Yannis Schumann
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 170/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2026-04-17 02:55:07 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 02:56:57 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 110.2 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 31.55 1.147 24.626
* 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-devel_2025-02-19/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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")
2026-04-17 02:56:36.077215 INFO::Formatting Data.
2026-04-17 02:56:36.078961 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:36.096731 INFO::Removing potential empty rows and columns
2026-04-17 02:56:36.468979 INFO::Found 0 missing values.
2026-04-17 02:56:36.473463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:36.474324 INFO::Done
2026-04-17 02:56:36.475032 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:36.489867 INFO::Starting hierarchical adjustment
2026-04-17 02:56:36.491003 INFO::Found 3 batches.
2026-04-17 02:56:36.491736 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:36.493201 INFO::Using default BPPARAM
2026-04-17 02:56:36.493952 INFO::Processing subtree level 1
2026-04-17 02:56:36.623934 INFO::Adjusting the last 1 batches sequentially
2026-04-17 02:56:36.630305 INFO::Done
2026-04-17 02:56:36.631176 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:36.63881 INFO::ASW Batch was -0.0650372932815926 prior to batch effect correction and is now -0.0650372932815926 .
2026-04-17 02:56:36.640399 INFO::Total function execution time is 0.564002752304077 s and adjustment time is 0.139501094818115 s ( 24.73 )
2026-04-17 02:56:36.665111 INFO::Formatting Data.
2026-04-17 02:56:36.66606 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:36.667272 INFO::Removing potential empty rows and columns
2026-04-17 02:56:36.670696 INFO::Found 0 missing values.
2026-04-17 02:56:36.672256 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.
2026-04-17 02:56:36.687167 INFO::Formatting Data.
2026-04-17 02:56:36.688137 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:36.689355 INFO::Removing potential empty rows and columns
2026-04-17 02:56:36.690732 INFO::Found 0 missing values.
2026-04-17 02:56:36.691934 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.
2026-04-17 02:56:36.713032 INFO::Formatting Data.
2026-04-17 02:56:36.713952 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:36.715071 INFO::Removing potential empty rows and columns
2026-04-17 02:56:36.716454 INFO::Found 0 missing values.
2026-04-17 02:56:36.717677 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.
2026-04-17 02:56:36.723676 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:36.724591 INFO::Done
2026-04-17 02:56:36.725326 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:36.72794 INFO::Starting hierarchical adjustment
2026-04-17 02:56:36.728952 INFO::Found 2 batches.
2026-04-17 02:56:36.729654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:36.730485 INFO::Using default BPPARAM
2026-04-17 02:56:36.731185 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:36.732454 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 02:56:36.76117 INFO::Done
2026-04-17 02:56:36.762049 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:36.764689 INFO::ASW Batch was -0.0102352841610904 prior to batch effect correction and is now -0.12964879236437 .
2026-04-17 02:56:36.765755 INFO::Total function execution time is 0.0527732372283936 s and adjustment time is 0.0323944091796875 s ( 61.38 )
2026-04-17 02:56:36.76924 INFO::Formatting Data.
2026-04-17 02:56:36.770125 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:36.781725 INFO::Formatting Data.
2026-04-17 02:56:36.7827 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:36.783876 INFO::Removing potential empty rows and columns
2026-04-17 02:56:36.785307 INFO::Found 0 missing values.
2026-04-17 02:56:36.789316 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:36.790127 INFO::Done
2026-04-17 02:56:36.790842 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:36.793533 INFO::Starting hierarchical adjustment
2026-04-17 02:56:36.794536 INFO::Found 2 batches.
2026-04-17 02:56:36.795256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:36.796105 INFO::Using default BPPARAM
2026-04-17 02:56:36.796842 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:36.798099 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 02:56:36.85225 INFO::Done
2026-04-17 02:56:36.853153 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:36.855839 INFO::ASW Batch was 0.0251745857353024 prior to batch effect correction and is now -0.10369457415769 .
2026-04-17 02:56:36.856905 INFO::Total function execution time is 0.0752208232879639 s and adjustment time is 0.0578892230987549 s ( 76.96 )
2026-04-17 02:56:36.858315 INFO::Formatting Data.
2026-04-17 02:56:36.859117 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:36.860337 INFO::Removing potential empty rows and columns
2026-04-17 02:56:36.861796 INFO::Found 0 missing values.
2026-04-17 02:56:36.865794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:36.866667 INFO::Done
2026-04-17 02:56:36.867415 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:36.870142 INFO::Starting hierarchical adjustment
2026-04-17 02:56:36.871133 INFO::Found 2 batches.
2026-04-17 02:56:36.87187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:36.87276 INFO::Using default BPPARAM
2026-04-17 02:56:36.873505 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:36.874773 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 02:56:36.895356 INFO::Done
2026-04-17 02:56:36.896257 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:36.898996 INFO::ASW Batch was 0.0251745857353024 prior to batch effect correction and is now -0.10369457415769 .
2026-04-17 02:56:36.900137 INFO::Total function execution time is 0.0417864322662354 s and adjustment time is 0.0243983268737793 s ( 58.39 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-17 02:56:41.096341 INFO::Formatting Data.
2026-04-17 02:56:41.097258 INFO::Recognized SummarizedExperiment
2026-04-17 02:56:41.097932 INFO::Typecasting input to dataframe.
2026-04-17 02:56:41.137774 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:41.139331 INFO::Removing potential empty rows and columns
2026-04-17 02:56:41.144397 INFO::Found 0 missing values.
2026-04-17 02:56:41.154199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:41.155044 INFO::Done
2026-04-17 02:56:41.15575 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:41.160529 INFO::Starting hierarchical adjustment
2026-04-17 02:56:41.161609 INFO::Found 2 batches.
2026-04-17 02:56:41.162277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:41.163609 INFO::Using default BPPARAM
2026-04-17 02:56:41.164289 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:41.165531 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 02:56:41.255922 INFO::Done
2026-04-17 02:56:41.256798 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:41.26127 INFO::ASW Batch was 0.0030095765825311 prior to batch effect correction and is now -0.0861267058010367 .
2026-04-17 02:56:41.262443 INFO::Total function execution time is 0.166613578796387 s and adjustment time is 0.0944755077362061 s ( 56.7 )
Warning: stack imbalance in '{', 73 then 75
2026-04-17 02:56:41.283597 INFO::Formatting Data.
2026-04-17 02:56:41.284446 INFO::Recognized SummarizedExperiment
2026-04-17 02:56:41.28512 INFO::Typecasting input to dataframe.
2026-04-17 02:56:41.295994 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:41.297379 INFO::Removing potential empty rows and columns
2026-04-17 02:56:41.30167 INFO::Found 0 missing values.
2026-04-17 02:56:41.310571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:41.31145 INFO::Done
2026-04-17 02:56:41.312152 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:41.316551 INFO::Starting hierarchical adjustment
2026-04-17 02:56:41.317595 INFO::Found 2 batches.
2026-04-17 02:56:41.318267 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:41.318995 INFO::Using default BPPARAM
2026-04-17 02:56:41.319667 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:41.320908 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 02:56:41.355226 INFO::Done
2026-04-17 02:56:41.35609 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:41.36081 INFO::ASW Batch was 0.00430749831964714 prior to batch effect correction and is now 0.00430749831964714 .
2026-04-17 02:56:41.362003 INFO::Total function execution time is 0.0783560276031494 s and adjustment time is 0.0377867221832275 s ( 48.22 )
2026-04-17 02:56:41.385567 INFO::Formatting Data.
2026-04-17 02:56:41.386551 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:41.387745 INFO::Removing potential empty rows and columns
2026-04-17 02:56:41.389175 INFO::Found 0 missing values.
2026-04-17 02:56:41.393407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:41.394366 INFO::Done
2026-04-17 02:56:41.395143 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:41.397855 INFO::Starting hierarchical adjustment
2026-04-17 02:56:41.398859 INFO::Found 3 batches.
2026-04-17 02:56:41.399602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:41.400398 INFO::Using default BPPARAM
2026-04-17 02:56:41.401157 INFO::Processing subtree level 1
2026-04-17 02:56:41.567359 INFO::Adjusting the last 1 batches sequentially
2026-04-17 02:56:41.578014 INFO::Done
2026-04-17 02:56:41.578955 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:41.586436 INFO::ASW Batch was -0.121125163517752 prior to batch effect correction and is now -0.167039133808909 .
2026-04-17 02:56:41.587887 INFO::Total function execution time is 0.202298879623413 s and adjustment time is 0.179330110549927 s ( 88.65 )
2026-04-17 02:56:41.625041 INFO::Skipping initial DF formatting
2026-04-17 02:56:41.626003 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:41.631613 INFO::Starting hierarchical adjustment
2026-04-17 02:56:41.632814 INFO::Found 5 batches.
2026-04-17 02:56:41.633631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:41.634499 INFO::Using default BPPARAM
2026-04-17 02:56:41.635279 INFO::Processing subtree level 1
2026-04-17 02:56:41.846424 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:41.8485 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 02:56:41.895377 INFO::Done
2026-04-17 02:56:41.896265 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:41.901888 INFO::ASW Batch was 0.516731878820738 prior to batch effect correction and is now 0.516731878820738 .
2026-04-17 02:56:41.902784 INFO::ASW Label was 0.387262937436805 prior to batch effect correction and is now 0.387262937436805 .
2026-04-17 02:56:41.903948 INFO::Total function execution time is 0.278962373733521 s and adjustment time is 0.2628014087677 s ( 94.21 )
2026-04-17 02:56:41.927646 INFO::Formatting Data.
2026-04-17 02:56:41.928675 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:41.929907 INFO::Removing potential empty rows and columns
2026-04-17 02:56:41.931327 INFO::Found 0 missing values.
2026-04-17 02:56:41.937093 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:41.937984 INFO::Done
2026-04-17 02:56:41.938747 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:41.94456 INFO::Starting hierarchical adjustment
2026-04-17 02:56:41.946029 INFO::Found 5 batches.
2026-04-17 02:56:41.946787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:41.94765 INFO::Using default BPPARAM
2026-04-17 02:56:41.948384 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.
2026-04-17 02:56:42.126063 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:42.128332 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 02:56:42.180008 INFO::Done
2026-04-17 02:56:42.180934 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:42.18513 INFO::ASW Batch was 0.224078669405531 prior to batch effect correction and is now -0.0452657060965385 .
2026-04-17 02:56:42.185964 INFO::ASW Label was 0.564854631228131 prior to batch effect correction and is now 0.818758322274579 .
2026-04-17 02:56:42.18707 INFO::Total function execution time is 0.259477138519287 s and adjustment time is 0.234512090682983 s ( 90.38 )
2026-04-17 02:56:42.188229 INFO::Formatting Data.
2026-04-17 02:56:42.191163 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:42.192422 INFO::Removing potential empty rows and columns
2026-04-17 02:56:42.193813 INFO::Found 0 missing values.
2026-04-17 02:56:42.199496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:42.200363 INFO::Done
2026-04-17 02:56:42.201137 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:42.20512 INFO::Starting hierarchical adjustment
2026-04-17 02:56:42.206215 INFO::Found 5 batches.
2026-04-17 02:56:42.206978 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:42.207846 INFO::Using default BPPARAM
2026-04-17 02:56:42.208604 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.
2026-04-17 02:56:42.425881 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:42.428177 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 02:56:42.479398 INFO::Done
2026-04-17 02:56:42.480429 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:42.486979 INFO::ASW Batch was 0.224078669405531 prior to batch effect correction and is now -0.0452657060965385 .
2026-04-17 02:56:42.48791 INFO::ASW Label was 0.564854631228131 prior to batch effect correction and is now 0.818758322274579 .
2026-04-17 02:56:42.489073 INFO::Total function execution time is 0.300796747207642 s and adjustment time is 0.273371458053589 s ( 90.88 )
2026-04-17 02:56:42.507172 INFO::Formatting Data.
2026-04-17 02:56:42.508193 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:42.509457 INFO::Removing potential empty rows and columns
2026-04-17 02:56:42.510842 INFO::Found 0 missing values.
2026-04-17 02:56:42.516687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:42.517569 INFO::Done
2026-04-17 02:56:42.518322 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:42.522339 INFO::Starting hierarchical adjustment
2026-04-17 02:56:42.523479 INFO::Found 5 batches.
2026-04-17 02:56:42.52425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:42.525162 INFO::Using default BPPARAM
2026-04-17 02:56:42.52593 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.
2026-04-17 02:56:42.727553 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:42.73789 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 02:56:42.77956 INFO::Done
2026-04-17 02:56:42.780432 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:42.784592 INFO::ASW Batch was 0.475321312091649 prior to batch effect correction and is now -0.100296789482088 .
2026-04-17 02:56:42.785414 INFO::ASW Label was 0.262793918187845 prior to batch effect correction and is now 0.880501562118375 .
2026-04-17 02:56:42.786533 INFO::Total function execution time is 0.279422998428345 s and adjustment time is 0.25631046295166 s ( 91.73 )
2026-04-17 02:56:42.787635 INFO::Formatting Data.
2026-04-17 02:56:42.788449 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:42.792171 INFO::Removing potential empty rows and columns
2026-04-17 02:56:42.793552 INFO::Found 0 missing values.
2026-04-17 02:56:42.799169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:42.800031 INFO::Done
2026-04-17 02:56:42.800772 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:42.804795 INFO::Starting hierarchical adjustment
2026-04-17 02:56:42.805851 INFO::Found 5 batches.
2026-04-17 02:56:42.806571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:42.807449 INFO::Using default BPPARAM
2026-04-17 02:56:42.808173 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.
2026-04-17 02:56:43.012539 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:43.018638 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 02:56:43.060423 INFO::Done
2026-04-17 02:56:43.065703 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:43.074476 INFO::ASW Batch was 0.475321312091649 prior to batch effect correction and is now -0.100296789482088 .
2026-04-17 02:56:43.075404 INFO::ASW Label was 0.262793918187845 prior to batch effect correction and is now 0.880501562118375 .
2026-04-17 02:56:43.076502 INFO::Total function execution time is 0.288837194442749 s and adjustment time is 0.254751205444336 s ( 88.2 )
2026-04-17 02:56:43.100038 INFO::Formatting Data.
2026-04-17 02:56:43.109265 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:43.110606 INFO::Removing potential empty rows and columns
2026-04-17 02:56:43.111984 INFO::Found 0 missing values.
2026-04-17 02:56:43.115612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:43.11632 INFO::Done
2026-04-17 02:56:43.117038 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:43.120848 INFO::Starting hierarchical adjustment
2026-04-17 02:56:43.121866 INFO::Found 2 batches.
2026-04-17 02:56:43.122591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:43.123445 INFO::Using default BPPARAM
2026-04-17 02:56:43.124184 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:43.125456 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 02:56:43.144634 INFO::Done
2026-04-17 02:56:43.1455 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:43.14942 INFO::ASW Batch was 0.736013175192274 prior to batch effect correction and is now 0.0424543368197714 .
2026-04-17 02:56:43.150266 INFO::ASW Label was 0.342643576612446 prior to batch effect correction and is now 0.847372151902659 .
2026-04-17 02:56:43.151361 INFO::Total function execution time is 0.0513882637023926 s and adjustment time is 0.0229461193084717 s ( 44.65 )
2026-04-17 02:56:43.152367 INFO::Formatting Data.
