Yannis Schumann
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 163/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2025-08-29 19:19:47 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 19:21:12 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 84.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* 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 26.834 1.465 19.215
* 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-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** 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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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")
2025-08-29 19:20:51.046146 INFO::Formatting Data.
2025-08-29 19:20:51.049488 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:51.06129 INFO::Removing potential empty rows and columns
2025-08-29 19:20:51.370163 INFO::Found 0 missing values.
2025-08-29 19:20:51.373736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:51.374724 INFO::Done
2025-08-29 19:20:51.375713 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:51.390901 INFO::Starting hierarchical adjustment
2025-08-29 19:20:51.392127 INFO::Found 3 batches.
2025-08-29 19:20:51.392747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:51.394468 INFO::Using default BPPARAM
2025-08-29 19:20:51.395132 INFO::Processing subtree level 1
2025-08-29 19:20:51.554887 INFO::Adjusting the last 1 batches sequentially
2025-08-29 19:20:51.560219 INFO::Done
2025-08-29 19:20:51.561209 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:51.566472 INFO::ASW Batch was -0.0163841368506903 prior to batch effect correction and is now -0.0163841368506903 .
2025-08-29 19:20:51.570041 INFO::Total function execution time is 0.523093938827515 s and adjustment time is 0.168190002441406 s ( 32.15 )
2025-08-29 19:20:51.592359 INFO::Formatting Data.
2025-08-29 19:20:51.593565 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:51.59506 INFO::Removing potential empty rows and columns
2025-08-29 19:20:51.596755 INFO::Found 0 missing values.
2025-08-29 19:20:51.597687 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.
2025-08-29 19:20:51.611803 INFO::Formatting Data.
2025-08-29 19:20:51.613077 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:51.614515 INFO::Removing potential empty rows and columns
2025-08-29 19:20:51.616142 INFO::Found 0 missing values.
2025-08-29 19:20:51.617565 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.
2025-08-29 19:20:51.638908 INFO::Formatting Data.
2025-08-29 19:20:51.640119 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:51.641526 INFO::Removing potential empty rows and columns
2025-08-29 19:20:51.643004 INFO::Found 0 missing values.
2025-08-29 19:20:51.643977 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.
2025-08-29 19:20:51.649139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:51.64979 INFO::Done
2025-08-29 19:20:51.650341 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:51.65261 INFO::Starting hierarchical adjustment
2025-08-29 19:20:51.653291 INFO::Found 2 batches.
2025-08-29 19:20:51.653818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:51.654773 INFO::Using default BPPARAM
2025-08-29 19:20:51.655299 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:51.656374 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 19:20:51.684867 INFO::Done
2025-08-29 19:20:51.685912 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:51.687951 INFO::ASW Batch was 0.0181909940612382 prior to batch effect correction and is now -0.100459455168775 .
2025-08-29 19:20:51.688928 INFO::Total function execution time is 0.0500369071960449 s and adjustment time is 0.0316741466522217 s ( 63.3 )
2025-08-29 19:20:51.692932 INFO::Formatting Data.
2025-08-29 19:20:51.693807 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:51.705249 INFO::Formatting Data.
2025-08-29 19:20:51.706395 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:51.707768 INFO::Removing potential empty rows and columns
2025-08-29 19:20:51.709036 INFO::Found 0 missing values.
2025-08-29 19:20:51.712685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:51.713276 INFO::Done
2025-08-29 19:20:51.714123 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:51.716787 INFO::Starting hierarchical adjustment
2025-08-29 19:20:51.717842 INFO::Found 2 batches.
2025-08-29 19:20:51.718628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:51.719569 INFO::Using default BPPARAM
2025-08-29 19:20:51.720404 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:51.721355 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 19:20:51.78072 INFO::Done
2025-08-29 19:20:51.781725 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:51.784583 INFO::ASW Batch was -0.075822077115495 prior to batch effect correction and is now -0.114994248215779 .
