Yannis Schumann
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 167/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.9.0.tar.gz |
| StartedAt: 2026-05-05 07:26:44 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 07:28:16 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 28.679 1.882 21.359
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.9.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-05-05 07:27:58.471357 INFO::Formatting Data.
2026-05-05 07:27:58.473399 INFO::Replacing NaNs with NAs.
2026-05-05 07:27:58.492642 INFO::Removing potential empty rows and columns
2026-05-05 07:27:58.966288 INFO::Found 0 missing values.
2026-05-05 07:27:58.971728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:27:58.972766 INFO::Done
2026-05-05 07:27:58.973669 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:27:58.995242 INFO::Starting hierarchical adjustment
2026-05-05 07:27:58.996627 INFO::Found 3 batches.
2026-05-05 07:27:58.997515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:27:58.999371 INFO::Using default BPPARAM
2026-05-05 07:27:59.000442 INFO::Processing subtree level 1
2026-05-05 07:27:59.158137 INFO::Adjusting the last 1 batches sequentially
2026-05-05 07:27:59.1612 INFO::Done
2026-05-05 07:27:59.162437 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:27:59.166903 INFO::ASW Batch was -0.163026157381245 prior to batch effect correction and is now -0.163026157381245 .
2026-05-05 07:27:59.168916 INFO::Total function execution time is 0.698345184326172 s and adjustment time is 0.164643526077271 s ( 23.58 )
2026-05-05 07:27:59.194143 INFO::Formatting Data.
2026-05-05 07:27:59.195403 INFO::Replacing NaNs with NAs.
2026-05-05 07:27:59.197071 INFO::Removing potential empty rows and columns
2026-05-05 07:27:59.199083 INFO::Found 0 missing values.
2026-05-05 07:27:59.20092 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.
2026-05-05 07:27:59.217889 INFO::Formatting Data.
2026-05-05 07:27:59.218978 INFO::Replacing NaNs with NAs.
2026-05-05 07:27:59.220394 INFO::Removing potential empty rows and columns
2026-05-05 07:27:59.222084 INFO::Found 0 missing values.
2026-05-05 07:27:59.223572 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.
2026-05-05 07:27:59.247792 INFO::Formatting Data.
2026-05-05 07:27:59.248938 INFO::Replacing NaNs with NAs.
2026-05-05 07:27:59.250328 INFO::Removing potential empty rows and columns
2026-05-05 07:27:59.25202 INFO::Found 0 missing values.
2026-05-05 07:27:59.253547 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.
2026-05-05 07:27:59.260963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:27:59.261963 INFO::Done
2026-05-05 07:27:59.262784 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:27:59.265882 INFO::Starting hierarchical adjustment
2026-05-05 07:27:59.267178 INFO::Found 2 batches.
2026-05-05 07:27:59.268095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:27:59.269191 INFO::Using default BPPARAM
2026-05-05 07:27:59.270051 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:27:59.271478 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 07:27:59.304751 INFO::Done
2026-05-05 07:27:59.305871 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:27:59.309197 INFO::ASW Batch was 0.0333426033516441 prior to batch effect correction and is now -0.126446350276424 .
2026-05-05 07:27:59.310628 INFO::Total function execution time is 0.062885046005249 s and adjustment time is 0.0377936363220215 s ( 60.1 )
2026-05-05 07:27:59.314893 INFO::Formatting Data.
2026-05-05 07:27:59.316132 INFO::Replacing NaNs with NAs.
2026-05-05 07:27:59.329677 INFO::Formatting Data.
2026-05-05 07:27:59.330853 INFO::Replacing NaNs with NAs.
2026-05-05 07:27:59.332541 INFO::Removing potential empty rows and columns
2026-05-05 07:27:59.334494 INFO::Found 0 missing values.
2026-05-05 07:27:59.339772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:27:59.340933 INFO::Done
2026-05-05 07:27:59.34198 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:27:59.345434 INFO::Starting hierarchical adjustment
2026-05-05 07:27:59.34687 INFO::Found 2 batches.
