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This page was generated on 2025-09-01 11:38 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 163/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.4.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_21
git_last_commit: dedce04
git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on nebbiolo1

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.

raw results


Summary

Package: BERT
Version: 1.4.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.4.0.tar.gz
StartedAt: 2025-08-31 20:23:52 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 20:25:22 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 90.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 23.056  1.228  16.432
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.4.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-08-31 20:24:44.750221 INFO::Formatting Data.
2025-08-31 20:24:44.751548 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:44.762285 INFO::Removing potential empty rows and columns
2025-08-31 20:24:44.998487 INFO::Found  0  missing values.
2025-08-31 20:24:45.001831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:45.002508 INFO::Done
2025-08-31 20:24:45.003054 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:45.014213 INFO::Starting hierarchical adjustment
2025-08-31 20:24:45.015092 INFO::Found  3  batches.
2025-08-31 20:24:45.01565 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:45.016789 INFO::Using default BPPARAM
2025-08-31 20:24:45.017354 INFO::Processing subtree level 1
2025-08-31 20:24:45.115555 INFO::Adjusting the last 1 batches sequentially
2025-08-31 20:24:45.117445 INFO::Done
2025-08-31 20:24:45.118166 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:45.120905 INFO::ASW Batch was 0.00231707727089579 prior to batch effect correction and is now 0.00231707727089579 .
2025-08-31 20:24:45.122072 INFO::Total function execution time is  0.372356653213501  s and adjustment time is  0.102510213851929 s ( 27.53 )
2025-08-31 20:24:45.135597 INFO::Formatting Data.
2025-08-31 20:24:45.136328 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:45.137271 INFO::Removing potential empty rows and columns
2025-08-31 20:24:45.138511 INFO::Found  0  missing values.
2025-08-31 20:24:45.139543 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.
2025-08-31 20:24:45.151352 INFO::Formatting Data.
2025-08-31 20:24:45.152297 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:45.153338 INFO::Removing potential empty rows and columns
2025-08-31 20:24:45.154477 INFO::Found  0  missing values.
2025-08-31 20:24:45.155497 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.
2025-08-31 20:24:45.173757 INFO::Formatting Data.
2025-08-31 20:24:45.174775 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:45.175868 INFO::Removing potential empty rows and columns
2025-08-31 20:24:45.177044 INFO::Found  0  missing values.
2025-08-31 20:24:45.178091 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.
2025-08-31 20:24:45.18311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:45.183735 INFO::Done
2025-08-31 20:24:45.184293 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:45.186472 INFO::Starting hierarchical adjustment
2025-08-31 20:24:45.187193 INFO::Found  2  batches.
2025-08-31 20:24:45.187756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:45.18844 INFO::Using default BPPARAM
2025-08-31 20:24:45.188995 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:45.189985 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-31 20:24:45.213471 INFO::Done
2025-08-31 20:24:45.214219 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:45.216319 INFO::ASW Batch was 0.0802379617531624 prior to batch effect correction and is now -0.130554839122708 .
2025-08-31 20:24:45.217221 INFO::Total function execution time is  0.0436320304870605  s and adjustment time is  0.0263833999633789 s ( 60.47 )
2025-08-31 20:24:45.220084 INFO::Formatting Data.
2025-08-31 20:24:45.220746 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:45.230086 INFO::Formatting Data.
2025-08-31 20:24:45.230945 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:45.254563 INFO::Removing potential empty rows and columns
2025-08-31 20:24:45.257929 INFO::Found  0  missing values.
2025-08-31 20:24:45.260956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:45.261601 INFO::Done
2025-08-31 20:24:45.262162 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:45.264167 INFO::Starting hierarchical adjustment
2025-08-31 20:24:45.264879 INFO::Found  2  batches.
2025-08-31 20:24:45.26539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:45.266008 INFO::Using default BPPARAM
2025-08-31 20:24:45.266512 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:45.267428 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-31 20:24:45.282123 INFO::Done
2025-08-31 20:24:45.282866 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:45.285022 INFO::ASW Batch was -0.0291088773008272 prior to batch effect correction and is now -0.124643337812302 .
