Yannis Schumann
| Snapshot Date: 2025-11-10 13:45 -0500 (Mon, 10 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-11 12:02 -0500 (Tue, 11 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-11-10 21:35:05 -0500 (Mon, 10 Nov 2025) |
| EndedAt: 2025-11-10 21:36:32 -0500 (Mon, 10 Nov 2025) |
| EllapsedTime: 87.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 23.288 1.167 16.707
* 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-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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")
2025-11-10 21:35:55.975754 INFO::Formatting Data.
2025-11-10 21:35:55.977195 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:55.98909 INFO::Removing potential empty rows and columns
2025-11-10 21:35:56.233727 INFO::Found 0 missing values.
2025-11-10 21:35:56.237049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:35:56.237687 INFO::Done
2025-11-10 21:35:56.238214 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:35:56.249313 INFO::Starting hierarchical adjustment
2025-11-10 21:35:56.250158 INFO::Found 3 batches.
2025-11-10 21:35:56.250691 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:35:56.251793 INFO::Using default BPPARAM
2025-11-10 21:35:56.252332 INFO::Processing subtree level 1
2025-11-10 21:35:56.353886 INFO::Adjusting the last 1 batches sequentially
2025-11-10 21:35:56.355825 INFO::Done
2025-11-10 21:35:56.35652 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:35:56.359158 INFO::ASW Batch was -0.107833045288117 prior to batch effect correction and is now -0.107833045288117 .
2025-11-10 21:35:56.360242 INFO::Total function execution time is 0.385217189788818 s and adjustment time is 0.105826854705811 s ( 27.47 )
2025-11-10 21:35:56.374057 INFO::Formatting Data.
2025-11-10 21:35:56.374841 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:56.375759 INFO::Removing potential empty rows and columns
2025-11-10 21:35:56.376829 INFO::Found 0 missing values.
2025-11-10 21:35:56.377784 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.
2025-11-10 21:35:56.388613 INFO::Formatting Data.
2025-11-10 21:35:56.389385 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:56.390303 INFO::Removing potential empty rows and columns
2025-11-10 21:35:56.391338 INFO::Found 0 missing values.
2025-11-10 21:35:56.392243 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.
2025-11-10 21:35:56.40827 INFO::Formatting Data.
2025-11-10 21:35:56.409184 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:56.410104 INFO::Removing potential empty rows and columns
2025-11-10 21:35:56.41121 INFO::Found 0 missing values.
2025-11-10 21:35:56.412205 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.
2025-11-10 21:35:56.416713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:35:56.417289 INFO::Done
2025-11-10 21:35:56.417806 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:35:56.419891 INFO::Starting hierarchical adjustment
2025-11-10 21:35:56.420608 INFO::Found 2 batches.
2025-11-10 21:35:56.421125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:35:56.421746 INFO::Using default BPPARAM
2025-11-10 21:35:56.422273 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:35:56.423257 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 21:35:56.446603 INFO::Done
2025-11-10 21:35:56.447416 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:35:56.449624 INFO::ASW Batch was 0.0014746933476518 prior to batch effect correction and is now -0.0969622056661945 .
2025-11-10 21:35:56.450471 INFO::Total function execution time is 0.0423328876495361 s and adjustment time is 0.0260848999023438 s ( 61.62 )
2025-11-10 21:35:56.453349 INFO::Formatting Data.
2025-11-10 21:35:56.453992 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:56.463253 INFO::Formatting Data.
2025-11-10 21:35:56.463979 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:56.464883 INFO::Removing potential empty rows and columns
2025-11-10 21:35:56.465921 INFO::Found 0 missing values.
2025-11-10 21:35:56.468783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:35:56.46932 INFO::Done
2025-11-10 21:35:56.469834 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:35:56.471857 INFO::Starting hierarchical adjustment
2025-11-10 21:35:56.472572 INFO::Found 2 batches.
2025-11-10 21:35:56.473091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:35:56.473887 INFO::Using default BPPARAM
2025-11-10 21:35:56.474493 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:35:56.47544 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 21:35:56.516516 INFO::Done
2025-11-10 21:35:56.517296 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:35:56.519447 INFO::ASW Batch was 0.0800779403025829 prior to batch effect correction and is now -0.120479898980517 .
2025-11-10 21:35:56.520283 INFO::Total function execution time is 0.057075023651123 s and adjustment time is 0.0440239906311035 s ( 77.13 )
2025-11-10 21:35:56.521414 INFO::Formatting Data.
2025-11-10 21:35:56.522057 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:56.522997 INFO::Removing potential empty rows and columns
2025-11-10 21:35:56.524075 INFO::Found 0 missing values.
2025-11-10 21:35:56.527068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:35:56.527632 INFO::Done
2025-11-10 21:35:56.528159 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:35:56.530373 INFO::Starting hierarchical adjustment
2025-11-10 21:35:56.531142 INFO::Found 2 batches.
2025-11-10 21:35:56.531667 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:35:56.532288 INFO::Using default BPPARAM
2025-11-10 21:35:56.532814 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:35:56.533725 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 21:35:56.549738 INFO::Done
2025-11-10 21:35:56.550465 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:35:56.552642 INFO::ASW Batch was 0.0800779403025829 prior to batch effect correction and is now -0.120479898980517 .
2025-11-10 21:35:56.553484 INFO::Total function execution time is 0.0320711135864258 s and adjustment time is 0.0187680721282959 s ( 58.52 )
2025-11-10 21:35:59.419814 INFO::Formatting Data.
2025-11-10 21:35:59.420715 INFO::Recognized SummarizedExperiment
2025-11-10 21:35:59.421336 INFO::Typecasting input to dataframe.
2025-11-10 21:35:59.453017 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:59.454307 INFO::Removing potential empty rows and columns
2025-11-10 21:35:59.458065 INFO::Found 0 missing values.
2025-11-10 21:35:59.465044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:35:59.465755 INFO::Done
2025-11-10 21:35:59.466303 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:35:59.469887 INFO::Starting hierarchical adjustment
2025-11-10 21:35:59.470605 INFO::Found 2 batches.
2025-11-10 21:35:59.471124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:35:59.472197 INFO::Using default BPPARAM
2025-11-10 21:35:59.472722 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:35:59.473678 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 21:35:59.531048 INFO::Done
2025-11-10 21:35:59.53181 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:35:59.535522 INFO::ASW Batch was 0.00339113724122052 prior to batch effect correction and is now -0.0950511157160565 .
2025-11-10 21:35:59.536433 INFO::Total function execution time is 0.116983652114868 s and adjustment time is 0.0605366230010986 s ( 51.75 )
2025-11-10 21:35:59.555553 INFO::Formatting Data.
2025-11-10 21:35:59.556361 INFO::Recognized SummarizedExperiment
2025-11-10 21:35:59.556911 INFO::Typecasting input to dataframe.
2025-11-10 21:35:59.566567 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:59.567778 INFO::Removing potential empty rows and columns
2025-11-10 21:35:59.571587 INFO::Found 0 missing values.
2025-11-10 21:35:59.578738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:35:59.579359 INFO::Done
2025-11-10 21:35:59.57989 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:35:59.583573 INFO::Starting hierarchical adjustment
2025-11-10 21:35:59.584334 INFO::Found 2 batches.
2025-11-10 21:35:59.584862 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:35:59.585479 INFO::Using default BPPARAM
2025-11-10 21:35:59.586001 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:35:59.587025 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 21:35:59.612266 INFO::Done
2025-11-10 21:35:59.613016 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:35:59.616839 INFO::ASW Batch was 0.00584363656344835 prior to batch effect correction and is now 0.00584363656344835 .
2025-11-10 21:35:59.617896 INFO::Total function execution time is 0.0623319149017334 s and adjustment time is 0.028050422668457 s ( 45 )
2025-11-10 21:35:59.635836 INFO::Formatting Data.
2025-11-10 21:35:59.636656 INFO::Replacing NaNs with NAs.
2025-11-10 21:35:59.63753 INFO::Removing potential empty rows and columns
2025-11-10 21:35:59.63854 INFO::Found 0 missing values.
2025-11-10 21:35:59.641459 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:35:59.641979 INFO::Done
2025-11-10 21:35:59.642493 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:35:59.644444 INFO::Starting hierarchical adjustment
2025-11-10 21:35:59.645113 INFO::Found 3 batches.
2025-11-10 21:35:59.64564 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:35:59.646227 INFO::Using default BPPARAM
2025-11-10 21:35:59.64674 INFO::Processing subtree level 1
2025-11-10 21:35:59.777131 INFO::Adjusting the last 1 batches sequentially
2025-11-10 21:35:59.778867 INFO::Done
2025-11-10 21:35:59.779492 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:35:59.781865 INFO::ASW Batch was -0.0429300911545304 prior to batch effect correction and is now -0.177803136661964 .
2025-11-10 21:35:59.782762 INFO::Total function execution time is 0.146962404251099 s and adjustment time is 0.133874177932739 s ( 91.09 )
2025-11-10 21:35:59.796711 INFO::Skipping initial DF formatting
2025-11-10 21:35:59.797391 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:35:59.801363 INFO::Starting hierarchical adjustment
2025-11-10 21:35:59.802112 INFO::Found 5 batches.
2025-11-10 21:35:59.80267 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:35:59.803287 INFO::Using default BPPARAM
2025-11-10 21:35:59.803824 INFO::Processing subtree level 1
2025-11-10 21:36:00.024492 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.026167 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 21:36:00.045931 INFO::Done
2025-11-10 21:36:00.046715 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.050937 INFO::ASW Batch was 0.578958601686919 prior to batch effect correction and is now 0.578958601686919 .
2025-11-10 21:36:00.051549 INFO::ASW Label was 0.354604447363931 prior to batch effect correction and is now 0.354604447363931 .
2025-11-10 21:36:00.052381 INFO::Total function execution time is 0.255728721618652 s and adjustment time is 0.243910789489746 s ( 95.38 )
2025-11-10 21:36:00.112002 INFO::Formatting Data.
2025-11-10 21:36:00.112751 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:00.113628 INFO::Removing potential empty rows and columns
2025-11-10 21:36:00.114557 INFO::Found 0 missing values.
2025-11-10 21:36:00.118432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:00.118982 INFO::Done
2025-11-10 21:36:00.119492 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:00.122368 INFO::Starting hierarchical adjustment
2025-11-10 21:36:00.123058 INFO::Found 5 batches.
2025-11-10 21:36:00.123615 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:00.124304 INFO::Using default BPPARAM
2025-11-10 21:36:00.124821 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.
2025-11-10 21:36:00.255414 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.256989 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 21:36:00.273691 INFO::Done
2025-11-10 21:36:00.274377 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.277637 INFO::ASW Batch was 0.463918415170459 prior to batch effect correction and is now -0.0464470666812716 .
2025-11-10 21:36:00.278252 INFO::ASW Label was 0.22313718898133 prior to batch effect correction and is now 0.810801857481606 .
2025-11-10 21:36:00.27906 INFO::Total function execution time is 0.167112588882446 s and adjustment time is 0.150741815567017 s ( 90.2 )
2025-11-10 21:36:00.279912 INFO::Formatting Data.
2025-11-10 21:36:00.280637 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:00.281558 INFO::Removing potential empty rows and columns
2025-11-10 21:36:00.282647 INFO::Found 0 missing values.
2025-11-10 21:36:00.286894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:00.287446 INFO::Done
2025-11-10 21:36:00.287954 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:00.290967 INFO::Starting hierarchical adjustment
2025-11-10 21:36:00.291684 INFO::Found 5 batches.
2025-11-10 21:36:00.292232 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:00.292866 INFO::Using default BPPARAM
2025-11-10 21:36:00.293401 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.
2025-11-10 21:36:00.420142 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.421979 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 21:36:00.440534 INFO::Done
2025-11-10 21:36:00.441411 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.445332 INFO::ASW Batch was 0.463918415170459 prior to batch effect correction and is now -0.0464470666812716 .
2025-11-10 21:36:00.446046 INFO::ASW Label was 0.22313718898133 prior to batch effect correction and is now 0.810801857481606 .
2025-11-10 21:36:00.447031 INFO::Total function execution time is 0.167087078094482 s and adjustment time is 0.148932933807373 s ( 89.13 )
2025-11-10 21:36:00.462662 INFO::Formatting Data.
2025-11-10 21:36:00.463524 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:00.464508 INFO::Removing potential empty rows and columns
2025-11-10 21:36:00.465576 INFO::Found 0 missing values.
2025-11-10 21:36:00.469914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:00.470495 INFO::Done
2025-11-10 21:36:00.471023 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:00.474448 INFO::Starting hierarchical adjustment
2025-11-10 21:36:00.475221 INFO::Found 5 batches.
2025-11-10 21:36:00.475777 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:00.476462 INFO::Using default BPPARAM
2025-11-10 21:36:00.477021 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.
2025-11-10 21:36:00.623798 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.625612 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 21:36:00.6418 INFO::Done
2025-11-10 21:36:00.642531 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.645908 INFO::ASW Batch was 0.355184937286325 prior to batch effect correction and is now -0.0971227144571827 .
2025-11-10 21:36:00.646589 INFO::ASW Label was 0.235171896406602 prior to batch effect correction and is now 0.861672337456393 .
2025-11-10 21:36:00.647438 INFO::Total function execution time is 0.184870719909668 s and adjustment time is 0.166690111160278 s ( 90.17 )
2025-11-10 21:36:00.648323 INFO::Formatting Data.
2025-11-10 21:36:00.648958 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:00.649901 INFO::Removing potential empty rows and columns
2025-11-10 21:36:00.650934 INFO::Found 0 missing values.
2025-11-10 21:36:00.654933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:00.655481 INFO::Done
2025-11-10 21:36:00.655997 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:00.658981 INFO::Starting hierarchical adjustment
2025-11-10 21:36:00.659692 INFO::Found 5 batches.
2025-11-10 21:36:00.660249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:00.660848 INFO::Using default BPPARAM
2025-11-10 21:36:00.66137 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.
2025-11-10 21:36:00.781153 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.782665 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 21:36:00.798112 INFO::Done
2025-11-10 21:36:00.798796 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.80225 INFO::ASW Batch was 0.355184937286325 prior to batch effect correction and is now -0.0971227144571827 .
2025-11-10 21:36:00.802955 INFO::ASW Label was 0.235171896406602 prior to batch effect correction and is now 0.861672337456393 .
2025-11-10 21:36:00.804003 INFO::Total function execution time is 0.155699729919434 s and adjustment time is 0.138546228408813 s ( 88.98 )
2025-11-10 21:36:00.816819 INFO::Formatting Data.
2025-11-10 21:36:00.81766 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:00.818588 INFO::Removing potential empty rows and columns
2025-11-10 21:36:00.8196 INFO::Found 0 missing values.
2025-11-10 21:36:00.822208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:00.822733 INFO::Done
2025-11-10 21:36:00.823247 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:00.82603 INFO::Starting hierarchical adjustment
2025-11-10 21:36:00.826721 INFO::Found 2 batches.
2025-11-10 21:36:00.827247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:00.827832 INFO::Using default BPPARAM
2025-11-10 21:36:00.82835 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.829222 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 21:36:00.84304 INFO::Done
2025-11-10 21:36:00.843677 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.846453 INFO::ASW Batch was 0.468812466295264 prior to batch effect correction and is now 0.128615059824355 .
2025-11-10 21:36:00.84701 INFO::ASW Label was 0.659945931136225 prior to batch effect correction and is now 0.846149935788949 .
2025-11-10 21:36:00.847746 INFO::Total function execution time is 0.0310051441192627 s and adjustment time is 0.0164401531219482 s ( 53.02 )
2025-11-10 21:36:00.848516 INFO::Formatting Data.
2025-11-10 21:36:00.849092 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:00.84991 INFO::Removing potential empty rows and columns
2025-11-10 21:36:00.850829 INFO::Found 0 missing values.
2025-11-10 21:36:00.85332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:00.853832 INFO::Done
2025-11-10 21:36:00.854331 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:00.857071 INFO::Starting hierarchical adjustment
2025-11-10 21:36:00.857753 INFO::Found 2 batches.
2025-11-10 21:36:00.858277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:00.85885 INFO::Using default BPPARAM
2025-11-10 21:36:00.859355 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.860211 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 21:36:00.874168 INFO::Done
2025-11-10 21:36:00.874791 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.877602 INFO::ASW Batch was 0.468812466295264 prior to batch effect correction and is now 0.128615059824355 .
2025-11-10 21:36:00.878163 INFO::ASW Label was 0.659945931136225 prior to batch effect correction and is now 0.846149935788949 .
2025-11-10 21:36:00.87891 INFO::Total function execution time is 0.0304186344146729 s and adjustment time is 0.0165314674377441 s ( 54.35 )
2025-11-10 21:36:00.889514 INFO::Formatting Data.
2025-11-10 21:36:00.890329 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:00.891342 INFO::Removing potential empty rows and columns
2025-11-10 21:36:00.892282 INFO::Found 0 missing values.
2025-11-10 21:36:00.894352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:00.894871 INFO::Done
2025-11-10 21:36:00.895411 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:00.897371 INFO::Starting hierarchical adjustment
2025-11-10 21:36:00.898071 INFO::Found 2 batches.
2025-11-10 21:36:00.898615 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:00.899199 INFO::Using default BPPARAM
2025-11-10 21:36:00.899693 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.900576 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 21:36:00.939923 INFO::Done
2025-11-10 21:36:00.940764 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.943747 INFO::ASW Batch was -0.0572758563169039 prior to batch effect correction and is now -0.102872784677346 .
2025-11-10 21:36:00.945029 INFO::Total function execution time is 0.0554986000061035 s and adjustment time is 0.0419306755065918 s ( 75.55 )
2025-11-10 21:36:00.95941 INFO::Formatting Data.
2025-11-10 21:36:00.960218 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:00.961141 INFO::Removing potential empty rows and columns
2025-11-10 21:36:00.96218 INFO::Found 0 missing values.
2025-11-10 21:36:00.963387 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.
2025-11-10 21:36:00.968222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:00.968796 INFO::Done
2025-11-10 21:36:00.969345 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:00.972336 INFO::Starting hierarchical adjustment
2025-11-10 21:36:00.973067 INFO::Found 2 batches.
2025-11-10 21:36:00.973628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:00.97426 INFO::Using default BPPARAM
2025-11-10 21:36:00.974795 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:00.975757 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 21:36:00.992851 INFO::Done
2025-11-10 21:36:00.993586 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:00.996718 INFO::ASW Batch was 0.58509813516722 prior to batch effect correction and is now 0.0268279830306656 .
2025-11-10 21:36:00.997375 INFO::ASW Label was 0.507218614255693 prior to batch effect correction and is now 0.895389793738919 .
2025-11-10 21:36:00.998174 INFO::Total function execution time is 0.0388450622558594 s and adjustment time is 0.0199148654937744 s ( 51.27 )
2025-11-10 21:36:00.998986 INFO::Formatting Data.
2025-11-10 21:36:00.999639 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:01.000587 INFO::Removing potential empty rows and columns
2025-11-10 21:36:01.001598 INFO::Found 0 missing values.
2025-11-10 21:36:01.002527 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.
2025-11-10 21:36:01.007087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:01.007665 INFO::Done
2025-11-10 21:36:01.008191 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:01.011111 INFO::Starting hierarchical adjustment
2025-11-10 21:36:01.011829 INFO::Found 2 batches.
2025-11-10 21:36:01.012363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:01.012948 INFO::Using default BPPARAM
2025-11-10 21:36:01.013489 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:01.014426 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 21:36:01.031111 INFO::Done
2025-11-10 21:36:01.031846 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:01.034822 INFO::ASW Batch was 0.58509813516722 prior to batch effect correction and is now 0.0268279830306656 .
2025-11-10 21:36:01.03545 INFO::ASW Label was 0.507218614255693 prior to batch effect correction and is now 0.895389793738919 .
2025-11-10 21:36:01.036267 INFO::Total function execution time is 0.0372920036315918 s and adjustment time is 0.0193929672241211 s ( 52 )
2025-11-10 21:36:01.246303 INFO::Formatting Data.
2025-11-10 21:36:01.247209 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:01.248188 INFO::Removing potential empty rows and columns
2025-11-10 21:36:01.249228 INFO::Found 0 missing values.
2025-11-10 21:36:01.252268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:01.252838 INFO::Done
2025-11-10 21:36:01.253376 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:01.255477 INFO::Starting hierarchical adjustment
2025-11-10 21:36:01.256216 INFO::Found 3 batches.
2025-11-10 21:36:01.256742 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:01.257369 INFO::Using default BPPARAM
2025-11-10 21:36:01.25789 INFO::Processing subtree level 1
2025-11-10 21:36:01.344287 INFO::Adjusting the last 1 batches sequentially
2025-11-10 21:36:01.34623 INFO::Done
2025-11-10 21:36:01.346966 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:01.349638 INFO::ASW Batch was -0.0454546829651907 prior to batch effect correction and is now -0.0454546829651907 .
2025-11-10 21:36:01.35065 INFO::Total function execution time is 0.104407072067261 s and adjustment time is 0.0901591777801514 s ( 86.35 )
2025-11-10 21:36:01.351771 INFO::Formatting Data.
2025-11-10 21:36:01.35246 INFO::Typecasting input to dataframe.
2025-11-10 21:36:01.353268 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:01.354254 INFO::Removing potential empty rows and columns
2025-11-10 21:36:01.355385 INFO::Found 0 missing values.
2025-11-10 21:36:01.358464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:01.359052 INFO::Done
2025-11-10 21:36:01.359596 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:01.361743 INFO::Starting hierarchical adjustment
2025-11-10 21:36:01.362492 INFO::Found 3 batches.
2025-11-10 21:36:01.363038 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:01.363678 INFO::Using default BPPARAM
2025-11-10 21:36:01.364277 INFO::Processing subtree level 1
2025-11-10 21:36:01.452864 INFO::Adjusting the last 1 batches sequentially
2025-11-10 21:36:01.454756 INFO::Done
2025-11-10 21:36:01.45544 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:01.457982 INFO::ASW Batch was -0.0454546829651907 prior to batch effect correction and is now -0.0454546829651907 .
2025-11-10 21:36:01.458968 INFO::Total function execution time is 0.107188940048218 s and adjustment time is 0.0924105644226074 s ( 86.21 )
2025-11-10 21:36:01.4718 INFO::Formatting Data.
2025-11-10 21:36:01.472613 INFO::Typecasting input to dataframe.
2025-11-10 21:36:01.473461 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:01.474384 INFO::Removing potential empty rows and columns
2025-11-10 21:36:01.475444 INFO::Found 0 missing values.
2025-11-10 21:36:01.478425 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:01.478961 INFO::Done
2025-11-10 21:36:01.479491 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:01.481486 INFO::Starting hierarchical adjustment
2025-11-10 21:36:01.482209 INFO::Found 3 batches.
2025-11-10 21:36:01.482732 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:01.483349 INFO::Using default BPPARAM
2025-11-10 21:36:01.483876 INFO::Processing subtree level 1
2025-11-10 21:36:01.569407 INFO::Adjusting the last 1 batches sequentially
2025-11-10 21:36:01.571294 INFO::Done
2025-11-10 21:36:01.572028 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:01.574732 INFO::ASW Batch was 0.0242012039463873 prior to batch effect correction and is now 0.0242012039463873 .
2025-11-10 21:36:01.57571 INFO::Total function execution time is 0.103952407836914 s and adjustment time is 0.0892205238342285 s ( 85.83 )
2025-11-10 21:36:01.713398 INFO::Formatting Data.
2025-11-10 21:36:01.714229 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:01.715346 INFO::Removing potential empty rows and columns
2025-11-10 21:36:01.718312 INFO::Found 1000 missing values.
2025-11-10 21:36:01.736938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:01.737659 INFO::Done
2025-11-10 21:36:01.738213 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:01.743586 INFO::Starting hierarchical adjustment
2025-11-10 21:36:01.744353 INFO::Found 10 batches.
2025-11-10 21:36:01.744885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:01.745517 INFO::Using default BPPARAM
2025-11-10 21:36:01.746035 INFO::Processing subtree level 1
2025-11-10 21:36:01.875511 INFO::Processing subtree level 2
2025-11-10 21:36:02.018335 INFO::Adjusting the last 1 batches sequentially
2025-11-10 21:36:02.021353 INFO::Done
2025-11-10 21:36:02.022466 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:02.031417 INFO::ASW Batch was 0.507615802370541 prior to batch effect correction and is now 0.507615802370541 .
2025-11-10 21:36:02.032218 INFO::ASW Label was 0.328965735404198 prior to batch effect correction and is now 0.328965735404197 .
2025-11-10 21:36:02.033171 INFO::Total function execution time is 0.319828987121582 s and adjustment time is 0.27709436416626 s ( 86.64 )
2025-11-10 21:36:02.034044 INFO::Formatting Data.
2025-11-10 21:36:02.034728 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:02.03608 INFO::Removing potential empty rows and columns
2025-11-10 21:36:02.039292 INFO::Found 1000 missing values.
2025-11-10 21:36:02.059247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:02.060013 INFO::Done
2025-11-10 21:36:02.060667 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:02.0663 INFO::Starting hierarchical adjustment
2025-11-10 21:36:02.067135 INFO::Found 10 batches.
2025-11-10 21:36:03.138461 INFO::Set up parallel execution backend with 2 workers
2025-11-10 21:36:03.14084 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-10 21:36:04.392627 INFO::Adjusting the last 2 batches sequentially
2025-11-10 21:36:04.394446 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 21:36:04.41079 INFO::Done
2025-11-10 21:36:04.411447 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:04.415871 INFO::ASW Batch was 0.507615802370541 prior to batch effect correction and is now 0.507615802370541 .
2025-11-10 21:36:04.416425 INFO::ASW Label was 0.328965735404198 prior to batch effect correction and is now 0.328965735404197 .
2025-11-10 21:36:04.417136 INFO::Total function execution time is 2.38312935829163 s and adjustment time is 2.34383130073547 s ( 98.35 )
2025-11-10 21:36:04.572455 INFO::Formatting Data.
2025-11-10 21:36:04.573275 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:04.574279 INFO::Removing potential empty rows and columns
2025-11-10 21:36:04.575454 INFO::Found 0 missing values.
2025-11-10 21:36:04.579378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:04.579991 INFO::Done
2025-11-10 21:36:04.580537 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 21:36:04.583607 INFO::Starting hierarchical adjustment
2025-11-10 21:36:04.584358 INFO::Found 3 batches.
2025-11-10 21:36:04.584887 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 21:36:04.585505 INFO::Using default BPPARAM
2025-11-10 21:36:04.58604 INFO::Processing subtree level 1
2025-11-10 21:36:04.697901 INFO::Adjusting the last 1 batches sequentially
2025-11-10 21:36:04.699869 INFO::Done
2025-11-10 21:36:04.700592 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 21:36:04.704085 INFO::ASW Batch was 0.356649313872814 prior to batch effect correction and is now -0.130405990283882 .
2025-11-10 21:36:04.704795 INFO::ASW Label was -0.227013313851359 prior to batch effect correction and is now 0.0213806930660948 .
2025-11-10 21:36:04.705803 INFO::Total function execution time is 0.133390665054321 s and adjustment time is 0.115652084350586 s ( 86.7 )
2025-11-10 21:36:04.836787 INFO::Formatting Data.
2025-11-10 21:36:04.837771 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:04.838754 INFO::Removing potential empty rows and columns
2025-11-10 21:36:04.839927 INFO::Found 2 missing values.
2025-11-10 21:36:04.843012 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:04.843604 INFO::Done
2025-11-10 21:36:04.874058 INFO::Found NA in Reference column
2025-11-10 21:36:04.88403 INFO::Require at least two references per batch.
2025-11-10 21:36:04.905669 INFO::Formatting Data.
2025-11-10 21:36:04.906511 INFO::Recognized SummarizedExperiment
2025-11-10 21:36:04.907039 INFO::Typecasting input to dataframe.
2025-11-10 21:36:04.91785 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:04.919304 INFO::Removing potential empty rows and columns
2025-11-10 21:36:04.92299 INFO::Found 0 missing values.
2025-11-10 21:36:04.929918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:04.931334 INFO::Done
2025-11-10 21:36:04.948525 INFO::Formatting Data.
2025-11-10 21:36:04.949422 INFO::Recognized SummarizedExperiment
2025-11-10 21:36:04.949984 INFO::Typecasting input to dataframe.
2025-11-10 21:36:04.968778 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:04.970252 INFO::Removing potential empty rows and columns
2025-11-10 21:36:04.973817 INFO::Found 0 missing values.
2025-11-10 21:36:04.984768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:04.985579 INFO::Done
2025-11-10 21:36:05.001624 INFO::Formatting Data.
2025-11-10 21:36:05.002447 INFO::Recognized SummarizedExperiment
2025-11-10 21:36:05.002963 INFO::Typecasting input to dataframe.
2025-11-10 21:36:05.021271 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:05.022441 INFO::Removing potential empty rows and columns
2025-11-10 21:36:05.023496 INFO::Found 0 missing values.
2025-11-10 21:36:05.024392 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.
2025-11-10 21:36:05.028464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:05.028972 INFO::Done
2025-11-10 21:36:05.038717 INFO::Formatting Data.
2025-11-10 21:36:05.039567 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:05.04042 INFO::Removing potential empty rows and columns
2025-11-10 21:36:05.041422 INFO::Found 0 missing values.
2025-11-10 21:36:05.044231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:05.044748 INFO::Done
2025-11-10 21:36:05.05664 INFO::Formatting Data.
2025-11-10 21:36:05.057579 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:05.058491 INFO::Removing potential empty rows and columns
2025-11-10 21:36:05.059615 INFO::Found 0 missing values.
2025-11-10 21:36:05.062746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:05.063349 INFO::Done
2025-11-10 21:36:05.095577 INFO::Formatting Data.
2025-11-10 21:36:05.096528 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:05.097665 INFO::Removing potential empty rows and columns
2025-11-10 21:36:05.098941 INFO::Found 1 missing values.
2025-11-10 21:36:05.101751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:05.102328 INFO::Done
2025-11-10 21:36:05.122055 INFO::Formatting Data.
2025-11-10 21:36:05.122977 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:05.123836 INFO::Removing potential empty rows and columns
2025-11-10 21:36:05.124781 INFO::Found 2 missing values.
2025-11-10 21:36:05.125682 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.
2025-11-10 21:36:05.127899 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:05.128438 INFO::Done
2025-11-10 21:36:05.138052 INFO::Formatting Data.
2025-11-10 21:36:05.138966 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:05.139964 INFO::Removing potential empty rows and columns
2025-11-10 21:36:05.141019 INFO::Found 2 missing values.
2025-11-10 21:36:05.142726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:05.143268 INFO::Done
2025-11-10 21:36:05.153519 INFO::Formatting Data.
2025-11-10 21:36:05.154303 INFO::Typecasting input to dataframe.
2025-11-10 21:36:05.155094 INFO::Replacing NaNs with NAs.
2025-11-10 21:36:05.155933 INFO::Removing potential empty rows and columns
2025-11-10 21:36:05.156932 INFO::Found 0 missing values.
2025-11-10 21:36:05.159682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 21:36:05.160202 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.302 3.413 20.459
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.288 | 1.167 | 16.707 | |
| compute_asw | 0.026 | 0.000 | 0.025 | |
| count_existing | 0.011 | 0.002 | 0.015 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.011 | 0.000 | 0.012 | |