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This page was generated on 2025-10-10 12:07 -0400 (Fri, 10 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 164/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.5.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-10-09 13:45 -0400 (Thu, 09 Oct 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)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BERT on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: BERT
Version: 1.5.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.5.0.tar.gz
StartedAt: 2025-10-10 05:49:06 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 05:50:27 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 81.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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 28.494  2.145  21.048
* 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


Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.5.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-10-10 05:50:11.44565 INFO::Formatting Data.
2025-10-10 05:50:11.447781 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:11.466027 INFO::Removing potential empty rows and columns
2025-10-10 05:50:12.0367 INFO::Found  0  missing values.
2025-10-10 05:50:12.041412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:12.04231 INFO::Done
2025-10-10 05:50:12.0431 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:12.058499 INFO::Starting hierarchical adjustment
2025-10-10 05:50:12.059781 INFO::Found  3  batches.
2025-10-10 05:50:12.060608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:12.06225 INFO::Using default BPPARAM
2025-10-10 05:50:12.06315 INFO::Processing subtree level 1
2025-10-10 05:50:12.195183 INFO::Adjusting the last 1 batches sequentially
2025-10-10 05:50:12.197684 INFO::Done
2025-10-10 05:50:12.198714 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:12.202512 INFO::ASW Batch was -0.0899310557785442 prior to batch effect correction and is now -0.0899310557785442 .
2025-10-10 05:50:12.204165 INFO::Total function execution time is  0.759495973587036  s and adjustment time is  0.138145446777344 s ( 18.19 )
2025-10-10 05:50:12.223795 INFO::Formatting Data.
2025-10-10 05:50:12.224899 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:12.2262 INFO::Removing potential empty rows and columns
2025-10-10 05:50:12.227782 INFO::Found  0  missing values.
2025-10-10 05:50:12.237946 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-10 05:50:12.255175 INFO::Formatting Data.
2025-10-10 05:50:12.256229 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:12.257602 INFO::Removing potential empty rows and columns
2025-10-10 05:50:12.259276 INFO::Found  0  missing values.
2025-10-10 05:50:12.260643 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-10 05:50:12.284451 INFO::Formatting Data.
2025-10-10 05:50:12.285542 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:12.286934 INFO::Removing potential empty rows and columns
2025-10-10 05:50:12.288533 INFO::Found  0  missing values.
2025-10-10 05:50:12.290047 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-10 05:50:12.29722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:12.298161 INFO::Done
2025-10-10 05:50:12.299003 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:12.30208 INFO::Starting hierarchical adjustment
2025-10-10 05:50:12.303254 INFO::Found  2  batches.
2025-10-10 05:50:12.304141 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:12.305275 INFO::Using default BPPARAM
2025-10-10 05:50:12.306077 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:12.307613 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 05:50:12.340014 INFO::Done
2025-10-10 05:50:12.34097 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:12.343862 INFO::ASW Batch was -0.055799741840214 prior to batch effect correction and is now -0.123125456853957 .
2025-10-10 05:50:12.345055 INFO::Total function execution time is  0.0606193542480469  s and adjustment time is  0.0369865894317627 s ( 61.01 )
2025-10-10 05:50:12.348923 INFO::Formatting Data.
2025-10-10 05:50:12.349933 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:12.362369 INFO::Formatting Data.
2025-10-10 05:50:12.363399 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:12.364622 INFO::Removing potential empty rows and columns
2025-10-10 05:50:12.366111 INFO::Found  0  missing values.
2025-10-10 05:50:12.370492 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:12.371464 INFO::Done
2025-10-10 05:50:12.37226 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:12.375359 INFO::Starting hierarchical adjustment
2025-10-10 05:50:12.376445 INFO::Found  2  batches.
2025-10-10 05:50:12.377268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:12.378141 INFO::Using default BPPARAM
2025-10-10 05:50:12.378986 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:12.380326 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 05:50:12.448788 INFO::Done
2025-10-10 05:50:12.44968 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:12.452351 INFO::ASW Batch was 0.0584851868074889 prior to batch effect correction and is now -0.125846937526551 .
2025-10-10 05:50:12.453488 INFO::Total function execution time is  0.0911812782287598  s and adjustment time is  0.0725157260894775 s ( 79.53 )
2025-10-10 05:50:12.455016 INFO::Formatting Data.
2025-10-10 05:50:12.455887 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:12.457157 INFO::Removing potential empty rows and columns
2025-10-10 05:50:12.458731 INFO::Found  0  missing values.
2025-10-10 05:50:12.462921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:12.46379 INFO::Done
2025-10-10 05:50:12.464534 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:12.467394 INFO::Starting hierarchical adjustment
2025-10-10 05:50:12.468483 INFO::Found  2  batches.
2025-10-10 05:50:12.46937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:12.470255 INFO::Using default BPPARAM
2025-10-10 05:50:12.471072 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:12.472424 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 05:50:12.494519 INFO::Done
2025-10-10 05:50:12.49546 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:12.498275 INFO::ASW Batch was 0.0584851868074889 prior to batch effect correction and is now -0.125846937526551 .
2025-10-10 05:50:12.499514 INFO::Total function execution time is  0.0444796085357666  s and adjustment time is  0.0262291431427002 s ( 58.97 )
2025-10-10 05:50:16.425776 INFO::Formatting Data.
2025-10-10 05:50:16.426768 INFO::Recognized SummarizedExperiment
2025-10-10 05:50:16.427442 INFO::Typecasting input to dataframe.
2025-10-10 05:50:16.468248 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:16.469934 INFO::Removing potential empty rows and columns
2025-10-10 05:50:16.475293 INFO::Found  0  missing values.
2025-10-10 05:50:16.485896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:16.486845 INFO::Done
2025-10-10 05:50:16.487606 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:16.493063 INFO::Starting hierarchical adjustment
2025-10-10 05:50:16.49432 INFO::Found  2  batches.
2025-10-10 05:50:16.495253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:16.496853 INFO::Using default BPPARAM
2025-10-10 05:50:16.497744 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:16.499262 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 05:50:16.580879 INFO::Done
2025-10-10 05:50:16.581784 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:16.586763 INFO::ASW Batch was 0.0252520399579016 prior to batch effect correction and is now -0.0953267898753793 .
2025-10-10 05:50:16.588021 INFO::Total function execution time is  0.162684202194214  s and adjustment time is  0.0867786407470703 s ( 53.34 )
2025-10-10 05:50:16.615486 INFO::Formatting Data.
2025-10-10 05:50:16.616487 INFO::Recognized SummarizedExperiment
2025-10-10 05:50:16.617332 INFO::Typecasting input to dataframe.
2025-10-10 05:50:16.6308 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:16.632408 INFO::Removing potential empty rows and columns
2025-10-10 05:50:16.637991 INFO::Found  0  missing values.
2025-10-10 05:50:16.648445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:16.649353 INFO::Done
2025-10-10 05:50:16.650088 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:16.655067 INFO::Starting hierarchical adjustment
2025-10-10 05:50:16.656187 INFO::Found  2  batches.
2025-10-10 05:50:16.656968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:16.657792 INFO::Using default BPPARAM
2025-10-10 05:50:16.658566 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:16.65995 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 05:50:16.695764 INFO::Done
2025-10-10 05:50:16.696682 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:16.701725 INFO::ASW Batch was -0.0033347120877159 prior to batch effect correction and is now -0.0033347120877159 .
2025-10-10 05:50:16.703059 INFO::Total function execution time is  0.0875430107116699  s and adjustment time is  0.0397531986236572 s ( 45.41 )
2025-10-10 05:50:16.72868 INFO::Formatting Data.
2025-10-10 05:50:16.729732 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:16.731014 INFO::Removing potential empty rows and columns
2025-10-10 05:50:16.732488 INFO::Found  0  missing values.
2025-10-10 05:50:16.736844 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:16.73773 INFO::Done
2025-10-10 05:50:16.73849 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:16.741459 INFO::Starting hierarchical adjustment
2025-10-10 05:50:16.742597 INFO::Found  3  batches.
2025-10-10 05:50:16.743403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:16.744281 INFO::Using default BPPARAM
2025-10-10 05:50:16.745078 INFO::Processing subtree level 1
2025-10-10 05:50:16.909863 INFO::Adjusting the last 1 batches sequentially
2025-10-10 05:50:16.912226 INFO::Done
2025-10-10 05:50:16.913128 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:16.916538 INFO::ASW Batch was -0.128321790934123 prior to batch effect correction and is now -0.162251103228208 .
2025-10-10 05:50:16.917907 INFO::Total function execution time is  0.18927526473999  s and adjustment time is  0.169856786727905 s ( 89.74 )
2025-10-10 05:50:16.937213 INFO::Skipping initial DF formatting
2025-10-10 05:50:16.938108 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:16.943447 INFO::Starting hierarchical adjustment
2025-10-10 05:50:16.944546 INFO::Found  5  batches.
2025-10-10 05:50:16.945343 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:16.946207 INFO::Using default BPPARAM
2025-10-10 05:50:16.946984 INFO::Processing subtree level 1
2025-10-10 05:50:17.202896 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:17.204983 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 05:50:17.231992 INFO::Done
2025-10-10 05:50:17.232912 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:17.304014 INFO::ASW Batch was 0.518114796780592 prior to batch effect correction and is now 0.518114796780592 .
2025-10-10 05:50:17.304904 INFO::ASW Label was 0.36705062980937 prior to batch effect correction and is now 0.367050629809371 .
2025-10-10 05:50:17.306036 INFO::Total function execution time is  0.368882417678833  s and adjustment time is  0.287604570388794 s ( 77.97 )
2025-10-10 05:50:17.33011 INFO::Formatting Data.
2025-10-10 05:50:17.331067 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:17.332271 INFO::Removing potential empty rows and columns
2025-10-10 05:50:17.333693 INFO::Found  0  missing values.
2025-10-10 05:50:17.339953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:17.340836 INFO::Done
2025-10-10 05:50:17.341595 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:17.345854 INFO::Starting hierarchical adjustment
2025-10-10 05:50:17.346975 INFO::Found  5  batches.
2025-10-10 05:50:17.347753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:17.348636 INFO::Using default BPPARAM
2025-10-10 05:50:17.349534 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-10-10 05:50:17.511375 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:17.513634 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 05:50:17.539778 INFO::Done
2025-10-10 05:50:17.540697 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:17.545638 INFO::ASW Batch was 0.501546865052661 prior to batch effect correction and is now -0.0967201019257862 .
2025-10-10 05:50:17.546686 INFO::ASW Label was 0.350694422220231 prior to batch effect correction and is now 0.673206850657308 .
2025-10-10 05:50:17.547885 INFO::Total function execution time is  0.21779203414917  s and adjustment time is  0.193053722381592 s ( 88.64 )
2025-10-10 05:50:17.549341 INFO::Formatting Data.
2025-10-10 05:50:17.55027 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:17.551708 INFO::Removing potential empty rows and columns
2025-10-10 05:50:17.553492 INFO::Found  0  missing values.
2025-10-10 05:50:17.560235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:17.561169 INFO::Done
2025-10-10 05:50:17.561984 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:17.566471 INFO::Starting hierarchical adjustment
2025-10-10 05:50:17.567657 INFO::Found  5  batches.
2025-10-10 05:50:17.568424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:17.569378 INFO::Using default BPPARAM
2025-10-10 05:50:17.57016 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-10-10 05:50:17.725253 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:17.727428 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 05:50:17.7517 INFO::Done
2025-10-10 05:50:17.752704 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:17.757301 INFO::ASW Batch was 0.501546865052661 prior to batch effect correction and is now -0.0967201019257862 .
2025-10-10 05:50:17.758212 INFO::ASW Label was 0.350694422220231 prior to batch effect correction and is now 0.673206850657308 .
2025-10-10 05:50:17.759475 INFO::Total function execution time is  0.210163831710815  s and adjustment time is  0.184273719787598 s ( 87.68 )
2025-10-10 05:50:17.779128 INFO::Formatting Data.
2025-10-10 05:50:17.780124 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:17.781404 INFO::Removing potential empty rows and columns
2025-10-10 05:50:17.782911 INFO::Found  0  missing values.
2025-10-10 05:50:17.789519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:17.790419 INFO::Done
2025-10-10 05:50:17.791244 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:17.795571 INFO::Starting hierarchical adjustment
2025-10-10 05:50:17.796763 INFO::Found  5  batches.
2025-10-10 05:50:17.797557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:17.798483 INFO::Using default BPPARAM
2025-10-10 05:50:17.79933 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-10-10 05:50:17.981701 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:17.984372 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 05:50:18.009473 INFO::Done
2025-10-10 05:50:18.010501 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:18.015686 INFO::ASW Batch was 0.255657935399199 prior to batch effect correction and is now -0.0356192972918393 .
2025-10-10 05:50:18.016694 INFO::ASW Label was 0.448546845453264 prior to batch effect correction and is now 0.865106103477211 .
2025-10-10 05:50:18.01795 INFO::Total function execution time is  0.238853454589844  s and adjustment time is  0.212932348251343 s ( 89.15 )
2025-10-10 05:50:18.019272 INFO::Formatting Data.
2025-10-10 05:50:18.02021 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:18.021566 INFO::Removing potential empty rows and columns
2025-10-10 05:50:18.023198 INFO::Found  0  missing values.
2025-10-10 05:50:18.029773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:18.030833 INFO::Done
2025-10-10 05:50:18.0317 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:18.036101 INFO::Starting hierarchical adjustment
2025-10-10 05:50:18.037326 INFO::Found  5  batches.
2025-10-10 05:50:18.038151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:18.039151 INFO::Using default BPPARAM
2025-10-10 05:50:18.039971 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-10-10 05:50:18.187541 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:18.189812 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 05:50:18.215233 INFO::Done
2025-10-10 05:50:18.216182 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:18.220846 INFO::ASW Batch was 0.255657935399199 prior to batch effect correction and is now -0.0356192972918393 .
2025-10-10 05:50:18.22177 INFO::ASW Label was 0.448546845453264 prior to batch effect correction and is now 0.865106103477211 .
2025-10-10 05:50:18.22297 INFO::Total function execution time is  0.203666687011719  s and adjustment time is  0.178128480911255 s ( 87.46 )
2025-10-10 05:50:18.242862 INFO::Formatting Data.
2025-10-10 05:50:18.243935 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:18.245294 INFO::Removing potential empty rows and columns
2025-10-10 05:50:18.246848 INFO::Found  0  missing values.
2025-10-10 05:50:18.25115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:18.252061 INFO::Done
2025-10-10 05:50:18.252864 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:18.257171 INFO::Starting hierarchical adjustment
2025-10-10 05:50:18.258318 INFO::Found  2  batches.
2025-10-10 05:50:18.259175 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:18.260098 INFO::Using default BPPARAM
2025-10-10 05:50:18.260888 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:18.262254 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 05:50:18.283625 INFO::Done
2025-10-10 05:50:18.284512 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:18.288826 INFO::ASW Batch was 0.628069492957295 prior to batch effect correction and is now 0.0324383467980422 .
2025-10-10 05:50:18.289766 INFO::ASW Label was 0.439068642260527 prior to batch effect correction and is now 0.821157999735579 .
2025-10-10 05:50:18.290938 INFO::Total function execution time is  0.048201322555542  s and adjustment time is  0.0255169868469238 s ( 52.94 )
2025-10-10 05:50:18.292102 INFO::Formatting Data.
2025-10-10 05:50:18.293028 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:18.294256 INFO::Removing potential empty rows and columns
2025-10-10 05:50:18.29574 INFO::Found  0  missing values.
2025-10-10 05:50:18.29986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:18.300711 INFO::Done
2025-10-10 05:50:18.301564 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:18.305879 INFO::Starting hierarchical adjustment
2025-10-10 05:50:18.307029 INFO::Found  2  batches.
2025-10-10 05:50:18.307845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:18.308761 INFO::Using default BPPARAM
2025-10-10 05:50:18.30962 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:18.311008 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 05:50:18.333001 INFO::Done
2025-10-10 05:50:18.333956 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:18.338511 INFO::ASW Batch was 0.628069492957295 prior to batch effect correction and is now 0.0324383467980422 .
2025-10-10 05:50:18.339605 INFO::ASW Label was 0.439068642260527 prior to batch effect correction and is now 0.821157999735579 .
2025-10-10 05:50:18.340873 INFO::Total function execution time is  0.0487382411956787  s and adjustment time is  0.0261714458465576 s ( 53.7 )
2025-10-10 05:50:18.358305 INFO::Formatting Data.
2025-10-10 05:50:18.359444 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:18.360796 INFO::Removing potential empty rows and columns
2025-10-10 05:50:18.362229 INFO::Found  0  missing values.
2025-10-10 05:50:18.365765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:18.366712 INFO::Done
2025-10-10 05:50:18.367562 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:18.370331 INFO::Starting hierarchical adjustment
2025-10-10 05:50:18.37143 INFO::Found  2  batches.
2025-10-10 05:50:18.372229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:18.373172 INFO::Using default BPPARAM
2025-10-10 05:50:18.373957 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:18.375341 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 05:50:18.422559 INFO::Done
2025-10-10 05:50:18.42349 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:18.426158 INFO::ASW Batch was 0.0657651239122492 prior to batch effect correction and is now -0.140642076265885 .
2025-10-10 05:50:18.427362 INFO::Total function execution time is  0.0691256523132324  s and adjustment time is  0.0513436794281006 s ( 74.28 )
2025-10-10 05:50:18.444197 INFO::Formatting Data.
2025-10-10 05:50:18.445308 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:18.446524 INFO::Removing potential empty rows and columns
2025-10-10 05:50:18.44804 INFO::Found  0  missing values.
2025-10-10 05:50:18.44965 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-10 05:50:18.456453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:18.457336 INFO::Done
2025-10-10 05:50:18.458106 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:18.462251 INFO::Starting hierarchical adjustment
2025-10-10 05:50:18.463364 INFO::Found  2  batches.
2025-10-10 05:50:18.464153 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:18.46506 INFO::Using default BPPARAM
2025-10-10 05:50:18.465843 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:18.467265 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 05:50:18.491236 INFO::Done
2025-10-10 05:50:18.492155 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:18.496315 INFO::ASW Batch was 0.47876222163162 prior to batch effect correction and is now -0.0105672896831536 .
2025-10-10 05:50:18.49723 INFO::ASW Label was 0.588185077423349 prior to batch effect correction and is now 0.939396047884179 .
2025-10-10 05:50:18.498364 INFO::Total function execution time is  0.0542411804199219  s and adjustment time is  0.0280635356903076 s ( 51.74 )
2025-10-10 05:50:18.499516 INFO::Formatting Data.
2025-10-10 05:50:18.500429 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:18.501889 INFO::Removing potential empty rows and columns
2025-10-10 05:50:18.503402 INFO::Found  0  missing values.
2025-10-10 05:50:18.504701 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-10 05:50:18.511515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:18.512411 INFO::Done
2025-10-10 05:50:18.513224 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:18.51739 INFO::Starting hierarchical adjustment
2025-10-10 05:50:18.518421 INFO::Found  2  batches.
2025-10-10 05:50:18.51924 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:18.520117 INFO::Using default BPPARAM
2025-10-10 05:50:18.520932 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:18.522281 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 05:50:18.546052 INFO::Done
2025-10-10 05:50:18.54698 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:18.551032 INFO::ASW Batch was 0.47876222163162 prior to batch effect correction and is now -0.0105672896831536 .
2025-10-10 05:50:18.551871 INFO::ASW Label was 0.588185077423349 prior to batch effect correction and is now 0.939396047884179 .
