Yannis Schumann
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:05 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 162/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-08-03 20:22:41 -0400 (Sun, 03 Aug 2025) |
| EndedAt: 2025-08-03 20:24:09 -0400 (Sun, 03 Aug 2025) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.531 1.258 17.579
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-08-03 20:23:32.278701 INFO::Formatting Data.
2025-08-03 20:23:32.280042 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:32.290769 INFO::Removing potential empty rows and columns
2025-08-03 20:23:32.526268 INFO::Found 0 missing values.
2025-08-03 20:23:32.529504 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:32.530111 INFO::Done
2025-08-03 20:23:32.530624 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:32.541616 INFO::Starting hierarchical adjustment
2025-08-03 20:23:32.542456 INFO::Found 3 batches.
2025-08-03 20:23:32.543006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:32.544152 INFO::Using default BPPARAM
2025-08-03 20:23:32.544698 INFO::Processing subtree level 1
2025-08-03 20:23:32.639749 INFO::Adjusting the last 1 batches sequentially
2025-08-03 20:23:32.641461 INFO::Done
2025-08-03 20:23:32.642101 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:32.644611 INFO::ASW Batch was -0.0953750164327233 prior to batch effect correction and is now -0.0953750164327233 .
2025-08-03 20:23:32.645705 INFO::Total function execution time is 0.36765193939209 s and adjustment time is 0.0991744995117188 s ( 26.98 )
2025-08-03 20:23:32.658642 INFO::Formatting Data.
2025-08-03 20:23:32.659381 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:32.660248 INFO::Removing potential empty rows and columns
2025-08-03 20:23:32.661295 INFO::Found 0 missing values.
2025-08-03 20:23:32.66221 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.
2025-08-03 20:23:32.672734 INFO::Formatting Data.
2025-08-03 20:23:32.673504 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:32.674392 INFO::Removing potential empty rows and columns
2025-08-03 20:23:32.675449 INFO::Found 0 missing values.
2025-08-03 20:23:32.676384 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.
2025-08-03 20:23:32.692085 INFO::Formatting Data.
2025-08-03 20:23:32.692945 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:32.693841 INFO::Removing potential empty rows and columns
2025-08-03 20:23:32.694884 INFO::Found 0 missing values.
2025-08-03 20:23:32.69581 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.
2025-08-03 20:23:32.700244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:32.700785 INFO::Done
2025-08-03 20:23:32.701304 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:32.703371 INFO::Starting hierarchical adjustment
2025-08-03 20:23:32.704078 INFO::Found 2 batches.
2025-08-03 20:23:32.704611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:32.705247 INFO::Using default BPPARAM
2025-08-03 20:23:32.705771 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:32.706722 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-03 20:23:32.728751 INFO::Done
2025-08-03 20:23:32.72946 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:32.731485 INFO::ASW Batch was -0.018400325004243 prior to batch effect correction and is now -0.112988056295399 .
2025-08-03 20:23:32.732301 INFO::Total function execution time is 0.0402908325195312 s and adjustment time is 0.0248129367828369 s ( 61.58 )
2025-08-03 20:23:32.735033 INFO::Formatting Data.
2025-08-03 20:23:32.735673 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:32.744244 INFO::Formatting Data.
2025-08-03 20:23:32.74494 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:32.745813 INFO::Removing potential empty rows and columns
2025-08-03 20:23:32.746841 INFO::Found 0 missing values.
2025-08-03 20:23:32.749652 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:32.750185 INFO::Done
2025-08-03 20:23:32.750703 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:32.7528 INFO::Starting hierarchical adjustment
2025-08-03 20:23:32.753504 INFO::Found 2 batches.
2025-08-03 20:23:32.754072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:32.7547 INFO::Using default BPPARAM
2025-08-03 20:23:32.755259 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:32.75619 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-03 20:23:32.794215 INFO::Done
2025-08-03 20:23:32.794877 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:32.796745 INFO::ASW Batch was 0.092851915916034 prior to batch effect correction and is now -0.12961494817329 .
