Yannis Schumann
| Snapshot Date: 2025-08-18 13:45 -0400 (Mon, 18 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-19 12:03 -0400 (Tue, 19 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
| 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 162/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2025-08-18 20:33:48 -0400 (Mon, 18 Aug 2025) |
| EndedAt: 2025-08-18 20:35:25 -0400 (Mon, 18 Aug 2025) |
| EllapsedTime: 97.1 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.5.0’
* 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 29.197 1.904 21.16
* 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 ‘1.5.0’ ** 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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-08-18 20:34:45.507527 INFO::Formatting Data.
2025-08-18 20:34:45.508832 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:45.51986 INFO::Removing potential empty rows and columns
2025-08-18 20:34:45.756619 INFO::Found 0 missing values.
2025-08-18 20:34:45.759882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:45.760485 INFO::Done
2025-08-18 20:34:45.761004 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:45.772155 INFO::Starting hierarchical adjustment
2025-08-18 20:34:45.772995 INFO::Found 3 batches.
2025-08-18 20:34:45.773527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:45.77464 INFO::Using default BPPARAM
2025-08-18 20:34:45.775186 INFO::Processing subtree level 1
2025-08-18 20:34:45.877702 INFO::Adjusting the last 1 batches sequentially
2025-08-18 20:34:45.879832 INFO::Done
2025-08-18 20:34:45.880623 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:45.883614 INFO::ASW Batch was 0.100855185302482 prior to batch effect correction and is now 0.100855185302482 .
2025-08-18 20:34:45.88484 INFO::Total function execution time is 0.377855539321899 s and adjustment time is 0.106979131698608 s ( 28.31 )
2025-08-18 20:34:45.899851 INFO::Formatting Data.
2025-08-18 20:34:45.900772 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:45.901735 INFO::Removing potential empty rows and columns
2025-08-18 20:34:45.90285 INFO::Found 0 missing values.
2025-08-18 20:34:45.903789 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.
2025-08-18 20:34:45.914646 INFO::Formatting Data.
2025-08-18 20:34:45.915447 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:45.916378 INFO::Removing potential empty rows and columns
2025-08-18 20:34:45.917438 INFO::Found 0 missing values.
2025-08-18 20:34:45.918372 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.
2025-08-18 20:34:45.934039 INFO::Formatting Data.
2025-08-18 20:34:45.934838 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:45.935735 INFO::Removing potential empty rows and columns
2025-08-18 20:34:45.936776 INFO::Found 0 missing values.
2025-08-18 20:34:45.937682 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.
2025-08-18 20:34:45.941854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:45.942394 INFO::Done
2025-08-18 20:34:45.94292 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:45.94509 INFO::Starting hierarchical adjustment
2025-08-18 20:34:45.945805 INFO::Found 2 batches.
2025-08-18 20:34:45.946312 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:45.946936 INFO::Using default BPPARAM
2025-08-18 20:34:45.947458 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:45.94839 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-18 20:34:45.971128 INFO::Done
2025-08-18 20:34:45.97193 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:45.974098 INFO::ASW Batch was 0.10359070129602 prior to batch effect correction and is now -0.121892814472434 .
2025-08-18 20:34:45.974943 INFO::Total function execution time is 0.0409791469573975 s and adjustment time is 0.0254509449005127 s ( 62.11 )
2025-08-18 20:34:45.97769 INFO::Formatting Data.
2025-08-18 20:34:45.97832 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:45.987212 INFO::Formatting Data.
2025-08-18 20:34:45.987974 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:45.988885 INFO::Removing potential empty rows and columns
2025-08-18 20:34:45.989956 INFO::Found 0 missing values.
2025-08-18 20:34:45.992912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:45.993449 INFO::Done
2025-08-18 20:34:45.993977 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:45.996161 INFO::Starting hierarchical adjustment
2025-08-18 20:34:45.996881 INFO::Found 2 batches.
2025-08-18 20:34:45.997415 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:45.998042 INFO::Using default BPPARAM
2025-08-18 20:34:45.998604 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:45.999572 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-18 20:34:46.056205 INFO::Done
2025-08-18 20:34:46.057121 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:46.059556 INFO::ASW Batch was 0.0591231734708557 prior to batch effect correction and is now -0.0975095850083899 .
2025-08-18 20:34:46.060443 INFO::Total function execution time is 0.0732650756835938 s and adjustment time is 0.0593888759613037 s ( 81.06 )
2025-08-18 20:34:46.061577 INFO::Formatting Data.
2025-08-18 20:34:46.0622 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:46.063101 INFO::Removing potential empty rows and columns
2025-08-18 20:34:46.064158 INFO::Found 0 missing values.
2025-08-18 20:34:46.066982 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:46.067514 INFO::Done
2025-08-18 20:34:46.068036 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:46.070067 INFO::Starting hierarchical adjustment
2025-08-18 20:34:46.070797 INFO::Found 2 batches.
2025-08-18 20:34:46.071322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:46.071972 INFO::Using default BPPARAM
2025-08-18 20:34:46.072496 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:46.073411 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-18 20:34:46.088276 INFO::Done
2025-08-18 20:34:46.088907 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:46.09088 INFO::ASW Batch was 0.0591231734708557 prior to batch effect correction and is now -0.0975095850083899 .
2025-08-18 20:34:46.091671 INFO::Total function execution time is 0.0300948619842529 s and adjustment time is 0.0176362991333008 s ( 58.6 )
2025-08-18 20:34:49.03064 INFO::Formatting Data.
2025-08-18 20:34:49.031356 INFO::Recognized SummarizedExperiment
2025-08-18 20:34:49.031832 INFO::Typecasting input to dataframe.
2025-08-18 20:34:49.063785 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:49.065139 INFO::Removing potential empty rows and columns
2025-08-18 20:34:49.069029 INFO::Found 0 missing values.
2025-08-18 20:34:49.076327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:49.077072 INFO::Done
2025-08-18 20:34:49.077635 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:49.081366 INFO::Starting hierarchical adjustment
2025-08-18 20:34:49.082127 INFO::Found 2 batches.
2025-08-18 20:34:49.082657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:49.083798 INFO::Using default BPPARAM
2025-08-18 20:34:49.084339 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:49.085337 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-18 20:34:49.142645 INFO::Done
2025-08-18 20:34:49.143424 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:49.147176 INFO::ASW Batch was 0.0182632143999791 prior to batch effect correction and is now -0.0922604271603214 .
2025-08-18 20:34:49.148072 INFO::Total function execution time is 0.117691278457642 s and adjustment time is 0.0606253147125244 s ( 51.51 )
2025-08-18 20:34:49.167285 INFO::Formatting Data.
2025-08-18 20:34:49.16804 INFO::Recognized SummarizedExperiment
2025-08-18 20:34:49.168554 INFO::Typecasting input to dataframe.
2025-08-18 20:34:49.178007 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:49.179194 INFO::Removing potential empty rows and columns
2025-08-18 20:34:49.182856 INFO::Found 0 missing values.
2025-08-18 20:34:49.190086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:49.1907 INFO::Done
2025-08-18 20:34:49.191238 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:49.194783 INFO::Starting hierarchical adjustment
2025-08-18 20:34:49.195506 INFO::Found 2 batches.
2025-08-18 20:34:49.196031 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:49.196626 INFO::Using default BPPARAM
2025-08-18 20:34:49.197149 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:49.198109 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-18 20:34:49.22322 INFO::Done
2025-08-18 20:34:49.223943 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:49.227471 INFO::ASW Batch was 0.010241855101032 prior to batch effect correction and is now 0.010241855101032 .
2025-08-18 20:34:49.228336 INFO::Total function execution time is 0.0610466003417969 s and adjustment time is 0.0278356075286865 s ( 45.6 )
2025-08-18 20:34:49.246839 INFO::Formatting Data.
2025-08-18 20:34:49.247643 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:49.248523 INFO::Removing potential empty rows and columns
2025-08-18 20:34:49.249561 INFO::Found 0 missing values.
2025-08-18 20:34:49.252525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:49.253064 INFO::Done
2025-08-18 20:34:49.253561 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:49.255541 INFO::Starting hierarchical adjustment
2025-08-18 20:34:49.256238 INFO::Found 3 batches.
2025-08-18 20:34:49.256766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:49.257345 INFO::Using default BPPARAM
2025-08-18 20:34:49.257872 INFO::Processing subtree level 1
2025-08-18 20:34:49.395273 INFO::Adjusting the last 1 batches sequentially
2025-08-18 20:34:49.397111 INFO::Done
2025-08-18 20:34:49.397775 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:49.400323 INFO::ASW Batch was -0.0251489864677172 prior to batch effect correction and is now -0.159075751246579 .
2025-08-18 20:34:49.401246 INFO::Total function execution time is 0.154521703720093 s and adjustment time is 0.140996932983398 s ( 91.25 )
2025-08-18 20:34:49.415606 INFO::Skipping initial DF formatting
2025-08-18 20:34:49.416319 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:49.42044 INFO::Starting hierarchical adjustment
2025-08-18 20:34:49.421228 INFO::Found 5 batches.
2025-08-18 20:34:49.4218 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:49.422413 INFO::Using default BPPARAM
2025-08-18 20:34:49.422954 INFO::Processing subtree level 1
2025-08-18 20:34:49.646897 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:49.648479 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-18 20:34:49.667734 INFO::Done
2025-08-18 20:34:49.668471 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:49.71591 INFO::ASW Batch was 0.544054125891898 prior to batch effect correction and is now 0.544054125891898 .
2025-08-18 20:34:49.717237 INFO::ASW Label was 0.365725368723742 prior to batch effect correction and is now 0.365725368723742 .
2025-08-18 20:34:49.718042 INFO::Total function execution time is 0.302542686462402 s and adjustment time is 0.246625423431396 s ( 81.52 )
2025-08-18 20:34:49.733879 INFO::Formatting Data.
2025-08-18 20:34:49.734632 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:49.735499 INFO::Removing potential empty rows and columns
2025-08-18 20:34:49.736456 INFO::Found 0 missing values.
2025-08-18 20:34:49.740419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:49.740961 INFO::Done
2025-08-18 20:34:49.741467 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:49.744612 INFO::Starting hierarchical adjustment
2025-08-18 20:34:49.745302 INFO::Found 5 batches.
2025-08-18 20:34:49.74583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:49.746428 INFO::Using default BPPARAM
2025-08-18 20:34:49.746977 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.
2025-08-18 20:34:49.88636 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:49.888173 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-18 20:34:49.905709 INFO::Done
2025-08-18 20:34:49.906451 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:49.909919 INFO::ASW Batch was 0.403597786032247 prior to batch effect correction and is now 0.0035129694282448 .
2025-08-18 20:34:49.910556 INFO::ASW Label was 0.421181107877444 prior to batch effect correction and is now 0.739321801101836 .
2025-08-18 20:34:49.911364 INFO::Total function execution time is 0.177542448043823 s and adjustment time is 0.160512924194336 s ( 90.41 )
2025-08-18 20:34:49.912325 INFO::Formatting Data.
2025-08-18 20:34:49.912992 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:49.913943 INFO::Removing potential empty rows and columns
2025-08-18 20:34:49.915047 INFO::Found 0 missing values.
2025-08-18 20:34:49.919256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:49.919813 INFO::Done
2025-08-18 20:34:49.920311 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:49.923495 INFO::Starting hierarchical adjustment
2025-08-18 20:34:49.924291 INFO::Found 5 batches.
2025-08-18 20:34:49.924836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:49.925423 INFO::Using default BPPARAM
2025-08-18 20:34:49.925961 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.
2025-08-18 20:34:50.062818 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:50.06481 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-18 20:34:50.084169 INFO::Done
2025-08-18 20:34:50.085035 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.088953 INFO::ASW Batch was 0.403597786032247 prior to batch effect correction and is now 0.0035129694282448 .
2025-08-18 20:34:50.089699 INFO::ASW Label was 0.421181107877444 prior to batch effect correction and is now 0.739321801101836 .
2025-08-18 20:34:50.09064 INFO::Total function execution time is 0.178317308425903 s and adjustment time is 0.15999436378479 s ( 89.72 )
2025-08-18 20:34:50.107234 INFO::Formatting Data.
2025-08-18 20:34:50.108173 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.109185 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.110261 INFO::Found 0 missing values.
2025-08-18 20:34:50.114514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:50.115127 INFO::Done
2025-08-18 20:34:50.115673 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:50.118951 INFO::Starting hierarchical adjustment
2025-08-18 20:34:50.119728 INFO::Found 5 batches.
2025-08-18 20:34:50.120276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:50.120924 INFO::Using default BPPARAM
2025-08-18 20:34:50.121465 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.
2025-08-18 20:34:50.251747 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:50.253395 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-18 20:34:50.269166 INFO::Done
2025-08-18 20:34:50.269898 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.273149 INFO::ASW Batch was 0.638629355114146 prior to batch effect correction and is now -0.0144891928399701 .
2025-08-18 20:34:50.273793 INFO::ASW Label was 0.164985468811569 prior to batch effect correction and is now 0.668148843869861 .
2025-08-18 20:34:50.274607 INFO::Total function execution time is 0.167516946792603 s and adjustment time is 0.14959716796875 s ( 89.3 )
2025-08-18 20:34:50.275434 INFO::Formatting Data.
2025-08-18 20:34:50.276061 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.276947 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.277935 INFO::Found 0 missing values.
2025-08-18 20:34:50.281831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:50.282348 INFO::Done
2025-08-18 20:34:50.282873 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:50.285805 INFO::Starting hierarchical adjustment
2025-08-18 20:34:50.286511 INFO::Found 5 batches.
2025-08-18 20:34:50.287072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:50.287726 INFO::Using default BPPARAM
2025-08-18 20:34:50.288258 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.
2025-08-18 20:34:50.418316 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:50.420257 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-18 20:34:50.438324 INFO::Done
2025-08-18 20:34:50.439332 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.442808 INFO::ASW Batch was 0.638629355114146 prior to batch effect correction and is now -0.0144891928399701 .
2025-08-18 20:34:50.443432 INFO::ASW Label was 0.164985468811569 prior to batch effect correction and is now 0.668148843869861 .
2025-08-18 20:34:50.444278 INFO::Total function execution time is 0.168832063674927 s and adjustment time is 0.151901483535767 s ( 89.97 )
2025-08-18 20:34:50.458146 INFO::Formatting Data.
2025-08-18 20:34:50.458998 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.459985 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.461016 INFO::Found 0 missing values.
2025-08-18 20:34:50.463671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:50.464214 INFO::Done
2025-08-18 20:34:50.464746 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:50.467798 INFO::Starting hierarchical adjustment
2025-08-18 20:34:50.468522 INFO::Found 2 batches.
2025-08-18 20:34:50.469083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:50.469722 INFO::Using default BPPARAM
2025-08-18 20:34:50.470251 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:50.47118 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-18 20:34:50.486089 INFO::Done
2025-08-18 20:34:50.486788 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.489701 INFO::ASW Batch was 0.741025456710747 prior to batch effect correction and is now -0.0260710669969388 .
2025-08-18 20:34:50.490277 INFO::ASW Label was 0.288202815737531 prior to batch effect correction and is now 0.878357075587817 .
2025-08-18 20:34:50.491035 INFO::Total function execution time is 0.0329904556274414 s and adjustment time is 0.0177011489868164 s ( 53.66 )
2025-08-18 20:34:50.49181 INFO::Formatting Data.
2025-08-18 20:34:50.492395 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.493242 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.494174 INFO::Found 0 missing values.
2025-08-18 20:34:50.496788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:50.497307 INFO::Done
2025-08-18 20:34:50.497815 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:50.50061 INFO::Starting hierarchical adjustment
2025-08-18 20:34:50.501286 INFO::Found 2 batches.
2025-08-18 20:34:50.501796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:50.502374 INFO::Using default BPPARAM
2025-08-18 20:34:50.50289 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:50.503762 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-18 20:34:50.518083 INFO::Done
2025-08-18 20:34:50.518757 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.521546 INFO::ASW Batch was 0.741025456710747 prior to batch effect correction and is now -0.0260710669969388 .
2025-08-18 20:34:50.522123 INFO::ASW Label was 0.288202815737531 prior to batch effect correction and is now 0.878357075587817 .
2025-08-18 20:34:50.522874 INFO::Total function execution time is 0.0310792922973633 s and adjustment time is 0.0169098377227783 s ( 54.41 )
2025-08-18 20:34:50.533767 INFO::Formatting Data.
2025-08-18 20:34:50.534606 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.535511 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.536465 INFO::Found 0 missing values.
2025-08-18 20:34:50.538559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:50.539101 INFO::Done
2025-08-18 20:34:50.539615 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:50.541538 INFO::Starting hierarchical adjustment
2025-08-18 20:34:50.54224 INFO::Found 2 batches.
2025-08-18 20:34:50.542779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:50.543379 INFO::Using default BPPARAM
2025-08-18 20:34:50.543902 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:50.544771 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-18 20:34:50.589395 INFO::Done
2025-08-18 20:34:50.590281 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.592625 INFO::ASW Batch was -0.149815640383614 prior to batch effect correction and is now -0.156706323196677 .
2025-08-18 20:34:50.593519 INFO::Total function execution time is 0.0598983764648438 s and adjustment time is 0.0472314357757568 s ( 78.85 )
2025-08-18 20:34:50.605613 INFO::Formatting Data.
2025-08-18 20:34:50.606369 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.607277 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.608307 INFO::Found 0 missing values.
2025-08-18 20:34:50.609415 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.
2025-08-18 20:34:50.614068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:50.614628 INFO::Done
2025-08-18 20:34:50.615145 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:50.618016 INFO::Starting hierarchical adjustment
2025-08-18 20:34:50.618752 INFO::Found 2 batches.
2025-08-18 20:34:50.619268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:50.619863 INFO::Using default BPPARAM
2025-08-18 20:34:50.620369 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:50.6213 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-18 20:34:50.638249 INFO::Done
2025-08-18 20:34:50.639005 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.642009 INFO::ASW Batch was 0.653045226399937 prior to batch effect correction and is now 0.122336548918426 .
2025-08-18 20:34:50.64267 INFO::ASW Label was 0.420545563941146 prior to batch effect correction and is now 0.775322797775095 .
2025-08-18 20:34:50.643431 INFO::Total function execution time is 0.0379199981689453 s and adjustment time is 0.0196547508239746 s ( 51.83 )
2025-08-18 20:34:50.644219 INFO::Formatting Data.
2025-08-18 20:34:50.644846 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.645759 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.646749 INFO::Found 0 missing values.
2025-08-18 20:34:50.647639 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.
2025-08-18 20:34:50.652012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:50.652557 INFO::Done
2025-08-18 20:34:50.653066 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:50.65584 INFO::Starting hierarchical adjustment
2025-08-18 20:34:50.656517 INFO::Found 2 batches.
2025-08-18 20:34:50.657052 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:50.657637 INFO::Using default BPPARAM
2025-08-18 20:34:50.658138 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:50.659047 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-18 20:34:50.676003 INFO::Done
2025-08-18 20:34:50.676737 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.679884 INFO::ASW Batch was 0.653045226399937 prior to batch effect correction and is now 0.122336548918426 .
2025-08-18 20:34:50.680515 INFO::ASW Label was 0.420545563941146 prior to batch effect correction and is now 0.775322797775095 .
2025-08-18 20:34:50.681374 INFO::Total function execution time is 0.0371620655059814 s and adjustment time is 0.0195877552032471 s ( 52.71 )
2025-08-18 20:34:50.883417 INFO::Formatting Data.
2025-08-18 20:34:50.884301 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.885215 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.886382 INFO::Found 0 missing values.
2025-08-18 20:34:50.88937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:50.889929 INFO::Done
2025-08-18 20:34:50.890435 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:50.892425 INFO::Starting hierarchical adjustment
2025-08-18 20:34:50.893115 INFO::Found 3 batches.
2025-08-18 20:34:50.893655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:50.894248 INFO::Using default BPPARAM
2025-08-18 20:34:50.894773 INFO::Processing subtree level 1
2025-08-18 20:34:50.986231 INFO::Adjusting the last 1 batches sequentially
2025-08-18 20:34:50.988144 INFO::Done
2025-08-18 20:34:50.988833 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:50.991439 INFO::ASW Batch was -0.0312182305144984 prior to batch effect correction and is now -0.0312182305144984 .
2025-08-18 20:34:50.992666 INFO::Total function execution time is 0.109256982803345 s and adjustment time is 0.0951430797576904 s ( 87.08 )
2025-08-18 20:34:50.993771 INFO::Formatting Data.
2025-08-18 20:34:50.994438 INFO::Typecasting input to dataframe.
2025-08-18 20:34:50.995229 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:50.996195 INFO::Removing potential empty rows and columns
2025-08-18 20:34:50.997334 INFO::Found 0 missing values.
2025-08-18 20:34:51.000476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:51.001043 INFO::Done
2025-08-18 20:34:51.001568 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:51.003643 INFO::Starting hierarchical adjustment
2025-08-18 20:34:51.00437 INFO::Found 3 batches.
2025-08-18 20:34:51.004907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:51.005545 INFO::Using default BPPARAM
2025-08-18 20:34:51.006104 INFO::Processing subtree level 1
2025-08-18 20:34:51.095017 INFO::Adjusting the last 1 batches sequentially
2025-08-18 20:34:51.097049 INFO::Done
2025-08-18 20:34:51.097795 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:51.100514 INFO::ASW Batch was -0.0312182305144984 prior to batch effect correction and is now -0.0312182305144984 .
2025-08-18 20:34:51.101494 INFO::Total function execution time is 0.107703924179077 s and adjustment time is 0.0927920341491699 s ( 86.15 )
2025-08-18 20:34:51.115913 INFO::Formatting Data.
2025-08-18 20:34:51.116949 INFO::Typecasting input to dataframe.
2025-08-18 20:34:51.117906 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:51.118953 INFO::Removing potential empty rows and columns
2025-08-18 20:34:51.120142 INFO::Found 0 missing values.
2025-08-18 20:34:51.123444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:51.124057 INFO::Done
2025-08-18 20:34:51.124617 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:51.126992 INFO::Starting hierarchical adjustment
2025-08-18 20:34:51.127748 INFO::Found 3 batches.
2025-08-18 20:34:51.128284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:51.128951 INFO::Using default BPPARAM
2025-08-18 20:34:51.12949 INFO::Processing subtree level 1
2025-08-18 20:34:51.221086 INFO::Adjusting the last 1 batches sequentially
2025-08-18 20:34:51.223032 INFO::Done
2025-08-18 20:34:51.223715 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:51.226306 INFO::ASW Batch was -0.0551069846295344 prior to batch effect correction and is now -0.0551069846295344 .
2025-08-18 20:34:51.227243 INFO::Total function execution time is 0.111593961715698 s and adjustment time is 0.0954382419586182 s ( 85.52 )
2025-08-18 20:34:51.375054 INFO::Formatting Data.
2025-08-18 20:34:51.375944 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:51.377079 INFO::Removing potential empty rows and columns
2025-08-18 20:34:51.379868 INFO::Found 1000 missing values.
2025-08-18 20:34:51.398727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:51.399487 INFO::Done
2025-08-18 20:34:51.400059 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:51.405604 INFO::Starting hierarchical adjustment
2025-08-18 20:34:51.406443 INFO::Found 10 batches.
2025-08-18 20:34:51.407229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:51.407863 INFO::Using default BPPARAM
2025-08-18 20:34:51.408414 INFO::Processing subtree level 1
2025-08-18 20:34:51.542668 INFO::Processing subtree level 2
2025-08-18 20:34:51.68875 INFO::Adjusting the last 1 batches sequentially
2025-08-18 20:34:51.691109 INFO::Done
2025-08-18 20:34:51.691972 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:51.69851 INFO::ASW Batch was 0.518135865634338 prior to batch effect correction and is now 0.518135865634338 .
2025-08-18 20:34:51.699306 INFO::ASW Label was 0.3542889233823 prior to batch effect correction and is now 0.3542889233823 .
2025-08-18 20:34:51.700394 INFO::Total function execution time is 0.325381994247437 s and adjustment time is 0.284793615341187 s ( 87.53 )
2025-08-18 20:34:51.701391 INFO::Formatting Data.
2025-08-18 20:34:51.702172 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:51.703653 INFO::Removing potential empty rows and columns
2025-08-18 20:34:51.706949 INFO::Found 1000 missing values.
2025-08-18 20:34:51.728711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:51.729647 INFO::Done
2025-08-18 20:34:51.730299 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:51.736433 INFO::Starting hierarchical adjustment
2025-08-18 20:34:51.737284 INFO::Found 10 batches.
2025-08-18 20:34:53.160139 INFO::Set up parallel execution backend with 2 workers
2025-08-18 20:34:53.162202 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-18 20:34:54.526047 INFO::Adjusting the last 2 batches sequentially
2025-08-18 20:34:54.528184 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-18 20:34:54.544698 INFO::Done
2025-08-18 20:34:54.545366 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:54.54995 INFO::ASW Batch was 0.518135865634338 prior to batch effect correction and is now 0.518135865634338 .
2025-08-18 20:34:54.550509 INFO::ASW Label was 0.3542889233823 prior to batch effect correction and is now 0.3542889233823 .
2025-08-18 20:34:54.55124 INFO::Total function execution time is 2.84992289543152 s and adjustment time is 2.80755162239075 s ( 98.51 )
2025-08-18 20:34:54.704837 INFO::Formatting Data.
2025-08-18 20:34:54.705713 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:54.70668 INFO::Removing potential empty rows and columns
2025-08-18 20:34:54.707784 INFO::Found 0 missing values.
2025-08-18 20:34:54.711298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:54.711824 INFO::Done
2025-08-18 20:34:54.712305 INFO::Acquiring quality metrics before batch effect correction.
2025-08-18 20:34:54.714942 INFO::Starting hierarchical adjustment
2025-08-18 20:34:54.715601 INFO::Found 3 batches.
2025-08-18 20:34:54.716095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-18 20:34:54.716681 INFO::Using default BPPARAM
2025-08-18 20:34:54.717174 INFO::Processing subtree level 1
2025-08-18 20:34:54.826294 INFO::Adjusting the last 1 batches sequentially
2025-08-18 20:34:54.82829 INFO::Done
2025-08-18 20:34:54.829006 INFO::Acquiring quality metrics after batch effect correction.
2025-08-18 20:34:54.832395 INFO::ASW Batch was 0.270985352069362 prior to batch effect correction and is now -0.115926989019991 .
2025-08-18 20:34:54.83304 INFO::ASW Label was -0.199281489771173 prior to batch effect correction and is now -0.0788802215370765 .
2025-08-18 20:34:54.833928 INFO::Total function execution time is 0.129202127456665 s and adjustment time is 0.112788915634155 s ( 87.3 )
2025-08-18 20:34:54.945283 INFO::Formatting Data.
2025-08-18 20:34:54.946136 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:54.947006 INFO::Removing potential empty rows and columns
2025-08-18 20:34:54.948004 INFO::Found 2 missing values.
2025-08-18 20:34:54.950773 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:54.951282 INFO::Done
2025-08-18 20:34:54.977094 INFO::Found NA in Reference column
2025-08-18 20:34:55.004169 INFO::Require at least two references per batch.
2025-08-18 20:34:55.027829 INFO::Formatting Data.
2025-08-18 20:34:55.028632 INFO::Recognized SummarizedExperiment
2025-08-18 20:34:55.02917 INFO::Typecasting input to dataframe.
2025-08-18 20:34:55.04142 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.04281 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.046388 INFO::Found 0 missing values.
2025-08-18 20:34:55.053052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.053642 INFO::Done
2025-08-18 20:34:55.069307 INFO::Formatting Data.
2025-08-18 20:34:55.070036 INFO::Recognized SummarizedExperiment
2025-08-18 20:34:55.070528 INFO::Typecasting input to dataframe.
2025-08-18 20:34:55.086405 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.087517 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.090766 INFO::Found 0 missing values.
2025-08-18 20:34:55.100663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.101252 INFO::Done
2025-08-18 20:34:55.115917 INFO::Formatting Data.
2025-08-18 20:34:55.11662 INFO::Recognized SummarizedExperiment
2025-08-18 20:34:55.117132 INFO::Typecasting input to dataframe.
2025-08-18 20:34:55.132461 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.133494 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.134511 INFO::Found 0 missing values.
2025-08-18 20:34:55.135396 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.
2025-08-18 20:34:55.13962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.14014 INFO::Done
2025-08-18 20:34:55.149194 INFO::Formatting Data.
2025-08-18 20:34:55.14992 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.150743 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.151659 INFO::Found 0 missing values.
2025-08-18 20:34:55.154306 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.154801 INFO::Done
2025-08-18 20:34:55.165294 INFO::Formatting Data.
2025-08-18 20:34:55.165987 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.16684 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.1678 INFO::Found 0 missing values.
2025-08-18 20:34:55.170472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.170996 INFO::Done
2025-08-18 20:34:55.199106 INFO::Formatting Data.
2025-08-18 20:34:55.200039 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.201127 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.202306 INFO::Found 1 missing values.
2025-08-18 20:34:55.20487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.205405 INFO::Done
2025-08-18 20:34:55.223564 INFO::Formatting Data.
2025-08-18 20:34:55.224381 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.22524 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.226165 INFO::Found 2 missing values.
2025-08-18 20:34:55.227041 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.
2025-08-18 20:34:55.229208 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.229751 INFO::Done
2025-08-18 20:34:55.239265 INFO::Formatting Data.
2025-08-18 20:34:55.2401 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.240942 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.241855 INFO::Found 2 missing values.
2025-08-18 20:34:55.243381 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.243897 INFO::Done
2025-08-18 20:34:55.254147 INFO::Formatting Data.
2025-08-18 20:34:55.254898 INFO::Typecasting input to dataframe.
2025-08-18 20:34:55.255695 INFO::Replacing NaNs with NAs.
2025-08-18 20:34:55.256541 INFO::Removing potential empty rows and columns
2025-08-18 20:34:55.257527 INFO::Found 0 missing values.
2025-08-18 20:34:55.26028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-18 20:34:55.260792 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.264 3.997 20.877
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.197 | 1.904 | 21.160 | |
| compute_asw | 0.028 | 0.000 | 0.028 | |
| count_existing | 0.015 | 0.001 | 0.016 | |
| generate_data_covariables | 0.011 | 0.003 | 0.014 | |
| generate_dataset | 0.013 | 0.000 | 0.013 | |