Yannis Schumann
| Snapshot Date: 2026-05-19 13:40 -0400 (Tue, 19 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_23 |
| git_last_commit: 0c9135c |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-20 11:32 -0400 (Wed, 20 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 172/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.8.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2026-05-19 21:48:11 -0400 (Tue, 19 May 2026) |
| EndedAt: 2026-05-19 21:49:46 -0400 (Tue, 19 May 2026) |
| EllapsedTime: 94.3 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-20 01:48:12 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 28.012 1.369 20.948
* 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 ‘1.8.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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")
2026-05-19 21:49:07.874976 INFO::Formatting Data.
2026-05-19 21:49:07.876523 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:07.889292 INFO::Removing potential empty rows and columns
2026-05-19 21:49:08.20659 INFO::Found 0 missing values.
2026-05-19 21:49:08.210801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:08.211759 INFO::Done
2026-05-19 21:49:08.212435 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:08.229236 INFO::Starting hierarchical adjustment
2026-05-19 21:49:08.230558 INFO::Found 3 batches.
2026-05-19 21:49:08.23135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:08.232823 INFO::Using default BPPARAM
2026-05-19 21:49:08.233523 INFO::Processing subtree level 1
2026-05-19 21:49:08.371946 INFO::Adjusting the last 1 batches sequentially
2026-05-19 21:49:08.374202 INFO::Done
2026-05-19 21:49:08.37503 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:08.378104 INFO::ASW Batch was -0.0663161827731457 prior to batch effect correction and is now -0.0663161827731457 .
2026-05-19 21:49:08.379372 INFO::Total function execution time is 0.505085229873657 s and adjustment time is 0.143882989883423 s ( 28.49 )
2026-05-19 21:49:08.397737 INFO::Formatting Data.
2026-05-19 21:49:08.398783 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:08.399905 INFO::Removing potential empty rows and columns
2026-05-19 21:49:08.401139 INFO::Found 0 missing values.
2026-05-19 21:49:08.402291 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.
2026-05-19 21:49:08.414909 INFO::Formatting Data.
2026-05-19 21:49:08.415991 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:08.41714 INFO::Removing potential empty rows and columns
2026-05-19 21:49:08.418433 INFO::Found 0 missing values.
2026-05-19 21:49:08.419548 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.
2026-05-19 21:49:08.437543 INFO::Formatting Data.
2026-05-19 21:49:08.438518 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:08.439634 INFO::Removing potential empty rows and columns
2026-05-19 21:49:08.440892 INFO::Found 0 missing values.
2026-05-19 21:49:08.442009 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.
2026-05-19 21:49:08.447363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:08.448206 INFO::Done
2026-05-19 21:49:08.448888 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:08.45148 INFO::Starting hierarchical adjustment
2026-05-19 21:49:08.452365 INFO::Found 2 batches.
2026-05-19 21:49:08.453052 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:08.453846 INFO::Using default BPPARAM
2026-05-19 21:49:08.454501 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:08.455732 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-19 21:49:08.479719 INFO::Done
2026-05-19 21:49:08.480578 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:08.483006 INFO::ASW Batch was -0.0567072005196644 prior to batch effect correction and is now -0.124852733266733 .
2026-05-19 21:49:08.483999 INFO::Total function execution time is 0.0465302467346191 s and adjustment time is 0.0274717807769775 s ( 59.04 )
2026-05-19 21:49:08.487244 INFO::Formatting Data.
2026-05-19 21:49:08.488044 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:08.498327 INFO::Formatting Data.
2026-05-19 21:49:08.499376 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:08.500484 INFO::Removing potential empty rows and columns
2026-05-19 21:49:08.501711 INFO::Found 0 missing values.
2026-05-19 21:49:08.504974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:08.505637 INFO::Done
2026-05-19 21:49:08.506251 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:08.508624 INFO::Starting hierarchical adjustment
2026-05-19 21:49:08.509596 INFO::Found 2 batches.