2025-10-10 05:50:18.553059 INFO::Total function execution time is  0.0535421371459961  s and adjustment time is  0.0278337001800537 s ( 51.98 )
2025-10-10 05:50:18.860811 INFO::Formatting Data.
2025-10-10 05:50:18.861834 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:18.863082 INFO::Removing potential empty rows and columns
2025-10-10 05:50:18.864521 INFO::Found  0  missing values.
2025-10-10 05:50:18.868899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:18.869703 INFO::Done
2025-10-10 05:50:18.870442 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:18.873218 INFO::Starting hierarchical adjustment
2025-10-10 05:50:18.874243 INFO::Found  3  batches.
2025-10-10 05:50:18.875051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:18.875897 INFO::Using default BPPARAM
2025-10-10 05:50:18.876649 INFO::Processing subtree level 1
2025-10-10 05:50:18.984092 INFO::Adjusting the last 1 batches sequentially
2025-10-10 05:50:18.986549 INFO::Done
2025-10-10 05:50:18.987465 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:18.990927 INFO::ASW Batch was -0.0767511183632649 prior to batch effect correction and is now -0.0767511183632649 .
2025-10-10 05:50:18.992227 INFO::Total function execution time is  0.131449222564697  s and adjustment time is  0.112512588500977 s ( 85.59 )
2025-10-10 05:50:18.993725 INFO::Formatting Data.
2025-10-10 05:50:18.994681 INFO::Typecasting input to dataframe.
2025-10-10 05:50:18.995768 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:18.997107 INFO::Removing potential empty rows and columns
2025-10-10 05:50:18.99873 INFO::Found  0  missing values.
2025-10-10 05:50:19.003337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:19.004169 INFO::Done
2025-10-10 05:50:19.004974 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:19.007884 INFO::Starting hierarchical adjustment
2025-10-10 05:50:19.008969 INFO::Found  3  batches.
2025-10-10 05:50:19.009749 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:19.010703 INFO::Using default BPPARAM
2025-10-10 05:50:19.011522 INFO::Processing subtree level 1
2025-10-10 05:50:19.120963 INFO::Adjusting the last 1 batches sequentially
2025-10-10 05:50:19.123567 INFO::Done
2025-10-10 05:50:19.12445 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:19.127946 INFO::ASW Batch was -0.0767511183632649 prior to batch effect correction and is now -0.0767511183632649 .
2025-10-10 05:50:19.129346 INFO::Total function execution time is  0.135571956634521  s and adjustment time is  0.114828586578369 s ( 84.7 )
2025-10-10 05:50:19.148504 INFO::Formatting Data.
2025-10-10 05:50:19.149602 INFO::Typecasting input to dataframe.
2025-10-10 05:50:19.150873 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:19.152309 INFO::Removing potential empty rows and columns
2025-10-10 05:50:19.153904 INFO::Found  0  missing values.
2025-10-10 05:50:19.158506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:19.159466 INFO::Done
2025-10-10 05:50:19.160258 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:19.16311 INFO::Starting hierarchical adjustment
2025-10-10 05:50:19.164175 INFO::Found  3  batches.
2025-10-10 05:50:19.165006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:19.165887 INFO::Using default BPPARAM
2025-10-10 05:50:19.166706 INFO::Processing subtree level 1
2025-10-10 05:50:19.276075 INFO::Adjusting the last 1 batches sequentially
2025-10-10 05:50:19.278579 INFO::Done
2025-10-10 05:50:19.279543 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:19.283221 INFO::ASW Batch was -0.059948478791237 prior to batch effect correction and is now -0.059948478791237 .
2025-10-10 05:50:19.284658 INFO::Total function execution time is  0.136192560195923  s and adjustment time is  0.114599704742432 s ( 84.15 )
2025-10-10 05:50:19.476284 INFO::Formatting Data.
2025-10-10 05:50:19.477401 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:19.478933 INFO::Removing potential empty rows and columns
2025-10-10 05:50:19.483208 INFO::Found  1000  missing values.
2025-10-10 05:50:19.511056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:19.512026 INFO::Done
2025-10-10 05:50:19.512835 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:19.520538 INFO::Starting hierarchical adjustment
2025-10-10 05:50:19.521767 INFO::Found  10  batches.
2025-10-10 05:50:19.52258 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:19.523585 INFO::Using default BPPARAM
2025-10-10 05:50:19.52439 INFO::Processing subtree level 1
2025-10-10 05:50:19.69218 INFO::Processing subtree level 2
2025-10-10 05:50:19.877426 INFO::Adjusting the last 1 batches sequentially
2025-10-10 05:50:19.880195 INFO::Done
2025-10-10 05:50:19.881087 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:19.888866 INFO::ASW Batch was 0.472436533326295 prior to batch effect correction and is now 0.472436533326295 .
2025-10-10 05:50:19.88983 INFO::ASW Label was 0.343519112263947 prior to batch effect correction and is now 0.343519112263947 .
2025-10-10 05:50:19.891213 INFO::Total function execution time is  0.414958000183105  s and adjustment time is  0.358668088912964 s ( 86.43 )
2025-10-10 05:50:19.892372 INFO::Formatting Data.
2025-10-10 05:50:19.89329 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:19.895023 INFO::Removing potential empty rows and columns
2025-10-10 05:50:19.899055 INFO::Found  1000  missing values.
2025-10-10 05:50:19.929652 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:19.930737 INFO::Done
2025-10-10 05:50:19.931552 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:19.939574 INFO::Starting hierarchical adjustment
2025-10-10 05:50:19.94086 INFO::Found  10  batches.
2025-10-10 05:50:20.992238 INFO::Set up parallel execution backend with 2 workers
2025-10-10 05:50:20.994327 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-10 05:50:22.266793 INFO::Adjusting the last 2 batches sequentially
2025-10-10 05:50:22.269292 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 05:50:22.294646 INFO::Done
2025-10-10 05:50:22.295546 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:22.302211 INFO::ASW Batch was 0.472436533326295 prior to batch effect correction and is now 0.472436533326295 .
2025-10-10 05:50:22.303121 INFO::ASW Label was 0.343519112263947 prior to batch effect correction and is now 0.343519112263947 .
2025-10-10 05:50:22.30415 INFO::Total function execution time is  2.41179823875427  s and adjustment time is  2.3540723323822 s ( 97.61 )
2025-10-10 05:50:22.489803 INFO::Formatting Data.
2025-10-10 05:50:22.490995 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:22.492402 INFO::Removing potential empty rows and columns
2025-10-10 05:50:22.494079 INFO::Found  0  missing values.
2025-10-10 05:50:22.500023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:22.500947 INFO::Done
2025-10-10 05:50:22.501781 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 05:50:22.505911 INFO::Starting hierarchical adjustment
2025-10-10 05:50:22.50708 INFO::Found  3  batches.
2025-10-10 05:50:22.507888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 05:50:22.508848 INFO::Using default BPPARAM
2025-10-10 05:50:22.509695 INFO::Processing subtree level 1
2025-10-10 05:50:22.639717 INFO::Adjusting the last 1 batches sequentially
2025-10-10 05:50:22.642266 INFO::Done
2025-10-10 05:50:22.643377 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 05:50:22.648696 INFO::ASW Batch was 0.297417856213757 prior to batch effect correction and is now -0.150575451113762 .
2025-10-10 05:50:22.649887 INFO::ASW Label was -0.228634617809956 prior to batch effect correction and is now -0.174062875840266 .
2025-10-10 05:50:22.651506 INFO::Total function execution time is  0.161677837371826  s and adjustment time is  0.135372638702393 s ( 83.73 )
2025-10-10 05:50:22.822858 INFO::Formatting Data.
2025-10-10 05:50:22.823874 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:22.825105 INFO::Removing potential empty rows and columns
2025-10-10 05:50:22.826563 INFO::Found  2  missing values.
2025-10-10 05:50:22.830932 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:22.831782 INFO::Done
2025-10-10 05:50:22.872792 INFO::Found NA in Reference column
2025-10-10 05:50:22.887157 INFO::Require at least two references per batch.
2025-10-10 05:50:22.918003 INFO::Formatting Data.
2025-10-10 05:50:22.919007 INFO::Recognized SummarizedExperiment
2025-10-10 05:50:22.919733 INFO::Typecasting input to dataframe.
2025-10-10 05:50:22.93378 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:22.935344 INFO::Removing potential empty rows and columns
2025-10-10 05:50:22.940541 INFO::Found  0  missing values.
2025-10-10 05:50:22.959589 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:22.960536 INFO::Done
2025-10-10 05:50:22.987798 INFO::Formatting Data.
2025-10-10 05:50:22.988772 INFO::Recognized SummarizedExperiment
2025-10-10 05:50:22.989575 INFO::Typecasting input to dataframe.
2025-10-10 05:50:23.016704 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:23.018356 INFO::Removing potential empty rows and columns
2025-10-10 05:50:23.023922 INFO::Found  0  missing values.
2025-10-10 05:50:23.041708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:23.042734 INFO::Done
2025-10-10 05:50:23.066001 INFO::Formatting Data.
2025-10-10 05:50:23.067022 INFO::Recognized SummarizedExperiment
2025-10-10 05:50:23.067788 INFO::Typecasting input to dataframe.
2025-10-10 05:50:23.09301 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:23.094388 INFO::Removing potential empty rows and columns
2025-10-10 05:50:23.096011 INFO::Found  0  missing values.
2025-10-10 05:50:23.097318 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-10 05:50:23.10394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:23.104831 INFO::Done
2025-10-10 05:50:23.119471 INFO::Formatting Data.
2025-10-10 05:50:23.120536 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:23.121848 INFO::Removing potential empty rows and columns
2025-10-10 05:50:23.12336 INFO::Found  0  missing values.
2025-10-10 05:50:23.128025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:23.129053 INFO::Done
2025-10-10 05:50:23.14589 INFO::Formatting Data.
2025-10-10 05:50:23.146981 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:23.148247 INFO::Removing potential empty rows and columns
2025-10-10 05:50:23.14984 INFO::Found  0  missing values.
2025-10-10 05:50:23.154523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:23.155496 INFO::Done
2025-10-10 05:50:23.200273 INFO::Formatting Data.
2025-10-10 05:50:23.201362 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:23.20284 INFO::Removing potential empty rows and columns
2025-10-10 05:50:23.204501 INFO::Found  1  missing values.
2025-10-10 05:50:23.208377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:23.209242 INFO::Done
2025-10-10 05:50:23.237855 INFO::Formatting Data.
2025-10-10 05:50:23.238887 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:23.240083 INFO::Removing potential empty rows and columns
2025-10-10 05:50:23.241461 INFO::Found  2  missing values.
2025-10-10 05:50:23.242787 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-10 05:50:23.246049 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:23.246924 INFO::Done
2025-10-10 05:50:23.261478 INFO::Formatting Data.
2025-10-10 05:50:23.262495 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:23.263755 INFO::Removing potential empty rows and columns
2025-10-10 05:50:23.265179 INFO::Found  2  missing values.
2025-10-10 05:50:23.267475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:23.268266 INFO::Done
2025-10-10 05:50:23.284058 INFO::Formatting Data.
2025-10-10 05:50:23.285174 INFO::Typecasting input to dataframe.
2025-10-10 05:50:23.286376 INFO::Replacing NaNs with NAs.
2025-10-10 05:50:23.287633 INFO::Removing potential empty rows and columns
2025-10-10 05:50:23.289172 INFO::Found  0  missing values.
2025-10-10 05:50:23.293672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 05:50:23.294565 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 21.047   4.593  25.205 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT28.494 2.14521.048
compute_asw0.0360.0000.036
count_existing0.0170.0000.018
generate_data_covariables0.0120.0030.015
generate_dataset0.0110.0040.015