Yannis Schumann
| Snapshot Date: 2025-11-21 13:40 -0500 (Fri, 21 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-22 11:39 -0500 (Sat, 22 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4567 |
| 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 167/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-11-21 18:38:19 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 18:38:54 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 35.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* 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 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 10.213 0.442 7.811
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-11-21 18:38:45.90302 INFO::Formatting Data.
2025-11-21 18:38:45.90482 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:45.909459 INFO::Removing potential empty rows and columns
2025-11-21 18:38:46.019127 INFO::Found 0 missing values.
2025-11-21 18:38:46.020409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:46.020631 INFO::Done
2025-11-21 18:38:46.020824 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:46.02658 INFO::Starting hierarchical adjustment
2025-11-21 18:38:46.026916 INFO::Found 3 batches.
2025-11-21 18:38:46.027116 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:46.027546 INFO::Using default BPPARAM
2025-11-21 18:38:46.027716 INFO::Processing subtree level 1
2025-11-21 18:38:46.078101 INFO::Adjusting the last 1 batches sequentially
2025-11-21 18:38:46.080581 INFO::Done
2025-11-21 18:38:46.080893 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:46.082848 INFO::ASW Batch was -0.104570078050748 prior to batch effect correction and is now -0.104570078050748 .
2025-11-21 18:38:46.083275 INFO::Total function execution time is 0.180727958679199 s and adjustment time is 0.0537030696868896 s ( 29.71 )
2025-11-21 18:38:46.090823 INFO::Formatting Data.
2025-11-21 18:38:46.091239 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:46.091567 INFO::Removing potential empty rows and columns
2025-11-21 18:38:46.092015 INFO::Found 0 missing values.
2025-11-21 18:38:46.09236 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-21 18:38:46.096499 INFO::Formatting Data.
2025-11-21 18:38:46.09674 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:46.097086 INFO::Removing potential empty rows and columns
2025-11-21 18:38:46.09771 INFO::Found 0 missing values.
2025-11-21 18:38:46.098049 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-21 18:38:46.104351 INFO::Formatting Data.
2025-11-21 18:38:46.104588 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:46.104891 INFO::Removing potential empty rows and columns
2025-11-21 18:38:46.105242 INFO::Found 0 missing values.
2025-11-21 18:38:46.105571 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-21 18:38:46.107162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:46.107381 INFO::Done
2025-11-21 18:38:46.107607 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:46.108511 INFO::Starting hierarchical adjustment
2025-11-21 18:38:46.108785 INFO::Found 2 batches.
2025-11-21 18:38:46.108985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:46.109234 INFO::Using default BPPARAM
2025-11-21 18:38:46.109403 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:46.109686 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 18:38:46.118441 INFO::Done
2025-11-21 18:38:46.11871 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:46.119432 INFO::ASW Batch was 0.0665822166744569 prior to batch effect correction and is now -0.119690796818732 .
2025-11-21 18:38:46.119694 INFO::Total function execution time is 0.0153539180755615 s and adjustment time is 0.00968599319458008 s ( 63.08 )
2025-11-21 18:38:46.120791 INFO::Formatting Data.
2025-11-21 18:38:46.120992 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:46.124669 INFO::Formatting Data.
2025-11-21 18:38:46.12495 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:46.125293 INFO::Removing potential empty rows and columns
2025-11-21 18:38:46.125682 INFO::Found 0 missing values.
2025-11-21 18:38:46.126814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:46.127023 INFO::Done
2025-11-21 18:38:46.127211 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:46.127972 INFO::Starting hierarchical adjustment
2025-11-21 18:38:46.128232 INFO::Found 2 batches.
2025-11-21 18:38:46.128405 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:46.128598 INFO::Using default BPPARAM
2025-11-21 18:38:46.128792 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:46.129086 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:46.153621 INFO::Done
2025-11-21 18:38:46.154059 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:46.154992 INFO::ASW Batch was -0.0029494082974043 prior to batch effect correction and is now -0.125593697788347 .
2025-11-21 18:38:46.155262 INFO::Total function execution time is 0.030623197555542 s and adjustment time is 0.0254268646240234 s ( 83.03 )
2025-11-21 18:38:46.1556 INFO::Formatting Data.
