Yannis Schumann
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 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 2025-11-20 12:04 -0500 (Thu, 20 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" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| 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: 2025-11-18 04:14:05 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 04:16:24 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 138.7 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 43.792 2.537 35.35
* 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")
2025-11-18 04:15:48.809527 INFO::Formatting Data.
2025-11-18 04:15:48.815952 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:48.849122 INFO::Removing potential empty rows and columns
2025-11-18 04:15:49.571613 INFO::Found 0 missing values.
2025-11-18 04:15:49.580833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:49.58233 INFO::Done
2025-11-18 04:15:49.583642 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:49.613211 INFO::Starting hierarchical adjustment
2025-11-18 04:15:49.615183 INFO::Found 3 batches.
2025-11-18 04:15:49.616551 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:49.619176 INFO::Using default BPPARAM
2025-11-18 04:15:49.620721 INFO::Processing subtree level 1
2025-11-18 04:15:49.902112 INFO::Adjusting the last 1 batches sequentially
2025-11-18 04:15:49.908295 INFO::Done
2025-11-18 04:15:49.909967 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:49.920058 INFO::ASW Batch was -0.0582989587131514 prior to batch effect correction and is now -0.0582989587131514 .
2025-11-18 04:15:49.923771 INFO::Total function execution time is 1.11473894119263 s and adjustment time is 0.293460130691528 s ( 26.33 )
2025-11-18 04:15:49.96351 INFO::Formatting Data.
2025-11-18 04:15:49.96623 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:49.968799 INFO::Removing potential empty rows and columns
2025-11-18 04:15:49.972285 INFO::Found 0 missing values.
2025-11-18 04:15:49.974968 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.
2025-11-18 04:15:50.005165 INFO::Formatting Data.
2025-11-18 04:15:50.006953 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:50.009193 INFO::Removing potential empty rows and columns
2025-11-18 04:15:50.012289 INFO::Found 0 missing values.
2025-11-18 04:15:50.014867 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.
2025-11-18 04:15:50.059176 INFO::Formatting Data.
2025-11-18 04:15:50.060991 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:50.06321 INFO::Removing potential empty rows and columns
2025-11-18 04:15:50.066213 INFO::Found 0 missing values.
2025-11-18 04:15:50.068852 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.
2025-11-18 04:15:50.081847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:50.083343 INFO::Done
2025-11-18 04:15:50.084731 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:50.089785 INFO::Starting hierarchical adjustment
2025-11-18 04:15:50.091829 INFO::Found 2 batches.
2025-11-18 04:15:50.09332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:50.094987 INFO::Using default BPPARAM
2025-11-18 04:15:50.096258 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:15:50.098394 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 04:15:50.151972 INFO::Done
2025-11-18 04:15:50.153362 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:50.158261 INFO::ASW Batch was -0.0861082762278634 prior to batch effect correction and is now -0.124423714004216 .
2025-11-18 04:15:50.160615 INFO::Total function execution time is 0.101400136947632 s and adjustment time is 0.060554027557373 s ( 59.72 )
2025-11-18 04:15:50.167357 INFO::Formatting Data.
2025-11-18 04:15:50.16963 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:50.191559 INFO::Formatting Data.
2025-11-18 04:15:50.193279 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:50.195559 INFO::Removing potential empty rows and columns
2025-11-18 04:15:50.200369 INFO::Found 0 missing values.
2025-11-18 04:15:50.209224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:50.21252 INFO::Done
2025-11-18 04:15:50.214281 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:50.218927 INFO::Starting hierarchical adjustment
2025-11-18 04:15:50.274848 INFO::Found 2 batches.
2025-11-18 04:15:50.276433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:50.278027 INFO::Using default BPPARAM
2025-11-18 04:15:50.279435 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:15:50.281789 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 04:15:50.330521 INFO::Done
2025-11-18 04:15:50.331968 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:50.336605 INFO::ASW Batch was -0.0273146197462337 prior to batch effect correction and is now -0.120246636658417 .