2025-08-31 20:24:45.28586 INFO::Total function execution time is  0.0558688640594482  s and adjustment time is  0.0173523426055908 s ( 31.06 )
2025-08-31 20:24:45.286891 INFO::Formatting Data.
2025-08-31 20:24:45.287471 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:45.288309 INFO::Removing potential empty rows and columns
2025-08-31 20:24:45.289278 INFO::Found  0  missing values.
2025-08-31 20:24:45.291976 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:45.292536 INFO::Done
2025-08-31 20:24:45.293066 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:45.295137 INFO::Starting hierarchical adjustment
2025-08-31 20:24:45.295882 INFO::Found  2  batches.
2025-08-31 20:24:45.296407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:45.297026 INFO::Using default BPPARAM
2025-08-31 20:24:45.297553 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:45.298498 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-31 20:24:45.312204 INFO::Done
2025-08-31 20:24:45.312846 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:45.314727 INFO::ASW Batch was -0.0291088773008272 prior to batch effect correction and is now -0.124643337812302 .
2025-08-31 20:24:45.315471 INFO::Total function execution time is  0.0285770893096924  s and adjustment time is  0.0164952278137207 s ( 57.72 )
2025-08-31 20:24:48.27244 INFO::Formatting Data.
2025-08-31 20:24:48.273186 INFO::Recognized SummarizedExperiment
2025-08-31 20:24:48.273706 INFO::Typecasting input to dataframe.
2025-08-31 20:24:48.302952 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:48.30413 INFO::Removing potential empty rows and columns
2025-08-31 20:24:48.307277 INFO::Found  0  missing values.
2025-08-31 20:24:48.314194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:48.314861 INFO::Done
2025-08-31 20:24:48.315404 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:48.319084 INFO::Starting hierarchical adjustment
2025-08-31 20:24:48.319838 INFO::Found  2  batches.
2025-08-31 20:24:48.320368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:48.321462 INFO::Using default BPPARAM
2025-08-31 20:24:48.322027 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:48.323026 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-31 20:24:48.379794 INFO::Done
2025-08-31 20:24:48.380572 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:48.384268 INFO::ASW Batch was 0.00195362277808041 prior to batch effect correction and is now -0.0869282280229005 .
2025-08-31 20:24:48.385167 INFO::Total function execution time is  0.112982511520386  s and adjustment time is  0.060081958770752 s ( 53.18 )
2025-08-31 20:24:48.404142 INFO::Formatting Data.
2025-08-31 20:24:48.40494 INFO::Recognized SummarizedExperiment
2025-08-31 20:24:48.405512 INFO::Typecasting input to dataframe.
2025-08-31 20:24:48.415008 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:48.416224 INFO::Removing potential empty rows and columns
2025-08-31 20:24:48.420265 INFO::Found  0  missing values.
2025-08-31 20:24:48.4278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:48.428678 INFO::Done
2025-08-31 20:24:48.429333 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:48.43326 INFO::Starting hierarchical adjustment
2025-08-31 20:24:48.434125 INFO::Found  2  batches.
2025-08-31 20:24:48.434697 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:48.435327 INFO::Using default BPPARAM
2025-08-31 20:24:48.435881 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:48.436916 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-31 20:24:48.462639 INFO::Done
2025-08-31 20:24:48.463363 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:48.467183 INFO::ASW Batch was -0.00738967361569529 prior to batch effect correction and is now -0.00738967361569529 .
2025-08-31 20:24:48.468052 INFO::Total function execution time is  0.0639073848724365  s and adjustment time is  0.0286571979522705 s ( 44.84 )
2025-08-31 20:24:48.486117 INFO::Formatting Data.
2025-08-31 20:24:48.486967 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:48.487874 INFO::Removing potential empty rows and columns
2025-08-31 20:24:48.488908 INFO::Found  0  missing values.
2025-08-31 20:24:48.491852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:48.492385 INFO::Done
2025-08-31 20:24:48.492916 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:48.494989 INFO::Starting hierarchical adjustment
2025-08-31 20:24:48.495703 INFO::Found  3  batches.
2025-08-31 20:24:48.496253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:48.496872 INFO::Using default BPPARAM
2025-08-31 20:24:48.497646 INFO::Processing subtree level 1
2025-08-31 20:24:48.772276 INFO::Adjusting the last 1 batches sequentially
2025-08-31 20:24:48.774321 INFO::Done
2025-08-31 20:24:48.775067 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:48.777822 INFO::ASW Batch was -0.0488728080545993 prior to batch effect correction and is now -0.154423241869365 .
2025-08-31 20:24:48.778827 INFO::Total function execution time is  0.292710542678833  s and adjustment time is  0.278734445571899 s ( 95.23 )
2025-08-31 20:24:48.85906 INFO::Skipping initial DF formatting
2025-08-31 20:24:48.860013 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:48.864435 INFO::Starting hierarchical adjustment
2025-08-31 20:24:48.865355 INFO::Found  5  batches.
2025-08-31 20:24:48.866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:48.866705 INFO::Using default BPPARAM
2025-08-31 20:24:48.867258 INFO::Processing subtree level 1
2025-08-31 20:24:49.059205 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:49.061275 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-31 20:24:49.085776 INFO::Done
2025-08-31 20:24:49.086673 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:49.091511 INFO::ASW Batch was 0.619975922852049 prior to batch effect correction and is now 0.619975922852049 .
2025-08-31 20:24:49.092248 INFO::ASW Label was 0.302069270043905 prior to batch effect correction and is now 0.302069270043905 .
2025-08-31 20:24:49.093241 INFO::Total function execution time is  0.234314441680908  s and adjustment time is  0.22057056427002 s ( 94.13 )
2025-08-31 20:24:49.113923 INFO::Formatting Data.
2025-08-31 20:24:49.114887 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:49.115979 INFO::Removing potential empty rows and columns
2025-08-31 20:24:49.127273 INFO::Found  0  missing values.
2025-08-31 20:24:49.133789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:49.134573 INFO::Done
2025-08-31 20:24:49.135294 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:49.139837 INFO::Starting hierarchical adjustment
2025-08-31 20:24:49.140789 INFO::Found  5  batches.
2025-08-31 20:24:49.141465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:49.142279 INFO::Using default BPPARAM
2025-08-31 20:24:49.142958 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.

2025-08-31 20:24:49.279745 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:49.281557 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-31 20:24:49.299794 INFO::Done
2025-08-31 20:24:49.300709 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:49.304395 INFO::ASW Batch was 0.225366778518379 prior to batch effect correction and is now -0.0681969450998025 .
2025-08-31 20:24:49.305138 INFO::ASW Label was 0.493864763608458 prior to batch effect correction and is now 0.860005874180952 .
2025-08-31 20:24:49.306084 INFO::Total function execution time is  0.19228196144104  s and adjustment time is  0.159181594848633 s ( 82.79 )
2025-08-31 20:24:49.307043 INFO::Formatting Data.
2025-08-31 20:24:49.307742 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:49.308704 INFO::Removing potential empty rows and columns
2025-08-31 20:24:49.309776 INFO::Found  0  missing values.
2025-08-31 20:24:49.314098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:49.314745 INFO::Done
2025-08-31 20:24:49.315345 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:49.318676 INFO::Starting hierarchical adjustment
2025-08-31 20:24:49.319462 INFO::Found  5  batches.
2025-08-31 20:24:49.320042 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:49.320752 INFO::Using default BPPARAM
2025-08-31 20:24:49.321344 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.

2025-08-31 20:24:49.471701 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:49.473566 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-31 20:24:49.490633 INFO::Done
2025-08-31 20:24:49.491446 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:49.495056 INFO::ASW Batch was 0.225366778518379 prior to batch effect correction and is now -0.0681969450998025 .
2025-08-31 20:24:49.495717 INFO::ASW Label was 0.493864763608458 prior to batch effect correction and is now 0.860005874180952 .
2025-08-31 20:24:49.49658 INFO::Total function execution time is  0.189534425735474  s and adjustment time is  0.171306133270264 s ( 90.38 )
2025-08-31 20:24:49.511145 INFO::Formatting Data.
2025-08-31 20:24:49.511985 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:49.512937 INFO::Removing potential empty rows and columns
2025-08-31 20:24:49.514023 INFO::Found  0  missing values.
2025-08-31 20:24:49.51831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:49.518909 INFO::Done
2025-08-31 20:24:49.51948 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:49.522715 INFO::Starting hierarchical adjustment
2025-08-31 20:24:49.523528 INFO::Found  5  batches.
2025-08-31 20:24:49.524127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:49.52484 INFO::Using default BPPARAM
2025-08-31 20:24:49.52549 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.

2025-08-31 20:24:49.656654 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:49.658408 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-31 20:24:49.674894 INFO::Done
2025-08-31 20:24:49.675678 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:49.679244 INFO::ASW Batch was 0.521195322490556 prior to batch effect correction and is now -0.0350476201591641 .
2025-08-31 20:24:49.679969 INFO::ASW Label was 0.316005449046799 prior to batch effect correction and is now 0.678999561545783 .
2025-08-31 20:24:49.68088 INFO::Total function execution time is  0.169787883758545  s and adjustment time is  0.151522636413574 s ( 89.24 )
2025-08-31 20:24:49.681835 INFO::Formatting Data.
2025-08-31 20:24:49.682518 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:49.683481 INFO::Removing potential empty rows and columns
2025-08-31 20:24:49.684591 INFO::Found  0  missing values.
2025-08-31 20:24:49.68899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:49.689595 INFO::Done
2025-08-31 20:24:49.690172 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:49.693406 INFO::Starting hierarchical adjustment
2025-08-31 20:24:49.6942 INFO::Found  5  batches.
2025-08-31 20:24:49.694802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:49.695501 INFO::Using default BPPARAM
2025-08-31 20:24:49.696106 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.

2025-08-31 20:24:49.824397 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:49.826212 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-31 20:24:49.842178 INFO::Done
2025-08-31 20:24:49.842982 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:49.846542 INFO::ASW Batch was 0.521195322490556 prior to batch effect correction and is now -0.0350476201591641 .
2025-08-31 20:24:49.847241 INFO::ASW Label was 0.316005449046799 prior to batch effect correction and is now 0.678999561545783 .
2025-08-31 20:24:49.848148 INFO::Total function execution time is  0.166357755661011  s and adjustment time is  0.148104190826416 s ( 89.03 )
2025-08-31 20:24:49.862209 INFO::Formatting Data.
2025-08-31 20:24:49.863072 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:49.864023 INFO::Removing potential empty rows and columns
2025-08-31 20:24:49.865062 INFO::Found  0  missing values.
2025-08-31 20:24:49.867853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:49.868405 INFO::Done
2025-08-31 20:24:49.868931 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:49.87213 INFO::Starting hierarchical adjustment
2025-08-31 20:24:49.872906 INFO::Found  2  batches.
2025-08-31 20:24:49.873429 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:49.874061 INFO::Using default BPPARAM
2025-08-31 20:24:49.874574 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:49.875531 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-31 20:24:49.892489 INFO::Done
2025-08-31 20:24:49.893359 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:49.897086 INFO::ASW Batch was 0.586284818349546 prior to batch effect correction and is now 0.0692739164583851 .
2025-08-31 20:24:49.897835 INFO::ASW Label was 0.50113846387674 prior to batch effect correction and is now 0.864604884976889 .
2025-08-31 20:24:49.898973 INFO::Total function execution time is  0.0368719100952148  s and adjustment time is  0.0196976661682129 s ( 53.42 )
2025-08-31 20:24:49.900039 INFO::Formatting Data.
2025-08-31 20:24:49.900812 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:49.901922 INFO::Removing potential empty rows and columns
2025-08-31 20:24:49.90318 INFO::Found  0  missing values.
2025-08-31 20:24:49.906576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:49.907238 INFO::Done
2025-08-31 20:24:49.907881 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:49.911498 INFO::Starting hierarchical adjustment
2025-08-31 20:24:49.912389 INFO::Found  2  batches.
2025-08-31 20:24:49.913065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:49.913847 INFO::Using default BPPARAM
2025-08-31 20:24:49.914505 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:49.91568 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-31 20:24:49.934628 INFO::Done
2025-08-31 20:24:49.935518 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:49.939757 INFO::ASW Batch was 0.586284818349546 prior to batch effect correction and is now 0.0692739164583851 .
2025-08-31 20:24:49.940541 INFO::ASW Label was 0.50113846387674 prior to batch effect correction and is now 0.864604884976889 .
2025-08-31 20:24:49.941528 INFO::Total function execution time is  0.0415244102478027  s and adjustment time is  0.022381067276001 s ( 53.9 )
2025-08-31 20:24:49.956763 INFO::Formatting Data.
2025-08-31 20:24:49.957732 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:49.958761 INFO::Removing potential empty rows and columns
2025-08-31 20:24:49.959827 INFO::Found  0  missing values.
2025-08-31 20:24:49.962162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:49.962759 INFO::Done
2025-08-31 20:24:49.963366 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:49.965557 INFO::Starting hierarchical adjustment
2025-08-31 20:24:49.966354 INFO::Found  2  batches.
2025-08-31 20:24:49.966949 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:49.967637 INFO::Using default BPPARAM
2025-08-31 20:24:49.968217 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:49.969214 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-31 20:24:50.00384 INFO::Done
2025-08-31 20:24:50.004704 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:50.007021 INFO::ASW Batch was 0.211648872677418 prior to batch effect correction and is now -0.161582707152699 .
2025-08-31 20:24:50.007978 INFO::Total function execution time is  0.0513768196105957  s and adjustment time is  0.0375998020172119 s ( 73.18 )
2025-08-31 20:24:50.021679 INFO::Formatting Data.
2025-08-31 20:24:50.022534 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:50.023615 INFO::Removing potential empty rows and columns
2025-08-31 20:24:50.024698 INFO::Found  0  missing values.
2025-08-31 20:24:50.025959 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.
2025-08-31 20:24:50.030774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:50.031369 INFO::Done
2025-08-31 20:24:50.031961 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:50.035192 INFO::Starting hierarchical adjustment
2025-08-31 20:24:50.035964 INFO::Found  2  batches.
2025-08-31 20:24:50.036518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:50.03717 INFO::Using default BPPARAM
2025-08-31 20:24:50.037731 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:50.038743 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-31 20:24:50.056172 INFO::Done
2025-08-31 20:24:50.056934 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:50.060328 INFO::ASW Batch was 0.364119985071676 prior to batch effect correction and is now 0.0409560398900886 .
2025-08-31 20:24:50.061066 INFO::ASW Label was 0.673968515624548 prior to batch effect correction and is now 0.879430851000763 .
2025-08-31 20:24:50.062036 INFO::Total function execution time is  0.0404567718505859  s and adjustment time is  0.0203402042388916 s ( 50.28 )
2025-08-31 20:24:50.063032 INFO::Formatting Data.
2025-08-31 20:24:50.063776 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:50.064872 INFO::Removing potential empty rows and columns
2025-08-31 20:24:50.066071 INFO::Found  0  missing values.
2025-08-31 20:24:50.067156 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.
2025-08-31 20:24:50.072997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:50.073695 INFO::Done
2025-08-31 20:24:50.074332 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:50.07785 INFO::Starting hierarchical adjustment
2025-08-31 20:24:50.078697 INFO::Found  2  batches.
2025-08-31 20:24:50.079373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:50.080134 INFO::Using default BPPARAM
2025-08-31 20:24:50.080794 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:50.081929 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-31 20:24:50.099771 INFO::Done
2025-08-31 20:24:50.100543 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:50.103733 INFO::ASW Batch was 0.364119985071676 prior to batch effect correction and is now 0.0409560398900886 .
2025-08-31 20:24:50.104374 INFO::ASW Label was 0.673968515624548 prior to batch effect correction and is now 0.879430851000763 .
2025-08-31 20:24:50.105253 INFO::Total function execution time is  0.042266845703125  s and adjustment time is  0.0212578773498535 s ( 50.29 )
2025-08-31 20:24:50.318842 INFO::Formatting Data.
2025-08-31 20:24:50.319731 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:50.320684 INFO::Removing potential empty rows and columns
2025-08-31 20:24:50.321734 INFO::Found  0  missing values.
2025-08-31 20:24:50.32482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:50.325408 INFO::Done
2025-08-31 20:24:50.325962 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:50.328078 INFO::Starting hierarchical adjustment
2025-08-31 20:24:50.32881 INFO::Found  3  batches.
2025-08-31 20:24:50.329358 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:50.329994 INFO::Using default BPPARAM
2025-08-31 20:24:50.330574 INFO::Processing subtree level 1
2025-08-31 20:24:50.423451 INFO::Adjusting the last 1 batches sequentially
2025-08-31 20:24:50.425495 INFO::Done
2025-08-31 20:24:50.4262 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:50.428924 INFO::ASW Batch was -0.11999735511481 prior to batch effect correction and is now -0.11999735511481 .
2025-08-31 20:24:50.429939 INFO::Total function execution time is  0.111152172088623  s and adjustment time is  0.0968105792999268 s ( 87.1 )
2025-08-31 20:24:50.431126 INFO::Formatting Data.
2025-08-31 20:24:50.431829 INFO::Typecasting input to dataframe.
2025-08-31 20:24:50.432615 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:50.433632 INFO::Removing potential empty rows and columns
2025-08-31 20:24:50.434797 INFO::Found  0  missing values.
2025-08-31 20:24:50.438028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:50.438592 INFO::Done
2025-08-31 20:24:50.439141 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:50.441361 INFO::Starting hierarchical adjustment
2025-08-31 20:24:50.44211 INFO::Found  3  batches.
2025-08-31 20:24:50.442673 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:50.443326 INFO::Using default BPPARAM
2025-08-31 20:24:50.443892 INFO::Processing subtree level 1
2025-08-31 20:24:50.539744 INFO::Adjusting the last 1 batches sequentially
2025-08-31 20:24:50.542242 INFO::Done
2025-08-31 20:24:50.543358 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:50.546555 INFO::ASW Batch was -0.11999735511481 prior to batch effect correction and is now -0.11999735511481 .
2025-08-31 20:24:50.547774 INFO::Total function execution time is  0.116581201553345  s and adjustment time is  0.100159883499146 s ( 85.91 )
2025-08-31 20:24:50.562318 INFO::Formatting Data.
2025-08-31 20:24:50.563315 INFO::Typecasting input to dataframe.
2025-08-31 20:24:50.5645 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:50.565642 INFO::Removing potential empty rows and columns
2025-08-31 20:24:50.566903 INFO::Found  0  missing values.
2025-08-31 20:24:50.570252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:50.570885 INFO::Done
2025-08-31 20:24:50.571445 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:50.573732 INFO::Starting hierarchical adjustment
2025-08-31 20:24:50.574478 INFO::Found  3  batches.
2025-08-31 20:24:50.575073 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:50.575764 INFO::Using default BPPARAM
2025-08-31 20:24:50.576339 INFO::Processing subtree level 1
2025-08-31 20:24:50.673568 INFO::Adjusting the last 1 batches sequentially
2025-08-31 20:24:50.675544 INFO::Done
2025-08-31 20:24:50.67622 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:50.678921 INFO::ASW Batch was -0.0528146960669388 prior to batch effect correction and is now -0.0528146960669388 .