2026-04-17 02:56:43.153195 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:43.15436 INFO::Removing potential empty rows and columns
2026-04-17 02:56:43.155679 INFO::Found 0 missing values.
2026-04-17 02:56:43.159353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:43.162689 INFO::Done
2026-04-17 02:56:43.163566 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:43.167453 INFO::Starting hierarchical adjustment
2026-04-17 02:56:43.168463 INFO::Found 2 batches.
2026-04-17 02:56:43.1692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:43.170008 INFO::Using default BPPARAM
2026-04-17 02:56:43.170717 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:43.171956 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 02:56:43.191145 INFO::Done
2026-04-17 02:56:43.191991 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:43.195712 INFO::ASW Batch was 0.736013175192274 prior to batch effect correction and is now 0.0424543368197714 .
2026-04-17 02:56:43.196451 INFO::ASW Label was 0.342643576612446 prior to batch effect correction and is now 0.847372151902659 .
2026-04-17 02:56:43.1975 INFO::Total function execution time is 0.0451209545135498 s and adjustment time is 0.0228521823883057 s ( 50.65 )
2026-04-17 02:56:43.211912 INFO::Formatting Data.
2026-04-17 02:56:43.21286 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:43.213958 INFO::Removing potential empty rows and columns
2026-04-17 02:56:43.215141 INFO::Found 0 missing values.
2026-04-17 02:56:43.217896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:43.218605 INFO::Done
2026-04-17 02:56:43.219298 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:43.221737 INFO::Starting hierarchical adjustment
2026-04-17 02:56:43.222667 INFO::Found 2 batches.
2026-04-17 02:56:43.223384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:43.224176 INFO::Using default BPPARAM
2026-04-17 02:56:43.224888 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:43.22605 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 02:56:43.266996 INFO::Done
2026-04-17 02:56:43.267863 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:43.270437 INFO::ASW Batch was -0.137081331928419 prior to batch effect correction and is now -0.124823954261362 .
2026-04-17 02:56:43.271473 INFO::Total function execution time is 0.0596365928649902 s and adjustment time is 0.0445001125335693 s ( 74.62 )
2026-04-17 02:56:43.286383 INFO::Formatting Data.
2026-04-17 02:56:43.287348 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:43.288452 INFO::Removing potential empty rows and columns
2026-04-17 02:56:43.289743 INFO::Found 0 missing values.
2026-04-17 02:56:43.291401 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.
2026-04-17 02:56:43.297471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:43.298309 INFO::Done
2026-04-17 02:56:43.299008 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:43.302728 INFO::Starting hierarchical adjustment
2026-04-17 02:56:43.303713 INFO::Found 2 batches.
2026-04-17 02:56:43.304407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:43.305214 INFO::Using default BPPARAM
2026-04-17 02:56:43.305901 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:43.307158 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 02:56:43.329072 INFO::Done
2026-04-17 02:56:43.329929 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:43.333805 INFO::ASW Batch was 0.716314290594086 prior to batch effect correction and is now 0.0332708863916622 .
2026-04-17 02:56:43.334652 INFO::ASW Label was 0.304686479469568 prior to batch effect correction and is now 0.789828938475876 .
2026-04-17 02:56:43.335703 INFO::Total function execution time is 0.0493850708007812 s and adjustment time is 0.0253341197967529 s ( 51.3 )
2026-04-17 02:56:43.336728 INFO::Formatting Data.
2026-04-17 02:56:43.337577 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:43.338806 INFO::Removing potential empty rows and columns
2026-04-17 02:56:43.340168 INFO::Found 0 missing values.
2026-04-17 02:56:43.341435 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.
2026-04-17 02:56:43.347764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:43.34863 INFO::Done
2026-04-17 02:56:43.349398 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:43.35333 INFO::Starting hierarchical adjustment
2026-04-17 02:56:43.354404 INFO::Found 2 batches.
2026-04-17 02:56:43.355156 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:43.355981 INFO::Using default BPPARAM
2026-04-17 02:56:43.356703 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:43.35801 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 02:56:43.380284 INFO::Done
2026-04-17 02:56:43.381162 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:43.385111 INFO::ASW Batch was 0.716314290594086 prior to batch effect correction and is now 0.0332708863916622 .
2026-04-17 02:56:43.385954 INFO::ASW Label was 0.304686479469568 prior to batch effect correction and is now 0.789828938475876 .
2026-04-17 02:56:43.387018 INFO::Total function execution time is 0.0503015518188477 s and adjustment time is 0.0260343551635742 s ( 51.76 )
2026-04-17 02:56:43.668835 INFO::Formatting Data.
2026-04-17 02:56:43.669765 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:43.670906 INFO::Removing potential empty rows and columns
2026-04-17 02:56:43.672253 INFO::Found 0 missing values.
2026-04-17 02:56:43.676293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:43.677119 INFO::Done
2026-04-17 02:56:43.677829 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:43.680428 INFO::Starting hierarchical adjustment
2026-04-17 02:56:43.681434 INFO::Found 3 batches.
2026-04-17 02:56:43.682147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:43.682952 INFO::Using default BPPARAM
2026-04-17 02:56:43.68368 INFO::Processing subtree level 1
2026-04-17 02:56:43.797611 INFO::Adjusting the last 1 batches sequentially
2026-04-17 02:56:43.79977 INFO::Done
2026-04-17 02:56:43.800529 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:43.807974 INFO::ASW Batch was -0.128867907729739 prior to batch effect correction and is now -0.128867907729739 .
2026-04-17 02:56:43.813413 INFO::Total function execution time is 0.144560098648071 s and adjustment time is 0.118543386459351 s ( 82 )
2026-04-17 02:56:43.814859 INFO::Formatting Data.
2026-04-17 02:56:43.815773 INFO::Typecasting input to dataframe.
2026-04-17 02:56:43.820953 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:43.822349 INFO::Removing potential empty rows and columns
2026-04-17 02:56:43.82387 INFO::Found 0 missing values.
2026-04-17 02:56:43.832305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:43.837336 INFO::Done
2026-04-17 02:56:43.838128 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:43.844994 INFO::Starting hierarchical adjustment
2026-04-17 02:56:43.84617 INFO::Found 3 batches.
2026-04-17 02:56:43.846909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:43.847784 INFO::Using default BPPARAM
2026-04-17 02:56:43.848498 INFO::Processing subtree level 1
2026-04-17 02:56:43.954791 INFO::Adjusting the last 1 batches sequentially
2026-04-17 02:56:43.96534 INFO::Done
2026-04-17 02:56:43.96629 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:43.973701 INFO::ASW Batch was -0.128867907729739 prior to batch effect correction and is now -0.128867907729739 .
2026-04-17 02:56:43.975032 INFO::Total function execution time is 0.160152196884155 s and adjustment time is 0.119361639022827 s ( 74.53 )
2026-04-17 02:56:44.013013 INFO::Formatting Data.
2026-04-17 02:56:44.014057 INFO::Typecasting input to dataframe.
2026-04-17 02:56:44.015218 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:44.016413 INFO::Removing potential empty rows and columns
2026-04-17 02:56:44.02002 INFO::Found 0 missing values.
2026-04-17 02:56:44.024193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:44.025072 INFO::Done
2026-04-17 02:56:44.02581 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:44.028463 INFO::Starting hierarchical adjustment
2026-04-17 02:56:44.030145 INFO::Found 3 batches.
2026-04-17 02:56:44.030859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:44.031703 INFO::Using default BPPARAM
2026-04-17 02:56:44.032415 INFO::Processing subtree level 1
2026-04-17 02:56:44.145556 INFO::Adjusting the last 1 batches sequentially
2026-04-17 02:56:44.14784 INFO::Done
2026-04-17 02:56:44.152701 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:44.156241 INFO::ASW Batch was -0.0318367555037374 prior to batch effect correction and is now -0.0318367555037374 .
2026-04-17 02:56:44.161784 INFO::Total function execution time is 0.148759841918945 s and adjustment time is 0.11789870262146 s ( 79.25 )
2026-04-17 02:56:44.39655 INFO::Formatting Data.
2026-04-17 02:56:44.40097 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:44.402558 INFO::Removing potential empty rows and columns
2026-04-17 02:56:44.407062 INFO::Found 1000 missing values.
2026-04-17 02:56:44.46514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:44.466177 INFO::Done
2026-04-17 02:56:44.467157 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:44.483761 INFO::Starting hierarchical adjustment
2026-04-17 02:56:44.489064 INFO::Found 10 batches.
2026-04-17 02:56:44.489923 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:44.490752 INFO::Using default BPPARAM
2026-04-17 02:56:44.491481 INFO::Processing subtree level 1
2026-04-17 02:56:44.78234 INFO::Processing subtree level 2
2026-04-17 02:56:45.235177 INFO::Adjusting the last 1 batches sequentially
2026-04-17 02:56:45.241908 INFO::Done
2026-04-17 02:56:45.242847 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:45.258897 INFO::ASW Batch was 0.472523025475629 prior to batch effect correction and is now 0.472523025475629 .
2026-04-17 02:56:45.259848 INFO::ASW Label was 0.34283436478325 prior to batch effect correction and is now 0.34283436478325 .
2026-04-17 02:56:45.265178 INFO::Total function execution time is 0.868601083755493 s and adjustment time is 0.757166624069214 s ( 87.17 )
2026-04-17 02:56:45.266443 INFO::Formatting Data.
2026-04-17 02:56:45.267308 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:45.273097 INFO::Removing potential empty rows and columns
2026-04-17 02:56:45.28138 INFO::Found 1000 missing values.
2026-04-17 02:56:45.454756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:45.455727 INFO::Done
2026-04-17 02:56:45.456483 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:45.477182 INFO::Starting hierarchical adjustment
2026-04-17 02:56:45.478461 INFO::Found 10 batches.
2026-04-17 02:56:46.941543 INFO::Set up parallel execution backend with 2 workers
2026-04-17 02:56:46.94288 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-17 02:56:48.888695 INFO::Adjusting the last 2 batches sequentially
2026-04-17 02:56:48.892619 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 02:56:48.917525 INFO::Done
2026-04-17 02:56:48.91837 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:48.925062 INFO::ASW Batch was 0.472523025475629 prior to batch effect correction and is now 0.472523025475629 .
2026-04-17 02:56:48.925914 INFO::ASW Label was 0.34283436478325 prior to batch effect correction and is now 0.34283436478325 .
2026-04-17 02:56:48.926928 INFO::Total function execution time is 3.66050291061401 s and adjustment time is 3.43930578231812 s ( 93.96 )
2026-04-17 02:56:49.153501 INFO::Formatting Data.
2026-04-17 02:56:49.154594 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.156011 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.158674 INFO::Found 0 missing values.
2026-04-17 02:56:49.164411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.165335 INFO::Done
2026-04-17 02:56:49.166107 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 02:56:49.170009 INFO::Starting hierarchical adjustment
2026-04-17 02:56:49.171088 INFO::Found 3 batches.
2026-04-17 02:56:49.171885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 02:56:49.172796 INFO::Using default BPPARAM
2026-04-17 02:56:49.173558 INFO::Processing subtree level 1
2026-04-17 02:56:49.320622 INFO::Adjusting the last 1 batches sequentially
2026-04-17 02:56:49.323144 INFO::Done
2026-04-17 02:56:49.324008 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 02:56:49.336769 INFO::ASW Batch was 0.192351595944959 prior to batch effect correction and is now -0.13516294569246 .
2026-04-17 02:56:49.337812 INFO::ASW Label was -0.162907835722237 prior to batch effect correction and is now 0.110342410023594 .
2026-04-17 02:56:49.339141 INFO::Total function execution time is 0.185645580291748 s and adjustment time is 0.152244567871094 s ( 82.01 )
2026-04-17 02:56:49.543694 INFO::Formatting Data.
2026-04-17 02:56:49.544776 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.546006 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.547515 INFO::Found 2 missing values.
2026-04-17 02:56:49.551762 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.552678 INFO::Done
2026-04-17 02:56:49.592828 INFO::Found NA in Reference column
2026-04-17 02:56:49.606822 INFO::Require at least two references per batch.
2026-04-17 02:56:49.63548 INFO::Formatting Data.
2026-04-17 02:56:49.636425 INFO::Recognized SummarizedExperiment
2026-04-17 02:56:49.637196 INFO::Typecasting input to dataframe.
2026-04-17 02:56:49.650754 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.652328 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.657965 INFO::Found 0 missing values.
2026-04-17 02:56:49.669085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.670004 INFO::Done
2026-04-17 02:56:49.698371 INFO::Formatting Data.
2026-04-17 02:56:49.699333 INFO::Recognized SummarizedExperiment
2026-04-17 02:56:49.700069 INFO::Typecasting input to dataframe.
2026-04-17 02:56:49.725607 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.72724 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.732959 INFO::Found 0 missing values.
2026-04-17 02:56:49.750934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.751872 INFO::Done
2026-04-17 02:56:49.773706 INFO::Formatting Data.
2026-04-17 02:56:49.774679 INFO::Recognized SummarizedExperiment
2026-04-17 02:56:49.77544 INFO::Typecasting input to dataframe.
2026-04-17 02:56:49.800225 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.80163 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.803197 INFO::Found 0 missing values.
2026-04-17 02:56:49.804507 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.
2026-04-17 02:56:49.811317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.812213 INFO::Done
2026-04-17 02:56:49.826229 INFO::Formatting Data.
2026-04-17 02:56:49.827282 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.828512 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.830057 INFO::Found 0 missing values.
2026-04-17 02:56:49.834466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.835378 INFO::Done
2026-04-17 02:56:49.851828 INFO::Formatting Data.
2026-04-17 02:56:49.852877 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.854096 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.855692 INFO::Found 0 missing values.
2026-04-17 02:56:49.860007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.860916 INFO::Done
2026-04-17 02:56:49.904663 INFO::Formatting Data.
2026-04-17 02:56:49.905731 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.90718 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.908867 INFO::Found 1 missing values.
2026-04-17 02:56:49.912669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.913514 INFO::Done
2026-04-17 02:56:49.952096 INFO::Formatting Data.
2026-04-17 02:56:49.95337 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.954603 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.956044 INFO::Found 2 missing values.
2026-04-17 02:56:49.957347 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.
2026-04-17 02:56:49.960744 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.961541 INFO::Done
2026-04-17 02:56:49.975803 INFO::Formatting Data.
2026-04-17 02:56:49.976861 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:49.978074 INFO::Removing potential empty rows and columns
2026-04-17 02:56:49.979395 INFO::Found 2 missing values.
2026-04-17 02:56:49.981705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:49.982489 INFO::Done
2026-04-17 02:56:49.999077 INFO::Formatting Data.
2026-04-17 02:56:50.000343 INFO::Typecasting input to dataframe.
2026-04-17 02:56:50.001765 INFO::Replacing NaNs with NAs.
2026-04-17 02:56:50.003214 INFO::Removing potential empty rows and columns
2026-04-17 02:56:50.004799 INFO::Found 0 missing values.
2026-04-17 02:56:50.009407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 02:56:50.010359 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.605 3.816 29.325
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.550 | 1.147 | 24.626 | |
| compute_asw | 0.034 | 0.000 | 0.034 | |
| count_existing | 0.018 | 0.000 | 0.018 | |
| generate_data_covariables | 0.016 | 0.000 | 0.016 | |
| generate_dataset | 0.015 | 0.000 | 0.015 | |