Yannis Schumann
| Snapshot Date: 2025-12-10 13:40 -0500 (Wed, 10 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-11 11:34 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4872 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4580 |
| 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 168/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-12-10 22:48:38 -0500 (Wed, 10 Dec 2025) |
| EndedAt: 2025-12-10 22:50:09 -0500 (Wed, 10 Dec 2025) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 24.841 2.062 18.174
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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")
2025-12-10 22:49:31.486404 INFO::Formatting Data.
2025-12-10 22:49:31.487668 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:31.498446 INFO::Removing potential empty rows and columns
2025-12-10 22:49:31.728003 INFO::Found 0 missing values.
2025-12-10 22:49:31.73113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:31.731796 INFO::Done
2025-12-10 22:49:31.732336 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:31.743504 INFO::Starting hierarchical adjustment
2025-12-10 22:49:31.744379 INFO::Found 3 batches.
2025-12-10 22:49:31.744937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:31.74602 INFO::Using default BPPARAM
2025-12-10 22:49:31.746557 INFO::Processing subtree level 1
2025-12-10 22:49:31.84448 INFO::Adjusting the last 1 batches sequentially
2025-12-10 22:49:31.846257 INFO::Done
2025-12-10 22:49:31.846954 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:31.849475 INFO::ASW Batch was -0.132778314438039 prior to batch effect correction and is now -0.132778314438039 .
2025-12-10 22:49:31.850532 INFO::Total function execution time is 0.364765644073486 s and adjustment time is 0.102037191390991 s ( 27.97 )
2025-12-10 22:49:31.863953 INFO::Formatting Data.
2025-12-10 22:49:31.864719 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:31.865639 INFO::Removing potential empty rows and columns
2025-12-10 22:49:31.866765 INFO::Found 0 missing values.
2025-12-10 22:49:31.867703 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.
2025-12-10 22:49:31.878357 INFO::Formatting Data.
2025-12-10 22:49:31.8791 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:31.880028 INFO::Removing potential empty rows and columns
2025-12-10 22:49:31.881174 INFO::Found 0 missing values.
2025-12-10 22:49:31.882139 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.
2025-12-10 22:49:31.898047 INFO::Formatting Data.
2025-12-10 22:49:31.898834 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:31.899698 INFO::Removing potential empty rows and columns
2025-12-10 22:49:31.900719 INFO::Found 0 missing values.
2025-12-10 22:49:31.901638 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.
2025-12-10 22:49:31.906038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:31.906592 INFO::Done
2025-12-10 22:49:31.907164 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:31.909259 INFO::Starting hierarchical adjustment
2025-12-10 22:49:31.909994 INFO::Found 2 batches.
2025-12-10 22:49:31.910516 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:31.911169 INFO::Using default BPPARAM
2025-12-10 22:49:31.911707 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:31.912649 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-10 22:49:31.933398 INFO::Done
2025-12-10 22:49:31.934153 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:31.936382 INFO::ASW Batch was -0.0512852630420064 prior to batch effect correction and is now -0.117197469237905 .
2025-12-10 22:49:31.93725 INFO::Total function execution time is 0.0392692089080811 s and adjustment time is 0.0235238075256348 s ( 59.9 )
2025-12-10 22:49:31.940238 INFO::Formatting Data.
2025-12-10 22:49:31.940901 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:31.950331 INFO::Formatting Data.
2025-12-10 22:49:31.951169 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:31.952173 INFO::Removing potential empty rows and columns
2025-12-10 22:49:31.953288 INFO::Found 0 missing values.
2025-12-10 22:49:31.956425 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:31.957036 INFO::Done
2025-12-10 22:49:31.9576 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:31.959968 INFO::Starting hierarchical adjustment
2025-12-10 22:49:31.960697 INFO::Found 2 batches.