2025-08-31 20:24:50.679986 INFO::Total function execution time is  0.11776876449585  s and adjustment time is  0.101217031478882 s ( 85.95 )
2025-08-31 20:24:50.82388 INFO::Formatting Data.
2025-08-31 20:24:50.82485 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:50.826049 INFO::Removing potential empty rows and columns
2025-08-31 20:24:50.828904 INFO::Found  1000  missing values.
2025-08-31 20:24:50.847745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:50.848664 INFO::Done
2025-08-31 20:24:50.849275 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:50.854961 INFO::Starting hierarchical adjustment
2025-08-31 20:24:50.855805 INFO::Found  10  batches.
2025-08-31 20:24:50.856378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:50.857025 INFO::Using default BPPARAM
2025-08-31 20:24:50.857594 INFO::Processing subtree level 1
2025-08-31 20:24:51.016334 INFO::Processing subtree level 2
2025-08-31 20:24:51.164814 INFO::Adjusting the last 1 batches sequentially
2025-08-31 20:24:51.167054 INFO::Done
2025-08-31 20:24:51.167789 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:51.173657 INFO::ASW Batch was 0.551315205218098 prior to batch effect correction and is now 0.551315205218098 .
2025-08-31 20:24:51.174375 INFO::ASW Label was 0.323155437520611 prior to batch effect correction and is now 0.323155437520611 .
2025-08-31 20:24:51.175453 INFO::Total function execution time is  0.351665258407593  s and adjustment time is  0.311410665512085 s ( 88.55 )
2025-08-31 20:24:51.176431 INFO::Formatting Data.
2025-08-31 20:24:51.177161 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:51.178516 INFO::Removing potential empty rows and columns
2025-08-31 20:24:51.18148 INFO::Found  1000  missing values.
2025-08-31 20:24:51.201011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:51.201966 INFO::Done
2025-08-31 20:24:51.202633 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:51.208505 INFO::Starting hierarchical adjustment
2025-08-31 20:24:51.209392 INFO::Found  10  batches.
2025-08-31 20:24:52.453092 INFO::Set up parallel execution backend with 2 workers
2025-08-31 20:24:52.455352 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-31 20:24:53.847484 INFO::Adjusting the last 2 batches sequentially
2025-08-31 20:24:53.84933 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-31 20:24:53.865567 INFO::Done
2025-08-31 20:24:53.866311 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:53.870973 INFO::ASW Batch was 0.551315205218098 prior to batch effect correction and is now 0.551315205218098 .
2025-08-31 20:24:53.871569 INFO::ASW Label was 0.323155437520611 prior to batch effect correction and is now 0.323155437520611 .
2025-08-31 20:24:53.872353 INFO::Total function execution time is  2.69597768783569  s and adjustment time is  2.65632700920105 s ( 98.53 )
2025-08-31 20:24:54.02481 INFO::Formatting Data.
2025-08-31 20:24:54.025749 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.02678 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.027948 INFO::Found  0  missing values.
2025-08-31 20:24:54.031515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.032058 INFO::Done
2025-08-31 20:24:54.032586 INFO::Acquiring quality metrics before batch effect correction.
2025-08-31 20:24:54.035225 INFO::Starting hierarchical adjustment
2025-08-31 20:24:54.035926 INFO::Found  3  batches.
2025-08-31 20:24:54.036435 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-31 20:24:54.037038 INFO::Using default BPPARAM
2025-08-31 20:24:54.037541 INFO::Processing subtree level 1
2025-08-31 20:24:54.146325 INFO::Adjusting the last 1 batches sequentially
2025-08-31 20:24:54.148309 INFO::Done
2025-08-31 20:24:54.149029 INFO::Acquiring quality metrics after batch effect correction.
2025-08-31 20:24:54.152698 INFO::ASW Batch was 0.231278242019531 prior to batch effect correction and is now -0.185790001881106 .
2025-08-31 20:24:54.153329 INFO::ASW Label was -0.201166220023948 prior to batch effect correction and is now 0.105391850866268 .
2025-08-31 20:24:54.154199 INFO::Total function execution time is  0.129498720169067  s and adjustment time is  0.112483024597168 s ( 86.86 )
2025-08-31 20:24:54.266388 INFO::Formatting Data.
2025-08-31 20:24:54.267435 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.268385 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.26944 INFO::Found  2  missing values.
2025-08-31 20:24:54.272231 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.272791 INFO::Done
2025-08-31 20:24:54.29947 INFO::Found NA in Reference column
2025-08-31 20:24:54.308688 INFO::Require at least two references per batch.
2025-08-31 20:24:54.328488 INFO::Formatting Data.
2025-08-31 20:24:54.329433 INFO::Recognized SummarizedExperiment
2025-08-31 20:24:54.330013 INFO::Typecasting input to dataframe.
2025-08-31 20:24:54.339604 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.340779 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.344163 INFO::Found  0  missing values.
2025-08-31 20:24:54.350801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.351466 INFO::Done
2025-08-31 20:24:54.367573 INFO::Formatting Data.
2025-08-31 20:24:54.368457 INFO::Recognized SummarizedExperiment
2025-08-31 20:24:54.369046 INFO::Typecasting input to dataframe.
2025-08-31 20:24:54.387945 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.389302 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.392839 INFO::Found  0  missing values.
2025-08-31 20:24:54.403714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.4045 INFO::Done
2025-08-31 20:24:54.420529 INFO::Formatting Data.
2025-08-31 20:24:54.421347 INFO::Recognized SummarizedExperiment
2025-08-31 20:24:54.421932 INFO::Typecasting input to dataframe.
2025-08-31 20:24:54.451235 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.452478 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.453695 INFO::Found  0  missing values.
2025-08-31 20:24:54.454698 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.
2025-08-31 20:24:54.459412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.460006 INFO::Done
2025-08-31 20:24:54.470811 INFO::Formatting Data.
2025-08-31 20:24:54.47175 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.4727 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.47375 INFO::Found  0  missing values.
2025-08-31 20:24:54.476798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.477366 INFO::Done
2025-08-31 20:24:54.489387 INFO::Formatting Data.
2025-08-31 20:24:54.490287 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.491225 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.492326 INFO::Found  0  missing values.
2025-08-31 20:24:54.495414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.496046 INFO::Done
2025-08-31 20:24:54.528059 INFO::Formatting Data.
2025-08-31 20:24:54.529001 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.530178 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.531635 INFO::Found  1  missing values.
2025-08-31 20:24:54.534548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.535133 INFO::Done
2025-08-31 20:24:54.554258 INFO::Formatting Data.
2025-08-31 20:24:54.555141 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.556128 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.557195 INFO::Found  2  missing values.
2025-08-31 20:24:54.55812 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.
2025-08-31 20:24:54.560386 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.560933 INFO::Done
2025-08-31 20:24:54.57124 INFO::Formatting Data.
2025-08-31 20:24:54.57221 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.573223 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.574281 INFO::Found  2  missing values.
2025-08-31 20:24:54.576118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.576689 INFO::Done
2025-08-31 20:24:54.588233 INFO::Formatting Data.
2025-08-31 20:24:54.589208 INFO::Typecasting input to dataframe.
2025-08-31 20:24:54.590143 INFO::Replacing NaNs with NAs.
2025-08-31 20:24:54.591135 INFO::Removing potential empty rows and columns
2025-08-31 20:24:54.592206 INFO::Found  0  missing values.
2025-08-31 20:24:54.59539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-31 20:24:54.595953 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 18.083   3.859  21.442

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT23.056 1.22816.432
compute_asw0.0240.0010.025
count_existing0.0120.0020.015
generate_data_covariables0.0120.0000.013
generate_dataset0.0110.0010.013