Yannis Schumann
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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 2025-08-15 12:06 -0400 (Fri, 15 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 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 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 24.04.3 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 13.7.7 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: 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: 2025-08-15 00:49:42 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 00:52:17 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 155.7 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 9.69 0.59 19.94
* 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")
2025-08-15 00:50:50.492868 INFO::Formatting Data.
2025-08-15 00:50:50.495843 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:50.511057 INFO::Removing potential empty rows and columns
2025-08-15 00:50:50.792153 INFO::Found 0 missing values.
2025-08-15 00:50:50.797499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:50:50.799057 INFO::Done
2025-08-15 00:50:50.80042 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:50:50.822147 INFO::Starting hierarchical adjustment
2025-08-15 00:50:50.824038 INFO::Found 3 batches.
2025-08-15 00:50:50.825434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:50:50.827578 INFO::Using default BPPARAM
2025-08-15 00:50:50.828895 INFO::Processing subtree level 1
2025-08-15 00:50:53.655015 INFO::Adjusting the last 1 batches sequentially
2025-08-15 00:50:53.657254 INFO::Done
2025-08-15 00:50:53.658577 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:50:53.66184 INFO::ASW Batch was -0.0617132350158586 prior to batch effect correction and is now -0.0617132350158586 .
2025-08-15 00:50:53.663572 INFO::Total function execution time is 3.17144703865051 s and adjustment time is 2.83354115486145 s ( 89.35 )
2025-08-15 00:50:53.685942 INFO::Formatting Data.
2025-08-15 00:50:53.687484 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:53.689258 INFO::Removing potential empty rows and columns
2025-08-15 00:50:53.691212 INFO::Found 0 missing values.
2025-08-15 00:50:53.693037 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.
2025-08-15 00:50:53.70478 INFO::Formatting Data.
2025-08-15 00:50:53.705762 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:53.707474 INFO::Removing potential empty rows and columns
2025-08-15 00:50:53.709395 INFO::Found 0 missing values.
2025-08-15 00:50:53.711171 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.
2025-08-15 00:50:53.736366 INFO::Formatting Data.
2025-08-15 00:50:53.7379 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:53.739637 INFO::Removing potential empty rows and columns
2025-08-15 00:50:53.741445 INFO::Found 0 missing values.
2025-08-15 00:50:53.743165 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.
2025-08-15 00:50:53.749606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:50:53.751035 INFO::Done
2025-08-15 00:50:53.75234 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:50:53.755807 INFO::Starting hierarchical adjustment
2025-08-15 00:50:53.757237 INFO::Found 2 batches.
2025-08-15 00:50:53.758525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:50:53.759867 INFO::Using default BPPARAM
2025-08-15 00:50:53.761027 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:50:53.762901 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 00:50:53.790099 INFO::Done
2025-08-15 00:50:53.791536 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:50:53.795131 INFO::ASW Batch was 0.00966171476172706 prior to batch effect correction and is now -0.124605765006792 .
2025-08-15 00:50:53.796744 INFO::Total function execution time is 0.0604510307312012 s and adjustment time is 0.0330259799957275 s ( 54.63 )
2025-08-15 00:50:53.801148 INFO::Formatting Data.
2025-08-15 00:50:53.802491 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:53.814399 INFO::Formatting Data.
2025-08-15 00:50:53.815958 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:53.817718 INFO::Removing potential empty rows and columns
2025-08-15 00:50:53.819598 INFO::Found 0 missing values.
2025-08-15 00:50:53.823865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:50:53.8251 INFO::Done
2025-08-15 00:50:53.826308 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:50:53.82962 INFO::Starting hierarchical adjustment
2025-08-15 00:50:53.831032 INFO::Found 2 batches.
2025-08-15 00:50:53.832163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:50:53.833391 INFO::Using default BPPARAM
2025-08-15 00:50:53.834559 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:50:53.836257 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 00:50:53.85726 INFO::Done
2025-08-15 00:50:53.858688 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:50:53.862088 INFO::ASW Batch was 0.024204266518579 prior to batch effect correction and is now -0.122024527878756 .
2025-08-15 00:50:53.863594 INFO::Total function execution time is 0.0492720603942871 s and adjustment time is 0.0263891220092773 s ( 53.56 )
2025-08-15 00:50:53.865556 INFO::Formatting Data.
2025-08-15 00:50:53.866806 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:53.868472 INFO::Removing potential empty rows and columns
2025-08-15 00:50:53.870324 INFO::Found 0 missing values.
2025-08-15 00:50:53.874727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:50:53.876002 INFO::Done
2025-08-15 00:50:53.877208 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:50:53.88048 INFO::Starting hierarchical adjustment
2025-08-15 00:50:53.881846 INFO::Found 2 batches.
2025-08-15 00:50:53.883012 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:50:53.884258 INFO::Using default BPPARAM
2025-08-15 00:50:53.885418 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:50:53.887121 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 00:50:53.907162 INFO::Done
2025-08-15 00:50:53.908549 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:50:53.911964 INFO::ASW Batch was 0.024204266518579 prior to batch effect correction and is now -0.122024527878756 .
2025-08-15 00:50:53.913506 INFO::Total function execution time is 0.047943115234375 s and adjustment time is 0.0254831314086914 s ( 53.15 )
2025-08-15 00:50:56.718313 INFO::Formatting Data.
2025-08-15 00:50:56.719716 INFO::Recognized SummarizedExperiment
2025-08-15 00:50:56.720866 INFO::Typecasting input to dataframe.
2025-08-15 00:50:56.762846 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:56.764925 INFO::Removing potential empty rows and columns
2025-08-15 00:50:56.769673 INFO::Found 0 missing values.
2025-08-15 00:50:56.778067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:50:56.779397 INFO::Done
2025-08-15 00:50:56.780556 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:50:56.786204 INFO::Starting hierarchical adjustment
2025-08-15 00:50:56.78766 INFO::Found 2 batches.
2025-08-15 00:50:56.788794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:50:56.790594 INFO::Using default BPPARAM
2025-08-15 00:50:56.791694 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:50:56.793494 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 00:50:56.857766 INFO::Done
2025-08-15 00:50:56.859068 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:50:56.864639 INFO::ASW Batch was -0.00211492237897812 prior to batch effect correction and is now -0.0937357562246563 .
2025-08-15 00:50:56.866261 INFO::Total function execution time is 0.148326873779297 s and adjustment time is 0.0702900886535645 s ( 47.39 )
2025-08-15 00:50:56.891711 INFO::Formatting Data.
2025-08-15 00:50:56.893105 INFO::Recognized SummarizedExperiment
2025-08-15 00:50:56.894241 INFO::Typecasting input to dataframe.
2025-08-15 00:50:56.905569 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:56.907516 INFO::Removing potential empty rows and columns
2025-08-15 00:50:56.911796 INFO::Found 0 missing values.
2025-08-15 00:50:56.920288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:50:56.921704 INFO::Done
2025-08-15 00:50:56.922976 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:50:56.928983 INFO::Starting hierarchical adjustment
2025-08-15 00:50:56.930513 INFO::Found 2 batches.
2025-08-15 00:50:56.931735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:50:56.933047 INFO::Using default BPPARAM
2025-08-15 00:50:56.93423 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:50:56.93618 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 00:50:56.969099 INFO::Done
2025-08-15 00:50:56.97046 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:50:56.976169 INFO::ASW Batch was -0.0107857781736252 prior to batch effect correction and is now -0.0107857781736252 .
2025-08-15 00:50:56.977788 INFO::Total function execution time is 0.0860340595245361 s and adjustment time is 0.0387670993804932 s ( 45.06 )
2025-08-15 00:50:57.005754 INFO::Formatting Data.
2025-08-15 00:50:57.007223 INFO::Replacing NaNs with NAs.
2025-08-15 00:50:57.008878 INFO::Removing potential empty rows and columns
2025-08-15 00:50:57.010615 INFO::Found 0 missing values.
2025-08-15 00:50:57.01471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:50:57.015898 INFO::Done
2025-08-15 00:50:57.017043 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:50:57.020202 INFO::Starting hierarchical adjustment
2025-08-15 00:50:57.021554 INFO::Found 3 batches.