2025-08-03 20:23:32.797495 INFO::Total function execution time is 0.0532960891723633 s and adjustment time is 0.0408122539520264 s ( 76.58 )
2025-08-03 20:23:32.798466 INFO::Formatting Data.
2025-08-03 20:23:32.79902 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:32.799819 INFO::Removing potential empty rows and columns
2025-08-03 20:23:32.800765 INFO::Found 0 missing values.
2025-08-03 20:23:32.803278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:32.803762 INFO::Done
2025-08-03 20:23:32.804242 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:32.806052 INFO::Starting hierarchical adjustment
2025-08-03 20:23:32.806705 INFO::Found 2 batches.
2025-08-03 20:23:32.807212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:32.807762 INFO::Using default BPPARAM
2025-08-03 20:23:32.808248 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:32.809051 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-03 20:23:32.822672 INFO::Done
2025-08-03 20:23:32.823343 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:32.825287 INFO::ASW Batch was 0.092851915916034 prior to batch effect correction and is now -0.12961494817329 .
2025-08-03 20:23:32.826025 INFO::Total function execution time is 0.0275514125823975 s and adjustment time is 0.0160865783691406 s ( 58.39 )
2025-08-03 20:23:35.851698 INFO::Formatting Data.
2025-08-03 20:23:35.852518 INFO::Recognized SummarizedExperiment
2025-08-03 20:23:35.852998 INFO::Typecasting input to dataframe.
2025-08-03 20:23:35.885938 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:35.887602 INFO::Removing potential empty rows and columns
2025-08-03 20:23:35.891538 INFO::Found 0 missing values.
2025-08-03 20:23:35.898925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:35.8996 INFO::Done
2025-08-03 20:23:35.900145 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:35.903821 INFO::Starting hierarchical adjustment
2025-08-03 20:23:35.904551 INFO::Found 2 batches.
2025-08-03 20:23:35.905064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:35.906184 INFO::Using default BPPARAM
2025-08-03 20:23:35.906716 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:35.907709 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-03 20:23:35.963341 INFO::Done
2025-08-03 20:23:35.964046 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:35.967602 INFO::ASW Batch was 0.0140489025239882 prior to batch effect correction and is now -0.0893296689570977 .
2025-08-03 20:23:35.968447 INFO::Total function execution time is 0.117053985595703 s and adjustment time is 0.0589072704315186 s ( 50.32 )
2025-08-03 20:23:35.987022 INFO::Formatting Data.
2025-08-03 20:23:35.987789 INFO::Recognized SummarizedExperiment
2025-08-03 20:23:35.988352 INFO::Typecasting input to dataframe.
2025-08-03 20:23:35.997672 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:35.998824 INFO::Removing potential empty rows and columns
2025-08-03 20:23:36.010502 INFO::Found 0 missing values.
2025-08-03 20:23:36.018634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:36.019377 INFO::Done
2025-08-03 20:23:36.020143 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:36.024231 INFO::Starting hierarchical adjustment
2025-08-03 20:23:36.025 INFO::Found 2 batches.
2025-08-03 20:23:36.025539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:36.026189 INFO::Using default BPPARAM
2025-08-03 20:23:36.026699 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:36.027678 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-03 20:23:36.054471 INFO::Done
2025-08-03 20:23:36.055233 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:36.058919 INFO::ASW Batch was -0.00868093920684156 prior to batch effect correction and is now -0.00868093920684156 .
2025-08-03 20:23:36.059941 INFO::Total function execution time is 0.072892427444458 s and adjustment time is 0.0296006202697754 s ( 40.61 )
2025-08-03 20:23:36.081498 INFO::Formatting Data.
2025-08-03 20:23:36.082316 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:36.083252 INFO::Removing potential empty rows and columns
2025-08-03 20:23:36.084315 INFO::Found 0 missing values.
2025-08-03 20:23:36.087297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:36.087843 INFO::Done
2025-08-03 20:23:36.08837 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:36.090403 INFO::Starting hierarchical adjustment
2025-08-03 20:23:36.091105 INFO::Found 3 batches.
2025-08-03 20:23:36.091611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:36.092207 INFO::Using default BPPARAM
2025-08-03 20:23:36.092711 INFO::Processing subtree level 1
2025-08-03 20:23:36.223456 INFO::Adjusting the last 1 batches sequentially
2025-08-03 20:23:36.225289 INFO::Done
2025-08-03 20:23:36.225936 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:36.22856 INFO::ASW Batch was 0.00424219325858821 prior to batch effect correction and is now -0.141208369337916 .
2025-08-03 20:23:36.229479 INFO::Total function execution time is 0.148041486740112 s and adjustment time is 0.134329319000244 s ( 90.74 )
2025-08-03 20:23:36.243305 INFO::Skipping initial DF formatting
2025-08-03 20:23:36.243994 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:36.247931 INFO::Starting hierarchical adjustment
2025-08-03 20:23:36.248707 INFO::Found 5 batches.
2025-08-03 20:23:36.249282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:36.249902 INFO::Using default BPPARAM
2025-08-03 20:23:36.250668 INFO::Processing subtree level 1
2025-08-03 20:23:36.472958 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:36.474591 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-03 20:23:36.494 INFO::Done
2025-08-03 20:23:36.494712 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:36.498804 INFO::ASW Batch was 0.518401371147371 prior to batch effect correction and is now 0.518401371147371 .
2025-08-03 20:23:36.499403 INFO::ASW Label was 0.391813373126711 prior to batch effect correction and is now 0.391813373126711 .
2025-08-03 20:23:36.500239 INFO::Total function execution time is 0.257003307342529 s and adjustment time is 0.245442628860474 s ( 95.5 )
2025-08-03 20:23:36.568995 INFO::Formatting Data.
2025-08-03 20:23:36.569757 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:36.570616 INFO::Removing potential empty rows and columns
2025-08-03 20:23:36.571588 INFO::Found 0 missing values.
2025-08-03 20:23:36.575345 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:36.57583 INFO::Done
2025-08-03 20:23:36.576326 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:36.579111 INFO::Starting hierarchical adjustment
2025-08-03 20:23:36.579788 INFO::Found 5 batches.
2025-08-03 20:23:36.580314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:36.580887 INFO::Using default BPPARAM
2025-08-03 20:23:36.581402 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.
2025-08-03 20:23:36.707535 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:36.709173 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-03 20:23:36.726055 INFO::Done
2025-08-03 20:23:36.726731 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:36.730149 INFO::ASW Batch was 0.583316095491505 prior to batch effect correction and is now -0.106650370812662 .
2025-08-03 20:23:36.730733 INFO::ASW Label was 0.16542473697413 prior to batch effect correction and is now 0.807107171497477 .
2025-08-03 20:23:36.731582 INFO::Total function execution time is 0.162631988525391 s and adjustment time is 0.146395206451416 s ( 90.02 )
2025-08-03 20:23:36.732441 INFO::Formatting Data.
2025-08-03 20:23:36.733077 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:36.734003 INFO::Removing potential empty rows and columns
2025-08-03 20:23:36.73511 INFO::Found 0 missing values.
2025-08-03 20:23:36.739458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:36.740022 INFO::Done
2025-08-03 20:23:36.740606 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:36.743633 INFO::Starting hierarchical adjustment
2025-08-03 20:23:36.744331 INFO::Found 5 batches.
2025-08-03 20:23:36.744847 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:36.745484 INFO::Using default BPPARAM
2025-08-03 20:23:36.745995 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.
2025-08-03 20:23:36.863663 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:36.865374 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-03 20:23:36.880973 INFO::Done
2025-08-03 20:23:36.881687 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:36.884913 INFO::ASW Batch was 0.583316095491505 prior to batch effect correction and is now -0.106650370812662 .
2025-08-03 20:23:36.885506 INFO::ASW Label was 0.16542473697413 prior to batch effect correction and is now 0.807107171497477 .
2025-08-03 20:23:36.886282 INFO::Total function execution time is 0.15383243560791 s and adjustment time is 0.136765241622925 s ( 88.91 )
2025-08-03 20:23:36.899199 INFO::Formatting Data.
2025-08-03 20:23:36.899897 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:36.900784 INFO::Removing potential empty rows and columns
2025-08-03 20:23:36.901767 INFO::Found 0 missing values.
2025-08-03 20:23:36.905684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:36.906202 INFO::Done
2025-08-03 20:23:36.906711 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:36.909756 INFO::Starting hierarchical adjustment
2025-08-03 20:23:36.910499 INFO::Found 5 batches.
2025-08-03 20:23:36.911027 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:36.91164 INFO::Using default BPPARAM
2025-08-03 20:23:36.912166 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.
2025-08-03 20:23:37.030994 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:37.032832 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-03 20:23:37.048484 INFO::Done
2025-08-03 20:23:37.049161 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.05233 INFO::ASW Batch was 0.396559282585036 prior to batch effect correction and is now -0.0853276800054 .
2025-08-03 20:23:37.052903 INFO::ASW Label was 0.332109971446999 prior to batch effect correction and is now 0.831247705444398 .
2025-08-03 20:23:37.053711 INFO::Total function execution time is 0.154572725296021 s and adjustment time is 0.1381516456604 s ( 89.38 )
2025-08-03 20:23:37.054525 INFO::Formatting Data.
2025-08-03 20:23:37.05513 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.055979 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.056942 INFO::Found 0 missing values.
2025-08-03 20:23:37.060778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.061328 INFO::Done
2025-08-03 20:23:37.061809 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.064641 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.065358 INFO::Found 5 batches.
2025-08-03 20:23:37.065878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.06647 INFO::Using default BPPARAM
2025-08-03 20:23:37.066974 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.
2025-08-03 20:23:37.188791 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:37.190371 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-03 20:23:37.207479 INFO::Done
2025-08-03 20:23:37.208237 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.211752 INFO::ASW Batch was 0.396559282585036 prior to batch effect correction and is now -0.0853276800054 .
2025-08-03 20:23:37.212386 INFO::ASW Label was 0.332109971446999 prior to batch effect correction and is now 0.831247705444398 .
2025-08-03 20:23:37.213401 INFO::Total function execution time is 0.158850431442261 s and adjustment time is 0.142236709594727 s ( 89.54 )
2025-08-03 20:23:37.227501 INFO::Formatting Data.
2025-08-03 20:23:37.22825 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.229172 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.230218 INFO::Found 0 missing values.
2025-08-03 20:23:37.23283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.233365 INFO::Done
2025-08-03 20:23:37.233855 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.236662 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.237338 INFO::Found 2 batches.
2025-08-03 20:23:37.237844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.23845 INFO::Using default BPPARAM
2025-08-03 20:23:37.238948 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:37.239801 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-03 20:23:37.25368 INFO::Done
2025-08-03 20:23:37.254262 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.256977 INFO::ASW Batch was 0.675862129052765 prior to batch effect correction and is now 0.051384474980838 .
2025-08-03 20:23:37.257543 INFO::ASW Label was 0.411720062534286 prior to batch effect correction and is now 0.853133557605194 .
2025-08-03 20:23:37.258266 INFO::Total function execution time is 0.0308318138122559 s and adjustment time is 0.0164825916290283 s ( 53.46 )
2025-08-03 20:23:37.258989 INFO::Formatting Data.
2025-08-03 20:23:37.259583 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.260377 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.261292 INFO::Found 0 missing values.