2025-08-29 19:20:51.785678 INFO::Total function execution time is 0.0805199146270752 s and adjustment time is 0.0630409717559814 s ( 78.29 )
2025-08-29 19:20:51.787199 INFO::Formatting Data.
2025-08-29 19:20:51.788068 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:51.789057 INFO::Removing potential empty rows and columns
2025-08-29 19:20:51.790241 INFO::Found 0 missing values.
2025-08-29 19:20:51.793968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:51.794689 INFO::Done
2025-08-29 19:20:51.795401 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:51.798053 INFO::Starting hierarchical adjustment
2025-08-29 19:20:51.7988 INFO::Found 2 batches.
2025-08-29 19:20:51.799262 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:51.79981 INFO::Using default BPPARAM
2025-08-29 19:20:51.800511 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:51.801668 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 19:20:51.82267 INFO::Done
2025-08-29 19:20:51.823353 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:51.825435 INFO::ASW Batch was -0.075822077115495 prior to batch effect correction and is now -0.114994248215779 .
2025-08-29 19:20:51.826566 INFO::Total function execution time is 0.0393569469451904 s and adjustment time is 0.0239560604095459 s ( 60.87 )
2025-08-29 19:20:55.142883 INFO::Formatting Data.
2025-08-29 19:20:55.143542 INFO::Recognized SummarizedExperiment
2025-08-29 19:20:55.144001 INFO::Typecasting input to dataframe.
2025-08-29 19:20:55.17964 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:55.181477 INFO::Removing potential empty rows and columns
2025-08-29 19:20:55.187052 INFO::Found 0 missing values.
2025-08-29 19:20:55.196292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:55.197326 INFO::Done
2025-08-29 19:20:55.198149 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:55.203 INFO::Starting hierarchical adjustment
2025-08-29 19:20:55.203844 INFO::Found 2 batches.
2025-08-29 19:20:55.204625 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:55.206101 INFO::Using default BPPARAM
2025-08-29 19:20:55.20684 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:55.208288 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 19:20:55.267083 INFO::Done
2025-08-29 19:20:55.267815 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:55.27279 INFO::ASW Batch was -0.0172768036362013 prior to batch effect correction and is now -0.0950382441226963 .
2025-08-29 19:20:55.274113 INFO::Total function execution time is 0.131383895874023 s and adjustment time is 0.0634498596191406 s ( 48.29 )
2025-08-29 19:20:55.302217 INFO::Formatting Data.
2025-08-29 19:20:55.303309 INFO::Recognized SummarizedExperiment
2025-08-29 19:20:55.304258 INFO::Typecasting input to dataframe.
2025-08-29 19:20:55.315994 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:55.317884 INFO::Removing potential empty rows and columns
2025-08-29 19:20:55.322418 INFO::Found 0 missing values.
2025-08-29 19:20:55.331597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:55.332469 INFO::Done
2025-08-29 19:20:55.333011 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:55.336337 INFO::Starting hierarchical adjustment
2025-08-29 19:20:55.33705 INFO::Found 2 batches.
2025-08-29 19:20:55.337532 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:55.33808 INFO::Using default BPPARAM
2025-08-29 19:20:55.33889 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:55.339785 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 19:20:55.367131 INFO::Done
2025-08-29 19:20:55.368079 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:55.373225 INFO::ASW Batch was 0.00686641701372077 prior to batch effect correction and is now 0.00686641701372077 .
2025-08-29 19:20:55.37451 INFO::Total function execution time is 0.0722880363464355 s and adjustment time is 0.030177116394043 s ( 41.75 )
2025-08-29 19:20:55.399725 INFO::Formatting Data.
2025-08-29 19:20:55.400462 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:55.401266 INFO::Removing potential empty rows and columns
2025-08-29 19:20:55.402827 INFO::Found 0 missing values.
2025-08-29 19:20:55.406746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:55.407516 INFO::Done
2025-08-29 19:20:55.408251 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:55.410228 INFO::Starting hierarchical adjustment
2025-08-29 19:20:55.410878 INFO::Found 3 batches.
2025-08-29 19:20:55.411342 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:55.411864 INFO::Using default BPPARAM
2025-08-29 19:20:55.412543 INFO::Processing subtree level 1
2025-08-29 19:20:55.611371 INFO::Adjusting the last 1 batches sequentially
2025-08-29 19:20:55.627623 INFO::Done
2025-08-29 19:20:55.628642 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:55.63624 INFO::ASW Batch was -0.136392877464843 prior to batch effect correction and is now -0.167642693340508 .
2025-08-29 19:20:55.63989 INFO::Total function execution time is 0.239169836044312 s and adjustment time is 0.216770887374878 s ( 90.63 )
2025-08-29 19:20:55.665628 INFO::Skipping initial DF formatting
2025-08-29 19:20:55.66671 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:55.673877 INFO::Starting hierarchical adjustment
2025-08-29 19:20:55.675204 INFO::Found 5 batches.
2025-08-29 19:20:55.675864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:55.67662 INFO::Using default BPPARAM
2025-08-29 19:20:55.677386 INFO::Processing subtree level 1
2025-08-29 19:20:56.035918 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:56.038405 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 19:20:56.096174 INFO::Done
2025-08-29 19:20:56.09728 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:56.113071 INFO::ASW Batch was 0.478699662797896 prior to batch effect correction and is now 0.478699662797896 .
2025-08-29 19:20:56.113956 INFO::ASW Label was 0.42176913621922 prior to batch effect correction and is now 0.42176913621922 .
2025-08-29 19:20:56.116447 INFO::Total function execution time is 0.450881004333496 s and adjustment time is 0.421238899230957 s ( 93.43 )
2025-08-29 19:20:56.22548 INFO::Formatting Data.
2025-08-29 19:20:56.226643 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:56.227995 INFO::Removing potential empty rows and columns
2025-08-29 19:20:56.229433 INFO::Found 0 missing values.
2025-08-29 19:20:56.23555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:56.236521 INFO::Done
2025-08-29 19:20:56.237351 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:56.241729 INFO::Starting hierarchical adjustment
2025-08-29 19:20:56.243013 INFO::Found 5 batches.
2025-08-29 19:20:56.243962 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:56.244942 INFO::Using default BPPARAM
2025-08-29 19:20:56.245752 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.
2025-08-29 19:20:56.462622 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:56.476882 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 19:20:56.517509 INFO::Done
2025-08-29 19:20:56.518261 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:56.523398 INFO::ASW Batch was 0.356576599759855 prior to batch effect correction and is now -0.0931170310593377 .
2025-08-29 19:20:56.524105 INFO::ASW Label was 0.371740050296378 prior to batch effect correction and is now 0.927182512172477 .
2025-08-29 19:20:56.524973 INFO::Total function execution time is 0.299635171890259 s and adjustment time is 0.274776935577393 s ( 91.7 )
2025-08-29 19:20:56.525895 INFO::Formatting Data.
2025-08-29 19:20:56.526548 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:56.52744 INFO::Removing potential empty rows and columns
2025-08-29 19:20:56.528502 INFO::Found 0 missing values.
2025-08-29 19:20:56.534872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:56.535996 INFO::Done
2025-08-29 19:20:56.536917 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:56.540892 INFO::Starting hierarchical adjustment
2025-08-29 19:20:56.541758 INFO::Found 5 batches.
2025-08-29 19:20:56.542636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:56.543553 INFO::Using default BPPARAM
2025-08-29 19:20:56.544409 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.
2025-08-29 19:20:56.739571 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:56.752324 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 19:20:56.787724 INFO::Done
2025-08-29 19:20:56.789624 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:56.796342 INFO::ASW Batch was 0.356576599759855 prior to batch effect correction and is now -0.0931170310593377 .
2025-08-29 19:20:56.797179 INFO::ASW Label was 0.371740050296378 prior to batch effect correction and is now 0.927182512172477 .
2025-08-29 19:20:56.799858 INFO::Total function execution time is 0.272579908370972 s and adjustment time is 0.246080160140991 s ( 90.28 )
2025-08-29 19:20:56.820745 INFO::Formatting Data.
2025-08-29 19:20:56.822091 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:56.823647 INFO::Removing potential empty rows and columns
2025-08-29 19:20:56.825747 INFO::Found 0 missing values.
2025-08-29 19:20:56.831223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:56.832177 INFO::Done
2025-08-29 19:20:56.833012 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:56.837461 INFO::Starting hierarchical adjustment
2025-08-29 19:20:56.838962 INFO::Found 5 batches.
2025-08-29 19:20:56.839814 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:56.840784 INFO::Using default BPPARAM
2025-08-29 19:20:56.841589 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.
2025-08-29 19:20:57.033659 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:57.044398 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 19:20:57.074856 INFO::Done
2025-08-29 19:20:57.07584 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:57.081063 INFO::ASW Batch was 0.444641148873731 prior to batch effect correction and is now -0.0563454331347212 .
2025-08-29 19:20:57.081857 INFO::ASW Label was 0.178854822394065 prior to batch effect correction and is now 0.795412362512962 .
2025-08-29 19:20:57.083372 INFO::Total function execution time is 0.26285982131958 s and adjustment time is 0.236189126968384 s ( 89.85 )
2025-08-29 19:20:57.084679 INFO::Formatting Data.
2025-08-29 19:20:57.085686 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:57.086865 INFO::Removing potential empty rows and columns
2025-08-29 19:20:57.088007 INFO::Found 0 missing values.
2025-08-29 19:20:57.093227 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:57.094023 INFO::Done
2025-08-29 19:20:57.094566 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:57.09902 INFO::Starting hierarchical adjustment
2025-08-29 19:20:57.10013 INFO::Found 5 batches.
2025-08-29 19:20:57.10098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:57.101943 INFO::Using default BPPARAM
2025-08-29 19:20:57.102504 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.
2025-08-29 19:20:57.311132 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:57.317738 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 19:20:57.346576 INFO::Done
2025-08-29 19:20:57.347582 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:57.352926 INFO::ASW Batch was 0.444641148873731 prior to batch effect correction and is now -0.0563454331347212 .
2025-08-29 19:20:57.354554 INFO::ASW Label was 0.178854822394065 prior to batch effect correction and is now 0.795412362512962 .
2025-08-29 19:20:57.356032 INFO::Total function execution time is 0.271320819854736 s and adjustment time is 0.246770143508911 s ( 90.95 )
2025-08-29 19:20:57.378263 INFO::Formatting Data.
2025-08-29 19:20:57.379408 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:57.380774 INFO::Removing potential empty rows and columns
2025-08-29 19:20:57.382142 INFO::Found 0 missing values.
2025-08-29 19:20:57.386437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:57.387354 INFO::Done
2025-08-29 19:20:57.388135 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:57.39238 INFO::Starting hierarchical adjustment
2025-08-29 19:20:57.393583 INFO::Found 2 batches.
2025-08-29 19:20:57.394555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:57.39546 INFO::Using default BPPARAM
2025-08-29 19:20:57.39626 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:57.39752 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 19:20:57.414334 INFO::Done
2025-08-29 19:20:57.415009 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:57.419215 INFO::ASW Batch was 0.542987650169201 prior to batch effect correction and is now 0.0736084722394486 .
2025-08-29 19:20:57.420241 INFO::ASW Label was 0.583069664285178 prior to batch effect correction and is now 0.889811780599215 .
2025-08-29 19:20:57.421234 INFO::Total function execution time is 0.0430450439453125 s and adjustment time is 0.0210959911346436 s ( 49.01 )
2025-08-29 19:20:57.421988 INFO::Formatting Data.
