Yannis Schumann
| Snapshot Date: 2026-05-20 13:40 -0400 (Wed, 20 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 2026-05-21 11:32 -0400 (Thu, 21 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: 2026-05-20 21:50:19 -0400 (Wed, 20 May 2026) |
| EndedAt: 2026-05-20 21:51:49 -0400 (Wed, 20 May 2026) |
| EllapsedTime: 90.2 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: 2026-05-21 01:50:20 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 24.979 1.4 18.76
* 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")
2026-05-20 21:51:13.290608 INFO::Formatting Data.
2026-05-20 21:51:13.291972 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:13.302781 INFO::Removing potential empty rows and columns
2026-05-20 21:51:13.5317 INFO::Found 0 missing values.
2026-05-20 21:51:13.53495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:13.535588 INFO::Done
2026-05-20 21:51:13.536165 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:13.548489 INFO::Starting hierarchical adjustment
2026-05-20 21:51:13.549451 INFO::Found 3 batches.
2026-05-20 21:51:13.550051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:13.551177 INFO::Using default BPPARAM
2026-05-20 21:51:13.551761 INFO::Processing subtree level 1
2026-05-20 21:51:13.64361 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:51:13.645379 INFO::Done
2026-05-20 21:51:13.646075 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:13.648607 INFO::ASW Batch was 0.0274612118332707 prior to batch effect correction and is now 0.0274612118332707 .
2026-05-20 21:51:13.649641 INFO::Total function execution time is 0.359630346298218 s and adjustment time is 0.0961120128631592 s ( 26.73 )
2026-05-20 21:51:13.663221 INFO::Formatting Data.
2026-05-20 21:51:13.663987 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:13.66492 INFO::Removing potential empty rows and columns
2026-05-20 21:51:13.666042 INFO::Found 0 missing values.
2026-05-20 21:51:13.667048 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.
2026-05-20 21:51:13.677962 INFO::Formatting Data.
2026-05-20 21:51:13.678708 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:13.679652 INFO::Removing potential empty rows and columns
2026-05-20 21:51:13.680771 INFO::Found 0 missing values.
2026-05-20 21:51:13.681741 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.
2026-05-20 21:51:13.697656 INFO::Formatting Data.
2026-05-20 21:51:13.698453 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:13.699383 INFO::Removing potential empty rows and columns
2026-05-20 21:51:13.70042 INFO::Found 0 missing values.
2026-05-20 21:51:13.701344 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.
2026-05-20 21:51:13.705878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:13.70644 INFO::Done
2026-05-20 21:51:13.707002 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:13.709055 INFO::Starting hierarchical adjustment
2026-05-20 21:51:13.709806 INFO::Found 2 batches.
2026-05-20 21:51:13.710366 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:13.711043 INFO::Using default BPPARAM
2026-05-20 21:51:13.711612 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:13.712586 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:51:13.733287 INFO::Done
2026-05-20 21:51:13.734071 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:13.736145 INFO::ASW Batch was 0.0162415075178771 prior to batch effect correction and is now -0.109734118066718 .
2026-05-20 21:51:13.736994 INFO::Total function execution time is 0.0393836498260498 s and adjustment time is 0.023611307144165 s ( 59.95 )
2026-05-20 21:51:13.739969 INFO::Formatting Data.
2026-05-20 21:51:13.740656 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:13.749711 INFO::Formatting Data.
2026-05-20 21:51:13.750471 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:13.751421 INFO::Removing potential empty rows and columns
2026-05-20 21:51:13.752514 INFO::Found 0 missing values.
2026-05-20 21:51:13.755539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:13.75613 INFO::Done
2026-05-20 21:51:13.756716 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:13.758863 INFO::Starting hierarchical adjustment
2026-05-20 21:51:13.759748 INFO::Found 2 batches.
2026-05-20 21:51:13.760403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:13.761087 INFO::Using default BPPARAM
2026-05-20 21:51:13.761651 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:13.76262 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:51:13.817039 INFO::Done
2026-05-20 21:51:13.817969 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:13.820191 INFO::ASW Batch was 0.0174162127536567 prior to batch effect correction and is now -0.1241026625667 .
2026-05-20 21:51:13.821041 INFO::Total function execution time is 0.0713784694671631 s and adjustment time is 0.0573489665985107 s ( 80.34 )
2026-05-20 21:51:13.822081 INFO::Formatting Data.
2026-05-20 21:51:13.822698 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:13.823572 INFO::Removing potential empty rows and columns
2026-05-20 21:51:13.824586 INFO::Found 0 missing values.
2026-05-20 21:51:13.827348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:13.827919 INFO::Done
2026-05-20 21:51:13.828448 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:13.830389 INFO::Starting hierarchical adjustment
2026-05-20 21:51:13.831098 INFO::Found 2 batches.
2026-05-20 21:51:13.831626 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:13.832255 INFO::Using default BPPARAM
2026-05-20 21:51:13.832792 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:13.833717 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:51:13.848373 INFO::Done
2026-05-20 21:51:13.849109 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:13.851124 INFO::ASW Batch was 0.0174162127536567 prior to batch effect correction and is now -0.1241026625667 .
2026-05-20 21:51:13.851925 INFO::Total function execution time is 0.0298428535461426 s and adjustment time is 0.0173883438110352 s ( 58.27 )
2026-05-20 21:51:16.678331 INFO::Formatting Data.
2026-05-20 21:51:16.679102 INFO::Recognized SummarizedExperiment
2026-05-20 21:51:16.679641 INFO::Typecasting input to dataframe.
2026-05-20 21:51:16.70753 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:16.708774 INFO::Removing potential empty rows and columns
2026-05-20 21:51:16.711965 INFO::Found 0 missing values.
2026-05-20 21:51:16.71798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:16.718557 INFO::Done
2026-05-20 21:51:16.719076 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:16.722202 INFO::Starting hierarchical adjustment
2026-05-20 21:51:16.722912 INFO::Found 2 batches.
2026-05-20 21:51:16.723424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:16.72444 INFO::Using default BPPARAM
2026-05-20 21:51:16.724967 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:16.725925 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:51:16.771346 INFO::Done
2026-05-20 21:51:16.772033 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:16.775063 INFO::ASW Batch was -0.0154133911554912 prior to batch effect correction and is now -0.0873236929537151 .
2026-05-20 21:51:16.775827 INFO::Total function execution time is 0.0977756977081299 s and adjustment time is 0.0485694408416748 s ( 49.67 )
2026-05-20 21:51:16.791632 INFO::Formatting Data.
2026-05-20 21:51:16.792284 INFO::Recognized SummarizedExperiment
2026-05-20 21:51:16.792796 INFO::Typecasting input to dataframe.
2026-05-20 21:51:16.801532 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:16.802599 INFO::Removing potential empty rows and columns
2026-05-20 21:51:16.805971 INFO::Found 0 missing values.
2026-05-20 21:51:16.812997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:16.813555 INFO::Done
2026-05-20 21:51:16.81411 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:16.817209 INFO::Starting hierarchical adjustment
2026-05-20 21:51:16.817872 INFO::Found 2 batches.
2026-05-20 21:51:16.818365 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:16.818967 INFO::Using default BPPARAM
2026-05-20 21:51:16.819475 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:16.820522 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:51:16.842507 INFO::Done
2026-05-20 21:51:16.843273 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:16.846894 INFO::ASW Batch was 0.0042664084816959 prior to batch effect correction and is now 0.0042664084816959 .
2026-05-20 21:51:16.847783 INFO::Total function execution time is 0.0560886859893799 s and adjustment time is 0.0247325897216797 s ( 44.1 )
2026-05-20 21:51:16.865868 INFO::Formatting Data.
2026-05-20 21:51:16.866723 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:16.867653 INFO::Removing potential empty rows and columns
2026-05-20 21:51:16.868717 INFO::Found 0 missing values.
2026-05-20 21:51:16.871815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:16.87238 INFO::Done
2026-05-20 21:51:16.872934 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:16.874958 INFO::Starting hierarchical adjustment
2026-05-20 21:51:16.875692 INFO::Found 3 batches.
2026-05-20 21:51:16.876266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:16.876917 INFO::Using default BPPARAM
2026-05-20 21:51:16.877472 INFO::Processing subtree level 1
2026-05-20 21:51:17.005946 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:51:17.00782 INFO::Done
2026-05-20 21:51:17.008496 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.011022 INFO::ASW Batch was 0.0239807499702122 prior to batch effect correction and is now -0.167702783957669 .
2026-05-20 21:51:17.01201 INFO::Total function execution time is 0.146193027496338 s and adjustment time is 0.132261753082275 s ( 90.47 )
2026-05-20 21:51:17.02658 INFO::Skipping initial DF formatting
2026-05-20 21:51:17.027383 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.031489 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.032357 INFO::Found 5 batches.