2025-08-15 00:50:57.02274 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:50:57.023972 INFO::Using default BPPARAM
2025-08-15 00:50:57.02511 INFO::Processing subtree level 1
2025-08-15 00:51:07.624653 INFO::Adjusting the last 1 batches sequentially
2025-08-15 00:51:07.626952 INFO::Done
2025-08-15 00:51:07.628266 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:07.631377 INFO::ASW Batch was -0.0541213470551057 prior to batch effect correction and is now -0.194279987630487 .
2025-08-15 00:51:07.632806 INFO::Total function execution time is 10.627151966095 s and adjustment time is 10.6055648326874 s ( 99.8 )
2025-08-15 00:51:07.654093 INFO::Skipping initial DF formatting
2025-08-15 00:51:07.655397 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:07.661537 INFO::Starting hierarchical adjustment
2025-08-15 00:51:07.662948 INFO::Found 5 batches.
2025-08-15 00:51:07.664019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:07.665147 INFO::Using default BPPARAM
2025-08-15 00:51:07.666209 INFO::Processing subtree level 1
2025-08-15 00:51:10.658697 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:10.660916 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 00:51:10.682136 INFO::Done
2025-08-15 00:51:10.683073 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:10.68823 INFO::ASW Batch was 0.580744313220168 prior to batch effect correction and is now 0.580744313220168 .
2025-08-15 00:51:10.689077 INFO::ASW Label was 0.370913252147789 prior to batch effect correction and is now 0.370913252147789 .
2025-08-15 00:51:10.690041 INFO::Total function execution time is 3.03612017631531 s and adjustment time is 3.01941013336182 s ( 99.45 )
2025-08-15 00:51:10.714757 INFO::Formatting Data.
2025-08-15 00:51:10.716315 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:10.718003 INFO::Removing potential empty rows and columns
2025-08-15 00:51:10.719808 INFO::Found 0 missing values.
2025-08-15 00:51:10.726055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:10.727325 INFO::Done
2025-08-15 00:51:10.728586 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:10.733532 INFO::Starting hierarchical adjustment
2025-08-15 00:51:10.735046 INFO::Found 5 batches.
2025-08-15 00:51:10.736237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:10.737546 INFO::Using default BPPARAM
2025-08-15 00:51:10.738747 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.
2025-08-15 00:51:13.836025 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:13.838308 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 00:51:13.85894 INFO::Done
2025-08-15 00:51:13.85989 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:13.863275 INFO::ASW Batch was 0.248504977836202 prior to batch effect correction and is now -0.0830256866641254 .
2025-08-15 00:51:13.864086 INFO::ASW Label was 0.479429831222388 prior to batch effect correction and is now 0.902817109386382 .
2025-08-15 00:51:13.865034 INFO::Total function execution time is 3.15049505233765 s and adjustment time is 3.12411880493164 s ( 99.16 )
2025-08-15 00:51:13.865975 INFO::Formatting Data.
2025-08-15 00:51:13.866761 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:13.867836 INFO::Removing potential empty rows and columns
2025-08-15 00:51:13.868939 INFO::Found 0 missing values.
2025-08-15 00:51:13.872347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:13.873104 INFO::Done
2025-08-15 00:51:13.873805 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:13.877987 INFO::Starting hierarchical adjustment
2025-08-15 00:51:13.87892 INFO::Found 5 batches.
2025-08-15 00:51:13.879631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:13.880397 INFO::Using default BPPARAM
2025-08-15 00:51:13.881325 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.
2025-08-15 00:51:17.089957 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:17.091627 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 00:51:17.108572 INFO::Done
2025-08-15 00:51:17.109972 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:17.114997 INFO::ASW Batch was 0.248504977836202 prior to batch effect correction and is now -0.0830256866641254 .
2025-08-15 00:51:17.116457 INFO::ASW Label was 0.479429831222388 prior to batch effect correction and is now 0.902817109386382 .
2025-08-15 00:51:17.118085 INFO::Total function execution time is 3.25200295448303 s and adjustment time is 3.22972798347473 s ( 99.32 )
2025-08-15 00:51:17.140875 INFO::Formatting Data.
2025-08-15 00:51:17.142436 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:17.144219 INFO::Removing potential empty rows and columns
2025-08-15 00:51:17.146063 INFO::Found 0 missing values.
2025-08-15 00:51:17.152011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:17.153304 INFO::Done
2025-08-15 00:51:17.154527 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:17.159282 INFO::Starting hierarchical adjustment
2025-08-15 00:51:17.160748 INFO::Found 5 batches.
2025-08-15 00:51:17.161951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:17.163214 INFO::Using default BPPARAM
2025-08-15 00:51:17.164444 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.
2025-08-15 00:51:20.499419 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:20.501382 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 00:51:20.523165 INFO::Done
2025-08-15 00:51:20.52455 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:20.529448 INFO::ASW Batch was 0.606847095631061 prior to batch effect correction and is now -0.100877992264171 .
2025-08-15 00:51:20.530819 INFO::ASW Label was 0.161096473287897 prior to batch effect correction and is now 0.841024081134729 .
2025-08-15 00:51:20.532414 INFO::Total function execution time is 3.39163303375244 s and adjustment time is 3.36259508132935 s ( 99.14 )
2025-08-15 00:51:20.534083 INFO::Formatting Data.
2025-08-15 00:51:20.535637 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:20.537641 INFO::Removing potential empty rows and columns
2025-08-15 00:51:20.539603 INFO::Found 0 missing values.
2025-08-15 00:51:20.546001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:20.547597 INFO::Done
2025-08-15 00:51:20.54906 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:20.554388 INFO::Starting hierarchical adjustment
2025-08-15 00:51:20.555955 INFO::Found 5 batches.
2025-08-15 00:51:20.557211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:20.55853 INFO::Using default BPPARAM
2025-08-15 00:51:20.559723 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.
2025-08-15 00:51:24.081278 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:24.083274 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 00:51:24.10206 INFO::Done
2025-08-15 00:51:24.103413 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:24.10827 INFO::ASW Batch was 0.606847095631061 prior to batch effect correction and is now -0.100877992264171 .
2025-08-15 00:51:24.109483 INFO::ASW Label was 0.161096473287897 prior to batch effect correction and is now 0.841024081134729 .
2025-08-15 00:51:24.110922 INFO::Total function execution time is 3.57692313194275 s and adjustment time is 3.54631900787354 s ( 99.14 )
2025-08-15 00:51:24.132465 INFO::Formatting Data.
2025-08-15 00:51:24.133981 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:24.135691 INFO::Removing potential empty rows and columns
2025-08-15 00:51:24.137499 INFO::Found 0 missing values.
2025-08-15 00:51:24.141564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:24.142747 INFO::Done
2025-08-15 00:51:24.143905 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:24.148515 INFO::Starting hierarchical adjustment
2025-08-15 00:51:24.149879 INFO::Found 2 batches.
2025-08-15 00:51:24.150996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:24.152202 INFO::Using default BPPARAM
2025-08-15 00:51:24.153321 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:24.154979 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 00:51:24.174304 INFO::Done
2025-08-15 00:51:24.175667 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:24.180436 INFO::ASW Batch was 0.746167910677881 prior to batch effect correction and is now 0.0734770086035832 .
2025-08-15 00:51:24.181757 INFO::ASW Label was 0.205907421889782 prior to batch effect correction and is now 0.764016240628729 .
2025-08-15 00:51:24.183317 INFO::Total function execution time is 0.0509400367736816 s and adjustment time is 0.0245969295501709 s ( 48.29 )
2025-08-15 00:51:24.184827 INFO::Formatting Data.
2025-08-15 00:51:24.186069 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:24.187601 INFO::Removing potential empty rows and columns
2025-08-15 00:51:24.189249 INFO::Found 0 missing values.
2025-08-15 00:51:24.19304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:24.194126 INFO::Done
2025-08-15 00:51:24.195197 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:24.19969 INFO::Starting hierarchical adjustment
2025-08-15 00:51:24.20102 INFO::Found 2 batches.
