Yannis Schumann
| Snapshot Date: 2026-03-04 13:45 -0500 (Wed, 04 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-05 11:57 -0500 (Thu, 05 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4894 |
| 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 | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-03-04 21:30:41 -0500 (Wed, 04 Mar 2026) |
| EndedAt: 2026-03-04 21:32:11 -0500 (Wed, 04 Mar 2026) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 25.367 1.195 17.895
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-03-04 21:31:32.855944 INFO::Formatting Data.
2026-03-04 21:31:32.857389 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:32.86908 INFO::Removing potential empty rows and columns
2026-03-04 21:31:33.171819 INFO::Found 0 missing values.
2026-03-04 21:31:33.17553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:33.17625 INFO::Done
2026-03-04 21:31:33.176865 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:33.189456 INFO::Starting hierarchical adjustment
2026-03-04 21:31:33.190437 INFO::Found 3 batches.
2026-03-04 21:31:33.19108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:33.192325 INFO::Using default BPPARAM
2026-03-04 21:31:33.192903 INFO::Processing subtree level 1
2026-03-04 21:31:33.302494 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:31:33.30455 INFO::Done
2026-03-04 21:31:33.305279 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:33.308235 INFO::ASW Batch was -0.07384848800625 prior to batch effect correction and is now -0.07384848800625 .
2026-03-04 21:31:33.309534 INFO::Total function execution time is 0.454451560974121 s and adjustment time is 0.114288806915283 s ( 25.15 )
2026-03-04 21:31:33.325821 INFO::Formatting Data.
2026-03-04 21:31:33.326857 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:33.327963 INFO::Removing potential empty rows and columns
2026-03-04 21:31:33.329293 INFO::Found 0 missing values.
2026-03-04 21:31:33.330374 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-04 21:31:33.342602 INFO::Formatting Data.
2026-03-04 21:31:33.343521 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:33.344586 INFO::Removing potential empty rows and columns
2026-03-04 21:31:33.345764 INFO::Found 0 missing values.
2026-03-04 21:31:33.346815 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-04 21:31:33.364903 INFO::Formatting Data.
2026-03-04 21:31:33.36586 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:33.366906 INFO::Removing potential empty rows and columns
2026-03-04 21:31:33.368103 INFO::Found 0 missing values.
2026-03-04 21:31:33.369175 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-04 21:31:33.374348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:33.375037 INFO::Done
2026-03-04 21:31:33.375617 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:33.37794 INFO::Starting hierarchical adjustment
2026-03-04 21:31:33.378712 INFO::Found 2 batches.
2026-03-04 21:31:33.379254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:33.379943 INFO::Using default BPPARAM
2026-03-04 21:31:33.380491 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:33.381519 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:31:33.405038 INFO::Done
2026-03-04 21:31:33.405904 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:33.408465 INFO::ASW Batch was -0.0158105997174982 prior to batch effect correction and is now -0.0985039044430981 .
2026-03-04 21:31:33.409415 INFO::Total function execution time is 0.044628381729126 s and adjustment time is 0.0264339447021484 s ( 59.23 )
2026-03-04 21:31:33.412837 INFO::Formatting Data.
2026-03-04 21:31:33.413574 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:33.424018 INFO::Formatting Data.
2026-03-04 21:31:33.425001 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:33.42608 INFO::Removing potential empty rows and columns
2026-03-04 21:31:33.427287 INFO::Found 0 missing values.
2026-03-04 21:31:33.430531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:33.431128 INFO::Done
2026-03-04 21:31:33.431703 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:33.46469 INFO::Starting hierarchical adjustment
2026-03-04 21:31:33.46658 INFO::Found 2 batches.
2026-03-04 21:31:33.467173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:33.467775 INFO::Using default BPPARAM
2026-03-04 21:31:33.468299 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:33.4693 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:33.484936 INFO::Done
2026-03-04 21:31:33.485824 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:33.488144 INFO::ASW Batch was 0.144264961571052 prior to batch effect correction and is now -0.0642362918859861 .
2026-03-04 21:31:33.489021 INFO::Total function execution time is 0.0651416778564453 s and adjustment time is 0.01851487159729 s ( 28.42 )
2026-03-04 21:31:33.490144 INFO::Formatting Data.
2026-03-04 21:31:33.490765 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:33.491675 INFO::Removing potential empty rows and columns
2026-03-04 21:31:33.492698 INFO::Found 0 missing values.
2026-03-04 21:31:33.495556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:33.496109 INFO::Done
2026-03-04 21:31:33.49663 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:33.498758 INFO::Starting hierarchical adjustment
2026-03-04 21:31:33.499471 INFO::Found 2 batches.
2026-03-04 21:31:33.49998 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:33.500597 INFO::Using default BPPARAM
2026-03-04 21:31:33.501099 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:33.502028 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:33.517418 INFO::Done
2026-03-04 21:31:33.518191 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:33.520444 INFO::ASW Batch was 0.144264961571052 prior to batch effect correction and is now -0.0642362918859861 .
2026-03-04 21:31:33.521329 INFO::Total function execution time is 0.0311806201934814 s and adjustment time is 0.0180432796478271 s ( 57.87 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-04 21:31:36.551456 INFO::Formatting Data.
2026-03-04 21:31:36.552242 INFO::Recognized SummarizedExperiment
2026-03-04 21:31:36.552737 INFO::Typecasting input to dataframe.
2026-03-04 21:31:36.584355 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:36.585687 INFO::Removing potential empty rows and columns
2026-03-04 21:31:36.589534 INFO::Found 0 missing values.
2026-03-04 21:31:36.596782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:36.597433 INFO::Done
2026-03-04 21:31:36.597985 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:36.601813 INFO::Starting hierarchical adjustment
2026-03-04 21:31:36.602574 INFO::Found 2 batches.
2026-03-04 21:31:36.603218 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:36.604398 INFO::Using default BPPARAM
2026-03-04 21:31:36.60495 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:36.605968 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:31:36.664433 INFO::Done
2026-03-04 21:31:36.665188 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:36.668912 INFO::ASW Batch was 0.00790988835711444 prior to batch effect correction and is now -0.0848176608755827 .
2026-03-04 21:31:36.669802 INFO::Total function execution time is 0.118675231933594 s and adjustment time is 0.0619909763336182 s ( 52.24 )
Warning: stack imbalance in '{', 73 then 75
2026-03-04 21:31:36.689733 INFO::Formatting Data.
2026-03-04 21:31:36.690525 INFO::Recognized SummarizedExperiment
2026-03-04 21:31:36.691068 INFO::Typecasting input to dataframe.
2026-03-04 21:31:36.700605 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:36.701804 INFO::Removing potential empty rows and columns
2026-03-04 21:31:36.705566 INFO::Found 0 missing values.
2026-03-04 21:31:36.713158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:36.713848 INFO::Done
2026-03-04 21:31:36.714385 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:36.718107 INFO::Starting hierarchical adjustment
2026-03-04 21:31:36.718855 INFO::Found 2 batches.
2026-03-04 21:31:36.719368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:36.719968 INFO::Using default BPPARAM
2026-03-04 21:31:36.720471 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:36.721463 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:31:36.74748 INFO::Done
2026-03-04 21:31:36.748287 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:36.752135 INFO::ASW Batch was -0.0042584618066631 prior to batch effect correction and is now -0.0042584618066631 .
2026-03-04 21:31:36.753113 INFO::Total function execution time is 0.0633389949798584 s and adjustment time is 0.02872633934021 s ( 45.35 )
2026-03-04 21:31:36.773324 INFO::Formatting Data.
2026-03-04 21:31:36.774179 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:36.77513 INFO::Removing potential empty rows and columns
2026-03-04 21:31:36.776207 INFO::Found 0 missing values.
2026-03-04 21:31:36.779283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:36.779825 INFO::Done
2026-03-04 21:31:36.78034 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:36.782443 INFO::Starting hierarchical adjustment
2026-03-04 21:31:36.783149 INFO::Found 3 batches.
2026-03-04 21:31:36.783684 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:36.78428 INFO::Using default BPPARAM
2026-03-04 21:31:36.784805 INFO::Processing subtree level 1
2026-03-04 21:31:36.937734 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:31:36.939906 INFO::Done
2026-03-04 21:31:36.940598 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:36.943357 INFO::ASW Batch was -0.159670342835605 prior to batch effect correction and is now -0.183567973608998 .
2026-03-04 21:31:36.94435 INFO::Total function execution time is 0.17107081413269 s and adjustment time is 0.156862020492554 s ( 91.69 )
2026-03-04 21:31:36.959449 INFO::Skipping initial DF formatting
2026-03-04 21:31:36.960197 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:36.964373 INFO::Starting hierarchical adjustment
2026-03-04 21:31:36.965183 INFO::Found 5 batches.
2026-03-04 21:31:36.965836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:36.966474 INFO::Using default BPPARAM
2026-03-04 21:31:36.967013 INFO::Processing subtree level 1
2026-03-04 21:31:37.208737 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:37.210569 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:31:37.232449 INFO::Done
2026-03-04 21:31:37.233353 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:37.238026 INFO::ASW Batch was 0.542514569170361 prior to batch effect correction and is now 0.542514569170361 .
2026-03-04 21:31:37.238693 INFO::ASW Label was 0.346837214503615 prior to batch effect correction and is now 0.346837214503615 .
2026-03-04 21:31:37.239594 INFO::Total function execution time is 0.280206680297852 s and adjustment time is 0.267356872558594 s ( 95.41 )
2026-03-04 21:31:37.310986 INFO::Formatting Data.
2026-03-04 21:31:37.311905 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:37.312886 INFO::Removing potential empty rows and columns
2026-03-04 21:31:37.314037 INFO::Found 0 missing values.
2026-03-04 21:31:37.318181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:37.318716 INFO::Done
2026-03-04 21:31:37.319207 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:37.322251 INFO::Starting hierarchical adjustment
2026-03-04 21:31:37.322973 INFO::Found 5 batches.
2026-03-04 21:31:37.323477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:37.324092 INFO::Using default BPPARAM
2026-03-04 21:31:37.324641 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:37.465057 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:37.466958 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:37.486437 INFO::Done
2026-03-04 21:31:37.487345 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:37.491445 INFO::ASW Batch was 0.500463590275428 prior to batch effect correction and is now -0.0641417030221231 .
2026-03-04 21:31:37.492184 INFO::ASW Label was 0.308557676503344 prior to batch effect correction and is now 0.790761050140373 .
2026-03-04 21:31:37.493157 INFO::Total function execution time is 0.182263135910034 s and adjustment time is 0.163540601730347 s ( 89.73 )
2026-03-04 21:31:37.494186 INFO::Formatting Data.
2026-03-04 21:31:37.494922 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:37.49597 INFO::Removing potential empty rows and columns
2026-03-04 21:31:37.497172 INFO::Found 0 missing values.
2026-03-04 21:31:37.502124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:37.502766 INFO::Done
2026-03-04 21:31:37.503418 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:37.507117 INFO::Starting hierarchical adjustment
2026-03-04 21:31:37.50788 INFO::Found 5 batches.
2026-03-04 21:31:37.508447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:37.509121 INFO::Using default BPPARAM
2026-03-04 21:31:37.518149 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:37.67287 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:37.674871 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:37.693709 INFO::Done
2026-03-04 21:31:37.69458 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:37.698605 INFO::ASW Batch was 0.500463590275428 prior to batch effect correction and is now -0.0641417030221231 .
2026-03-04 21:31:37.699337 INFO::ASW Label was 0.308557676503344 prior to batch effect correction and is now 0.790761050140373 .
2026-03-04 21:31:37.700319 INFO::Total function execution time is 0.206137657165527 s and adjustment time is 0.185912609100342 s ( 90.19 )
2026-03-04 21:31:37.716688 INFO::Formatting Data.
2026-03-04 21:31:37.717663 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:37.718765 INFO::Removing potential empty rows and columns
2026-03-04 21:31:37.720018 INFO::Found 0 missing values.
2026-03-04 21:31:37.724746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:37.725304 INFO::Done
2026-03-04 21:31:37.725893 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:37.729697 INFO::Starting hierarchical adjustment
2026-03-04 21:31:37.730483 INFO::Found 5 batches.
2026-03-04 21:31:37.731061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:37.731739 INFO::Using default BPPARAM
2026-03-04 21:31:37.732313 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:37.881016 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:37.883629 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:37.91047 INFO::Done
2026-03-04 21:31:37.911748 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:37.917361 INFO::ASW Batch was 0.403580970976038 prior to batch effect correction and is now -0.0413823083564717 .
2026-03-04 21:31:37.918432 INFO::ASW Label was 0.303846291519261 prior to batch effect correction and is now 0.818509563730148 .
2026-03-04 21:31:37.919944 INFO::Total function execution time is 0.203255891799927 s and adjustment time is 0.180047512054443 s ( 88.58 )
2026-03-04 21:31:37.921436 INFO::Formatting Data.
2026-03-04 21:31:37.92249 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:37.923943 INFO::Removing potential empty rows and columns
2026-03-04 21:31:37.925649 INFO::Found 0 missing values.
2026-03-04 21:31:37.932792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:37.933869 INFO::Done
2026-03-04 21:31:37.934729 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:37.939861 INFO::Starting hierarchical adjustment
2026-03-04 21:31:37.941153 INFO::Found 5 batches.
2026-03-04 21:31:37.942077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:37.943079 INFO::Using default BPPARAM
2026-03-04 21:31:37.943896 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:38.098132 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:38.10021 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:38.11916 INFO::Done
2026-03-04 21:31:38.120016 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:38.124088 INFO::ASW Batch was 0.403580970976038 prior to batch effect correction and is now -0.0413823083564717 .
2026-03-04 21:31:38.124914 INFO::ASW Label was 0.303846291519261 prior to batch effect correction and is now 0.818509563730148 .
2026-03-04 21:31:38.126066 INFO::Total function execution time is 0.204720735549927 s and adjustment time is 0.178272485733032 s ( 87.08 )
2026-03-04 21:31:38.142722 INFO::Formatting Data.
2026-03-04 21:31:38.14369 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:38.144774 INFO::Removing potential empty rows and columns
2026-03-04 21:31:38.145999 INFO::Found 0 missing values.
2026-03-04 21:31:38.149111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:38.149734 INFO::Done
2026-03-04 21:31:38.150281 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:38.154011 INFO::Starting hierarchical adjustment
2026-03-04 21:31:38.154839 INFO::Found 2 batches.
2026-03-04 21:31:38.155406 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:38.156054 INFO::Using default BPPARAM
2026-03-04 21:31:38.156642 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:38.157646 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:38.175758 INFO::Done
2026-03-04 21:31:38.176692 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:38.180828 INFO::ASW Batch was 0.713809448451173 prior to batch effect correction and is now 0.0188905357543538 .
2026-03-04 21:31:38.181597 INFO::ASW Label was 0.305245982507917 prior to batch effect correction and is now 0.870545548794666 .
2026-03-04 21:31:38.182617 INFO::Total function execution time is 0.040057897567749 s and adjustment time is 0.0210473537445068 s ( 52.54 )
2026-03-04 21:31:38.183797 INFO::Formatting Data.
2026-03-04 21:31:38.18461 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:38.185731 INFO::Removing potential empty rows and columns
2026-03-04 21:31:38.187047 INFO::Found 0 missing values.
2026-03-04 21:31:38.190718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:38.1914 INFO::Done
2026-03-04 21:31:38.192043 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:38.196113 INFO::Starting hierarchical adjustment
2026-03-04 21:31:38.197034 INFO::Found 2 batches.
2026-03-04 21:31:38.197713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:38.198485 INFO::Using default BPPARAM
2026-03-04 21:31:38.199174 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:38.200343 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 21:31:38.222456 INFO::Done
2026-03-04 21:31:38.223877 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:38.228396 INFO::ASW Batch was 0.713809448451173 prior to batch effect correction and is now 0.0188905357543538 .
2026-03-04 21:31:38.229328 INFO::ASW Label was 0.305245982507917 prior to batch effect correction and is now 0.870545548794666 .
2026-03-04 21:31:38.230498 INFO::Total function execution time is 0.0466859340667725 s and adjustment time is 0.0255420207977295 s ( 54.71 )
2026-03-04 21:31:38.251259 INFO::Formatting Data.
2026-03-04 21:31:38.252864 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:38.254649 INFO::Removing potential empty rows and columns
2026-03-04 21:31:38.256484 INFO::Found 0 missing values.
2026-03-04 21:31:38.260744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:38.261774 INFO::Done
2026-03-04 21:31:38.262754 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:38.266502 INFO::Starting hierarchical adjustment
2026-03-04 21:31:38.267874 INFO::Found 2 batches.
2026-03-04 21:31:38.268844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:38.269925 INFO::Using default BPPARAM
2026-03-04 21:31:38.270891 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:38.272543 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:31:38.3352 INFO::Done
2026-03-04 21:31:38.336588 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:38.340495 INFO::ASW Batch was 0.108570297772705 prior to batch effect correction and is now -0.121820011136708 .
2026-03-04 21:31:38.342114 INFO::Total function execution time is 0.0910708904266357 s and adjustment time is 0.0675969123840332 s ( 74.22 )
2026-03-04 21:31:38.360395 INFO::Formatting Data.
2026-03-04 21:31:38.361376 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:38.3624 INFO::Removing potential empty rows and columns
2026-03-04 21:31:38.36354 INFO::Found 0 missing values.
2026-03-04 21:31:38.364898 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-04 21:31:38.370539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:38.371254 INFO::Done
2026-03-04 21:31:38.371845 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:38.375244 INFO::Starting hierarchical adjustment
2026-03-04 21:31:38.376033 INFO::Found 2 batches.
2026-03-04 21:31:38.376622 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:38.377287 INFO::Using default BPPARAM
2026-03-04 21:31:38.377882 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:38.378914 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:31:38.399695 INFO::Done
2026-03-04 21:31:38.400733 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:38.404645 INFO::ASW Batch was 0.401282897458413 prior to batch effect correction and is now 0.0164506400736301 .
2026-03-04 21:31:38.405396 INFO::ASW Label was 0.665266893315391 prior to batch effect correction and is now 0.915795064661876 .
2026-03-04 21:31:38.406388 INFO::Total function execution time is 0.0461323261260986 s and adjustment time is 0.0237476825714111 s ( 51.48 )
2026-03-04 21:31:38.407418 INFO::Formatting Data.
2026-03-04 21:31:38.408176 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:38.409329 INFO::Removing potential empty rows and columns
2026-03-04 21:31:38.410535 INFO::Found 0 missing values.
2026-03-04 21:31:38.411634 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-04 21:31:38.417156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:38.417832 INFO::Done
2026-03-04 21:31:38.418433 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:38.421995 INFO::Starting hierarchical adjustment
2026-03-04 21:31:38.422773 INFO::Found 2 batches.
2026-03-04 21:31:38.423374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:38.424084 INFO::Using default BPPARAM
2026-03-04 21:31:38.424691 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:38.425805 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:31:38.446094 INFO::Done
2026-03-04 21:31:38.446887 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:38.450201 INFO::ASW Batch was 0.401282897458413 prior to batch effect correction and is now 0.0164506400736301 .
2026-03-04 21:31:38.450869 INFO::ASW Label was 0.665266893315391 prior to batch effect correction and is now 0.915795064661876 .
2026-03-04 21:31:38.451762 INFO::Total function execution time is 0.0443994998931885 s and adjustment time is 0.0234634876251221 s ( 52.85 )
2026-03-04 21:31:38.675365 INFO::Formatting Data.
2026-03-04 21:31:38.676249 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:38.677202 INFO::Removing potential empty rows and columns
2026-03-04 21:31:38.678273 INFO::Found 0 missing values.
2026-03-04 21:31:38.681368 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:38.681915 INFO::Done
2026-03-04 21:31:38.68242 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:38.6846 INFO::Starting hierarchical adjustment
2026-03-04 21:31:38.685304 INFO::Found 3 batches.
2026-03-04 21:31:38.685838 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:38.68643 INFO::Using default BPPARAM
2026-03-04 21:31:38.686953 INFO::Processing subtree level 1
2026-03-04 21:31:38.786519 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:31:38.788924 INFO::Done
2026-03-04 21:31:38.789819 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:38.793075 INFO::ASW Batch was -0.074843964122726 prior to batch effect correction and is now -0.074843964122726 .
2026-03-04 21:31:38.794257 INFO::Total function execution time is 0.118896484375 s and adjustment time is 0.103669404983521 s ( 87.19 )
2026-03-04 21:31:38.795547 INFO::Formatting Data.
2026-03-04 21:31:38.796267 INFO::Typecasting input to dataframe.
2026-03-04 21:31:38.797138 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:38.798248 INFO::Removing potential empty rows and columns
2026-03-04 21:31:38.799532 INFO::Found 0 missing values.
2026-03-04 21:31:38.803075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:38.803655 INFO::Done
2026-03-04 21:31:38.8042 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:38.806663 INFO::Starting hierarchical adjustment
2026-03-04 21:31:38.807426 INFO::Found 3 batches.
2026-03-04 21:31:38.807987 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:38.808659 INFO::Using default BPPARAM
2026-03-04 21:31:38.809231 INFO::Processing subtree level 1
2026-03-04 21:31:38.907093 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:31:38.909258 INFO::Done
2026-03-04 21:31:38.91005 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:38.912941 INFO::ASW Batch was -0.074843964122726 prior to batch effect correction and is now -0.074843964122726 .
2026-03-04 21:31:38.914012 INFO::Total function execution time is 0.118473052978516 s and adjustment time is 0.101950645446777 s ( 86.05 )
2026-03-04 21:31:38.929912 INFO::Formatting Data.
2026-03-04 21:31:38.930875 INFO::Typecasting input to dataframe.
2026-03-04 21:31:38.931857 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:38.932868 INFO::Removing potential empty rows and columns
2026-03-04 21:31:38.934019 INFO::Found 0 missing values.
2026-03-04 21:31:38.937254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:38.937809 INFO::Done
2026-03-04 21:31:38.938335 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:38.940626 INFO::Starting hierarchical adjustment
2026-03-04 21:31:38.941348 INFO::Found 3 batches.
2026-03-04 21:31:38.941944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:38.942576 INFO::Using default BPPARAM
2026-03-04 21:31:38.943125 INFO::Processing subtree level 1
2026-03-04 21:31:39.037629 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:31:39.039862 INFO::Done
2026-03-04 21:31:39.040697 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:39.043773 INFO::ASW Batch was -0.00230911196980503 prior to batch effect correction and is now -0.00230911196980503 .
2026-03-04 21:31:39.044882 INFO::Total function execution time is 0.115293979644775 s and adjustment time is 0.0985956192016602 s ( 85.52 )
2026-03-04 21:31:39.1946 INFO::Formatting Data.
2026-03-04 21:31:39.195473 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:39.196651 INFO::Removing potential empty rows and columns
2026-03-04 21:31:39.199477 INFO::Found 1000 missing values.
2026-03-04 21:31:39.218418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:39.219242 INFO::Done
2026-03-04 21:31:39.219833 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:39.225613 INFO::Starting hierarchical adjustment
2026-03-04 21:31:39.22644 INFO::Found 10 batches.
2026-03-04 21:31:39.227014 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:39.227653 INFO::Using default BPPARAM
2026-03-04 21:31:39.22818 INFO::Processing subtree level 1
2026-03-04 21:31:39.368574 INFO::Processing subtree level 2
2026-03-04 21:31:39.515687 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:31:39.518197 INFO::Done
2026-03-04 21:31:39.519039 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:39.525756 INFO::ASW Batch was 0.481540102900471 prior to batch effect correction and is now 0.481540102900471 .
2026-03-04 21:31:39.526573 INFO::ASW Label was 0.352973498924973 prior to batch effect correction and is now 0.352973498924973 .
2026-03-04 21:31:39.527708 INFO::Total function execution time is 0.333183526992798 s and adjustment time is 0.291866302490234 s ( 87.6 )
2026-03-04 21:31:39.528751 INFO::Formatting Data.
2026-03-04 21:31:39.529503 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:39.530942 INFO::Removing potential empty rows and columns
2026-03-04 21:31:39.534158 INFO::Found 1000 missing values.
2026-03-04 21:31:39.5561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:39.557088 INFO::Done
2026-03-04 21:31:39.55774 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:39.56402 INFO::Starting hierarchical adjustment
2026-03-04 21:31:39.564872 INFO::Found 10 batches.
2026-03-04 21:31:41.225224 INFO::Set up parallel execution backend with 2 workers
2026-03-04 21:31:41.228438 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-04 21:31:42.443364 INFO::Adjusting the last 2 batches sequentially
2026-03-04 21:31:42.453373 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 21:31:42.469969 INFO::Done
2026-03-04 21:31:42.470617 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:42.475287 INFO::ASW Batch was 0.481540102900471 prior to batch effect correction and is now 0.481540102900471 .
2026-03-04 21:31:42.475852 INFO::ASW Label was 0.352973498924973 prior to batch effect correction and is now 0.352973498924973 .
2026-03-04 21:31:42.476603 INFO::Total function execution time is 2.94795775413513 s and adjustment time is 2.90524911880493 s ( 98.55 )
2026-03-04 21:31:42.617886 INFO::Formatting Data.
2026-03-04 21:31:42.61869 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:42.619589 INFO::Removing potential empty rows and columns
2026-03-04 21:31:42.62063 INFO::Found 0 missing values.
2026-03-04 21:31:42.624113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:42.62465 INFO::Done
2026-03-04 21:31:42.62514 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 21:31:42.627794 INFO::Starting hierarchical adjustment
2026-03-04 21:31:42.628454 INFO::Found 3 batches.
2026-03-04 21:31:42.628974 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 21:31:42.62957 INFO::Using default BPPARAM
2026-03-04 21:31:42.630067 INFO::Processing subtree level 1
2026-03-04 21:31:42.731614 INFO::Adjusting the last 1 batches sequentially
2026-03-04 21:31:42.733307 INFO::Done
2026-03-04 21:31:42.73394 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 21:31:42.737102 INFO::ASW Batch was 0.231576125700235 prior to batch effect correction and is now -0.173338636371364 .
2026-03-04 21:31:42.737724 INFO::ASW Label was -0.192473123190491 prior to batch effect correction and is now 0.0355342378622995 .
2026-03-04 21:31:42.73863 INFO::Total function execution time is 0.120788335800171 s and adjustment time is 0.104959964752197 s ( 86.9 )
2026-03-04 21:31:42.854457 INFO::Formatting Data.
2026-03-04 21:31:42.855302 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:42.856208 INFO::Removing potential empty rows and columns
2026-03-04 21:31:42.857216 INFO::Found 2 missing values.
2026-03-04 21:31:42.859921 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:42.860438 INFO::Done
2026-03-04 21:31:42.88694 INFO::Found NA in Reference column
2026-03-04 21:31:42.896111 INFO::Require at least two references per batch.
2026-03-04 21:31:42.916439 INFO::Formatting Data.
2026-03-04 21:31:42.917178 INFO::Recognized SummarizedExperiment
2026-03-04 21:31:42.917717 INFO::Typecasting input to dataframe.
2026-03-04 21:31:42.92721 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:42.928437 INFO::Removing potential empty rows and columns
2026-03-04 21:31:42.931909 INFO::Found 0 missing values.
2026-03-04 21:31:42.938189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:42.938759 INFO::Done
2026-03-04 21:31:42.953801 INFO::Formatting Data.
2026-03-04 21:31:42.95447 INFO::Recognized SummarizedExperiment
2026-03-04 21:31:42.954982 INFO::Typecasting input to dataframe.
2026-03-04 21:31:42.971339 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:42.972485 INFO::Removing potential empty rows and columns
2026-03-04 21:31:42.975776 INFO::Found 0 missing values.
2026-03-04 21:31:42.985848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:42.986476 INFO::Done
2026-03-04 21:31:43.001497 INFO::Formatting Data.
2026-03-04 21:31:43.002226 INFO::Recognized SummarizedExperiment
2026-03-04 21:31:43.002742 INFO::Typecasting input to dataframe.
2026-03-04 21:31:43.01856 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:43.019532 INFO::Removing potential empty rows and columns
2026-03-04 21:31:43.020551 INFO::Found 0 missing values.
2026-03-04 21:31:43.021417 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-04 21:31:43.025589 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:43.026147 INFO::Done
2026-03-04 21:31:43.035788 INFO::Formatting Data.
2026-03-04 21:31:43.036528 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:43.037345 INFO::Removing potential empty rows and columns
2026-03-04 21:31:43.038303 INFO::Found 0 missing values.
2026-03-04 21:31:43.041118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:43.041642 INFO::Done
2026-03-04 21:31:43.052978 INFO::Formatting Data.
2026-03-04 21:31:43.053869 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:43.054953 INFO::Removing potential empty rows and columns
2026-03-04 21:31:43.056016 INFO::Found 0 missing values.
2026-03-04 21:31:43.058977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:43.059549 INFO::Done
2026-03-04 21:31:43.090702 INFO::Formatting Data.
2026-03-04 21:31:43.091595 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:43.09274 INFO::Removing potential empty rows and columns
2026-03-04 21:31:43.093989 INFO::Found 1 missing values.
2026-03-04 21:31:43.096864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:43.097418 INFO::Done
2026-03-04 21:31:43.118373 INFO::Formatting Data.
2026-03-04 21:31:43.119243 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:43.120173 INFO::Removing potential empty rows and columns
2026-03-04 21:31:43.121205 INFO::Found 2 missing values.
2026-03-04 21:31:43.122145 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-04 21:31:43.124522 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:43.125088 INFO::Done
2026-03-04 21:31:43.135803 INFO::Formatting Data.
2026-03-04 21:31:43.136653 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:43.137592 INFO::Removing potential empty rows and columns
2026-03-04 21:31:43.138585 INFO::Found 2 missing values.
2026-03-04 21:31:43.140319 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:43.140886 INFO::Done
2026-03-04 21:31:43.151782 INFO::Formatting Data.
2026-03-04 21:31:43.152571 INFO::Typecasting input to dataframe.
2026-03-04 21:31:43.153378 INFO::Replacing NaNs with NAs.
2026-03-04 21:31:43.154266 INFO::Removing potential empty rows and columns
2026-03-04 21:31:43.155276 INFO::Found 0 missing values.
2026-03-04 21:31:43.158373 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 21:31:43.158955 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.729 4.415 21.821
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.367 | 1.195 | 17.895 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.011 | |