Yannis Schumann
| Snapshot Date: 2025-08-15 13:45 -0400 (Fri, 15 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 2025-08-16 12:04 -0400 (Sat, 16 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" | 4818 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 162/2317 | 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: 2025-08-15 19:20:51 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 19:22:16 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 84.5 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 27.434 1.495 19.653
* 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")
2025-08-15 19:21:54.790528 INFO::Formatting Data.
2025-08-15 19:21:54.794062 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:54.810534 INFO::Removing potential empty rows and columns
2025-08-15 19:21:55.138512 INFO::Found 0 missing values.
2025-08-15 19:21:55.142249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:21:55.142907 INFO::Done
2025-08-15 19:21:55.143429 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:21:55.160152 INFO::Starting hierarchical adjustment
2025-08-15 19:21:55.161531 INFO::Found 3 batches.
2025-08-15 19:21:55.162429 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:21:55.163844 INFO::Using default BPPARAM
2025-08-15 19:21:55.164656 INFO::Processing subtree level 1
2025-08-15 19:21:55.317918 INFO::Adjusting the last 1 batches sequentially
2025-08-15 19:21:55.325762 INFO::Done
2025-08-15 19:21:55.327501 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:21:55.332938 INFO::ASW Batch was -0.0661011053569423 prior to batch effect correction and is now -0.0661011053569423 .
2025-08-15 19:21:55.335356 INFO::Total function execution time is 0.545296907424927 s and adjustment time is 0.164524078369141 s ( 30.17 )
2025-08-15 19:21:55.356841 INFO::Formatting Data.
2025-08-15 19:21:55.35881 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:55.360456 INFO::Removing potential empty rows and columns
2025-08-15 19:21:55.362055 INFO::Found 0 missing values.
2025-08-15 19:21:55.363419 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.
2025-08-15 19:21:55.379144 INFO::Formatting Data.
2025-08-15 19:21:55.38013 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:55.381111 INFO::Removing potential empty rows and columns
2025-08-15 19:21:55.382925 INFO::Found 0 missing values.
2025-08-15 19:21:55.383994 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.
2025-08-15 19:21:55.404471 INFO::Formatting Data.
2025-08-15 19:21:55.405274 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:55.406455 INFO::Removing potential empty rows and columns
2025-08-15 19:21:55.407438 INFO::Found 0 missing values.
2025-08-15 19:21:55.4083 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.
2025-08-15 19:21:55.412262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:21:55.41282 INFO::Done
2025-08-15 19:21:55.413332 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:21:55.416343 INFO::Starting hierarchical adjustment
2025-08-15 19:21:55.41736 INFO::Found 2 batches.
2025-08-15 19:21:55.418174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:21:55.418827 INFO::Using default BPPARAM
2025-08-15 19:21:55.419697 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:21:55.421046 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 19:21:55.453003 INFO::Done
2025-08-15 19:21:55.453729 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:21:55.455864 INFO::ASW Batch was 0.0217083109110414 prior to batch effect correction and is now -0.121670525639135 .
2025-08-15 19:21:55.456926 INFO::Total function execution time is 0.0525200366973877 s and adjustment time is 0.035836935043335 s ( 68.23 )
2025-08-15 19:21:55.459875 INFO::Formatting Data.
2025-08-15 19:21:55.460491 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:55.471964 INFO::Formatting Data.
2025-08-15 19:21:55.472931 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:55.474742 INFO::Removing potential empty rows and columns
2025-08-15 19:21:55.476418 INFO::Found 0 missing values.
2025-08-15 19:21:55.479847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:21:55.480416 INFO::Done
2025-08-15 19:21:55.480908 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:21:55.48298 INFO::Starting hierarchical adjustment
2025-08-15 19:21:55.483996 INFO::Found 2 batches.
2025-08-15 19:21:55.484827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:21:55.485744 INFO::Using default BPPARAM
2025-08-15 19:21:55.48655 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:21:55.487878 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 19:21:55.548383 INFO::Done
2025-08-15 19:21:55.549165 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:21:55.552044 INFO::ASW Batch was -0.0482567501374994 prior to batch effect correction and is now -0.114913956409257 .