2025-08-15 00:51:24.202097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:24.2033 INFO::Using default BPPARAM
2025-08-15 00:51:24.204396 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:24.206032 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-15 00:51:24.222559 INFO::Done
2025-08-15 00:51:24.223519 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:24.226955 INFO::ASW Batch was 0.746167910677881 prior to batch effect correction and is now 0.0734770086035832 .
2025-08-15 00:51:24.227801 INFO::ASW Label was 0.205907421889782 prior to batch effect correction and is now 0.764016240628729 .
2025-08-15 00:51:24.228787 INFO::Total function execution time is 0.0440549850463867 s and adjustment time is 0.0217258930206299 s ( 49.32 )
2025-08-15 00:51:24.244079 INFO::Formatting Data.
2025-08-15 00:51:24.245654 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:24.247414 INFO::Removing potential empty rows and columns
2025-08-15 00:51:24.249172 INFO::Found 0 missing values.
2025-08-15 00:51:24.252549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:24.253828 INFO::Done
2025-08-15 00:51:24.255084 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:24.257898 INFO::Starting hierarchical adjustment
2025-08-15 00:51:24.25883 INFO::Found 2 batches.
2025-08-15 00:51:24.259567 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:24.260365 INFO::Using default BPPARAM
2025-08-15 00:51:24.261078 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:24.262175 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 00:51:24.28779 INFO::Done
2025-08-15 00:51:24.288845 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:24.291631 INFO::ASW Batch was -0.124002345530532 prior to batch effect correction and is now -0.127234723639177 .
2025-08-15 00:51:24.292734 INFO::Total function execution time is 0.048820972442627 s and adjustment time is 0.02907395362854 s ( 59.55 )
2025-08-15 00:51:24.308701 INFO::Formatting Data.
2025-08-15 00:51:24.309712 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:24.310899 INFO::Removing potential empty rows and columns
2025-08-15 00:51:24.312027 INFO::Found 0 missing values.
2025-08-15 00:51:24.313276 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.
2025-08-15 00:51:24.3172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:24.317998 INFO::Done
2025-08-15 00:51:24.318711 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:24.321775 INFO::Starting hierarchical adjustment
2025-08-15 00:51:24.322673 INFO::Found 2 batches.
2025-08-15 00:51:24.323403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:24.324187 INFO::Using default BPPARAM
2025-08-15 00:51:24.324898 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:24.325997 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 00:51:24.340146 INFO::Done
2025-08-15 00:51:24.341072 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:24.344259 INFO::ASW Batch was 0.644228783492475 prior to batch effect correction and is now -0.0344628224229572 .
2025-08-15 00:51:24.345078 INFO::ASW Label was 0.398641327179037 prior to batch effect correction and is now 0.893698530796849 .
2025-08-15 00:51:24.346042 INFO::Total function execution time is 0.0374429225921631 s and adjustment time is 0.0175690650939941 s ( 46.92 )
2025-08-15 00:51:24.346999 INFO::Formatting Data.
2025-08-15 00:51:24.347797 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:24.348885 INFO::Removing potential empty rows and columns
2025-08-15 00:51:24.350004 INFO::Found 0 missing values.
2025-08-15 00:51:24.351115 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.
2025-08-15 00:51:24.355073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:24.355839 INFO::Done
2025-08-15 00:51:24.356553 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:24.359582 INFO::Starting hierarchical adjustment
2025-08-15 00:51:24.360505 INFO::Found 2 batches.
2025-08-15 00:51:24.36123 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:24.36201 INFO::Using default BPPARAM
2025-08-15 00:51:24.362723 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:24.363827 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 00:51:24.378164 INFO::Done
2025-08-15 00:51:24.379175 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:24.382486 INFO::ASW Batch was 0.644228783492475 prior to batch effect correction and is now -0.0344628224229572 .
2025-08-15 00:51:24.383328 INFO::ASW Label was 0.398641327179037 prior to batch effect correction and is now 0.893698530796849 .
2025-08-15 00:51:24.384335 INFO::Total function execution time is 0.0373430252075195 s and adjustment time is 0.0177810192108154 s ( 47.62 )
2025-08-15 00:51:24.590453 INFO::Formatting Data.
2025-08-15 00:51:24.59214 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:24.59406 INFO::Removing potential empty rows and columns
2025-08-15 00:51:24.596092 INFO::Found 0 missing values.
2025-08-15 00:51:24.601131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:24.602094 INFO::Done
2025-08-15 00:51:24.602974 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:24.605562 INFO::Starting hierarchical adjustment
2025-08-15 00:51:24.606694 INFO::Found 3 batches.
2025-08-15 00:51:24.607562 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:24.608518 INFO::Using default BPPARAM
2025-08-15 00:51:24.609478 INFO::Processing subtree level 1
2025-08-15 00:51:27.801127 INFO::Adjusting the last 1 batches sequentially
2025-08-15 00:51:27.803328 INFO::Done
2025-08-15 00:51:27.804618 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:27.807917 INFO::ASW Batch was -0.123277273212489 prior to batch effect correction and is now -0.123277273212489 .
2025-08-15 00:51:27.8096 INFO::Total function execution time is 3.21933197975159 s and adjustment time is 3.19678902626038 s ( 99.3 )
2025-08-15 00:51:27.810967 INFO::Formatting Data.
2025-08-15 00:51:27.812033 INFO::Typecasting input to dataframe.
2025-08-15 00:51:27.813506 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:27.815177 INFO::Removing potential empty rows and columns
2025-08-15 00:51:27.816965 INFO::Found 0 missing values.
2025-08-15 00:51:27.821732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:27.822592 INFO::Done
2025-08-15 00:51:27.823561 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:27.826786 INFO::Starting hierarchical adjustment
2025-08-15 00:51:27.828158 INFO::Found 3 batches.
2025-08-15 00:51:27.829303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:27.83055 INFO::Using default BPPARAM
2025-08-15 00:51:27.831667 INFO::Processing subtree level 1
2025-08-15 00:51:30.781663 INFO::Adjusting the last 1 batches sequentially
2025-08-15 00:51:30.783967 INFO::Done
2025-08-15 00:51:30.785345 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:30.788757 INFO::ASW Batch was -0.123277273212489 prior to batch effect correction and is now -0.123277273212489 .
2025-08-15 00:51:30.790387 INFO::Total function execution time is 2.97934794425964 s and adjustment time is 2.9559850692749 s ( 99.22 )
2025-08-15 00:51:30.812249 INFO::Formatting Data.
2025-08-15 00:51:30.81387 INFO::Typecasting input to dataframe.
2025-08-15 00:51:30.815625 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:30.817407 INFO::Removing potential empty rows and columns
2025-08-15 00:51:30.8193 INFO::Found 0 missing values.
2025-08-15 00:51:30.823847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:30.82507 INFO::Done
2025-08-15 00:51:30.826277 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:30.829638 INFO::Starting hierarchical adjustment
2025-08-15 00:51:30.831119 INFO::Found 3 batches.
2025-08-15 00:51:30.832335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:30.83364 INFO::Using default BPPARAM
2025-08-15 00:51:30.834821 INFO::Processing subtree level 1
2025-08-15 00:51:33.670028 INFO::Adjusting the last 1 batches sequentially
2025-08-15 00:51:33.671728 INFO::Done
2025-08-15 00:51:33.672566 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:33.674643 INFO::ASW Batch was 0.00261767836694898 prior to batch effect correction and is now 0.00261767836694898 .
2025-08-15 00:51:33.675586 INFO::Total function execution time is 2.86354613304138 s and adjustment time is 2.84087014198303 s ( 99.21 )
2025-08-15 00:51:36.570256 INFO::Formatting Data.
2025-08-15 00:51:36.571886 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:36.574016 INFO::Removing potential empty rows and columns
2025-08-15 00:51:36.577771 INFO::Found 1000 missing values.
2025-08-15 00:51:36.594025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:36.595007 INFO::Done
2025-08-15 00:51:36.595853 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:36.602157 INFO::Starting hierarchical adjustment
2025-08-15 00:51:36.603164 INFO::Found 10 batches.
2025-08-15 00:51:36.603918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:36.604715 INFO::Using default BPPARAM
2025-08-15 00:51:36.60543 INFO::Processing subtree level 1
2025-08-15 00:51:39.724199 INFO::Processing subtree level 2
2025-08-15 00:51:42.676826 INFO::Adjusting the last 1 batches sequentially
2025-08-15 00:51:42.679276 INFO::Done
2025-08-15 00:51:42.680527 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:42.689249 INFO::ASW Batch was 0.491792942930033 prior to batch effect correction and is now 0.491792942930033 .
2025-08-15 00:51:42.69056 INFO::ASW Label was 0.333642340972578 prior to batch effect correction and is now 0.333642340972578 .
2025-08-15 00:51:42.692061 INFO::Total function execution time is 6.12192511558533 s and adjustment time is 6.07622289657593 s ( 99.25 )
2025-08-15 00:51:42.69347 INFO::Formatting Data.
2025-08-15 00:51:42.694661 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:42.696484 INFO::Removing potential empty rows and columns
2025-08-15 00:51:42.698981 INFO::Found 1000 missing values.
2025-08-15 00:51:42.714098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:42.715475 INFO::Done
2025-08-15 00:51:42.716696 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:42.726213 INFO::Starting hierarchical adjustment
2025-08-15 00:51:42.72779 INFO::Found 10 batches.
2025-08-15 00:51:43.532607 INFO::Set up parallel execution backend with 2 workers
2025-08-15 00:51:43.53415 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-15 00:51:46.650807 INFO::Adjusting the last 2 batches sequentially
2025-08-15 00:51:46.652994 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-15 00:51:46.676152 INFO::Done
2025-08-15 00:51:46.677516 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:46.686346 INFO::ASW Batch was 0.491792942930033 prior to batch effect correction and is now 0.491792942930033 .
2025-08-15 00:51:46.687661 INFO::ASW Label was 0.333642340972578 prior to batch effect correction and is now 0.333642340972578 .
2025-08-15 00:51:46.689189 INFO::Total function execution time is 3.99570989608765 s and adjustment time is 3.94857788085938 s ( 98.82 )
2025-08-15 00:51:49.919493 INFO::Formatting Data.
2025-08-15 00:51:49.921244 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:49.92319 INFO::Removing potential empty rows and columns
2025-08-15 00:51:49.925253 INFO::Found 0 missing values.
2025-08-15 00:51:49.930953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:49.932481 INFO::Done
2025-08-15 00:51:49.933902 INFO::Acquiring quality metrics before batch effect correction.
2025-08-15 00:51:49.938791 INFO::Starting hierarchical adjustment
2025-08-15 00:51:49.940521 INFO::Found 3 batches.
2025-08-15 00:51:49.941899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-15 00:51:49.943352 INFO::Using default BPPARAM
2025-08-15 00:51:49.944701 INFO::Processing subtree level 1
2025-08-15 00:51:53.451499 INFO::Adjusting the last 1 batches sequentially
2025-08-15 00:51:53.453868 INFO::Done
2025-08-15 00:51:53.455319 INFO::Acquiring quality metrics after batch effect correction.
2025-08-15 00:51:53.460032 INFO::ASW Batch was 0.215328308388923 prior to batch effect correction and is now -0.160626066024596 .
2025-08-15 00:51:53.461451 INFO::ASW Label was -0.185925404744342 prior to batch effect correction and is now -0.0679204101432664 .
2025-08-15 00:51:53.463156 INFO::Total function execution time is 3.54376292228699 s and adjustment time is 3.51359796524048 s ( 99.15 )
2025-08-15 00:51:53.657114 INFO::Formatting Data.
2025-08-15 00:51:53.658656 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:53.660428 INFO::Removing potential empty rows and columns
2025-08-15 00:51:53.662254 INFO::Found 2 missing values.
2025-08-15 00:51:53.666485 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:53.667723 INFO::Done
2025-08-15 00:51:53.724604 INFO::Found NA in Reference column
2025-08-15 00:51:53.741386 INFO::Require at least two references per batch.
2025-08-15 00:51:53.765409 INFO::Formatting Data.
2025-08-15 00:51:53.766395 INFO::Recognized SummarizedExperiment
2025-08-15 00:51:53.767157 INFO::Typecasting input to dataframe.
2025-08-15 00:51:53.775208 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:53.776602 INFO::Removing potential empty rows and columns
2025-08-15 00:51:53.779672 INFO::Found 0 missing values.
2025-08-15 00:51:53.788761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:53.790156 INFO::Done
2025-08-15 00:51:53.813778 INFO::Formatting Data.
2025-08-15 00:51:53.815255 INFO::Recognized SummarizedExperiment
2025-08-15 00:51:53.816519 INFO::Typecasting input to dataframe.
2025-08-15 00:51:53.841452 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:53.843467 INFO::Removing potential empty rows and columns
2025-08-15 00:51:53.846532 INFO::Found 0 missing values.
2025-08-15 00:51:53.854793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:53.855694 INFO::Done
2025-08-15 00:51:53.870586 INFO::Formatting Data.
2025-08-15 00:51:53.871583 INFO::Recognized SummarizedExperiment
2025-08-15 00:51:53.872341 INFO::Typecasting input to dataframe.
2025-08-15 00:51:53.887223 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:53.888463 INFO::Removing potential empty rows and columns
2025-08-15 00:51:53.889771 INFO::Found 0 missing values.
2025-08-15 00:51:53.890892 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.
2025-08-15 00:51:53.894842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:53.895623 INFO::Done
2025-08-15 00:51:53.911337 INFO::Formatting Data.
2025-08-15 00:51:53.912939 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:53.914762 INFO::Removing potential empty rows and columns
2025-08-15 00:51:53.916754 INFO::Found 0 missing values.
2025-08-15 00:51:53.921713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:53.922746 INFO::Done
2025-08-15 00:51:53.943795 INFO::Formatting Data.
2025-08-15 00:51:53.945318 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:53.947078 INFO::Removing potential empty rows and columns
2025-08-15 00:51:53.94898 INFO::Found 0 missing values.
2025-08-15 00:51:53.953495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:53.954715 INFO::Done
2025-08-15 00:51:53.993049 INFO::Formatting Data.
2025-08-15 00:51:53.994077 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:53.99529 INFO::Removing potential empty rows and columns
2025-08-15 00:51:53.996551 INFO::Found 1 missing values.
2025-08-15 00:51:53.999049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:53.999801 INFO::Done
2025-08-15 00:51:54.02339 INFO::Formatting Data.
2025-08-15 00:51:54.024537 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:54.025655 INFO::Removing potential empty rows and columns
2025-08-15 00:51:54.026808 INFO::Found 2 missing values.
2025-08-15 00:51:54.027927 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.
2025-08-15 00:51:54.031158 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:54.03236 INFO::Done
2025-08-15 00:51:54.052486 INFO::Formatting Data.
2025-08-15 00:51:54.054038 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:54.055862 INFO::Removing potential empty rows and columns
2025-08-15 00:51:54.057642 INFO::Found 2 missing values.
2025-08-15 00:51:54.060387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:54.061584 INFO::Done
2025-08-15 00:51:54.082651 INFO::Formatting Data.
2025-08-15 00:51:54.084089 INFO::Typecasting input to dataframe.
2025-08-15 00:51:54.085703 INFO::Replacing NaNs with NAs.
2025-08-15 00:51:54.087355 INFO::Removing potential empty rows and columns
2025-08-15 00:51:54.089176 INFO::Found 0 missing values.
2025-08-15 00:51:54.093806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-15 00:51:54.095118 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
31.04 1.43 79.14
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.69 | 0.59 | 19.94 | |
| compute_asw | 0.04 | 0.00 | 0.05 | |
| count_existing | 0.02 | 0.00 | 0.02 | |
| generate_data_covariables | 0.03 | 0.00 | 0.03 | |
| generate_dataset | 0.01 | 0.00 | 0.01 | |