2026-05-19 21:49:08.510349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:08.511085 INFO::Using default BPPARAM
2026-05-19 21:49:08.511688 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:08.512765 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-19 21:49:08.562143 INFO::Done
2026-05-19 21:49:08.563039 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:08.565394 INFO::ASW Batch was -0.0217758299840915 prior to batch effect correction and is now -0.0897191959792718 .
2026-05-19 21:49:08.566383 INFO::Total function execution time is 0.0681707859039307 s and adjustment time is 0.0526854991912842 s ( 77.28 )
2026-05-19 21:49:08.567591 INFO::Formatting Data.
2026-05-19 21:49:08.568293 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:08.569253 INFO::Removing potential empty rows and columns
2026-05-19 21:49:08.570348 INFO::Found 0 missing values.
2026-05-19 21:49:08.573393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:08.57405 INFO::Done
2026-05-19 21:49:08.574623 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:08.57684 INFO::Starting hierarchical adjustment
2026-05-19 21:49:08.577604 INFO::Found 2 batches.
2026-05-19 21:49:08.578184 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:08.57886 INFO::Using default BPPARAM
2026-05-19 21:49:08.579438 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:08.580541 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-19 21:49:08.597095 INFO::Done
2026-05-19 21:49:08.597981 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:08.600388 INFO::ASW Batch was -0.0217758299840915 prior to batch effect correction and is now -0.0897191959792718 .
2026-05-19 21:49:08.601382 INFO::Total function execution time is 0.0337734222412109 s and adjustment time is 0.0195977687835693 s ( 58.03 )
2026-05-19 21:49:11.80081 INFO::Formatting Data.
2026-05-19 21:49:11.80166 INFO::Recognized SummarizedExperiment
2026-05-19 21:49:11.802251 INFO::Typecasting input to dataframe.
2026-05-19 21:49:11.833754 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:11.835315 INFO::Removing potential empty rows and columns
2026-05-19 21:49:11.83887 INFO::Found 0 missing values.
2026-05-19 21:49:11.84555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:11.846324 INFO::Done
2026-05-19 21:49:11.84692 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:11.850425 INFO::Starting hierarchical adjustment
2026-05-19 21:49:11.851241 INFO::Found 2 batches.
2026-05-19 21:49:11.851808 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:11.852963 INFO::Using default BPPARAM
2026-05-19 21:49:11.853519 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:11.854578 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-19 21:49:11.910763 INFO::Done
2026-05-19 21:49:11.911813 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:11.915709 INFO::ASW Batch was 0.0272136735744563 prior to batch effect correction and is now -0.0921693162560468 .
2026-05-19 21:49:11.916793 INFO::Total function execution time is 0.116239547729492 s and adjustment time is 0.0595798492431641 s ( 51.26 )
2026-05-19 21:49:11.935344 INFO::Formatting Data.
2026-05-19 21:49:11.936212 INFO::Recognized SummarizedExperiment
2026-05-19 21:49:11.936817 INFO::Typecasting input to dataframe.
2026-05-19 21:49:11.945732 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:11.946949 INFO::Removing potential empty rows and columns
2026-05-19 21:49:11.950346 INFO::Found 0 missing values.
2026-05-19 21:49:11.95694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:11.957592 INFO::Done
2026-05-19 21:49:11.95817 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:11.961442 INFO::Starting hierarchical adjustment
2026-05-19 21:49:11.962158 INFO::Found 2 batches.
2026-05-19 21:49:11.962672 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:11.963265 INFO::Using default BPPARAM
2026-05-19 21:49:11.963792 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:11.96474 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-19 21:49:11.988275 INFO::Done
2026-05-19 21:49:11.989127 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:11.992984 INFO::ASW Batch was 0.00946831215289967 prior to batch effect correction and is now 0.00946831215289967 .
2026-05-19 21:49:11.993989 INFO::Total function execution time is 0.0586361885070801 s and adjustment time is 0.0261964797973633 s ( 44.68 )
2026-05-19 21:49:12.013939 INFO::Formatting Data.
2026-05-19 21:49:12.014935 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:12.015997 INFO::Removing potential empty rows and columns
2026-05-19 21:49:12.017169 INFO::Found 0 missing values.
2026-05-19 21:49:12.02039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:12.02101 INFO::Done
2026-05-19 21:49:12.021569 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:12.023757 INFO::Starting hierarchical adjustment
2026-05-19 21:49:12.024546 INFO::Found 3 batches.
2026-05-19 21:49:12.025136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:12.025808 INFO::Using default BPPARAM
2026-05-19 21:49:12.026368 INFO::Processing subtree level 1
2026-05-19 21:49:12.166986 INFO::Adjusting the last 1 batches sequentially
2026-05-19 21:49:12.168998 INFO::Done
2026-05-19 21:49:12.169748 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:12.172434 INFO::ASW Batch was -0.0190460403845173 prior to batch effect correction and is now -0.171249054049995 .
2026-05-19 21:49:12.173509 INFO::Total function execution time is 0.159617900848389 s and adjustment time is 0.144585371017456 s ( 90.58 )
2026-05-19 21:49:12.188772 INFO::Skipping initial DF formatting
2026-05-19 21:49:12.189613 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:12.193913 INFO::Starting hierarchical adjustment
2026-05-19 21:49:12.194797 INFO::Found 5 batches.
2026-05-19 21:49:12.195448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:12.196154 INFO::Using default BPPARAM
2026-05-19 21:49:12.19678 INFO::Processing subtree level 1
2026-05-19 21:49:12.323599 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:12.325747 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-19 21:49:12.347179 INFO::Done
2026-05-19 21:49:12.348173 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:12.352917 INFO::ASW Batch was 0.501414309945911 prior to batch effect correction and is now 0.501414309945911 .
2026-05-19 21:49:12.353629 INFO::ASW Label was 0.397013996967726 prior to batch effect correction and is now 0.397013996967726 .
2026-05-19 21:49:12.354578 INFO::Total function execution time is 0.165907621383667 s and adjustment time is 0.152523756027222 s ( 91.93 )
2026-05-19 21:49:12.372975 INFO::Formatting Data.
2026-05-19 21:49:12.373906 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:12.374996 INFO::Removing potential empty rows and columns
2026-05-19 21:49:12.376103 INFO::Found 0 missing values.
2026-05-19 21:49:12.380399 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:12.381038 INFO::Done
2026-05-19 21:49:12.381611 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:12.38483 INFO::Starting hierarchical adjustment
2026-05-19 21:49:12.385612 INFO::Found 5 batches.
2026-05-19 21:49:12.386242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:12.386935 INFO::Using default BPPARAM
2026-05-19 21:49:12.387529 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.
2026-05-19 21:49:12.496512 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:12.498286 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-19 21:49:12.515182 INFO::Done
2026-05-19 21:49:12.51602 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:12.519651 INFO::ASW Batch was 0.417825955453563 prior to batch effect correction and is now -0.0666277286162346 .
2026-05-19 21:49:12.520422 INFO::ASW Label was 0.365821018431546 prior to batch effect correction and is now 0.798802154338979 .
2026-05-19 21:49:12.521384 INFO::Total function execution time is 0.148496866226196 s and adjustment time is 0.129701614379883 s ( 87.34 )
2026-05-19 21:49:12.522334 INFO::Formatting Data.
2026-05-19 21:49:12.523048 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:12.524037 INFO::Removing potential empty rows and columns
2026-05-19 21:49:12.525115 INFO::Found 0 missing values.
2026-05-19 21:49:12.529448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:12.530123 INFO::Done
2026-05-19 21:49:12.530716 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:12.533982 INFO::Starting hierarchical adjustment
2026-05-19 21:49:12.534769 INFO::Found 5 batches.
