Yannis Schumann
| Snapshot Date: 2025-11-20 15:01 -0500 (Thu, 20 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 2025-11-24 12:03 -0500 (Mon, 24 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4873 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4654 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4600 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /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: 2025-11-20 22:12:29 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 22:14:00 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 4.5.2 (2025-10-31)
* 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 24.364 1.625 18.486
* 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
2025-11-20 22:13:21.14918 INFO::Formatting Data.
2025-11-20 22:13:21.150438 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:21.161204 INFO::Removing potential empty rows and columns
2025-11-20 22:13:21.442307 INFO::Found 0 missing values.
2025-11-20 22:13:21.445569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:21.44621 INFO::Done
2025-11-20 22:13:21.446744 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:21.457252 INFO::Starting hierarchical adjustment
2025-11-20 22:13:21.45804 INFO::Found 3 batches.
2025-11-20 22:13:21.458569 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:21.459612 INFO::Using default BPPARAM
2025-11-20 22:13:21.460147 INFO::Processing subtree level 1
2025-11-20 22:13:21.556612 INFO::Adjusting the last 1 batches sequentially
2025-11-20 22:13:21.558235 INFO::Done
2025-11-20 22:13:21.558869 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:21.561287 INFO::ASW Batch was 0.00533990949840633 prior to batch effect correction and is now 0.00533990949840633 .
2025-11-20 22:13:21.562284 INFO::Total function execution time is 0.413737535476685 s and adjustment time is 0.100341320037842 s ( 24.25 )
2025-11-20 22:13:21.575152 INFO::Formatting Data.
2025-11-20 22:13:21.575873 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:21.576761 INFO::Removing potential empty rows and columns
2025-11-20 22:13:21.577893 INFO::Found 0 missing values.
2025-11-20 22:13:21.578811 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.
2025-11-20 22:13:21.589067 INFO::Formatting Data.
2025-11-20 22:13:21.58976 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:21.590603 INFO::Removing potential empty rows and columns
2025-11-20 22:13:21.591598 INFO::Found 0 missing values.
2025-11-20 22:13:21.592502 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.
2025-11-20 22:13:21.60792 INFO::Formatting Data.
2025-11-20 22:13:21.608671 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:21.60955 INFO::Removing potential empty rows and columns
2025-11-20 22:13:21.610564 INFO::Found 0 missing values.
2025-11-20 22:13:21.611459 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.
2025-11-20 22:13:21.61576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:21.616286 INFO::Done
2025-11-20 22:13:21.616775 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:21.618682 INFO::Starting hierarchical adjustment
2025-11-20 22:13:21.619348 INFO::Found 2 batches.
2025-11-20 22:13:21.619857 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:21.620459 INFO::Using default BPPARAM
2025-11-20 22:13:21.620958 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:21.621828 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 22:13:21.642542 INFO::Done
2025-11-20 22:13:21.643335 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:21.645393 INFO::ASW Batch was 0.0116567398206499 prior to batch effect correction and is now -0.103714391863446 .
2025-11-20 22:13:21.646204 INFO::Total function execution time is 0.0383231639862061 s and adjustment time is 0.0232861042022705 s ( 60.76 )
2025-11-20 22:13:21.648896 INFO::Formatting Data.
2025-11-20 22:13:21.649531 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:21.658258 INFO::Formatting Data.
2025-11-20 22:13:21.659001 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:21.659911 INFO::Removing potential empty rows and columns
2025-11-20 22:13:21.660955 INFO::Found 0 missing values.
2025-11-20 22:13:21.663908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:21.664448 INFO::Done
2025-11-20 22:13:21.664968 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:21.666964 INFO::Starting hierarchical adjustment
2025-11-20 22:13:21.667684 INFO::Found 2 batches.
2025-11-20 22:13:21.668219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:21.668816 INFO::Using default BPPARAM
2025-11-20 22:13:21.689387 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:21.691954 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 22:13:21.705374 INFO::Done
2025-11-20 22:13:21.705988 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:21.707821 INFO::ASW Batch was 0.0115524512846472 prior to batch effect correction and is now -0.0409798396744363 .
2025-11-20 22:13:21.708544 INFO::Total function execution time is 0.050356388092041 s and adjustment time is 0.0378298759460449 s ( 75.12 )
2025-11-20 22:13:21.709504 INFO::Formatting Data.
2025-11-20 22:13:21.710055 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:21.710822 INFO::Removing potential empty rows and columns
2025-11-20 22:13:21.711724 INFO::Found 0 missing values.
2025-11-20 22:13:21.714223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:21.714705 INFO::Done
2025-11-20 22:13:21.715178 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:21.716944 INFO::Starting hierarchical adjustment
2025-11-20 22:13:21.717588 INFO::Found 2 batches.
2025-11-20 22:13:21.718061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:21.718619 INFO::Using default BPPARAM
2025-11-20 22:13:21.719069 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:21.719876 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 22:13:21.733434 INFO::Done
2025-11-20 22:13:21.734039 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:21.735892 INFO::ASW Batch was 0.0115524512846472 prior to batch effect correction and is now -0.0409798396744363 .
2025-11-20 22:13:21.736638 INFO::Total function execution time is 0.0271313190460205 s and adjustment time is 0.0159564018249512 s ( 58.81 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-20 22:13:24.574349 INFO::Formatting Data.
2025-11-20 22:13:24.575164 INFO::Recognized SummarizedExperiment
2025-11-20 22:13:24.575658 INFO::Typecasting input to dataframe.
2025-11-20 22:13:24.606639 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:24.607971 INFO::Removing potential empty rows and columns
2025-11-20 22:13:24.611917 INFO::Found 0 missing values.
2025-11-20 22:13:24.619441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:24.620149 INFO::Done
2025-11-20 22:13:24.620687 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:24.62447 INFO::Starting hierarchical adjustment
2025-11-20 22:13:24.625258 INFO::Found 2 batches.
2025-11-20 22:13:24.62579 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:24.626974 INFO::Using default BPPARAM
2025-11-20 22:13:24.627513 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:24.628549 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 22:13:24.687407 INFO::Done
2025-11-20 22:13:24.688198 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:24.691958 INFO::ASW Batch was -0.00461442736754413 prior to batch effect correction and is now -0.100497563816919 .
2025-11-20 22:13:24.692832 INFO::Total function execution time is 0.118816614151001 s and adjustment time is 0.0623035430908203 s ( 52.44 )
Warning: stack imbalance in '{', 73 then 74
2025-11-20 22:13:24.712255 INFO::Formatting Data.
2025-11-20 22:13:24.713059 INFO::Recognized SummarizedExperiment
2025-11-20 22:13:24.713611 INFO::Typecasting input to dataframe.
2025-11-20 22:13:24.723444 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:24.724665 INFO::Removing potential empty rows and columns
2025-11-20 22:13:24.728549 INFO::Found 0 missing values.
2025-11-20 22:13:24.735767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:24.736697 INFO::Done
2025-11-20 22:13:24.737253 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:24.740844 INFO::Starting hierarchical adjustment
2025-11-20 22:13:24.741585 INFO::Found 2 batches.
2025-11-20 22:13:24.742101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:24.742717 INFO::Using default BPPARAM
2025-11-20 22:13:24.74324 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:24.744217 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 22:13:24.769815 INFO::Done
2025-11-20 22:13:24.770554 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:24.774168 INFO::ASW Batch was -0.0167199392115748 prior to batch effect correction and is now -0.0167199392115748 .
2025-11-20 22:13:24.775035 INFO::Total function execution time is 0.0627791881561279 s and adjustment time is 0.0283472537994385 s ( 45.15 )
2025-11-20 22:13:24.794043 INFO::Formatting Data.
2025-11-20 22:13:24.794873 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:24.795796 INFO::Removing potential empty rows and columns
2025-11-20 22:13:24.7971 INFO::Found 0 missing values.
2025-11-20 22:13:24.800099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:24.800651 INFO::Done
2025-11-20 22:13:24.801173 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:24.81311 INFO::Starting hierarchical adjustment
2025-11-20 22:13:24.814296 INFO::Found 3 batches.
2025-11-20 22:13:24.814845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:24.815511 INFO::Using default BPPARAM
2025-11-20 22:13:24.816016 INFO::Processing subtree level 1
2025-11-20 22:13:24.963914 INFO::Adjusting the last 1 batches sequentially
2025-11-20 22:13:24.965958 INFO::Done
2025-11-20 22:13:24.966645 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:24.969321 INFO::ASW Batch was -0.082062904685279 prior to batch effect correction and is now -0.15551915941211 .
2025-11-20 22:13:24.970339 INFO::Total function execution time is 0.176295280456543 s and adjustment time is 0.151896953582764 s ( 86.16 )
2025-11-20 22:13:24.986841 INFO::Skipping initial DF formatting
2025-11-20 22:13:24.987598 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:24.99182 INFO::Starting hierarchical adjustment
2025-11-20 22:13:24.992678 INFO::Found 5 batches.
2025-11-20 22:13:24.99324 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:24.99386 INFO::Using default BPPARAM
2025-11-20 22:13:24.99441 INFO::Processing subtree level 1
2025-11-20 22:13:25.308198 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:25.310027 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 22:13:25.330207 INFO::Done
2025-11-20 22:13:25.33106 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:25.394879 INFO::ASW Batch was 0.451079150052949 prior to batch effect correction and is now 0.451079150052949 .
2025-11-20 22:13:25.396696 INFO::ASW Label was 0.409483007704736 prior to batch effect correction and is now 0.409483007704736 .
2025-11-20 22:13:25.397693 INFO::Total function execution time is 0.410926103591919 s and adjustment time is 0.337634325027466 s ( 82.16 )
2025-11-20 22:13:25.416485 INFO::Formatting Data.
2025-11-20 22:13:25.417443 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:25.418477 INFO::Removing potential empty rows and columns
2025-11-20 22:13:25.419523 INFO::Found 0 missing values.
2025-11-20 22:13:25.423843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:25.424455 INFO::Done
2025-11-20 22:13:25.425004 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:25.428451 INFO::Starting hierarchical adjustment
2025-11-20 22:13:25.42923 INFO::Found 5 batches.
2025-11-20 22:13:25.429773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:25.430467 INFO::Using default BPPARAM
2025-11-20 22:13:25.431017 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.
2025-11-20 22:13:25.589063 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:25.592103 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 22:13:25.621841 INFO::Done
2025-11-20 22:13:25.623034 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:25.628696 INFO::ASW Batch was 0.472477775779161 prior to batch effect correction and is now -0.0233133993288535 .
2025-11-20 22:13:25.629703 INFO::ASW Label was 0.298403247171631 prior to batch effect correction and is now 0.751186107610961 .
2025-11-20 22:13:25.631137 INFO::Total function execution time is 0.214668750762939 s and adjustment time is 0.19267725944519 s ( 89.76 )
2025-11-20 22:13:25.632535 INFO::Formatting Data.
2025-11-20 22:13:25.633648 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:25.634718 INFO::Removing potential empty rows and columns
2025-11-20 22:13:25.635828 INFO::Found 0 missing values.
2025-11-20 22:13:25.642359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:25.642929 INFO::Done
2025-11-20 22:13:25.643481 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:25.646776 INFO::Starting hierarchical adjustment
2025-11-20 22:13:25.647507 INFO::Found 5 batches.
2025-11-20 22:13:25.648046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:25.648664 INFO::Using default BPPARAM
2025-11-20 22:13:25.64922 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.
2025-11-20 22:13:25.795168 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:25.796923 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 22:13:25.814223 INFO::Done
2025-11-20 22:13:25.815003 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:25.818515 INFO::ASW Batch was 0.472477775779161 prior to batch effect correction and is now -0.0233133993288535 .
2025-11-20 22:13:25.81918 INFO::ASW Label was 0.298403247171631 prior to batch effect correction and is now 0.751186107610961 .
2025-11-20 22:13:25.820018 INFO::Total function execution time is 0.187607288360596 s and adjustment time is 0.166802167892456 s ( 88.91 )
2025-11-20 22:13:25.834672 INFO::Formatting Data.
2025-11-20 22:13:25.835529 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:25.836573 INFO::Removing potential empty rows and columns
2025-11-20 22:13:25.837646 INFO::Found 0 missing values.
2025-11-20 22:13:25.841981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:25.842568 INFO::Done
2025-11-20 22:13:25.843086 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:25.84647 INFO::Starting hierarchical adjustment
2025-11-20 22:13:25.847242 INFO::Found 5 batches.
2025-11-20 22:13:25.847767 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:25.84841 INFO::Using default BPPARAM
2025-11-20 22:13:25.848945 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.
2025-11-20 22:13:25.994426 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:25.996398 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 22:13:26.025699 INFO::Done
2025-11-20 22:13:26.0267 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.030733 INFO::ASW Batch was 0.629207832998456 prior to batch effect correction and is now -0.0383169878634537 .
2025-11-20 22:13:26.03144 INFO::ASW Label was 0.201557611151754 prior to batch effect correction and is now 0.736208131309647 .
2025-11-20 22:13:26.032347 INFO::Total function execution time is 0.197756052017212 s and adjustment time is 0.178525686264038 s ( 90.28 )
2025-11-20 22:13:26.033347 INFO::Formatting Data.
2025-11-20 22:13:26.034037 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.035028 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.036218 INFO::Found 0 missing values.
2025-11-20 22:13:26.040746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.041363 INFO::Done
2025-11-20 22:13:26.041945 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.045432 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.046257 INFO::Found 5 batches.
2025-11-20 22:13:26.046901 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.0476 INFO::Using default BPPARAM
2025-11-20 22:13:26.048183 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.
2025-11-20 22:13:26.192201 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:26.194063 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 22:13:26.213504 INFO::Done
2025-11-20 22:13:26.214411 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.2181 INFO::ASW Batch was 0.629207832998456 prior to batch effect correction and is now -0.0383169878634537 .
2025-11-20 22:13:26.21883 INFO::ASW Label was 0.201557611151754 prior to batch effect correction and is now 0.736208131309647 .
2025-11-20 22:13:26.219766 INFO::Total function execution time is 0.186418533325195 s and adjustment time is 0.16740345954895 s ( 89.8 )
2025-11-20 22:13:26.235372 INFO::Formatting Data.
2025-11-20 22:13:26.236264 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.237329 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.238489 INFO::Found 0 missing values.
2025-11-20 22:13:26.241538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.242146 INFO::Done
2025-11-20 22:13:26.24272 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.246034 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.246842 INFO::Found 2 batches.
2025-11-20 22:13:26.247458 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.24817 INFO::Using default BPPARAM
2025-11-20 22:13:26.248786 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:26.249875 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 22:13:26.266888 INFO::Done
2025-11-20 22:13:26.267632 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.270804 INFO::ASW Batch was 0.795905223435187 prior to batch effect correction and is now -0.0225055900649972 .
2025-11-20 22:13:26.271454 INFO::ASW Label was 0.245789184370211 prior to batch effect correction and is now 0.863855955139003 .
2025-11-20 22:13:26.272272 INFO::Total function execution time is 0.0370132923126221 s and adjustment time is 0.0201947689056396 s ( 54.56 )
2025-11-20 22:13:26.27309 INFO::Formatting Data.
2025-11-20 22:13:26.273747 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.274642 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.275676 INFO::Found 0 missing values.
2025-11-20 22:13:26.278558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.279132 INFO::Done
2025-11-20 22:13:26.27967 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.282784 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.283559 INFO::Found 2 batches.
2025-11-20 22:13:26.284127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.284763 INFO::Using default BPPARAM
2025-11-20 22:13:26.285316 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:26.286276 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 22:13:26.301541 INFO::Done
2025-11-20 22:13:26.302223 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.305206 INFO::ASW Batch was 0.795905223435187 prior to batch effect correction and is now -0.0225055900649972 .
2025-11-20 22:13:26.30579 INFO::ASW Label was 0.245789184370211 prior to batch effect correction and is now 0.863855955139003 .
2025-11-20 22:13:26.306583 INFO::Total function execution time is 0.0335190296173096 s and adjustment time is 0.0181331634521484 s ( 54.1 )
2025-11-20 22:13:26.318417 INFO::Formatting Data.
2025-11-20 22:13:26.319208 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.320167 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.321099 INFO::Found 0 missing values.
2025-11-20 22:13:26.323318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.323867 INFO::Done
2025-11-20 22:13:26.324405 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.326421 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.327112 INFO::Found 2 batches.
2025-11-20 22:13:26.327634 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.328235 INFO::Using default BPPARAM
2025-11-20 22:13:26.328757 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:26.329647 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 22:13:26.36237 INFO::Done
2025-11-20 22:13:26.363108 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.365133 INFO::ASW Batch was 0.022312634632299 prior to batch effect correction and is now -0.174079215851736 .
2025-11-20 22:13:26.365944 INFO::Total function execution time is 0.0476841926574707 s and adjustment time is 0.0353639125823975 s ( 74.16 )
2025-11-20 22:13:26.377967 INFO::Formatting Data.
2025-11-20 22:13:26.378773 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.379663 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.380667 INFO::Found 0 missing values.
2025-11-20 22:13:26.381908 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.
2025-11-20 22:13:26.386525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.387069 INFO::Done
2025-11-20 22:13:26.387584 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.390527 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.391221 INFO::Found 2 batches.
2025-11-20 22:13:26.39174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.39236 INFO::Using default BPPARAM
2025-11-20 22:13:26.39286 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:26.393809 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 22:13:26.410742 INFO::Done
2025-11-20 22:13:26.411442 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.414395 INFO::ASW Batch was 0.580144126232876 prior to batch effect correction and is now 0.0566772585425118 .
2025-11-20 22:13:26.414974 INFO::ASW Label was 0.410477645818692 prior to batch effect correction and is now 0.845534762343921 .
2025-11-20 22:13:26.415716 INFO::Total function execution time is 0.0378518104553223 s and adjustment time is 0.0196466445922852 s ( 51.9 )
2025-11-20 22:13:26.416525 INFO::Formatting Data.
2025-11-20 22:13:26.417142 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.418044 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.419033 INFO::Found 0 missing values.
2025-11-20 22:13:26.419935 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.
2025-11-20 22:13:26.424411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.424947 INFO::Done
2025-11-20 22:13:26.425475 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.428527 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.429245 INFO::Found 2 batches.
2025-11-20 22:13:26.429773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.430402 INFO::Using default BPPARAM
2025-11-20 22:13:26.430914 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:26.431864 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 22:13:26.449698 INFO::Done
2025-11-20 22:13:26.450557 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.453914 INFO::ASW Batch was 0.580144126232876 prior to batch effect correction and is now 0.0566772585425118 .
2025-11-20 22:13:26.45462 INFO::ASW Label was 0.410477645818692 prior to batch effect correction and is now 0.845534762343921 .
2025-11-20 22:13:26.455518 INFO::Total function execution time is 0.0389926433563232 s and adjustment time is 0.0205631256103516 s ( 52.74 )
2025-11-20 22:13:26.668785 INFO::Formatting Data.
2025-11-20 22:13:26.669557 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.670455 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.671495 INFO::Found 0 missing values.
2025-11-20 22:13:26.674523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.675045 INFO::Done
2025-11-20 22:13:26.675566 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.677577 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.678282 INFO::Found 3 batches.
2025-11-20 22:13:26.6788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.679407 INFO::Using default BPPARAM
2025-11-20 22:13:26.679917 INFO::Processing subtree level 1
2025-11-20 22:13:26.77122 INFO::Adjusting the last 1 batches sequentially
2025-11-20 22:13:26.773196 INFO::Done
2025-11-20 22:13:26.773917 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.776627 INFO::ASW Batch was -0.0811837804185896 prior to batch effect correction and is now -0.0811837804185896 .
2025-11-20 22:13:26.777646 INFO::Total function execution time is 0.108886003494263 s and adjustment time is 0.0950181484222412 s ( 87.26 )
2025-11-20 22:13:26.778802 INFO::Formatting Data.
2025-11-20 22:13:26.779525 INFO::Typecasting input to dataframe.
2025-11-20 22:13:26.780339 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.781335 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.782497 INFO::Found 0 missing values.
2025-11-20 22:13:26.785645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.786203 INFO::Done
2025-11-20 22:13:26.786728 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.788899 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.789658 INFO::Found 3 batches.
2025-11-20 22:13:26.790235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.790871 INFO::Using default BPPARAM
2025-11-20 22:13:26.791424 INFO::Processing subtree level 1
2025-11-20 22:13:26.883839 INFO::Adjusting the last 1 batches sequentially
2025-11-20 22:13:26.886025 INFO::Done
2025-11-20 22:13:26.886806 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:26.88966 INFO::ASW Batch was -0.0811837804185896 prior to batch effect correction and is now -0.0811837804185896 .
2025-11-20 22:13:26.890718 INFO::Total function execution time is 0.111899375915527 s and adjustment time is 0.0964665412902832 s ( 86.21 )
2025-11-20 22:13:26.906485 INFO::Formatting Data.
2025-11-20 22:13:26.907521 INFO::Typecasting input to dataframe.
2025-11-20 22:13:26.908528 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:26.909539 INFO::Removing potential empty rows and columns
2025-11-20 22:13:26.910698 INFO::Found 0 missing values.
2025-11-20 22:13:26.913956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:26.914577 INFO::Done
2025-11-20 22:13:26.915122 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:26.917477 INFO::Starting hierarchical adjustment
2025-11-20 22:13:26.918269 INFO::Found 3 batches.
2025-11-20 22:13:26.918815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:26.919474 INFO::Using default BPPARAM
2025-11-20 22:13:26.919999 INFO::Processing subtree level 1
2025-11-20 22:13:27.016728 INFO::Adjusting the last 1 batches sequentially
2025-11-20 22:13:27.018816 INFO::Done
2025-11-20 22:13:27.019584 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:27.022467 INFO::ASW Batch was -0.0526598923067028 prior to batch effect correction and is now -0.0526598923067028 .
2025-11-20 22:13:27.023645 INFO::Total function execution time is 0.117292404174805 s and adjustment time is 0.100690841674805 s ( 85.85 )
2025-11-20 22:13:27.169096 INFO::Formatting Data.
2025-11-20 22:13:27.170048 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:27.171278 INFO::Removing potential empty rows and columns
2025-11-20 22:13:27.174168 INFO::Found 1000 missing values.
2025-11-20 22:13:27.193315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:27.194252 INFO::Done
2025-11-20 22:13:27.194851 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:27.200914 INFO::Starting hierarchical adjustment
2025-11-20 22:13:27.201804 INFO::Found 10 batches.
2025-11-20 22:13:27.202368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:27.203043 INFO::Using default BPPARAM
2025-11-20 22:13:27.203604 INFO::Processing subtree level 1
2025-11-20 22:13:27.362239 INFO::Processing subtree level 2
2025-11-20 22:13:27.507482 INFO::Adjusting the last 1 batches sequentially
2025-11-20 22:13:27.509716 INFO::Done
2025-11-20 22:13:27.510508 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:27.516519 INFO::ASW Batch was 0.50620034164611 prior to batch effect correction and is now 0.50620034164611 .
2025-11-20 22:13:27.517198 INFO::ASW Label was 0.332538616250768 prior to batch effect correction and is now 0.332538616250768 .
2025-11-20 22:13:27.5182 INFO::Total function execution time is 0.349201202392578 s and adjustment time is 0.308068037033081 s ( 88.22 )
2025-11-20 22:13:27.519103 INFO::Formatting Data.
2025-11-20 22:13:27.519812 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:27.521153 INFO::Removing potential empty rows and columns
2025-11-20 22:13:27.52404 INFO::Found 1000 missing values.
2025-11-20 22:13:27.543451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:27.544277 INFO::Done
2025-11-20 22:13:27.544867 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:27.550725 INFO::Starting hierarchical adjustment
2025-11-20 22:13:27.551551 INFO::Found 10 batches.
2025-11-20 22:13:29.127048 INFO::Set up parallel execution backend with 2 workers
2025-11-20 22:13:29.129204 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-20 22:13:30.333108 INFO::Adjusting the last 2 batches sequentially
2025-11-20 22:13:30.335236 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 22:13:30.351791 INFO::Done
2025-11-20 22:13:30.352434 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:30.356882 INFO::ASW Batch was 0.50620034164611 prior to batch effect correction and is now 0.50620034164611 .
2025-11-20 22:13:30.357443 INFO::ASW Label was 0.332538616250768 prior to batch effect correction and is now 0.332538616250768 .
2025-11-20 22:13:30.358145 INFO::Total function execution time is 2.83908867835999 s and adjustment time is 2.80040860176086 s ( 98.64 )
2025-11-20 22:13:30.520433 INFO::Formatting Data.
2025-11-20 22:13:30.52122 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:30.522077 INFO::Removing potential empty rows and columns
2025-11-20 22:13:30.5231 INFO::Found 0 missing values.
2025-11-20 22:13:30.526613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:30.527138 INFO::Done
2025-11-20 22:13:30.527632 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 22:13:30.530291 INFO::Starting hierarchical adjustment
2025-11-20 22:13:30.530962 INFO::Found 3 batches.
2025-11-20 22:13:30.531493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 22:13:30.532065 INFO::Using default BPPARAM
2025-11-20 22:13:30.532604 INFO::Processing subtree level 1
2025-11-20 22:13:30.635445 INFO::Adjusting the last 1 batches sequentially
2025-11-20 22:13:30.637148 INFO::Done
2025-11-20 22:13:30.637756 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 22:13:30.640806 INFO::ASW Batch was 0.173341327818227 prior to batch effect correction and is now -0.145401061521942 .
2025-11-20 22:13:30.641403 INFO::ASW Label was -0.198881288739465 prior to batch effect correction and is now -0.0579966097079682 .
2025-11-20 22:13:30.642275 INFO::Total function execution time is 0.121875762939453 s and adjustment time is 0.106295108795166 s ( 87.22 )
2025-11-20 22:13:30.763558 INFO::Formatting Data.
2025-11-20 22:13:30.764413 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:30.765342 INFO::Removing potential empty rows and columns
2025-11-20 22:13:30.766354 INFO::Found 2 missing values.
2025-11-20 22:13:30.769096 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:30.769623 INFO::Done
2025-11-20 22:13:30.795068 INFO::Found NA in Reference column
2025-11-20 22:13:30.803854 INFO::Require at least two references per batch.
2025-11-20 22:13:30.824965 INFO::Formatting Data.
2025-11-20 22:13:30.825689 INFO::Recognized SummarizedExperiment
2025-11-20 22:13:30.826218 INFO::Typecasting input to dataframe.
2025-11-20 22:13:30.836133 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:30.837185 INFO::Removing potential empty rows and columns
2025-11-20 22:13:30.840447 INFO::Found 0 missing values.
2025-11-20 22:13:30.84669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:30.847242 INFO::Done
2025-11-20 22:13:30.861901 INFO::Formatting Data.
2025-11-20 22:13:30.862558 INFO::Recognized SummarizedExperiment
2025-11-20 22:13:30.863065 INFO::Typecasting input to dataframe.
2025-11-20 22:13:30.879385 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:30.880513 INFO::Removing potential empty rows and columns
2025-11-20 22:13:30.88378 INFO::Found 0 missing values.
2025-11-20 22:13:30.893806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:30.894394 INFO::Done
2025-11-20 22:13:30.909002 INFO::Formatting Data.
2025-11-20 22:13:30.909718 INFO::Recognized SummarizedExperiment
2025-11-20 22:13:30.910226 INFO::Typecasting input to dataframe.
2025-11-20 22:13:30.926358 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:30.927508 INFO::Removing potential empty rows and columns
2025-11-20 22:13:30.928638 INFO::Found 0 missing values.
2025-11-20 22:13:30.929607 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.
2025-11-20 22:13:30.934139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:30.934681 INFO::Done
2025-11-20 22:13:30.944778 INFO::Formatting Data.
2025-11-20 22:13:30.945516 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:30.946307 INFO::Removing potential empty rows and columns
2025-11-20 22:13:30.947228 INFO::Found 0 missing values.
2025-11-20 22:13:30.949851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:30.950363 INFO::Done
2025-11-20 22:13:30.961061 INFO::Formatting Data.
2025-11-20 22:13:30.961848 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:30.962855 INFO::Removing potential empty rows and columns
2025-11-20 22:13:30.963835 INFO::Found 0 missing values.
2025-11-20 22:13:30.96663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:30.967196 INFO::Done
2025-11-20 22:13:30.997209 INFO::Formatting Data.
2025-11-20 22:13:30.998015 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:30.999024 INFO::Removing potential empty rows and columns
2025-11-20 22:13:31.000199 INFO::Found 1 missing values.
2025-11-20 22:13:31.002856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:31.003515 INFO::Done
2025-11-20 22:13:31.021716 INFO::Formatting Data.
2025-11-20 22:13:31.022502 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:31.023385 INFO::Removing potential empty rows and columns
2025-11-20 22:13:31.024294 INFO::Found 2 missing values.
2025-11-20 22:13:31.025151 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.
2025-11-20 22:13:31.027261 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:31.027767 INFO::Done
2025-11-20 22:13:31.037465 INFO::Formatting Data.
2025-11-20 22:13:31.03818 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:31.039029 INFO::Removing potential empty rows and columns
2025-11-20 22:13:31.039927 INFO::Found 2 missing values.
2025-11-20 22:13:31.041441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:31.041936 INFO::Done
2025-11-20 22:13:31.051428 INFO::Formatting Data.
2025-11-20 22:13:31.052104 INFO::Typecasting input to dataframe.
2025-11-20 22:13:31.052879 INFO::Replacing NaNs with NAs.
2025-11-20 22:13:31.053695 INFO::Removing potential empty rows and columns
2025-11-20 22:13:31.054655 INFO::Found 0 missing values.
2025-11-20 22:13:31.057333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 22:13:31.057849 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.089 4.333 20.902
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.364 | 1.625 | 18.486 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.013 | 0.001 | 0.015 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |