Yannis Schumann
| Snapshot Date: 2025-12-16 13:40 -0500 (Tue, 16 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-17 11:35 -0500 (Wed, 17 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4589 |
| 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 168/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2025-12-16 18:36:17 -0500 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 18:36:54 -0500 (Tue, 16 Dec 2025) |
| EllapsedTime: 37.5 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 10.348 0.441 7.66
* 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/4.6-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-12-16 18:36:45.322319 INFO::Formatting Data.
2025-12-16 18:36:45.324769 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:45.329644 INFO::Removing potential empty rows and columns
2025-12-16 18:36:45.464535 INFO::Found 0 missing values.
2025-12-16 18:36:45.465805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:45.46603 INFO::Done
2025-12-16 18:36:45.466219 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:45.472225 INFO::Starting hierarchical adjustment
2025-12-16 18:36:45.472541 INFO::Found 3 batches.
2025-12-16 18:36:45.472719 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:45.47315 INFO::Using default BPPARAM
2025-12-16 18:36:45.473309 INFO::Processing subtree level 1
2025-12-16 18:36:45.545446 INFO::Adjusting the last 1 batches sequentially
2025-12-16 18:36:45.547156 INFO::Done
2025-12-16 18:36:45.547469 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:45.549332 INFO::ASW Batch was -0.0405791682867847 prior to batch effect correction and is now -0.0405791682867847 .
2025-12-16 18:36:45.550448 INFO::Total function execution time is 0.228193998336792 s and adjustment time is 0.0746698379516602 s ( 32.72 )
2025-12-16 18:36:45.558895 INFO::Formatting Data.
2025-12-16 18:36:45.55918 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:45.559524 INFO::Removing potential empty rows and columns
2025-12-16 18:36:45.560009 INFO::Found 0 missing values.
2025-12-16 18:36:45.560352 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.
2025-12-16 18:36:45.564679 INFO::Formatting Data.
2025-12-16 18:36:45.564925 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:45.56523 INFO::Removing potential empty rows and columns
2025-12-16 18:36:45.565892 INFO::Found 0 missing values.
2025-12-16 18:36:45.566252 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.
2025-12-16 18:36:45.574948 INFO::Formatting Data.
2025-12-16 18:36:45.575299 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:45.575664 INFO::Removing potential empty rows and columns
2025-12-16 18:36:45.576077 INFO::Found 0 missing values.
2025-12-16 18:36:45.576408 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.
2025-12-16 18:36:45.582678 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:45.582942 INFO::Done
2025-12-16 18:36:45.583155 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:45.584104 INFO::Starting hierarchical adjustment
2025-12-16 18:36:45.584415 INFO::Found 2 batches.
2025-12-16 18:36:45.584645 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:45.584936 INFO::Using default BPPARAM
2025-12-16 18:36:45.585154 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:45.585587 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-16 18:36:45.597109 INFO::Done
2025-12-16 18:36:45.597464 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:45.598398 INFO::ASW Batch was 0.0431940648204716 prior to batch effect correction and is now -0.122485640150361 .
2025-12-16 18:36:45.598744 INFO::Total function execution time is 0.0238461494445801 s and adjustment time is 0.0127389430999756 s ( 53.42 )
2025-12-16 18:36:45.60019 INFO::Formatting Data.
2025-12-16 18:36:45.60063 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:45.604232 INFO::Formatting Data.
2025-12-16 18:36:45.604472 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:45.604764 INFO::Removing potential empty rows and columns
2025-12-16 18:36:45.605117 INFO::Found 0 missing values.
2025-12-16 18:36:45.606176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:45.606374 INFO::Done
2025-12-16 18:36:45.606539 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:45.607201 INFO::Starting hierarchical adjustment
2025-12-16 18:36:45.607426 INFO::Found 2 batches.
2025-12-16 18:36:45.607596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:45.6078 INFO::Using default BPPARAM
2025-12-16 18:36:45.607974 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:45.608249 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-16 18:36:45.637688 INFO::Done
2025-12-16 18:36:45.637992 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:45.638706 INFO::ASW Batch was -0.0413341192716271 prior to batch effect correction and is now -0.126901137806742 .