2026-05-05 07:27:59.348475 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:27:59.34968 INFO::Using default BPPARAM
2026-05-05 07:27:59.350682 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:27:59.352338 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 07:27:59.376345 INFO::Done
2026-05-05 07:27:59.37742 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:27:59.380825 INFO::ASW Batch was -0.0460589548075857 prior to batch effect correction and is now -0.116702599082361 .
2026-05-05 07:27:59.382235 INFO::Total function execution time is 0.052609920501709 s and adjustment time is 0.0298066139221191 s ( 56.66 )
2026-05-05 07:27:59.38411 INFO::Formatting Data.
2026-05-05 07:27:59.385203 INFO::Replacing NaNs with NAs.
2026-05-05 07:27:59.386681 INFO::Removing potential empty rows and columns
2026-05-05 07:27:59.388456 INFO::Found 0 missing values.
2026-05-05 07:27:59.393248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:27:59.394345 INFO::Done
2026-05-05 07:27:59.395192 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:27:59.398398 INFO::Starting hierarchical adjustment
2026-05-05 07:27:59.399605 INFO::Found 2 batches.
2026-05-05 07:27:59.400489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:27:59.401406 INFO::Using default BPPARAM
2026-05-05 07:27:59.402272 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:27:59.403754 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 07:27:59.436965 INFO::Done
2026-05-05 07:27:59.438231 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:27:59.441519 INFO::ASW Batch was -0.0460589548075857 prior to batch effect correction and is now -0.116702599082361 .
2026-05-05 07:27:59.442785 INFO::Total function execution time is 0.0587279796600342 s and adjustment time is 0.0375490188598633 s ( 63.94 )
2026-05-05 07:28:03.837034 INFO::Formatting Data.
2026-05-05 07:28:03.838062 INFO::Recognized SummarizedExperiment
2026-05-05 07:28:03.838848 INFO::Typecasting input to dataframe.
2026-05-05 07:28:03.884413 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:03.886053 INFO::Removing potential empty rows and columns
2026-05-05 07:28:03.891036 INFO::Found 0 missing values.
2026-05-05 07:28:03.901133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:03.902232 INFO::Done
2026-05-05 07:28:03.903068 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:03.908054 INFO::Starting hierarchical adjustment
2026-05-05 07:28:03.909248 INFO::Found 2 batches.
2026-05-05 07:28:03.910076 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:03.911536 INFO::Using default BPPARAM
2026-05-05 07:28:03.912484 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:03.913961 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 07:28:03.990126 INFO::Done
2026-05-05 07:28:03.991042 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:03.995853 INFO::ASW Batch was 0.0215714297753119 prior to batch effect correction and is now -0.0946735258386256 .
2026-05-05 07:28:03.9971 INFO::Total function execution time is 0.160572528839111 s and adjustment time is 0.081106424331665 s ( 50.51 )
2026-05-05 07:28:04.022869 INFO::Formatting Data.
2026-05-05 07:28:04.023865 INFO::Recognized SummarizedExperiment
2026-05-05 07:28:04.024611 INFO::Typecasting input to dataframe.
2026-05-05 07:28:04.037356 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:04.039085 INFO::Removing potential empty rows and columns
2026-05-05 07:28:04.044008 INFO::Found 0 missing values.
2026-05-05 07:28:04.053696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:04.054634 INFO::Done
2026-05-05 07:28:04.055468 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:04.060468 INFO::Starting hierarchical adjustment
2026-05-05 07:28:04.061724 INFO::Found 2 batches.
2026-05-05 07:28:04.062636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:04.063596 INFO::Using default BPPARAM
2026-05-05 07:28:04.064517 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:04.06611 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 07:28:04.10224 INFO::Done
2026-05-05 07:28:04.10328 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:04.108662 INFO::ASW Batch was -0.0158229709334169 prior to batch effect correction and is now -0.0158229709334169 .
2026-05-05 07:28:04.11007 INFO::Total function execution time is 0.0871140956878662 s and adjustment time is 0.0407769680023193 s ( 46.81 )
2026-05-05 07:28:04.138298 INFO::Formatting Data.
2026-05-05 07:28:04.139524 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:04.141081 INFO::Removing potential empty rows and columns
2026-05-05 07:28:04.14285 INFO::Found 0 missing values.
2026-05-05 07:28:04.14793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:04.148971 INFO::Done
2026-05-05 07:28:04.14997 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:04.153189 INFO::Starting hierarchical adjustment
2026-05-05 07:28:04.154488 INFO::Found 3 batches.
2026-05-05 07:28:04.15545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:04.156507 INFO::Using default BPPARAM
2026-05-05 07:28:04.157718 INFO::Processing subtree level 1
2026-05-05 07:28:04.345114 INFO::Adjusting the last 1 batches sequentially
2026-05-05 07:28:04.355714 INFO::Done
2026-05-05 07:28:04.356675 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:04.364525 INFO::ASW Batch was -0.116246352580394 prior to batch effect correction and is now -0.170793296226264 .
2026-05-05 07:28:04.370129 INFO::Total function execution time is 0.231799602508545 s and adjustment time is 0.201457023620605 s ( 86.91 )
2026-05-05 07:28:04.40437 INFO::Skipping initial DF formatting
2026-05-05 07:28:04.405383 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:04.41131 INFO::Starting hierarchical adjustment
2026-05-05 07:28:04.412679 INFO::Found 5 batches.
2026-05-05 07:28:04.413662 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:04.414708 INFO::Using default BPPARAM
2026-05-05 07:28:04.415663 INFO::Processing subtree level 1
2026-05-05 07:28:04.582039 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:04.584814 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 07:28:04.614387 INFO::Done
2026-05-05 07:28:04.615459 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:04.622341 INFO::ASW Batch was 0.583171384671825 prior to batch effect correction and is now 0.583171384671825 .
2026-05-05 07:28:04.623412 INFO::ASW Label was 0.359401557523035 prior to batch effect correction and is now 0.359401557523035 .
2026-05-05 07:28:04.624751 INFO::Total function execution time is 0.220419883728027 s and adjustment time is 0.201926231384277 s ( 91.61 )
2026-05-05 07:28:04.650643 INFO::Formatting Data.
2026-05-05 07:28:04.651839 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:04.653227 INFO::Removing potential empty rows and columns
2026-05-05 07:28:04.654811 INFO::Found 0 missing values.
2026-05-05 07:28:04.661599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:04.662854 INFO::Done
2026-05-05 07:28:04.664262 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:04.669949 INFO::Starting hierarchical adjustment
2026-05-05 07:28:04.671234 INFO::Found 5 batches.
2026-05-05 07:28:04.672166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:04.673151 INFO::Using default BPPARAM
2026-05-05 07:28:04.674044 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.
2026-05-05 07:28:04.815743 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:04.82088 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 07:28:04.846919 INFO::Done
2026-05-05 07:28:04.848061 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:04.853135 INFO::ASW Batch was 0.38214515131014 prior to batch effect correction and is now -0.109816432961421 .
2026-05-05 07:28:04.854213 INFO::ASW Label was 0.287299057325152 prior to batch effect correction and is now 0.907311419084471 .
2026-05-05 07:28:04.855501 INFO::Total function execution time is 0.204858064651489 s and adjustment time is 0.175918579101562 s ( 85.87 )
2026-05-05 07:28:04.856964 INFO::Formatting Data.
2026-05-05 07:28:04.858074 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:04.859483 INFO::Removing potential empty rows and columns
2026-05-05 07:28:04.861168 INFO::Found 0 missing values.
2026-05-05 07:28:04.867633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:04.868616 INFO::Done
2026-05-05 07:28:04.86947 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:04.874021 INFO::Starting hierarchical adjustment
2026-05-05 07:28:04.875299 INFO::Found 5 batches.
2026-05-05 07:28:04.876208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:04.87718 INFO::Using default BPPARAM
2026-05-05 07:28:04.878098 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.