2025-12-10 22:49:31.961278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:31.961941 INFO::Using default BPPARAM
2025-12-10 22:49:31.962484 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:31.963472 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-10 22:49:32.002292 INFO::Done
2025-12-10 22:49:32.003008 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:32.004939 INFO::ASW Batch was 0.00345406191638572 prior to batch effect correction and is now -0.115902068210807 .
2025-12-10 22:49:32.005696 INFO::Total function execution time is 0.0554442405700684 s and adjustment time is 0.041719913482666 s ( 75.25 )
2025-12-10 22:49:32.006673 INFO::Formatting Data.
2025-12-10 22:49:32.00724 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:32.008041 INFO::Removing potential empty rows and columns
2025-12-10 22:49:32.008982 INFO::Found 0 missing values.
2025-12-10 22:49:32.011532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:32.012071 INFO::Done
2025-12-10 22:49:32.012559 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:32.014383 INFO::Starting hierarchical adjustment
2025-12-10 22:49:32.015038 INFO::Found 2 batches.
2025-12-10 22:49:32.015526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:32.016089 INFO::Using default BPPARAM
2025-12-10 22:49:32.01657 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:32.017409 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-10 22:49:32.031376 INFO::Done
2025-12-10 22:49:32.032066 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:32.03404 INFO::ASW Batch was 0.00345406191638572 prior to batch effect correction and is now -0.115902068210807 .
2025-12-10 22:49:32.034814 INFO::Total function execution time is 0.0281181335449219 s and adjustment time is 0.0164394378662109 s ( 58.47 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-10 22:49:34.947068 INFO::Formatting Data.
2025-12-10 22:49:34.947777 INFO::Recognized SummarizedExperiment
2025-12-10 22:49:34.948271 INFO::Typecasting input to dataframe.
2025-12-10 22:49:34.976546 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:34.977687 INFO::Removing potential empty rows and columns
2025-12-10 22:49:34.980721 INFO::Found 0 missing values.
2025-12-10 22:49:34.986415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:34.986951 INFO::Done
2025-12-10 22:49:34.987408 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:34.990623 INFO::Starting hierarchical adjustment
2025-12-10 22:49:34.99127 INFO::Found 2 batches.
2025-12-10 22:49:34.99173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:34.992728 INFO::Using default BPPARAM
2025-12-10 22:49:34.993218 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:34.994092 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-10 22:49:35.041385 INFO::Done
2025-12-10 22:49:35.042244 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:35.045496 INFO::ASW Batch was 0.000963136191996272 prior to batch effect correction and is now -0.0923222150358397 .
2025-12-10 22:49:35.046317 INFO::Total function execution time is 0.0995352268218994 s and adjustment time is 0.0501673221588135 s ( 50.4 )
Warning: stack imbalance in '{', 73 then 75
2025-12-10 22:49:35.063254 INFO::Formatting Data.
2025-12-10 22:49:35.063997 INFO::Recognized SummarizedExperiment
2025-12-10 22:49:35.06451 INFO::Typecasting input to dataframe.
2025-12-10 22:49:35.073018 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:35.074111 INFO::Removing potential empty rows and columns
2025-12-10 22:49:35.077191 INFO::Found 0 missing values.
2025-12-10 22:49:35.083241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:35.083826 INFO::Done
2025-12-10 22:49:35.084299 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:35.087659 INFO::Starting hierarchical adjustment
2025-12-10 22:49:35.088428 INFO::Found 2 batches.
2025-12-10 22:49:35.088976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:35.089618 INFO::Using default BPPARAM
2025-12-10 22:49:35.090167 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:35.09117 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-10 22:49:35.117536 INFO::Done
2025-12-10 22:49:35.118302 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:35.122039 INFO::ASW Batch was -0.00422844136869983 prior to batch effect correction and is now -0.00422844136869983 .
2025-12-10 22:49:35.122945 INFO::Total function execution time is 0.0596868991851807 s and adjustment time is 0.0292127132415771 s ( 48.94 )
2025-12-10 22:49:35.142539 INFO::Formatting Data.