2026-05-19 21:49:12.535362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:12.536051 INFO::Using default BPPARAM
2026-05-19 21:49:12.536662 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.
2026-05-19 21:49:12.646706 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:12.64846 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-19 21:49:12.665103 INFO::Done
2026-05-19 21:49:12.665922 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:12.669295 INFO::ASW Batch was 0.417825955453563 prior to batch effect correction and is now -0.0666277286162346 .
2026-05-19 21:49:12.669994 INFO::ASW Label was 0.365821018431546 prior to batch effect correction and is now 0.798802154338979 .
2026-05-19 21:49:12.670868 INFO::Total function execution time is 0.148530244827271 s and adjustment time is 0.130466222763062 s ( 87.84 )
2026-05-19 21:49:12.685068 INFO::Formatting Data.
2026-05-19 21:49:12.686049 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:12.68707 INFO::Removing potential empty rows and columns
2026-05-19 21:49:12.688139 INFO::Found 0 missing values.
2026-05-19 21:49:12.692511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:12.693156 INFO::Done
2026-05-19 21:49:12.693747 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:12.696907 INFO::Starting hierarchical adjustment
2026-05-19 21:49:12.697739 INFO::Found 5 batches.
2026-05-19 21:49:12.698318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:12.699018 INFO::Using default BPPARAM
2026-05-19 21:49:12.699591 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.
2026-05-19 21:49:12.807663 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:12.809445 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-19 21:49:12.825992 INFO::Done
2026-05-19 21:49:12.826836 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:12.830254 INFO::ASW Batch was 0.286706081547462 prior to batch effect correction and is now -0.035058518971719 .
2026-05-19 21:49:12.83099 INFO::ASW Label was 0.447037261909729 prior to batch effect correction and is now 0.859035247240059 .
2026-05-19 21:49:12.83191 INFO::Total function execution time is 0.146959066390991 s and adjustment time is 0.128387928009033 s ( 87.36 )
2026-05-19 21:49:12.832827 INFO::Formatting Data.
2026-05-19 21:49:12.833507 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:12.834476 INFO::Removing potential empty rows and columns
2026-05-19 21:49:12.835534 INFO::Found 0 missing values.
2026-05-19 21:49:12.839841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:12.840462 INFO::Done
2026-05-19 21:49:12.841046 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:12.8442 INFO::Starting hierarchical adjustment
2026-05-19 21:49:12.844981 INFO::Found 5 batches.
2026-05-19 21:49:12.845558 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:12.846268 INFO::Using default BPPARAM
2026-05-19 21:49:12.846867 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.
2026-05-19 21:49:12.957182 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:12.959152 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-19 21:49:12.976931 INFO::Done
2026-05-19 21:49:12.977836 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:12.981472 INFO::ASW Batch was 0.286706081547462 prior to batch effect correction and is now -0.035058518971719 .
2026-05-19 21:49:12.982218 INFO::ASW Label was 0.447037261909729 prior to batch effect correction and is now 0.859035247240059 .
2026-05-19 21:49:12.983168 INFO::Total function execution time is 0.150369882583618 s and adjustment time is 0.132046937942505 s ( 87.81 )
2026-05-19 21:49:12.998049 INFO::Formatting Data.
2026-05-19 21:49:12.998964 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:12.999983 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.001093 INFO::Found 0 missing values.
2026-05-19 21:49:13.003967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:13.00456 INFO::Done
2026-05-19 21:49:13.005139 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:13.008253 INFO::Starting hierarchical adjustment
2026-05-19 21:49:13.009012 INFO::Found 2 batches.
2026-05-19 21:49:13.009589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:13.010278 INFO::Using default BPPARAM
2026-05-19 21:49:13.010872 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:13.011871 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-19 21:49:13.028221 INFO::Done
2026-05-19 21:49:13.029075 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:13.032327 INFO::ASW Batch was 0.548167079370894 prior to batch effect correction and is now 0.00446405958175861 .