2026-05-05 07:28:05.051493 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:05.054718 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 07:28:05.081169 INFO::Done
2026-05-05 07:28:05.082445 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:05.088276 INFO::ASW Batch was 0.38214515131014 prior to batch effect correction and is now -0.109816432961421 .
2026-05-05 07:28:05.089586 INFO::ASW Label was 0.287299057325152 prior to batch effect correction and is now 0.907311419084471 .
2026-05-05 07:28:05.091239 INFO::Total function execution time is 0.23421573638916 s and adjustment time is 0.206073760986328 s ( 87.98 )
2026-05-05 07:28:05.114393 INFO::Formatting Data.
2026-05-05 07:28:05.115801 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:05.117555 INFO::Removing potential empty rows and columns
2026-05-05 07:28:05.119476 INFO::Found 0 missing values.
2026-05-05 07:28:05.127568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:05.128769 INFO::Done
2026-05-05 07:28:05.129922 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:05.135472 INFO::Starting hierarchical adjustment
2026-05-05 07:28:05.137029 INFO::Found 5 batches.
2026-05-05 07:28:05.138212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:05.139447 INFO::Using default BPPARAM
2026-05-05 07:28:05.140623 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.
2026-05-05 07:28:05.281534 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:05.283829 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 07:28:05.307689 INFO::Done
2026-05-05 07:28:05.308701 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:05.313715 INFO::ASW Batch was 0.618696228218455 prior to batch effect correction and is now -0.0843842397478269 .
2026-05-05 07:28:05.314798 INFO::ASW Label was 0.17984378962497 prior to batch effect correction and is now 0.708223302767804 .
2026-05-05 07:28:05.31617 INFO::Total function execution time is 0.201864957809448 s and adjustment time is 0.170914888381958 s ( 84.67 )
2026-05-05 07:28:05.317581 INFO::Formatting Data.
2026-05-05 07:28:05.318661 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:05.320141 INFO::Removing potential empty rows and columns
2026-05-05 07:28:05.321835 INFO::Found 0 missing values.
2026-05-05 07:28:05.329058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:05.330134 INFO::Done
2026-05-05 07:28:05.331071 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:05.335928 INFO::Starting hierarchical adjustment
2026-05-05 07:28:05.337272 INFO::Found 5 batches.
2026-05-05 07:28:05.338284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:05.339318 INFO::Using default BPPARAM
2026-05-05 07:28:05.340303 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.
2026-05-05 07:28:05.494697 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:05.497178 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 07:28:05.521753 INFO::Done
2026-05-05 07:28:05.522855 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:05.528199 INFO::ASW Batch was 0.618696228218455 prior to batch effect correction and is now -0.0843842397478269 .
2026-05-05 07:28:05.529303 INFO::ASW Label was 0.17984378962497 prior to batch effect correction and is now 0.708223302767804 .
2026-05-05 07:28:05.530702 INFO::Total function execution time is 0.213109970092773 s and adjustment time is 0.184760093688965 s ( 86.7 )
2026-05-05 07:28:05.55179 INFO::Formatting Data.
2026-05-05 07:28:05.552994 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:05.554555 INFO::Removing potential empty rows and columns
2026-05-05 07:28:05.556272 INFO::Found 0 missing values.
2026-05-05 07:28:05.560867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:05.561956 INFO::Done
2026-05-05 07:28:05.562904 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:05.567788 INFO::Starting hierarchical adjustment
2026-05-05 07:28:05.569156 INFO::Found 2 batches.
2026-05-05 07:28:05.570204 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:05.571267 INFO::Using default BPPARAM
2026-05-05 07:28:05.572257 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:05.573816 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 07:28:05.596773 INFO::Done
2026-05-05 07:28:05.597946 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:05.603067 INFO::ASW Batch was 0.210018541848317 prior to batch effect correction and is now 0.0754972997147811 .
2026-05-05 07:28:05.60423 INFO::ASW Label was 0.831252592369241 prior to batch effect correction and is now 0.894372565664604 .