2025-08-29 19:20:57.422747 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:57.424002 INFO::Removing potential empty rows and columns
2025-08-29 19:20:57.425419 INFO::Found 0 missing values.
2025-08-29 19:20:57.429568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:57.430186 INFO::Done
2025-08-29 19:20:57.430706 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:57.433371 INFO::Starting hierarchical adjustment
2025-08-29 19:20:57.434086 INFO::Found 2 batches.
2025-08-29 19:20:57.434589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:57.435138 INFO::Using default BPPARAM
2025-08-29 19:20:57.43562 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:57.436464 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 19:20:57.450209 INFO::Done
2025-08-29 19:20:57.450915 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:57.453713 INFO::ASW Batch was 0.542987650169201 prior to batch effect correction and is now 0.0736084722394486 .
2025-08-29 19:20:57.454334 INFO::ASW Label was 0.583069664285178 prior to batch effect correction and is now 0.889811780599215 .
2025-08-29 19:20:57.455081 INFO::Total function execution time is 0.0331149101257324 s and adjustment time is 0.0162370204925537 s ( 49.03 )
2025-08-29 19:20:57.471045 INFO::Formatting Data.
2025-08-29 19:20:57.471967 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:57.473392 INFO::Removing potential empty rows and columns
2025-08-29 19:20:57.474601 INFO::Found 0 missing values.
2025-08-29 19:20:57.477006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:57.477595 INFO::Done
2025-08-29 19:20:57.478109 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:57.479999 INFO::Starting hierarchical adjustment
2025-08-29 19:20:57.48102 INFO::Found 2 batches.
2025-08-29 19:20:57.481798 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:57.482679 INFO::Using default BPPARAM
2025-08-29 19:20:57.483446 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:57.484762 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 19:20:57.524318 INFO::Done
2025-08-29 19:20:57.525018 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:57.526897 INFO::ASW Batch was 0.0855113926648032 prior to batch effect correction and is now -0.141310767243414 .
2025-08-29 19:20:57.527993 INFO::Total function execution time is 0.0569648742675781 s and adjustment time is 0.0435218811035156 s ( 76.4 )
2025-08-29 19:20:57.545067 INFO::Formatting Data.
2025-08-29 19:20:57.54619 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:57.547453 INFO::Removing potential empty rows and columns
2025-08-29 19:20:57.548826 INFO::Found 0 missing values.
2025-08-29 19:20:57.55034 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.
2025-08-29 19:20:57.557013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:57.55801 INFO::Done
2025-08-29 19:20:57.558974 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:57.562069 INFO::Starting hierarchical adjustment
2025-08-29 19:20:57.562831 INFO::Found 2 batches.
2025-08-29 19:20:57.563596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:57.564451 INFO::Using default BPPARAM
2025-08-29 19:20:57.565211 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:57.566577 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 19:20:57.583512 INFO::Done
2025-08-29 19:20:57.584478 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:57.588544 INFO::ASW Batch was 0.649096172927233 prior to batch effect correction and is now 0.0110817488033907 .
2025-08-29 19:20:57.589421 INFO::ASW Label was 0.35036084290477 prior to batch effect correction and is now 0.88977756110722 .
2025-08-29 19:20:57.590547 INFO::Total function execution time is 0.0455999374389648 s and adjustment time is 0.0207979679107666 s ( 45.61 )
2025-08-29 19:20:57.591614 INFO::Formatting Data.
2025-08-29 19:20:57.592448 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:57.593455 INFO::Removing potential empty rows and columns
2025-08-29 19:20:57.594378 INFO::Found 0 missing values.
2025-08-29 19:20:57.595312 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.
2025-08-29 19:20:57.602668 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:57.603658 INFO::Done
2025-08-29 19:20:57.604488 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:57.608771 INFO::Starting hierarchical adjustment
2025-08-29 19:20:57.609572 INFO::Found 2 batches.
2025-08-29 19:20:57.610091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:57.610653 INFO::Using default BPPARAM
2025-08-29 19:20:57.611155 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:20:57.612484 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 19:20:57.630258 INFO::Done
2025-08-29 19:20:57.631238 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:57.63519 INFO::ASW Batch was 0.649096172927233 prior to batch effect correction and is now 0.0110817488033907 .
2025-08-29 19:20:57.635902 INFO::ASW Label was 0.35036084290477 prior to batch effect correction and is now 0.88977756110722 .
2025-08-29 19:20:57.637086 INFO::Total function execution time is 0.0454809665679932 s and adjustment time is 0.0208079814910889 s ( 45.75 )
2025-08-29 19:20:57.879546 INFO::Formatting Data.
2025-08-29 19:20:57.880292 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:57.881109 INFO::Removing potential empty rows and columns
2025-08-29 19:20:57.882188 INFO::Found 0 missing values.
2025-08-29 19:20:57.886214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:57.88702 INFO::Done
2025-08-29 19:20:57.887719 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:57.890631 INFO::Starting hierarchical adjustment
2025-08-29 19:20:57.8914 INFO::Found 3 batches.
2025-08-29 19:20:57.89188 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:57.892413 INFO::Using default BPPARAM
2025-08-29 19:20:57.892881 INFO::Processing subtree level 1
2025-08-29 19:20:58.010324 INFO::Adjusting the last 1 batches sequentially
2025-08-29 19:20:58.02453 INFO::Done
2025-08-29 19:20:58.025573 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:58.032623 INFO::ASW Batch was -0.0997712434083838 prior to batch effect correction and is now -0.0997712434083838 .
2025-08-29 19:20:58.035724 INFO::Total function execution time is 0.154994010925293 s and adjustment time is 0.133170127868652 s ( 85.92 )
2025-08-29 19:20:58.038301 INFO::Formatting Data.
2025-08-29 19:20:58.040407 INFO::Typecasting input to dataframe.
2025-08-29 19:20:58.041575 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:58.043551 INFO::Removing potential empty rows and columns
2025-08-29 19:20:58.045638 INFO::Found 0 missing values.
2025-08-29 19:20:58.05084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:58.052002 INFO::Done
2025-08-29 19:20:58.052554 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:58.054568 INFO::Starting hierarchical adjustment
2025-08-29 19:20:58.055289 INFO::Found 3 batches.
2025-08-29 19:20:58.055961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:58.05684 INFO::Using default BPPARAM
2025-08-29 19:20:58.057979 INFO::Processing subtree level 1
2025-08-29 19:20:58.170977 INFO::Adjusting the last 1 batches sequentially
2025-08-29 19:20:58.186003 INFO::Done
2025-08-29 19:20:58.187592 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:58.196468 INFO::ASW Batch was -0.0997712434083838 prior to batch effect correction and is now -0.0997712434083838 .
2025-08-29 19:20:58.199734 INFO::Total function execution time is 0.160501003265381 s and adjustment time is 0.130365133285522 s ( 81.22 )
2025-08-29 19:20:58.228344 INFO::Formatting Data.
2025-08-29 19:20:58.229926 INFO::Typecasting input to dataframe.
2025-08-29 19:20:58.231546 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:58.232833 INFO::Removing potential empty rows and columns
2025-08-29 19:20:58.235299 INFO::Found 0 missing values.
2025-08-29 19:20:58.239263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:58.240093 INFO::Done
2025-08-29 19:20:58.240961 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:58.244133 INFO::Starting hierarchical adjustment
2025-08-29 19:20:58.245378 INFO::Found 3 batches.
2025-08-29 19:20:58.245985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:58.246591 INFO::Using default BPPARAM
2025-08-29 19:20:58.24713 INFO::Processing subtree level 1
2025-08-29 19:20:58.379012 INFO::Adjusting the last 1 batches sequentially
2025-08-29 19:20:58.386959 INFO::Done
2025-08-29 19:20:58.388722 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:58.394506 INFO::ASW Batch was -0.0788060855613163 prior to batch effect correction and is now -0.0788060855613163 .
2025-08-29 19:20:58.397395 INFO::Total function execution time is 0.16840386390686 s and adjustment time is 0.142052888870239 s ( 84.35 )
2025-08-29 19:20:58.585743 INFO::Formatting Data.
2025-08-29 19:20:58.586758 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:58.588811 INFO::Removing potential empty rows and columns
2025-08-29 19:20:58.593774 INFO::Found 1000 missing values.
2025-08-29 19:20:58.620747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:58.621683 INFO::Done
2025-08-29 19:20:58.62236 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:58.627898 INFO::Starting hierarchical adjustment
2025-08-29 19:20:58.629157 INFO::Found 10 batches.
2025-08-29 19:20:58.629864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:20:58.630626 INFO::Using default BPPARAM
2025-08-29 19:20:58.631445 INFO::Processing subtree level 1
2025-08-29 19:20:58.769976 INFO::Processing subtree level 2
2025-08-29 19:20:58.9409 INFO::Adjusting the last 1 batches sequentially
2025-08-29 19:20:58.945165 INFO::Done
2025-08-29 19:20:58.94598 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:20:58.952371 INFO::ASW Batch was 0.515064287863682 prior to batch effect correction and is now 0.515064287863682 .
2025-08-29 19:20:58.953546 INFO::ASW Label was 0.321919991595797 prior to batch effect correction and is now 0.321919991595797 .
2025-08-29 19:20:58.954596 INFO::Total function execution time is 0.368906021118164 s and adjustment time is 0.316228866577148 s ( 85.72 )
2025-08-29 19:20:58.955446 INFO::Formatting Data.
2025-08-29 19:20:58.956113 INFO::Replacing NaNs with NAs.
2025-08-29 19:20:58.957318 INFO::Removing potential empty rows and columns
2025-08-29 19:20:58.96174 INFO::Found 1000 missing values.
2025-08-29 19:20:58.980911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:20:58.981772 INFO::Done
2025-08-29 19:20:58.982347 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:20:58.987682 INFO::Starting hierarchical adjustment
2025-08-29 19:20:58.988503 INFO::Found 10 batches.
2025-08-29 19:21:00.406187 INFO::Set up parallel execution backend with 2 workers
2025-08-29 19:21:00.407028 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-29 19:21:01.741734 INFO::Adjusting the last 2 batches sequentially
2025-08-29 19:21:01.743319 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 19:21:01.765521 INFO::Done
2025-08-29 19:21:01.766473 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:21:01.770711 INFO::ASW Batch was 0.515064287863682 prior to batch effect correction and is now 0.515064287863682 .
2025-08-29 19:21:01.771291 INFO::ASW Label was 0.321919991595797 prior to batch effect correction and is now 0.321919991595797 .
2025-08-29 19:21:01.771962 INFO::Total function execution time is 2.81653881072998 s and adjustment time is 2.77703976631165 s ( 98.6 )
2025-08-29 19:21:02.003152 INFO::Formatting Data.
2025-08-29 19:21:02.00504 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.006961 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.008702 INFO::Found 0 missing values.
2025-08-29 19:21:02.012898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.01378 INFO::Done
2025-08-29 19:21:02.014544 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 19:21:02.017461 INFO::Starting hierarchical adjustment
2025-08-29 19:21:02.018124 INFO::Found 3 batches.
2025-08-29 19:21:02.018588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 19:21:02.019549 INFO::Using default BPPARAM
2025-08-29 19:21:02.020032 INFO::Processing subtree level 1
2025-08-29 19:21:02.165668 INFO::Adjusting the last 1 batches sequentially
2025-08-29 19:21:02.180734 INFO::Done
2025-08-29 19:21:02.184403 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 19:21:02.21123 INFO::ASW Batch was 0.293088283498618 prior to batch effect correction and is now -0.16319253330639 .
2025-08-29 19:21:02.214834 INFO::ASW Label was -0.205351386780945 prior to batch effect correction and is now -0.0793580747168809 .
2025-08-29 19:21:02.220381 INFO::Total function execution time is 0.21557092666626 s and adjustment time is 0.162683010101318 s ( 75.47 )
2025-08-29 19:21:02.413096 INFO::Formatting Data.
2025-08-29 19:21:02.413942 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.414838 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.41584 INFO::Found 2 missing values.
2025-08-29 19:21:02.418396 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.418909 INFO::Done
2025-08-29 19:21:02.458807 INFO::Found NA in Reference column
2025-08-29 19:21:02.474074 INFO::Require at least two references per batch.
2025-08-29 19:21:02.505621 INFO::Formatting Data.
2025-08-29 19:21:02.507652 INFO::Recognized SummarizedExperiment
2025-08-29 19:21:02.50849 INFO::Typecasting input to dataframe.
2025-08-29 19:21:02.523154 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.524329 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.529099 INFO::Found 0 missing values.
2025-08-29 19:21:02.535677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.536343 INFO::Done
2025-08-29 19:21:02.557683 INFO::Formatting Data.
2025-08-29 19:21:02.558564 INFO::Recognized SummarizedExperiment
2025-08-29 19:21:02.559348 INFO::Typecasting input to dataframe.
2025-08-29 19:21:02.580887 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.582022 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.584985 INFO::Found 0 missing values.
2025-08-29 19:21:02.595823 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.596474 INFO::Done
2025-08-29 19:21:02.615226 INFO::Formatting Data.
2025-08-29 19:21:02.615944 INFO::Recognized SummarizedExperiment
2025-08-29 19:21:02.616462 INFO::Typecasting input to dataframe.
2025-08-29 19:21:02.63655 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.637545 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.638975 INFO::Found 0 missing values.
2025-08-29 19:21:02.640338 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.
2025-08-29 19:21:02.64629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.646978 INFO::Done
2025-08-29 19:21:02.662805 INFO::Formatting Data.
2025-08-29 19:21:02.6636 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.664506 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.665732 INFO::Found 0 missing values.
2025-08-29 19:21:02.668703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.669461 INFO::Done
2025-08-29 19:21:02.687307 INFO::Formatting Data.
2025-08-29 19:21:02.688089 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.688923 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.689885 INFO::Found 0 missing values.
2025-08-29 19:21:02.692495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.693295 INFO::Done
2025-08-29 19:21:02.7428 INFO::Formatting Data.
2025-08-29 19:21:02.743966 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.74547 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.7472 INFO::Found 1 missing values.
2025-08-29 19:21:02.751183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.751917 INFO::Done
2025-08-29 19:21:02.78823 INFO::Formatting Data.
2025-08-29 19:21:02.789388 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.790714 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.792124 INFO::Found 2 missing values.
2025-08-29 19:21:02.793476 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.
2025-08-29 19:21:02.797086 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.798028 INFO::Done
2025-08-29 19:21:02.817265 INFO::Formatting Data.
2025-08-29 19:21:02.818398 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.819673 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.820597 INFO::Found 2 missing values.
2025-08-29 19:21:02.822063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.82256 INFO::Done
2025-08-29 19:21:02.837142 INFO::Formatting Data.
2025-08-29 19:21:02.837905 INFO::Typecasting input to dataframe.
2025-08-29 19:21:02.838682 INFO::Replacing NaNs with NAs.
2025-08-29 19:21:02.839494 INFO::Removing potential empty rows and columns
2025-08-29 19:21:02.840403 INFO::Found 0 missing values.
2025-08-29 19:21:02.842882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 19:21:02.843372 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.334 4.531 25.116
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.834 | 1.465 | 19.215 | |
| compute_asw | 0.026 | 0.001 | 0.027 | |
| count_existing | 0.017 | 0.001 | 0.018 | |
| generate_data_covariables | 0.011 | 0.001 | 0.013 | |
| generate_dataset | 0.014 | 0.000 | 0.015 | |