2025-11-21 18:38:46.155792 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:46.159385 INFO::Removing potential empty rows and columns
2025-11-21 18:38:46.165029 INFO::Found 0 missing values.
2025-11-21 18:38:46.166198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:46.166424 INFO::Done
2025-11-21 18:38:46.166603 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:46.167429 INFO::Starting hierarchical adjustment
2025-11-21 18:38:46.167679 INFO::Found 2 batches.
2025-11-21 18:38:46.167876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:46.168098 INFO::Using default BPPARAM
2025-11-21 18:38:46.168297 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:46.168628 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:46.176721 INFO::Done
2025-11-21 18:38:46.176993 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:46.177732 INFO::ASW Batch was -0.0029494082974043 prior to batch effect correction and is now -0.125593697788347 .
2025-11-21 18:38:46.177998 INFO::Total function execution time is 0.0223860740661621 s and adjustment time is 0.00907802581787109 s ( 40.55 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-21 18:38:47.507471 INFO::Formatting Data.
2025-11-21 18:38:47.507764 INFO::Recognized SummarizedExperiment
2025-11-21 18:38:47.507931 INFO::Typecasting input to dataframe.
2025-11-21 18:38:47.518811 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:47.519239 INFO::Removing potential empty rows and columns
2025-11-21 18:38:47.520284 INFO::Found 0 missing values.
2025-11-21 18:38:47.522237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:47.522415 INFO::Done
2025-11-21 18:38:47.522562 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:47.523683 INFO::Starting hierarchical adjustment
2025-11-21 18:38:47.523885 INFO::Found 2 batches.
2025-11-21 18:38:47.524033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:47.524352 INFO::Using default BPPARAM
2025-11-21 18:38:47.524498 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:47.524765 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 18:38:47.545694 INFO::Done
2025-11-21 18:38:47.545997 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:47.547282 INFO::ASW Batch was -0.00817915478697113 prior to batch effect correction and is now -0.0882048465211941 .
2025-11-21 18:38:47.547558 INFO::Total function execution time is 0.0402228832244873 s and adjustment time is 0.0218188762664795 s ( 54.24 )
Warning: stack imbalance in '{', 73 then 75
2025-11-21 18:38:47.554634 INFO::Formatting Data.
2025-11-21 18:38:47.554926 INFO::Recognized SummarizedExperiment
2025-11-21 18:38:47.555104 INFO::Typecasting input to dataframe.
2025-11-21 18:38:47.558203 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:47.558567 INFO::Removing potential empty rows and columns
2025-11-21 18:38:47.55972 INFO::Found 0 missing values.
2025-11-21 18:38:47.562054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:47.562251 INFO::Done
2025-11-21 18:38:47.562414 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:47.563627 INFO::Starting hierarchical adjustment
2025-11-21 18:38:47.563839 INFO::Found 2 batches.
2025-11-21 18:38:47.563991 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:47.564172 INFO::Using default BPPARAM
2025-11-21 18:38:47.564318 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:47.564615 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 18:38:47.572519 INFO::Done
2025-11-21 18:38:47.572723 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:47.57387 INFO::ASW Batch was 0.0270353502341646 prior to batch effect correction and is now 0.0270353502341646 .
2025-11-21 18:38:47.574142 INFO::Total function execution time is 0.0195269584655762 s and adjustment time is 0.00872206687927246 s ( 44.67 )
2025-11-21 18:38:47.580435 INFO::Formatting Data.
2025-11-21 18:38:47.580656 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:47.580964 INFO::Removing potential empty rows and columns
2025-11-21 18:38:47.581267 INFO::Found 0 missing values.
2025-11-21 18:38:47.582106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:47.582268 INFO::Done
2025-11-21 18:38:47.58244 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:47.583034 INFO::Starting hierarchical adjustment
2025-11-21 18:38:47.583229 INFO::Found 3 batches.
2025-11-21 18:38:47.583376 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:47.583556 INFO::Using default BPPARAM
2025-11-21 18:38:47.583701 INFO::Processing subtree level 1
2025-11-21 18:38:47.652755 INFO::Adjusting the last 1 batches sequentially
2025-11-21 18:38:47.653865 INFO::Done
2025-11-21 18:38:47.654448 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:47.656066 INFO::ASW Batch was -0.0785021279994534 prior to batch effect correction and is now -0.164372377698683 .
2025-11-21 18:38:47.656754 INFO::Total function execution time is 0.0761561393737793 s and adjustment time is 0.0706701278686523 s ( 92.8 )
2025-11-21 18:38:47.663007 INFO::Skipping initial DF formatting
2025-11-21 18:38:47.663421 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:47.66476 INFO::Starting hierarchical adjustment
2025-11-21 18:38:47.665009 INFO::Found 5 batches.
2025-11-21 18:38:47.665173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:47.665397 INFO::Using default BPPARAM
2025-11-21 18:38:47.665554 INFO::Processing subtree level 1
2025-11-21 18:38:47.714184 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:47.716795 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 18:38:47.724855 INFO::Done
2025-11-21 18:38:47.725307 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:47.728063 INFO::ASW Batch was 0.465693712408124 prior to batch effect correction and is now 0.465693712408124 .
2025-11-21 18:38:47.728344 INFO::ASW Label was 0.430127400292258 prior to batch effect correction and is now 0.430127400292258 .
2025-11-21 18:38:47.729026 INFO::Total function execution time is 0.0658421516418457 s and adjustment time is 0.0598819255828857 s ( 90.95 )
2025-11-21 18:38:47.737241 INFO::Formatting Data.
2025-11-21 18:38:47.73752 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:47.73807 INFO::Removing potential empty rows and columns
2025-11-21 18:38:47.738446 INFO::Found 0 missing values.
2025-11-21 18:38:47.739739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:47.739943 INFO::Done
2025-11-21 18:38:47.740117 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:47.741173 INFO::Starting hierarchical adjustment
2025-11-21 18:38:47.74143 INFO::Found 5 batches.
2025-11-21 18:38:47.741596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:47.741825 INFO::Using default BPPARAM
2025-11-21 18:38:47.741989 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:47.793696 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:47.795594 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:47.804371 INFO::Done
2025-11-21 18:38:47.804858 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:47.8065 INFO::ASW Batch was 0.700225400724876 prior to batch effect correction and is now -0.0325180731343177 .
2025-11-21 18:38:47.806875 INFO::ASW Label was 0.115868919372615 prior to batch effect correction and is now 0.710729746879625 .
2025-11-21 18:38:47.807756 INFO::Total function execution time is 0.0703139305114746 s and adjustment time is 0.0629751682281494 s ( 89.56 )
2025-11-21 18:38:47.808127 INFO::Formatting Data.
2025-11-21 18:38:47.808366 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:47.808761 INFO::Removing potential empty rows and columns
2025-11-21 18:38:47.809161 INFO::Found 0 missing values.
2025-11-21 18:38:47.81039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:47.810566 INFO::Done
2025-11-21 18:38:47.81073 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:47.811672 INFO::Starting hierarchical adjustment
2025-11-21 18:38:47.81201 INFO::Found 5 batches.
2025-11-21 18:38:47.812168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:47.812389 INFO::Using default BPPARAM
2025-11-21 18:38:47.812542 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:47.858458 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:47.860381 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:47.867702 INFO::Done
2025-11-21 18:38:47.86805 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:47.869537 INFO::ASW Batch was 0.700225400724876 prior to batch effect correction and is now -0.0325180731343177 .
2025-11-21 18:38:47.869768 INFO::ASW Label was 0.115868919372615 prior to batch effect correction and is now 0.710729746879625 .
2025-11-21 18:38:47.870163 INFO::Total function execution time is 0.0619018077850342 s and adjustment time is 0.0558459758758545 s ( 90.22 )
2025-11-21 18:38:47.876798 INFO::Formatting Data.
2025-11-21 18:38:47.877046 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:47.877334 INFO::Removing potential empty rows and columns
2025-11-21 18:38:47.877664 INFO::Found 0 missing values.
2025-11-21 18:38:47.878833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:47.879003 INFO::Done
2025-11-21 18:38:47.879161 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:47.880603 INFO::Starting hierarchical adjustment
2025-11-21 18:38:47.880959 INFO::Found 5 batches.