2025-08-15 19:21:55.553211 INFO::Total function execution time is 0.0813679695129395 s and adjustment time is 0.0645260810852051 s ( 79.3 )
2025-08-15 19:21:55.554683 INFO::Formatting Data.
2025-08-15 19:21:55.555562 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:55.556611 INFO::Removing potential empty rows and columns
2025-08-15 19:21:55.557547 INFO::Found 0 missing values.
2025-08-15 19:21:55.560959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:21:55.561745 INFO::Done
2025-08-15 19:21:55.562256 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:21:55.565112 INFO::Starting hierarchical adjustment
2025-08-15 19:21:55.566138 INFO::Found 2 batches.
2025-08-15 19:21:55.566881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:21:55.567708 INFO::Using default BPPARAM
2025-08-15 19:21:55.568436 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:21:55.569751 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 19:21:55.587682 INFO::Done
2025-08-15 19:21:55.58862 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:21:55.591589 INFO::ASW Batch was -0.0482567501374994 prior to batch effect correction and is now -0.114913956409257 .
2025-08-15 19:21:55.592463 INFO::Total function execution time is 0.0378310680389404 s and adjustment time is 0.0217080116271973 s ( 57.38 )
2025-08-15 19:21:59.131343 INFO::Formatting Data.
2025-08-15 19:21:59.132335 INFO::Recognized SummarizedExperiment
2025-08-15 19:21:59.133101 INFO::Typecasting input to dataframe.
2025-08-15 19:21:59.171866 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:59.173668 INFO::Removing potential empty rows and columns
2025-08-15 19:21:59.179047 INFO::Found 0 missing values.
2025-08-15 19:21:59.187806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:21:59.188749 INFO::Done
2025-08-15 19:21:59.189609 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:21:59.193742 INFO::Starting hierarchical adjustment
2025-08-15 19:21:59.194814 INFO::Found 2 batches.
2025-08-15 19:21:59.195583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:21:59.197051 INFO::Using default BPPARAM
2025-08-15 19:21:59.197782 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:21:59.199283 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 19:21:59.261956 INFO::Done
2025-08-15 19:21:59.262665 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:21:59.267555 INFO::ASW Batch was -0.00759643030861081 prior to batch effect correction and is now -0.092687676151594 .
2025-08-15 19:21:59.268853 INFO::Total function execution time is 0.137836933135986 s and adjustment time is 0.0673618316650391 s ( 48.87 )
2025-08-15 19:21:59.296482 INFO::Formatting Data.
2025-08-15 19:21:59.297594 INFO::Recognized SummarizedExperiment
2025-08-15 19:21:59.298446 INFO::Typecasting input to dataframe.
2025-08-15 19:21:59.3097 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:59.311316 INFO::Removing potential empty rows and columns
2025-08-15 19:21:59.315361 INFO::Found 0 missing values.
2025-08-15 19:21:59.324351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:21:59.325219 INFO::Done
2025-08-15 19:21:59.326027 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:21:59.33042 INFO::Starting hierarchical adjustment
2025-08-15 19:21:59.33162 INFO::Found 2 batches.
2025-08-15 19:21:59.332461 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:21:59.333341 INFO::Using default BPPARAM
2025-08-15 19:21:59.334082 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:21:59.335054 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 19:21:59.368107 INFO::Done
2025-08-15 19:21:59.368834 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:21:59.372695 INFO::ASW Batch was 0.0167226592106084 prior to batch effect correction and is now 0.0167226592106084 .
2025-08-15 19:21:59.373833 INFO::Total function execution time is 0.0772528648376465 s and adjustment time is 0.0367169380187988 s ( 47.53 )
2025-08-15 19:21:59.398456 INFO::Formatting Data.
2025-08-15 19:21:59.399493 INFO::Replacing NaNs with NAs.
2025-08-15 19:21:59.400882 INFO::Removing potential empty rows and columns
2025-08-15 19:21:59.402468 INFO::Found 0 missing values.
2025-08-15 19:21:59.405289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:21:59.405863 INFO::Done
2025-08-15 19:21:59.406353 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:21:59.408173 INFO::Starting hierarchical adjustment
2025-08-15 19:21:59.408836 INFO::Found 3 batches.
2025-08-15 19:21:59.4093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:21:59.409817 INFO::Using default BPPARAM
2025-08-15 19:21:59.410277 INFO::Processing subtree level 1
2025-08-15 19:21:59.605299 INFO::Adjusting the last 1 batches sequentially
2025-08-15 19:21:59.631734 INFO::Done
2025-08-15 19:21:59.633035 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:21:59.644542 INFO::ASW Batch was -0.0556097313929038 prior to batch effect correction and is now -0.138147959873232 .
2025-08-15 19:21:59.647216 INFO::Total function execution time is 0.248091220855713 s and adjustment time is 0.222992181777954 s ( 89.88 )
2025-08-15 19:21:59.67215 INFO::Skipping initial DF formatting
2025-08-15 19:21:59.673194 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:21:59.677857 INFO::Starting hierarchical adjustment
2025-08-15 19:21:59.678955 INFO::Found 5 batches.
2025-08-15 19:21:59.679547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:21:59.680198 INFO::Using default BPPARAM
2025-08-15 19:21:59.680804 INFO::Processing subtree level 1
2025-08-15 19:22:00.215051 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:00.218698 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 19:22:00.29438 INFO::Done
2025-08-15 19:22:00.2974 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:00.313582 INFO::ASW Batch was 0.56252201344544 prior to batch effect correction and is now 0.56252201344544 .
2025-08-15 19:22:00.31441 INFO::ASW Label was 0.327205370133333 prior to batch effect correction and is now 0.327205370133333 .
2025-08-15 19:22:00.318529 INFO::Total function execution time is 0.646431922912598 s and adjustment time is 0.615607023239136 s ( 95.23 )
2025-08-15 19:22:00.425181 INFO::Formatting Data.
2025-08-15 19:22:00.426221 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:00.427394 INFO::Removing potential empty rows and columns
2025-08-15 19:22:00.428746 INFO::Found 0 missing values.
2025-08-15 19:22:00.434792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:00.435711 INFO::Done
2025-08-15 19:22:00.436596 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:00.44083 INFO::Starting hierarchical adjustment
2025-08-15 19:22:00.442012 INFO::Found 5 batches.
2025-08-15 19:22:00.442842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:00.443786 INFO::Using default BPPARAM
2025-08-15 19:22:00.44456 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.
2025-08-15 19:22:00.670258 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:00.679699 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 19:22:00.716077 INFO::Done
2025-08-15 19:22:00.717465 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:00.722897 INFO::ASW Batch was 0.417079340026405 prior to batch effect correction and is now -0.0932723592679584 .
2025-08-15 19:22:00.723926 INFO::ASW Label was 0.374372025705566 prior to batch effect correction and is now 0.888895268737973 .
2025-08-15 19:22:00.725171 INFO::Total function execution time is 0.300036907196045 s and adjustment time is 0.274257898330688 s ( 91.41 )
2025-08-15 19:22:00.726427 INFO::Formatting Data.
2025-08-15 19:22:00.727503 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:00.729269 INFO::Removing potential empty rows and columns
2025-08-15 19:22:00.730785 INFO::Found 0 missing values.
2025-08-15 19:22:00.737035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:00.738334 INFO::Done
2025-08-15 19:22:00.739316 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:00.744092 INFO::Starting hierarchical adjustment
2025-08-15 19:22:00.745383 INFO::Found 5 batches.
2025-08-15 19:22:00.746259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:00.747148 INFO::Using default BPPARAM
2025-08-15 19:22:00.747957 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.
2025-08-15 19:22:00.946009 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:00.957157 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 19:22:00.989726 INFO::Done
2025-08-15 19:22:00.991262 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:00.997526 INFO::ASW Batch was 0.417079340026405 prior to batch effect correction and is now -0.0932723592679584 .
2025-08-15 19:22:00.998813 INFO::ASW Label was 0.374372025705566 prior to batch effect correction and is now 0.888895268737973 .
2025-08-15 19:22:01.0002 INFO::Total function execution time is 0.273722171783447 s and adjustment time is 0.24458384513855 s ( 89.35 )
2025-08-15 19:22:01.022941 INFO::Formatting Data.
2025-08-15 19:22:01.024196 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:01.025689 INFO::Removing potential empty rows and columns
2025-08-15 19:22:01.027289 INFO::Found 0 missing values.
2025-08-15 19:22:01.032337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:01.032995 INFO::Done
2025-08-15 19:22:01.033517 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:01.038216 INFO::Starting hierarchical adjustment
2025-08-15 19:22:01.0396 INFO::Found 5 batches.
2025-08-15 19:22:01.040518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:01.041516 INFO::Using default BPPARAM
2025-08-15 19:22:01.042339 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.
2025-08-15 19:22:01.254358 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:01.264325 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 19:22:01.296582 INFO::Done
2025-08-15 19:22:01.297997 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:01.304973 INFO::ASW Batch was 0.334640948812153 prior to batch effect correction and is now -0.0612061694951511 .
2025-08-15 19:22:01.306586 INFO::ASW Label was 0.312640709065895 prior to batch effect correction and is now 0.789070669848885 .
2025-08-15 19:22:01.307933 INFO::Total function execution time is 0.285088062286377 s and adjustment time is 0.257266998291016 s ( 90.24 )
2025-08-15 19:22:01.3094 INFO::Formatting Data.
2025-08-15 19:22:01.310113 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:01.311072 INFO::Removing potential empty rows and columns
2025-08-15 19:22:01.312177 INFO::Found 0 missing values.
2025-08-15 19:22:01.31586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:01.316445 INFO::Done
2025-08-15 19:22:01.316988 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:01.321453 INFO::Starting hierarchical adjustment
2025-08-15 19:22:01.323161 INFO::Found 5 batches.
2025-08-15 19:22:01.324255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:01.325124 INFO::Using default BPPARAM
2025-08-15 19:22:01.325826 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.
2025-08-15 19:22:01.504851 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:01.508135 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 19:22:01.541958 INFO::Done
2025-08-15 19:22:01.543382 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:01.549196 INFO::ASW Batch was 0.334640948812153 prior to batch effect correction and is now -0.0612061694951511 .
2025-08-15 19:22:01.55055 INFO::ASW Label was 0.312640709065895 prior to batch effect correction and is now 0.789070669848885 .
2025-08-15 19:22:01.551932 INFO::Total function execution time is 0.242549896240234 s and adjustment time is 0.219525098800659 s ( 90.51 )
2025-08-15 19:22:01.582286 INFO::Formatting Data.
2025-08-15 19:22:01.583683 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:01.585431 INFO::Removing potential empty rows and columns
2025-08-15 19:22:01.587479 INFO::Found 0 missing values.
2025-08-15 19:22:01.591585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:01.592602 INFO::Done
2025-08-15 19:22:01.593465 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:01.598862 INFO::Starting hierarchical adjustment
2025-08-15 19:22:01.600246 INFO::Found 2 batches.
2025-08-15 19:22:01.601276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:01.602398 INFO::Using default BPPARAM
2025-08-15 19:22:01.603314 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:01.604649 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 19:22:01.627316 INFO::Done
2025-08-15 19:22:01.628553 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:01.633831 INFO::ASW Batch was 0.521364405589158 prior to batch effect correction and is now 0.00581006030690831 .
2025-08-15 19:22:01.63524 INFO::ASW Label was 0.539832535949822 prior to batch effect correction and is now 0.922224039469382 .
2025-08-15 19:22:01.636702 INFO::Total function execution time is 0.0545029640197754 s and adjustment time is 0.0272901058197021 s ( 50.07 )
2025-08-15 19:22:01.637838 INFO::Formatting Data.
2025-08-15 19:22:01.639656 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:01.641224 INFO::Removing potential empty rows and columns
2025-08-15 19:22:01.643069 INFO::Found 0 missing values.
2025-08-15 19:22:01.648224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:01.649086 INFO::Done
2025-08-15 19:22:01.649781 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:01.654919 INFO::Starting hierarchical adjustment
2025-08-15 19:22:01.657945 INFO::Found 2 batches.
2025-08-15 19:22:01.659045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:01.660125 INFO::Using default BPPARAM
2025-08-15 19:22:01.661045 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:01.662698 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 19:22:01.687691 INFO::Done
2025-08-15 19:22:01.688692 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:01.692367 INFO::ASW Batch was 0.521364405589158 prior to batch effect correction and is now 0.00581006030690831 .
2025-08-15 19:22:01.693184 INFO::ASW Label was 0.539832535949822 prior to batch effect correction and is now 0.922224039469382 .
2025-08-15 19:22:01.69414 INFO::Total function execution time is 0.0563631057739258 s and adjustment time is 0.0300710201263428 s ( 53.35 )
2025-08-15 19:22:01.715261 INFO::Formatting Data.
2025-08-15 19:22:01.716346 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:01.717904 INFO::Removing potential empty rows and columns
2025-08-15 19:22:01.719322 INFO::Found 0 missing values.
2025-08-15 19:22:01.722041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:01.722788 INFO::Done
2025-08-15 19:22:01.723468 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:01.726071 INFO::Starting hierarchical adjustment
2025-08-15 19:22:01.72743 INFO::Found 2 batches.
2025-08-15 19:22:01.72838 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:01.729453 INFO::Using default BPPARAM
2025-08-15 19:22:01.730351 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:01.731958 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 19:22:01.781927 INFO::Done
2025-08-15 19:22:01.783044 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:01.786326 INFO::ASW Batch was -0.049970485626985 prior to batch effect correction and is now -0.152545051908774 .
2025-08-15 19:22:01.787659 INFO::Total function execution time is 0.072577953338623 s and adjustment time is 0.0547609329223633 s ( 75.45 )
2025-08-15 19:22:01.808345 INFO::Formatting Data.
2025-08-15 19:22:01.809634 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:01.811221 INFO::Removing potential empty rows and columns
2025-08-15 19:22:01.812962 INFO::Found 0 missing values.
2025-08-15 19:22:01.814698 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.
2025-08-15 19:22:01.821784 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:01.822955 INFO::Done
2025-08-15 19:22:01.823996 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:01.829046 INFO::Starting hierarchical adjustment
2025-08-15 19:22:01.830168 INFO::Found 2 batches.
2025-08-15 19:22:01.831331 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:01.83244 INFO::Using default BPPARAM
2025-08-15 19:22:01.833418 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:01.83486 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 19:22:01.861358 INFO::Done
2025-08-15 19:22:01.862512 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:01.867632 INFO::ASW Batch was 0.683043976590266 prior to batch effect correction and is now 0.156620876324094 .
2025-08-15 19:22:01.868507 INFO::ASW Label was 0.391477082088342 prior to batch effect correction and is now 0.78961360008461 .
2025-08-15 19:22:01.869593 INFO::Total function execution time is 0.0613939762115479 s and adjustment time is 0.0313699245452881 s ( 51.1 )
2025-08-15 19:22:01.870844 INFO::Formatting Data.
2025-08-15 19:22:01.871866 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:01.873413 INFO::Removing potential empty rows and columns
2025-08-15 19:22:01.875001 INFO::Found 0 missing values.
2025-08-15 19:22:01.876532 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.
2025-08-15 19:22:01.884212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:01.885325 INFO::Done
2025-08-15 19:22:01.886291 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:01.890572 INFO::Starting hierarchical adjustment
2025-08-15 19:22:01.8921 INFO::Found 2 batches.
2025-08-15 19:22:01.893033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:01.89412 INFO::Using default BPPARAM
2025-08-15 19:22:01.89502 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:01.896786 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 19:22:01.921869 INFO::Done
2025-08-15 19:22:01.923312 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:01.927335 INFO::ASW Batch was 0.683043976590266 prior to batch effect correction and is now 0.156620876324094 .
2025-08-15 19:22:01.928147 INFO::ASW Label was 0.391477082088342 prior to batch effect correction and is now 0.78961360008461 .
2025-08-15 19:22:01.929086 INFO::Total function execution time is 0.0583431720733643 s and adjustment time is 0.03000807762146 s ( 51.43 )
2025-08-15 19:22:02.234593 INFO::Formatting Data.
2025-08-15 19:22:02.235817 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:02.237231 INFO::Removing potential empty rows and columns
2025-08-15 19:22:02.238668 INFO::Found 0 missing values.
2025-08-15 19:22:02.242866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:02.243881 INFO::Done
2025-08-15 19:22:02.244748 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:02.247669 INFO::Starting hierarchical adjustment
2025-08-15 19:22:02.248734 INFO::Found 3 batches.
2025-08-15 19:22:02.249487 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:02.25055 INFO::Using default BPPARAM
2025-08-15 19:22:02.251245 INFO::Processing subtree level 1
2025-08-15 19:22:02.381682 INFO::Adjusting the last 1 batches sequentially
2025-08-15 19:22:02.389448 INFO::Done
2025-08-15 19:22:02.391847 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:02.39738 INFO::ASW Batch was -0.0718260606545413 prior to batch effect correction and is now -0.0718260606545413 .
2025-08-15 19:22:02.399014 INFO::Total function execution time is 0.164502143859863 s and adjustment time is 0.140878915786743 s ( 85.64 )
2025-08-15 19:22:02.400595 INFO::Formatting Data.
2025-08-15 19:22:02.401728 INFO::Typecasting input to dataframe.
2025-08-15 19:22:02.403234 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:02.40545 INFO::Removing potential empty rows and columns
2025-08-15 19:22:02.407306 INFO::Found 0 missing values.
2025-08-15 19:22:02.412627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:02.413572 INFO::Done
2025-08-15 19:22:02.414549 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:02.417467 INFO::Starting hierarchical adjustment
2025-08-15 19:22:02.418192 INFO::Found 3 batches.
2025-08-15 19:22:02.418725 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:02.41934 INFO::Using default BPPARAM
2025-08-15 19:22:02.419842 INFO::Processing subtree level 1
2025-08-15 19:22:02.544104 INFO::Adjusting the last 1 batches sequentially
2025-08-15 19:22:02.549319 INFO::Done
2025-08-15 19:22:02.550285 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:02.555098 INFO::ASW Batch was -0.0718260606545413 prior to batch effect correction and is now -0.0718260606545413 .
2025-08-15 19:22:02.556835 INFO::Total function execution time is 0.156286001205444 s and adjustment time is 0.131247997283936 s ( 83.98 )
2025-08-15 19:22:02.578783 INFO::Formatting Data.
2025-08-15 19:22:02.579727 INFO::Typecasting input to dataframe.
2025-08-15 19:22:02.581404 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:02.583095 INFO::Removing potential empty rows and columns
2025-08-15 19:22:02.585045 INFO::Found 0 missing values.
2025-08-15 19:22:02.588668 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:02.589416 INFO::Done
2025-08-15 19:22:02.589928 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:02.592398 INFO::Starting hierarchical adjustment
2025-08-15 19:22:02.593602 INFO::Found 3 batches.
2025-08-15 19:22:02.594404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:02.595303 INFO::Using default BPPARAM
2025-08-15 19:22:02.596073 INFO::Processing subtree level 1
2025-08-15 19:22:02.838899 INFO::Adjusting the last 1 batches sequentially
2025-08-15 19:22:02.856473 INFO::Done
2025-08-15 19:22:02.859032 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:02.872428 INFO::ASW Batch was -0.08096896606645 prior to batch effect correction and is now -0.08096896606645 .
2025-08-15 19:22:02.874881 INFO::Total function execution time is 0.295923948287964 s and adjustment time is 0.26297402381897 s ( 88.87 )
2025-08-15 19:22:03.124647 INFO::Formatting Data.
2025-08-15 19:22:03.125752 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:03.127333 INFO::Removing potential empty rows and columns
2025-08-15 19:22:03.131625 INFO::Found 1000 missing values.
2025-08-15 19:22:03.15728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:03.158268 INFO::Done
2025-08-15 19:22:03.159099 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:03.166397 INFO::Starting hierarchical adjustment
2025-08-15 19:22:03.167226 INFO::Found 10 batches.
2025-08-15 19:22:03.167733 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:03.168319 INFO::Using default BPPARAM
2025-08-15 19:22:03.168815 INFO::Processing subtree level 1
2025-08-15 19:22:03.34178 INFO::Processing subtree level 2
2025-08-15 19:22:03.562944 INFO::Adjusting the last 1 batches sequentially
2025-08-15 19:22:03.58638 INFO::Done
2025-08-15 19:22:03.588211 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:03.606999 INFO::ASW Batch was 0.513902486213537 prior to batch effect correction and is now 0.513902486213537 .
2025-08-15 19:22:03.608059 INFO::ASW Label was 0.306659403196086 prior to batch effect correction and is now 0.306659403196086 .
2025-08-15 19:22:03.610785 INFO::Total function execution time is 0.486219167709351 s and adjustment time is 0.419081926345825 s ( 86.19 )
2025-08-15 19:22:03.611728 INFO::Formatting Data.
2025-08-15 19:22:03.612413 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:03.615466 INFO::Removing potential empty rows and columns
2025-08-15 19:22:03.618677 INFO::Found 1000 missing values.
2025-08-15 19:22:03.646639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:03.649208 INFO::Done
2025-08-15 19:22:03.650291 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:03.656033 INFO::Starting hierarchical adjustment
2025-08-15 19:22:03.657389 INFO::Found 10 batches.
2025-08-15 19:22:04.76486 INFO::Set up parallel execution backend with 2 workers
2025-08-15 19:22:04.76584 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-15 19:22:06.061908 INFO::Adjusting the last 2 batches sequentially
2025-08-15 19:22:06.063776 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 19:22:06.081363 INFO::Done
2025-08-15 19:22:06.082017 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:06.088105 INFO::ASW Batch was 0.513902486213537 prior to batch effect correction and is now 0.513902486213537 .
2025-08-15 19:22:06.088983 INFO::ASW Label was 0.306659403196086 prior to batch effect correction and is now 0.306659403196086 .
2025-08-15 19:22:06.08999 INFO::Total function execution time is 2.47825789451599 s and adjustment time is 2.4241681098938 s ( 97.82 )
2025-08-15 19:22:06.369185 INFO::Formatting Data.
2025-08-15 19:22:06.370493 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:06.372611 INFO::Removing potential empty rows and columns
2025-08-15 19:22:06.374307 INFO::Found 0 missing values.
2025-08-15 19:22:06.380852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:06.381765 INFO::Done
2025-08-15 19:22:06.382482 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 19:22:06.385594 INFO::Starting hierarchical adjustment
2025-08-15 19:22:06.386311 INFO::Found 3 batches.
2025-08-15 19:22:06.387183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 19:22:06.387922 INFO::Using default BPPARAM
2025-08-15 19:22:06.38881 INFO::Processing subtree level 1
2025-08-15 19:22:06.564537 INFO::Adjusting the last 1 batches sequentially
2025-08-15 19:22:06.5857 INFO::Done
2025-08-15 19:22:06.589838 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 19:22:06.602976 INFO::ASW Batch was 0.134082938895497 prior to batch effect correction and is now -0.140536704398628 .
2025-08-15 19:22:06.606044 INFO::ASW Label was -0.194705793758138 prior to batch effect correction and is now 0.018605678787046 .
2025-08-15 19:22:06.610934 INFO::Total function execution time is 0.240295886993408 s and adjustment time is 0.199414014816284 s ( 82.99 )
2025-08-15 19:22:06.838105 INFO::Formatting Data.
2025-08-15 19:22:06.838927 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:06.840373 INFO::Removing potential empty rows and columns
2025-08-15 19:22:06.841899 INFO::Found 2 missing values.
2025-08-15 19:22:06.845984 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:06.846885 INFO::Done
2025-08-15 19:22:06.893896 INFO::Found NA in Reference column
2025-08-15 19:22:06.908005 INFO::Require at least two references per batch.
2025-08-15 19:22:06.937626 INFO::Formatting Data.
2025-08-15 19:22:06.938379 INFO::Recognized SummarizedExperiment
2025-08-15 19:22:06.939237 INFO::Typecasting input to dataframe.
2025-08-15 19:22:06.952154 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:06.953876 INFO::Removing potential empty rows and columns
2025-08-15 19:22:06.958216 INFO::Found 0 missing values.
2025-08-15 19:22:06.964697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:06.965626 INFO::Done
2025-08-15 19:22:06.985694 INFO::Formatting Data.
2025-08-15 19:22:06.986828 INFO::Recognized SummarizedExperiment
2025-08-15 19:22:06.98774 INFO::Typecasting input to dataframe.
2025-08-15 19:22:07.012139 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:07.014417 INFO::Removing potential empty rows and columns
2025-08-15 19:22:07.020972 INFO::Found 0 missing values.
2025-08-15 19:22:07.031859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:07.03282 INFO::Done
2025-08-15 19:22:07.053016 INFO::Formatting Data.
2025-08-15 19:22:07.053773 INFO::Recognized SummarizedExperiment
2025-08-15 19:22:07.054515 INFO::Typecasting input to dataframe.
2025-08-15 19:22:07.077047 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:07.078003 INFO::Removing potential empty rows and columns
2025-08-15 19:22:07.07894 INFO::Found 0 missing values.
2025-08-15 19:22:07.079762 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.
2025-08-15 19:22:07.084713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:07.085504 INFO::Done
2025-08-15 19:22:07.100012 INFO::Formatting Data.
2025-08-15 19:22:07.100808 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:07.101997 INFO::Removing potential empty rows and columns
2025-08-15 19:22:07.103474 INFO::Found 0 missing values.
2025-08-15 19:22:07.107829 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:07.108692 INFO::Done
2025-08-15 19:22:07.126489 INFO::Formatting Data.
2025-08-15 19:22:07.127254 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:07.128077 INFO::Removing potential empty rows and columns
2025-08-15 19:22:07.129249 INFO::Found 0 missing values.
2025-08-15 19:22:07.132618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:07.133407 INFO::Done
2025-08-15 19:22:07.178543 INFO::Formatting Data.
2025-08-15 19:22:07.17976 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:07.181049 INFO::Removing potential empty rows and columns
2025-08-15 19:22:07.182811 INFO::Found 1 missing values.
2025-08-15 19:22:07.186849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:07.187627 INFO::Done
2025-08-15 19:22:07.2165 INFO::Formatting Data.
2025-08-15 19:22:07.217606 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:07.218655 INFO::Removing potential empty rows and columns
2025-08-15 19:22:07.219629 INFO::Found 2 missing values.
2025-08-15 19:22:07.220762 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.
2025-08-15 19:22:07.223724 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:07.224275 INFO::Done
2025-08-15 19:22:07.243087 INFO::Formatting Data.
2025-08-15 19:22:07.24416 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:07.24538 INFO::Removing potential empty rows and columns
2025-08-15 19:22:07.246971 INFO::Found 2 missing values.
2025-08-15 19:22:07.249199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:07.249988 INFO::Done
2025-08-15 19:22:07.269176 INFO::Formatting Data.
2025-08-15 19:22:07.27029 INFO::Typecasting input to dataframe.
2025-08-15 19:22:07.271552 INFO::Replacing NaNs with NAs.
2025-08-15 19:22:07.272861 INFO::Removing potential empty rows and columns
2025-08-15 19:22:07.274358 INFO::Found 0 missing values.
2025-08-15 19:22:07.278688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 19:22:07.279652 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.695 4.555 25.538
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.434 | 1.495 | 19.653 | |
| compute_asw | 0.030 | 0.001 | 0.032 | |
| count_existing | 0.019 | 0.001 | 0.020 | |
| generate_data_covariables | 0.013 | 0.000 | 0.014 | |
| generate_dataset | 0.013 | 0.001 | 0.015 | |