2025-12-16 18:36:45.638962 INFO::Total function execution time is 0.0347390174865723 s and adjustment time is 0.0302870273590088 s ( 87.18 )
2025-12-16 18:36:45.639267 INFO::Formatting Data.
2025-12-16 18:36:45.639467 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:45.639765 INFO::Removing potential empty rows and columns
2025-12-16 18:36:45.640126 INFO::Found 0 missing values.
2025-12-16 18:36:45.641085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:45.641285 INFO::Done
2025-12-16 18:36:45.64146 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:45.642134 INFO::Starting hierarchical adjustment
2025-12-16 18:36:45.642431 INFO::Found 2 batches.
2025-12-16 18:36:45.642616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:45.64284 INFO::Using default BPPARAM
2025-12-16 18:36:45.643027 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:45.643337 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-16 18:36:45.649562 INFO::Done
2025-12-16 18:36:45.649875 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:45.650691 INFO::ASW Batch was -0.0413341192716271 prior to batch effect correction and is now -0.126901137806742 .
2025-12-16 18:36:45.65098 INFO::Total function execution time is 0.0116879940032959 s and adjustment time is 0.0071871280670166 s ( 61.49 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-16 18:36:46.964265 INFO::Formatting Data.
2025-12-16 18:36:46.964517 INFO::Recognized SummarizedExperiment
2025-12-16 18:36:46.964673 INFO::Typecasting input to dataframe.
2025-12-16 18:36:46.974949 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:46.975399 INFO::Removing potential empty rows and columns
2025-12-16 18:36:46.976886 INFO::Found 0 missing values.
2025-12-16 18:36:46.979052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:46.979259 INFO::Done
2025-12-16 18:36:46.979413 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:46.980627 INFO::Starting hierarchical adjustment
2025-12-16 18:36:46.980864 INFO::Found 2 batches.
2025-12-16 18:36:46.981045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:46.981502 INFO::Using default BPPARAM
2025-12-16 18:36:46.981695 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:46.982058 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-16 18:36:47.003691 INFO::Done
2025-12-16 18:36:47.004009 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.005555 INFO::ASW Batch was 0.000996497693483852 prior to batch effect correction and is now -0.0894096187118763 .
2025-12-16 18:36:47.005884 INFO::Total function execution time is 0.0417091846466064 s and adjustment time is 0.0228497982025146 s ( 54.78 )
Warning: stack imbalance in '{', 73 then 75
2025-12-16 18:36:47.013418 INFO::Formatting Data.
2025-12-16 18:36:47.01374 INFO::Recognized SummarizedExperiment
2025-12-16 18:36:47.013937 INFO::Typecasting input to dataframe.
2025-12-16 18:36:47.017435 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.017864 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.019066 INFO::Found 0 missing values.
2025-12-16 18:36:47.021311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.021486 INFO::Done
2025-12-16 18:36:47.021639 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.022908 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.02313 INFO::Found 2 batches.
2025-12-16 18:36:47.023286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.023472 INFO::Using default BPPARAM
2025-12-16 18:36:47.023616 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.023905 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-16 18:36:47.032116 INFO::Done
2025-12-16 18:36:47.032343 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.033788 INFO::ASW Batch was -0.00124636596913402 prior to batch effect correction and is now -0.00124636596913402 .
2025-12-16 18:36:47.034086 INFO::Total function execution time is 0.0206811428070068 s and adjustment time is 0.00902891159057617 s ( 43.66 )
2025-12-16 18:36:47.041304 INFO::Formatting Data.
2025-12-16 18:36:47.041551 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.041832 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.042152 INFO::Found 0 missing values.
2025-12-16 18:36:47.043046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.043218 INFO::Done
2025-12-16 18:36:47.043377 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.044005 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.044208 INFO::Found 3 batches.
2025-12-16 18:36:47.044356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.044538 INFO::Using default BPPARAM
2025-12-16 18:36:47.044684 INFO::Processing subtree level 1
2025-12-16 18:36:47.132765 INFO::Adjusting the last 1 batches sequentially
2025-12-16 18:36:47.135063 INFO::Done
2025-12-16 18:36:47.135571 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.137602 INFO::ASW Batch was -0.0811418402135901 prior to batch effect correction and is now -0.159100458075918 .
2025-12-16 18:36:47.138228 INFO::Total function execution time is 0.0968930721282959 s and adjustment time is 0.0908749103546143 s ( 93.79 )
2025-12-16 18:36:47.147677 INFO::Skipping initial DF formatting
2025-12-16 18:36:47.148078 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.149668 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.149956 INFO::Found 5 batches.
2025-12-16 18:36:47.150141 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.150367 INFO::Using default BPPARAM
2025-12-16 18:36:47.150545 INFO::Processing subtree level 1
2025-12-16 18:36:47.221833 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.22468 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-16 18:36:47.233618 INFO::Done
2025-12-16 18:36:47.234305 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.236702 INFO::ASW Batch was 0.520801141634334 prior to batch effect correction and is now 0.520801141634334 .
2025-12-16 18:36:47.236946 INFO::ASW Label was 0.375243193596276 prior to batch effect correction and is now 0.375243193596276 .
2025-12-16 18:36:47.237691 INFO::Total function execution time is 0.0900158882141113 s and adjustment time is 0.0837287902832031 s ( 93.02 )
2025-12-16 18:36:47.247975 INFO::Formatting Data.
2025-12-16 18:36:47.248285 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.248683 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.249165 INFO::Found 0 missing values.
2025-12-16 18:36:47.250676 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.250918 INFO::Done
2025-12-16 18:36:47.251126 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.252351 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.252667 INFO::Found 5 batches.
2025-12-16 18:36:47.252912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.253174 INFO::Using default BPPARAM
2025-12-16 18:36:47.255961 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.
2025-12-16 18:36:47.310115 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.314965 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-16 18:36:47.323278 INFO::Done
2025-12-16 18:36:47.323677 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.325138 INFO::ASW Batch was 0.587770318760578 prior to batch effect correction and is now -0.0918687918899615 .
2025-12-16 18:36:47.325369 INFO::ASW Label was 0.179824500735187 prior to batch effect correction and is now 0.812849923050568 .
2025-12-16 18:36:47.325892 INFO::Total function execution time is 0.07796311378479 s and adjustment time is 0.0706779956817627 s ( 90.66 )
2025-12-16 18:36:47.326212 INFO::Formatting Data.
2025-12-16 18:36:47.326393 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.326799 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.330821 INFO::Found 0 missing values.
2025-12-16 18:36:47.332502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.33271 INFO::Done
2025-12-16 18:36:47.332906 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.334068 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.334338 INFO::Found 5 batches.
2025-12-16 18:36:47.334501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.334929 INFO::Using default BPPARAM
2025-12-16 18:36:47.335105 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.
2025-12-16 18:36:47.394762 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.3996 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-16 18:36:47.407399 INFO::Done
2025-12-16 18:36:47.407644 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.409473 INFO::ASW Batch was 0.587770318760578 prior to batch effect correction and is now -0.0918687918899615 .
2025-12-16 18:36:47.409707 INFO::ASW Label was 0.179824500735187 prior to batch effect correction and is now 0.812849923050568 .
2025-12-16 18:36:47.410233 INFO::Total function execution time is 0.0839829444885254 s and adjustment time is 0.0731220245361328 s ( 87.07 )
2025-12-16 18:36:47.416207 INFO::Formatting Data.
2025-12-16 18:36:47.41647 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.416773 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.417118 INFO::Found 0 missing values.
2025-12-16 18:36:47.418315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.418488 INFO::Done
2025-12-16 18:36:47.418652 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.41961 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.419843 INFO::Found 5 batches.
2025-12-16 18:36:47.420002 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.420206 INFO::Using default BPPARAM
2025-12-16 18:36:47.420363 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.
2025-12-16 18:36:47.488714 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.492962 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-16 18:36:47.506187 INFO::Done
2025-12-16 18:36:47.506488 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.508189 INFO::ASW Batch was 0.394329853596795 prior to batch effect correction and is now -0.0306198580363725 .
2025-12-16 18:36:47.508408 INFO::ASW Label was 0.509501250895523 prior to batch effect correction and is now 0.766401613406421 .
2025-12-16 18:36:47.508995 INFO::Total function execution time is 0.0927939414978027 s and adjustment time is 0.0863738059997559 s ( 93.08 )
2025-12-16 18:36:47.50931 INFO::Formatting Data.
2025-12-16 18:36:47.509498 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.5098 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.510142 INFO::Found 0 missing values.
2025-12-16 18:36:47.511388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.511559 INFO::Done
2025-12-16 18:36:47.511832 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.512735 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.512966 INFO::Found 5 batches.
2025-12-16 18:36:47.513131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.513487 INFO::Using default BPPARAM
2025-12-16 18:36:47.513653 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.
2025-12-16 18:36:47.580131 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.586861 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-16 18:36:47.597172 INFO::Done
2025-12-16 18:36:47.597676 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.59987 INFO::ASW Batch was 0.394329853596795 prior to batch effect correction and is now -0.0306198580363725 .
2025-12-16 18:36:47.600201 INFO::ASW Label was 0.509501250895523 prior to batch effect correction and is now 0.766401613406421 .
2025-12-16 18:36:47.600869 INFO::Total function execution time is 0.0915060043334961 s and adjustment time is 0.0842359066009521 s ( 92.06 )
2025-12-16 18:36:47.60895 INFO::Formatting Data.
2025-12-16 18:36:47.609274 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.609626 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.610053 INFO::Found 0 missing values.
2025-12-16 18:36:47.610986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.611168 INFO::Done
2025-12-16 18:36:47.611342 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.612417 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.612676 INFO::Found 2 batches.
2025-12-16 18:36:47.61288 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.613161 INFO::Using default BPPARAM
2025-12-16 18:36:47.613352 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.613657 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-16 18:36:47.619079 INFO::Done
2025-12-16 18:36:47.619308 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.620263 INFO::ASW Batch was 0.201584330570658 prior to batch effect correction and is now 0.0529595996985835 .
2025-12-16 18:36:47.620493 INFO::ASW Label was 0.843221345029777 prior to batch effect correction and is now 0.906515972215845 .
2025-12-16 18:36:47.620765 INFO::Total function execution time is 0.011864185333252 s and adjustment time is 0.00644612312316895 s ( 54.33 )
2025-12-16 18:36:47.621002 INFO::Formatting Data.
2025-12-16 18:36:47.621172 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.621447 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.621774 INFO::Found 0 missing values.
2025-12-16 18:36:47.622585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.622758 INFO::Done
2025-12-16 18:36:47.622922 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.623826 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.624053 INFO::Found 2 batches.
2025-12-16 18:36:47.624225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.624425 INFO::Using default BPPARAM
2025-12-16 18:36:47.624583 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.62486 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-16 18:36:47.630063 INFO::Done
2025-12-16 18:36:47.630296 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.631243 INFO::ASW Batch was 0.201584330570658 prior to batch effect correction and is now 0.0529595996985835 .
2025-12-16 18:36:47.631429 INFO::ASW Label was 0.843221345029777 prior to batch effect correction and is now 0.906515972215845 .
2025-12-16 18:36:47.631682 INFO::Total function execution time is 0.0106630325317383 s and adjustment time is 0.00604701042175293 s ( 56.71 )
2025-12-16 18:36:47.636575 INFO::Formatting Data.
2025-12-16 18:36:47.636842 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.637137 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.637446 INFO::Found 0 missing values.
2025-12-16 18:36:47.638119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.638297 INFO::Done
2025-12-16 18:36:47.638459 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.639133 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.639369 INFO::Found 2 batches.
2025-12-16 18:36:47.639534 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.639769 INFO::Using default BPPARAM
2025-12-16 18:36:47.639919 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.640183 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-16 18:36:47.652517 INFO::Done
2025-12-16 18:36:47.652882 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.653677 INFO::ASW Batch was 0.228141410467575 prior to batch effect correction and is now -0.0344600904880534 .
2025-12-16 18:36:47.654019 INFO::Total function execution time is 0.0174839496612549 s and adjustment time is 0.0131728649139404 s ( 75.34 )
2025-12-16 18:36:47.659561 INFO::Formatting Data.
2025-12-16 18:36:47.659868 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.660216 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.660617 INFO::Found 0 missing values.
2025-12-16 18:36:47.661066 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.
2025-12-16 18:36:47.662464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.66265 INFO::Done
2025-12-16 18:36:47.662815 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.663761 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.663998 INFO::Found 2 batches.
2025-12-16 18:36:47.66415 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.664401 INFO::Using default BPPARAM
2025-12-16 18:36:47.664599 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.66492 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-16 18:36:47.670881 INFO::Done
2025-12-16 18:36:47.671148 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.672437 INFO::ASW Batch was 0.66052853646379 prior to batch effect correction and is now 0.158256166423596 .
2025-12-16 18:36:47.672758 INFO::ASW Label was 0.423766214844841 prior to batch effect correction and is now 0.808584771387106 .
2025-12-16 18:36:47.673074 INFO::Total function execution time is 0.0135400295257568 s and adjustment time is 0.00689411163330078 s ( 50.92 )
2025-12-16 18:36:47.673361 INFO::Formatting Data.
2025-12-16 18:36:47.673553 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.673869 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.674194 INFO::Found 0 missing values.
2025-12-16 18:36:47.6745 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.
2025-12-16 18:36:47.675902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.676081 INFO::Done
2025-12-16 18:36:47.676243 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.677154 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.677365 INFO::Found 2 batches.
2025-12-16 18:36:47.67752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.677706 INFO::Using default BPPARAM
2025-12-16 18:36:47.677882 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:47.678158 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-16 18:36:47.686138 INFO::Done
2025-12-16 18:36:47.686394 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.68737 INFO::ASW Batch was 0.66052853646379 prior to batch effect correction and is now 0.158256166423596 .
2025-12-16 18:36:47.687567 INFO::ASW Label was 0.423766214844841 prior to batch effect correction and is now 0.808584771387106 .
2025-12-16 18:36:47.687817 INFO::Total function execution time is 0.0144500732421875 s and adjustment time is 0.00880193710327148 s ( 60.91 )
2025-12-16 18:36:47.760069 INFO::Formatting Data.
2025-12-16 18:36:47.760387 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.760718 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.761075 INFO::Found 0 missing values.
2025-12-16 18:36:47.762012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.762189 INFO::Done
2025-12-16 18:36:47.762356 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.763054 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.763282 INFO::Found 3 batches.
2025-12-16 18:36:47.763449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.763642 INFO::Using default BPPARAM
2025-12-16 18:36:47.763796 INFO::Processing subtree level 1
2025-12-16 18:36:47.822361 INFO::Adjusting the last 1 batches sequentially
2025-12-16 18:36:47.824236 INFO::Done
2025-12-16 18:36:47.824599 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.826289 INFO::ASW Batch was -0.0582821371943505 prior to batch effect correction and is now -0.0582821371943505 .
2025-12-16 18:36:47.82691 INFO::Total function execution time is 0.0668950080871582 s and adjustment time is 0.0609989166259766 s ( 91.19 )
2025-12-16 18:36:47.827374 INFO::Formatting Data.
2025-12-16 18:36:47.827567 INFO::Typecasting input to dataframe.
2025-12-16 18:36:47.828216 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.828643 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.829105 INFO::Found 0 missing values.
2025-12-16 18:36:47.830355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.830696 INFO::Done
2025-12-16 18:36:47.830963 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.831688 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.83193 INFO::Found 3 batches.
2025-12-16 18:36:47.832232 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.832451 INFO::Using default BPPARAM
2025-12-16 18:36:47.832613 INFO::Processing subtree level 1
2025-12-16 18:36:47.88349 INFO::Adjusting the last 1 batches sequentially
2025-12-16 18:36:47.885976 INFO::Done
2025-12-16 18:36:47.886631 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.88841 INFO::ASW Batch was -0.0582821371943505 prior to batch effect correction and is now -0.0582821371943505 .
2025-12-16 18:36:47.889122 INFO::Total function execution time is 0.0618140697479248 s and adjustment time is 0.0540809631347656 s ( 87.49 )
2025-12-16 18:36:47.896306 INFO::Formatting Data.
2025-12-16 18:36:47.896581 INFO::Typecasting input to dataframe.
2025-12-16 18:36:47.896882 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:47.897203 INFO::Removing potential empty rows and columns
2025-12-16 18:36:47.897618 INFO::Found 0 missing values.
2025-12-16 18:36:47.898549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:47.898718 INFO::Done
2025-12-16 18:36:47.898894 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:47.899577 INFO::Starting hierarchical adjustment
2025-12-16 18:36:47.899813 INFO::Found 3 batches.
2025-12-16 18:36:47.899977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:47.900188 INFO::Using default BPPARAM
2025-12-16 18:36:47.900387 INFO::Processing subtree level 1
2025-12-16 18:36:47.952381 INFO::Adjusting the last 1 batches sequentially
2025-12-16 18:36:47.95458 INFO::Done
2025-12-16 18:36:47.954985 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:47.957396 INFO::ASW Batch was -0.0255887215907312 prior to batch effect correction and is now -0.0255887215907312 .
2025-12-16 18:36:47.958323 INFO::Total function execution time is 0.0621581077575684 s and adjustment time is 0.0548019409179688 s ( 88.17 )
2025-12-16 18:36:48.047404 INFO::Formatting Data.
2025-12-16 18:36:48.047674 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:48.048088 INFO::Removing potential empty rows and columns
2025-12-16 18:36:48.049066 INFO::Found 1000 missing values.
2025-12-16 18:36:48.055681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:48.055987 INFO::Done
2025-12-16 18:36:48.056241 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:48.05835 INFO::Starting hierarchical adjustment
2025-12-16 18:36:48.058628 INFO::Found 10 batches.
2025-12-16 18:36:48.058807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:48.059057 INFO::Using default BPPARAM
2025-12-16 18:36:48.059234 INFO::Processing subtree level 1
2025-12-16 18:36:48.133967 INFO::Processing subtree level 2
2025-12-16 18:36:48.270039 INFO::Adjusting the last 1 batches sequentially
2025-12-16 18:36:48.271488 INFO::Done
2025-12-16 18:36:48.271731 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:48.274501 INFO::ASW Batch was 0.518199021724486 prior to batch effect correction and is now 0.518199021724486 .
2025-12-16 18:36:48.275223 INFO::ASW Label was 0.322905836872616 prior to batch effect correction and is now 0.322905836872616 .
2025-12-16 18:36:48.280987 INFO::Total function execution time is 0.232418060302734 s and adjustment time is 0.212905168533325 s ( 91.6 )
2025-12-16 18:36:48.282164 INFO::Formatting Data.
2025-12-16 18:36:48.282658 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:48.318614 INFO::Removing potential empty rows and columns
2025-12-16 18:36:48.319594 INFO::Found 1000 missing values.
2025-12-16 18:36:48.326589 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:48.326859 INFO::Done
2025-12-16 18:36:48.327042 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:48.329178 INFO::Starting hierarchical adjustment
2025-12-16 18:36:48.329488 INFO::Found 10 batches.
2025-12-16 18:36:48.871489 INFO::Set up parallel execution backend with 2 workers
2025-12-16 18:36:48.871832 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-16 18:36:49.527168 INFO::Adjusting the last 2 batches sequentially
2025-12-16 18:36:49.527789 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-16 18:36:49.533616 INFO::Done
2025-12-16 18:36:49.533858 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:49.535738 INFO::ASW Batch was 0.518199021724486 prior to batch effect correction and is now 0.518199021724486 .
2025-12-16 18:36:49.535923 INFO::ASW Label was 0.322905836872616 prior to batch effect correction and is now 0.322905836872616 .
2025-12-16 18:36:49.536182 INFO::Total function execution time is 1.25403809547424 s and adjustment time is 1.20419502258301 s ( 96.03 )
2025-12-16 18:36:49.614461 INFO::Formatting Data.
2025-12-16 18:36:49.614868 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.616246 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.616853 INFO::Found 0 missing values.
2025-12-16 18:36:49.618314 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.618519 INFO::Done
2025-12-16 18:36:49.618732 INFO::Acquiring quality metrics before batch effect correction.
2025-12-16 18:36:49.619829 INFO::Starting hierarchical adjustment
2025-12-16 18:36:49.620094 INFO::Found 3 batches.
2025-12-16 18:36:49.620285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-16 18:36:49.620526 INFO::Using default BPPARAM
2025-12-16 18:36:49.620712 INFO::Processing subtree level 1
2025-12-16 18:36:49.672989 INFO::Adjusting the last 1 batches sequentially
2025-12-16 18:36:49.675868 INFO::Done
2025-12-16 18:36:49.676312 INFO::Acquiring quality metrics after batch effect correction.
2025-12-16 18:36:49.678506 INFO::ASW Batch was 0.133702505344927 prior to batch effect correction and is now -0.140568316743182 .
2025-12-16 18:36:49.678852 INFO::ASW Label was -0.181096947846586 prior to batch effect correction and is now -0.0172119316985758 .
2025-12-16 18:36:49.679482 INFO::Total function execution time is 0.0650510787963867 s and adjustment time is 0.0558040142059326 s ( 85.78 )
2025-12-16 18:36:49.743595 INFO::Formatting Data.
2025-12-16 18:36:49.743977 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.744322 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.744731 INFO::Found 2 missing values.
2025-12-16 18:36:49.745736 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.745935 INFO::Done
2025-12-16 18:36:49.762334 INFO::Found NA in Reference column
2025-12-16 18:36:49.7664 INFO::Require at least two references per batch.
2025-12-16 18:36:49.776742 INFO::Formatting Data.
2025-12-16 18:36:49.777002 INFO::Recognized SummarizedExperiment
2025-12-16 18:36:49.777179 INFO::Typecasting input to dataframe.
2025-12-16 18:36:49.780974 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.781398 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.782798 INFO::Found 0 missing values.
2025-12-16 18:36:49.785983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.786204 INFO::Done
2025-12-16 18:36:49.793758 INFO::Formatting Data.
2025-12-16 18:36:49.794018 INFO::Recognized SummarizedExperiment
2025-12-16 18:36:49.794208 INFO::Typecasting input to dataframe.
2025-12-16 18:36:49.802619 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.803127 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.805469 INFO::Found 0 missing values.
2025-12-16 18:36:49.810858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.811115 INFO::Done
2025-12-16 18:36:49.818508 INFO::Formatting Data.
2025-12-16 18:36:49.818818 INFO::Recognized SummarizedExperiment
2025-12-16 18:36:49.819004 INFO::Typecasting input to dataframe.
2025-12-16 18:36:49.825207 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.825573 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.825978 INFO::Found 0 missing values.
2025-12-16 18:36:49.826295 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.
2025-12-16 18:36:49.827936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.828131 INFO::Done
2025-12-16 18:36:49.833132 INFO::Formatting Data.
2025-12-16 18:36:49.833395 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.833699 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.83406 INFO::Found 0 missing values.
2025-12-16 18:36:49.83513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.835323 INFO::Done
2025-12-16 18:36:49.840553 INFO::Formatting Data.
2025-12-16 18:36:49.840972 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.841336 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.841768 INFO::Found 0 missing values.
2025-12-16 18:36:49.842758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.842933 INFO::Done
2025-12-16 18:36:49.85639 INFO::Formatting Data.
2025-12-16 18:36:49.856715 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.857119 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.857543 INFO::Found 1 missing values.
2025-12-16 18:36:49.858456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.858643 INFO::Done
2025-12-16 18:36:49.87322 INFO::Formatting Data.
2025-12-16 18:36:49.873574 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.873887 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.87422 INFO::Found 2 missing values.
2025-12-16 18:36:49.874702 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.
2025-12-16 18:36:49.875606 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.875812 INFO::Done
2025-12-16 18:36:49.890902 INFO::Formatting Data.
2025-12-16 18:36:49.891586 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.891988 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.892352 INFO::Found 2 missing values.
2025-12-16 18:36:49.893043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.893222 INFO::Done
2025-12-16 18:36:49.898549 INFO::Formatting Data.
2025-12-16 18:36:49.89884 INFO::Typecasting input to dataframe.
2025-12-16 18:36:49.899134 INFO::Replacing NaNs with NAs.
2025-12-16 18:36:49.899437 INFO::Removing potential empty rows and columns
2025-12-16 18:36:49.899799 INFO::Found 0 missing values.
2025-12-16 18:36:49.900798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-16 18:36:49.900996 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.356 1.764 9.804
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.348 | 0.441 | 7.660 | |
| compute_asw | 0.01 | 0.00 | 0.01 | |
| count_existing | 0.005 | 0.000 | 0.006 | |
| generate_data_covariables | 0.005 | 0.001 | 0.007 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |