Yannis Schumann
| Snapshot Date: 2025-12-01 13:40 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-02 11:34 -0500 (Tue, 02 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 167/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-12-01 21:26:55 -0500 (Mon, 01 Dec 2025) |
| EndedAt: 2025-12-01 21:28:25 -0500 (Mon, 01 Dec 2025) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.7.0’
* 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 23.686 1.145 16.745
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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")
2025-12-01 21:27:47.428959 INFO::Formatting Data.
2025-12-01 21:27:47.430559 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:47.442671 INFO::Removing potential empty rows and columns
2025-12-01 21:27:47.709928 INFO::Found 0 missing values.
2025-12-01 21:27:47.713709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:47.714521 INFO::Done
2025-12-01 21:27:47.715193 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:47.728798 INFO::Starting hierarchical adjustment
2025-12-01 21:27:47.729905 INFO::Found 3 batches.
2025-12-01 21:27:47.730604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:47.732104 INFO::Using default BPPARAM
2025-12-01 21:27:47.732712 INFO::Processing subtree level 1
2025-12-01 21:27:47.85008 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:27:47.852119 INFO::Done
2025-12-01 21:27:47.852918 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:47.85587 INFO::ASW Batch was -0.0857798887653273 prior to batch effect correction and is now -0.0857798887653273 .
2025-12-01 21:27:47.857033 INFO::Total function execution time is 0.428957223892212 s and adjustment time is 0.1224524974823 s ( 28.55 )
2025-12-01 21:27:47.873082 INFO::Formatting Data.
2025-12-01 21:27:47.873915 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:47.874939 INFO::Removing potential empty rows and columns
2025-12-01 21:27:47.876272 INFO::Found 0 missing values.
2025-12-01 21:27:47.877339 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.
2025-12-01 21:27:47.891253 INFO::Formatting Data.
2025-12-01 21:27:47.892221 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:47.893314 INFO::Removing potential empty rows and columns
2025-12-01 21:27:47.894686 INFO::Found 0 missing values.
2025-12-01 21:27:47.895832 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.
2025-12-01 21:27:47.931301 INFO::Formatting Data.
2025-12-01 21:27:47.932618 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:47.934077 INFO::Removing potential empty rows and columns
2025-12-01 21:27:47.935817 INFO::Found 0 missing values.
2025-12-01 21:27:47.937268 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.
2025-12-01 21:27:47.94453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:47.945411 INFO::Done
2025-12-01 21:27:47.946272 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:47.950163 INFO::Starting hierarchical adjustment
2025-12-01 21:27:47.951243 INFO::Found 2 batches.
2025-12-01 21:27:47.952001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:47.952977 INFO::Using default BPPARAM
2025-12-01 21:27:47.953731 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:47.955024 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:27:47.986875 INFO::Done
2025-12-01 21:27:47.987745 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:47.990203 INFO::ASW Batch was -0.000203888007036573 prior to batch effect correction and is now -0.0695551635693426 .
2025-12-01 21:27:47.991239 INFO::Total function execution time is 0.0602524280548096 s and adjustment time is 0.0358104705810547 s ( 59.43 )
2025-12-01 21:27:47.99489 INFO::Formatting Data.
2025-12-01 21:27:47.995609 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:48.007818 INFO::Formatting Data.
2025-12-01 21:27:48.008703 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:48.009805 INFO::Removing potential empty rows and columns
2025-12-01 21:27:48.011037 INFO::Found 0 missing values.
2025-12-01 21:27:48.01494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:48.015592 INFO::Done
2025-12-01 21:27:48.016176 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:48.018719 INFO::Starting hierarchical adjustment
2025-12-01 21:27:48.01957 INFO::Found 2 batches.
2025-12-01 21:27:48.020219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:48.020925 INFO::Using default BPPARAM
2025-12-01 21:27:48.02149 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:48.022636 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:27:48.115479 INFO::Done
2025-12-01 21:27:48.116317 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:48.118715 INFO::ASW Batch was 0.012717164604474 prior to batch effect correction and is now -0.0909653509541789 .
2025-12-01 21:27:48.119616 INFO::Total function execution time is 0.111905336380005 s and adjustment time is 0.0960502624511719 s ( 85.83 )
2025-12-01 21:27:48.120867 INFO::Formatting Data.
2025-12-01 21:27:48.121922 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:48.122971 INFO::Removing potential empty rows and columns
2025-12-01 21:27:48.124196 INFO::Found 0 missing values.
2025-12-01 21:27:48.127614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:48.128273 INFO::Done
2025-12-01 21:27:48.128887 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:48.131175 INFO::Starting hierarchical adjustment
2025-12-01 21:27:48.131998 INFO::Found 2 batches.
2025-12-01 21:27:48.132608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:48.133294 INFO::Using default BPPARAM
2025-12-01 21:27:48.133898 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:48.134984 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:27:48.154397 INFO::Done
2025-12-01 21:27:48.155257 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:48.157763 INFO::ASW Batch was 0.012717164604474 prior to batch effect correction and is now -0.0909653509541789 .
2025-12-01 21:27:48.158774 INFO::Total function execution time is 0.0378899574279785 s and adjustment time is 0.0225207805633545 s ( 59.44 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-01 21:27:51.338248 INFO::Formatting Data.
2025-12-01 21:27:51.338988 INFO::Recognized SummarizedExperiment
2025-12-01 21:27:51.339478 INFO::Typecasting input to dataframe.
2025-12-01 21:27:51.367714 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:51.368828 INFO::Removing potential empty rows and columns
2025-12-01 21:27:51.371843 INFO::Found 0 missing values.
2025-12-01 21:27:51.37747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:51.378026 INFO::Done
2025-12-01 21:27:51.378503 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:51.381625 INFO::Starting hierarchical adjustment
2025-12-01 21:27:51.382288 INFO::Found 2 batches.
2025-12-01 21:27:51.38277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:51.383797 INFO::Using default BPPARAM
2025-12-01 21:27:51.384278 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:51.385164 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:27:51.431888 INFO::Done
2025-12-01 21:27:51.432529 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:51.435625 INFO::ASW Batch was -0.0149010401497061 prior to batch effect correction and is now -0.0881635150993133 .
2025-12-01 21:27:51.436411 INFO::Total function execution time is 0.0984368324279785 s and adjustment time is 0.049696683883667 s ( 50.49 )
Warning: stack imbalance in '{', 73 then 75
2025-12-01 21:27:51.452841 INFO::Formatting Data.
2025-12-01 21:27:51.453494 INFO::Recognized SummarizedExperiment
2025-12-01 21:27:51.453977 INFO::Typecasting input to dataframe.
2025-12-01 21:27:51.461848 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:51.462826 INFO::Removing potential empty rows and columns
2025-12-01 21:27:51.465779 INFO::Found 0 missing values.
2025-12-01 21:27:51.471531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:51.472047 INFO::Done
2025-12-01 21:27:51.472505 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:51.475516 INFO::Starting hierarchical adjustment
2025-12-01 21:27:51.476152 INFO::Found 2 batches.
2025-12-01 21:27:51.476643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:51.477286 INFO::Using default BPPARAM
2025-12-01 21:27:51.477829 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:51.478778 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:27:51.504093 INFO::Done
2025-12-01 21:27:51.504815 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:51.508387 INFO::ASW Batch was 0.00286347997449355 prior to batch effect correction and is now 0.00286347997449355 .
2025-12-01 21:27:51.509245 INFO::Total function execution time is 0.0563921928405762 s and adjustment time is 0.0280270576477051 s ( 49.7 )
2025-12-01 21:27:51.527544 INFO::Formatting Data.
2025-12-01 21:27:51.528373 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:51.52933 INFO::Removing potential empty rows and columns
2025-12-01 21:27:51.530381 INFO::Found 0 missing values.
2025-12-01 21:27:51.533557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:51.534099 INFO::Done
2025-12-01 21:27:51.534638 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:51.536662 INFO::Starting hierarchical adjustment
2025-12-01 21:27:51.537357 INFO::Found 3 batches.
2025-12-01 21:27:51.537885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:51.538484 INFO::Using default BPPARAM
2025-12-01 21:27:51.539003 INFO::Processing subtree level 1
2025-12-01 21:27:51.674342 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:27:51.676183 INFO::Done
2025-12-01 21:27:51.676853 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:51.679359 INFO::ASW Batch was -0.121647622223036 prior to batch effect correction and is now -0.159409710088562 .
2025-12-01 21:27:51.680288 INFO::Total function execution time is 0.152796506881714 s and adjustment time is 0.138936519622803 s ( 90.93 )
2025-12-01 21:27:51.694715 INFO::Skipping initial DF formatting
2025-12-01 21:27:51.695412 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:51.699419 INFO::Starting hierarchical adjustment
2025-12-01 21:27:51.700218 INFO::Found 5 batches.
2025-12-01 21:27:51.700763 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:51.7014 INFO::Using default BPPARAM
2025-12-01 21:27:51.701947 INFO::Processing subtree level 1
2025-12-01 21:27:51.821481 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:51.823254 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:27:51.843231 INFO::Done
2025-12-01 21:27:51.844001 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:51.84837 INFO::ASW Batch was 0.528255166620927 prior to batch effect correction and is now 0.528255166620927 .
2025-12-01 21:27:51.849039 INFO::ASW Label was 0.38307149617004 prior to batch effect correction and is now 0.38307149617004 .
2025-12-01 21:27:51.849912 INFO::Total function execution time is 0.155231475830078 s and adjustment time is 0.143147230148315 s ( 92.22 )
2025-12-01 21:27:51.867979 INFO::Formatting Data.
2025-12-01 21:27:51.868801 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:51.869722 INFO::Removing potential empty rows and columns
2025-12-01 21:27:51.870732 INFO::Found 0 missing values.
2025-12-01 21:27:51.874802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:51.875365 INFO::Done
2025-12-01 21:27:51.875902 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:51.878907 INFO::Starting hierarchical adjustment
2025-12-01 21:27:51.879618 INFO::Found 5 batches.
2025-12-01 21:27:51.880162 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:51.880797 INFO::Using default BPPARAM
2025-12-01 21:27:51.881357 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.
2025-12-01 21:27:51.988429 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:51.990013 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:27:52.005711 INFO::Done
2025-12-01 21:27:52.00664 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.009852 INFO::ASW Batch was 0.332961101848856 prior to batch effect correction and is now -0.0286453663413318 .
2025-12-01 21:27:52.010495 INFO::ASW Label was 0.494310909676598 prior to batch effect correction and is now 0.792033687541073 .
2025-12-01 21:27:52.011328 INFO::Total function execution time is 0.143421411514282 s and adjustment time is 0.12621283531189 s ( 88 )
2025-12-01 21:27:52.012174 INFO::Formatting Data.
2025-12-01 21:27:52.012817 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.013694 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.014706 INFO::Found 0 missing values.
2025-12-01 21:27:52.018741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.019318 INFO::Done
2025-12-01 21:27:52.019851 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.022792 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.023506 INFO::Found 5 batches.
2025-12-01 21:27:52.024053 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.024701 INFO::Using default BPPARAM
2025-12-01 21:27:52.025255 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.
2025-12-01 21:27:52.132133 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:52.133738 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:27:52.149528 INFO::Done
2025-12-01 21:27:52.15025 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.153449 INFO::ASW Batch was 0.332961101848856 prior to batch effect correction and is now -0.0286453663413318 .
2025-12-01 21:27:52.154087 INFO::ASW Label was 0.494310909676598 prior to batch effect correction and is now 0.792033687541073 .
2025-12-01 21:27:52.155153 INFO::Total function execution time is 0.142982482910156 s and adjustment time is 0.126103162765503 s ( 88.19 )
2025-12-01 21:27:52.168677 INFO::Formatting Data.
2025-12-01 21:27:52.169502 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.170464 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.171509 INFO::Found 0 missing values.
2025-12-01 21:27:52.17565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.176267 INFO::Done
2025-12-01 21:27:52.17682 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.17991 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.180651 INFO::Found 5 batches.
2025-12-01 21:27:52.181195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.181829 INFO::Using default BPPARAM
2025-12-01 21:27:52.182367 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.
2025-12-01 21:27:52.299166 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:52.300935 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:27:52.316564 INFO::Done
2025-12-01 21:27:52.317315 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.320601 INFO::ASW Batch was 0.490623926302162 prior to batch effect correction and is now -0.0710003068765669 .
