Yannis Schumann
| Snapshot Date: 2025-11-06 13:45 -0500 (Thu, 06 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-07 12:00 -0500 (Fri, 07 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-11-06 18:37:55 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 18:38:26 -0500 (Thu, 06 Nov 2025) |
| EllapsedTime: 31.4 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 9.794 0.477 7.241
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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")
2025-11-06 18:38:18.793238 INFO::Formatting Data.
2025-11-06 18:38:18.795003 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:18.799836 INFO::Removing potential empty rows and columns
2025-11-06 18:38:18.913601 INFO::Found 0 missing values.
2025-11-06 18:38:18.915076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:18.915322 INFO::Done
2025-11-06 18:38:18.915552 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:18.921458 INFO::Starting hierarchical adjustment
2025-11-06 18:38:18.921791 INFO::Found 3 batches.
2025-11-06 18:38:18.921989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:18.922448 INFO::Using default BPPARAM
2025-11-06 18:38:18.922629 INFO::Processing subtree level 1
2025-11-06 18:38:18.972184 INFO::Adjusting the last 1 batches sequentially
2025-11-06 18:38:18.97385 INFO::Done
2025-11-06 18:38:18.974132 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:18.975495 INFO::ASW Batch was -0.111019434618045 prior to batch effect correction and is now -0.111019434618045 .
2025-11-06 18:38:18.976801 INFO::Total function execution time is 0.183652877807617 s and adjustment time is 0.052128791809082 s ( 28.38 )
2025-11-06 18:38:18.98374 INFO::Formatting Data.
2025-11-06 18:38:18.983993 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:18.984302 INFO::Removing potential empty rows and columns
2025-11-06 18:38:18.984684 INFO::Found 0 missing values.
2025-11-06 18:38:18.984992 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.
2025-11-06 18:38:18.988915 INFO::Formatting Data.
2025-11-06 18:38:18.989145 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:18.989419 INFO::Removing potential empty rows and columns
2025-11-06 18:38:18.989752 INFO::Found 0 missing values.
2025-11-06 18:38:18.990037 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.
2025-11-06 18:38:18.996677 INFO::Formatting Data.
2025-11-06 18:38:18.996948 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:18.99725 INFO::Removing potential empty rows and columns
2025-11-06 18:38:18.997619 INFO::Found 0 missing values.
2025-11-06 18:38:18.997933 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.
2025-11-06 18:38:18.999491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:18.999695 INFO::Done
2025-11-06 18:38:18.999918 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:19.000723 INFO::Starting hierarchical adjustment
2025-11-06 18:38:19.000956 INFO::Found 2 batches.
2025-11-06 18:38:19.001133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:19.001366 INFO::Using default BPPARAM
2025-11-06 18:38:19.001537 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:19.001834 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 18:38:19.011183 INFO::Done
2025-11-06 18:38:19.01146 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:19.012217 INFO::ASW Batch was 0.0535261924378097 prior to batch effect correction and is now -0.118513780938808 .
2025-11-06 18:38:19.012511 INFO::Total function execution time is 0.0158519744873047 s and adjustment time is 0.0102519989013672 s ( 64.67 )
2025-11-06 18:38:19.014015 INFO::Formatting Data.
2025-11-06 18:38:19.014295 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:19.017983 INFO::Formatting Data.
2025-11-06 18:38:19.01827 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:19.018581 INFO::Removing potential empty rows and columns
2025-11-06 18:38:19.018971 INFO::Found 0 missing values.
2025-11-06 18:38:19.020059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:19.020273 INFO::Done
2025-11-06 18:38:19.020446 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:19.021311 INFO::Starting hierarchical adjustment
2025-11-06 18:38:19.021667 INFO::Found 2 batches.
2025-11-06 18:38:19.02186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:19.022084 INFO::Using default BPPARAM
2025-11-06 18:38:19.022261 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:19.022541 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 18:38:19.04222 INFO::Done
2025-11-06 18:38:19.042479 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:19.043151 INFO::ASW Batch was 0.00454076281356958 prior to batch effect correction and is now -0.112593136909213 .
2025-11-06 18:38:19.043402 INFO::Total function execution time is 0.025460958480835 s and adjustment time is 0.0206189155578613 s ( 80.98 )
2025-11-06 18:38:19.043708 INFO::Formatting Data.
2025-11-06 18:38:19.043875 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:19.044124 INFO::Removing potential empty rows and columns
2025-11-06 18:38:19.044418 INFO::Found 0 missing values.
2025-11-06 18:38:19.045203 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:19.045354 INFO::Done
2025-11-06 18:38:19.045493 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:19.046063 INFO::Starting hierarchical adjustment
2025-11-06 18:38:19.046275 INFO::Found 2 batches.
2025-11-06 18:38:19.046425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:19.046602 INFO::Using default BPPARAM
2025-11-06 18:38:19.04674 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:19.046987 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 18:38:19.051679 INFO::Done
2025-11-06 18:38:19.051908 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:19.05256 INFO::ASW Batch was 0.00454076281356958 prior to batch effect correction and is now -0.112593136909213 .
2025-11-06 18:38:19.0528 INFO::Total function execution time is 0.00908493995666504 s and adjustment time is 0.00543785095214844 s ( 59.86 )
2025-11-06 18:38:20.242143 INFO::Formatting Data.
2025-11-06 18:38:20.242444 INFO::Recognized SummarizedExperiment
2025-11-06 18:38:20.242613 INFO::Typecasting input to dataframe.
2025-11-06 18:38:20.253274 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.253732 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.254965 INFO::Found 0 missing values.
2025-11-06 18:38:20.257124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.257325 INFO::Done
2025-11-06 18:38:20.257483 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.258752 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.258997 INFO::Found 2 batches.
2025-11-06 18:38:20.259154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.259506 INFO::Using default BPPARAM
2025-11-06 18:38:20.259664 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.259978 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 18:38:20.277917 INFO::Done
2025-11-06 18:38:20.278167 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.279404 INFO::ASW Batch was 0.001211380998981 prior to batch effect correction and is now -0.0927524985299653 .
2025-11-06 18:38:20.279677 INFO::Total function execution time is 0.0376381874084473 s and adjustment time is 0.0189609527587891 s ( 50.38 )
2025-11-06 18:38:20.285994 INFO::Formatting Data.
2025-11-06 18:38:20.286216 INFO::Recognized SummarizedExperiment
2025-11-06 18:38:20.286379 INFO::Typecasting input to dataframe.
2025-11-06 18:38:20.28938 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.289729 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.290814 INFO::Found 0 missing values.
2025-11-06 18:38:20.292853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.293016 INFO::Done
2025-11-06 18:38:20.29317 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.294294 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.294504 INFO::Found 2 batches.
2025-11-06 18:38:20.294651 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.294825 INFO::Using default BPPARAM
2025-11-06 18:38:20.294965 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.295247 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 18:38:20.303184 INFO::Done
2025-11-06 18:38:20.303426 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.304616 INFO::ASW Batch was 0.00567223160928926 prior to batch effect correction and is now 0.00567223160928926 .
2025-11-06 18:38:20.304902 INFO::Total function execution time is 0.0188970565795898 s and adjustment time is 0.00871515274047852 s ( 46.12 )
2025-11-06 18:38:20.312529 INFO::Formatting Data.
2025-11-06 18:38:20.312821 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.313126 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.313468 INFO::Found 0 missing values.
2025-11-06 18:38:20.314388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.314565 INFO::Done
2025-11-06 18:38:20.314728 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.315479 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.315699 INFO::Found 3 batches.
2025-11-06 18:38:20.315854 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.316041 INFO::Using default BPPARAM
2025-11-06 18:38:20.316191 INFO::Processing subtree level 1
2025-11-06 18:38:20.383438 INFO::Adjusting the last 1 batches sequentially
2025-11-06 18:38:20.385122 INFO::Done
2025-11-06 18:38:20.385533 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.387615 INFO::ASW Batch was -0.0363317451658504 prior to batch effect correction and is now -0.161505559489179 .
2025-11-06 18:38:20.388161 INFO::Total function execution time is 0.0756170749664307 s and adjustment time is 0.0694620609283447 s ( 91.86 )
2025-11-06 18:38:20.395451 INFO::Skipping initial DF formatting
2025-11-06 18:38:20.395746 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.397213 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.397482 INFO::Found 5 batches.
2025-11-06 18:38:20.397829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.398054 INFO::Using default BPPARAM
2025-11-06 18:38:20.398222 INFO::Processing subtree level 1
2025-11-06 18:38:20.520012 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.522644 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 18:38:20.533992 INFO::Done
2025-11-06 18:38:20.534345 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.536701 INFO::ASW Batch was 0.575098707571718 prior to batch effect correction and is now 0.575098707571718 .
2025-11-06 18:38:20.538247 INFO::ASW Label was 0.357312510011355 prior to batch effect correction and is now 0.357312510011355 .
2025-11-06 18:38:20.538714 INFO::Total function execution time is 0.143306016921997 s and adjustment time is 0.136558055877686 s ( 95.29 )
2025-11-06 18:38:20.583207 INFO::Formatting Data.
2025-11-06 18:38:20.58355 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.583956 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.584315 INFO::Found 0 missing values.
2025-11-06 18:38:20.585693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.585871 INFO::Done
2025-11-06 18:38:20.586036 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.587086 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.587302 INFO::Found 5 batches.
2025-11-06 18:38:20.58747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.587683 INFO::Using default BPPARAM
2025-11-06 18:38:20.587869 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.
2025-11-06 18:38:20.664342 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.666457 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 18:38:20.679953 INFO::Done
2025-11-06 18:38:20.681431 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.684049 INFO::ASW Batch was 0.323623264525062 prior to batch effect correction and is now -0.065648029321361 .
2025-11-06 18:38:20.684556 INFO::ASW Label was 0.401860800466377 prior to batch effect correction and is now 0.863528672860514 .
2025-11-06 18:38:20.685048 INFO::Total function execution time is 0.101819038391113 s and adjustment time is 0.0926480293273926 s ( 90.99 )
2025-11-06 18:38:20.68566 INFO::Formatting Data.
2025-11-06 18:38:20.685932 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.686366 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.686963 INFO::Found 0 missing values.
2025-11-06 18:38:20.68949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.689908 INFO::Done
2025-11-06 18:38:20.690299 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.692 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.692487 INFO::Found 5 batches.
2025-11-06 18:38:20.692739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.69298 INFO::Using default BPPARAM
2025-11-06 18:38:20.693151 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.
2025-11-06 18:38:20.7662 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.767854 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 18:38:20.776617 INFO::Done
2025-11-06 18:38:20.777032 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.778585 INFO::ASW Batch was 0.323623264525062 prior to batch effect correction and is now -0.065648029321361 .
2025-11-06 18:38:20.778826 INFO::ASW Label was 0.401860800466377 prior to batch effect correction and is now 0.863528672860514 .
2025-11-06 18:38:20.779496 INFO::Total function execution time is 0.0937778949737549 s and adjustment time is 0.0841820240020752 s ( 89.77 )
2025-11-06 18:38:20.791152 INFO::Formatting Data.
2025-11-06 18:38:20.791511 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.791944 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.792371 INFO::Found 0 missing values.
2025-11-06 18:38:20.793861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.794057 INFO::Done
2025-11-06 18:38:20.794259 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.79556 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.795818 INFO::Found 5 batches.
2025-11-06 18:38:20.796019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.796271 INFO::Using default BPPARAM
2025-11-06 18:38:20.796453 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.
2025-11-06 18:38:20.861733 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.863639 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 18:38:20.872506 INFO::Done
2025-11-06 18:38:20.872975 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.874781 INFO::ASW Batch was 0.545103855951479 prior to batch effect correction and is now -0.0337822147860339 .
2025-11-06 18:38:20.875035 INFO::ASW Label was 0.255187540353663 prior to batch effect correction and is now 0.736604797228341 .
2025-11-06 18:38:20.875363 INFO::Total function execution time is 0.0842399597167969 s and adjustment time is 0.0767309665679932 s ( 91.09 )
2025-11-06 18:38:20.875726 INFO::Formatting Data.
2025-11-06 18:38:20.875961 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.876314 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.876736 INFO::Found 0 missing values.
2025-11-06 18:38:20.878264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.878473 INFO::Done
2025-11-06 18:38:20.878668 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.879795 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.880066 INFO::Found 5 batches.
2025-11-06 18:38:20.880265 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.880521 INFO::Using default BPPARAM
2025-11-06 18:38:20.880813 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.
2025-11-06 18:38:20.94771 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.950015 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 18:38:20.960899 INFO::Done
2025-11-06 18:38:20.961476 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.964238 INFO::ASW Batch was 0.545103855951479 prior to batch effect correction and is now -0.0337822147860339 .
2025-11-06 18:38:20.964582 INFO::ASW Label was 0.255187540353663 prior to batch effect correction and is now 0.736604797228341 .
2025-11-06 18:38:20.965047 INFO::Total function execution time is 0.089231014251709 s and adjustment time is 0.0808751583099365 s ( 90.64 )
2025-11-06 18:38:20.975169 INFO::Formatting Data.
2025-11-06 18:38:20.97547 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.975863 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.976312 INFO::Found 0 missing values.
2025-11-06 18:38:20.977276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.977466 INFO::Done
2025-11-06 18:38:20.977659 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.978698 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.979103 INFO::Found 2 batches.
2025-11-06 18:38:20.979304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.979552 INFO::Using default BPPARAM
2025-11-06 18:38:20.979746 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.980048 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 18:38:20.985988 INFO::Done
2025-11-06 18:38:20.986305 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:20.9875 INFO::ASW Batch was 0.522446000306634 prior to batch effect correction and is now 0.0855362974963801 .
2025-11-06 18:38:20.987768 INFO::ASW Label was 0.518316762602065 prior to batch effect correction and is now 0.848202700143592 .
2025-11-06 18:38:20.988092 INFO::Total function execution time is 0.0129489898681641 s and adjustment time is 0.00693392753601074 s ( 53.55 )
2025-11-06 18:38:20.988416 INFO::Formatting Data.
2025-11-06 18:38:20.988658 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:20.988985 INFO::Removing potential empty rows and columns
2025-11-06 18:38:20.989412 INFO::Found 0 missing values.
2025-11-06 18:38:20.990486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:20.990681 INFO::Done
2025-11-06 18:38:20.990862 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:20.99197 INFO::Starting hierarchical adjustment
2025-11-06 18:38:20.992289 INFO::Found 2 batches.
2025-11-06 18:38:20.992518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:20.992876 INFO::Using default BPPARAM
2025-11-06 18:38:20.993098 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:20.993477 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 18:38:20.999798 INFO::Done
2025-11-06 18:38:21.000061 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:21.001141 INFO::ASW Batch was 0.522446000306634 prior to batch effect correction and is now 0.0855362974963801 .
2025-11-06 18:38:21.001354 INFO::ASW Label was 0.518316762602065 prior to batch effect correction and is now 0.848202700143592 .
2025-11-06 18:38:21.001628 INFO::Total function execution time is 0.013206958770752 s and adjustment time is 0.00756001472473145 s ( 57.24 )
2025-11-06 18:38:21.006851 INFO::Formatting Data.
2025-11-06 18:38:21.007136 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:21.007467 INFO::Removing potential empty rows and columns
2025-11-06 18:38:21.007823 INFO::Found 0 missing values.
2025-11-06 18:38:21.00859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:21.008791 INFO::Done
2025-11-06 18:38:21.009003 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:21.009677 INFO::Starting hierarchical adjustment
2025-11-06 18:38:21.009954 INFO::Found 2 batches.
2025-11-06 18:38:21.010144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:21.010376 INFO::Using default BPPARAM
2025-11-06 18:38:21.010574 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:21.010871 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 18:38:21.023417 INFO::Done
2025-11-06 18:38:21.023709 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:21.024435 INFO::ASW Batch was -0.12313425239291 prior to batch effect correction and is now -0.163912063250352 .
2025-11-06 18:38:21.024727 INFO::Total function execution time is 0.0179991722106934 s and adjustment time is 0.01350998878479 s ( 75.06 )
2025-11-06 18:38:21.030678 INFO::Formatting Data.
2025-11-06 18:38:21.03095 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:21.031248 INFO::Removing potential empty rows and columns
2025-11-06 18:38:21.031615 INFO::Found 0 missing values.
2025-11-06 18:38:21.032097 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.
2025-11-06 18:38:21.033728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:21.033936 INFO::Done
2025-11-06 18:38:21.034107 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:21.035187 INFO::Starting hierarchical adjustment
2025-11-06 18:38:21.035431 INFO::Found 2 batches.
2025-11-06 18:38:21.035624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:21.035831 INFO::Using default BPPARAM
2025-11-06 18:38:21.036017 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:21.036322 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 18:38:21.042979 INFO::Done
2025-11-06 18:38:21.043297 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:21.044521 INFO::ASW Batch was 0.489507711240555 prior to batch effect correction and is now 0.00714173227876962 .
2025-11-06 18:38:21.044746 INFO::ASW Label was 0.601824932455385 prior to batch effect correction and is now 0.929270441459601 .
2025-11-06 18:38:21.045055 INFO::Total function execution time is 0.0144009590148926 s and adjustment time is 0.00756597518920898 s ( 52.54 )
2025-11-06 18:38:21.04533 INFO::Formatting Data.
2025-11-06 18:38:21.045515 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:21.04583 INFO::Removing potential empty rows and columns
2025-11-06 18:38:21.046169 INFO::Found 0 missing values.
2025-11-06 18:38:21.046461 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.
2025-11-06 18:38:21.047947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:21.048136 INFO::Done
2025-11-06 18:38:21.048333 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:21.049581 INFO::Starting hierarchical adjustment
2025-11-06 18:38:21.049875 INFO::Found 2 batches.
2025-11-06 18:38:21.050066 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:21.050289 INFO::Using default BPPARAM
2025-11-06 18:38:21.050445 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:21.050781 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 18:38:21.057838 INFO::Done
2025-11-06 18:38:21.058135 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:21.059309 INFO::ASW Batch was 0.489507711240555 prior to batch effect correction and is now 0.00714173227876962 .
2025-11-06 18:38:21.059531 INFO::ASW Label was 0.601824932455385 prior to batch effect correction and is now 0.929270441459601 .
2025-11-06 18:38:21.059822 INFO::Total function execution time is 0.014477014541626 s and adjustment time is 0.00800204277038574 s ( 55.27 )
2025-11-06 18:38:21.136139 INFO::Formatting Data.
2025-11-06 18:38:21.136453 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:21.13675 INFO::Removing potential empty rows and columns
2025-11-06 18:38:21.137123 INFO::Found 0 missing values.
2025-11-06 18:38:21.138038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:21.138224 INFO::Done
2025-11-06 18:38:21.13838 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:21.139042 INFO::Starting hierarchical adjustment
2025-11-06 18:38:21.139252 INFO::Found 3 batches.
2025-11-06 18:38:21.139408 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:21.139583 INFO::Using default BPPARAM
2025-11-06 18:38:21.139724 INFO::Processing subtree level 1
2025-11-06 18:38:21.184124 INFO::Adjusting the last 1 batches sequentially
2025-11-06 18:38:21.185514 INFO::Done
2025-11-06 18:38:21.185836 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:21.187403 INFO::ASW Batch was -0.0881208942094074 prior to batch effect correction and is now -0.0881208942094074 .
2025-11-06 18:38:21.187928 INFO::Total function execution time is 0.0518248081207275 s and adjustment time is 0.0462980270385742 s ( 89.34 )
2025-11-06 18:38:21.188292 INFO::Formatting Data.
2025-11-06 18:38:21.188499 INFO::Typecasting input to dataframe.
2025-11-06 18:38:21.188757 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:21.189065 INFO::Removing potential empty rows and columns
2025-11-06 18:38:21.189434 INFO::Found 0 missing values.
2025-11-06 18:38:21.190409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:21.191016 INFO::Done
2025-11-06 18:38:21.191309 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:21.192335 INFO::Starting hierarchical adjustment
2025-11-06 18:38:21.19269 INFO::Found 3 batches.
2025-11-06 18:38:21.192876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:21.193101 INFO::Using default BPPARAM
2025-11-06 18:38:21.193264 INFO::Processing subtree level 1
2025-11-06 18:38:21.229839 INFO::Adjusting the last 1 batches sequentially
2025-11-06 18:38:21.231513 INFO::Done
2025-11-06 18:38:21.231792 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:21.233133 INFO::ASW Batch was -0.0881208942094074 prior to batch effect correction and is now -0.0881208942094074 .
2025-11-06 18:38:21.233604 INFO::Total function execution time is 0.045292854309082 s and adjustment time is 0.038884162902832 s ( 85.85 )
2025-11-06 18:38:21.239743 INFO::Formatting Data.
2025-11-06 18:38:21.240041 INFO::Typecasting input to dataframe.
2025-11-06 18:38:21.240321 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:21.240626 INFO::Removing potential empty rows and columns
2025-11-06 18:38:21.241014 INFO::Found 0 missing values.
2025-11-06 18:38:21.241941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:21.242112 INFO::Done
2025-11-06 18:38:21.242293 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:21.242949 INFO::Starting hierarchical adjustment
2025-11-06 18:38:21.243175 INFO::Found 3 batches.
2025-11-06 18:38:21.243335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:21.24356 INFO::Using default BPPARAM
2025-11-06 18:38:21.247882 INFO::Processing subtree level 1
2025-11-06 18:38:21.290023 INFO::Adjusting the last 1 batches sequentially
2025-11-06 18:38:21.291451 INFO::Done
2025-11-06 18:38:21.291846 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:21.293356 INFO::ASW Batch was -0.0677353606146803 prior to batch effect correction and is now -0.0677353606146803 .
2025-11-06 18:38:21.293932 INFO::Total function execution time is 0.0541930198669434 s and adjustment time is 0.0483229160308838 s ( 89.17 )
2025-11-06 18:38:21.367091 INFO::Formatting Data.
2025-11-06 18:38:21.367555 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:21.367987 INFO::Removing potential empty rows and columns
2025-11-06 18:38:21.368953 INFO::Found 1000 missing values.
2025-11-06 18:38:21.37472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:21.374956 INFO::Done
2025-11-06 18:38:21.375151 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:21.377238 INFO::Starting hierarchical adjustment
2025-11-06 18:38:21.377517 INFO::Found 10 batches.
2025-11-06 18:38:21.377687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:21.377971 INFO::Using default BPPARAM
2025-11-06 18:38:21.378282 INFO::Processing subtree level 1
2025-11-06 18:38:21.442085 INFO::Processing subtree level 2
2025-11-06 18:38:21.513914 INFO::Adjusting the last 1 batches sequentially
2025-11-06 18:38:21.517396 INFO::Done
2025-11-06 18:38:21.518737 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:21.521683 INFO::ASW Batch was 0.422235445092243 prior to batch effect correction and is now 0.422235445092243 .
2025-11-06 18:38:21.521975 INFO::ASW Label was 0.403809565175064 prior to batch effect correction and is now 0.403809565175064 .
2025-11-06 18:38:21.522435 INFO::Total function execution time is 0.155344009399414 s and adjustment time is 0.139904022216797 s ( 90.06 )
2025-11-06 18:38:21.522784 INFO::Formatting Data.
2025-11-06 18:38:21.522991 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:21.523421 INFO::Removing potential empty rows and columns
2025-11-06 18:38:21.52443 INFO::Found 1000 missing values.
2025-11-06 18:38:21.530601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:21.530929 INFO::Done
2025-11-06 18:38:21.531126 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:21.533268 INFO::Starting hierarchical adjustment
2025-11-06 18:38:21.533562 INFO::Found 10 batches.
2025-11-06 18:38:21.978448 INFO::Set up parallel execution backend with 2 workers
2025-11-06 18:38:21.978734 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-06 18:38:22.492758 INFO::Adjusting the last 2 batches sequentially
2025-11-06 18:38:22.493356 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 18:38:22.498983 INFO::Done
2025-11-06 18:38:22.499212 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:22.501065 INFO::ASW Batch was 0.422235445092243 prior to batch effect correction and is now 0.422235445092243 .
2025-11-06 18:38:22.501252 INFO::ASW Label was 0.403809565175064 prior to batch effect correction and is now 0.403809565175064 .
2025-11-06 18:38:22.501493 INFO::Total function execution time is 0.978718996047974 s and adjustment time is 0.965476989746094 s ( 98.65 )
2025-11-06 18:38:22.574493 INFO::Formatting Data.
2025-11-06 18:38:22.574828 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.575346 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.575914 INFO::Found 0 missing values.
2025-11-06 18:38:22.577417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.577646 INFO::Done
2025-11-06 18:38:22.577885 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 18:38:22.579191 INFO::Starting hierarchical adjustment
2025-11-06 18:38:22.579519 INFO::Found 3 batches.
2025-11-06 18:38:22.57971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 18:38:22.579984 INFO::Using default BPPARAM
2025-11-06 18:38:22.580167 INFO::Processing subtree level 1
2025-11-06 18:38:22.635041 INFO::Adjusting the last 1 batches sequentially
2025-11-06 18:38:22.637223 INFO::Done
2025-11-06 18:38:22.63751 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 18:38:22.641864 INFO::ASW Batch was 0.184892455855461 prior to batch effect correction and is now -0.144639377580589 .
2025-11-06 18:38:22.64219 INFO::ASW Label was -0.189335561771923 prior to batch effect correction and is now -0.135367631370251 .
2025-11-06 18:38:22.642721 INFO::Total function execution time is 0.0682559013366699 s and adjustment time is 0.0577719211578369 s ( 84.64 )
2025-11-06 18:38:22.694053 INFO::Formatting Data.
2025-11-06 18:38:22.694392 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.69475 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.695209 INFO::Found 2 missing values.
2025-11-06 18:38:22.696255 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.696448 INFO::Done
2025-11-06 18:38:22.709289 INFO::Found NA in Reference column
2025-11-06 18:38:22.713415 INFO::Require at least two references per batch.
2025-11-06 18:38:22.722676 INFO::Formatting Data.
2025-11-06 18:38:22.722958 INFO::Recognized SummarizedExperiment
2025-11-06 18:38:22.723156 INFO::Typecasting input to dataframe.
2025-11-06 18:38:22.727807 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.728262 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.729784 INFO::Found 0 missing values.
2025-11-06 18:38:22.73262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.732827 INFO::Done
2025-11-06 18:38:22.739014 INFO::Formatting Data.
2025-11-06 18:38:22.739301 INFO::Recognized SummarizedExperiment
2025-11-06 18:38:22.739496 INFO::Typecasting input to dataframe.
2025-11-06 18:38:22.745865 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.746331 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.7477 INFO::Found 0 missing values.
2025-11-06 18:38:22.752711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.753036 INFO::Done
2025-11-06 18:38:22.75964 INFO::Formatting Data.
2025-11-06 18:38:22.759898 INFO::Recognized SummarizedExperiment
2025-11-06 18:38:22.760064 INFO::Typecasting input to dataframe.
2025-11-06 18:38:22.765593 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.76597 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.766352 INFO::Found 0 missing values.
2025-11-06 18:38:22.766653 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.
2025-11-06 18:38:22.768147 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.76834 INFO::Done
2025-11-06 18:38:22.7726 INFO::Formatting Data.
2025-11-06 18:38:22.772853 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.773146 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.773477 INFO::Found 0 missing values.
2025-11-06 18:38:22.77461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.77479 INFO::Done
2025-11-06 18:38:22.779246 INFO::Formatting Data.
2025-11-06 18:38:22.779507 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.779872 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.780232 INFO::Found 0 missing values.
2025-11-06 18:38:22.781359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.783498 INFO::Done
2025-11-06 18:38:22.796454 INFO::Formatting Data.
2025-11-06 18:38:22.798358 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.798811 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.799227 INFO::Found 1 missing values.
2025-11-06 18:38:22.800205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.800463 INFO::Done
2025-11-06 18:38:22.807733 INFO::Formatting Data.
2025-11-06 18:38:22.808004 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.808306 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.808614 INFO::Found 2 missing values.
2025-11-06 18:38:22.808952 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.
2025-11-06 18:38:22.809676 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.809881 INFO::Done
2025-11-06 18:38:22.813711 INFO::Formatting Data.
2025-11-06 18:38:22.813949 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.814221 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.814533 INFO::Found 2 missing values.
2025-11-06 18:38:22.815055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.815217 INFO::Done
2025-11-06 18:38:22.819124 INFO::Formatting Data.
2025-11-06 18:38:22.819361 INFO::Typecasting input to dataframe.
2025-11-06 18:38:22.819605 INFO::Replacing NaNs with NAs.
2025-11-06 18:38:22.819852 INFO::Removing potential empty rows and columns
2025-11-06 18:38:22.820241 INFO::Found 0 missing values.
2025-11-06 18:38:22.821141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 18:38:22.821297 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.834 1.754 8.718
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.794 | 0.477 | 7.241 | |
| compute_asw | 0.009 | 0.000 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.004 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |