Yannis Schumann
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_21 |
| git_last_commit: dedce04 |
| git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | 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 | | ||||||||
| kunpeng2 | 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: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz |
| StartedAt: 2025-10-14 00:28:39 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 00:31:08 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 148.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 44.013 2.766 34.573
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.4.0’ ** 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 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-10-14 00:30:31.398303 INFO::Formatting Data.
2025-10-14 00:30:31.407523 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:31.459174 INFO::Removing potential empty rows and columns
2025-10-14 00:30:32.128003 INFO::Found 0 missing values.
2025-10-14 00:30:32.137556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:32.139142 INFO::Done
2025-10-14 00:30:32.140657 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:32.168594 INFO::Starting hierarchical adjustment
2025-10-14 00:30:32.170655 INFO::Found 3 batches.
2025-10-14 00:30:32.172211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:32.175401 INFO::Using default BPPARAM
2025-10-14 00:30:32.17725 INFO::Processing subtree level 1
2025-10-14 00:30:32.489168 INFO::Adjusting the last 1 batches sequentially
2025-10-14 00:30:32.497304 INFO::Done
2025-10-14 00:30:32.498916 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:32.50772 INFO::ASW Batch was -0.0544174986858565 prior to batch effect correction and is now -0.0544174986858565 .
2025-10-14 00:30:32.510353 INFO::Total function execution time is 1.11345291137695 s and adjustment time is 0.327080965042114 s ( 29.38 )
2025-10-14 00:30:32.546561 INFO::Formatting Data.
2025-10-14 00:30:32.548431 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:32.550783 INFO::Removing potential empty rows and columns
2025-10-14 00:30:32.553989 INFO::Found 0 missing values.
2025-10-14 00:30:32.556602 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.
2025-10-14 00:30:32.586319 INFO::Formatting Data.
2025-10-14 00:30:32.588288 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:32.590944 INFO::Removing potential empty rows and columns
2025-10-14 00:30:32.594194 INFO::Found 0 missing values.
2025-10-14 00:30:32.597053 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.
2025-10-14 00:30:32.647028 INFO::Formatting Data.
2025-10-14 00:30:32.648818 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:32.651193 INFO::Removing potential empty rows and columns
2025-10-14 00:30:32.653911 INFO::Found 0 missing values.
2025-10-14 00:30:32.656476 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.
2025-10-14 00:30:32.670564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:32.672363 INFO::Done
2025-10-14 00:30:32.673847 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:32.678638 INFO::Starting hierarchical adjustment
2025-10-14 00:30:32.680584 INFO::Found 2 batches.
2025-10-14 00:30:32.68201 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:32.683743 INFO::Using default BPPARAM
2025-10-14 00:30:32.68525 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:32.687695 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 00:30:32.747836 INFO::Done
2025-10-14 00:30:32.749715 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:32.755129 INFO::ASW Batch was 0.00282075873220982 prior to batch effect correction and is now -0.115215434411645 .
2025-10-14 00:30:32.757234 INFO::Total function execution time is 0.110239028930664 s and adjustment time is 0.0676100254058838 s ( 61.33 )
2025-10-14 00:30:32.763878 INFO::Formatting Data.
2025-10-14 00:30:32.765663 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:32.790034 INFO::Formatting Data.
2025-10-14 00:30:32.842967 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:32.845208 INFO::Removing potential empty rows and columns
2025-10-14 00:30:32.847771 INFO::Found 0 missing values.
2025-10-14 00:30:32.856725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:32.858383 INFO::Done
2025-10-14 00:30:32.860337 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:32.865803 INFO::Starting hierarchical adjustment
2025-10-14 00:30:32.867995 INFO::Found 2 batches.
2025-10-14 00:30:32.870617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:32.872291 INFO::Using default BPPARAM
2025-10-14 00:30:32.873557 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:32.875576 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 00:30:32.916023 INFO::Done
2025-10-14 00:30:32.917539 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:32.922364 INFO::ASW Batch was 0.0312229523200041 prior to batch effect correction and is now -0.0913561429098494 .
2025-10-14 00:30:32.92444 INFO::Total function execution time is 0.134456872940063 s and adjustment time is 0.04848313331604 s ( 36.06 )
2025-10-14 00:30:32.927119 INFO::Formatting Data.
2025-10-14 00:30:32.928703 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:32.930836 INFO::Removing potential empty rows and columns
2025-10-14 00:30:32.933651 INFO::Found 0 missing values.
2025-10-14 00:30:32.941617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:32.943121 INFO::Done
2025-10-14 00:30:32.944535 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:32.94921 INFO::Starting hierarchical adjustment
2025-10-14 00:30:32.951078 INFO::Found 2 batches.
2025-10-14 00:30:32.952421 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:32.953949 INFO::Using default BPPARAM
2025-10-14 00:30:32.955254 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:32.958038 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 00:30:33.002881 INFO::Done
2025-10-14 00:30:33.004493 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:33.009853 INFO::ASW Batch was 0.0312229523200041 prior to batch effect correction and is now -0.0913561429098494 .
2025-10-14 00:30:33.012153 INFO::Total function execution time is 0.0849809646606445 s and adjustment time is 0.0521469116210938 s ( 61.36 )
2025-10-14 00:30:39.478677 INFO::Formatting Data.
2025-10-14 00:30:39.48 INFO::Recognized SummarizedExperiment
2025-10-14 00:30:39.481093 INFO::Typecasting input to dataframe.
2025-10-14 00:30:39.548422 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:39.551245 INFO::Removing potential empty rows and columns
2025-10-14 00:30:39.562032 INFO::Found 0 missing values.
2025-10-14 00:30:39.584965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:39.586454 INFO::Done
2025-10-14 00:30:39.587763 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:39.598757 INFO::Starting hierarchical adjustment
2025-10-14 00:30:39.600797 INFO::Found 2 batches.
2025-10-14 00:30:39.60221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:39.606425 INFO::Using default BPPARAM
2025-10-14 00:30:39.607713 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:39.609879 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 00:30:39.768576 INFO::Done
2025-10-14 00:30:39.770164 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:39.779639 INFO::ASW Batch was 0.015182069588952 prior to batch effect correction and is now -0.0963058329050925 .
2025-10-14 00:30:39.781636 INFO::Total function execution time is 0.303567886352539 s and adjustment time is 0.168154954910278 s ( 55.39 )
2025-10-14 00:30:39.832056 INFO::Formatting Data.
2025-10-14 00:30:39.833647 INFO::Recognized SummarizedExperiment
2025-10-14 00:30:39.834992 INFO::Typecasting input to dataframe.
2025-10-14 00:30:39.860026 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:39.862652 INFO::Removing potential empty rows and columns
2025-10-14 00:30:39.87371 INFO::Found 0 missing values.
2025-10-14 00:30:39.896228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:39.897716 INFO::Done
2025-10-14 00:30:39.899055 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:39.907657 INFO::Starting hierarchical adjustment
2025-10-14 00:30:39.909407 INFO::Found 2 batches.
2025-10-14 00:30:39.910669 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:39.912036 INFO::Using default BPPARAM
2025-10-14 00:30:39.913329 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:39.915893 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 00:30:39.990396 INFO::Done
2025-10-14 00:30:39.991846 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:40.00142 INFO::ASW Batch was 0.000236717096431503 prior to batch effect correction and is now 0.000236717096431503 .
2025-10-14 00:30:40.003424 INFO::Total function execution time is 0.171351909637451 s and adjustment time is 0.0812890529632568 s ( 47.44 )
2025-10-14 00:30:40.054781 INFO::Formatting Data.
2025-10-14 00:30:40.056571 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:40.058826 INFO::Removing potential empty rows and columns
2025-10-14 00:30:40.061667 INFO::Found 0 missing values.
2025-10-14 00:30:40.069925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:40.071601 INFO::Done
2025-10-14 00:30:40.073196 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:40.078148 INFO::Starting hierarchical adjustment
2025-10-14 00:30:40.080194 INFO::Found 3 batches.
2025-10-14 00:30:40.081805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:40.083276 INFO::Using default BPPARAM
2025-10-14 00:30:40.084734 INFO::Processing subtree level 1
2025-10-14 00:30:40.753651 INFO::Adjusting the last 1 batches sequentially
2025-10-14 00:30:40.759533 INFO::Done
2025-10-14 00:30:40.764703 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:40.794533 INFO::ASW Batch was -0.0450012577305114 prior to batch effect correction and is now -0.15454395992553 .
2025-10-14 00:30:40.802288 INFO::Total function execution time is 0.747395992279053 s and adjustment time is 0.67976713180542 s ( 90.95 )
2025-10-14 00:30:40.946301 INFO::Skipping initial DF formatting
2025-10-14 00:30:40.948028 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:40.957689 INFO::Starting hierarchical adjustment
2025-10-14 00:30:40.959649 INFO::Found 5 batches.
2025-10-14 00:30:40.961151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:40.96276 INFO::Using default BPPARAM
2025-10-14 00:30:40.96411 INFO::Processing subtree level 1
2025-10-14 00:30:41.416124 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:41.426152 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 00:30:41.50295 INFO::Done
2025-10-14 00:30:41.504729 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:41.51728 INFO::ASW Batch was 0.560830506367835 prior to batch effect correction and is now 0.560830506367835 .
2025-10-14 00:30:41.519119 INFO::ASW Label was 0.375175720226282 prior to batch effect correction and is now 0.375175720226282 .
2025-10-14 00:30:41.521629 INFO::Total function execution time is 0.575364828109741 s and adjustment time is 0.54363489151001 s ( 94.49 )
2025-10-14 00:30:41.578558 INFO::Formatting Data.
2025-10-14 00:30:41.580403 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:41.582687 INFO::Removing potential empty rows and columns
2025-10-14 00:30:41.585534 INFO::Found 0 missing values.
2025-10-14 00:30:41.599064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:41.601547 INFO::Done
2025-10-14 00:30:41.6034 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:41.61137 INFO::Starting hierarchical adjustment
2025-10-14 00:30:41.614097 INFO::Found 5 batches.
2025-10-14 00:30:41.615747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:41.617549 INFO::Using default BPPARAM
2025-10-14 00:30:41.619079 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.
2025-10-14 00:30:41.945715 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:41.955349 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 00:30:42.011727 INFO::Done
2025-10-14 00:30:42.013336 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:42.021887 INFO::ASW Batch was 0.348162139250525 prior to batch effect correction and is now -0.0801304872118675 .
2025-10-14 00:30:42.023678 INFO::ASW Label was 0.425484399771975 prior to batch effect correction and is now 0.824749748260392 .
2025-10-14 00:30:42.026346 INFO::Total function execution time is 0.447821140289307 s and adjustment time is 0.398080110549927 s ( 88.89 )
2025-10-14 00:30:42.028541 INFO::Formatting Data.
2025-10-14 00:30:42.030169 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:42.032411 INFO::Removing potential empty rows and columns
2025-10-14 00:30:42.03501 INFO::Found 0 missing values.
2025-10-14 00:30:42.047306 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:42.048702 INFO::Done
2025-10-14 00:30:42.049902 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:42.057293 INFO::Starting hierarchical adjustment
2025-10-14 00:30:42.059722 INFO::Found 5 batches.
2025-10-14 00:30:42.061077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:42.062674 INFO::Using default BPPARAM
2025-10-14 00:30:42.06411 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.
2025-10-14 00:30:42.39486 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:42.407331 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 00:30:42.46649 INFO::Done
2025-10-14 00:30:42.468121 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:42.476623 INFO::ASW Batch was 0.348162139250525 prior to batch effect correction and is now -0.0801304872118675 .
2025-10-14 00:30:42.478691 INFO::ASW Label was 0.425484399771975 prior to batch effect correction and is now 0.824749748260392 .
2025-10-14 00:30:42.480724 INFO::Total function execution time is 0.452185869216919 s and adjustment time is 0.407108068466187 s ( 90.03 )
2025-10-14 00:30:42.519017 INFO::Formatting Data.
2025-10-14 00:30:42.520789 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:42.523032 INFO::Removing potential empty rows and columns
2025-10-14 00:30:42.525633 INFO::Found 0 missing values.
2025-10-14 00:30:42.537532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:42.540375 INFO::Done
2025-10-14 00:30:42.542566 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:42.550347 INFO::Starting hierarchical adjustment
2025-10-14 00:30:42.552405 INFO::Found 5 batches.
2025-10-14 00:30:42.553871 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:42.555545 INFO::Using default BPPARAM
2025-10-14 00:30:42.557186 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.
2025-10-14 00:30:42.87366 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:42.88363 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 00:30:42.9357 INFO::Done
2025-10-14 00:30:42.93729 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:42.945923 INFO::ASW Batch was 0.327338756709328 prior to batch effect correction and is now 0.0653571350672726 .
2025-10-14 00:30:42.947634 INFO::ASW Label was 0.505340726464277 prior to batch effect correction and is now 0.683421372985998 .
2025-10-14 00:30:42.950792 INFO::Total function execution time is 0.431809902191162 s and adjustment time is 0.3836989402771 s ( 88.86 )
2025-10-14 00:30:42.952949 INFO::Formatting Data.
2025-10-14 00:30:42.954747 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:42.957053 INFO::Removing potential empty rows and columns
2025-10-14 00:30:42.959724 INFO::Found 0 missing values.
2025-10-14 00:30:42.970937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:42.972476 INFO::Done
2025-10-14 00:30:42.973872 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:42.981513 INFO::Starting hierarchical adjustment
2025-10-14 00:30:42.98353 INFO::Found 5 batches.
2025-10-14 00:30:42.984837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:42.986382 INFO::Using default BPPARAM
2025-10-14 00:30:42.9878 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.
2025-10-14 00:30:43.288916 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:43.30115 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 00:30:43.351901 INFO::Done
2025-10-14 00:30:43.354085 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:43.3618 INFO::ASW Batch was 0.327338756709328 prior to batch effect correction and is now 0.0653571350672726 .
2025-10-14 00:30:43.363945 INFO::ASW Label was 0.505340726464277 prior to batch effect correction and is now 0.683421372985998 .
2025-10-14 00:30:43.366167 INFO::Total function execution time is 0.413323879241943 s and adjustment time is 0.368865013122559 s ( 89.24 )
2025-10-14 00:30:43.405033 INFO::Formatting Data.
2025-10-14 00:30:43.406848 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:43.409133 INFO::Removing potential empty rows and columns
2025-10-14 00:30:43.411879 INFO::Found 0 missing values.
2025-10-14 00:30:43.419765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:43.421316 INFO::Done
2025-10-14 00:30:43.422647 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:43.429596 INFO::Starting hierarchical adjustment
2025-10-14 00:30:43.43143 INFO::Found 2 batches.
2025-10-14 00:30:43.432738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:43.434578 INFO::Using default BPPARAM
2025-10-14 00:30:43.436049 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:43.438441 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 00:30:43.476154 INFO::Done
2025-10-14 00:30:43.477661 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:43.484746 INFO::ASW Batch was 0.525052655638461 prior to batch effect correction and is now 0.099259979420863 .
2025-10-14 00:30:43.486356 INFO::ASW Label was 0.599897113076367 prior to batch effect correction and is now 0.866227994824225 .
2025-10-14 00:30:43.488338 INFO::Total function execution time is 0.0834259986877441 s and adjustment time is 0.0450439453125 s ( 53.99 )
2025-10-14 00:30:43.490447 INFO::Formatting Data.
2025-10-14 00:30:43.492047 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:43.494406 INFO::Removing potential empty rows and columns
2025-10-14 00:30:43.49709 INFO::Found 0 missing values.
2025-10-14 00:30:43.504418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:43.505871 INFO::Done
2025-10-14 00:30:43.507191 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:43.513851 INFO::Starting hierarchical adjustment
2025-10-14 00:30:43.51576 INFO::Found 2 batches.
2025-10-14 00:30:43.517086 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:43.518556 INFO::Using default BPPARAM
2025-10-14 00:30:43.519818 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:43.522025 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 00:30:43.559403 INFO::Done
2025-10-14 00:30:43.560951 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:43.568041 INFO::ASW Batch was 0.525052655638461 prior to batch effect correction and is now 0.099259979420863 .
2025-10-14 00:30:43.5696 INFO::ASW Label was 0.599897113076367 prior to batch effect correction and is now 0.866227994824225 .
2025-10-14 00:30:43.571527 INFO::Total function execution time is 0.0811071395874023 s and adjustment time is 0.0440001487731934 s ( 54.25 )
2025-10-14 00:30:43.601799 INFO::Formatting Data.
2025-10-14 00:30:43.6035 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:43.605602 INFO::Removing potential empty rows and columns
2025-10-14 00:30:43.607872 INFO::Found 0 missing values.
2025-10-14 00:30:43.613258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:43.614757 INFO::Done
2025-10-14 00:30:43.616064 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:43.620451 INFO::Starting hierarchical adjustment
2025-10-14 00:30:43.622252 INFO::Found 2 batches.
2025-10-14 00:30:43.623517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:43.624971 INFO::Using default BPPARAM
2025-10-14 00:30:43.626282 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:43.628436 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 00:30:43.709454 INFO::Done
2025-10-14 00:30:43.710893 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:43.715178 INFO::ASW Batch was -0.0599366772801692 prior to batch effect correction and is now -0.153235983656837 .
2025-10-14 00:30:43.717103 INFO::Total function execution time is 0.115412950515747 s and adjustment time is 0.0875260829925537 s ( 75.84 )
2025-10-14 00:30:43.748041 INFO::Formatting Data.
2025-10-14 00:30:43.749768 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:43.751806 INFO::Removing potential empty rows and columns
2025-10-14 00:30:43.754265 INFO::Found 0 missing values.
2025-10-14 00:30:43.756979 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.
2025-10-14 00:30:43.768529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:43.769933 INFO::Done
2025-10-14 00:30:43.771201 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:43.777815 INFO::Starting hierarchical adjustment
2025-10-14 00:30:43.780153 INFO::Found 2 batches.
2025-10-14 00:30:43.781493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:43.782884 INFO::Using default BPPARAM
2025-10-14 00:30:43.784146 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:43.786279 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 00:30:43.828738 INFO::Done
2025-10-14 00:30:43.830225 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:43.84118 INFO::ASW Batch was 0.677518022318577 prior to batch effect correction and is now 0.231407554656169 .
2025-10-14 00:30:43.842946 INFO::ASW Label was 0.463229395998855 prior to batch effect correction and is now 0.783751620805021 .
2025-10-14 00:30:43.844859 INFO::Total function execution time is 0.0969169139862061 s and adjustment time is 0.0489749908447266 s ( 50.53 )
2025-10-14 00:30:43.846669 INFO::Formatting Data.
2025-10-14 00:30:43.848149 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:43.850458 INFO::Removing potential empty rows and columns
2025-10-14 00:30:43.853005 INFO::Found 0 missing values.
2025-10-14 00:30:43.871677 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.
2025-10-14 00:30:43.884177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:43.885635 INFO::Done
2025-10-14 00:30:43.88697 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:43.894068 INFO::Starting hierarchical adjustment
2025-10-14 00:30:43.895981 INFO::Found 2 batches.
2025-10-14 00:30:43.897303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:43.898828 INFO::Using default BPPARAM
2025-10-14 00:30:43.900179 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:43.902554 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 00:30:43.946072 INFO::Done
2025-10-14 00:30:43.947611 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:43.954807 INFO::ASW Batch was 0.677518022318577 prior to batch effect correction and is now 0.231407554656169 .
2025-10-14 00:30:43.95636 INFO::ASW Label was 0.463229395998855 prior to batch effect correction and is now 0.783751620805021 .
2025-10-14 00:30:43.958375 INFO::Total function execution time is 0.111696004867554 s and adjustment time is 0.0504608154296875 s ( 45.18 )
2025-10-14 00:30:44.541739 INFO::Formatting Data.
2025-10-14 00:30:44.543478 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:44.545736 INFO::Removing potential empty rows and columns
2025-10-14 00:30:44.548383 INFO::Found 0 missing values.
2025-10-14 00:30:44.556743 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:44.558106 INFO::Done
2025-10-14 00:30:44.55964 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:44.565201 INFO::Starting hierarchical adjustment
2025-10-14 00:30:44.567176 INFO::Found 3 batches.
2025-10-14 00:30:44.5686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:44.570183 INFO::Using default BPPARAM
2025-10-14 00:30:44.57157 INFO::Processing subtree level 1
2025-10-14 00:30:44.801535 INFO::Adjusting the last 1 batches sequentially
2025-10-14 00:30:44.811645 INFO::Done
2025-10-14 00:30:44.815061 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:44.827186 INFO::ASW Batch was -0.00835098581074937 prior to batch effect correction and is now -0.00835098581074937 .
2025-10-14 00:30:44.830906 INFO::Total function execution time is 0.289121150970459 s and adjustment time is 0.244836807250977 s ( 84.68 )
2025-10-14 00:30:44.834145 INFO::Formatting Data.
2025-10-14 00:30:44.835877 INFO::Typecasting input to dataframe.
2025-10-14 00:30:44.837835 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:44.840219 INFO::Removing potential empty rows and columns
2025-10-14 00:30:44.843707 INFO::Found 0 missing values.
2025-10-14 00:30:44.854383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:44.85589 INFO::Done
2025-10-14 00:30:44.857225 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:44.862266 INFO::Starting hierarchical adjustment
2025-10-14 00:30:44.864737 INFO::Found 3 batches.
2025-10-14 00:30:44.866157 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:44.867752 INFO::Using default BPPARAM
2025-10-14 00:30:44.870411 INFO::Processing subtree level 1
2025-10-14 00:30:45.10329 INFO::Adjusting the last 1 batches sequentially
2025-10-14 00:30:45.114754 INFO::Done
2025-10-14 00:30:45.117491 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:45.129723 INFO::ASW Batch was -0.00835098581074937 prior to batch effect correction and is now -0.00835098581074937 .
2025-10-14 00:30:45.132796 INFO::Total function execution time is 0.298657894134521 s and adjustment time is 0.250365972518921 s ( 83.83 )
2025-10-14 00:30:45.174861 INFO::Formatting Data.
2025-10-14 00:30:45.176601 INFO::Typecasting input to dataframe.
2025-10-14 00:30:45.179298 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:45.181368 INFO::Removing potential empty rows and columns
2025-10-14 00:30:45.184066 INFO::Found 0 missing values.
2025-10-14 00:30:45.191609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:45.193035 INFO::Done
2025-10-14 00:30:45.194323 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:45.198861 INFO::Starting hierarchical adjustment
2025-10-14 00:30:45.200907 INFO::Found 3 batches.
2025-10-14 00:30:45.2023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:45.203828 INFO::Using default BPPARAM
2025-10-14 00:30:45.205189 INFO::Processing subtree level 1
2025-10-14 00:30:45.428279 INFO::Adjusting the last 1 batches sequentially
2025-10-14 00:30:45.439551 INFO::Done
2025-10-14 00:30:45.44229 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:45.453056 INFO::ASW Batch was -0.102551194009559 prior to batch effect correction and is now -0.102551194009559 .
2025-10-14 00:30:45.456108 INFO::Total function execution time is 0.280582904815674 s and adjustment time is 0.239176034927368 s ( 85.24 )
2025-10-14 00:30:45.844856 INFO::Formatting Data.
2025-10-14 00:30:45.846548 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:45.849184 INFO::Removing potential empty rows and columns
2025-10-14 00:30:45.856815 INFO::Found 1000 missing values.
2025-10-14 00:30:45.916052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:45.917786 INFO::Done
2025-10-14 00:30:45.91932 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:45.931893 INFO::Starting hierarchical adjustment
2025-10-14 00:30:45.933843 INFO::Found 10 batches.
2025-10-14 00:30:45.935769 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:45.937394 INFO::Using default BPPARAM
2025-10-14 00:30:45.938794 INFO::Processing subtree level 1
2025-10-14 00:30:46.227703 INFO::Processing subtree level 2
2025-10-14 00:30:46.606145 INFO::Adjusting the last 1 batches sequentially
2025-10-14 00:30:46.61201 INFO::Done
2025-10-14 00:30:46.613689 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:46.629327 INFO::ASW Batch was 0.538066808949283 prior to batch effect correction and is now 0.538066808949283 .
2025-10-14 00:30:46.631175 INFO::ASW Label was 0.282415209144313 prior to batch effect correction and is now 0.282415209144313 .
2025-10-14 00:30:46.634017 INFO::Total function execution time is 0.789040088653564 s and adjustment time is 0.678544044494629 s ( 86 )
2025-10-14 00:30:46.636435 INFO::Formatting Data.
2025-10-14 00:30:46.638147 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:46.641557 INFO::Removing potential empty rows and columns
2025-10-14 00:30:46.650534 INFO::Found 1000 missing values.
2025-10-14 00:30:46.712971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:46.714481 INFO::Done
2025-10-14 00:30:46.715881 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:46.728495 INFO::Starting hierarchical adjustment
2025-10-14 00:30:46.730417 INFO::Found 10 batches.
2025-10-14 00:30:48.498444 INFO::Set up parallel execution backend with 2 workers
2025-10-14 00:30:48.499812 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-14 00:30:50.310433 INFO::Adjusting the last 2 batches sequentially
2025-10-14 00:30:50.312803 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 00:30:50.360725 INFO::Done
2025-10-14 00:30:50.362023 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:50.373301 INFO::ASW Batch was 0.538066808949283 prior to batch effect correction and is now 0.538066808949283 .
2025-10-14 00:30:50.37533 INFO::ASW Label was 0.282415209144313 prior to batch effect correction and is now 0.282415209144313 .
2025-10-14 00:30:50.377374 INFO::Total function execution time is 3.74075102806091 s and adjustment time is 3.63068509101868 s ( 97.06 )
2025-10-14 00:30:50.775361 INFO::Formatting Data.
2025-10-14 00:30:50.778076 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:50.780666 INFO::Removing potential empty rows and columns
2025-10-14 00:30:50.783992 INFO::Found 0 missing values.
2025-10-14 00:30:50.795627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:50.797578 INFO::Done
2025-10-14 00:30:50.799316 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 00:30:50.806101 INFO::Starting hierarchical adjustment
2025-10-14 00:30:50.807974 INFO::Found 3 batches.
2025-10-14 00:30:50.810315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 00:30:50.811971 INFO::Using default BPPARAM
2025-10-14 00:30:50.813391 INFO::Processing subtree level 1
2025-10-14 00:30:51.099104 INFO::Adjusting the last 1 batches sequentially
2025-10-14 00:30:51.113268 INFO::Done
2025-10-14 00:30:51.115181 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 00:30:51.128999 INFO::ASW Batch was 0.197000194333075 prior to batch effect correction and is now -0.156306066942263 .
2025-10-14 00:30:51.132465 INFO::ASW Label was -0.103580674152293 prior to batch effect correction and is now 0.104605315201803 .
2025-10-14 00:30:51.136958 INFO::Total function execution time is 0.361318111419678 s and adjustment time is 0.305615186691284 s ( 84.58 )
2025-10-14 00:30:51.483693 INFO::Formatting Data.
2025-10-14 00:30:51.485486 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:51.487687 INFO::Removing potential empty rows and columns
2025-10-14 00:30:51.491709 INFO::Found 2 missing values.
2025-10-14 00:30:51.500042 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:51.501605 INFO::Done
2025-10-14 00:30:51.585354 INFO::Found NA in Reference column
2025-10-14 00:30:51.612916 INFO::Require at least two references per batch.
2025-10-14 00:30:51.675939 INFO::Formatting Data.
2025-10-14 00:30:51.677949 INFO::Recognized SummarizedExperiment
2025-10-14 00:30:51.679487 INFO::Typecasting input to dataframe.
2025-10-14 00:30:51.709621 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:51.712341 INFO::Removing potential empty rows and columns
2025-10-14 00:30:51.724508 INFO::Found 0 missing values.
2025-10-14 00:30:51.750686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:51.7539 INFO::Done
2025-10-14 00:30:51.801274 INFO::Formatting Data.
2025-10-14 00:30:51.802804 INFO::Recognized SummarizedExperiment
2025-10-14 00:30:51.804435 INFO::Typecasting input to dataframe.
2025-10-14 00:30:51.855464 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:51.858127 INFO::Removing potential empty rows and columns
2025-10-14 00:30:51.870733 INFO::Found 0 missing values.
2025-10-14 00:30:51.909504 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:51.911016 INFO::Done
2025-10-14 00:30:51.952291 INFO::Formatting Data.
2025-10-14 00:30:51.953818 INFO::Recognized SummarizedExperiment
2025-10-14 00:30:51.955028 INFO::Typecasting input to dataframe.
2025-10-14 00:30:52.001326 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:52.003612 INFO::Removing potential empty rows and columns
2025-10-14 00:30:52.00779 INFO::Found 0 missing values.
2025-10-14 00:30:52.010287 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.
2025-10-14 00:30:52.022832 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:52.024391 INFO::Done
2025-10-14 00:30:52.05189 INFO::Formatting Data.
2025-10-14 00:30:52.053653 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:52.055974 INFO::Removing potential empty rows and columns
2025-10-14 00:30:52.058827 INFO::Found 0 missing values.
2025-10-14 00:30:52.06698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:52.068511 INFO::Done
2025-10-14 00:30:52.101269 INFO::Formatting Data.
2025-10-14 00:30:52.103262 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:52.105598 INFO::Removing potential empty rows and columns
2025-10-14 00:30:52.108294 INFO::Found 0 missing values.
2025-10-14 00:30:52.116759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:52.118366 INFO::Done
2025-10-14 00:30:52.208576 INFO::Formatting Data.
2025-10-14 00:30:52.211259 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:52.214015 INFO::Removing potential empty rows and columns
2025-10-14 00:30:52.217407 INFO::Found 1 missing values.
2025-10-14 00:30:52.224916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:52.226688 INFO::Done
2025-10-14 00:30:52.283361 INFO::Formatting Data.
2025-10-14 00:30:52.285313 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:52.287452 INFO::Removing potential empty rows and columns
2025-10-14 00:30:52.289816 INFO::Found 2 missing values.
2025-10-14 00:30:52.292329 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.
2025-10-14 00:30:52.301381 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:52.303026 INFO::Done
2025-10-14 00:30:52.333836 INFO::Formatting Data.
2025-10-14 00:30:52.335595 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:52.337745 INFO::Removing potential empty rows and columns
2025-10-14 00:30:52.340163 INFO::Found 2 missing values.
2025-10-14 00:30:52.344498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:52.346119 INFO::Done
2025-10-14 00:30:52.376165 INFO::Formatting Data.
2025-10-14 00:30:52.378124 INFO::Typecasting input to dataframe.
2025-10-14 00:30:52.38023 INFO::Replacing NaNs with NAs.
2025-10-14 00:30:52.382422 INFO::Removing potential empty rows and columns
2025-10-14 00:30:52.385074 INFO::Found 0 missing values.
2025-10-14 00:30:52.393194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 00:30:52.394647 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.182 6.975 43.853
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 44.013 | 2.766 | 34.573 | |
| compute_asw | 0.057 | 0.003 | 0.064 | |
| count_existing | 0.028 | 0.002 | 0.031 | |
| generate_data_covariables | 0.025 | 0.002 | 0.028 | |
| generate_dataset | 0.025 | 0.003 | 0.028 | |