2025-11-18 04:15:50.338662 INFO::Total function execution time is 0.147151947021484 s and adjustment time is 0.0562350749969482 s ( 38.22 )
2025-11-18 04:15:50.341193 INFO::Formatting Data.
2025-11-18 04:15:50.342627 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:50.344785 INFO::Removing potential empty rows and columns
2025-11-18 04:15:50.34759 INFO::Found 0 missing values.
2025-11-18 04:15:50.355877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:50.35733 INFO::Done
2025-11-18 04:15:50.358624 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:50.363052 INFO::Starting hierarchical adjustment
2025-11-18 04:15:50.366974 INFO::Found 2 batches.
2025-11-18 04:15:50.368332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:50.369593 INFO::Using default BPPARAM
2025-11-18 04:15:50.370735 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:15:50.372925 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 04:15:50.420255 INFO::Done
2025-11-18 04:15:50.421849 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:50.429625 INFO::ASW Batch was -0.0273146197462337 prior to batch effect correction and is now -0.120246636658417 .
2025-11-18 04:15:50.431668 INFO::Total function execution time is 0.0904450416564941 s and adjustment time is 0.0536248683929443 s ( 59.29 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-18 04:15:57.426429 INFO::Formatting Data.
2025-11-18 04:15:57.427869 INFO::Recognized SummarizedExperiment
2025-11-18 04:15:57.429188 INFO::Typecasting input to dataframe.
2025-11-18 04:15:57.509121 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:57.512708 INFO::Removing potential empty rows and columns
2025-11-18 04:15:57.524022 INFO::Found 0 missing values.
2025-11-18 04:15:57.545303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:57.546735 INFO::Done
2025-11-18 04:15:57.548025 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:57.557619 INFO::Starting hierarchical adjustment
2025-11-18 04:15:57.559619 INFO::Found 2 batches.
2025-11-18 04:15:57.561062 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:57.563469 INFO::Using default BPPARAM
2025-11-18 04:15:57.567219 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:15:57.572446 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 04:15:57.747216 INFO::Done
2025-11-18 04:15:57.748768 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:57.75781 INFO::ASW Batch was -0.00391756137928122 prior to batch effect correction and is now -0.0906091120498806 .
2025-11-18 04:15:57.759791 INFO::Total function execution time is 0.334007978439331 s and adjustment time is 0.188015937805176 s ( 56.29 )
Warning: stack imbalance in '{', 73 then 74
2025-11-18 04:15:57.814717 INFO::Formatting Data.
2025-11-18 04:15:57.819567 INFO::Recognized SummarizedExperiment
2025-11-18 04:15:57.821075 INFO::Typecasting input to dataframe.
2025-11-18 04:15:57.847019 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:57.849694 INFO::Removing potential empty rows and columns
2025-11-18 04:15:57.861787 INFO::Found 0 missing values.
2025-11-18 04:15:57.887903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:57.889588 INFO::Done
2025-11-18 04:15:57.891039 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:57.902921 INFO::Starting hierarchical adjustment
2025-11-18 04:15:57.904899 INFO::Found 2 batches.
2025-11-18 04:15:57.906265 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:57.907838 INFO::Using default BPPARAM
2025-11-18 04:15:57.9103 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:15:57.912816 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 04:15:57.995026 INFO::Done
2025-11-18 04:15:57.996477 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:58.005282 INFO::ASW Batch was 0.00263890993228031 prior to batch effect correction and is now 0.00263890993228031 .
2025-11-18 04:15:58.007319 INFO::Total function execution time is 0.192559003829956 s and adjustment time is 0.0905420780181885 s ( 47.02 )
2025-11-18 04:15:58.059465 INFO::Formatting Data.
2025-11-18 04:15:58.061086 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:58.063127 INFO::Removing potential empty rows and columns
2025-11-18 04:15:58.065687 INFO::Found 0 missing values.
2025-11-18 04:15:58.075229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:58.076744 INFO::Done
2025-11-18 04:15:58.078009 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:58.084793 INFO::Starting hierarchical adjustment
2025-11-18 04:15:58.086782 INFO::Found 3 batches.
2025-11-18 04:15:58.08819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:58.089696 INFO::Using default BPPARAM
2025-11-18 04:15:58.091002 INFO::Processing subtree level 1
2025-11-18 04:15:58.443165 INFO::Adjusting the last 1 batches sequentially
2025-11-18 04:15:58.452872 INFO::Done
2025-11-18 04:15:58.456756 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:58.468883 INFO::ASW Batch was -0.145329756241925 prior to batch effect correction and is now -0.181788617422964 .
2025-11-18 04:15:58.471955 INFO::Total function execution time is 0.411855936050415 s and adjustment time is 0.366418123245239 s ( 88.97 )
2025-11-18 04:15:58.514473 INFO::Skipping initial DF formatting
2025-11-18 04:15:58.516044 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:58.525639 INFO::Starting hierarchical adjustment
2025-11-18 04:15:58.527705 INFO::Found 5 batches.
2025-11-18 04:15:58.530221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:58.532077 INFO::Using default BPPARAM
2025-11-18 04:15:58.533618 INFO::Processing subtree level 1
2025-11-18 04:15:59.100794 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:15:59.118402 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 04:15:59.200093 INFO::Done
2025-11-18 04:15:59.203392 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:59.221308 INFO::ASW Batch was 0.506055062712858 prior to batch effect correction and is now 0.506055062712858 .
2025-11-18 04:15:59.222821 INFO::ASW Label was 0.35052657892713 prior to batch effect correction and is now 0.35052657892713 .
2025-11-18 04:15:59.227594 INFO::Total function execution time is 0.713115930557251 s and adjustment time is 0.672816038131714 s ( 94.35 )
2025-11-18 04:15:59.390077 INFO::Formatting Data.
2025-11-18 04:15:59.391629 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:59.393823 INFO::Removing potential empty rows and columns
2025-11-18 04:15:59.396272 INFO::Found 0 missing values.
2025-11-18 04:15:59.407149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:59.408727 INFO::Done
2025-11-18 04:15:59.409921 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:59.416677 INFO::Starting hierarchical adjustment
2025-11-18 04:15:59.418606 INFO::Found 5 batches.
2025-11-18 04:15:59.420028 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:59.421578 INFO::Using default BPPARAM
2025-11-18 04:15:59.423033 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.
2025-11-18 04:15:59.790824 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:15:59.804232 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 04:15:59.862372 INFO::Done
2025-11-18 04:15:59.864013 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:15:59.875663 INFO::ASW Batch was 0.343557287216535 prior to batch effect correction and is now -0.0836356594406271 .
2025-11-18 04:15:59.877475 INFO::ASW Label was 0.282894293395001 prior to batch effect correction and is now 0.899446353668044 .
2025-11-18 04:15:59.879756 INFO::Total function execution time is 0.489681005477905 s and adjustment time is 0.444104909896851 s ( 90.69 )
2025-11-18 04:15:59.88267 INFO::Formatting Data.
2025-11-18 04:15:59.884577 INFO::Replacing NaNs with NAs.
2025-11-18 04:15:59.887195 INFO::Removing potential empty rows and columns
2025-11-18 04:15:59.890244 INFO::Found 0 missing values.
2025-11-18 04:15:59.903128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:15:59.904733 INFO::Done
2025-11-18 04:15:59.906179 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:15:59.914167 INFO::Starting hierarchical adjustment
2025-11-18 04:15:59.916762 INFO::Found 5 batches.
2025-11-18 04:15:59.918259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:15:59.91972 INFO::Using default BPPARAM
2025-11-18 04:15:59.921061 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.
2025-11-18 04:16:00.23946 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:00.24922 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 04:16:00.30694 INFO::Done
2025-11-18 04:16:00.309091 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:00.320494 INFO::ASW Batch was 0.343557287216535 prior to batch effect correction and is now -0.0836356594406271 .
2025-11-18 04:16:00.322331 INFO::ASW Label was 0.282894293395001 prior to batch effect correction and is now 0.899446353668044 .
2025-11-18 04:16:00.324669 INFO::Total function execution time is 0.442038059234619 s and adjustment time is 0.391139030456543 s ( 88.49 )
2025-11-18 04:16:00.366173 INFO::Formatting Data.
2025-11-18 04:16:00.368033 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:00.370405 INFO::Removing potential empty rows and columns
2025-11-18 04:16:00.373206 INFO::Found 0 missing values.
2025-11-18 04:16:00.384809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:00.386348 INFO::Done
2025-11-18 04:16:00.387839 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:00.395455 INFO::Starting hierarchical adjustment
2025-11-18 04:16:00.397602 INFO::Found 5 batches.
2025-11-18 04:16:00.399187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:00.400999 INFO::Using default BPPARAM
2025-11-18 04:16:00.402645 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.
2025-11-18 04:16:00.72839 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:00.742491 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 04:16:00.800854 INFO::Done
2025-11-18 04:16:00.802565 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:00.812137 INFO::ASW Batch was 0.527492583070101 prior to batch effect correction and is now -0.0760292126537666 .
2025-11-18 04:16:00.81427 INFO::ASW Label was 0.305688135501533 prior to batch effect correction and is now 0.702438857333094 .
2025-11-18 04:16:00.816335 INFO::Total function execution time is 0.450201988220215 s and adjustment time is 0.403700113296509 s ( 89.67 )
2025-11-18 04:16:00.81899 INFO::Formatting Data.
2025-11-18 04:16:00.820701 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:00.822931 INFO::Removing potential empty rows and columns
2025-11-18 04:16:00.826059 INFO::Found 0 missing values.
2025-11-18 04:16:00.837879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:00.839471 INFO::Done
2025-11-18 04:16:00.840983 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:00.848205 INFO::Starting hierarchical adjustment
2025-11-18 04:16:00.85082 INFO::Found 5 batches.
2025-11-18 04:16:00.852403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:00.854134 INFO::Using default BPPARAM
2025-11-18 04:16:00.856333 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.
2025-11-18 04:16:01.170971 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:01.18378 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 04:16:01.248957 INFO::Done
2025-11-18 04:16:01.250934 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:01.26068 INFO::ASW Batch was 0.527492583070101 prior to batch effect correction and is now -0.0760292126537666 .
2025-11-18 04:16:01.262402 INFO::ASW Label was 0.305688135501533 prior to batch effect correction and is now 0.702438857333094 .
2025-11-18 04:16:01.265007 INFO::Total function execution time is 0.445991039276123 s and adjustment time is 0.399186134338379 s ( 89.51 )
2025-11-18 04:16:01.307118 INFO::Formatting Data.
2025-11-18 04:16:01.309027 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:01.311466 INFO::Removing potential empty rows and columns
2025-11-18 04:16:01.314516 INFO::Found 0 missing values.
2025-11-18 04:16:01.322419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:01.324013 INFO::Done
2025-11-18 04:16:01.325438 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:01.332858 INFO::Starting hierarchical adjustment
2025-11-18 04:16:01.334896 INFO::Found 2 batches.
2025-11-18 04:16:01.3364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:01.338099 INFO::Using default BPPARAM
2025-11-18 04:16:01.33956 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:01.341985 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 04:16:01.380146 INFO::Done
2025-11-18 04:16:01.381717 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:01.391727 INFO::ASW Batch was 0.447518919506471 prior to batch effect correction and is now 0.0769598206524647 .
2025-11-18 04:16:01.393407 INFO::ASW Label was 0.504561847609811 prior to batch effect correction and is now 0.783329368201628 .
2025-11-18 04:16:01.395331 INFO::Total function execution time is 0.0883719921112061 s and adjustment time is 0.0456569194793701 s ( 51.66 )
2025-11-18 04:16:01.397308 INFO::Formatting Data.
2025-11-18 04:16:01.398882 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:01.401052 INFO::Removing potential empty rows and columns
2025-11-18 04:16:01.403608 INFO::Found 0 missing values.
2025-11-18 04:16:01.410957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:01.412488 INFO::Done
2025-11-18 04:16:01.413862 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:01.420925 INFO::Starting hierarchical adjustment
2025-11-18 04:16:01.42289 INFO::Found 2 batches.
2025-11-18 04:16:01.424332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:01.425793 INFO::Using default BPPARAM
2025-11-18 04:16:01.427095 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:01.429335 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 04:16:01.467177 INFO::Done
2025-11-18 04:16:01.468775 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:01.47597 INFO::ASW Batch was 0.447518919506471 prior to batch effect correction and is now 0.0769598206524647 .
2025-11-18 04:16:01.477566 INFO::ASW Label was 0.504561847609811 prior to batch effect correction and is now 0.783329368201628 .
2025-11-18 04:16:01.479558 INFO::Total function execution time is 0.0822699069976807 s and adjustment time is 0.0446500778198242 s ( 54.27 )
2025-11-18 04:16:01.510769 INFO::Formatting Data.
2025-11-18 04:16:01.512547 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:01.514615 INFO::Removing potential empty rows and columns
2025-11-18 04:16:01.516892 INFO::Found 0 missing values.
2025-11-18 04:16:01.522305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:01.523766 INFO::Done
2025-11-18 04:16:01.525074 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:01.529421 INFO::Starting hierarchical adjustment
2025-11-18 04:16:01.53129 INFO::Found 2 batches.
2025-11-18 04:16:01.532647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:01.534239 INFO::Using default BPPARAM
2025-11-18 04:16:01.535642 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:01.537882 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 04:16:01.616122 INFO::Done
2025-11-18 04:16:01.617653 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:01.62217 INFO::ASW Batch was -0.143510881601973 prior to batch effect correction and is now -0.166914419618002 .
2025-11-18 04:16:01.624133 INFO::Total function execution time is 0.113496780395508 s and adjustment time is 0.0851640701293945 s ( 75.04 )
2025-11-18 04:16:01.656967 INFO::Formatting Data.
2025-11-18 04:16:01.658717 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:01.660834 INFO::Removing potential empty rows and columns
2025-11-18 04:16:01.663446 INFO::Found 0 missing values.
2025-11-18 04:16:01.667017 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.
2025-11-18 04:16:01.680527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:01.682158 INFO::Done
2025-11-18 04:16:01.683647 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:01.690822 INFO::Starting hierarchical adjustment
2025-11-18 04:16:01.692824 INFO::Found 2 batches.
2025-11-18 04:16:01.694207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:01.696248 INFO::Using default BPPARAM
2025-11-18 04:16:01.69795 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:01.700511 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 04:16:01.745103 INFO::Done
2025-11-18 04:16:01.746757 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:01.754417 INFO::ASW Batch was 0.723037196772582 prior to batch effect correction and is now 0.0497245101456109 .
2025-11-18 04:16:01.755854 INFO::ASW Label was 0.342414585078463 prior to batch effect correction and is now 0.849861866941664 .
2025-11-18 04:16:01.757585 INFO::Total function execution time is 0.100743055343628 s and adjustment time is 0.0526800155639648 s ( 52.29 )
2025-11-18 04:16:01.759346 INFO::Formatting Data.
2025-11-18 04:16:01.761253 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:01.763628 INFO::Removing potential empty rows and columns
2025-11-18 04:16:01.768178 INFO::Found 0 missing values.
2025-11-18 04:16:01.773227 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.
2025-11-18 04:16:01.787095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:01.788855 INFO::Done
2025-11-18 04:16:01.790454 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:01.800951 INFO::Starting hierarchical adjustment
2025-11-18 04:16:01.803074 INFO::Found 2 batches.
2025-11-18 04:16:01.80494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:01.806845 INFO::Using default BPPARAM
2025-11-18 04:16:01.8094 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:01.812076 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 04:16:01.861586 INFO::Done
2025-11-18 04:16:01.863552 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:01.871618 INFO::ASW Batch was 0.723037196772582 prior to batch effect correction and is now 0.0497245101456109 .
2025-11-18 04:16:01.873333 INFO::ASW Label was 0.342414585078463 prior to batch effect correction and is now 0.849861866941664 .
2025-11-18 04:16:01.875604 INFO::Total function execution time is 0.116202116012573 s and adjustment time is 0.0589039325714111 s ( 50.69 )
2025-11-18 04:16:02.463624 INFO::Formatting Data.
2025-11-18 04:16:02.465227 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:02.467239 INFO::Removing potential empty rows and columns
2025-11-18 04:16:02.470127 INFO::Found 0 missing values.
2025-11-18 04:16:02.477929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:02.479914 INFO::Done
2025-11-18 04:16:02.481228 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:02.486071 INFO::Starting hierarchical adjustment
2025-11-18 04:16:02.487953 INFO::Found 3 batches.
2025-11-18 04:16:02.489335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:02.490844 INFO::Using default BPPARAM
2025-11-18 04:16:02.492211 INFO::Processing subtree level 1
2025-11-18 04:16:02.712669 INFO::Adjusting the last 1 batches sequentially
2025-11-18 04:16:02.724403 INFO::Done
2025-11-18 04:16:02.72668 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:02.739499 INFO::ASW Batch was 0.0139142315703384 prior to batch effect correction and is now 0.0139142315703384 .
2025-11-18 04:16:02.742571 INFO::Total function execution time is 0.278963088989258 s and adjustment time is 0.236778020858765 s ( 84.88 )
2025-11-18 04:16:02.745526 INFO::Formatting Data.
2025-11-18 04:16:02.747625 INFO::Typecasting input to dataframe.
2025-11-18 04:16:02.749534 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:02.752354 INFO::Removing potential empty rows and columns
2025-11-18 04:16:02.755977 INFO::Found 0 missing values.
2025-11-18 04:16:02.764964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:02.76648 INFO::Done
2025-11-18 04:16:02.767844 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:02.772634 INFO::Starting hierarchical adjustment
2025-11-18 04:16:02.775048 INFO::Found 3 batches.
2025-11-18 04:16:02.776548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:02.778909 INFO::Using default BPPARAM
2025-11-18 04:16:02.780355 INFO::Processing subtree level 1
2025-11-18 04:16:02.997386 INFO::Adjusting the last 1 batches sequentially
2025-11-18 04:16:03.007284 INFO::Done
2025-11-18 04:16:03.010125 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:03.02393 INFO::ASW Batch was 0.0139142315703384 prior to batch effect correction and is now 0.0139142315703384 .
2025-11-18 04:16:03.026988 INFO::Total function execution time is 0.28148889541626 s and adjustment time is 0.232592821121216 s ( 82.63 )
2025-11-18 04:16:03.073439 INFO::Formatting Data.
2025-11-18 04:16:03.07525 INFO::Typecasting input to dataframe.
2025-11-18 04:16:03.077286 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:03.080783 INFO::Removing potential empty rows and columns
2025-11-18 04:16:03.08375 INFO::Found 0 missing values.
2025-11-18 04:16:03.090757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:03.092086 INFO::Done
2025-11-18 04:16:03.093313 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:03.098892 INFO::Starting hierarchical adjustment
2025-11-18 04:16:03.100796 INFO::Found 3 batches.
2025-11-18 04:16:03.102166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:03.103728 INFO::Using default BPPARAM
2025-11-18 04:16:03.105099 INFO::Processing subtree level 1
2025-11-18 04:16:03.334049 INFO::Adjusting the last 1 batches sequentially
2025-11-18 04:16:03.344326 INFO::Done
2025-11-18 04:16:03.346906 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:03.35892 INFO::ASW Batch was -0.0555186568643894 prior to batch effect correction and is now -0.0555186568643894 .
2025-11-18 04:16:03.362694 INFO::Total function execution time is 0.288823127746582 s and adjustment time is 0.243892192840576 s ( 84.44 )
2025-11-18 04:16:03.773304 INFO::Formatting Data.
2025-11-18 04:16:03.775803 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:03.779221 INFO::Removing potential empty rows and columns
2025-11-18 04:16:03.787332 INFO::Found 1000 missing values.
2025-11-18 04:16:03.847892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:03.849476 INFO::Done
2025-11-18 04:16:03.850834 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:03.863117 INFO::Starting hierarchical adjustment
2025-11-18 04:16:03.865192 INFO::Found 10 batches.
2025-11-18 04:16:03.866691 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:03.868302 INFO::Using default BPPARAM
2025-11-18 04:16:03.869719 INFO::Processing subtree level 1
2025-11-18 04:16:04.191373 INFO::Processing subtree level 2
2025-11-18 04:16:04.604426 INFO::Adjusting the last 1 batches sequentially
2025-11-18 04:16:04.617434 INFO::Done
2025-11-18 04:16:04.622522 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:04.643565 INFO::ASW Batch was 0.487298640741135 prior to batch effect correction and is now 0.487298640741135 .
2025-11-18 04:16:04.645816 INFO::ASW Label was 0.320206842605534 prior to batch effect correction and is now 0.320206842605534 .
2025-11-18 04:16:04.648306 INFO::Total function execution time is 0.874998092651367 s and adjustment time is 0.752626180648804 s ( 86.01 )
2025-11-18 04:16:04.651851 INFO::Formatting Data.
2025-11-18 04:16:04.654486 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:04.657643 INFO::Removing potential empty rows and columns
2025-11-18 04:16:04.666145 INFO::Found 1000 missing values.
2025-11-18 04:16:04.72582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:04.727434 INFO::Done
2025-11-18 04:16:04.728902 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:04.741176 INFO::Starting hierarchical adjustment
2025-11-18 04:16:04.744308 INFO::Found 10 batches.
2025-11-18 04:16:06.070505 INFO::Set up parallel execution backend with 2 workers
2025-11-18 04:16:06.072287 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-18 04:16:07.872271 INFO::Adjusting the last 2 batches sequentially
2025-11-18 04:16:07.874535 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 04:16:07.921872 INFO::Done
2025-11-18 04:16:07.923194 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:07.935878 INFO::ASW Batch was 0.487298640741135 prior to batch effect correction and is now 0.487298640741135 .
2025-11-18 04:16:07.937256 INFO::ASW Label was 0.320206842605534 prior to batch effect correction and is now 0.320206842605534 .
2025-11-18 04:16:07.93928 INFO::Total function execution time is 3.28758502006531 s and adjustment time is 3.17798399925232 s ( 96.67 )
2025-11-18 04:16:08.339172 INFO::Formatting Data.
2025-11-18 04:16:08.340899 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:08.3431 INFO::Removing potential empty rows and columns
2025-11-18 04:16:08.346211 INFO::Found 0 missing values.
2025-11-18 04:16:08.356996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:08.358438 INFO::Done
2025-11-18 04:16:08.360367 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 04:16:08.366836 INFO::Starting hierarchical adjustment
2025-11-18 04:16:08.3687 INFO::Found 3 batches.
2025-11-18 04:16:08.37003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 04:16:08.373082 INFO::Using default BPPARAM
2025-11-18 04:16:08.374527 INFO::Processing subtree level 1
2025-11-18 04:16:08.665721 INFO::Adjusting the last 1 batches sequentially
2025-11-18 04:16:08.677948 INFO::Done
2025-11-18 04:16:08.680249 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 04:16:08.697948 INFO::ASW Batch was 0.281748925747067 prior to batch effect correction and is now -0.144213461546573 .
2025-11-18 04:16:08.700506 INFO::ASW Label was -0.211306570429576 prior to batch effect correction and is now 0.0136921913097934 .
2025-11-18 04:16:08.703834 INFO::Total function execution time is 0.36429500579834 s and adjustment time is 0.309574127197266 s ( 84.98 )
2025-11-18 04:16:09.048925 INFO::Formatting Data.
2025-11-18 04:16:09.050745 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.053656 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.056682 INFO::Found 2 missing values.
2025-11-18 04:16:09.065285 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.066853 INFO::Done
2025-11-18 04:16:09.145062 INFO::Found NA in Reference column
2025-11-18 04:16:09.175628 INFO::Require at least two references per batch.
2025-11-18 04:16:09.23382 INFO::Formatting Data.
2025-11-18 04:16:09.235364 INFO::Recognized SummarizedExperiment
2025-11-18 04:16:09.236562 INFO::Typecasting input to dataframe.
2025-11-18 04:16:09.260264 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.262758 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.272881 INFO::Found 0 missing values.
2025-11-18 04:16:09.295921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.297425 INFO::Done
2025-11-18 04:16:09.34111 INFO::Formatting Data.
2025-11-18 04:16:09.342605 INFO::Recognized SummarizedExperiment
2025-11-18 04:16:09.343892 INFO::Typecasting input to dataframe.
2025-11-18 04:16:09.391459 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.3942 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.405336 INFO::Found 0 missing values.
2025-11-18 04:16:09.447281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.450002 INFO::Done
2025-11-18 04:16:09.49312 INFO::Formatting Data.
2025-11-18 04:16:09.494618 INFO::Recognized SummarizedExperiment
2025-11-18 04:16:09.495874 INFO::Typecasting input to dataframe.
2025-11-18 04:16:09.542087 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.544564 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.547085 INFO::Found 0 missing values.
2025-11-18 04:16:09.549331 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.
2025-11-18 04:16:09.561441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.563097 INFO::Done
2025-11-18 04:16:09.592613 INFO::Formatting Data.
2025-11-18 04:16:09.594606 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.596999 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.599638 INFO::Found 0 missing values.
2025-11-18 04:16:09.607335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.60884 INFO::Done
2025-11-18 04:16:09.640863 INFO::Formatting Data.
2025-11-18 04:16:09.64272 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.644843 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.647681 INFO::Found 0 missing values.
2025-11-18 04:16:09.65599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.657544 INFO::Done
2025-11-18 04:16:09.746929 INFO::Formatting Data.
2025-11-18 04:16:09.748817 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.751435 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.754608 INFO::Found 1 missing values.
2025-11-18 04:16:09.762297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.763832 INFO::Done
2025-11-18 04:16:09.820112 INFO::Formatting Data.
2025-11-18 04:16:09.82178 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.823753 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.826169 INFO::Found 2 missing values.
2025-11-18 04:16:09.82989 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.
2025-11-18 04:16:09.836053 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.837516 INFO::Done
2025-11-18 04:16:09.865949 INFO::Formatting Data.
2025-11-18 04:16:09.867675 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.870184 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.873399 INFO::Found 2 missing values.
2025-11-18 04:16:09.877814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.879365 INFO::Done
2025-11-18 04:16:09.908381 INFO::Formatting Data.
2025-11-18 04:16:09.9101 INFO::Typecasting input to dataframe.
2025-11-18 04:16:09.911912 INFO::Replacing NaNs with NAs.
2025-11-18 04:16:09.914595 INFO::Removing potential empty rows and columns
2025-11-18 04:16:09.917276 INFO::Found 0 missing values.
2025-11-18 04:16:09.925612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 04:16:09.92707 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
34.688 6.631 43.748
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.792 | 2.537 | 35.350 | |
| compute_asw | 0.055 | 0.002 | 0.060 | |
| count_existing | 0.028 | 0.002 | 0.032 | |
| generate_data_covariables | 0.026 | 0.004 | 0.032 | |
| generate_dataset | 0.024 | 0.001 | 0.029 | |