2026-05-05 07:28:05.605673 INFO::Total function execution time is 0.0539326667785645 s and adjustment time is 0.0278730392456055 s ( 51.68 )
2026-05-05 07:28:05.607154 INFO::Formatting Data.
2026-05-05 07:28:05.608431 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:05.610091 INFO::Removing potential empty rows and columns
2026-05-05 07:28:05.612007 INFO::Found 0 missing values.
2026-05-05 07:28:05.617035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:05.618147 INFO::Done
2026-05-05 07:28:05.619153 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:05.62424 INFO::Starting hierarchical adjustment
2026-05-05 07:28:05.62567 INFO::Found 2 batches.
2026-05-05 07:28:05.626742 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:05.627921 INFO::Using default BPPARAM
2026-05-05 07:28:05.628959 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:05.630794 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 07:28:05.653188 INFO::Done
2026-05-05 07:28:05.654235 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:05.658726 INFO::ASW Batch was 0.210018541848317 prior to batch effect correction and is now 0.0754972997147811 .
2026-05-05 07:28:05.659795 INFO::ASW Label was 0.831252592369241 prior to batch effect correction and is now 0.894372565664604 .
2026-05-05 07:28:05.661018 INFO::Total function execution time is 0.0539264678955078 s and adjustment time is 0.0278465747833252 s ( 51.64 )
2026-05-05 07:28:05.678648 INFO::Formatting Data.
2026-05-05 07:28:05.679856 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:05.681213 INFO::Removing potential empty rows and columns
2026-05-05 07:28:05.68266 INFO::Found 0 missing values.
2026-05-05 07:28:05.686029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:05.687011 INFO::Done
2026-05-05 07:28:05.68787 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:05.690799 INFO::Starting hierarchical adjustment
2026-05-05 07:28:05.692046 INFO::Found 2 batches.
2026-05-05 07:28:05.692914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:05.693871 INFO::Using default BPPARAM
2026-05-05 07:28:05.694689 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:05.696129 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 07:28:05.743418 INFO::Done
2026-05-05 07:28:05.744434 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:05.74747 INFO::ASW Batch was 0.28349122254951 prior to batch effect correction and is now -0.114827411132713 .
2026-05-05 07:28:05.748814 INFO::Total function execution time is 0.0702304840087891 s and adjustment time is 0.0515780448913574 s ( 73.44 )
2026-05-05 07:28:05.766934 INFO::Formatting Data.
2026-05-05 07:28:05.768067 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:05.769372 INFO::Removing potential empty rows and columns
2026-05-05 07:28:05.771034 INFO::Found 0 missing values.
2026-05-05 07:28:05.772756 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.
2026-05-05 07:28:05.779953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:05.780936 INFO::Done
2026-05-05 07:28:05.781867 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:05.786283 INFO::Starting hierarchical adjustment
2026-05-05 07:28:05.787521 INFO::Found 2 batches.
2026-05-05 07:28:05.788435 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:05.789352 INFO::Using default BPPARAM
2026-05-05 07:28:05.7902 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:05.791743 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 07:28:05.816104 INFO::Done
2026-05-05 07:28:05.817065 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:05.821493 INFO::ASW Batch was 0.555369344356933 prior to batch effect correction and is now -0.00310271543750173 .
2026-05-05 07:28:05.822472 INFO::ASW Label was 0.523627634010962 prior to batch effect correction and is now 0.912903018477216 .
2026-05-05 07:28:05.823662 INFO::Total function execution time is 0.0567529201507568 s and adjustment time is 0.0288088321685791 s ( 50.76 )
2026-05-05 07:28:05.824884 INFO::Formatting Data.
2026-05-05 07:28:05.825907 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:05.827342 INFO::Removing potential empty rows and columns
2026-05-05 07:28:05.828917 INFO::Found 0 missing values.
2026-05-05 07:28:05.830363 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.
2026-05-05 07:28:05.83787 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:05.838815 INFO::Done
2026-05-05 07:28:05.83968 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:05.844195 INFO::Starting hierarchical adjustment
2026-05-05 07:28:05.845426 INFO::Found 2 batches.
2026-05-05 07:28:05.846304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:05.847175 INFO::Using default BPPARAM
2026-05-05 07:28:05.848123 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:05.849562 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 07:28:05.87392 INFO::Done
2026-05-05 07:28:05.874882 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:05.87915 INFO::ASW Batch was 0.555369344356933 prior to batch effect correction and is now -0.00310271543750173 .
2026-05-05 07:28:05.880169 INFO::ASW Label was 0.523627634010962 prior to batch effect correction and is now 0.912903018477216 .
2026-05-05 07:28:05.881351 INFO::Total function execution time is 0.0565006732940674 s and adjustment time is 0.028717041015625 s ( 50.83 )
2026-05-05 07:28:06.182328 INFO::Formatting Data.
2026-05-05 07:28:06.183368 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:06.184679 INFO::Removing potential empty rows and columns
2026-05-05 07:28:06.186242 INFO::Found 0 missing values.
2026-05-05 07:28:06.190703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:06.19167 INFO::Done
2026-05-05 07:28:06.192424 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:06.195352 INFO::Starting hierarchical adjustment
2026-05-05 07:28:06.19664 INFO::Found 3 batches.
2026-05-05 07:28:06.197472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:06.198338 INFO::Using default BPPARAM
2026-05-05 07:28:06.199084 INFO::Processing subtree level 1
2026-05-05 07:28:06.309765 INFO::Adjusting the last 1 batches sequentially
2026-05-05 07:28:06.312318 INFO::Done
2026-05-05 07:28:06.313318 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:06.317322 INFO::ASW Batch was -0.0643350683419137 prior to batch effect correction and is now -0.0643350683419137 .
2026-05-05 07:28:06.318911 INFO::Total function execution time is 0.136547327041626 s and adjustment time is 0.11591649055481 s ( 84.89 )
2026-05-05 07:28:06.320576 INFO::Formatting Data.
2026-05-05 07:28:06.32168 INFO::Typecasting input to dataframe.
2026-05-05 07:28:06.322889 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:06.324363 INFO::Removing potential empty rows and columns
2026-05-05 07:28:06.326059 INFO::Found 0 missing values.
2026-05-05 07:28:06.330914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:06.331953 INFO::Done
2026-05-05 07:28:06.332817 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:06.335971 INFO::Starting hierarchical adjustment
2026-05-05 07:28:06.337225 INFO::Found 3 batches.
2026-05-05 07:28:06.338161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:06.339147 INFO::Using default BPPARAM
2026-05-05 07:28:06.340044 INFO::Processing subtree level 1
2026-05-05 07:28:06.454542 INFO::Adjusting the last 1 batches sequentially
2026-05-05 07:28:06.457038 INFO::Done
2026-05-05 07:28:06.458021 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:06.461679 INFO::ASW Batch was -0.0643350683419137 prior to batch effect correction and is now -0.0643350683419137 .
2026-05-05 07:28:06.463204 INFO::Total function execution time is 0.142592191696167 s and adjustment time is 0.120046615600586 s ( 84.19 )
2026-05-05 07:28:06.483127 INFO::Formatting Data.
2026-05-05 07:28:06.484377 INFO::Typecasting input to dataframe.
2026-05-05 07:28:06.485754 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:06.487194 INFO::Removing potential empty rows and columns
2026-05-05 07:28:06.488931 INFO::Found 0 missing values.
2026-05-05 07:28:06.493726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:06.494734 INFO::Done
2026-05-05 07:28:06.495575 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:06.498661 INFO::Starting hierarchical adjustment
2026-05-05 07:28:06.499922 INFO::Found 3 batches.
2026-05-05 07:28:06.500807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:06.501809 INFO::Using default BPPARAM
2026-05-05 07:28:06.502663 INFO::Processing subtree level 1
2026-05-05 07:28:06.616023 INFO::Adjusting the last 1 batches sequentially
2026-05-05 07:28:06.618557 INFO::Done
2026-05-05 07:28:06.619732 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:06.624141 INFO::ASW Batch was -0.10495726918626 prior to batch effect correction and is now -0.10495726918626 .
2026-05-05 07:28:06.625784 INFO::Total function execution time is 0.142602205276489 s and adjustment time is 0.118890285491943 s ( 83.37 )
2026-05-05 07:28:06.819887 INFO::Formatting Data.
2026-05-05 07:28:06.821112 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:06.822931 INFO::Removing potential empty rows and columns
2026-05-05 07:28:06.827299 INFO::Found 1000 missing values.
2026-05-05 07:28:06.857914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:06.85893 INFO::Done
2026-05-05 07:28:06.859827 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:06.868252 INFO::Starting hierarchical adjustment
2026-05-05 07:28:06.869585 INFO::Found 10 batches.
2026-05-05 07:28:06.870485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:06.871453 INFO::Using default BPPARAM
2026-05-05 07:28:06.87232 INFO::Processing subtree level 1
2026-05-05 07:28:07.07534 INFO::Processing subtree level 2
2026-05-05 07:28:07.381285 INFO::Adjusting the last 1 batches sequentially
2026-05-05 07:28:07.384225 INFO::Done
2026-05-05 07:28:07.385157 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:07.458829 INFO::ASW Batch was 0.533552219495872 prior to batch effect correction and is now 0.533552219495872 .
2026-05-05 07:28:07.460231 INFO::ASW Label was 0.294193513923949 prior to batch effect correction and is now 0.294193513923949 .
2026-05-05 07:28:07.461615 INFO::Total function execution time is 0.64179801940918 s and adjustment time is 0.514943361282349 s ( 80.23 )
2026-05-05 07:28:07.462873 INFO::Formatting Data.
2026-05-05 07:28:07.46385 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:07.465476 INFO::Removing potential empty rows and columns
2026-05-05 07:28:07.469778 INFO::Found 1000 missing values.
2026-05-05 07:28:07.499884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:07.500879 INFO::Done
2026-05-05 07:28:07.508994 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:07.517881 INFO::Starting hierarchical adjustment
2026-05-05 07:28:07.519096 INFO::Found 10 batches.
2026-05-05 07:28:08.744798 INFO::Set up parallel execution backend with 2 workers
2026-05-05 07:28:08.746665 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-05 07:28:10.218622 INFO::Adjusting the last 2 batches sequentially
2026-05-05 07:28:10.223052 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 07:28:10.248949 INFO::Done
2026-05-05 07:28:10.249901 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:10.256898 INFO::ASW Batch was 0.533552219495872 prior to batch effect correction and is now 0.533552219495872 .
2026-05-05 07:28:10.257883 INFO::ASW Label was 0.294193513923949 prior to batch effect correction and is now 0.294193513923949 .
2026-05-05 07:28:10.259076 INFO::Total function execution time is 2.7962212562561 s and adjustment time is 2.73010683059692 s ( 97.64 )
2026-05-05 07:28:10.49763 INFO::Formatting Data.
2026-05-05 07:28:10.498944 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:10.500628 INFO::Removing potential empty rows and columns
2026-05-05 07:28:10.502617 INFO::Found 0 missing values.
2026-05-05 07:28:10.509388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:10.510444 INFO::Done
2026-05-05 07:28:10.511499 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 07:28:10.516483 INFO::Starting hierarchical adjustment
2026-05-05 07:28:10.517897 INFO::Found 3 batches.
2026-05-05 07:28:10.518927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 07:28:10.520048 INFO::Using default BPPARAM
2026-05-05 07:28:10.521024 INFO::Processing subtree level 1
2026-05-05 07:28:10.682923 INFO::Adjusting the last 1 batches sequentially
2026-05-05 07:28:10.689821 INFO::Done
2026-05-05 07:28:10.690955 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 07:28:10.700472 INFO::ASW Batch was 0.200617249413019 prior to batch effect correction and is now -0.153149206747179 .
2026-05-05 07:28:10.705507 INFO::ASW Label was -0.194955169758104 prior to batch effect correction and is now 0.0564649701216362 .
2026-05-05 07:28:10.707205 INFO::Total function execution time is 0.209593772888184 s and adjustment time is 0.172200441360474 s ( 82.16 )
2026-05-05 07:28:10.912976 INFO::Formatting Data.
2026-05-05 07:28:10.914164 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:10.915557 INFO::Removing potential empty rows and columns
2026-05-05 07:28:10.917263 INFO::Found 2 missing values.
2026-05-05 07:28:10.921979 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:10.922967 INFO::Done
2026-05-05 07:28:10.96625 INFO::Found NA in Reference column
2026-05-05 07:28:10.981361 INFO::Require at least two references per batch.
2026-05-05 07:28:11.013604 INFO::Formatting Data.
2026-05-05 07:28:11.014616 INFO::Recognized SummarizedExperiment
2026-05-05 07:28:11.015406 INFO::Typecasting input to dataframe.
2026-05-05 07:28:11.030226 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.031988 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.037761 INFO::Found 0 missing values.
2026-05-05 07:28:11.048877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.049889 INFO::Done
2026-05-05 07:28:11.074569 INFO::Formatting Data.
2026-05-05 07:28:11.075705 INFO::Recognized SummarizedExperiment
2026-05-05 07:28:11.076566 INFO::Typecasting input to dataframe.
2026-05-05 07:28:11.104892 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.106781 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.112768 INFO::Found 0 missing values.
2026-05-05 07:28:11.132055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.133013 INFO::Done
2026-05-05 07:28:11.157643 INFO::Formatting Data.
2026-05-05 07:28:11.158698 INFO::Recognized SummarizedExperiment
2026-05-05 07:28:11.159517 INFO::Typecasting input to dataframe.
2026-05-05 07:28:11.186963 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.188488 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.190232 INFO::Found 0 missing values.
2026-05-05 07:28:11.191779 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.
2026-05-05 07:28:11.199142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.200127 INFO::Done
2026-05-05 07:28:11.216073 INFO::Formatting Data.
2026-05-05 07:28:11.217327 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.218834 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.220531 INFO::Found 0 missing values.
2026-05-05 07:28:11.225414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.226415 INFO::Done
2026-05-05 07:28:11.244717 INFO::Formatting Data.
2026-05-05 07:28:11.245844 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.247176 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.248779 INFO::Found 0 missing values.
2026-05-05 07:28:11.253651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.254598 INFO::Done
2026-05-05 07:28:11.303381 INFO::Formatting Data.
2026-05-05 07:28:11.304577 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.306386 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.308544 INFO::Found 1 missing values.
2026-05-05 07:28:11.313152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.314176 INFO::Done
2026-05-05 07:28:11.3462 INFO::Formatting Data.
2026-05-05 07:28:11.347387 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.348935 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.350713 INFO::Found 2 missing values.
2026-05-05 07:28:11.352312 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.
2026-05-05 07:28:11.356702 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.357766 INFO::Done
2026-05-05 07:28:11.374261 INFO::Formatting Data.
2026-05-05 07:28:11.375454 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.376967 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.378816 INFO::Found 2 missing values.
2026-05-05 07:28:11.381761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.382753 INFO::Done
2026-05-05 07:28:11.400074 INFO::Formatting Data.
2026-05-05 07:28:11.401234 INFO::Typecasting input to dataframe.
2026-05-05 07:28:11.40255 INFO::Replacing NaNs with NAs.
2026-05-05 07:28:11.404123 INFO::Removing potential empty rows and columns
2026-05-05 07:28:11.405805 INFO::Found 0 missing values.
2026-05-05 07:28:11.410965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 07:28:11.412052 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
23.111 4.563 27.902
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.679 | 1.882 | 21.359 | |
| compute_asw | 0.033 | 0.000 | 0.032 | |
| count_existing | 0.017 | 0.000 | 0.017 | |
| generate_data_covariables | 0.015 | 0.000 | 0.015 | |
| generate_dataset | 0.013 | 0.000 | 0.013 | |