Yannis Schumann
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 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 2025-11-21 11:39 -0500 (Fri, 21 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" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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: 2025-11-20 18:40:13 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 18:40:49 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 36.6 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 10.244 0.429 7.844
* 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")
2025-11-20 18:40:40.095345 INFO::Formatting Data.
2025-11-20 18:40:40.096919 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:40.101279 INFO::Removing potential empty rows and columns
2025-11-20 18:40:40.223395 INFO::Found 0 missing values.
2025-11-20 18:40:40.224657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:40.224875 INFO::Done
2025-11-20 18:40:40.225078 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:40.230584 INFO::Starting hierarchical adjustment
2025-11-20 18:40:40.230929 INFO::Found 3 batches.
2025-11-20 18:40:40.231122 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:40.231561 INFO::Using default BPPARAM
2025-11-20 18:40:40.231737 INFO::Processing subtree level 1
2025-11-20 18:40:40.294701 INFO::Adjusting the last 1 batches sequentially
2025-11-20 18:40:40.296219 INFO::Done
2025-11-20 18:40:40.29651 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:40.297874 INFO::ASW Batch was -0.0286949928236273 prior to batch effect correction and is now -0.0286949928236273 .
2025-11-20 18:40:40.298538 INFO::Total function execution time is 0.203557014465332 s and adjustment time is 0.0653469562530518 s ( 32.1 )
2025-11-20 18:40:40.307036 INFO::Formatting Data.
2025-11-20 18:40:40.307341 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:40.307777 INFO::Removing potential empty rows and columns
2025-11-20 18:40:40.308347 INFO::Found 0 missing values.
2025-11-20 18:40:40.308738 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.
2025-11-20 18:40:40.31337 INFO::Formatting Data.
2025-11-20 18:40:40.313671 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:40.315902 INFO::Removing potential empty rows and columns
2025-11-20 18:40:40.3167 INFO::Found 0 missing values.
2025-11-20 18:40:40.317193 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.
2025-11-20 18:40:40.324905 INFO::Formatting Data.
2025-11-20 18:40:40.325166 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:40.326257 INFO::Removing potential empty rows and columns
2025-11-20 18:40:40.326673 INFO::Found 0 missing values.
2025-11-20 18:40:40.327042 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.
2025-11-20 18:40:40.336188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:40.336516 INFO::Done
2025-11-20 18:40:40.336764 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:40.337801 INFO::Starting hierarchical adjustment
2025-11-20 18:40:40.338159 INFO::Found 2 batches.
2025-11-20 18:40:40.338414 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:40.33872 INFO::Using default BPPARAM
2025-11-20 18:40:40.338912 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:40.339254 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 18:40:40.349068 INFO::Done
2025-11-20 18:40:40.34932 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:40.350011 INFO::ASW Batch was -0.0416716502939463 prior to batch effect correction and is now -0.118151708481542 .
2025-11-20 18:40:40.350278 INFO::Total function execution time is 0.0254030227661133 s and adjustment time is 0.0109760761260986 s ( 43.21 )
2025-11-20 18:40:40.351347 INFO::Formatting Data.
2025-11-20 18:40:40.351587 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:40.357458 INFO::Formatting Data.
2025-11-20 18:40:40.357755 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:40.358082 INFO::Removing potential empty rows and columns
2025-11-20 18:40:40.358456 INFO::Found 0 missing values.
2025-11-20 18:40:40.35948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:40.359676 INFO::Done
2025-11-20 18:40:40.359848 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:40.360621 INFO::Starting hierarchical adjustment
2025-11-20 18:40:40.360857 INFO::Found 2 batches.
2025-11-20 18:40:40.361023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:40.361225 INFO::Using default BPPARAM
2025-11-20 18:40:40.361402 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:40.361682 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 18:40:40.38452 INFO::Done
2025-11-20 18:40:40.384805 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:40.385552 INFO::ASW Batch was -0.0716154128672362 prior to batch effect correction and is now -0.126050447822803 .
2025-11-20 18:40:40.385827 INFO::Total function execution time is 0.0283911228179932 s and adjustment time is 0.0236940383911133 s ( 83.46 )
2025-11-20 18:40:40.386161 INFO::Formatting Data.
