INFO::Done
2025-12-05 07:34:42.23322 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:42.238572 INFO::ASW Batch was 0.36303751795341 prior to batch effect correction and is now -0.0261268168442883 .
2025-12-05 07:34:42.239579 INFO::ASW Label was 0.399920494067098 prior to batch effect correction and is now 0.805452010930988 .
2025-12-05 07:34:42.240815 INFO::Total function execution time is 0.202508449554443 s and adjustment time is 0.175527811050415 s ( 86.68 )
2025-12-05 07:34:42.260569 INFO::Formatting Data.
2025-12-05 07:34:42.261719 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:42.263081 INFO::Removing potential empty rows and columns
2025-12-05 07:34:42.264582 INFO::Found 0 missing values.
2025-12-05 07:34:42.268675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:42.269558 INFO::Done
2025-12-05 07:34:42.270345 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:42.274568 INFO::Starting hierarchical adjustment
2025-12-05 07:34:42.275756 INFO::Found 2 batches.
2025-12-05 07:34:42.276572 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:42.277539 INFO::Using default BPPARAM
2025-12-05 07:34:42.27837 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:42.279751 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 07:34:42.30063 INFO::Done
2025-12-05 07:34:42.301556 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:42.30567 INFO::ASW Batch was 0.557168202426829 prior to batch effect correction and is now 0.0651344413038073 .
2025-12-05 07:34:42.306545 INFO::ASW Label was 0.522569313434618 prior to batch effect correction and is now 0.884986988787107 .
2025-12-05 07:34:42.307716 INFO::Total function execution time is 0.0472135543823242 s and adjustment time is 0.0250928401947021 s ( 53.15 )
2025-12-05 07:34:42.30882 INFO::Formatting Data.
2025-12-05 07:34:42.309729 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:42.31101 INFO::Removing potential empty rows and columns
2025-12-05 07:34:42.31242 INFO::Found 0 missing values.
2025-12-05 07:34:42.316505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:42.317372 INFO::Done
2025-12-05 07:34:42.318155 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:42.322245 INFO::Starting hierarchical adjustment
2025-12-05 07:34:42.323333 INFO::Found 2 batches.
2025-12-05 07:34:42.324131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:42.325063 INFO::Using default BPPARAM
2025-12-05 07:34:42.3259 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:42.327253 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 07:34:42.347881 INFO::Done
2025-12-05 07:34:42.348813 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:42.35283 INFO::ASW Batch was 0.557168202426829 prior to batch effect correction and is now 0.0651344413038073 .
2025-12-05 07:34:42.353689 INFO::ASW Label was 0.522569313434618 prior to batch effect correction and is now 0.884986988787107 .
2025-12-05 07:34:42.354786 INFO::Total function execution time is 0.0459742546081543 s and adjustment time is 0.0247645378112793 s ( 53.87 )
2025-12-05 07:34:42.370771 INFO::Formatting Data.
2025-12-05 07:34:42.371788 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:42.373043 INFO::Removing potential empty rows and columns
2025-12-05 07:34:42.374357 INFO::Found 0 missing values.
2025-12-05 07:34:42.377608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:42.378451 INFO::Done
2025-12-05 07:34:42.379293 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:42.381996 INFO::Starting hierarchical adjustment
2025-12-05 07:34:42.383086 INFO::Found 2 batches.
2025-12-05 07:34:42.383909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:42.384891 INFO::Using default BPPARAM
2025-12-05 07:34:42.385746 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:42.387218 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 07:34:42.43387 INFO::Done
2025-12-05 07:34:42.434856 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:42.437599 INFO::ASW Batch was -0.143959487337951 prior to batch effect correction and is now -0.151065852392946 .
2025-12-05 07:34:42.438825 INFO::Total function execution time is 0.0681173801422119 s and adjustment time is 0.0509719848632812 s ( 74.83 )
2025-12-05 07:34:42.455912 INFO::Formatting Data.
2025-12-05 07:34:42.457123 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:42.45849 INFO::Removing potential empty rows and columns
2025-12-05 07:34:42.460098 INFO::Found 0 missing values.
2025-12-05 07:34:42.461879 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.
2025-12-05 07:34:42.468869 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:42.469764 INFO::Done
2025-12-05 07:34:42.470548 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:42.474655 INFO::Starting hierarchical adjustment
2025-12-05 07:34:42.475819 INFO::Found 2 batches.
2025-12-05 07:34:42.476628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:42.477553 INFO::Using default BPPARAM
2025-12-05 07:34:42.478349 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:42.479782 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 07:34:42.503543 INFO::Done
2025-12-05 07:34:42.504459 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:42.50861 INFO::ASW Batch was 0.31773036606689 prior to batch effect correction and is now -0.0110298915580657 .
2025-12-05 07:34:42.509567 INFO::ASW Label was 0.715503338164242 prior to batch effect correction and is now 0.937341763675465 .
2025-12-05 07:34:42.510677 INFO::Total function execution time is 0.0548429489135742 s and adjustment time is 0.0279321670532227 s ( 50.93 )
2025-12-05 07:34:42.511874 INFO::Formatting Data.
2025-12-05 07:34:42.512791 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:42.514117 INFO::Removing potential empty rows and columns
2025-12-05 07:34:42.515574 INFO::Found 0 missing values.
2025-12-05 07:34:42.51689 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.
2025-12-05 07:34:42.52364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:42.524523 INFO::Done
2025-12-05 07:34:42.525342 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:42.529438 INFO::Starting hierarchical adjustment
2025-12-05 07:34:42.530543 INFO::Found 2 batches.
2025-12-05 07:34:42.531401 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:42.532345 INFO::Using default BPPARAM
2025-12-05 07:34:42.533211 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:42.534621 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 07:34:42.558185 INFO::Done
2025-12-05 07:34:42.559161 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:42.563421 INFO::ASW Batch was 0.31773036606689 prior to batch effect correction and is now -0.0110298915580657 .
2025-12-05 07:34:42.564338 INFO::ASW Label was 0.715503338164242 prior to batch effect correction and is now 0.937341763675465 .
2025-12-05 07:34:42.565532 INFO::Total function execution time is 0.0536549091339111 s and adjustment time is 0.027843713760376 s ( 51.89 )
2025-12-05 07:34:42.873481 INFO::Formatting Data.
2025-12-05 07:34:42.874599 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:42.875928 INFO::Removing potential empty rows and columns
2025-12-05 07:34:42.877425 INFO::Found 0 missing values.
2025-12-05 07:34:42.881877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:42.882779 INFO::Done
2025-12-05 07:34:42.883554 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:42.886376 INFO::Starting hierarchical adjustment
2025-12-05 07:34:42.887519 INFO::Found 3 batches.
2025-12-05 07:34:42.888335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:42.889278 INFO::Using default BPPARAM
2025-12-05 07:34:42.89005 INFO::Processing subtree level 1
2025-12-05 07:34:42.995622 INFO::Adjusting the last 1 batches sequentially
2025-12-05 07:34:42.998106 INFO::Done
2025-12-05 07:34:42.99915 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:43.002831 INFO::ASW Batch was -0.0156018112957019 prior to batch effect correction and is now -0.0156018112957019 .
2025-12-05 07:34:43.004339 INFO::Total function execution time is 0.130837678909302 s and adjustment time is 0.11078929901123 s ( 84.68 )
2025-12-05 07:34:43.006019 INFO::Formatting Data.
2025-12-05 07:34:43.007132 INFO::Typecasting input to dataframe.
2025-12-05 07:34:43.00837 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:43.00984 INFO::Removing potential empty rows and columns
2025-12-05 07:34:43.011625 INFO::Found 0 missing values.
2025-12-05 07:34:43.016626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:43.017688 INFO::Done
2025-12-05 07:34:43.018586 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:43.02179 INFO::Starting hierarchical adjustment
2025-12-05 07:34:43.023085 INFO::Found 3 batches.
2025-12-05 07:34:43.023984 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:43.025009 INFO::Using default BPPARAM
2025-12-05 07:34:43.025864 INFO::Processing subtree level 1
2025-12-05 07:34:43.134304 INFO::Adjusting the last 1 batches sequentially
2025-12-05 07:34:43.136724 INFO::Done
2025-12-05 07:34:43.137647 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:43.141134 INFO::ASW Batch was -0.0156018112957019 prior to batch effect correction and is now -0.0156018112957019 .
2025-12-05 07:34:43.142542 INFO::Total function execution time is 0.136512517929077 s and adjustment time is 0.11396861076355 s ( 83.49 )
2025-12-05 07:34:43.161641 INFO::Formatting Data.
2025-12-05 07:34:43.162689 INFO::Typecasting input to dataframe.
2025-12-05 07:34:43.163925 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:43.165327 INFO::Removing potential empty rows and columns
2025-12-05 07:34:43.166854 INFO::Found 0 missing values.
2025-12-05 07:34:43.171278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:43.172192 INFO::Done
2025-12-05 07:34:43.173022 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:43.175822 INFO::Starting hierarchical adjustment
2025-12-05 07:34:43.176919 INFO::Found 3 batches.
2025-12-05 07:34:43.177744 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:43.178654 INFO::Using default BPPARAM
2025-12-05 07:34:43.179525 INFO::Processing subtree level 1
2025-12-05 07:34:43.286914 INFO::Adjusting the last 1 batches sequentially
2025-12-05 07:34:43.289543 INFO::Done
2025-12-05 07:34:43.290587 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:43.294454 INFO::ASW Batch was -0.107780744378424 prior to batch effect correction and is now -0.107780744378424 .
2025-12-05 07:34:43.29603 INFO::Total function execution time is 0.134358644485474 s and adjustment time is 0.112840890884399 s ( 83.98 )
2025-12-05 07:34:43.480307 INFO::Formatting Data.
2025-12-05 07:34:43.481462 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:43.483158 INFO::Removing potential empty rows and columns
2025-12-05 07:34:43.487691 INFO::Found 1000 missing values.
2025-12-05 07:34:43.518839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:43.519925 INFO::Done
2025-12-05 07:34:43.520995 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:43.529094 INFO::Starting hierarchical adjustment
2025-12-05 07:34:43.530298 INFO::Found 10 batches.
2025-12-05 07:34:43.53113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:43.532056 INFO::Using default BPPARAM
2025-12-05 07:34:43.532893 INFO::Processing subtree level 1
2025-12-05 07:34:43.704368 INFO::Processing subtree level 2
2025-12-05 07:34:43.891166 INFO::Adjusting the last 1 batches sequentially
2025-12-05 07:34:43.893945 INFO::Done
2025-12-05 07:34:43.894872 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:43.902832 INFO::ASW Batch was 0.518797287953002 prior to batch effect correction and is now 0.518797287953002 .
2025-12-05 07:34:43.903901 INFO::ASW Label was 0.332983392354375 prior to batch effect correction and is now 0.332983392354375 .
2025-12-05 07:34:43.905282 INFO::Total function execution time is 0.424988269805908 s and adjustment time is 0.363879919052124 s ( 85.62 )
2025-12-05 07:34:43.906512 INFO::Formatting Data.
2025-12-05 07:34:43.907504 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:43.909331 INFO::Removing potential empty rows and columns
2025-12-05 07:34:43.913533 INFO::Found 1000 missing values.
2025-12-05 07:34:43.941441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:43.942398 INFO::Done
2025-12-05 07:34:43.943206 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:43.950857 INFO::Starting hierarchical adjustment
2025-12-05 07:34:43.952006 INFO::Found 10 batches.
2025-12-05 07:34:45.004302 INFO::Set up parallel execution backend with 2 workers
2025-12-05 07:34:45.007112 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-05 07:34:46.249111 INFO::Adjusting the last 2 batches sequentially
2025-12-05 07:34:46.251553 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 07:34:46.277374 INFO::Done
2025-12-05 07:34:46.278263 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:46.285297 INFO::ASW Batch was 0.518797287953002 prior to batch effect correction and is now 0.518797287953002 .
2025-12-05 07:34:46.286313 INFO::ASW Label was 0.332983392354375 prior to batch effect correction and is now 0.332983392354375 .
2025-12-05 07:34:46.287608 INFO::Total function execution time is 2.38108849525452 s and adjustment time is 2.32557344436646 s ( 97.67 )
2025-12-05 07:34:46.479653 INFO::Formatting Data.
2025-12-05 07:34:46.48085 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:46.48219 INFO::Removing potential empty rows and columns
2025-12-05 07:34:46.48385 INFO::Found 0 missing values.
2025-12-05 07:34:46.4899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:46.49089 INFO::Done
2025-12-05 07:34:46.491671 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 07:34:46.495729 INFO::Starting hierarchical adjustment
2025-12-05 07:34:46.496904 INFO::Found 3 batches.
2025-12-05 07:34:46.497705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 07:34:46.498614 INFO::Using default BPPARAM
2025-12-05 07:34:46.499462 INFO::Processing subtree level 1
2025-12-05 07:34:46.629039 INFO::Adjusting the last 1 batches sequentially
2025-12-05 07:34:46.631592 INFO::Done
2025-12-05 07:34:46.632591 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 07:34:46.637584 INFO::ASW Batch was 0.200679163119422 prior to batch effect correction and is now -0.15847393297904 .
2025-12-05 07:34:46.638636 INFO::ASW Label was -0.154672129688588 prior to batch effect correction and is now 0.212756566148722 .
2025-12-05 07:34:46.640102 INFO::Total function execution time is 0.16048526763916 s and adjustment time is 0.134913206100464 s ( 84.07 )
2025-12-05 07:34:46.827826 INFO::Formatting Data.
2025-12-05 07:34:46.828903 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:46.830206 INFO::Removing potential empty rows and columns
2025-12-05 07:34:46.831766 INFO::Found 2 missing values.
2025-12-05 07:34:46.836362 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:46.837217 INFO::Done
2025-12-05 07:34:46.878121 INFO::Found NA in Reference column
2025-12-05 07:34:46.892636 INFO::Require at least two references per batch.
2025-12-05 07:34:46.923875 INFO::Formatting Data.
2025-12-05 07:34:46.92487 INFO::Recognized SummarizedExperiment
2025-12-05 07:34:46.925658 INFO::Typecasting input to dataframe.
2025-12-05 07:34:46.940317 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:46.94196 INFO::Removing potential empty rows and columns
2025-12-05 07:34:46.947523 INFO::Found 0 missing values.
2025-12-05 07:34:46.958402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:46.959398 INFO::Done
2025-12-05 07:34:46.982531 INFO::Formatting Data.
2025-12-05 07:34:46.983535 INFO::Recognized SummarizedExperiment
2025-12-05 07:34:46.984292 INFO::Typecasting input to dataframe.
2025-12-05 07:34:47.009974 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:47.011648 INFO::Removing potential empty rows and columns
2025-12-05 07:34:47.017144 INFO::Found 0 missing values.
2025-12-05 07:34:47.03499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:47.035916 INFO::Done
2025-12-05 07:34:47.05895 INFO::Formatting Data.
2025-12-05 07:34:47.059922 INFO::Recognized SummarizedExperiment
2025-12-05 07:34:47.060689 INFO::Typecasting input to dataframe.
2025-12-05 07:34:47.085321 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:47.086688 INFO::Removing potential empty rows and columns
2025-12-05 07:34:47.088332 INFO::Found 0 missing values.
2025-12-05 07:34:47.089703 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.
2025-12-05 07:34:47.096559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:47.097486 INFO::Done
2025-12-05 07:34:47.112082 INFO::Formatting Data.
2025-12-05 07:34:47.113113 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:47.114326 INFO::Removing potential empty rows and columns
2025-12-05 07:34:47.115814 INFO::Found 0 missing values.
2025-12-05 07:34:47.120291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:47.121235 INFO::Done
2025-12-05 07:34:47.13764 INFO::Formatting Data.
2025-12-05 07:34:47.138642 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:47.139901 INFO::Removing potential empty rows and columns
2025-12-05 07:34:47.141403 INFO::Found 0 missing values.
2025-12-05 07:34:47.145962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:47.14681 INFO::Done
2025-12-05 07:34:47.190802 INFO::Formatting Data.
2025-12-05 07:34:47.191876 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:47.193322 INFO::Removing potential empty rows and columns
2025-12-05 07:34:47.195017 INFO::Found 1 missing values.
2025-12-05 07:34:47.198892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:47.199695 INFO::Done
2025-12-05 07:34:47.227192 INFO::Formatting Data.
2025-12-05 07:34:47.228243 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:47.229519 INFO::Removing potential empty rows and columns
2025-12-05 07:34:47.231012 INFO::Found 2 missing values.
2025-12-05 07:34:47.232411 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.
2025-12-05 07:34:47.235992 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:47.236953 INFO::Done
2025-12-05 07:34:47.25235 INFO::Formatting Data.
2025-12-05 07:34:47.253457 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:47.254753 INFO::Removing potential empty rows and columns
2025-12-05 07:34:47.256164 INFO::Found 2 missing values.
2025-12-05 07:34:47.258657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:47.259567 INFO::Done
2025-12-05 07:34:47.27506 INFO::Formatting Data.
2025-12-05 07:34:47.276067 INFO::Typecasting input to dataframe.
2025-12-05 07:34:47.277203 INFO::Replacing NaNs with NAs.
2025-12-05 07:34:47.278394 INFO::Removing potential empty rows and columns
2025-12-05 07:34:47.27988 INFO::Found 0 missing values.
2025-12-05 07:34:47.285032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 07:34:47.286067 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.983 4.458 24.030
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.755 | 1.124 | 19.058 | |
| compute_asw | 0.033 | 0.000 | 0.033 | |
| count_existing | 0.017 | 0.000 | 0.017 | |
| generate_data_covariables | 0.015 | 0.000 | 0.015 | |
| generate_dataset | 0.014 | 0.000 | 0.013 | |