Yannis Schumann
| Snapshot Date: 2025-11-11 13:40 -0500 (Tue, 11 Nov 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-12 11:32 -0500 (Wed, 12 Nov 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" | 4823 |
| 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 166/2325 | 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 | | ||||||||
|
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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-11-11 21:26:14 -0500 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 21:27:45 -0500 (Tue, 11 Nov 2025) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 23.823 1.699 17.788
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
2025-11-11 21:27:06.143798 INFO::Formatting Data.
2025-11-11 21:27:06.145107 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:06.155809 INFO::Removing potential empty rows and columns
2025-11-11 21:27:06.394972 INFO::Found 0 missing values.
2025-11-11 21:27:06.398633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:06.399402 INFO::Done
2025-11-11 21:27:06.400005 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:06.412704 INFO::Starting hierarchical adjustment
2025-11-11 21:27:06.413713 INFO::Found 3 batches.
2025-11-11 21:27:06.41434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:06.415645 INFO::Using default BPPARAM
2025-11-11 21:27:06.416265 INFO::Processing subtree level 1
2025-11-11 21:27:06.529446 INFO::Adjusting the last 1 batches sequentially
2025-11-11 21:27:06.531617 INFO::Done
2025-11-11 21:27:06.532392 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:06.535229 INFO::ASW Batch was -0.00709481933181945 prior to batch effect correction and is now -0.00709481933181945 .
2025-11-11 21:27:06.53641 INFO::Total function execution time is 0.393163204193115 s and adjustment time is 0.118094205856323 s ( 30.04 )
2025-11-11 21:27:06.563552 INFO::Formatting Data.
2025-11-11 21:27:06.564769 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:06.565966 INFO::Removing potential empty rows and columns
2025-11-11 21:27:06.567286 INFO::Found 0 missing values.
2025-11-11 21:27:06.568444 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.
2025-11-11 21:27:06.581198 INFO::Formatting Data.
2025-11-11 21:27:06.582005 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:06.582962 INFO::Removing potential empty rows and columns
2025-11-11 21:27:06.584056 INFO::Found 0 missing values.
2025-11-11 21:27:06.585018 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.
2025-11-11 21:27:06.600951 INFO::Formatting Data.
2025-11-11 21:27:06.601699 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:06.602597 INFO::Removing potential empty rows and columns
2025-11-11 21:27:06.603625 INFO::Found 0 missing values.
2025-11-11 21:27:06.604525 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.
2025-11-11 21:27:06.608817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:06.609375 INFO::Done
2025-11-11 21:27:06.609912 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:06.612208 INFO::Starting hierarchical adjustment
2025-11-11 21:27:06.612913 INFO::Found 2 batches.
2025-11-11 21:27:06.61343 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:06.614108 INFO::Using default BPPARAM
2025-11-11 21:27:06.61466 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:06.615633 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 21:27:06.641067 INFO::Done
2025-11-11 21:27:06.641873 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:06.644098 INFO::ASW Batch was 0.00897383243560155 prior to batch effect correction and is now -0.120625213627434 .
2025-11-11 21:27:06.645008 INFO::Total function execution time is 0.0440876483917236 s and adjustment time is 0.0282473564147949 s ( 64.07 )
2025-11-11 21:27:06.647995 INFO::Formatting Data.
2025-11-11 21:27:06.648669 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:06.657617 INFO::Formatting Data.
2025-11-11 21:27:06.658329 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:06.65922 INFO::Removing potential empty rows and columns
2025-11-11 21:27:06.660254 INFO::Found 0 missing values.
2025-11-11 21:27:06.663129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:06.663681 INFO::Done
2025-11-11 21:27:06.664209 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:06.666272 INFO::Starting hierarchical adjustment
2025-11-11 21:27:06.666984 INFO::Found 2 batches.
2025-11-11 21:27:06.66752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:06.668184 INFO::Using default BPPARAM
2025-11-11 21:27:06.668747 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:06.670088 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 21:27:06.720361 INFO::Done
2025-11-11 21:27:06.721072 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:06.723042 INFO::ASW Batch was -0.0246787201658367 prior to batch effect correction and is now -0.123924004089757 .
2025-11-11 21:27:06.723804 INFO::Total function execution time is 0.0662243366241455 s and adjustment time is 0.0535132884979248 s ( 80.81 )
2025-11-11 21:27:06.724783 INFO::Formatting Data.
2025-11-11 21:27:06.725362 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:06.72618 INFO::Removing potential empty rows and columns
2025-11-11 21:27:06.727133 INFO::Found 0 missing values.
2025-11-11 21:27:06.729684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:06.730212 INFO::Done
2025-11-11 21:27:06.730689 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:06.732483 INFO::Starting hierarchical adjustment
2025-11-11 21:27:06.733141 INFO::Found 2 batches.
2025-11-11 21:27:06.733627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:06.734196 INFO::Using default BPPARAM
2025-11-11 21:27:06.734679 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:06.735544 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 21:27:06.748998 INFO::Done
2025-11-11 21:27:06.749609 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:06.751443 INFO::ASW Batch was -0.0246787201658367 prior to batch effect correction and is now -0.123924004089757 .
2025-11-11 21:27:06.752167 INFO::Total function execution time is 0.0273809432983398 s and adjustment time is 0.015977144241333 s ( 58.35 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-11 21:27:10.045236 INFO::Formatting Data.
2025-11-11 21:27:10.04606 INFO::Recognized SummarizedExperiment
2025-11-11 21:27:10.046552 INFO::Typecasting input to dataframe.
2025-11-11 21:27:10.077736 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:10.079376 INFO::Removing potential empty rows and columns
2025-11-11 21:27:10.083269 INFO::Found 0 missing values.
2025-11-11 21:27:10.090387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:10.091048 INFO::Done
2025-11-11 21:27:10.091599 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:10.095515 INFO::Starting hierarchical adjustment
2025-11-11 21:27:10.096269 INFO::Found 2 batches.
2025-11-11 21:27:10.096795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:10.098003 INFO::Using default BPPARAM
2025-11-11 21:27:10.098541 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:10.099527 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 21:27:10.155741 INFO::Done
2025-11-11 21:27:10.156439 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:10.159487 INFO::ASW Batch was -0.0236925798157544 prior to batch effect correction and is now -0.0915707341666395 .
2025-11-11 21:27:10.160281 INFO::Total function execution time is 0.115385770797729 s and adjustment time is 0.0596189498901367 s ( 51.67 )
Warning: stack imbalance in '{', 73 then 74
2025-11-11 21:27:10.17757 INFO::Formatting Data.
2025-11-11 21:27:10.178359 INFO::Recognized SummarizedExperiment
2025-11-11 21:27:10.178893 INFO::Typecasting input to dataframe.
2025-11-11 21:27:10.187742 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:10.188958 INFO::Removing potential empty rows and columns
2025-11-11 21:27:10.192324 INFO::Found 0 missing values.
2025-11-11 21:27:10.198875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:10.199438 INFO::Done
2025-11-11 21:27:10.199966 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:10.203285 INFO::Starting hierarchical adjustment
2025-11-11 21:27:10.203993 INFO::Found 2 batches.
2025-11-11 21:27:10.204486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:10.205117 INFO::Using default BPPARAM
2025-11-11 21:27:10.205615 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:10.206566 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 21:27:10.23024 INFO::Done
2025-11-11 21:27:10.231089 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:10.235294 INFO::ASW Batch was 0.00951288542069842 prior to batch effect correction and is now 0.00951288542069842 .
2025-11-11 21:27:10.236329 INFO::Total function execution time is 0.0587196350097656 s and adjustment time is 0.0263569355010986 s ( 44.89 )
2025-11-11 21:27:10.256426 INFO::Formatting Data.
2025-11-11 21:27:10.257359 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:10.258345 INFO::Removing potential empty rows and columns
2025-11-11 21:27:10.259442 INFO::Found 0 missing values.
2025-11-11 21:27:10.262533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:10.263133 INFO::Done
2025-11-11 21:27:10.263684 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:10.265734 INFO::Starting hierarchical adjustment
2025-11-11 21:27:10.266446 INFO::Found 3 batches.
2025-11-11 21:27:10.266984 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:10.26759 INFO::Using default BPPARAM
2025-11-11 21:27:10.268133 INFO::Processing subtree level 1
2025-11-11 21:27:10.437402 INFO::Adjusting the last 1 batches sequentially
2025-11-11 21:27:10.439961 INFO::Done
2025-11-11 21:27:10.440685 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:10.443828 INFO::ASW Batch was -0.0662902757000003 prior to batch effect correction and is now -0.153486139725741 .
2025-11-11 21:27:10.44499 INFO::Total function execution time is 0.188546180725098 s and adjustment time is 0.173585891723633 s ( 92.07 )
2025-11-11 21:27:10.462405 INFO::Skipping initial DF formatting
2025-11-11 21:27:10.46325 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:10.467977 INFO::Starting hierarchical adjustment
2025-11-11 21:27:10.468868 INFO::Found 5 batches.
2025-11-11 21:27:10.469447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:10.470139 INFO::Using default BPPARAM
2025-11-11 21:27:10.470702 INFO::Processing subtree level 1
2025-11-11 21:27:10.627569 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:10.629679 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 21:27:10.651218 INFO::Done
2025-11-11 21:27:10.652141 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:10.656829 INFO::ASW Batch was 0.511720915054626 prior to batch effect correction and is now 0.511720915054626 .
2025-11-11 21:27:10.657523 INFO::ASW Label was 0.441768011244844 prior to batch effect correction and is now 0.441768011244844 .
2025-11-11 21:27:10.658444 INFO::Total function execution time is 0.196158885955811 s and adjustment time is 0.182532548904419 s ( 93.05 )
2025-11-11 21:27:10.677262 INFO::Formatting Data.
2025-11-11 21:27:10.678233 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:10.679265 INFO::Removing potential empty rows and columns
2025-11-11 21:27:10.680316 INFO::Found 0 missing values.
2025-11-11 21:27:10.684532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:10.685104 INFO::Done
2025-11-11 21:27:10.685632 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:10.689554 INFO::Starting hierarchical adjustment
2025-11-11 21:27:10.690388 INFO::Found 5 batches.
2025-11-11 21:27:10.690985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:10.691711 INFO::Using default BPPARAM
2025-11-11 21:27:10.692322 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.
2025-11-11 21:27:10.860861 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:10.862982 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 21:27:10.887143 INFO::Done
2025-11-11 21:27:10.888207 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:10.892154 INFO::ASW Batch was 0.254827392809794 prior to batch effect correction and is now -0.0887589182376165 .
2025-11-11 21:27:10.89289 INFO::ASW Label was 0.434969565019749 prior to batch effect correction and is now 0.880500392236391 .
2025-11-11 21:27:10.893801 INFO::Total function execution time is 0.216655731201172 s and adjustment time is 0.196855545043945 s ( 90.86 )
2025-11-11 21:27:10.894771 INFO::Formatting Data.
2025-11-11 21:27:10.895487 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:10.896472 INFO::Removing potential empty rows and columns
2025-11-11 21:27:10.897607 INFO::Found 0 missing values.
2025-11-11 21:27:10.90209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:10.902671 INFO::Done
2025-11-11 21:27:10.903252 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:10.906737 INFO::Starting hierarchical adjustment
2025-11-11 21:27:10.907529 INFO::Found 5 batches.
2025-11-11 21:27:10.908094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:10.908801 INFO::Using default BPPARAM
2025-11-11 21:27:10.90938 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.
2025-11-11 21:27:11.054939 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:11.0573 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 21:27:11.076726 INFO::Done
2025-11-11 21:27:11.077666 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:11.081402 INFO::ASW Batch was 0.254827392809794 prior to batch effect correction and is now -0.0887589182376165 .
2025-11-11 21:27:11.082123 INFO::ASW Label was 0.434969565019749 prior to batch effect correction and is now 0.880500392236391 .
2025-11-11 21:27:11.083072 INFO::Total function execution time is 0.188308954238892 s and adjustment time is 0.169302701950073 s ( 89.91 )
2025-11-11 21:27:11.098479 INFO::Formatting Data.
2025-11-11 21:27:11.099451 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:11.100524 INFO::Removing potential empty rows and columns
2025-11-11 21:27:11.101626 INFO::Found 0 missing values.
2025-11-11 21:27:11.106027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:11.106703 INFO::Done
2025-11-11 21:27:11.10728 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:11.11083 INFO::Starting hierarchical adjustment
2025-11-11 21:27:11.111703 INFO::Found 5 batches.
2025-11-11 21:27:11.112305 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:11.113018 INFO::Using default BPPARAM
2025-11-11 21:27:11.113611 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.
2025-11-11 21:27:11.271737 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:11.275299 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 21:27:11.296485 INFO::Done
2025-11-11 21:27:11.29748 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:11.301388 INFO::ASW Batch was 0.132188038241442 prior to batch effect correction and is now -0.104109086534342 .
2025-11-11 21:27:11.302219 INFO::ASW Label was 0.642812906876566 prior to batch effect correction and is now 0.879065073015532 .
2025-11-11 21:27:11.303189 INFO::Total function execution time is 0.20480751991272 s and adjustment time is 0.18486762046814 s ( 90.26 )
2025-11-11 21:27:11.304245 INFO::Formatting Data.
2025-11-11 21:27:11.304967 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:11.306067 INFO::Removing potential empty rows and columns
2025-11-11 21:27:11.307343 INFO::Found 0 missing values.
2025-11-11 21:27:11.312238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:11.313127 INFO::Done
2025-11-11 21:27:11.313778 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:11.317515 INFO::Starting hierarchical adjustment
2025-11-11 21:27:11.318491 INFO::Found 5 batches.
2025-11-11 21:27:11.319096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:11.319773 INFO::Using default BPPARAM
2025-11-11 21:27:11.320343 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.
2025-11-11 21:27:11.447304 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:11.449402 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 21:27:11.46721 INFO::Done
2025-11-11 21:27:11.468165 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:11.471947 INFO::ASW Batch was 0.132188038241442 prior to batch effect correction and is now -0.104109086534342 .
2025-11-11 21:27:11.472697 INFO::ASW Label was 0.642812906876566 prior to batch effect correction and is now 0.879065073015532 .
2025-11-11 21:27:11.47364 INFO::Total function execution time is 0.169433832168579 s and adjustment time is 0.148855447769165 s ( 87.85 )
2025-11-11 21:27:11.488862 INFO::Formatting Data.
2025-11-11 21:27:11.489894 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:11.491071 INFO::Removing potential empty rows and columns
2025-11-11 21:27:11.492233 INFO::Found 0 missing values.
2025-11-11 21:27:11.495295 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:11.495936 INFO::Done
2025-11-11 21:27:11.4965 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:11.499967 INFO::Starting hierarchical adjustment
2025-11-11 21:27:11.500744 INFO::Found 2 batches.
2025-11-11 21:27:11.501331 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:11.502022 INFO::Using default BPPARAM
2025-11-11 21:27:11.502596 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:11.50363 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 21:27:11.521594 INFO::Done
2025-11-11 21:27:11.522555 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:11.52617 INFO::ASW Batch was 0.481098572521712 prior to batch effect correction and is now 0.0567837945630228 .
2025-11-11 21:27:11.526933 INFO::ASW Label was 0.587801771855587 prior to batch effect correction and is now 0.87258142842879 .
2025-11-11 21:27:11.527859 INFO::Total function execution time is 0.0391805171966553 s and adjustment time is 0.0209319591522217 s ( 53.42 )
2025-11-11 21:27:11.528691 INFO::Formatting Data.
2025-11-11 21:27:11.529375 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:11.530342 INFO::Removing potential empty rows and columns
2025-11-11 21:27:11.531398 INFO::Found 0 missing values.
2025-11-11 21:27:11.534336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:11.534934 INFO::Done
2025-11-11 21:27:11.535476 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:11.538987 INFO::Starting hierarchical adjustment
2025-11-11 21:27:11.539779 INFO::Found 2 batches.
2025-11-11 21:27:11.54035 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:11.54102 INFO::Using default BPPARAM
2025-11-11 21:27:11.541622 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:11.542669 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 21:27:11.559792 INFO::Done
2025-11-11 21:27:11.560652 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:11.563976 INFO::ASW Batch was 0.481098572521712 prior to batch effect correction and is now 0.0567837945630228 .
2025-11-11 21:27:11.564668 INFO::ASW Label was 0.587801771855587 prior to batch effect correction and is now 0.87258142842879 .
2025-11-11 21:27:11.565547 INFO::Total function execution time is 0.0368554592132568 s and adjustment time is 0.0201241970062256 s ( 54.6 )
2025-11-11 21:27:11.577656 INFO::Formatting Data.
2025-11-11 21:27:11.578616 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:11.579606 INFO::Removing potential empty rows and columns
2025-11-11 21:27:11.580607 INFO::Found 0 missing values.
2025-11-11 21:27:11.582958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:11.583515 INFO::Done
2025-11-11 21:27:11.584091 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:11.586284 INFO::Starting hierarchical adjustment
2025-11-11 21:27:11.587051 INFO::Found 2 batches.
2025-11-11 21:27:11.587674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:11.588302 INFO::Using default BPPARAM
2025-11-11 21:27:11.588894 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:11.589854 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 21:27:11.624668 INFO::Done
2025-11-11 21:27:11.625564 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:11.62797 INFO::ASW Batch was 0.124067805383316 prior to batch effect correction and is now -0.167812267442742 .
2025-11-11 21:27:11.628929 INFO::Total function execution time is 0.0513885021209717 s and adjustment time is 0.0377535820007324 s ( 73.47 )
2025-11-11 21:27:11.641961 INFO::Formatting Data.
2025-11-11 21:27:11.642918 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:11.643906 INFO::Removing potential empty rows and columns
2025-11-11 21:27:11.64499 INFO::Found 0 missing values.
2025-11-11 21:27:11.646209 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.
2025-11-11 21:27:11.651265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:11.651926 INFO::Done
2025-11-11 21:27:11.65247 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:11.656218 INFO::Starting hierarchical adjustment
2025-11-11 21:27:11.657017 INFO::Found 2 batches.
2025-11-11 21:27:11.657568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:11.658255 INFO::Using default BPPARAM
2025-11-11 21:27:11.658784 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:11.659788 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 21:27:11.677911 INFO::Done
2025-11-11 21:27:11.67872 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:11.68201 INFO::ASW Batch was 0.470671812044892 prior to batch effect correction and is now 0.162515015226308 .
2025-11-11 21:27:11.682709 INFO::ASW Label was 0.614119075194418 prior to batch effect correction and is now 0.674341674578469 .
2025-11-11 21:27:11.683606 INFO::Total function execution time is 0.0418038368225098 s and adjustment time is 0.0209996700286865 s ( 50.23 )
2025-11-11 21:27:11.684472 INFO::Formatting Data.
2025-11-11 21:27:11.685129 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:11.686166 INFO::Removing potential empty rows and columns
2025-11-11 21:27:11.6872 INFO::Found 0 missing values.
2025-11-11 21:27:11.688152 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.
2025-11-11 21:27:11.693156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:11.693727 INFO::Done
2025-11-11 21:27:11.694291 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:11.697381 INFO::Starting hierarchical adjustment
2025-11-11 21:27:11.698121 INFO::Found 2 batches.
2025-11-11 21:27:11.6987 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:11.699347 INFO::Using default BPPARAM
2025-11-11 21:27:11.699899 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:11.700858 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 21:27:11.718145 INFO::Done
2025-11-11 21:27:11.718925 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:11.722134 INFO::ASW Batch was 0.470671812044892 prior to batch effect correction and is now 0.162515015226308 .
2025-11-11 21:27:11.722755 INFO::ASW Label was 0.614119075194418 prior to batch effect correction and is now 0.674341674578469 .
2025-11-11 21:27:11.72359 INFO::Total function execution time is 0.0391528606414795 s and adjustment time is 0.0201473236083984 s ( 51.46 )
2025-11-11 21:27:11.972582 INFO::Formatting Data.
2025-11-11 21:27:11.973747 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:11.975014 INFO::Removing potential empty rows and columns
2025-11-11 21:27:11.976405 INFO::Found 0 missing values.
2025-11-11 21:27:11.980055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:11.980802 INFO::Done
2025-11-11 21:27:11.981406 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:11.984193 INFO::Starting hierarchical adjustment
2025-11-11 21:27:11.985066 INFO::Found 3 batches.
2025-11-11 21:27:11.985663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:11.986412 INFO::Using default BPPARAM
2025-11-11 21:27:11.986991 INFO::Processing subtree level 1
2025-11-11 21:27:12.114438 INFO::Adjusting the last 1 batches sequentially
2025-11-11 21:27:12.117011 INFO::Done
2025-11-11 21:27:12.117963 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:12.121129 INFO::ASW Batch was -0.111108160210456 prior to batch effect correction and is now -0.111108160210456 .
2025-11-11 21:27:12.122212 INFO::Total function execution time is 0.150066137313843 s and adjustment time is 0.132081270217896 s ( 88.02 )
2025-11-11 21:27:12.123393 INFO::Formatting Data.
2025-11-11 21:27:12.124156 INFO::Typecasting input to dataframe.
2025-11-11 21:27:12.124961 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:12.126009 INFO::Removing potential empty rows and columns
2025-11-11 21:27:12.127297 INFO::Found 0 missing values.
2025-11-11 21:27:12.131145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:12.13181 INFO::Done
2025-11-11 21:27:12.132451 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:12.135267 INFO::Starting hierarchical adjustment
2025-11-11 21:27:12.136131 INFO::Found 3 batches.
2025-11-11 21:27:12.13675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:12.137598 INFO::Using default BPPARAM
2025-11-11 21:27:12.138289 INFO::Processing subtree level 1
2025-11-11 21:27:12.267559 INFO::Adjusting the last 1 batches sequentially
2025-11-11 21:27:12.270967 INFO::Done
2025-11-11 21:27:12.27234 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:12.277195 INFO::ASW Batch was -0.111108160210456 prior to batch effect correction and is now -0.111108160210456 .
2025-11-11 21:27:12.278968 INFO::Total function execution time is 0.15538215637207 s and adjustment time is 0.134909391403198 s ( 86.82 )
2025-11-11 21:27:12.297893 INFO::Formatting Data.
2025-11-11 21:27:12.298929 INFO::Typecasting input to dataframe.
2025-11-11 21:27:12.299838 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:12.300919 INFO::Removing potential empty rows and columns
2025-11-11 21:27:12.302123 INFO::Found 0 missing values.
2025-11-11 21:27:12.305288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:12.305868 INFO::Done
2025-11-11 21:27:12.306439 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:12.308856 INFO::Starting hierarchical adjustment
2025-11-11 21:27:12.309601 INFO::Found 3 batches.
2025-11-11 21:27:12.310183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:12.310834 INFO::Using default BPPARAM
2025-11-11 21:27:12.311418 INFO::Processing subtree level 1
2025-11-11 21:27:12.407134 INFO::Adjusting the last 1 batches sequentially
2025-11-11 21:27:12.4096 INFO::Done
2025-11-11 21:27:12.410425 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:12.413218 INFO::ASW Batch was -0.108806524420643 prior to batch effect correction and is now -0.108806524420643 .
2025-11-11 21:27:12.414247 INFO::Total function execution time is 0.116517782211304 s and adjustment time is 0.100113868713379 s ( 85.92 )
2025-11-11 21:27:12.568145 INFO::Formatting Data.
2025-11-11 21:27:12.569274 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:12.57055 INFO::Removing potential empty rows and columns
2025-11-11 21:27:12.573588 INFO::Found 1000 missing values.
2025-11-11 21:27:12.593576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:12.594547 INFO::Done
2025-11-11 21:27:12.595217 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:12.601463 INFO::Starting hierarchical adjustment
2025-11-11 21:27:12.602424 INFO::Found 10 batches.
2025-11-11 21:27:12.603038 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:12.603789 INFO::Using default BPPARAM
2025-11-11 21:27:12.604383 INFO::Processing subtree level 1
2025-11-11 21:27:12.777951 INFO::Processing subtree level 2
2025-11-11 21:27:12.949558 INFO::Adjusting the last 1 batches sequentially
2025-11-11 21:27:12.952533 INFO::Done
2025-11-11 21:27:12.953536 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:12.960853 INFO::ASW Batch was 0.483809063553947 prior to batch effect correction and is now 0.483809063553947 .
2025-11-11 21:27:12.961906 INFO::ASW Label was 0.344426462246578 prior to batch effect correction and is now 0.344426462246578 .
2025-11-11 21:27:12.963241 INFO::Total function execution time is 0.395214796066284 s and adjustment time is 0.35024881362915 s ( 88.62 )
2025-11-11 21:27:12.964417 INFO::Formatting Data.
2025-11-11 21:27:12.965281 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:12.967033 INFO::Removing potential empty rows and columns
2025-11-11 21:27:12.970673 INFO::Found 1000 missing values.
2025-11-11 21:27:12.994098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:12.99527 INFO::Done
2025-11-11 21:27:12.996 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:13.002864 INFO::Starting hierarchical adjustment
2025-11-11 21:27:13.003964 INFO::Found 10 batches.
2025-11-11 21:27:14.274635 INFO::Set up parallel execution backend with 2 workers
2025-11-11 21:27:14.27753 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-11 21:27:15.934591 INFO::Adjusting the last 2 batches sequentially
2025-11-11 21:27:15.937731 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 21:27:15.954105 INFO::Done
2025-11-11 21:27:15.954716 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:15.959378 INFO::ASW Batch was 0.483809063553947 prior to batch effect correction and is now 0.483809063553947 .
2025-11-11 21:27:15.960008 INFO::ASW Label was 0.344426462246578 prior to batch effect correction and is now 0.344426462246578 .
2025-11-11 21:27:15.960756 INFO::Total function execution time is 2.99646425247192 s and adjustment time is 2.95041489601135 s ( 98.46 )
2025-11-11 21:27:16.122884 INFO::Formatting Data.
2025-11-11 21:27:16.124245 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.125766 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.127474 INFO::Found 0 missing values.
2025-11-11 21:27:16.132257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.132986 INFO::Done
2025-11-11 21:27:16.133649 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 21:27:16.13771 INFO::Starting hierarchical adjustment
2025-11-11 21:27:16.138599 INFO::Found 3 batches.
2025-11-11 21:27:16.139241 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 21:27:16.140038 INFO::Using default BPPARAM
2025-11-11 21:27:16.140773 INFO::Processing subtree level 1
2025-11-11 21:27:16.286514 INFO::Adjusting the last 1 batches sequentially
2025-11-11 21:27:16.289795 INFO::Done
2025-11-11 21:27:16.290964 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 21:27:16.295996 INFO::ASW Batch was 0.111161450478514 prior to batch effect correction and is now -0.154567450291496 .
2025-11-11 21:27:16.296979 INFO::ASW Label was -0.149326512842048 prior to batch effect correction and is now 0.014804602301011 .
2025-11-11 21:27:16.298354 INFO::Total function execution time is 0.175655603408813 s and adjustment time is 0.151276588439941 s ( 86.12 )
2025-11-11 21:27:16.427023 INFO::Formatting Data.
2025-11-11 21:27:16.427932 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.428898 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.429974 INFO::Found 2 missing values.
2025-11-11 21:27:16.432728 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.433314 INFO::Done
2025-11-11 21:27:16.460716 INFO::Found NA in Reference column
2025-11-11 21:27:16.469773 INFO::Require at least two references per batch.
2025-11-11 21:27:16.489456 INFO::Formatting Data.
2025-11-11 21:27:16.490326 INFO::Recognized SummarizedExperiment
2025-11-11 21:27:16.490917 INFO::Typecasting input to dataframe.
2025-11-11 21:27:16.50105 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.502285 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.505766 INFO::Found 0 missing values.
2025-11-11 21:27:16.512534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.513153 INFO::Done
2025-11-11 21:27:16.52937 INFO::Formatting Data.
2025-11-11 21:27:16.530258 INFO::Recognized SummarizedExperiment
2025-11-11 21:27:16.530826 INFO::Typecasting input to dataframe.
2025-11-11 21:27:16.548673 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.55002 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.553507 INFO::Found 0 missing values.
2025-11-11 21:27:16.564076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.564785 INFO::Done
2025-11-11 21:27:16.580991 INFO::Formatting Data.
2025-11-11 21:27:16.58201 INFO::Recognized SummarizedExperiment
2025-11-11 21:27:16.582618 INFO::Typecasting input to dataframe.
2025-11-11 21:27:16.60057 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.601785 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.603001 INFO::Found 0 missing values.
2025-11-11 21:27:16.604033 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.
2025-11-11 21:27:16.608625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.609241 INFO::Done
2025-11-11 21:27:16.619892 INFO::Formatting Data.
2025-11-11 21:27:16.620705 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.621582 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.622598 INFO::Found 0 missing values.
2025-11-11 21:27:16.625663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.626248 INFO::Done
2025-11-11 21:27:16.63694 INFO::Formatting Data.
2025-11-11 21:27:16.637722 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.638602 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.639607 INFO::Found 0 missing values.
2025-11-11 21:27:16.642419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.642965 INFO::Done
2025-11-11 21:27:16.670818 INFO::Formatting Data.
2025-11-11 21:27:16.67165 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.672674 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.673813 INFO::Found 1 missing values.
2025-11-11 21:27:16.676348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.676957 INFO::Done
2025-11-11 21:27:16.694793 INFO::Formatting Data.
2025-11-11 21:27:16.695616 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.696476 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.697396 INFO::Found 2 missing values.
2025-11-11 21:27:16.69832 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.
2025-11-11 21:27:16.700511 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.701043 INFO::Done
2025-11-11 21:27:16.710939 INFO::Formatting Data.
2025-11-11 21:27:16.711739 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.712646 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.713588 INFO::Found 2 missing values.
2025-11-11 21:27:16.715157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.715715 INFO::Done
2025-11-11 21:27:16.725342 INFO::Formatting Data.
2025-11-11 21:27:16.726087 INFO::Typecasting input to dataframe.
2025-11-11 21:27:16.726878 INFO::Replacing NaNs with NAs.
2025-11-11 21:27:16.727744 INFO::Removing potential empty rows and columns
2025-11-11 21:27:16.728817 INFO::Found 0 missing values.
2025-11-11 21:27:16.731895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 21:27:16.732448 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.791 4.330 22.538
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.823 | 1.699 | 17.788 | |
| compute_asw | 0.027 | 0.002 | 0.029 | |
| count_existing | 0.014 | 0.003 | 0.018 | |
| generate_data_covariables | 0.014 | 0.001 | 0.015 | |
| generate_dataset | 0.011 | 0.003 | 0.015 | |