Yannis Schumann
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-27 12:02 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-11-25 01:06:02 -0500 (Tue, 25 Nov 2025) |
| EndedAt: 2025-11-25 01:08:28 -0500 (Tue, 25 Nov 2025) |
| EllapsedTime: 146.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* 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 ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 43.828 2.549 33.958
* 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 ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
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")
2025-11-25 01:07:45.761527 INFO::Formatting Data.
2025-11-25 01:07:45.768786 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:45.801939 INFO::Removing potential empty rows and columns
2025-11-25 01:07:46.499785 INFO::Found 0 missing values.
2025-11-25 01:07:46.508293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:46.509817 INFO::Done
2025-11-25 01:07:46.511158 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:46.539598 INFO::Starting hierarchical adjustment
2025-11-25 01:07:46.54177 INFO::Found 3 batches.
2025-11-25 01:07:46.543397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:46.546538 INFO::Using default BPPARAM
2025-11-25 01:07:46.548194 INFO::Processing subtree level 1
2025-11-25 01:07:46.81528 INFO::Adjusting the last 1 batches sequentially
2025-11-25 01:07:46.821529 INFO::Done
2025-11-25 01:07:46.823128 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:46.833224 INFO::ASW Batch was -0.0346453186464688 prior to batch effect correction and is now -0.0346453186464688 .
2025-11-25 01:07:46.836011 INFO::Total function execution time is 1.07660007476807 s and adjustment time is 0.280196905136108 s ( 26.03 )
2025-11-25 01:07:46.872089 INFO::Formatting Data.
2025-11-25 01:07:46.873851 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:46.876088 INFO::Removing potential empty rows and columns
2025-11-25 01:07:46.881336 INFO::Found 0 missing values.
2025-11-25 01:07:46.885133 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 01:07:46.917377 INFO::Formatting Data.
2025-11-25 01:07:46.919057 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:46.921286 INFO::Removing potential empty rows and columns
2025-11-25 01:07:46.924384 INFO::Found 0 missing values.
2025-11-25 01:07:46.926941 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 01:07:46.970455 INFO::Formatting Data.
2025-11-25 01:07:46.972176 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:46.975407 INFO::Removing potential empty rows and columns
2025-11-25 01:07:46.978561 INFO::Found 0 missing values.
2025-11-25 01:07:46.981068 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 01:07:46.993969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:46.995889 INFO::Done
2025-11-25 01:07:46.997456 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:47.002444 INFO::Starting hierarchical adjustment
2025-11-25 01:07:47.004432 INFO::Found 2 batches.
2025-11-25 01:07:47.006556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:47.008495 INFO::Using default BPPARAM
2025-11-25 01:07:47.009822 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:47.012097 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 01:07:47.069335 INFO::Done
2025-11-25 01:07:47.071323 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:47.076947 INFO::ASW Batch was -0.0205346490303347 prior to batch effect correction and is now -0.115280175882859 .
2025-11-25 01:07:47.079539 INFO::Total function execution time is 0.108987808227539 s and adjustment time is 0.0652480125427246 s ( 59.87 )
2025-11-25 01:07:47.086578 INFO::Formatting Data.
2025-11-25 01:07:47.088313 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:47.11236 INFO::Formatting Data.
2025-11-25 01:07:47.11407 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:47.116163 INFO::Removing potential empty rows and columns
2025-11-25 01:07:47.11864 INFO::Found 0 missing values.
2025-11-25 01:07:47.126647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:47.128227 INFO::Done
2025-11-25 01:07:47.129791 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:47.134933 INFO::Starting hierarchical adjustment
2025-11-25 01:07:47.186245 INFO::Found 2 batches.
2025-11-25 01:07:47.187686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:47.189172 INFO::Using default BPPARAM
2025-11-25 01:07:47.190532 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:47.192686 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:47.230869 INFO::Done
2025-11-25 01:07:47.232347 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:47.236782 INFO::ASW Batch was 0.00464196600726287 prior to batch effect correction and is now -0.0628286145881357 .
2025-11-25 01:07:47.238605 INFO::Total function execution time is 0.126328945159912 s and adjustment time is 0.0450129508972168 s ( 35.63 )
2025-11-25 01:07:47.241426 INFO::Formatting Data.
2025-11-25 01:07:47.24329 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:47.245339 INFO::Removing potential empty rows and columns
2025-11-25 01:07:47.247847 INFO::Found 0 missing values.
2025-11-25 01:07:47.256073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:47.257602 INFO::Done
2025-11-25 01:07:47.258994 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:47.263987 INFO::Starting hierarchical adjustment
2025-11-25 01:07:47.265903 INFO::Found 2 batches.
2025-11-25 01:07:47.267315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:47.268857 INFO::Using default BPPARAM
2025-11-25 01:07:47.270034 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:47.27219 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:47.312084 INFO::Done
2025-11-25 01:07:47.313691 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:47.318219 INFO::ASW Batch was 0.00464196600726287 prior to batch effect correction and is now -0.0628286145881357 .
2025-11-25 01:07:47.320061 INFO::Total function execution time is 0.078603982925415 s and adjustment time is 0.0465269088745117 s ( 59.19 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-25 01:07:53.739138 INFO::Formatting Data.
2025-11-25 01:07:53.740441 INFO::Recognized SummarizedExperiment
2025-11-25 01:07:53.741558 INFO::Typecasting input to dataframe.
2025-11-25 01:07:53.808844 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:53.811979 INFO::Removing potential empty rows and columns
2025-11-25 01:07:53.825169 INFO::Found 0 missing values.
2025-11-25 01:07:53.848406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:53.849855 INFO::Done
2025-11-25 01:07:53.851174 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:53.862995 INFO::Starting hierarchical adjustment
2025-11-25 01:07:53.864904 INFO::Found 2 batches.
2025-11-25 01:07:53.866682 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:53.869085 INFO::Using default BPPARAM
2025-11-25 01:07:53.871003 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:53.873697 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 01:07:54.041587 INFO::Done
2025-11-25 01:07:54.043532 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:54.053053 INFO::ASW Batch was 0.0137200414713744 prior to batch effect correction and is now -0.103701199149014 .
2025-11-25 01:07:54.055051 INFO::Total function execution time is 0.316618204116821 s and adjustment time is 0.177117824554443 s ( 55.94 )
Warning: stack imbalance in '{', 73 then 75
2025-11-25 01:07:54.104269 INFO::Formatting Data.
2025-11-25 01:07:54.105787 INFO::Recognized SummarizedExperiment
2025-11-25 01:07:54.10706 INFO::Typecasting input to dataframe.
2025-11-25 01:07:54.131946 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:54.134706 INFO::Removing potential empty rows and columns
2025-11-25 01:07:54.145497 INFO::Found 0 missing values.
2025-11-25 01:07:54.167976 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:54.169482 INFO::Done
2025-11-25 01:07:54.17079 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:54.180943 INFO::Starting hierarchical adjustment
2025-11-25 01:07:54.182775 INFO::Found 2 batches.
2025-11-25 01:07:54.184104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:54.185769 INFO::Using default BPPARAM
2025-11-25 01:07:54.187441 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:54.189922 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 01:07:54.268672 INFO::Done
2025-11-25 01:07:54.27019 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:54.280124 INFO::ASW Batch was -0.00982558117672552 prior to batch effect correction and is now -0.00982558117672552 .
2025-11-25 01:07:54.28291 INFO::Total function execution time is 0.177889108657837 s and adjustment time is 0.0862369537353516 s ( 48.48 )
2025-11-25 01:07:54.333436 INFO::Formatting Data.
2025-11-25 01:07:54.335065 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:54.33711 INFO::Removing potential empty rows and columns
2025-11-25 01:07:54.340198 INFO::Found 0 missing values.
2025-11-25 01:07:54.34796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:54.349387 INFO::Done
2025-11-25 01:07:54.350764 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:54.355234 INFO::Starting hierarchical adjustment
2025-11-25 01:07:54.357116 INFO::Found 3 batches.
2025-11-25 01:07:54.358515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:54.360902 INFO::Using default BPPARAM
2025-11-25 01:07:54.362288 INFO::Processing subtree level 1
2025-11-25 01:07:54.729766 INFO::Adjusting the last 1 batches sequentially
2025-11-25 01:07:54.742325 INFO::Done
2025-11-25 01:07:54.744972 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:54.758436 INFO::ASW Batch was -0.0533823619155378 prior to batch effect correction and is now -0.160093859846406 .
2025-11-25 01:07:54.762056 INFO::Total function execution time is 0.42857813835144 s and adjustment time is 0.38555383682251 s ( 89.96 )
2025-11-25 01:07:54.802963 INFO::Skipping initial DF formatting
2025-11-25 01:07:54.804546 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:54.81798 INFO::Starting hierarchical adjustment
2025-11-25 01:07:54.819934 INFO::Found 5 batches.
2025-11-25 01:07:54.821331 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:54.822964 INFO::Using default BPPARAM
2025-11-25 01:07:54.824326 INFO::Processing subtree level 1
2025-11-25 01:07:55.416427 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:55.453173 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 01:07:55.527529 INFO::Done
2025-11-25 01:07:55.52977 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:55.544898 INFO::ASW Batch was 0.494646747503043 prior to batch effect correction and is now 0.494646747503043 .
2025-11-25 01:07:55.546404 INFO::ASW Label was 0.418070356869032 prior to batch effect correction and is now 0.418070356869032 .
2025-11-25 01:07:55.54916 INFO::Total function execution time is 0.746166944503784 s and adjustment time is 0.707898855209351 s ( 94.87 )
2025-11-25 01:07:55.697486 INFO::Formatting Data.
2025-11-25 01:07:55.699275 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:55.701374 INFO::Removing potential empty rows and columns
2025-11-25 01:07:55.703896 INFO::Found 0 missing values.
2025-11-25 01:07:55.714762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:55.716269 INFO::Done
2025-11-25 01:07:55.717623 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:55.724636 INFO::Starting hierarchical adjustment
2025-11-25 01:07:55.726421 INFO::Found 5 batches.
2025-11-25 01:07:55.727817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:55.729444 INFO::Using default BPPARAM
2025-11-25 01:07:55.730936 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:56.087219 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:56.097029 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:56.15416 INFO::Done
2025-11-25 01:07:56.155794 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:56.16456 INFO::ASW Batch was 0.500841866081822 prior to batch effect correction and is now -0.0876343279176412 .
2025-11-25 01:07:56.166367 INFO::ASW Label was 0.292868232145051 prior to batch effect correction and is now 0.768763865692436 .
2025-11-25 01:07:56.169047 INFO::Total function execution time is 0.471566915512085 s and adjustment time is 0.428042888641357 s ( 90.77 )
2025-11-25 01:07:56.171203 INFO::Formatting Data.
2025-11-25 01:07:56.172889 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:56.175329 INFO::Removing potential empty rows and columns
2025-11-25 01:07:56.177966 INFO::Found 0 missing values.
2025-11-25 01:07:56.18943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:56.190939 INFO::Done
2025-11-25 01:07:56.192241 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:56.199341 INFO::Starting hierarchical adjustment
2025-11-25 01:07:56.201243 INFO::Found 5 batches.
2025-11-25 01:07:56.202587 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:56.204092 INFO::Using default BPPARAM
2025-11-25 01:07:56.206201 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:56.516809 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:56.53042 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:56.594146 INFO::Done
2025-11-25 01:07:56.598041 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:56.607067 INFO::ASW Batch was 0.500841866081822 prior to batch effect correction and is now -0.0876343279176412 .
2025-11-25 01:07:56.608758 INFO::ASW Label was 0.292868232145051 prior to batch effect correction and is now 0.768763865692436 .
2025-11-25 01:07:56.610821 INFO::Total function execution time is 0.439579963684082 s and adjustment time is 0.393244028091431 s ( 89.46 )
2025-11-25 01:07:56.648641 INFO::Formatting Data.
2025-11-25 01:07:56.65031 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:56.652413 INFO::Removing potential empty rows and columns
2025-11-25 01:07:56.654983 INFO::Found 0 missing values.
2025-11-25 01:07:56.666363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:56.668048 INFO::Done
2025-11-25 01:07:56.669447 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:56.678993 INFO::Starting hierarchical adjustment
2025-11-25 01:07:56.680718 INFO::Found 5 batches.
2025-11-25 01:07:56.682034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:56.684915 INFO::Using default BPPARAM
2025-11-25 01:07:56.686554 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:57.021563 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:57.038292 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:57.096674 INFO::Done
2025-11-25 01:07:57.098251 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:57.106179 INFO::ASW Batch was 0.304214382306626 prior to batch effect correction and is now -0.0407893094760777 .
2025-11-25 01:07:57.107859 INFO::ASW Label was 0.498492525062433 prior to batch effect correction and is now 0.815821360183954 .
2025-11-25 01:07:57.110004 INFO::Total function execution time is 0.461351156234741 s and adjustment time is 0.416247129440308 s ( 90.22 )
2025-11-25 01:07:57.112292 INFO::Formatting Data.
2025-11-25 01:07:57.113964 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:57.116252 INFO::Removing potential empty rows and columns
2025-11-25 01:07:57.11886 INFO::Found 0 missing values.
2025-11-25 01:07:57.131022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:57.132829 INFO::Done
2025-11-25 01:07:57.134191 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:57.141794 INFO::Starting hierarchical adjustment
2025-11-25 01:07:57.143724 INFO::Found 5 batches.
2025-11-25 01:07:57.145838 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:57.1479 INFO::Using default BPPARAM
2025-11-25 01:07:57.149393 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:57.491905 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:57.508306 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:57.570853 INFO::Done
2025-11-25 01:07:57.572615 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:57.581879 INFO::ASW Batch was 0.304214382306626 prior to batch effect correction and is now -0.0407893094760777 .
2025-11-25 01:07:57.583792 INFO::ASW Label was 0.498492525062433 prior to batch effect correction and is now 0.815821360183954 .
2025-11-25 01:07:57.58602 INFO::Total function execution time is 0.473704099655151 s and adjustment time is 0.427477836608887 s ( 90.24 )
2025-11-25 01:07:57.625599 INFO::Formatting Data.
2025-11-25 01:07:57.627804 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:57.630604 INFO::Removing potential empty rows and columns
2025-11-25 01:07:57.633856 INFO::Found 0 missing values.
2025-11-25 01:07:57.642385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:57.643977 INFO::Done
2025-11-25 01:07:57.64639 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:57.653781 INFO::Starting hierarchical adjustment
2025-11-25 01:07:57.659537 INFO::Found 2 batches.
2025-11-25 01:07:57.661251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:57.66296 INFO::Using default BPPARAM
2025-11-25 01:07:57.664333 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:57.666678 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:57.708819 INFO::Done
2025-11-25 01:07:57.710796 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:57.719823 INFO::ASW Batch was 0.462459515144012 prior to batch effect correction and is now 0.00631421619356909 .
2025-11-25 01:07:57.721441 INFO::ASW Label was 0.631777516866944 prior to batch effect correction and is now 0.927347109132789 .
2025-11-25 01:07:57.72336 INFO::Total function execution time is 0.0979471206665039 s and adjustment time is 0.0533831119537354 s ( 54.5 )
2025-11-25 01:07:57.725724 INFO::Formatting Data.
2025-11-25 01:07:57.727362 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:57.729516 INFO::Removing potential empty rows and columns
2025-11-25 01:07:57.733181 INFO::Found 0 missing values.
2025-11-25 01:07:57.741225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:57.742957 INFO::Done
2025-11-25 01:07:57.744652 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:57.753496 INFO::Starting hierarchical adjustment
2025-11-25 01:07:57.755474 INFO::Found 2 batches.
2025-11-25 01:07:57.757906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:57.75987 INFO::Using default BPPARAM
2025-11-25 01:07:57.761542 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:57.763967 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 01:07:57.806987 INFO::Done
2025-11-25 01:07:57.808682 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:57.816807 INFO::ASW Batch was 0.462459515144012 prior to batch effect correction and is now 0.00631421619356909 .
2025-11-25 01:07:57.819529 INFO::ASW Label was 0.631777516866944 prior to batch effect correction and is now 0.927347109132789 .
2025-11-25 01:07:57.821716 INFO::Total function execution time is 0.0960509777069092 s and adjustment time is 0.0519039630889893 s ( 54.04 )
2025-11-25 01:07:57.854911 INFO::Formatting Data.
2025-11-25 01:07:57.856748 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:57.859006 INFO::Removing potential empty rows and columns
2025-11-25 01:07:57.861514 INFO::Found 0 missing values.
2025-11-25 01:07:57.867499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:57.869035 INFO::Done
2025-11-25 01:07:57.870494 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:57.875231 INFO::Starting hierarchical adjustment
2025-11-25 01:07:57.877142 INFO::Found 2 batches.
2025-11-25 01:07:57.878631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:57.880313 INFO::Using default BPPARAM
2025-11-25 01:07:57.882108 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:57.884397 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 01:07:57.971924 INFO::Done
2025-11-25 01:07:57.973544 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:57.979041 INFO::ASW Batch was 0.265306743537403 prior to batch effect correction and is now -0.0853597068810635 .
2025-11-25 01:07:57.981443 INFO::Total function execution time is 0.126610994338989 s and adjustment time is 0.0951881408691406 s ( 75.18 )
2025-11-25 01:07:58.01482 INFO::Formatting Data.
2025-11-25 01:07:58.016697 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:58.018978 INFO::Removing potential empty rows and columns
2025-11-25 01:07:58.022639 INFO::Found 0 missing values.
2025-11-25 01:07:58.025302 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 01:07:58.038573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:58.040114 INFO::Done
2025-11-25 01:07:58.041807 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:58.049423 INFO::Starting hierarchical adjustment
2025-11-25 01:07:58.05178 INFO::Found 2 batches.
2025-11-25 01:07:58.053205 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:58.054716 INFO::Using default BPPARAM
2025-11-25 01:07:58.056058 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:58.058384 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 01:07:58.101415 INFO::Done
2025-11-25 01:07:58.102939 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:58.109867 INFO::ASW Batch was 0.628635409255643 prior to batch effect correction and is now 0.00029817371930435 .
2025-11-25 01:07:58.111378 INFO::ASW Label was 0.365959926675026 prior to batch effect correction and is now 0.914790863812174 .
2025-11-25 01:07:58.113276 INFO::Total function execution time is 0.0985860824584961 s and adjustment time is 0.0500209331512451 s ( 50.74 )
2025-11-25 01:07:58.115272 INFO::Formatting Data.
2025-11-25 01:07:58.11682 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:58.119071 INFO::Removing potential empty rows and columns
2025-11-25 01:07:58.12185 INFO::Found 0 missing values.
2025-11-25 01:07:58.124378 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 01:07:58.137103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:58.138543 INFO::Done
2025-11-25 01:07:58.13987 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:58.147615 INFO::Starting hierarchical adjustment
2025-11-25 01:07:58.149569 INFO::Found 2 batches.
2025-11-25 01:07:58.150979 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:58.15261 INFO::Using default BPPARAM
2025-11-25 01:07:58.154349 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:07:58.157207 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 01:07:58.199133 INFO::Done
2025-11-25 01:07:58.200596 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:58.20778 INFO::ASW Batch was 0.628635409255643 prior to batch effect correction and is now 0.00029817371930435 .
2025-11-25 01:07:58.209389 INFO::ASW Label was 0.365959926675026 prior to batch effect correction and is now 0.914790863812174 .
2025-11-25 01:07:58.211387 INFO::Total function execution time is 0.0961689949035645 s and adjustment time is 0.0499551296234131 s ( 51.95 )
2025-11-25 01:07:58.906565 INFO::Formatting Data.
2025-11-25 01:07:58.908248 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:58.910302 INFO::Removing potential empty rows and columns
2025-11-25 01:07:58.912885 INFO::Found 0 missing values.
2025-11-25 01:07:58.920679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:58.922195 INFO::Done
2025-11-25 01:07:58.923502 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:58.928163 INFO::Starting hierarchical adjustment
2025-11-25 01:07:58.930035 INFO::Found 3 batches.
2025-11-25 01:07:58.931403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:58.932984 INFO::Using default BPPARAM
2025-11-25 01:07:58.934453 INFO::Processing subtree level 1
2025-11-25 01:07:59.176674 INFO::Adjusting the last 1 batches sequentially
2025-11-25 01:07:59.190339 INFO::Done
2025-11-25 01:07:59.192773 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:59.205663 INFO::ASW Batch was -0.0155403023326363 prior to batch effect correction and is now -0.0155403023326363 .
2025-11-25 01:07:59.209959 INFO::Total function execution time is 0.303328037261963 s and adjustment time is 0.260621070861816 s ( 85.92 )
2025-11-25 01:07:59.213655 INFO::Formatting Data.
2025-11-25 01:07:59.216108 INFO::Typecasting input to dataframe.
2025-11-25 01:07:59.218185 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:59.221397 INFO::Removing potential empty rows and columns
2025-11-25 01:07:59.225048 INFO::Found 0 missing values.
2025-11-25 01:07:59.235358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:59.236964 INFO::Done
2025-11-25 01:07:59.238444 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:59.243456 INFO::Starting hierarchical adjustment
2025-11-25 01:07:59.24598 INFO::Found 3 batches.
2025-11-25 01:07:59.247524 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:59.24927 INFO::Using default BPPARAM
2025-11-25 01:07:59.251565 INFO::Processing subtree level 1
2025-11-25 01:07:59.498841 INFO::Adjusting the last 1 batches sequentially
2025-11-25 01:07:59.509698 INFO::Done
2025-11-25 01:07:59.511786 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:59.523709 INFO::ASW Batch was -0.0155403023326363 prior to batch effect correction and is now -0.0155403023326363 .
2025-11-25 01:07:59.526886 INFO::Total function execution time is 0.313176870346069 s and adjustment time is 0.264212846755981 s ( 84.37 )
2025-11-25 01:07:59.566716 INFO::Formatting Data.
2025-11-25 01:07:59.568589 INFO::Typecasting input to dataframe.
2025-11-25 01:07:59.570731 INFO::Replacing NaNs with NAs.
2025-11-25 01:07:59.575333 INFO::Removing potential empty rows and columns
2025-11-25 01:07:59.578134 INFO::Found 0 missing values.
2025-11-25 01:07:59.586311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:07:59.588043 INFO::Done
2025-11-25 01:07:59.589482 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:07:59.594279 INFO::Starting hierarchical adjustment
2025-11-25 01:07:59.596225 INFO::Found 3 batches.
2025-11-25 01:07:59.597602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:07:59.599244 INFO::Using default BPPARAM
2025-11-25 01:07:59.600669 INFO::Processing subtree level 1
2025-11-25 01:07:59.832244 INFO::Adjusting the last 1 batches sequentially
2025-11-25 01:07:59.845487 INFO::Done
2025-11-25 01:07:59.847472 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:07:59.861864 INFO::ASW Batch was -0.0875777023617503 prior to batch effect correction and is now -0.0875777023617503 .
2025-11-25 01:07:59.866479 INFO::Total function execution time is 0.299697875976562 s and adjustment time is 0.249604940414429 s ( 83.29 )
2025-11-25 01:08:00.275995 INFO::Formatting Data.
2025-11-25 01:08:00.277903 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:00.280702 INFO::Removing potential empty rows and columns
2025-11-25 01:08:00.288786 INFO::Found 1000 missing values.
2025-11-25 01:08:00.351761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:00.354274 INFO::Done
2025-11-25 01:08:00.35573 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:08:00.36899 INFO::Starting hierarchical adjustment
2025-11-25 01:08:00.371224 INFO::Found 10 batches.
2025-11-25 01:08:00.372861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:08:00.374726 INFO::Using default BPPARAM
2025-11-25 01:08:00.376389 INFO::Processing subtree level 1
2025-11-25 01:08:00.676146 INFO::Processing subtree level 2
2025-11-25 01:08:01.067456 INFO::Adjusting the last 1 batches sequentially
2025-11-25 01:08:01.072892 INFO::Done
2025-11-25 01:08:01.074581 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:08:01.089865 INFO::ASW Batch was 0.487880365540142 prior to batch effect correction and is now 0.487880365540142 .
2025-11-25 01:08:01.091706 INFO::ASW Label was 0.351702932682263 prior to batch effect correction and is now 0.351702932682263 .
2025-11-25 01:08:01.094397 INFO::Total function execution time is 0.818280935287476 s and adjustment time is 0.70212197303772 s ( 85.8 )
2025-11-25 01:08:01.096896 INFO::Formatting Data.
2025-11-25 01:08:01.098694 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:01.101911 INFO::Removing potential empty rows and columns
2025-11-25 01:08:01.110375 INFO::Found 1000 missing values.
2025-11-25 01:08:01.169771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:01.171483 INFO::Done
2025-11-25 01:08:01.172934 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:08:01.185701 INFO::Starting hierarchical adjustment
2025-11-25 01:08:01.187838 INFO::Found 10 batches.
2025-11-25 01:08:02.857725 INFO::Set up parallel execution backend with 2 workers
2025-11-25 01:08:02.859306 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-25 01:08:04.630629 INFO::Adjusting the last 2 batches sequentially
2025-11-25 01:08:04.633159 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 01:08:04.679624 INFO::Done
2025-11-25 01:08:04.680914 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:08:04.691937 INFO::ASW Batch was 0.487880365540142 prior to batch effect correction and is now 0.487880365540142 .
2025-11-25 01:08:04.693293 INFO::ASW Label was 0.351702932682263 prior to batch effect correction and is now 0.351702932682263 .
2025-11-25 01:08:04.694836 INFO::Total function execution time is 3.59811305999756 s and adjustment time is 3.49227213859558 s ( 97.06 )
2025-11-25 01:08:05.099775 INFO::Formatting Data.
2025-11-25 01:08:05.101521 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:05.103782 INFO::Removing potential empty rows and columns
2025-11-25 01:08:05.107832 INFO::Found 0 missing values.
2025-11-25 01:08:05.118682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:05.12019 INFO::Done
2025-11-25 01:08:05.122129 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 01:08:05.130214 INFO::Starting hierarchical adjustment
2025-11-25 01:08:05.132052 INFO::Found 3 batches.
2025-11-25 01:08:05.133387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 01:08:05.134974 INFO::Using default BPPARAM
2025-11-25 01:08:05.136358 INFO::Processing subtree level 1
2025-11-25 01:08:05.44232 INFO::Adjusting the last 1 batches sequentially
2025-11-25 01:08:05.454606 INFO::Done
2025-11-25 01:08:05.456628 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 01:08:05.473645 INFO::ASW Batch was 0.216079511363736 prior to batch effect correction and is now -0.164865301003162 .
2025-11-25 01:08:05.475387 INFO::ASW Label was -0.192209136842458 prior to batch effect correction and is now -0.016277503764352 .
2025-11-25 01:08:05.481672 INFO::Total function execution time is 0.380638122558594 s and adjustment time is 0.322914123535156 s ( 84.83 )
2025-11-25 01:08:05.875997 INFO::Formatting Data.
2025-11-25 01:08:05.877955 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:05.880218 INFO::Removing potential empty rows and columns
2025-11-25 01:08:05.883379 INFO::Found 2 missing values.
2025-11-25 01:08:05.891727 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:05.893295 INFO::Done
2025-11-25 01:08:05.98018 INFO::Found NA in Reference column
2025-11-25 01:08:06.009272 INFO::Require at least two references per batch.
2025-11-25 01:08:06.070047 INFO::Formatting Data.
2025-11-25 01:08:06.072009 INFO::Recognized SummarizedExperiment
2025-11-25 01:08:06.073435 INFO::Typecasting input to dataframe.
2025-11-25 01:08:06.099551 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.102547 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.114212 INFO::Found 0 missing values.
2025-11-25 01:08:06.143732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.145441 INFO::Done
2025-11-25 01:08:06.19086 INFO::Formatting Data.
2025-11-25 01:08:06.193085 INFO::Recognized SummarizedExperiment
2025-11-25 01:08:06.194394 INFO::Typecasting input to dataframe.
2025-11-25 01:08:06.242216 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.246375 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.259041 INFO::Found 0 missing values.
2025-11-25 01:08:06.299775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.301875 INFO::Done
2025-11-25 01:08:06.35228 INFO::Formatting Data.
2025-11-25 01:08:06.353926 INFO::Recognized SummarizedExperiment
2025-11-25 01:08:06.355339 INFO::Typecasting input to dataframe.
2025-11-25 01:08:06.40359 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.407617 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.410337 INFO::Found 0 missing values.
2025-11-25 01:08:06.412656 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 01:08:06.427071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.429296 INFO::Done
2025-11-25 01:08:06.458124 INFO::Formatting Data.
2025-11-25 01:08:06.461362 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.463566 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.466199 INFO::Found 0 missing values.
2025-11-25 01:08:06.473954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.475497 INFO::Done
2025-11-25 01:08:06.508311 INFO::Formatting Data.
2025-11-25 01:08:06.510657 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.513723 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.516621 INFO::Found 0 missing values.
2025-11-25 01:08:06.524863 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.526379 INFO::Done
2025-11-25 01:08:06.620364 INFO::Formatting Data.
2025-11-25 01:08:06.623096 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.626156 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.62959 INFO::Found 1 missing values.
2025-11-25 01:08:06.636874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.639091 INFO::Done
2025-11-25 01:08:06.696288 INFO::Formatting Data.
2025-11-25 01:08:06.698142 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.700327 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.702943 INFO::Found 2 missing values.
2025-11-25 01:08:06.705488 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 01:08:06.71175 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.713333 INFO::Done
2025-11-25 01:08:06.742858 INFO::Formatting Data.
2025-11-25 01:08:06.744821 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.747081 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.749601 INFO::Found 2 missing values.
2025-11-25 01:08:06.753874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.755384 INFO::Done
2025-11-25 01:08:06.786191 INFO::Formatting Data.
2025-11-25 01:08:06.78794 INFO::Typecasting input to dataframe.
2025-11-25 01:08:06.789947 INFO::Replacing NaNs with NAs.
2025-11-25 01:08:06.792036 INFO::Removing potential empty rows and columns
2025-11-25 01:08:06.79468 INFO::Found 0 missing values.
2025-11-25 01:08:06.802519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 01:08:06.804036 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.110 6.851 44.753
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.828 | 2.549 | 33.958 | |
| compute_asw | 0.061 | 0.002 | 0.070 | |
| count_existing | 0.030 | 0.001 | 0.034 | |
| generate_data_covariables | 0.030 | 0.002 | 0.035 | |
| generate_dataset | 0.025 | 0.001 | 0.026 | |