2025-11-20 18:40:40.38636 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:40.386644 INFO::Removing potential empty rows and columns
2025-11-20 18:40:40.386983 INFO::Found 0 missing values.
2025-11-20 18:40:40.387993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:40.388217 INFO::Done
2025-11-20 18:40:40.388431 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:40.389178 INFO::Starting hierarchical adjustment
2025-11-20 18:40:40.389482 INFO::Found 2 batches.
2025-11-20 18:40:40.389693 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:40.389912 INFO::Using default BPPARAM
2025-11-20 18:40:40.390105 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:40.390468 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 18:40:40.396717 INFO::Done
2025-11-20 18:40:40.396989 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:40.397772 INFO::ASW Batch was -0.0716154128672362 prior to batch effect correction and is now -0.126050447822803 .
2025-11-20 18:40:40.39808 INFO::Total function execution time is 0.0118989944458008 s and adjustment time is 0.00729703903198242 s ( 61.32 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-20 18:40:41.727807 INFO::Formatting Data.
2025-11-20 18:40:41.728102 INFO::Recognized SummarizedExperiment
2025-11-20 18:40:41.728271 INFO::Typecasting input to dataframe.
2025-11-20 18:40:41.73921 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:41.739658 INFO::Removing potential empty rows and columns
2025-11-20 18:40:41.740746 INFO::Found 0 missing values.
2025-11-20 18:40:41.742677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:41.742841 INFO::Done
2025-11-20 18:40:41.742985 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:41.744138 INFO::Starting hierarchical adjustment
2025-11-20 18:40:41.744342 INFO::Found 2 batches.
2025-11-20 18:40:41.744492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:41.744804 INFO::Using default BPPARAM
2025-11-20 18:40:41.744951 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:41.745225 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 18:40:41.762742 INFO::Done
2025-11-20 18:40:41.763023 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:41.764358 INFO::ASW Batch was -0.0283534622731763 prior to batch effect correction and is now -0.0918668091709835 .
2025-11-20 18:40:41.764643 INFO::Total function execution time is 0.0369551181793213 s and adjustment time is 0.0184071063995361 s ( 49.81 )
Warning: stack imbalance in '{', 73 then 74
2025-11-20 18:40:41.773307 INFO::Formatting Data.
2025-11-20 18:40:41.773631 INFO::Recognized SummarizedExperiment
2025-11-20 18:40:41.773852 INFO::Typecasting input to dataframe.
2025-11-20 18:40:41.777694 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:41.778174 INFO::Removing potential empty rows and columns
2025-11-20 18:40:41.779638 INFO::Found 0 missing values.
2025-11-20 18:40:41.782422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:41.78264 INFO::Done
2025-11-20 18:40:41.782836 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:41.784187 INFO::Starting hierarchical adjustment
2025-11-20 18:40:41.784439 INFO::Found 2 batches.
2025-11-20 18:40:41.784629 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:41.784857 INFO::Using default BPPARAM
2025-11-20 18:40:41.78502 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:41.785371 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 18:40:41.795016 INFO::Done
2025-11-20 18:40:41.795308 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:41.796613 INFO::ASW Batch was -0.0177650174412136 prior to batch effect correction and is now -0.0177650174412136 .
2025-11-20 18:40:41.796908 INFO::Total function execution time is 0.0236289501190186 s and adjustment time is 0.0106170177459717 s ( 44.93 )
2025-11-20 18:40:41.804031 INFO::Formatting Data.
2025-11-20 18:40:41.804299 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:41.804599 INFO::Removing potential empty rows and columns
2025-11-20 18:40:41.804924 INFO::Found 0 missing values.
2025-11-20 18:40:41.805808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:41.805976 INFO::Done
2025-11-20 18:40:41.806135 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:41.806839 INFO::Starting hierarchical adjustment
2025-11-20 18:40:41.807044 INFO::Found 3 batches.
2025-11-20 18:40:41.807194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:41.807378 INFO::Using default BPPARAM
2025-11-20 18:40:41.807541 INFO::Processing subtree level 1
2025-11-20 18:40:41.880468 INFO::Adjusting the last 1 batches sequentially
2025-11-20 18:40:41.881886 INFO::Done
2025-11-20 18:40:41.882274 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:41.884922 INFO::ASW Batch was -0.0396571993167073 prior to batch effect correction and is now -0.14910019456701 .
2025-11-20 18:40:41.885777 INFO::Total function execution time is 0.0816018581390381 s and adjustment time is 0.074882984161377 s ( 91.77 )
2025-11-20 18:40:41.894236 INFO::Skipping initial DF formatting
2025-11-20 18:40:41.894508 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:41.895995 INFO::Starting hierarchical adjustment
2025-11-20 18:40:41.896285 INFO::Found 5 batches.
2025-11-20 18:40:41.896468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:41.89671 INFO::Using default BPPARAM
2025-11-20 18:40:41.896871 INFO::Processing subtree level 1
2025-11-20 18:40:41.956108 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:41.957821 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 18:40:41.966552 INFO::Done
2025-11-20 18:40:41.967045 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:41.969827 INFO::ASW Batch was 0.545050498817792 prior to batch effect correction and is now 0.545050498817792 .
2025-11-20 18:40:41.970991 INFO::ASW Label was 0.320999279171066 prior to batch effect correction and is now 0.320999279171066 .
2025-11-20 18:40:41.971692 INFO::Total function execution time is 0.0773220062255859 s and adjustment time is 0.0703220367431641 s ( 90.95 )
2025-11-20 18:40:41.981162 INFO::Formatting Data.
2025-11-20 18:40:41.981485 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:41.981908 INFO::Removing potential empty rows and columns
2025-11-20 18:40:41.982436 INFO::Found 0 missing values.
2025-11-20 18:40:41.984121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:41.984338 INFO::Done
2025-11-20 18:40:41.984563 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:41.985664 INFO::Starting hierarchical adjustment
2025-11-20 18:40:41.985936 INFO::Found 5 batches.
2025-11-20 18:40:41.986108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:41.986392 INFO::Using default BPPARAM
2025-11-20 18:40:41.986554 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.
2025-11-20 18:40:42.046525 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.050815 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 18:40:42.059115 INFO::Done
2025-11-20 18:40:42.059357 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.061236 INFO::ASW Batch was 0.311527186203081 prior to batch effect correction and is now -0.0294937202488888 .
2025-11-20 18:40:42.061447 INFO::ASW Label was 0.30406385908284 prior to batch effect correction and is now 0.807497028449904 .
2025-11-20 18:40:42.061878 INFO::Total function execution time is 0.0806071758270264 s and adjustment time is 0.0732400417327881 s ( 90.86 )
2025-11-20 18:40:42.062142 INFO::Formatting Data.
2025-11-20 18:40:42.062319 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.062596 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.062921 INFO::Found 0 missing values.
2025-11-20 18:40:42.064099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.064269 INFO::Done
2025-11-20 18:40:42.064443 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.065345 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.065716 INFO::Found 5 batches.
2025-11-20 18:40:42.065882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.066092 INFO::Using default BPPARAM
2025-11-20 18:40:42.066332 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.
2025-11-20 18:40:42.11633 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.119553 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 18:40:42.133633 INFO::Done
2025-11-20 18:40:42.134079 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.135767 INFO::ASW Batch was 0.311527186203081 prior to batch effect correction and is now -0.0294937202488888 .
2025-11-20 18:40:42.135976 INFO::ASW Label was 0.30406385908284 prior to batch effect correction and is now 0.807497028449904 .
2025-11-20 18:40:42.136639 INFO::Total function execution time is 0.0742709636688232 s and adjustment time is 0.0680851936340332 s ( 91.67 )
2025-11-20 18:40:42.143649 INFO::Formatting Data.
2025-11-20 18:40:42.143897 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.144338 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.144707 INFO::Found 0 missing values.
2025-11-20 18:40:42.145955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.146138 INFO::Done
2025-11-20 18:40:42.146317 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.147278 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.147513 INFO::Found 5 batches.
2025-11-20 18:40:42.147677 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.147881 INFO::Using default BPPARAM
2025-11-20 18:40:42.148245 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.
2025-11-20 18:40:42.196897 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.199658 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 18:40:42.208754 INFO::Done
2025-11-20 18:40:42.209432 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.210956 INFO::ASW Batch was 0.44396604309068 prior to batch effect correction and is now 0.023850435571085 .
2025-11-20 18:40:42.211162 INFO::ASW Label was 0.262440021677141 prior to batch effect correction and is now 0.704388817250509 .
2025-11-20 18:40:42.211452 INFO::Total function execution time is 0.0678160190582275 s and adjustment time is 0.0612668991088867 s ( 90.34 )
2025-11-20 18:40:42.211751 INFO::Formatting Data.
2025-11-20 18:40:42.211931 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.212216 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.212547 INFO::Found 0 missing values.
2025-11-20 18:40:42.213712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.213882 INFO::Done
2025-11-20 18:40:42.214059 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.214927 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.215157 INFO::Found 5 batches.
2025-11-20 18:40:42.215318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.215531 INFO::Using default BPPARAM
2025-11-20 18:40:42.215752 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.
2025-11-20 18:40:42.269024 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.271861 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 18:40:42.281891 INFO::Done
2025-11-20 18:40:42.28218 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.283778 INFO::ASW Batch was 0.44396604309068 prior to batch effect correction and is now 0.023850435571085 .
2025-11-20 18:40:42.284282 INFO::ASW Label was 0.262440021677141 prior to batch effect correction and is now 0.704388817250509 .
2025-11-20 18:40:42.284976 INFO::Total function execution time is 0.0729470252990723 s and adjustment time is 0.0667598247528076 s ( 91.52 )
2025-11-20 18:40:42.29157 INFO::Formatting Data.
2025-11-20 18:40:42.291802 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.29211 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.292487 INFO::Found 0 missing values.
2025-11-20 18:40:42.293346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.29352 INFO::Done
2025-11-20 18:40:42.293685 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.29461 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.294845 INFO::Found 2 batches.
2025-11-20 18:40:42.295009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.295231 INFO::Using default BPPARAM
2025-11-20 18:40:42.295394 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.295659 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 18:40:42.30027 INFO::Done
2025-11-20 18:40:42.300472 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.301327 INFO::ASW Batch was 0.492069573582845 prior to batch effect correction and is now -0.0214804369703387 .
2025-11-20 18:40:42.30151 INFO::ASW Label was 0.606423301948546 prior to batch effect correction and is now 0.926272219675629 .
2025-11-20 18:40:42.301764 INFO::Total function execution time is 0.0102128982543945 s and adjustment time is 0.00547504425048828 s ( 53.61 )
2025-11-20 18:40:42.301979 INFO::Formatting Data.
2025-11-20 18:40:42.302144 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.302381 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.302662 INFO::Found 0 missing values.
2025-11-20 18:40:42.303431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.303591 INFO::Done
2025-11-20 18:40:42.303752 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.304555 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.304775 INFO::Found 2 batches.
2025-11-20 18:40:42.304932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.305116 INFO::Using default BPPARAM
2025-11-20 18:40:42.305265 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.305516 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 18:40:42.310035 INFO::Done
2025-11-20 18:40:42.310269 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.31113 INFO::ASW Batch was 0.492069573582845 prior to batch effect correction and is now -0.0214804369703387 .
2025-11-20 18:40:42.311308 INFO::ASW Label was 0.606423301948546 prior to batch effect correction and is now 0.926272219675629 .
2025-11-20 18:40:42.311538 INFO::Total function execution time is 0.00954890251159668 s and adjustment time is 0.0052947998046875 s ( 55.45 )
2025-11-20 18:40:42.316444 INFO::Formatting Data.
2025-11-20 18:40:42.316716 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.317015 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.317317 INFO::Found 0 missing values.
2025-11-20 18:40:42.317961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.318123 INFO::Done
2025-11-20 18:40:42.31829 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.318928 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.319146 INFO::Found 2 batches.
2025-11-20 18:40:42.319298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.319503 INFO::Using default BPPARAM
2025-11-20 18:40:42.319656 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.319919 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 18:40:42.332646 INFO::Done
2025-11-20 18:40:42.332939 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.333771 INFO::ASW Batch was 0.171391429391613 prior to batch effect correction and is now -0.109606095817725 .
2025-11-20 18:40:42.334091 INFO::Total function execution time is 0.017672061920166 s and adjustment time is 0.0135200023651123 s ( 76.5 )
2025-11-20 18:40:42.339985 INFO::Formatting Data.
2025-11-20 18:40:42.340272 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.34061 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.34103 INFO::Found 0 missing values.
2025-11-20 18:40:42.341564 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.
2025-11-20 18:40:42.343251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.343432 INFO::Done
2025-11-20 18:40:42.343602 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.344619 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.344867 INFO::Found 2 batches.
2025-11-20 18:40:42.345044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.345255 INFO::Using default BPPARAM
2025-11-20 18:40:42.345445 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.345762 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 18:40:42.352461 INFO::Done
2025-11-20 18:40:42.352746 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.35386 INFO::ASW Batch was 0.372627529184984 prior to batch effect correction and is now 0.0050155792196618 .
2025-11-20 18:40:42.354084 INFO::ASW Label was 0.672015916909663 prior to batch effect correction and is now 0.909882332383275 .
2025-11-20 18:40:42.354444 INFO::Total function execution time is 0.0144820213317871 s and adjustment time is 0.0076141357421875 s ( 52.58 )
2025-11-20 18:40:42.354725 INFO::Formatting Data.
2025-11-20 18:40:42.354937 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.355276 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.355627 INFO::Found 0 missing values.
2025-11-20 18:40:42.355902 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.
2025-11-20 18:40:42.357205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.357382 INFO::Done
2025-11-20 18:40:42.357533 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.358403 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.358624 INFO::Found 2 batches.
2025-11-20 18:40:42.358795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.358977 INFO::Using default BPPARAM
2025-11-20 18:40:42.359136 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:42.35939 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 18:40:42.365324 INFO::Done
2025-11-20 18:40:42.365549 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.366428 INFO::ASW Batch was 0.372627529184984 prior to batch effect correction and is now 0.0050155792196618 .
2025-11-20 18:40:42.366612 INFO::ASW Label was 0.672015916909663 prior to batch effect correction and is now 0.909882332383275 .
2025-11-20 18:40:42.36686 INFO::Total function execution time is 0.012131929397583 s and adjustment time is 0.00673317909240723 s ( 55.5 )
2025-11-20 18:40:42.436575 INFO::Formatting Data.
2025-11-20 18:40:42.436921 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.437286 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.437699 INFO::Found 0 missing values.
2025-11-20 18:40:42.438669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.438841 INFO::Done
2025-11-20 18:40:42.439008 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.43976 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.440045 INFO::Found 3 batches.
2025-11-20 18:40:42.440205 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.440394 INFO::Using default BPPARAM
2025-11-20 18:40:42.440544 INFO::Processing subtree level 1
2025-11-20 18:40:42.480172 INFO::Adjusting the last 1 batches sequentially
2025-11-20 18:40:42.481732 INFO::Done
2025-11-20 18:40:42.481961 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.483003 INFO::ASW Batch was 0.00434421265510276 prior to batch effect correction and is now 0.00434421265510276 .
2025-11-20 18:40:42.483693 INFO::Total function execution time is 0.0469920635223389 s and adjustment time is 0.0418009757995605 s ( 88.95 )
2025-11-20 18:40:42.484027 INFO::Formatting Data.
2025-11-20 18:40:42.484212 INFO::Typecasting input to dataframe.
2025-11-20 18:40:42.484462 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.484879 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.485225 INFO::Found 0 missing values.
2025-11-20 18:40:42.486137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.48645 INFO::Done
2025-11-20 18:40:42.486618 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.487251 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.487479 INFO::Found 3 batches.
2025-11-20 18:40:42.487636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.48784 INFO::Using default BPPARAM
2025-11-20 18:40:42.487986 INFO::Processing subtree level 1
2025-11-20 18:40:42.532223 INFO::Adjusting the last 1 batches sequentially
2025-11-20 18:40:42.533765 INFO::Done
2025-11-20 18:40:42.534241 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.537398 INFO::ASW Batch was 0.00434421265510276 prior to batch effect correction and is now 0.00434421265510276 .
2025-11-20 18:40:42.537971 INFO::Total function execution time is 0.0538089275360107 s and adjustment time is 0.0463089942932129 s ( 86.06 )
2025-11-20 18:40:42.544898 INFO::Formatting Data.
2025-11-20 18:40:42.545177 INFO::Typecasting input to dataframe.
2025-11-20 18:40:42.545508 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.545874 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.546267 INFO::Found 0 missing values.
2025-11-20 18:40:42.547249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.547427 INFO::Done
2025-11-20 18:40:42.547597 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.548249 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.548689 INFO::Found 3 batches.
2025-11-20 18:40:42.548859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.549081 INFO::Using default BPPARAM
2025-11-20 18:40:42.54923 INFO::Processing subtree level 1
2025-11-20 18:40:42.597805 INFO::Adjusting the last 1 batches sequentially
2025-11-20 18:40:42.607975 INFO::Done
2025-11-20 18:40:42.608388 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.610657 INFO::ASW Batch was -0.0550222119026583 prior to batch effect correction and is now -0.0550222119026583 .
2025-11-20 18:40:42.611572 INFO::Total function execution time is 0.0665521621704102 s and adjustment time is 0.0593640804290771 s ( 89.2 )
2025-11-20 18:40:42.713053 INFO::Formatting Data.
2025-11-20 18:40:42.71336 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.713789 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.71494 INFO::Found 1000 missing values.
2025-11-20 18:40:42.720705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:42.720935 INFO::Done
2025-11-20 18:40:42.721121 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:42.723325 INFO::Starting hierarchical adjustment
2025-11-20 18:40:42.723609 INFO::Found 10 batches.
2025-11-20 18:40:42.72381 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:42.724087 INFO::Using default BPPARAM
2025-11-20 18:40:42.724342 INFO::Processing subtree level 1
2025-11-20 18:40:42.803968 INFO::Processing subtree level 2
2025-11-20 18:40:42.978652 INFO::Adjusting the last 1 batches sequentially
2025-11-20 18:40:42.981973 INFO::Done
2025-11-20 18:40:42.982628 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:42.988686 INFO::ASW Batch was 0.473586287024577 prior to batch effect correction and is now 0.473586287024577 .
2025-11-20 18:40:42.989012 INFO::ASW Label was 0.367299026379914 prior to batch effect correction and is now 0.367299026379914 .
2025-11-20 18:40:42.989911 INFO::Total function execution time is 0.276863098144531 s and adjustment time is 0.25837779045105 s ( 93.32 )
2025-11-20 18:40:42.99027 INFO::Formatting Data.
2025-11-20 18:40:42.990503 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:42.991256 INFO::Removing potential empty rows and columns
2025-11-20 18:40:42.992358 INFO::Found 1000 missing values.
2025-11-20 18:40:43.031826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:43.032227 INFO::Done
2025-11-20 18:40:43.032478 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:43.035143 INFO::Starting hierarchical adjustment
2025-11-20 18:40:43.035517 INFO::Found 10 batches.
2025-11-20 18:40:43.571606 INFO::Set up parallel execution backend with 2 workers
2025-11-20 18:40:43.571908 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-20 18:40:44.195641 INFO::Adjusting the last 2 batches sequentially
2025-11-20 18:40:44.196304 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 18:40:44.202609 INFO::Done
2025-11-20 18:40:44.20284 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:44.204738 INFO::ASW Batch was 0.473586287024577 prior to batch effect correction and is now 0.473586287024577 .
2025-11-20 18:40:44.204911 INFO::ASW Label was 0.367299026379914 prior to batch effect correction and is now 0.367299026379914 .
2025-11-20 18:40:44.205151 INFO::Total function execution time is 1.2148859500885 s and adjustment time is 1.16718006134033 s ( 96.07 )
2025-11-20 18:40:44.287996 INFO::Formatting Data.
2025-11-20 18:40:44.288424 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.288781 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.289234 INFO::Found 0 missing values.
2025-11-20 18:40:44.290578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.290824 INFO::Done
2025-11-20 18:40:44.291064 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 18:40:44.29231 INFO::Starting hierarchical adjustment
2025-11-20 18:40:44.292605 INFO::Found 3 batches.
2025-11-20 18:40:44.292815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 18:40:44.293061 INFO::Using default BPPARAM
2025-11-20 18:40:44.293236 INFO::Processing subtree level 1
2025-11-20 18:40:44.36516 INFO::Adjusting the last 1 batches sequentially
2025-11-20 18:40:44.367054 INFO::Done
2025-11-20 18:40:44.367363 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 18:40:44.369704 INFO::ASW Batch was 0.100643791634609 prior to batch effect correction and is now -0.146612516394193 .
2025-11-20 18:40:44.369955 INFO::ASW Label was -0.175826333548698 prior to batch effect correction and is now 0.0242402977070182 .
2025-11-20 18:40:44.370682 INFO::Total function execution time is 0.082690954208374 s and adjustment time is 0.07452392578125 s ( 90.12 )
2025-11-20 18:40:44.437225 INFO::Formatting Data.
2025-11-20 18:40:44.437561 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.437894 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.438323 INFO::Found 2 missing values.
2025-11-20 18:40:44.43934 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.439546 INFO::Done
2025-11-20 18:40:44.451674 INFO::Found NA in Reference column
2025-11-20 18:40:44.456046 INFO::Require at least two references per batch.
2025-11-20 18:40:44.466399 INFO::Formatting Data.
2025-11-20 18:40:44.466679 INFO::Recognized SummarizedExperiment
2025-11-20 18:40:44.466856 INFO::Typecasting input to dataframe.
2025-11-20 18:40:44.471561 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.47205 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.473565 INFO::Found 0 missing values.
2025-11-20 18:40:44.476374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.476591 INFO::Done
2025-11-20 18:40:44.482768 INFO::Formatting Data.
2025-11-20 18:40:44.483004 INFO::Recognized SummarizedExperiment
2025-11-20 18:40:44.483173 INFO::Typecasting input to dataframe.
2025-11-20 18:40:44.490818 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.491307 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.492748 INFO::Found 0 missing values.
2025-11-20 18:40:44.498066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.498317 INFO::Done
2025-11-20 18:40:44.506331 INFO::Formatting Data.
2025-11-20 18:40:44.506589 INFO::Recognized SummarizedExperiment
2025-11-20 18:40:44.506774 INFO::Typecasting input to dataframe.
2025-11-20 18:40:44.512439 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.512794 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.513185 INFO::Found 0 missing values.
2025-11-20 18:40:44.513488 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.
2025-11-20 18:40:44.517235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.5176 INFO::Done
2025-11-20 18:40:44.525515 INFO::Formatting Data.
2025-11-20 18:40:44.525891 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.526255 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.52665 INFO::Found 0 missing values.
2025-11-20 18:40:44.527694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.527886 INFO::Done
2025-11-20 18:40:44.534628 INFO::Formatting Data.
2025-11-20 18:40:44.534982 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.535394 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.535856 INFO::Found 0 missing values.
2025-11-20 18:40:44.537169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.53739 INFO::Done
2025-11-20 18:40:44.555679 INFO::Formatting Data.
2025-11-20 18:40:44.556023 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.556427 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.557025 INFO::Found 1 missing values.
2025-11-20 18:40:44.558034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.558232 INFO::Done
2025-11-20 18:40:44.568517 INFO::Formatting Data.
2025-11-20 18:40:44.56882 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.56914 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.569481 INFO::Found 2 missing values.
2025-11-20 18:40:44.5698 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.
2025-11-20 18:40:44.570621 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.570836 INFO::Done
2025-11-20 18:40:44.578772 INFO::Formatting Data.
2025-11-20 18:40:44.579299 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.57967 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.580066 INFO::Found 2 missing values.
2025-11-20 18:40:44.580829 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.581016 INFO::Done
2025-11-20 18:40:44.588581 INFO::Formatting Data.
2025-11-20 18:40:44.588955 INFO::Typecasting input to dataframe.
2025-11-20 18:40:44.589257 INFO::Replacing NaNs with NAs.
2025-11-20 18:40:44.589592 INFO::Removing potential empty rows and columns
2025-11-20 18:40:44.589955 INFO::Found 0 missing values.
2025-11-20 18:40:44.590944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 18:40:44.591143 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.465 1.722 9.875
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.244 | 0.429 | 7.844 | |
| compute_asw | 0.010 | 0.000 | 0.011 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.005 | 0.001 | 0.006 | |
| generate_dataset | 0.006 | 0.000 | 0.006 | |