2025-11-21 18:38:47.881138 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:47.881358 INFO::Using default BPPARAM
2025-11-21 18:38:47.881516 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:47.938477 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:47.942714 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:47.952219 INFO::Done
2025-11-21 18:38:47.952652 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:47.958153 INFO::ASW Batch was 0.33794157342579 prior to batch effect correction and is now -0.0932387418786308 .
2025-11-21 18:38:47.958495 INFO::ASW Label was 0.32841178536123 prior to batch effect correction and is now 0.828612476334657 .
2025-11-21 18:38:47.95919 INFO::Total function execution time is 0.0820901393890381 s and adjustment time is 0.0714070796966553 s ( 86.99 )
2025-11-21 18:38:47.95958 INFO::Formatting Data.
2025-11-21 18:38:47.959829 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:47.960243 INFO::Removing potential empty rows and columns
2025-11-21 18:38:47.960679 INFO::Found 0 missing values.
2025-11-21 18:38:47.962226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:47.962444 INFO::Done
2025-11-21 18:38:47.96262 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:47.963569 INFO::Starting hierarchical adjustment
2025-11-21 18:38:47.963817 INFO::Found 5 batches.
2025-11-21 18:38:47.963989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:47.964209 INFO::Using default BPPARAM
2025-11-21 18:38:47.964367 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:48.018894 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:48.02087 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:48.031734 INFO::Done
2025-11-21 18:38:48.032016 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.033611 INFO::ASW Batch was 0.33794157342579 prior to batch effect correction and is now -0.0932387418786308 .
2025-11-21 18:38:48.033825 INFO::ASW Label was 0.32841178536123 prior to batch effect correction and is now 0.828612476334657 .
2025-11-21 18:38:48.034618 INFO::Total function execution time is 0.0745952129364014 s and adjustment time is 0.067950963973999 s ( 91.09 )
2025-11-21 18:38:48.048468 INFO::Formatting Data.
2025-11-21 18:38:48.048863 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.049269 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.04975 INFO::Found 0 missing values.
2025-11-21 18:38:48.050747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.050936 INFO::Done
2025-11-21 18:38:48.051127 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.052184 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.052437 INFO::Found 2 batches.
2025-11-21 18:38:48.052617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.052875 INFO::Using default BPPARAM
2025-11-21 18:38:48.053043 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:48.053372 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:48.058921 INFO::Done
2025-11-21 18:38:48.059187 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.060464 INFO::ASW Batch was 0.722477192097163 prior to batch effect correction and is now 0.0936358821905406 .
2025-11-21 18:38:48.060703 INFO::ASW Label was 0.382196606709374 prior to batch effect correction and is now 0.80953838674603 .
2025-11-21 18:38:48.061139 INFO::Total function execution time is 0.0127551555633545 s and adjustment time is 0.00652885437011719 s ( 51.19 )
2025-11-21 18:38:48.061532 INFO::Formatting Data.
2025-11-21 18:38:48.061931 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.062396 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.063064 INFO::Found 0 missing values.
2025-11-21 18:38:48.064075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.064296 INFO::Done
2025-11-21 18:38:48.064507 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.065595 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.066394 INFO::Found 2 batches.
2025-11-21 18:38:48.066603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.066852 INFO::Using default BPPARAM
2025-11-21 18:38:48.067071 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:48.067542 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 18:38:48.073441 INFO::Done
2025-11-21 18:38:48.073712 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.074813 INFO::ASW Batch was 0.722477192097163 prior to batch effect correction and is now 0.0936358821905406 .
2025-11-21 18:38:48.075107 INFO::ASW Label was 0.382196606709374 prior to batch effect correction and is now 0.80953838674603 .
2025-11-21 18:38:48.07548 INFO::Total function execution time is 0.0139811038970947 s and adjustment time is 0.00712108612060547 s ( 50.93 )
2025-11-21 18:38:48.08178 INFO::Formatting Data.
2025-11-21 18:38:48.082072 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.08243 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.082826 INFO::Found 0 missing values.
2025-11-21 18:38:48.083627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.083818 INFO::Done
2025-11-21 18:38:48.083981 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.084595 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.084808 INFO::Found 2 batches.
2025-11-21 18:38:48.084994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.085228 INFO::Using default BPPARAM
2025-11-21 18:38:48.085402 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:48.085691 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 18:38:48.102085 INFO::Done
2025-11-21 18:38:48.102348 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.102993 INFO::ASW Batch was -0.0313212099724593 prior to batch effect correction and is now -0.124204226181206 .