2025-12-10 22:49:35.143421 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:35.144431 INFO::Removing potential empty rows and columns
2025-12-10 22:49:35.145521 INFO::Found 0 missing values.
2025-12-10 22:49:35.14865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:35.149231 INFO::Done
2025-12-10 22:49:35.150031 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:35.152162 INFO::Starting hierarchical adjustment
2025-12-10 22:49:35.152894 INFO::Found 3 batches.
2025-12-10 22:49:35.153419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:35.154033 INFO::Using default BPPARAM
2025-12-10 22:49:35.154567 INFO::Processing subtree level 1
2025-12-10 22:49:35.29149 INFO::Adjusting the last 1 batches sequentially
2025-12-10 22:49:35.29326 INFO::Done
2025-12-10 22:49:35.2939 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:35.296372 INFO::ASW Batch was 0.113090501791613 prior to batch effect correction and is now -0.145400059263606 .
2025-12-10 22:49:35.297316 INFO::Total function execution time is 0.15485143661499 s and adjustment time is 0.140514850616455 s ( 90.74 )
2025-12-10 22:49:35.311553 INFO::Skipping initial DF formatting
2025-12-10 22:49:35.312265 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:35.316393 INFO::Starting hierarchical adjustment
2025-12-10 22:49:35.317175 INFO::Found 5 batches.
2025-12-10 22:49:35.317723 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:35.318369 INFO::Using default BPPARAM
2025-12-10 22:49:35.318933 INFO::Processing subtree level 1
2025-12-10 22:49:35.442519 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:35.444119 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-10 22:49:35.464314 INFO::Done
2025-12-10 22:49:35.465054 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:35.469397 INFO::ASW Batch was 0.546835208221244 prior to batch effect correction and is now 0.546835208221244 .
2025-12-10 22:49:35.470022 INFO::ASW Label was 0.3270508096649 prior to batch effect correction and is now 0.3270508096649 .
2025-12-10 22:49:35.470875 INFO::Total function execution time is 0.159367322921753 s and adjustment time is 0.147277593612671 s ( 92.41 )
2025-12-10 22:49:35.488556 INFO::Formatting Data.
2025-12-10 22:49:35.489351 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:35.490291 INFO::Removing potential empty rows and columns
2025-12-10 22:49:35.491288 INFO::Found 0 missing values.
2025-12-10 22:49:35.495335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:35.495887 INFO::Done
2025-12-10 22:49:35.496413 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:35.499426 INFO::Starting hierarchical adjustment
2025-12-10 22:49:35.500143 INFO::Found 5 batches.
2025-12-10 22:49:35.500675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:35.501314 INFO::Using default BPPARAM
2025-12-10 22:49:35.501871 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.
2025-12-10 22:49:35.633227 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:35.635141 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-10 22:49:35.652442 INFO::Done
2025-12-10 22:49:35.653266 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:35.656922 INFO::ASW Batch was 0.515220256563377 prior to batch effect correction and is now -0.0817297225379627 .
2025-12-10 22:49:35.657621 INFO::ASW Label was 0.169547551751617 prior to batch effect correction and is now 0.873745062465517 .
2025-12-10 22:49:35.658567 INFO::Total function execution time is 0.170041561126709 s and adjustment time is 0.152376413345337 s ( 89.61 )
2025-12-10 22:49:35.659522 INFO::Formatting Data.
2025-12-10 22:49:35.660213 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:35.66118 INFO::Removing potential empty rows and columns
2025-12-10 22:49:35.662273 INFO::Found 0 missing values.
2025-12-10 22:49:35.666458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:35.667053 INFO::Done
2025-12-10 22:49:35.667596 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:35.67077 INFO::Starting hierarchical adjustment
2025-12-10 22:49:35.671522 INFO::Found 5 batches.
2025-12-10 22:49:35.672084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:35.672776 INFO::Using default BPPARAM
2025-12-10 22:49:35.673347 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.
2025-12-10 22:49:35.798231 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:35.800018 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-10 22:49:35.817034 INFO::Done
2025-12-10 22:49:35.817799 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:35.82127 INFO::ASW Batch was 0.515220256563377 prior to batch effect correction and is now -0.0817297225379627 .
2025-12-10 22:49:35.821929 INFO::ASW Label was 0.169547551751617 prior to batch effect correction and is now 0.873745062465517 .
2025-12-10 22:49:35.822817 INFO::Total function execution time is 0.163305521011353 s and adjustment time is 0.145639419555664 s ( 89.18 )
2025-12-10 22:49:35.837012 INFO::Formatting Data.
2025-12-10 22:49:35.837876 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:35.838845 INFO::Removing potential empty rows and columns
2025-12-10 22:49:35.839884 INFO::Found 0 missing values.
2025-12-10 22:49:35.844033 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:35.844633 INFO::Done
2025-12-10 22:49:35.845189 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:35.848254 INFO::Starting hierarchical adjustment
2025-12-10 22:49:35.848993 INFO::Found 5 batches.
2025-12-10 22:49:35.849536 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:35.850197 INFO::Using default BPPARAM
2025-12-10 22:49:35.85073 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.
2025-12-10 22:49:35.970607 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:35.972454 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-10 22:49:35.989445 INFO::Done
2025-12-10 22:49:35.990284 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:35.993944 INFO::ASW Batch was 0.428297010428525 prior to batch effect correction and is now -0.0839935325391069 .
2025-12-10 22:49:35.994652 INFO::ASW Label was 0.32304133427724 prior to batch effect correction and is now 0.831664878531678 .
2025-12-10 22:49:35.995547 INFO::Total function execution time is 0.158622741699219 s and adjustment time is 0.14055061340332 s ( 88.61 )
2025-12-10 22:49:35.996446 INFO::Formatting Data.
2025-12-10 22:49:35.997148 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:35.998103 INFO::Removing potential empty rows and columns
2025-12-10 22:49:35.999147 INFO::Found 0 missing values.
2025-12-10 22:49:36.003401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.004036 INFO::Done
2025-12-10 22:49:36.004583 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.007827 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.008588 INFO::Found 5 batches.
2025-12-10 22:49:36.009199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.009864 INFO::Using default BPPARAM
2025-12-10 22:49:36.010413 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.
2025-12-10 22:49:36.131181 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:36.133481 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-10 22:49:36.157987 INFO::Done
2025-12-10 22:49:36.159055 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.164077 INFO::ASW Batch was 0.428297010428525 prior to batch effect correction and is now -0.0839935325391069 .
2025-12-10 22:49:36.165039 INFO::ASW Label was 0.32304133427724 prior to batch effect correction and is now 0.831664878531678 .
2025-12-10 22:49:36.166377 INFO::Total function execution time is 0.16984224319458 s and adjustment time is 0.149473905563354 s ( 88.01 )
2025-12-10 22:49:36.187284 INFO::Formatting Data.
2025-12-10 22:49:36.188401 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:36.189778 INFO::Removing potential empty rows and columns
2025-12-10 22:49:36.191292 INFO::Found 0 missing values.
2025-12-10 22:49:36.19586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.196713 INFO::Done
2025-12-10 22:49:36.197551 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.201953 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.203009 INFO::Found 2 batches.
2025-12-10 22:49:36.203819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.204762 INFO::Using default BPPARAM
2025-12-10 22:49:36.205596 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:36.207191 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-10 22:49:36.230353 INFO::Done
2025-12-10 22:49:36.231396 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.235963 INFO::ASW Batch was 0.313203801804459 prior to batch effect correction and is now -0.0218556713809768 .
2025-12-10 22:49:36.236924 INFO::ASW Label was 0.737088459211292 prior to batch effect correction and is now 0.948458444062475 .