2025-08-03 20:23:37.263746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.264263 INFO::Done
2025-08-03 20:23:37.264739 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.267416 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.268069 INFO::Found 2 batches.
2025-08-03 20:23:37.268572 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.269141 INFO::Using default BPPARAM
2025-08-03 20:23:37.269635 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:37.270467 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-03 20:23:37.284197 INFO::Done
2025-08-03 20:23:37.284804 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.287571 INFO::ASW Batch was 0.675862129052765 prior to batch effect correction and is now 0.051384474980838 .
2025-08-03 20:23:37.288134 INFO::ASW Label was 0.411720062534286 prior to batch effect correction and is now 0.853133557605194 .
2025-08-03 20:23:37.288863 INFO::Total function execution time is 0.029879093170166 s and adjustment time is 0.0162515640258789 s ( 54.39 )
2025-08-03 20:23:37.299136 INFO::Formatting Data.
2025-08-03 20:23:37.299868 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.300704 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.301569 INFO::Found 0 missing values.
2025-08-03 20:23:37.303521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.304027 INFO::Done
2025-08-03 20:23:37.304534 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.306294 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.306944 INFO::Found 2 batches.
2025-08-03 20:23:37.307469 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.308034 INFO::Using default BPPARAM
2025-08-03 20:23:37.308546 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:37.309393 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-03 20:23:37.345639 INFO::Done
2025-08-03 20:23:37.346431 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.348589 INFO::ASW Batch was -0.0535898173386098 prior to batch effect correction and is now -0.18910243235062 .
2025-08-03 20:23:37.349415 INFO::Total function execution time is 0.0503585338592529 s and adjustment time is 0.0387682914733887 s ( 76.98 )
2025-08-03 20:23:37.36089 INFO::Formatting Data.
2025-08-03 20:23:37.361613 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.362503 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.363534 INFO::Found 0 missing values.
2025-08-03 20:23:37.364657 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.
2025-08-03 20:23:37.36906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.369606 INFO::Done
2025-08-03 20:23:37.370104 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.372937 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.373608 INFO::Found 2 batches.
2025-08-03 20:23:37.374133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.374743 INFO::Using default BPPARAM
2025-08-03 20:23:37.375264 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:37.376178 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-03 20:23:37.392494 INFO::Done
2025-08-03 20:23:37.393172 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.395996 INFO::ASW Batch was 0.527237460263528 prior to batch effect correction and is now -0.0343732370813433 .
2025-08-03 20:23:37.396576 INFO::ASW Label was 0.544673061286318 prior to batch effect correction and is now 0.920498616342617 .
2025-08-03 20:23:37.397327 INFO::Total function execution time is 0.0365126132965088 s and adjustment time is 0.0189967155456543 s ( 52.03 )
2025-08-03 20:23:37.398079 INFO::Formatting Data.
2025-08-03 20:23:37.398685 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.39955 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.400487 INFO::Found 0 missing values.
2025-08-03 20:23:37.401354 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.
2025-08-03 20:23:37.405506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.406011 INFO::Done
2025-08-03 20:23:37.406492 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.409172 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.409814 INFO::Found 2 batches.
2025-08-03 20:23:37.41032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.410888 INFO::Using default BPPARAM
2025-08-03 20:23:37.411382 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:37.412237 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-03 20:23:37.427394 INFO::Done
2025-08-03 20:23:37.428029 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.430746 INFO::ASW Batch was 0.527237460263528 prior to batch effect correction and is now -0.0343732370813433 .
2025-08-03 20:23:37.431322 INFO::ASW Label was 0.544673061286318 prior to batch effect correction and is now 0.920498616342617 .
2025-08-03 20:23:37.432076 INFO::Total function execution time is 0.0340020656585693 s and adjustment time is 0.0176928043365479 s ( 52.03 )
2025-08-03 20:23:37.625825 INFO::Formatting Data.
2025-08-03 20:23:37.62671 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.627615 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.628839 INFO::Found 0 missing values.
2025-08-03 20:23:37.631783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.632331 INFO::Done
2025-08-03 20:23:37.632836 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.634803 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.635491 INFO::Found 3 batches.
2025-08-03 20:23:37.635994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.636591 INFO::Using default BPPARAM
2025-08-03 20:23:37.637101 INFO::Processing subtree level 1
2025-08-03 20:23:37.718453 INFO::Adjusting the last 1 batches sequentially
2025-08-03 20:23:37.720224 INFO::Done
2025-08-03 20:23:37.720872 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.72333 INFO::ASW Batch was 0.0498949027038349 prior to batch effect correction and is now 0.0498949027038349 .
2025-08-03 20:23:37.724289 INFO::Total function execution time is 0.0984725952148438 s and adjustment time is 0.0848522186279297 s ( 86.17 )
2025-08-03 20:23:37.725528 INFO::Formatting Data.
2025-08-03 20:23:37.726194 INFO::Typecasting input to dataframe.
2025-08-03 20:23:37.726945 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.727866 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.728989 INFO::Found 0 missing values.
2025-08-03 20:23:37.73207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.732635 INFO::Done
2025-08-03 20:23:37.733177 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.735201 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.735896 INFO::Found 3 batches.
2025-08-03 20:23:37.736433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.737025 INFO::Using default BPPARAM
2025-08-03 20:23:37.737562 INFO::Processing subtree level 1
2025-08-03 20:23:37.817742 INFO::Adjusting the last 1 batches sequentially
2025-08-03 20:23:37.819487 INFO::Done
2025-08-03 20:23:37.820114 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.822781 INFO::ASW Batch was 0.0498949027038349 prior to batch effect correction and is now 0.0498949027038349 .
2025-08-03 20:23:37.823709 INFO::Total function execution time is 0.0981755256652832 s and adjustment time is 0.0837235450744629 s ( 85.28 )
2025-08-03 20:23:37.8362 INFO::Formatting Data.
2025-08-03 20:23:37.836982 INFO::Typecasting input to dataframe.
2025-08-03 20:23:37.837821 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:37.838735 INFO::Removing potential empty rows and columns
2025-08-03 20:23:37.839851 INFO::Found 0 missing values.
2025-08-03 20:23:37.842771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:37.843313 INFO::Done
2025-08-03 20:23:37.843818 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:37.845777 INFO::Starting hierarchical adjustment
2025-08-03 20:23:37.846483 INFO::Found 3 batches.
2025-08-03 20:23:37.846989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:37.847606 INFO::Using default BPPARAM
2025-08-03 20:23:37.848132 INFO::Processing subtree level 1
2025-08-03 20:23:37.928558 INFO::Adjusting the last 1 batches sequentially
2025-08-03 20:23:37.930312 INFO::Done
2025-08-03 20:23:37.93093 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:37.933367 INFO::ASW Batch was -0.0716907881135729 prior to batch effect correction and is now -0.0716907881135729 .
2025-08-03 20:23:37.934274 INFO::Total function execution time is 0.0981245040893555 s and adjustment time is 0.0839512348175049 s ( 85.56 )
2025-08-03 20:23:38.062499 INFO::Formatting Data.
2025-08-03 20:23:38.063272 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:38.06435 INFO::Removing potential empty rows and columns
2025-08-03 20:23:38.067045 INFO::Found 1000 missing values.
2025-08-03 20:23:38.08559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:38.086334 INFO::Done
2025-08-03 20:23:38.086882 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:38.092272 INFO::Starting hierarchical adjustment
2025-08-03 20:23:38.093022 INFO::Found 10 batches.
2025-08-03 20:23:38.093566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:38.094181 INFO::Using default BPPARAM
2025-08-03 20:23:38.094711 INFO::Processing subtree level 1
2025-08-03 20:23:38.216786 INFO::Processing subtree level 2
2025-08-03 20:23:38.348931 INFO::Adjusting the last 1 batches sequentially
2025-08-03 20:23:38.350893 INFO::Done
2025-08-03 20:23:38.351607 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:38.357434 INFO::ASW Batch was 0.528130602871737 prior to batch effect correction and is now 0.528130602871737 .
2025-08-03 20:23:38.358173 INFO::ASW Label was 0.309174680489753 prior to batch effect correction and is now 0.309174680489753 .
2025-08-03 20:23:38.359117 INFO::Total function execution time is 0.29664421081543 s and adjustment time is 0.258014440536499 s ( 86.98 )
2025-08-03 20:23:38.359984 INFO::Formatting Data.
2025-08-03 20:23:38.360674 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:38.361919 INFO::Removing potential empty rows and columns
2025-08-03 20:23:38.364848 INFO::Found 1000 missing values.
2025-08-03 20:23:38.384645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:38.393419 INFO::Done
2025-08-03 20:23:38.394192 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:38.399927 INFO::Starting hierarchical adjustment
2025-08-03 20:23:38.400757 INFO::Found 10 batches.
2025-08-03 20:23:39.370096 INFO::Set up parallel execution backend with 2 workers
2025-08-03 20:23:39.37204 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-03 20:23:40.436931 INFO::Adjusting the last 2 batches sequentially
2025-08-03 20:23:40.43859 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-03 20:23:40.453859 INFO::Done
2025-08-03 20:23:40.454492 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:40.458735 INFO::ASW Batch was 0.528130602871737 prior to batch effect correction and is now 0.528130602871737 .
2025-08-03 20:23:40.459288 INFO::ASW Label was 0.309174680489753 prior to batch effect correction and is now 0.309174680489753 .
2025-08-03 20:23:40.459958 INFO::Total function execution time is 2.10002112388611 s and adjustment time is 2.05326795578003 s ( 97.77 )
2025-08-03 20:23:40.603947 INFO::Formatting Data.
2025-08-03 20:23:40.604907 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:40.606673 INFO::Removing potential empty rows and columns
2025-08-03 20:23:40.607928 INFO::Found 0 missing values.
2025-08-03 20:23:40.611712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:40.612291 INFO::Done
2025-08-03 20:23:40.612807 INFO::Acquiring quality metrics before batch effect correction.
2025-08-03 20:23:40.615788 INFO::Starting hierarchical adjustment
2025-08-03 20:23:40.616524 INFO::Found 3 batches.
2025-08-03 20:23:40.617045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-03 20:23:40.617672 INFO::Using default BPPARAM
2025-08-03 20:23:40.618209 INFO::Processing subtree level 1
2025-08-03 20:23:40.726348 INFO::Adjusting the last 1 batches sequentially
2025-08-03 20:23:40.728312 INFO::Done
2025-08-03 20:23:40.729007 INFO::Acquiring quality metrics after batch effect correction.
2025-08-03 20:23:40.732523 INFO::ASW Batch was 0.138608103638064 prior to batch effect correction and is now -0.144162414666796 .
2025-08-03 20:23:40.733182 INFO::ASW Label was -0.188531154406823 prior to batch effect correction and is now -0.054485547686057 .
2025-08-03 20:23:40.734139 INFO::Total function execution time is 0.130311965942383 s and adjustment time is 0.111899614334106 s ( 85.87 )
2025-08-03 20:23:40.851948 INFO::Formatting Data.
2025-08-03 20:23:40.852845 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:40.853719 INFO::Removing potential empty rows and columns
2025-08-03 20:23:40.854717 INFO::Found 2 missing values.
2025-08-03 20:23:40.857427 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:40.857928 INFO::Done
2025-08-03 20:23:40.882825 INFO::Found NA in Reference column
2025-08-03 20:23:40.891446 INFO::Require at least two references per batch.
2025-08-03 20:23:40.910467 INFO::Formatting Data.
2025-08-03 20:23:40.911216 INFO::Recognized SummarizedExperiment
2025-08-03 20:23:40.911732 INFO::Typecasting input to dataframe.
2025-08-03 20:23:40.920814 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:40.921928 INFO::Removing potential empty rows and columns
2025-08-03 20:23:40.930961 INFO::Found 0 missing values.
2025-08-03 20:23:40.93777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:40.938457 INFO::Done
2025-08-03 20:23:40.95396 INFO::Formatting Data.
2025-08-03 20:23:40.954658 INFO::Recognized SummarizedExperiment
2025-08-03 20:23:40.955148 INFO::Typecasting input to dataframe.
2025-08-03 20:23:40.971424 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:40.972597 INFO::Removing potential empty rows and columns
2025-08-03 20:23:40.975902 INFO::Found 0 missing values.
2025-08-03 20:23:40.985802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:40.98644 INFO::Done
2025-08-03 20:23:41.001048 INFO::Formatting Data.
2025-08-03 20:23:41.001761 INFO::Recognized SummarizedExperiment
2025-08-03 20:23:41.002266 INFO::Typecasting input to dataframe.
2025-08-03 20:23:41.017879 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:41.01891 INFO::Removing potential empty rows and columns
2025-08-03 20:23:41.019944 INFO::Found 0 missing values.
2025-08-03 20:23:41.020828 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.
2025-08-03 20:23:41.025044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:41.025572 INFO::Done
2025-08-03 20:23:41.035006 INFO::Formatting Data.
2025-08-03 20:23:41.035784 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:41.036591 INFO::Removing potential empty rows and columns
2025-08-03 20:23:41.037507 INFO::Found 0 missing values.
2025-08-03 20:23:41.040195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:41.040686 INFO::Done
2025-08-03 20:23:41.0512 INFO::Formatting Data.
2025-08-03 20:23:41.051922 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:41.052722 INFO::Removing potential empty rows and columns
2025-08-03 20:23:41.053664 INFO::Found 0 missing values.
2025-08-03 20:23:41.05639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:41.056891 INFO::Done
2025-08-03 20:23:41.087012 INFO::Formatting Data.
2025-08-03 20:23:41.087955 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:41.089054 INFO::Removing potential empty rows and columns
2025-08-03 20:23:41.090298 INFO::Found 1 missing values.
2025-08-03 20:23:41.093016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:41.093592 INFO::Done
2025-08-03 20:23:41.114048 INFO::Formatting Data.
2025-08-03 20:23:41.114933 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:41.115852 INFO::Removing potential empty rows and columns
2025-08-03 20:23:41.116807 INFO::Found 2 missing values.
2025-08-03 20:23:41.117728 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.
2025-08-03 20:23:41.120021 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:41.120597 INFO::Done
2025-08-03 20:23:41.130697 INFO::Formatting Data.
2025-08-03 20:23:41.131603 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:41.132492 INFO::Removing potential empty rows and columns
2025-08-03 20:23:41.133437 INFO::Found 2 missing values.
2025-08-03 20:23:41.135018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:41.135572 INFO::Done
2025-08-03 20:23:41.146279 INFO::Formatting Data.
2025-08-03 20:23:41.147053 INFO::Typecasting input to dataframe.
2025-08-03 20:23:41.147874 INFO::Replacing NaNs with NAs.
2025-08-03 20:23:41.148773 INFO::Removing potential empty rows and columns
2025-08-03 20:23:41.149826 INFO::Found 0 missing values.
2025-08-03 20:23:41.152696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-03 20:23:41.153226 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.116 3.199 20.154
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.531 | 1.258 | 17.579 | |
| compute_asw | 0.024 | 0.000 | 0.025 | |
| count_existing | 0.012 | 0.002 | 0.014 | |
| generate_data_covariables | 0.010 | 0.001 | 0.012 | |
| generate_dataset | 0.009 | 0.002 | 0.011 | |