2025-11-21 18:38:48.103265 INFO::Total function execution time is 0.0215189456939697 s and adjustment time is 0.0173048973083496 s ( 80.42 )
2025-11-21 18:38:48.10777 INFO::Formatting Data.
2025-11-21 18:38:48.107996 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.108273 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.108605 INFO::Found 0 missing values.
2025-11-21 18:38:48.109021 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-21 18:38:48.11043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.110608 INFO::Done
2025-11-21 18:38:48.110774 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.111661 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.111889 INFO::Found 2 batches.
2025-11-21 18:38:48.112052 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.112233 INFO::Using default BPPARAM
2025-11-21 18:38:48.112393 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:48.112663 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 18:38:48.117798 INFO::Done
2025-11-21 18:38:48.118 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.118895 INFO::ASW Batch was 0.555879247620918 prior to batch effect correction and is now 0.00387514179138246 .
2025-11-21 18:38:48.119071 INFO::ASW Label was 0.448878231619366 prior to batch effect correction and is now 0.89748166367733 .
2025-11-21 18:38:48.11932 INFO::Total function execution time is 0.0115549564361572 s and adjustment time is 0.00594401359558105 s ( 51.44 )
2025-11-21 18:38:48.119548 INFO::Formatting Data.
2025-11-21 18:38:48.119718 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.119979 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.120267 INFO::Found 0 missing values.
2025-11-21 18:38:48.120516 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-21 18:38:48.121787 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.121957 INFO::Done
2025-11-21 18:38:48.122107 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.124349 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.124751 INFO::Found 2 batches.
2025-11-21 18:38:48.124992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.125235 INFO::Using default BPPARAM
2025-11-21 18:38:48.125434 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:48.125804 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 18:38:48.132024 INFO::Done
2025-11-21 18:38:48.132277 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.133237 INFO::ASW Batch was 0.555879247620918 prior to batch effect correction and is now 0.00387514179138246 .
2025-11-21 18:38:48.133438 INFO::ASW Label was 0.448878231619366 prior to batch effect correction and is now 0.89748166367733 .
2025-11-21 18:38:48.133679 INFO::Total function execution time is 0.0141279697418213 s and adjustment time is 0.00736498832702637 s ( 52.13 )
2025-11-21 18:38:48.205024 INFO::Formatting Data.
2025-11-21 18:38:48.205327 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.205662 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.205991 INFO::Found 0 missing values.
2025-11-21 18:38:48.206878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.207064 INFO::Done
2025-11-21 18:38:48.207215 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.207896 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.208107 INFO::Found 3 batches.
2025-11-21 18:38:48.208271 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.208458 INFO::Using default BPPARAM
2025-11-21 18:38:48.20862 INFO::Processing subtree level 1
2025-11-21 18:38:48.268629 INFO::Adjusting the last 1 batches sequentially
2025-11-21 18:38:48.270416 INFO::Done
2025-11-21 18:38:48.270754 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.272466 INFO::ASW Batch was 0.0142564915198749 prior to batch effect correction and is now 0.0142564915198749 .
2025-11-21 18:38:48.273016 INFO::Total function execution time is 0.0679640769958496 s and adjustment time is 0.0623328685760498 s ( 91.71 )
2025-11-21 18:38:48.273525 INFO::Formatting Data.
2025-11-21 18:38:48.273755 INFO::Typecasting input to dataframe.
2025-11-21 18:38:48.274035 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.274426 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.274936 INFO::Found 0 missing values.
2025-11-21 18:38:48.27598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.276196 INFO::Done
2025-11-21 18:38:48.2764 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.277125 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.277398 INFO::Found 3 batches.
2025-11-21 18:38:48.277587 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.277861 INFO::Using default BPPARAM
2025-11-21 18:38:48.278083 INFO::Processing subtree level 1
2025-11-21 18:38:48.32543 INFO::Adjusting the last 1 batches sequentially
2025-11-21 18:38:48.326738 INFO::Done
2025-11-21 18:38:48.32699 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.328341 INFO::ASW Batch was 0.0142564915198749 prior to batch effect correction and is now 0.0142564915198749 .
2025-11-21 18:38:48.328857 INFO::Total function execution time is 0.0552690029144287 s and adjustment time is 0.0493888854980469 s ( 89.36 )
2025-11-21 18:38:48.33554 INFO::Formatting Data.
2025-11-21 18:38:48.335793 INFO::Typecasting input to dataframe.
2025-11-21 18:38:48.336073 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.336388 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.336791 INFO::Found 0 missing values.
2025-11-21 18:38:48.337677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.337904 INFO::Done
2025-11-21 18:38:48.338076 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.338694 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.338942 INFO::Found 3 batches.
2025-11-21 18:38:48.339112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.339338 INFO::Using default BPPARAM
2025-11-21 18:38:48.339513 INFO::Processing subtree level 1
2025-11-21 18:38:48.390469 INFO::Adjusting the last 1 batches sequentially
2025-11-21 18:38:48.391673 INFO::Done
2025-11-21 18:38:48.391967 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.393295 INFO::ASW Batch was -0.0707636501440044 prior to batch effect correction and is now -0.0707636501440044 .
2025-11-21 18:38:48.393715 INFO::Total function execution time is 0.0581619739532471 s and adjustment time is 0.052772045135498 s ( 90.73 )
2025-11-21 18:38:48.448527 INFO::Formatting Data.
2025-11-21 18:38:48.448787 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.4492 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.450118 INFO::Found 1000 missing values.
2025-11-21 18:38:48.455921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.456157 INFO::Done
2025-11-21 18:38:48.456364 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.458442 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.4587 INFO::Found 10 batches.
2025-11-21 18:38:48.458864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:48.459088 INFO::Using default BPPARAM
2025-11-21 18:38:48.459252 INFO::Processing subtree level 1
2025-11-21 18:38:48.525558 INFO::Processing subtree level 2
2025-11-21 18:38:48.669358 INFO::Adjusting the last 1 batches sequentially
2025-11-21 18:38:48.67111 INFO::Done
2025-11-21 18:38:48.671385 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:48.679028 INFO::ASW Batch was 0.473312433242494 prior to batch effect correction and is now 0.473312433242494 .
2025-11-21 18:38:48.679444 INFO::ASW Label was 0.357718565983805 prior to batch effect correction and is now 0.357718565983805 .
2025-11-21 18:38:48.680145 INFO::Total function execution time is 0.231474161148071 s and adjustment time is 0.212447881698608 s ( 91.78 )
2025-11-21 18:38:48.68053 INFO::Formatting Data.
2025-11-21 18:38:48.680746 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:48.681402 INFO::Removing potential empty rows and columns
2025-11-21 18:38:48.682426 INFO::Found 1000 missing values.
2025-11-21 18:38:48.732445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:48.732839 INFO::Done
2025-11-21 18:38:48.733072 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:48.735696 INFO::Starting hierarchical adjustment
2025-11-21 18:38:48.736075 INFO::Found 10 batches.
2025-11-21 18:38:49.323895 INFO::Set up parallel execution backend with 2 workers
2025-11-21 18:38:49.324231 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-21 18:38:49.933921 INFO::Adjusting the last 2 batches sequentially
2025-11-21 18:38:49.934708 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 18:38:49.941789 INFO::Done
2025-11-21 18:38:49.942049 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:49.944355 INFO::ASW Batch was 0.473312433242494 prior to batch effect correction and is now 0.473312433242494 .
2025-11-21 18:38:49.944586 INFO::ASW Label was 0.357718565983805 prior to batch effect correction and is now 0.357718565983805 .
2025-11-21 18:38:49.94489 INFO::Total function execution time is 1.26435494422913 s and adjustment time is 1.20576596260071 s ( 95.37 )
2025-11-21 18:38:50.02557 INFO::Formatting Data.
2025-11-21 18:38:50.026035 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.026521 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.027223 INFO::Found 0 missing values.
2025-11-21 18:38:50.029429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.029799 INFO::Done
2025-11-21 18:38:50.030247 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 18:38:50.031835 INFO::Starting hierarchical adjustment
2025-11-21 18:38:50.032218 INFO::Found 3 batches.
2025-11-21 18:38:50.032455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 18:38:50.032752 INFO::Using default BPPARAM
2025-11-21 18:38:50.032975 INFO::Processing subtree level 1
2025-11-21 18:38:50.087461 INFO::Adjusting the last 1 batches sequentially
2025-11-21 18:38:50.088715 INFO::Done
2025-11-21 18:38:50.08895 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 18:38:50.090919 INFO::ASW Batch was 0.170437184395926 prior to batch effect correction and is now -0.146927026477019 .
2025-11-21 18:38:50.091117 INFO::ASW Label was -0.192719242080689 prior to batch effect correction and is now -0.00388359848253334 .
2025-11-21 18:38:50.091482 INFO::Total function execution time is 0.0659990310668945 s and adjustment time is 0.0565810203552246 s ( 85.73 )
2025-11-21 18:38:50.156615 INFO::Formatting Data.
2025-11-21 18:38:50.156978 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.15738 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.157837 INFO::Found 2 missing values.
2025-11-21 18:38:50.158849 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.15905 INFO::Done
2025-11-21 18:38:50.170202 INFO::Found NA in Reference column
2025-11-21 18:38:50.174072 INFO::Require at least two references per batch.
2025-11-21 18:38:50.183581 INFO::Formatting Data.
2025-11-21 18:38:50.183931 INFO::Recognized SummarizedExperiment
2025-11-21 18:38:50.184164 INFO::Typecasting input to dataframe.
2025-11-21 18:38:50.18887 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.189396 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.191001 INFO::Found 0 missing values.
2025-11-21 18:38:50.194056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.194245 INFO::Done
2025-11-21 18:38:50.200681 INFO::Formatting Data.
2025-11-21 18:38:50.200967 INFO::Recognized SummarizedExperiment
2025-11-21 18:38:50.201198 INFO::Typecasting input to dataframe.
2025-11-21 18:38:50.20768 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.20813 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.209484 INFO::Found 0 missing values.
2025-11-21 18:38:50.214119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.214374 INFO::Done
2025-11-21 18:38:50.22076 INFO::Formatting Data.
2025-11-21 18:38:50.22102 INFO::Recognized SummarizedExperiment
2025-11-21 18:38:50.22121 INFO::Typecasting input to dataframe.
2025-11-21 18:38:50.227272 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.227638 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.228043 INFO::Found 0 missing values.
2025-11-21 18:38:50.228375 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-21 18:38:50.230088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.23026 INFO::Done
2025-11-21 18:38:50.234529 INFO::Formatting Data.
2025-11-21 18:38:50.234785 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.235068 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.235385 INFO::Found 0 missing values.
2025-11-21 18:38:50.236283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.236449 INFO::Done
2025-11-21 18:38:50.242085 INFO::Formatting Data.
2025-11-21 18:38:50.242369 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.242689 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.24307 INFO::Found 0 missing values.
2025-11-21 18:38:50.244008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.244177 INFO::Done
2025-11-21 18:38:50.255501 INFO::Formatting Data.
2025-11-21 18:38:50.255832 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.256233 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.256752 INFO::Found 1 missing values.
2025-11-21 18:38:50.257831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.258042 INFO::Done
2025-11-21 18:38:50.266816 INFO::Formatting Data.
2025-11-21 18:38:50.267177 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.267525 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.267897 INFO::Found 2 missing values.
2025-11-21 18:38:50.268264 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-21 18:38:50.269221 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.269457 INFO::Done
2025-11-21 18:38:50.274392 INFO::Formatting Data.
2025-11-21 18:38:50.274953 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.275378 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.275804 INFO::Found 2 missing values.
2025-11-21 18:38:50.276526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.276716 INFO::Done
2025-11-21 18:38:50.281239 INFO::Formatting Data.
2025-11-21 18:38:50.28152 INFO::Typecasting input to dataframe.
2025-11-21 18:38:50.281822 INFO::Replacing NaNs with NAs.
2025-11-21 18:38:50.282145 INFO::Removing potential empty rows and columns
2025-11-21 18:38:50.28251 INFO::Found 0 missing values.
2025-11-21 18:38:50.283487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 18:38:50.285962 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.303 1.648 9.589
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.213 | 0.442 | 7.811 | |
| compute_asw | 0.011 | 0.000 | 0.013 | |
| count_existing | 0.005 | 0.000 | 0.008 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.005 | 0.000 | 0.005 | |