2025-12-10 22:49:36.238185 INFO::Total function execution time is 0.0509979724884033 s and adjustment time is 0.0275368690490723 s ( 54 )
2025-12-10 22:49:36.239427 INFO::Formatting Data.
2025-12-10 22:49:36.240417 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:36.24183 INFO::Removing potential empty rows and columns
2025-12-10 22:49:36.243381 INFO::Found 0 missing values.
2025-12-10 22:49:36.247577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.248183 INFO::Done
2025-12-10 22:49:36.248713 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.25171 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.252433 INFO::Found 2 batches.
2025-12-10 22:49:36.252977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.253599 INFO::Using default BPPARAM
2025-12-10 22:49:36.254171 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:36.255108 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-10 22:49:36.269772 INFO::Done
2025-12-10 22:49:36.270491 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.273495 INFO::ASW Batch was 0.313203801804459 prior to batch effect correction and is now -0.0218556713809768 .
2025-12-10 22:49:36.274125 INFO::ASW Label was 0.737088459211292 prior to batch effect correction and is now 0.948458444062475 .
2025-12-10 22:49:36.274923 INFO::Total function execution time is 0.0355966091156006 s and adjustment time is 0.0174670219421387 s ( 49.07 )
2025-12-10 22:49:36.286359 INFO::Formatting Data.
2025-12-10 22:49:36.287187 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:36.288094 INFO::Removing potential empty rows and columns
2025-12-10 22:49:36.289013 INFO::Found 0 missing values.
2025-12-10 22:49:36.291167 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.291711 INFO::Done
2025-12-10 22:49:36.292243 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.294206 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.294924 INFO::Found 2 batches.
2025-12-10 22:49:36.295452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.296073 INFO::Using default BPPARAM
2025-12-10 22:49:36.296622 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:36.29753 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-10 22:49:36.329076 INFO::Done
2025-12-10 22:49:36.329807 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.331865 INFO::ASW Batch was -0.200747531708029 prior to batch effect correction and is now -0.207120705801393 .
2025-12-10 22:49:36.332699 INFO::Total function execution time is 0.0464284420013428 s and adjustment time is 0.0342767238616943 s ( 73.83 )
2025-12-10 22:49:36.344881 INFO::Formatting Data.
2025-12-10 22:49:36.345672 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:36.346578 INFO::Removing potential empty rows and columns
2025-12-10 22:49:36.34757 INFO::Found 0 missing values.
2025-12-10 22:49:36.348713 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.
2025-12-10 22:49:36.35337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.353969 INFO::Done
2025-12-10 22:49:36.354494 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.357448 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.358156 INFO::Found 2 batches.
2025-12-10 22:49:36.358693 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.359333 INFO::Using default BPPARAM
2025-12-10 22:49:36.359893 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:36.360822 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-10 22:49:36.377294 INFO::Done
2025-12-10 22:49:36.378046 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.38106 INFO::ASW Batch was 0.371806331653552 prior to batch effect correction and is now -0.0132935739514724 .
2025-12-10 22:49:36.381662 INFO::ASW Label was 0.68235282708149 prior to batch effect correction and is now 0.943381465987249 .
2025-12-10 22:49:36.382481 INFO::Total function execution time is 0.0377001762390137 s and adjustment time is 0.0192408561706543 s ( 51.04 )
2025-12-10 22:49:36.383296 INFO::Formatting Data.
2025-12-10 22:49:36.383923 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:36.384856 INFO::Removing potential empty rows and columns
2025-12-10 22:49:36.385847 INFO::Found 0 missing values.
2025-12-10 22:49:36.386741 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.
2025-12-10 22:49:36.39133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.391911 INFO::Done
2025-12-10 22:49:36.392432 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.395376 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.396084 INFO::Found 2 batches.
2025-12-10 22:49:36.396645 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.397268 INFO::Using default BPPARAM
2025-12-10 22:49:36.397795 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:36.398736 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-10 22:49:36.415214 INFO::Done
2025-12-10 22:49:36.415953 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.418993 INFO::ASW Batch was 0.371806331653552 prior to batch effect correction and is now -0.0132935739514724 .
2025-12-10 22:49:36.419662 INFO::ASW Label was 0.68235282708149 prior to batch effect correction and is now 0.943381465987249 .
2025-12-10 22:49:36.420491 INFO::Total function execution time is 0.0372178554534912 s and adjustment time is 0.0192346572875977 s ( 51.68 )
2025-12-10 22:49:36.644539 INFO::Formatting Data.
2025-12-10 22:49:36.645355 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:36.646255 INFO::Removing potential empty rows and columns
2025-12-10 22:49:36.647313 INFO::Found 0 missing values.
2025-12-10 22:49:36.650275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.65082 INFO::Done
2025-12-10 22:49:36.651346 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.653483 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.654197 INFO::Found 3 batches.
2025-12-10 22:49:36.65474 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.655362 INFO::Using default BPPARAM
2025-12-10 22:49:36.655916 INFO::Processing subtree level 1
2025-12-10 22:49:36.743323 INFO::Adjusting the last 1 batches sequentially
2025-12-10 22:49:36.745023 INFO::Done
2025-12-10 22:49:36.745667 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.748085 INFO::ASW Batch was -0.120193402141508 prior to batch effect correction and is now -0.120193402141508 .
2025-12-10 22:49:36.749027 INFO::Total function execution time is 0.104547262191772 s and adjustment time is 0.090961217880249 s ( 87 )
2025-12-10 22:49:36.750067 INFO::Formatting Data.
2025-12-10 22:49:36.75071 INFO::Typecasting input to dataframe.
2025-12-10 22:49:36.751474 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:36.752359 INFO::Removing potential empty rows and columns
2025-12-10 22:49:36.753435 INFO::Found 0 missing values.
2025-12-10 22:49:36.756438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.757018 INFO::Done
2025-12-10 22:49:36.757544 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.759544 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.760268 INFO::Found 3 batches.
2025-12-10 22:49:36.760826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.761448 INFO::Using default BPPARAM
2025-12-10 22:49:36.762014 INFO::Processing subtree level 1
2025-12-10 22:49:36.847015 INFO::Adjusting the last 1 batches sequentially
2025-12-10 22:49:36.848807 INFO::Done
2025-12-10 22:49:36.849487 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.852051 INFO::ASW Batch was -0.120193402141508 prior to batch effect correction and is now -0.120193402141508 .
2025-12-10 22:49:36.853034 INFO::Total function execution time is 0.102930545806885 s and adjustment time is 0.0886533260345459 s ( 86.13 )
2025-12-10 22:49:36.866429 INFO::Formatting Data.
2025-12-10 22:49:36.867241 INFO::Typecasting input to dataframe.
2025-12-10 22:49:36.868125 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:36.869046 INFO::Removing potential empty rows and columns
2025-12-10 22:49:36.87015 INFO::Found 0 missing values.
2025-12-10 22:49:36.873089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:36.873628 INFO::Done
2025-12-10 22:49:36.87417 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:36.876174 INFO::Starting hierarchical adjustment
2025-12-10 22:49:36.876884 INFO::Found 3 batches.
2025-12-10 22:49:36.877628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:36.87826 INFO::Using default BPPARAM
2025-12-10 22:49:36.878847 INFO::Processing subtree level 1
2025-12-10 22:49:36.964237 INFO::Adjusting the last 1 batches sequentially
2025-12-10 22:49:36.966065 INFO::Done
2025-12-10 22:49:36.966741 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:36.96926 INFO::ASW Batch was -0.098146120998581 prior to batch effect correction and is now -0.098146120998581 .
2025-12-10 22:49:36.970221 INFO::Total function execution time is 0.103840827941895 s and adjustment time is 0.0893101692199707 s ( 86.01 )
2025-12-10 22:49:37.107347 INFO::Formatting Data.
2025-12-10 22:49:37.108213 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:37.109343 INFO::Removing potential empty rows and columns
2025-12-10 22:49:37.112308 INFO::Found 1000 missing values.
2025-12-10 22:49:37.131465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:37.132272 INFO::Done
2025-12-10 22:49:37.132879 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:37.138504 INFO::Starting hierarchical adjustment
2025-12-10 22:49:37.139354 INFO::Found 10 batches.
2025-12-10 22:49:37.139929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:37.140616 INFO::Using default BPPARAM
2025-12-10 22:49:37.141177 INFO::Processing subtree level 1
2025-12-10 22:49:37.288564 INFO::Processing subtree level 2
2025-12-10 22:49:37.563879 INFO::Adjusting the last 1 batches sequentially
2025-12-10 22:49:37.565862 INFO::Done
2025-12-10 22:49:37.566541 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:37.572123 INFO::ASW Batch was 0.549994828877806 prior to batch effect correction and is now 0.549994828877806 .
2025-12-10 22:49:37.572826 INFO::ASW Label was 0.323147575895789 prior to batch effect correction and is now 0.323147575895789 .
2025-12-10 22:49:37.573745 INFO::Total function execution time is 0.46644926071167 s and adjustment time is 0.426653861999512 s ( 91.47 )
2025-12-10 22:49:37.574597 INFO::Formatting Data.
2025-12-10 22:49:37.575247 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:37.576407 INFO::Removing potential empty rows and columns
2025-12-10 22:49:37.639465 INFO::Found 1000 missing values.
2025-12-10 22:49:37.658028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:37.658739 INFO::Done
2025-12-10 22:49:37.65932 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:37.664543 INFO::Starting hierarchical adjustment
2025-12-10 22:49:37.665265 INFO::Found 10 batches.
2025-12-10 22:49:38.639854 INFO::Set up parallel execution backend with 2 workers
2025-12-10 22:49:38.640998 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-10 22:49:39.768312 INFO::Adjusting the last 2 batches sequentially
2025-12-10 22:49:39.771345 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-10 22:49:39.793977 INFO::Done
2025-12-10 22:49:39.794768 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:39.799891 INFO::ASW Batch was 0.549994828877806 prior to batch effect correction and is now 0.549994828877806 .
2025-12-10 22:49:39.800518 INFO::ASW Label was 0.323147575895789 prior to batch effect correction and is now 0.323147575895789 .
2025-12-10 22:49:39.801266 INFO::Total function execution time is 2.22670364379883 s and adjustment time is 2.12882113456726 s ( 95.6 )
2025-12-10 22:49:39.947984 INFO::Formatting Data.
2025-12-10 22:49:39.948758 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:39.949702 INFO::Removing potential empty rows and columns
2025-12-10 22:49:39.950803 INFO::Found 0 missing values.
2025-12-10 22:49:39.954361 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:39.954904 INFO::Done
2025-12-10 22:49:39.955413 INFO::Acquiring quality metrics before batch effect correction.
2025-12-10 22:49:39.95807 INFO::Starting hierarchical adjustment
2025-12-10 22:49:39.95875 INFO::Found 3 batches.
2025-12-10 22:49:39.959285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-10 22:49:39.95992 INFO::Using default BPPARAM
2025-12-10 22:49:39.960443 INFO::Processing subtree level 1
2025-12-10 22:49:40.066119 INFO::Adjusting the last 1 batches sequentially
2025-12-10 22:49:40.067934 INFO::Done
2025-12-10 22:49:40.068582 INFO::Acquiring quality metrics after batch effect correction.
2025-12-10 22:49:40.071769 INFO::ASW Batch was 0.175182538007979 prior to batch effect correction and is now -0.150438770202874 .
2025-12-10 22:49:40.07239 INFO::ASW Label was -0.259350605430115 prior to batch effect correction and is now -0.141884439191604 .
2025-12-10 22:49:40.07333 INFO::Total function execution time is 0.125381231307983 s and adjustment time is 0.109291076660156 s ( 87.17 )
2025-12-10 22:49:40.188593 INFO::Formatting Data.
2025-12-10 22:49:40.189402 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.190288 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.191306 INFO::Found 2 missing values.
2025-12-10 22:49:40.194068 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.194628 INFO::Done
2025-12-10 22:49:40.221183 INFO::Found NA in Reference column
2025-12-10 22:49:40.230128 INFO::Require at least two references per batch.
2025-12-10 22:49:40.249398 INFO::Formatting Data.
2025-12-10 22:49:40.250113 INFO::Recognized SummarizedExperiment
2025-12-10 22:49:40.25063 INFO::Typecasting input to dataframe.
2025-12-10 22:49:40.259573 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.260657 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.264047 INFO::Found 0 missing values.
2025-12-10 22:49:40.270371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.270919 INFO::Done
2025-12-10 22:49:40.285417 INFO::Formatting Data.
2025-12-10 22:49:40.286107 INFO::Recognized SummarizedExperiment
2025-12-10 22:49:40.286623 INFO::Typecasting input to dataframe.
2025-12-10 22:49:40.303127 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.30429 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.307669 INFO::Found 0 missing values.
2025-12-10 22:49:40.317791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.318395 INFO::Done
2025-12-10 22:49:40.332764 INFO::Formatting Data.
2025-12-10 22:49:40.333451 INFO::Recognized SummarizedExperiment
2025-12-10 22:49:40.333966 INFO::Typecasting input to dataframe.
2025-12-10 22:49:40.349279 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.350253 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.351308 INFO::Found 0 missing values.
2025-12-10 22:49:40.352183 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.
2025-12-10 22:49:40.356226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.356745 INFO::Done
2025-12-10 22:49:40.366352 INFO::Formatting Data.
2025-12-10 22:49:40.367176 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.368051 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.369034 INFO::Found 0 missing values.
2025-12-10 22:49:40.371707 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.372245 INFO::Done
2025-12-10 22:49:40.382873 INFO::Formatting Data.
2025-12-10 22:49:40.383621 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.384464 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.385514 INFO::Found 0 missing values.
2025-12-10 22:49:40.388263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.388768 INFO::Done
2025-12-10 22:49:40.416501 INFO::Formatting Data.
2025-12-10 22:49:40.417335 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.41834 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.419468 INFO::Found 1 missing values.
2025-12-10 22:49:40.421901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.422441 INFO::Done
2025-12-10 22:49:40.440239 INFO::Formatting Data.
2025-12-10 22:49:40.440989 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.441816 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.442711 INFO::Found 2 missing values.
2025-12-10 22:49:40.44359 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.
2025-12-10 22:49:40.445776 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.446332 INFO::Done
2025-12-10 22:49:40.456444 INFO::Formatting Data.
2025-12-10 22:49:40.457259 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.458187 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.459114 INFO::Found 2 missing values.
2025-12-10 22:49:40.460632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.461199 INFO::Done
2025-12-10 22:49:40.470949 INFO::Formatting Data.
2025-12-10 22:49:40.471666 INFO::Typecasting input to dataframe.
2025-12-10 22:49:40.472446 INFO::Replacing NaNs with NAs.
2025-12-10 22:49:40.473288 INFO::Removing potential empty rows and columns
2025-12-10 22:49:40.474236 INFO::Found 0 missing values.
2025-12-10 22:49:40.476915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-10 22:49:40.47744 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.855 3.536 20.108
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.841 | 2.062 | 18.174 | |
| compute_asw | 0.022 | 0.004 | 0.025 | |
| count_existing | 0.014 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.011 | 0.002 | 0.012 | |