2025-12-01 21:27:52.321222 INFO::ASW Label was 0.296326621473479 prior to batch effect correction and is now 0.790657480107903 .
2025-12-01 21:27:52.322053 INFO::Total function execution time is 0.153470516204834 s and adjustment time is 0.136043548583984 s ( 88.64 )
2025-12-01 21:27:52.32291 INFO::Formatting Data.
2025-12-01 21:27:52.32358 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.324484 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.32548 INFO::Found 0 missing values.
2025-12-01 21:27:52.32966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.330223 INFO::Done
2025-12-01 21:27:52.330742 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.333622 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.334332 INFO::Found 5 batches.
2025-12-01 21:27:52.33489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.335507 INFO::Using default BPPARAM
2025-12-01 21:27:52.336056 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.
2025-12-01 21:27:52.441237 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:52.442776 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:27:52.45816 INFO::Done
2025-12-01 21:27:52.458871 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.461979 INFO::ASW Batch was 0.490623926302162 prior to batch effect correction and is now -0.0710003068765669 .
2025-12-01 21:27:52.462583 INFO::ASW Label was 0.296326621473479 prior to batch effect correction and is now 0.790657480107903 .
2025-12-01 21:27:52.463452 INFO::Total function execution time is 0.140563488006592 s and adjustment time is 0.123933792114258 s ( 88.17 )
2025-12-01 21:27:52.476703 INFO::Formatting Data.
2025-12-01 21:27:52.477519 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.478469 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.479469 INFO::Found 0 missing values.
2025-12-01 21:27:52.482331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.48291 INFO::Done
2025-12-01 21:27:52.48343 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.486344 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.487068 INFO::Found 2 batches.
2025-12-01 21:27:52.487608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.48826 INFO::Using default BPPARAM
2025-12-01 21:27:52.488843 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:52.489762 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:27:52.50422 INFO::Done
2025-12-01 21:27:52.5049 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.507779 INFO::ASW Batch was 0.575680380393616 prior to batch effect correction and is now 0.0303483648883186 .
2025-12-01 21:27:52.508386 INFO::ASW Label was 0.367064687906604 prior to batch effect correction and is now 0.897667773451594 .
2025-12-01 21:27:52.509181 INFO::Total function execution time is 0.0325682163238525 s and adjustment time is 0.0172932147979736 s ( 53.1 )
2025-12-01 21:27:52.509953 INFO::Formatting Data.
2025-12-01 21:27:52.510578 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.511429 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.512504 INFO::Found 0 missing values.
2025-12-01 21:27:52.515132 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.515697 INFO::Done
2025-12-01 21:27:52.516235 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.519062 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.519766 INFO::Found 2 batches.
2025-12-01 21:27:52.520298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.520916 INFO::Using default BPPARAM
2025-12-01 21:27:52.521472 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:52.522391 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:27:52.53695 INFO::Done
2025-12-01 21:27:52.537634 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.540528 INFO::ASW Batch was 0.575680380393616 prior to batch effect correction and is now 0.0303483648883186 .
2025-12-01 21:27:52.541147 INFO::ASW Label was 0.367064687906604 prior to batch effect correction and is now 0.897667773451594 .
2025-12-01 21:27:52.541935 INFO::Total function execution time is 0.0319762229919434 s and adjustment time is 0.017301082611084 s ( 54.11 )
2025-12-01 21:27:52.553381 INFO::Formatting Data.
2025-12-01 21:27:52.554166 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.555076 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.555982 INFO::Found 0 missing values.
2025-12-01 21:27:52.558114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.558644 INFO::Done
2025-12-01 21:27:52.559172 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.561077 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.561772 INFO::Found 2 batches.
2025-12-01 21:27:52.562315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.562929 INFO::Using default BPPARAM
2025-12-01 21:27:52.563476 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:52.564397 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:27:52.595673 INFO::Done
2025-12-01 21:27:52.596437 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.598466 INFO::ASW Batch was 0.0164136747637867 prior to batch effect correction and is now -0.140670793826077 .
2025-12-01 21:27:52.599279 INFO::Total function execution time is 0.0459740161895752 s and adjustment time is 0.0340044498443604 s ( 73.96 )
2025-12-01 21:27:52.611415 INFO::Formatting Data.
2025-12-01 21:27:52.612211 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.613113 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.614111 INFO::Found 0 missing values.
2025-12-01 21:27:52.615229 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.
2025-12-01 21:27:52.619809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.620365 INFO::Done
2025-12-01 21:27:52.62091 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.623779 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.624488 INFO::Found 2 batches.
2025-12-01 21:27:52.625019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.625645 INFO::Using default BPPARAM
2025-12-01 21:27:52.626186 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:52.627114 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:27:52.643257 INFO::Done
2025-12-01 21:27:52.64396 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.64685 INFO::ASW Batch was 0.673741862443638 prior to batch effect correction and is now 0.0530952640110797 .
2025-12-01 21:27:52.647441 INFO::ASW Label was 0.357553155510326 prior to batch effect correction and is now 0.862682445576953 .
2025-12-01 21:27:52.648245 INFO::Total function execution time is 0.0369195938110352 s and adjustment time is 0.0188987255096436 s ( 51.19 )
2025-12-01 21:27:52.649035 INFO::Formatting Data.
2025-12-01 21:27:52.64965 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.650574 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.651545 INFO::Found 0 missing values.
2025-12-01 21:27:52.652441 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.
2025-12-01 21:27:52.656928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.657486 INFO::Done
2025-12-01 21:27:52.658024 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.660865 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.661556 INFO::Found 2 batches.
2025-12-01 21:27:52.662119 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.662724 INFO::Using default BPPARAM
2025-12-01 21:27:52.66327 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:52.664307 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:27:52.680445 INFO::Done
2025-12-01 21:27:52.681168 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:52.684063 INFO::ASW Batch was 0.673741862443638 prior to batch effect correction and is now 0.0530952640110797 .
2025-12-01 21:27:52.684703 INFO::ASW Label was 0.357553155510326 prior to batch effect correction and is now 0.862682445576953 .
2025-12-01 21:27:52.685513 INFO::Total function execution time is 0.0364902019500732 s and adjustment time is 0.0190062522888184 s ( 52.09 )
2025-12-01 21:27:52.904002 INFO::Formatting Data.
2025-12-01 21:27:52.904987 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:52.905982 INFO::Removing potential empty rows and columns
2025-12-01 21:27:52.907154 INFO::Found 0 missing values.
2025-12-01 21:27:52.910404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:52.910998 INFO::Done
2025-12-01 21:27:52.911528 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:52.91384 INFO::Starting hierarchical adjustment
2025-12-01 21:27:52.914546 INFO::Found 3 batches.
2025-12-01 21:27:52.915084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:52.915769 INFO::Using default BPPARAM
2025-12-01 21:27:52.916317 INFO::Processing subtree level 1
2025-12-01 21:27:53.006409 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:27:53.008266 INFO::Done
2025-12-01 21:27:53.008932 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:53.011387 INFO::ASW Batch was -0.0429961938816422 prior to batch effect correction and is now -0.0429961938816422 .
2025-12-01 21:27:53.012372 INFO::Total function execution time is 0.108752250671387 s and adjustment time is 0.0938501358032227 s ( 86.3 )
2025-12-01 21:27:53.013577 INFO::Formatting Data.
2025-12-01 21:27:53.014249 INFO::Typecasting input to dataframe.
2025-12-01 21:27:53.015036 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:53.015963 INFO::Removing potential empty rows and columns
2025-12-01 21:27:53.017042 INFO::Found 0 missing values.
2025-12-01 21:27:53.020064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:53.020653 INFO::Done
2025-12-01 21:27:53.021201 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:53.023256 INFO::Starting hierarchical adjustment
2025-12-01 21:27:53.023993 INFO::Found 3 batches.
2025-12-01 21:27:53.024542 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:53.025188 INFO::Using default BPPARAM
2025-12-01 21:27:53.025797 INFO::Processing subtree level 1
2025-12-01 21:27:53.113472 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:27:53.115324 INFO::Done
2025-12-01 21:27:53.116 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:53.118623 INFO::ASW Batch was -0.0429961938816422 prior to batch effect correction and is now -0.0429961938816422 .
2025-12-01 21:27:53.119689 INFO::Total function execution time is 0.106182336807251 s and adjustment time is 0.0914745330810547 s ( 86.15 )
2025-12-01 21:27:53.133427 INFO::Formatting Data.
2025-12-01 21:27:53.134332 INFO::Typecasting input to dataframe.
2025-12-01 21:27:53.135237 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:53.136177 INFO::Removing potential empty rows and columns
2025-12-01 21:27:53.137297 INFO::Found 0 missing values.
2025-12-01 21:27:53.140331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:53.140892 INFO::Done
2025-12-01 21:27:53.141425 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:53.143471 INFO::Starting hierarchical adjustment
2025-12-01 21:27:53.144396 INFO::Found 3 batches.
2025-12-01 21:27:53.144956 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:53.14558 INFO::Using default BPPARAM
2025-12-01 21:27:53.146135 INFO::Processing subtree level 1
2025-12-01 21:27:53.236729 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:27:53.238556 INFO::Done
2025-12-01 21:27:53.239228 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:53.241702 INFO::ASW Batch was -0.0367427665223382 prior to batch effect correction and is now -0.0367427665223382 .
2025-12-01 21:27:53.242641 INFO::Total function execution time is 0.10929274559021 s and adjustment time is 0.0945022106170654 s ( 86.47 )
2025-12-01 21:27:53.386118 INFO::Formatting Data.
2025-12-01 21:27:53.387003 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:53.388165 INFO::Removing potential empty rows and columns
2025-12-01 21:27:53.390899 INFO::Found 1000 missing values.
2025-12-01 21:27:53.409647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:53.410408 INFO::Done
2025-12-01 21:27:53.410985 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:53.416383 INFO::Starting hierarchical adjustment
2025-12-01 21:27:53.417172 INFO::Found 10 batches.
2025-12-01 21:27:53.417713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:53.418379 INFO::Using default BPPARAM
2025-12-01 21:27:53.418925 INFO::Processing subtree level 1
2025-12-01 21:27:53.56254 INFO::Processing subtree level 2
2025-12-01 21:27:53.827845 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:27:53.829864 INFO::Done
2025-12-01 21:27:53.830524 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:53.836013 INFO::ASW Batch was 0.501022197257308 prior to batch effect correction and is now 0.501022197257308 .
2025-12-01 21:27:53.836699 INFO::ASW Label was 0.319159727511943 prior to batch effect correction and is now 0.319159727511943 .
2025-12-01 21:27:53.837597 INFO::Total function execution time is 0.451535940170288 s and adjustment time is 0.412819623947144 s ( 91.43 )
2025-12-01 21:27:53.838432 INFO::Formatting Data.
2025-12-01 21:27:53.839098 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:53.840257 INFO::Removing potential empty rows and columns
2025-12-01 21:27:53.892906 INFO::Found 1000 missing values.
2025-12-01 21:27:53.910655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:53.911429 INFO::Done
2025-12-01 21:27:53.912036 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:53.917182 INFO::Starting hierarchical adjustment
2025-12-01 21:27:53.917925 INFO::Found 10 batches.
2025-12-01 21:27:54.914531 INFO::Set up parallel execution backend with 2 workers
2025-12-01 21:27:54.915968 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-01 21:27:56.023126 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:27:56.02616 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:27:56.042029 INFO::Done
2025-12-01 21:27:56.042685 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:56.047136 INFO::ASW Batch was 0.501022197257308 prior to batch effect correction and is now 0.501022197257308 .
2025-12-01 21:27:56.047716 INFO::ASW Label was 0.319159727511943 prior to batch effect correction and is now 0.319159727511943 .
2025-12-01 21:27:56.04844 INFO::Total function execution time is 2.21003937721252 s and adjustment time is 2.12423968315125 s ( 96.12 )
2025-12-01 21:27:56.197106 INFO::Formatting Data.
2025-12-01 21:27:56.19821 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.199246 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.200355 INFO::Found 0 missing values.
2025-12-01 21:27:56.204117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.204664 INFO::Done
2025-12-01 21:27:56.205198 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:27:56.208028 INFO::Starting hierarchical adjustment
2025-12-01 21:27:56.208727 INFO::Found 3 batches.
2025-12-01 21:27:56.209274 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:27:56.209931 INFO::Using default BPPARAM
2025-12-01 21:27:56.210458 INFO::Processing subtree level 1
2025-12-01 21:27:56.340477 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:27:56.34269 INFO::Done
2025-12-01 21:27:56.343469 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:27:56.34714 INFO::ASW Batch was 0.264245516743639 prior to batch effect correction and is now -0.147550306648442 .
2025-12-01 21:27:56.347817 INFO::ASW Label was -0.188608027721891 prior to batch effect correction and is now 0.00160920158026879 .
2025-12-01 21:27:56.348842 INFO::Total function execution time is 0.151835203170776 s and adjustment time is 0.134058952331543 s ( 88.29 )
2025-12-01 21:27:56.472073 INFO::Formatting Data.
2025-12-01 21:27:56.472969 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.473872 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.474876 INFO::Found 2 missing values.
2025-12-01 21:27:56.477593 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.478153 INFO::Done
2025-12-01 21:27:56.503949 INFO::Found NA in Reference column
2025-12-01 21:27:56.512903 INFO::Require at least two references per batch.
2025-12-01 21:27:56.532291 INFO::Formatting Data.
2025-12-01 21:27:56.533056 INFO::Recognized SummarizedExperiment
2025-12-01 21:27:56.533593 INFO::Typecasting input to dataframe.
2025-12-01 21:27:56.542827 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.543957 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.547275 INFO::Found 0 missing values.
2025-12-01 21:27:56.5537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.554334 INFO::Done
2025-12-01 21:27:56.570252 INFO::Formatting Data.
2025-12-01 21:27:56.57101 INFO::Recognized SummarizedExperiment
2025-12-01 21:27:56.571536 INFO::Typecasting input to dataframe.
2025-12-01 21:27:56.588857 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.590162 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.5937 INFO::Found 0 missing values.
2025-12-01 21:27:56.60406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.604682 INFO::Done
2025-12-01 21:27:56.619843 INFO::Formatting Data.
2025-12-01 21:27:56.620554 INFO::Recognized SummarizedExperiment
2025-12-01 21:27:56.621099 INFO::Typecasting input to dataframe.
2025-12-01 21:27:56.637069 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.638104 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.639214 INFO::Found 0 missing values.
2025-12-01 21:27:56.640117 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.
2025-12-01 21:27:56.644422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.644972 INFO::Done
2025-12-01 21:27:56.65531 INFO::Formatting Data.
2025-12-01 21:27:56.656184 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.657125 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.658154 INFO::Found 0 missing values.
2025-12-01 21:27:56.66106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.661608 INFO::Done
2025-12-01 21:27:56.672807 INFO::Formatting Data.
2025-12-01 21:27:56.673616 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.674488 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.675469 INFO::Found 0 missing values.
2025-12-01 21:27:56.678251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.67877 INFO::Done
2025-12-01 21:27:56.707122 INFO::Formatting Data.
2025-12-01 21:27:56.707941 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.708968 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.71008 INFO::Found 1 missing values.
2025-12-01 21:27:56.712487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.713048 INFO::Done
2025-12-01 21:27:56.73077 INFO::Formatting Data.
2025-12-01 21:27:56.731601 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.732464 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.733374 INFO::Found 2 missing values.
2025-12-01 21:27:56.734253 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.
2025-12-01 21:27:56.736504 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.737059 INFO::Done
2025-12-01 21:27:56.747233 INFO::Formatting Data.
2025-12-01 21:27:56.748057 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.748963 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.74987 INFO::Found 2 missing values.
2025-12-01 21:27:56.751405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.751965 INFO::Done
2025-12-01 21:27:56.76161 INFO::Formatting Data.
2025-12-01 21:27:56.762341 INFO::Typecasting input to dataframe.
2025-12-01 21:27:56.763111 INFO::Replacing NaNs with NAs.
2025-12-01 21:27:56.763932 INFO::Removing potential empty rows and columns
2025-12-01 21:27:56.764881 INFO::Found 0 missing values.
2025-12-01 21:27:56.76755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:27:56.768075 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.987 4.095 20.897
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.686 | 1.145 | 16.745 | |
| compute_asw | 0.023 | 0.001 | 0.024 | |
| count_existing | 0.011 | 0.002 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |