Yannis Schumann
| Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 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 2025-08-12 12:07 -0400 (Tue, 12 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-08-11 23:49:12 -0400 (Mon, 11 Aug 2025) |
| EndedAt: 2025-08-11 23:52:02 -0400 (Mon, 11 Aug 2025) |
| EllapsedTime: 169.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 10.22 0.66 20.37
* 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: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2025-08-11 23:50:21.042148 INFO::Formatting Data.
2025-08-11 23:50:21.044336 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:21.05368 INFO::Removing potential empty rows and columns
2025-08-11 23:50:21.268906 INFO::Found 0 missing values.
2025-08-11 23:50:21.274769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:21.276299 INFO::Done
2025-08-11 23:50:21.277685 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:21.299045 INFO::Starting hierarchical adjustment
2025-08-11 23:50:21.300911 INFO::Found 3 batches.
2025-08-11 23:50:21.302301 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:21.304472 INFO::Using default BPPARAM
2025-08-11 23:50:21.305388 INFO::Processing subtree level 1
2025-08-11 23:50:24.047574 INFO::Adjusting the last 1 batches sequentially
2025-08-11 23:50:24.049791 INFO::Done
2025-08-11 23:50:24.051112 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:24.054394 INFO::ASW Batch was -0.0940188501118773 prior to batch effect correction and is now -0.0940188501118773 .
2025-08-11 23:50:24.056112 INFO::Total function execution time is 3.01429104804993 s and adjustment time is 2.74920010566711 s ( 91.21 )
2025-08-11 23:50:24.078964 INFO::Formatting Data.
2025-08-11 23:50:24.080584 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:24.082479 INFO::Removing potential empty rows and columns
2025-08-11 23:50:24.084469 INFO::Found 0 missing values.
2025-08-11 23:50:24.086354 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.
2025-08-11 23:50:24.098267 INFO::Formatting Data.
2025-08-11 23:50:24.099319 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:24.100511 INFO::Removing potential empty rows and columns
2025-08-11 23:50:24.101689 INFO::Found 0 missing values.
2025-08-11 23:50:24.102885 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.
2025-08-11 23:50:24.118826 INFO::Formatting Data.
2025-08-11 23:50:24.119828 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:24.121023 INFO::Removing potential empty rows and columns
2025-08-11 23:50:24.122218 INFO::Found 0 missing values.
2025-08-11 23:50:24.123715 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.
2025-08-11 23:50:24.128197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:24.12899 INFO::Done
2025-08-11 23:50:24.129716 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:24.131903 INFO::Starting hierarchical adjustment
2025-08-11 23:50:24.133294 INFO::Found 2 batches.
2025-08-11 23:50:24.1346 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:24.135464 INFO::Using default BPPARAM
2025-08-11 23:50:24.136188 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:24.137306 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-11 23:50:24.154833 INFO::Done
2025-08-11 23:50:24.155919 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:24.159012 INFO::ASW Batch was -0.00995568626959872 prior to batch effect correction and is now -0.0590213335693202 .
2025-08-11 23:50:24.160056 INFO::Total function execution time is 0.0413010120391846 s and adjustment time is 0.0217959880828857 s ( 52.77 )
2025-08-11 23:50:24.162896 INFO::Formatting Data.
2025-08-11 23:50:24.163724 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:24.170896 INFO::Formatting Data.
2025-08-11 23:50:24.171784 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:24.17281 INFO::Removing potential empty rows and columns
2025-08-11 23:50:24.174005 INFO::Found 0 missing values.
2025-08-11 23:50:24.177287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:24.178104 INFO::Done
2025-08-11 23:50:24.178829 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:24.180961 INFO::Starting hierarchical adjustment
2025-08-11 23:50:24.181846 INFO::Found 2 batches.
2025-08-11 23:50:24.182555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:24.183324 INFO::Using default BPPARAM
2025-08-11 23:50:24.184022 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:24.185113 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-11 23:50:24.199485 INFO::Done
2025-08-11 23:50:24.20038 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:24.202577 INFO::ASW Batch was -0.00990895728031496 prior to batch effect correction and is now -0.119866829217439 .
2025-08-11 23:50:24.203552 INFO::Total function execution time is 0.0326929092407227 s and adjustment time is 0.0177409648895264 s ( 54.27 )
2025-08-11 23:50:24.204737 INFO::Formatting Data.
2025-08-11 23:50:24.205995 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:24.207664 INFO::Removing potential empty rows and columns
2025-08-11 23:50:24.209544 INFO::Found 0 missing values.
2025-08-11 23:50:24.212137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:24.212871 INFO::Done
2025-08-11 23:50:24.213579 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:24.2158 INFO::Starting hierarchical adjustment
2025-08-11 23:50:24.216935 INFO::Found 2 batches.
2025-08-11 23:50:24.218157 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:24.219199 INFO::Using default BPPARAM
2025-08-11 23:50:24.219923 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:24.221046 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-11 23:50:24.234265 INFO::Done
2025-08-11 23:50:24.235719 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:24.238683 INFO::ASW Batch was -0.00990895728031496 prior to batch effect correction and is now -0.119866829217439 .
2025-08-11 23:50:24.239729 INFO::Total function execution time is 0.0349559783935547 s and adjustment time is 0.0175127983093262 s ( 50.1 )
2025-08-11 23:50:26.838584 INFO::Formatting Data.
2025-08-11 23:50:26.839548 INFO::Recognized SummarizedExperiment
2025-08-11 23:50:26.840648 INFO::Typecasting input to dataframe.
2025-08-11 23:50:26.869962 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:26.871442 INFO::Removing potential empty rows and columns
2025-08-11 23:50:26.874616 INFO::Found 0 missing values.
2025-08-11 23:50:26.880023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:26.880864 INFO::Done
2025-08-11 23:50:26.881588 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:26.885245 INFO::Starting hierarchical adjustment
2025-08-11 23:50:26.88613 INFO::Found 2 batches.
2025-08-11 23:50:26.886883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:26.88814 INFO::Using default BPPARAM
2025-08-11 23:50:26.888932 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:26.890325 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-11 23:50:26.935809 INFO::Done
2025-08-11 23:50:26.936733 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:26.940523 INFO::ASW Batch was 0.0164896131987001 prior to batch effect correction and is now -0.0928983607556831 .
2025-08-11 23:50:26.9416 INFO::Total function execution time is 0.103279113769531 s and adjustment time is 0.0497498512268066 s ( 48.17 )
2025-08-11 23:50:26.960542 INFO::Formatting Data.
2025-08-11 23:50:26.961505 INFO::Recognized SummarizedExperiment
2025-08-11 23:50:26.962299 INFO::Typecasting input to dataframe.
2025-08-11 23:50:26.971239 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:26.972593 INFO::Removing potential empty rows and columns
2025-08-11 23:50:26.975437 INFO::Found 0 missing values.
2025-08-11 23:50:26.980953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:26.981858 INFO::Done
2025-08-11 23:50:26.982596 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:26.986403 INFO::Starting hierarchical adjustment
2025-08-11 23:50:26.987346 INFO::Found 2 batches.
2025-08-11 23:50:26.988075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:26.988879 INFO::Using default BPPARAM
2025-08-11 23:50:26.9896 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:26.990804 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-11 23:50:27.019938 INFO::Done
2025-08-11 23:50:27.021412 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:27.027696 INFO::ASW Batch was 0.0158020705393438 prior to batch effect correction and is now 0.0158020705393438 .
2025-08-11 23:50:27.029543 INFO::Total function execution time is 0.0688850879669189 s and adjustment time is 0.0326378345489502 s ( 47.38 )
2025-08-11 23:50:27.055242 INFO::Formatting Data.
2025-08-11 23:50:27.056242 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:27.057332 INFO::Removing potential empty rows and columns
2025-08-11 23:50:27.058541 INFO::Found 0 missing values.
2025-08-11 23:50:27.06138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:27.062147 INFO::Done
2025-08-11 23:50:27.062893 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:27.065215 INFO::Starting hierarchical adjustment
2025-08-11 23:50:27.066155 INFO::Found 3 batches.
2025-08-11 23:50:27.066918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:27.067759 INFO::Using default BPPARAM
2025-08-11 23:50:27.068516 INFO::Processing subtree level 1
2025-08-11 23:50:38.057355 INFO::Adjusting the last 1 batches sequentially
2025-08-11 23:50:38.059732 INFO::Done
2025-08-11 23:50:38.061149 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:38.06464 INFO::ASW Batch was -0.119432248557642 prior to batch effect correction and is now -0.171557942766905 .
2025-08-11 23:50:38.066345 INFO::Total function execution time is 11.011087179184 s and adjustment time is 10.9936540126801 s ( 99.84 )
2025-08-11 23:50:38.090807 INFO::Skipping initial DF formatting
2025-08-11 23:50:38.092348 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:38.099232 INFO::Starting hierarchical adjustment
2025-08-11 23:50:38.101062 INFO::Found 5 batches.
2025-08-11 23:50:38.102294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:38.103499 INFO::Using default BPPARAM
2025-08-11 23:50:38.104687 INFO::Processing subtree level 1
2025-08-11 23:50:41.248878 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:41.250982 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-11 23:50:41.275208 INFO::Done
2025-08-11 23:50:41.276674 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:41.283467 INFO::ASW Batch was 0.50350932340185 prior to batch effect correction and is now 0.50350932340185 .
2025-08-11 23:50:41.284868 INFO::ASW Label was 0.37314265260786 prior to batch effect correction and is now 0.37314265260786 .
2025-08-11 23:50:41.28641 INFO::Total function execution time is 3.19571399688721 s and adjustment time is 3.17434287071228 s ( 99.33 )
2025-08-11 23:50:41.312246 INFO::Formatting Data.
2025-08-11 23:50:41.31327 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:41.314361 INFO::Removing potential empty rows and columns
2025-08-11 23:50:41.315522 INFO::Found 0 missing values.
2025-08-11 23:50:41.319006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:41.319751 INFO::Done
2025-08-11 23:50:41.320486 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:41.323646 INFO::Starting hierarchical adjustment
2025-08-11 23:50:41.324572 INFO::Found 5 batches.
2025-08-11 23:50:41.325305 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:41.326217 INFO::Using default BPPARAM
2025-08-11 23:50:41.326991 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.
2025-08-11 23:50:44.602382 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:44.604477 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-11 23:50:44.622058 INFO::Done
2025-08-11 23:50:44.623322 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:44.627618 INFO::ASW Batch was 0.503122620107507 prior to batch effect correction and is now -0.0591986999256987 .
2025-08-11 23:50:44.628798 INFO::ASW Label was 0.222473034376057 prior to batch effect correction and is now 0.795165429988025 .
2025-08-11 23:50:44.630005 INFO::Total function execution time is 3.31781220436096 s and adjustment time is 3.29755711555481 s ( 99.39 )
2025-08-11 23:50:44.631077 INFO::Formatting Data.
2025-08-11 23:50:44.631863 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:44.632888 INFO::Removing potential empty rows and columns
2025-08-11 23:50:44.634066 INFO::Found 0 missing values.
2025-08-11 23:50:44.638215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:44.639297 INFO::Done
2025-08-11 23:50:44.640321 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:44.644677 INFO::Starting hierarchical adjustment
2025-08-11 23:50:44.645992 INFO::Found 5 batches.
2025-08-11 23:50:44.647045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:44.648178 INFO::Using default BPPARAM
2025-08-11 23:50:44.649216 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.
2025-08-11 23:50:47.937178 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:47.939291 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-11 23:50:47.958587 INFO::Done
2025-08-11 23:50:47.960032 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:47.965047 INFO::ASW Batch was 0.503122620107507 prior to batch effect correction and is now -0.0591986999256987 .
2025-08-11 23:50:47.966441 INFO::ASW Label was 0.222473034376057 prior to batch effect correction and is now 0.795165429988025 .
2025-08-11 23:50:47.968095 INFO::Total function execution time is 3.33692097663879 s and adjustment time is 3.31273102760315 s ( 99.28 )
2025-08-11 23:50:47.983488 INFO::Formatting Data.
2025-08-11 23:50:47.984495 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:47.985877 INFO::Removing potential empty rows and columns
2025-08-11 23:50:47.987262 INFO::Found 0 missing values.
2025-08-11 23:50:47.990634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:47.991381 INFO::Done
2025-08-11 23:50:47.992102 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:47.995238 INFO::Starting hierarchical adjustment
2025-08-11 23:50:47.99617 INFO::Found 5 batches.
2025-08-11 23:50:47.996893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:47.997672 INFO::Using default BPPARAM
2025-08-11 23:50:47.998384 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.
2025-08-11 23:50:51.354662 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:51.356657 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-11 23:50:51.375128 INFO::Done
2025-08-11 23:50:51.376494 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:51.38116 INFO::ASW Batch was 0.367887707563566 prior to batch effect correction and is now -0.0834042460927473 .
2025-08-11 23:50:51.382501 INFO::ASW Label was 0.325001994294245 prior to batch effect correction and is now 0.834559160830848 .
2025-08-11 23:50:51.384084 INFO::Total function execution time is 3.4005970954895 s and adjustment time is 3.37900996208191 s ( 99.37 )
2025-08-11 23:50:51.385651 INFO::Formatting Data.
2025-08-11 23:50:51.386894 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:51.388544 INFO::Removing potential empty rows and columns
2025-08-11 23:50:51.390285 INFO::Found 0 missing values.
2025-08-11 23:50:51.395214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:51.396371 INFO::Done
2025-08-11 23:50:51.397421 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:51.401692 INFO::Starting hierarchical adjustment
2025-08-11 23:50:51.403014 INFO::Found 5 batches.
2025-08-11 23:50:51.404093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:51.405273 INFO::Using default BPPARAM
2025-08-11 23:50:51.406403 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.
2025-08-11 23:50:54.677642 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:54.679647 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-11 23:50:54.698192 INFO::Done
2025-08-11 23:50:54.699535 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:54.704051 INFO::ASW Batch was 0.367887707563566 prior to batch effect correction and is now -0.0834042460927473 .
2025-08-11 23:50:54.705225 INFO::ASW Label was 0.325001994294245 prior to batch effect correction and is now 0.834559160830848 .
2025-08-11 23:50:54.706471 INFO::Total function execution time is 3.32089805603027 s and adjustment time is 3.29533696174622 s ( 99.23 )
2025-08-11 23:50:54.724837 INFO::Formatting Data.
2025-08-11 23:50:54.725891 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:54.726977 INFO::Removing potential empty rows and columns
2025-08-11 23:50:54.728126 INFO::Found 0 missing values.
2025-08-11 23:50:54.73055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:54.731278 INFO::Done
2025-08-11 23:50:54.731987 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:54.735149 INFO::Starting hierarchical adjustment
2025-08-11 23:50:54.736097 INFO::Found 2 batches.
2025-08-11 23:50:54.736872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:54.73766 INFO::Using default BPPARAM
2025-08-11 23:50:54.738373 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:54.739426 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-11 23:50:54.753263 INFO::Done
2025-08-11 23:50:54.754487 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:54.757806 INFO::ASW Batch was 0.346364363517796 prior to batch effect correction and is now -0.0346578932219491 .
2025-08-11 23:50:54.758682 INFO::ASW Label was 0.671967642185663 prior to batch effect correction and is now 0.92139353045996 .
2025-08-11 23:50:54.759701 INFO::Total function execution time is 0.0349709987640381 s and adjustment time is 0.0172860622406006 s ( 49.43 )
2025-08-11 23:50:54.760796 INFO::Formatting Data.
2025-08-11 23:50:54.761712 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:54.762869 INFO::Removing potential empty rows and columns
2025-08-11 23:50:54.764037 INFO::Found 0 missing values.
2025-08-11 23:50:54.766758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:54.767529 INFO::Done
2025-08-11 23:50:54.768379 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:54.772217 INFO::Starting hierarchical adjustment
2025-08-11 23:50:54.77321 INFO::Found 2 batches.
2025-08-11 23:50:54.773952 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:54.774805 INFO::Using default BPPARAM
2025-08-11 23:50:54.775547 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:54.776661 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-11 23:50:54.789158 INFO::Done
2025-08-11 23:50:54.790115 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:54.793535 INFO::ASW Batch was 0.346364363517796 prior to batch effect correction and is now -0.0346578932219491 .
2025-08-11 23:50:54.794333 INFO::ASW Label was 0.671967642185663 prior to batch effect correction and is now 0.92139353045996 .
2025-08-11 23:50:54.795313 INFO::Total function execution time is 0.0345349311828613 s and adjustment time is 0.0160820484161377 s ( 46.57 )
2025-08-11 23:50:54.810582 INFO::Formatting Data.
2025-08-11 23:50:54.81166 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:54.81288 INFO::Removing potential empty rows and columns
2025-08-11 23:50:54.814033 INFO::Found 0 missing values.
2025-08-11 23:50:54.816335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:54.817107 INFO::Done
2025-08-11 23:50:54.817872 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:54.819922 INFO::Starting hierarchical adjustment
2025-08-11 23:50:54.82082 INFO::Found 2 batches.
2025-08-11 23:50:54.821607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:54.822463 INFO::Using default BPPARAM
2025-08-11 23:50:54.823187 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:54.824261 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-11 23:50:54.854301 INFO::Done
2025-08-11 23:50:54.855261 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:54.857473 INFO::ASW Batch was -0.14216915178951 prior to batch effect correction and is now -0.196165010074995 .
2025-08-11 23:50:54.858591 INFO::Total function execution time is 0.0480940341949463 s and adjustment time is 0.0335800647735596 s ( 69.82 )
2025-08-11 23:50:54.877055 INFO::Formatting Data.
2025-08-11 23:50:54.878595 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:54.880349 INFO::Removing potential empty rows and columns
2025-08-11 23:50:54.882176 INFO::Found 0 missing values.
2025-08-11 23:50:54.884111 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.
2025-08-11 23:50:54.890829 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:54.892184 INFO::Done
2025-08-11 23:50:54.893469 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:54.898381 INFO::Starting hierarchical adjustment
2025-08-11 23:50:54.899793 INFO::Found 2 batches.
2025-08-11 23:50:54.900993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:54.902248 INFO::Using default BPPARAM
2025-08-11 23:50:54.903381 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:54.90508 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-11 23:50:54.927233 INFO::Done
2025-08-11 23:50:54.928772 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:54.933803 INFO::ASW Batch was 0.434718509318974 prior to batch effect correction and is now 0.0519386826886773 .
2025-08-11 23:50:54.935072 INFO::ASW Label was 0.641057056334733 prior to batch effect correction and is now 0.899215758009739 .
2025-08-11 23:50:54.936614 INFO::Total function execution time is 0.0596728324890137 s and adjustment time is 0.0276198387145996 s ( 46.29 )
2025-08-11 23:50:54.938102 INFO::Formatting Data.
2025-08-11 23:50:54.939377 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:54.941045 INFO::Removing potential empty rows and columns
2025-08-11 23:50:54.942797 INFO::Found 0 missing values.
2025-08-11 23:50:54.944441 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.
2025-08-11 23:50:54.950634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:54.951859 INFO::Done
2025-08-11 23:50:54.953016 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:54.957738 INFO::Starting hierarchical adjustment
2025-08-11 23:50:54.95918 INFO::Found 2 batches.
2025-08-11 23:50:54.960352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:54.961615 INFO::Using default BPPARAM
2025-08-11 23:50:54.962777 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:50:54.964574 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-11 23:50:54.98645 INFO::Done
2025-08-11 23:50:54.98789 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:54.992845 INFO::ASW Batch was 0.434718509318974 prior to batch effect correction and is now 0.0519386826886773 .
2025-08-11 23:50:54.994179 INFO::ASW Label was 0.641057056334733 prior to batch effect correction and is now 0.899215758009739 .
2025-08-11 23:50:54.995816 INFO::Total function execution time is 0.0576729774475098 s and adjustment time is 0.0274338722229004 s ( 47.57 )
2025-08-11 23:50:55.862983 INFO::Formatting Data.
2025-08-11 23:50:55.864751 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:55.866784 INFO::Removing potential empty rows and columns
2025-08-11 23:50:55.868965 INFO::Found 0 missing values.
2025-08-11 23:50:55.874343 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:55.87582 INFO::Done
2025-08-11 23:50:55.877158 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:55.880968 INFO::Starting hierarchical adjustment
2025-08-11 23:50:55.882718 INFO::Found 3 batches.
2025-08-11 23:50:55.884095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:55.885529 INFO::Using default BPPARAM
2025-08-11 23:50:55.886922 INFO::Processing subtree level 1
2025-08-11 23:50:58.8514 INFO::Adjusting the last 1 batches sequentially
2025-08-11 23:50:58.853579 INFO::Done
2025-08-11 23:50:58.854447 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:50:58.856827 INFO::ASW Batch was -0.0136192762834024 prior to batch effect correction and is now -0.0136192762834024 .
2025-08-11 23:50:58.857887 INFO::Total function execution time is 2.9951479434967 s and adjustment time is 2.97115206718445 s ( 99.2 )
2025-08-11 23:50:58.858964 INFO::Formatting Data.
2025-08-11 23:50:58.859825 INFO::Typecasting input to dataframe.
2025-08-11 23:50:58.860771 INFO::Replacing NaNs with NAs.
2025-08-11 23:50:58.861808 INFO::Removing potential empty rows and columns
2025-08-11 23:50:58.862953 INFO::Found 0 missing values.
2025-08-11 23:50:58.86565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:50:58.866448 INFO::Done
2025-08-11 23:50:58.867158 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:50:58.869444 INFO::Starting hierarchical adjustment
2025-08-11 23:50:58.870736 INFO::Found 3 batches.
2025-08-11 23:50:58.871814 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:50:58.87298 INFO::Using default BPPARAM
2025-08-11 23:50:58.87404 INFO::Processing subtree level 1
2025-08-11 23:51:01.977277 INFO::Adjusting the last 1 batches sequentially
2025-08-11 23:51:01.979191 INFO::Done
2025-08-11 23:51:01.980041 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:51:01.982408 INFO::ASW Batch was -0.0136192762834024 prior to batch effect correction and is now -0.0136192762834024 .
2025-08-11 23:51:01.983865 INFO::Total function execution time is 3.12474584579468 s and adjustment time is 3.10866498947144 s ( 99.49 )
2025-08-11 23:51:02.007226 INFO::Formatting Data.
2025-08-11 23:51:02.008892 INFO::Typecasting input to dataframe.
2025-08-11 23:51:02.010662 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:02.012428 INFO::Removing potential empty rows and columns
2025-08-11 23:51:02.014255 INFO::Found 0 missing values.
2025-08-11 23:51:02.018822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:02.02014 INFO::Done
2025-08-11 23:51:02.021392 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:51:02.024787 INFO::Starting hierarchical adjustment
2025-08-11 23:51:02.026254 INFO::Found 3 batches.
2025-08-11 23:51:02.027461 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:51:02.028788 INFO::Using default BPPARAM
2025-08-11 23:51:02.029589 INFO::Processing subtree level 1
2025-08-11 23:51:05.072381 INFO::Adjusting the last 1 batches sequentially
2025-08-11 23:51:05.075007 INFO::Done
2025-08-11 23:51:05.076397 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:51:05.079847 INFO::ASW Batch was -0.0647989707146536 prior to batch effect correction and is now -0.0647989707146536 .
2025-08-11 23:51:05.081571 INFO::Total function execution time is 3.07445311546326 s and adjustment time is 3.04893398284912 s ( 99.17 )
2025-08-11 23:51:08.232369 INFO::Formatting Data.
2025-08-11 23:51:08.233519 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:08.235402 INFO::Removing potential empty rows and columns
2025-08-11 23:51:08.238922 INFO::Found 1000 missing values.
2025-08-11 23:51:08.259921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:08.2614 INFO::Done
2025-08-11 23:51:08.262587 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:51:08.272142 INFO::Starting hierarchical adjustment
2025-08-11 23:51:08.273686 INFO::Found 10 batches.
2025-08-11 23:51:08.274903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:51:08.276136 INFO::Using default BPPARAM
2025-08-11 23:51:08.277238 INFO::Processing subtree level 1
2025-08-11 23:51:11.591441 INFO::Processing subtree level 2
2025-08-11 23:51:14.579144 INFO::Adjusting the last 1 batches sequentially
2025-08-11 23:51:14.58163 INFO::Done
2025-08-11 23:51:14.582908 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:51:14.591835 INFO::ASW Batch was 0.50560397602825 prior to batch effect correction and is now 0.50560397602825 .
2025-08-11 23:51:14.59318 INFO::ASW Label was 0.314201198975033 prior to batch effect correction and is now 0.314201198975033 .
2025-08-11 23:51:14.594753 INFO::Total function execution time is 6.36241602897644 s and adjustment time is 6.30816698074341 s ( 99.15 )
2025-08-11 23:51:14.596191 INFO::Formatting Data.
2025-08-11 23:51:14.597405 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:14.598823 INFO::Removing potential empty rows and columns
2025-08-11 23:51:14.601079 INFO::Found 1000 missing values.
2025-08-11 23:51:14.623263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:14.624752 INFO::Done
2025-08-11 23:51:14.626054 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:51:14.635974 INFO::Starting hierarchical adjustment
2025-08-11 23:51:14.637674 INFO::Found 10 batches.
2025-08-11 23:51:15.381287 INFO::Set up parallel execution backend with 2 workers
2025-08-11 23:51:15.382275 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-11 23:51:18.628592 INFO::Adjusting the last 2 batches sequentially
2025-08-11 23:51:18.631051 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-11 23:51:18.656386 INFO::Done
2025-08-11 23:51:18.657971 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:51:18.668486 INFO::ASW Batch was 0.50560397602825 prior to batch effect correction and is now 0.50560397602825 .
2025-08-11 23:51:18.670082 INFO::ASW Label was 0.314201198975033 prior to batch effect correction and is now 0.314201198975033 .
2025-08-11 23:51:18.671888 INFO::Total function execution time is 4.07565689086914 s and adjustment time is 4.01891088485718 s ( 98.61 )
2025-08-11 23:51:21.783589 INFO::Formatting Data.
2025-08-11 23:51:21.78471 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:21.785897 INFO::Removing potential empty rows and columns
2025-08-11 23:51:21.787075 INFO::Found 0 missing values.
2025-08-11 23:51:21.790237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:21.790995 INFO::Done
2025-08-11 23:51:21.791707 INFO::Acquiring quality metrics before batch effect correction.
2025-08-11 23:51:21.794563 INFO::Starting hierarchical adjustment
2025-08-11 23:51:21.795478 INFO::Found 3 batches.
2025-08-11 23:51:21.7962 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-11 23:51:21.797034 INFO::Using default BPPARAM
2025-08-11 23:51:21.797774 INFO::Processing subtree level 1
2025-08-11 23:51:24.991721 INFO::Adjusting the last 1 batches sequentially
2025-08-11 23:51:24.993962 INFO::Done
2025-08-11 23:51:24.995233 INFO::Acquiring quality metrics after batch effect correction.
2025-08-11 23:51:24.999389 INFO::ASW Batch was 0.27713813078799 prior to batch effect correction and is now -0.17138879729951 .
2025-08-11 23:51:25.000711 INFO::ASW Label was -0.194312265732129 prior to batch effect correction and is now 0.133145535718926 .
2025-08-11 23:51:25.002134 INFO::Total function execution time is 3.21858906745911 s and adjustment time is 3.19856977462769 s ( 99.38 )
2025-08-11 23:51:25.148968 INFO::Formatting Data.
2025-08-11 23:51:25.150018 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.151135 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.152287 INFO::Found 2 missing values.
2025-08-11 23:51:25.15494 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.155746 INFO::Done
2025-08-11 23:51:25.195067 INFO::Found NA in Reference column
2025-08-11 23:51:25.207735 INFO::Require at least two references per batch.
2025-08-11 23:51:25.228509 INFO::Formatting Data.
2025-08-11 23:51:25.229498 INFO::Recognized SummarizedExperiment
2025-08-11 23:51:25.230258 INFO::Typecasting input to dataframe.
2025-08-11 23:51:25.240729 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.242168 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.24499 INFO::Found 0 missing values.
2025-08-11 23:51:25.250585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.251567 INFO::Done
2025-08-11 23:51:25.270851 INFO::Formatting Data.
2025-08-11 23:51:25.271852 INFO::Recognized SummarizedExperiment
2025-08-11 23:51:25.27262 INFO::Typecasting input to dataframe.
2025-08-11 23:51:25.288029 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.28951 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.292419 INFO::Found 0 missing values.
2025-08-11 23:51:25.300694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.301641 INFO::Done
2025-08-11 23:51:25.31651 INFO::Formatting Data.
2025-08-11 23:51:25.317723 INFO::Recognized SummarizedExperiment
2025-08-11 23:51:25.318945 INFO::Typecasting input to dataframe.
2025-08-11 23:51:25.334184 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.335453 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.336684 INFO::Found 0 missing values.
2025-08-11 23:51:25.337801 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.
2025-08-11 23:51:25.341714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.342497 INFO::Done
2025-08-11 23:51:25.356008 INFO::Formatting Data.
2025-08-11 23:51:25.357249 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.358582 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.360127 INFO::Found 0 missing values.
2025-08-11 23:51:25.36348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.364353 INFO::Done
2025-08-11 23:51:25.379888 INFO::Formatting Data.
2025-08-11 23:51:25.381569 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.383549 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.385699 INFO::Found 0 missing values.
2025-08-11 23:51:25.389927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.390756 INFO::Done
2025-08-11 23:51:25.43074 INFO::Formatting Data.
2025-08-11 23:51:25.432359 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.43437 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.436462 INFO::Found 1 missing values.
2025-08-11 23:51:25.440672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.44202 INFO::Done
2025-08-11 23:51:25.469812 INFO::Formatting Data.
2025-08-11 23:51:25.470946 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.472055 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.473161 INFO::Found 2 missing values.
2025-08-11 23:51:25.47427 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.
2025-08-11 23:51:25.476466 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.477224 INFO::Done
2025-08-11 23:51:25.490977 INFO::Formatting Data.
2025-08-11 23:51:25.491992 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.493125 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.494221 INFO::Found 2 missing values.
2025-08-11 23:51:25.495936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.496668 INFO::Done
2025-08-11 23:51:25.515494 INFO::Formatting Data.
2025-08-11 23:51:25.517277 INFO::Typecasting input to dataframe.
2025-08-11 23:51:25.518907 INFO::Replacing NaNs with NAs.
2025-08-11 23:51:25.520222 INFO::Removing potential empty rows and columns
2025-08-11 23:51:25.52221 INFO::Found 0 missing values.
2025-08-11 23:51:25.527032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-11 23:51:25.528368 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
31.64 1.54 81.11
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.22 | 0.66 | 20.37 | |
| compute_asw | 0.04 | 0.02 | 0.05 | |
| count_existing | 0.03 | 0.00 | 0.03 | |
| generate_data_covariables | 0.02 | 0.00 | 0.01 | |
| generate_dataset | 0.03 | 0.00 | 0.03 | |