2026-05-19 21:49:13.033045 INFO::ASW Label was 0.530567526284135 prior to batch effect correction and is now 0.92026972873458 .
2026-05-19 21:49:13.033912 INFO::Total function execution time is 0.0359382629394531 s and adjustment time is 0.0193042755126953 s ( 53.72 )
2026-05-19 21:49:13.034821 INFO::Formatting Data.
2026-05-19 21:49:13.035492 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:13.03645 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.03753 INFO::Found 0 missing values.
2026-05-19 21:49:13.040458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:13.041065 INFO::Done
2026-05-19 21:49:13.04169 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:13.04486 INFO::Starting hierarchical adjustment
2026-05-19 21:49:13.045646 INFO::Found 2 batches.
2026-05-19 21:49:13.046248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:13.046961 INFO::Using default BPPARAM
2026-05-19 21:49:13.047531 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:13.048543 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-19 21:49:13.064106 INFO::Done
2026-05-19 21:49:13.064959 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:13.068155 INFO::ASW Batch was 0.548167079370894 prior to batch effect correction and is now 0.00446405958175861 .
2026-05-19 21:49:13.068855 INFO::ASW Label was 0.530567526284135 prior to batch effect correction and is now 0.92026972873458 .
2026-05-19 21:49:13.069724 INFO::Total function execution time is 0.0349152088165283 s and adjustment time is 0.01859450340271 s ( 53.26 )
2026-05-19 21:49:13.091866 INFO::Formatting Data.
2026-05-19 21:49:13.092959 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:13.094053 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.095143 INFO::Found 0 missing values.
2026-05-19 21:49:13.097558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:13.098165 INFO::Done
2026-05-19 21:49:13.098773 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:13.101181 INFO::Starting hierarchical adjustment
2026-05-19 21:49:13.101954 INFO::Found 2 batches.
2026-05-19 21:49:13.102546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:13.10326 INFO::Using default BPPARAM
2026-05-19 21:49:13.103849 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:13.104827 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-19 21:49:13.141027 INFO::Done
2026-05-19 21:49:13.141866 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:13.144064 INFO::ASW Batch was 0.203140350989247 prior to batch effect correction and is now -0.116462143417043 .
2026-05-19 21:49:13.145008 INFO::Total function execution time is 0.0535273551940918 s and adjustment time is 0.039172887802124 s ( 73.18 )
2026-05-19 21:49:13.158493 INFO::Formatting Data.
2026-05-19 21:49:13.15944 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:13.160496 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.161584 INFO::Found 0 missing values.
2026-05-19 21:49:13.162852 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.
2026-05-19 21:49:13.167775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:13.168414 INFO::Done
2026-05-19 21:49:13.169041 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:13.172191 INFO::Starting hierarchical adjustment
2026-05-19 21:49:13.172974 INFO::Found 2 batches.
2026-05-19 21:49:13.173547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:13.174218 INFO::Using default BPPARAM
2026-05-19 21:49:13.17481 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:13.175845 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-19 21:49:13.193553 INFO::Done
2026-05-19 21:49:13.19445 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:13.197787 INFO::ASW Batch was 0.529070169075456 prior to batch effect correction and is now 0.0708751020773111 .
2026-05-19 21:49:13.198487 INFO::ASW Label was 0.570251920850508 prior to batch effect correction and is now 0.86845463481452 .
2026-05-19 21:49:13.199354 INFO::Total function execution time is 0.0409636497497559 s and adjustment time is 0.0206930637359619 s ( 50.52 )
2026-05-19 21:49:13.20026 INFO::Formatting Data.
2026-05-19 21:49:13.201026 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:13.202035 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.203089 INFO::Found 0 missing values.
2026-05-19 21:49:13.204086 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.
2026-05-19 21:49:13.209124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:13.20977 INFO::Done
2026-05-19 21:49:13.210358 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:13.213536 INFO::Starting hierarchical adjustment
2026-05-19 21:49:13.214334 INFO::Found 2 batches.
2026-05-19 21:49:13.21493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:13.215615 INFO::Using default BPPARAM
2026-05-19 21:49:13.216208 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:13.217234 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-19 21:49:13.235209 INFO::Done
2026-05-19 21:49:13.236112 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:13.239448 INFO::ASW Batch was 0.529070169075456 prior to batch effect correction and is now 0.0708751020773111 .
2026-05-19 21:49:13.240169 INFO::ASW Label was 0.570251920850508 prior to batch effect correction and is now 0.86845463481452 .
2026-05-19 21:49:13.241088 INFO::Total function execution time is 0.0408554077148438 s and adjustment time is 0.0209755897521973 s ( 51.34 )
2026-05-19 21:49:13.464025 INFO::Formatting Data.
2026-05-19 21:49:13.464983 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:13.466011 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.467149 INFO::Found 0 missing values.
2026-05-19 21:49:13.470462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:13.47112 INFO::Done
2026-05-19 21:49:13.47171 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:13.47383 INFO::Starting hierarchical adjustment
2026-05-19 21:49:13.474585 INFO::Found 3 batches.
2026-05-19 21:49:13.475166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:13.475827 INFO::Using default BPPARAM
2026-05-19 21:49:13.476444 INFO::Processing subtree level 1
2026-05-19 21:49:13.571115 INFO::Adjusting the last 1 batches sequentially
2026-05-19 21:49:13.573289 INFO::Done
2026-05-19 21:49:13.57413 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:13.577036 INFO::ASW Batch was -0.100248616576448 prior to batch effect correction and is now -0.100248616576448 .
2026-05-19 21:49:13.578143 INFO::Total function execution time is 0.114141702651978 s and adjustment time is 0.0988101959228516 s ( 86.57 )
2026-05-19 21:49:13.579431 INFO::Formatting Data.
2026-05-19 21:49:13.580181 INFO::Typecasting input to dataframe.
2026-05-19 21:49:13.581061 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:13.582144 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.583363 INFO::Found 0 missing values.
2026-05-19 21:49:13.58672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:13.587402 INFO::Done
2026-05-19 21:49:13.588007 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:13.590406 INFO::Starting hierarchical adjustment
2026-05-19 21:49:13.591244 INFO::Found 3 batches.
2026-05-19 21:49:13.591861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:13.592566 INFO::Using default BPPARAM
2026-05-19 21:49:13.593183 INFO::Processing subtree level 1
2026-05-19 21:49:13.687715 INFO::Adjusting the last 1 batches sequentially
2026-05-19 21:49:13.690143 INFO::Done
2026-05-19 21:49:13.691545 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:13.694749 INFO::ASW Batch was -0.100248616576448 prior to batch effect correction and is now -0.100248616576448 .
2026-05-19 21:49:13.695993 INFO::Total function execution time is 0.116523265838623 s and adjustment time is 0.0990078449249268 s ( 84.97 )
2026-05-19 21:49:13.710879 INFO::Formatting Data.
2026-05-19 21:49:13.711903 INFO::Typecasting input to dataframe.
2026-05-19 21:49:13.712962 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:13.714061 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.715309 INFO::Found 0 missing values.
2026-05-19 21:49:13.718582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:13.719231 INFO::Done
2026-05-19 21:49:13.719842 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:13.722102 INFO::Starting hierarchical adjustment
2026-05-19 21:49:13.722904 INFO::Found 3 batches.
2026-05-19 21:49:13.723521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:13.724219 INFO::Using default BPPARAM
2026-05-19 21:49:13.724844 INFO::Processing subtree level 1
2026-05-19 21:49:13.821226 INFO::Adjusting the last 1 batches sequentially
2026-05-19 21:49:13.824057 INFO::Done
2026-05-19 21:49:13.825111 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:13.828317 INFO::ASW Batch was -0.0815269614989412 prior to batch effect correction and is now -0.0815269614989412 .
2026-05-19 21:49:13.829575 INFO::Total function execution time is 0.118804216384888 s and adjustment time is 0.10120415687561 s ( 85.19 )
2026-05-19 21:49:13.98789 INFO::Formatting Data.
2026-05-19 21:49:13.989092 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:13.990428 INFO::Removing potential empty rows and columns
2026-05-19 21:49:13.993511 INFO::Found 1000 missing values.
2026-05-19 21:49:14.014363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:14.015514 INFO::Done
2026-05-19 21:49:14.016302 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:14.022736 INFO::Starting hierarchical adjustment
2026-05-19 21:49:14.023789 INFO::Found 10 batches.
2026-05-19 21:49:14.02447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:14.025241 INFO::Using default BPPARAM
2026-05-19 21:49:14.025906 INFO::Processing subtree level 1
2026-05-19 21:49:14.196627 INFO::Processing subtree level 2
2026-05-19 21:49:14.360234 INFO::Adjusting the last 1 batches sequentially
2026-05-19 21:49:14.362868 INFO::Done
2026-05-19 21:49:14.363812 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:14.370125 INFO::ASW Batch was 0.495299255998136 prior to batch effect correction and is now 0.495299255998136 .
2026-05-19 21:49:14.37098 INFO::ASW Label was 0.34798901335023 prior to batch effect correction and is now 0.34798901335023 .
2026-05-19 21:49:14.372159 INFO::Total function execution time is 0.384407758712769 s and adjustment time is 0.339263916015625 s ( 88.26 )
2026-05-19 21:49:14.373196 INFO::Formatting Data.
2026-05-19 21:49:14.37397 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:14.375419 INFO::Removing potential empty rows and columns
2026-05-19 21:49:14.378594 INFO::Found 1000 missing values.
2026-05-19 21:49:14.399694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:14.400714 INFO::Done
2026-05-19 21:49:14.401415 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:14.407616 INFO::Starting hierarchical adjustment
2026-05-19 21:49:14.408575 INFO::Found 10 batches.
2026-05-19 21:49:16.487541 INFO::Set up parallel execution backend with 2 workers
2026-05-19 21:49:16.490773 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-19 21:49:17.816932 INFO::Adjusting the last 2 batches sequentially
2026-05-19 21:49:17.820368 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-19 21:49:17.838045 INFO::Done
2026-05-19 21:49:17.838862 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:17.843931 INFO::ASW Batch was 0.495299255998136 prior to batch effect correction and is now 0.495299255998136 .
2026-05-19 21:49:17.844628 INFO::ASW Label was 0.34798901335023 prior to batch effect correction and is now 0.34798901335023 .
2026-05-19 21:49:17.845586 INFO::Total function execution time is 3.47243905067444 s and adjustment time is 3.42962789535522 s ( 98.77 )
2026-05-19 21:49:18.011006 INFO::Formatting Data.
2026-05-19 21:49:18.012115 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.013276 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.014502 INFO::Found 0 missing values.
2026-05-19 21:49:18.018652 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.019323 INFO::Done
2026-05-19 21:49:18.019972 INFO::Acquiring quality metrics before batch effect correction.
2026-05-19 21:49:18.023229 INFO::Starting hierarchical adjustment
2026-05-19 21:49:18.024051 INFO::Found 3 batches.
2026-05-19 21:49:18.024638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-19 21:49:18.025349 INFO::Using default BPPARAM
2026-05-19 21:49:18.025969 INFO::Processing subtree level 1
2026-05-19 21:49:18.148673 INFO::Adjusting the last 1 batches sequentially
2026-05-19 21:49:18.15078 INFO::Done
2026-05-19 21:49:18.151494 INFO::Acquiring quality metrics after batch effect correction.
2026-05-19 21:49:18.154897 INFO::ASW Batch was 0.239137093966225 prior to batch effect correction and is now -0.152291765964575 .
2026-05-19 21:49:18.155557 INFO::ASW Label was -0.197640773681738 prior to batch effect correction and is now -0.106986980360254 .
2026-05-19 21:49:18.156553 INFO::Total function execution time is 0.14565372467041 s and adjustment time is 0.126852989196777 s ( 87.09 )
2026-05-19 21:49:18.281481 INFO::Formatting Data.
2026-05-19 21:49:18.282494 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.28352 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.284626 INFO::Found 2 missing values.
2026-05-19 21:49:18.287628 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.288238 INFO::Done
2026-05-19 21:49:18.317124 INFO::Found NA in Reference column
2026-05-19 21:49:18.326957 INFO::Require at least two references per batch.
2026-05-19 21:49:18.347014 INFO::Formatting Data.
2026-05-19 21:49:18.347852 INFO::Recognized SummarizedExperiment
2026-05-19 21:49:18.348428 INFO::Typecasting input to dataframe.
2026-05-19 21:49:18.357742 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.359012 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.362615 INFO::Found 0 missing values.
2026-05-19 21:49:18.36942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.370155 INFO::Done
2026-05-19 21:49:18.385321 INFO::Formatting Data.
2026-05-19 21:49:18.386154 INFO::Recognized SummarizedExperiment
2026-05-19 21:49:18.386744 INFO::Typecasting input to dataframe.
2026-05-19 21:49:18.404926 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.406516 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.410322 INFO::Found 0 missing values.
2026-05-19 21:49:18.421812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.422779 INFO::Done
2026-05-19 21:49:18.440079 INFO::Formatting Data.
2026-05-19 21:49:18.441089 INFO::Recognized SummarizedExperiment
2026-05-19 21:49:18.441756 INFO::Typecasting input to dataframe.
2026-05-19 21:49:18.459331 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.46057 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.461903 INFO::Found 0 missing values.
2026-05-19 21:49:18.462917 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.
2026-05-19 21:49:18.467728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.468368 INFO::Done
2026-05-19 21:49:18.479363 INFO::Formatting Data.
2026-05-19 21:49:18.480297 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.481297 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.482393 INFO::Found 0 missing values.
2026-05-19 21:49:18.485451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.486045 INFO::Done
2026-05-19 21:49:18.498101 INFO::Formatting Data.
2026-05-19 21:49:18.499076 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.500058 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.501136 INFO::Found 0 missing values.
2026-05-19 21:49:18.504323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.504956 INFO::Done
2026-05-19 21:49:18.536589 INFO::Formatting Data.
2026-05-19 21:49:18.537553 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.538723 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.539937 INFO::Found 1 missing values.
2026-05-19 21:49:18.542562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.543144 INFO::Done
2026-05-19 21:49:18.57308 INFO::Formatting Data.
2026-05-19 21:49:18.574362 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.57542 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.576501 INFO::Found 2 missing values.
2026-05-19 21:49:18.577488 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.
2026-05-19 21:49:18.579835 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.580433 INFO::Done
2026-05-19 21:49:18.591476 INFO::Formatting Data.
2026-05-19 21:49:18.592317 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.593239 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.594221 INFO::Found 2 missing values.
2026-05-19 21:49:18.596059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.596671 INFO::Done
2026-05-19 21:49:18.607468 INFO::Formatting Data.
2026-05-19 21:49:18.60844 INFO::Typecasting input to dataframe.
2026-05-19 21:49:18.609409 INFO::Replacing NaNs with NAs.
2026-05-19 21:49:18.610469 INFO::Removing potential empty rows and columns
2026-05-19 21:49:18.611639 INFO::Found 0 missing values.
2026-05-19 21:49:18.614911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-19 21:49:18.615535 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.234 4.810 22.690
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.012 | 1.369 | 20.948 | |
| compute_asw | 0.024 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.001 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.010 | 0.001 | 0.012 | |