2026-05-20 21:51:17.03301 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.033695 INFO::Using default BPPARAM
2026-05-20 21:51:17.034286 INFO::Processing subtree level 1
2026-05-20 21:51:17.145836 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.147633 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:51:17.167706 INFO::Done
2026-05-20 21:51:17.168483 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.172966 INFO::ASW Batch was 0.579756706178296 prior to batch effect correction and is now 0.579756706178296 .
2026-05-20 21:51:17.173666 INFO::ASW Label was 0.337652824001987 prior to batch effect correction and is now 0.337652824001987 .
2026-05-20 21:51:17.174597 INFO::Total function execution time is 0.148084402084351 s and adjustment time is 0.135471820831299 s ( 91.48 )
2026-05-20 21:51:17.192848 INFO::Formatting Data.
2026-05-20 21:51:17.193733 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:17.194756 INFO::Removing potential empty rows and columns
2026-05-20 21:51:17.195819 INFO::Found 0 missing values.
2026-05-20 21:51:17.200195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:17.200839 INFO::Done
2026-05-20 21:51:17.201415 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.204505 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.205282 INFO::Found 5 batches.
2026-05-20 21:51:17.205901 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.206573 INFO::Using default BPPARAM
2026-05-20 21:51:17.20718 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.
2026-05-20 21:51:17.3085 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.310978 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:51:17.334655 INFO::Done
2026-05-20 21:51:17.33554 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.339257 INFO::ASW Batch was 0.52658404839472 prior to batch effect correction and is now -0.0762660453104705 .
2026-05-20 21:51:17.339972 INFO::ASW Label was 0.168242922001992 prior to batch effect correction and is now 0.76375248206963 .
2026-05-20 21:51:17.340939 INFO::Total function execution time is 0.148165464401245 s and adjustment time is 0.129409074783325 s ( 87.34 )
2026-05-20 21:51:17.341889 INFO::Formatting Data.
2026-05-20 21:51:17.342633 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:17.343624 INFO::Removing potential empty rows and columns
2026-05-20 21:51:17.344709 INFO::Found 0 missing values.
2026-05-20 21:51:17.349059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:17.349735 INFO::Done
2026-05-20 21:51:17.350441 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.353733 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.354505 INFO::Found 5 batches.
2026-05-20 21:51:17.355101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.355795 INFO::Using default BPPARAM
2026-05-20 21:51:17.356375 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.
2026-05-20 21:51:17.467783 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.469759 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:51:17.486771 INFO::Done
2026-05-20 21:51:17.487613 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.491097 INFO::ASW Batch was 0.52658404839472 prior to batch effect correction and is now -0.0762660453104705 .
2026-05-20 21:51:17.491805 INFO::ASW Label was 0.168242922001992 prior to batch effect correction and is now 0.76375248206963 .
2026-05-20 21:51:17.492714 INFO::Total function execution time is 0.150840759277344 s and adjustment time is 0.132364511489868 s ( 87.75 )
2026-05-20 21:51:17.507 INFO::Formatting Data.
2026-05-20 21:51:17.507936 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:17.508977 INFO::Removing potential empty rows and columns
2026-05-20 21:51:17.510067 INFO::Found 0 missing values.
2026-05-20 21:51:17.514566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:17.515257 INFO::Done
2026-05-20 21:51:17.51588 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.519031 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.519853 INFO::Found 5 batches.
2026-05-20 21:51:17.520425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.521118 INFO::Using default BPPARAM
2026-05-20 21:51:17.52171 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.
2026-05-20 21:51:17.627974 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.629863 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:51:17.64715 INFO::Done
2026-05-20 21:51:17.648014 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.651656 INFO::ASW Batch was 0.711220260639119 prior to batch effect correction and is now -0.0906861085280693 .
2026-05-20 21:51:17.652447 INFO::ASW Label was 0.138378297460612 prior to batch effect correction and is now 0.695245517024182 .
2026-05-20 21:51:17.653378 INFO::Total function execution time is 0.146473169326782 s and adjustment time is 0.127411603927612 s ( 86.99 )
2026-05-20 21:51:17.654323 INFO::Formatting Data.
2026-05-20 21:51:17.655029 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:17.656043 INFO::Removing potential empty rows and columns
2026-05-20 21:51:17.657135 INFO::Found 0 missing values.
2026-05-20 21:51:17.661578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:17.662268 INFO::Done
2026-05-20 21:51:17.66288 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.666296 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.667152 INFO::Found 5 batches.
2026-05-20 21:51:17.667761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.668485 INFO::Using default BPPARAM
2026-05-20 21:51:17.6691 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.
2026-05-20 21:51:17.781843 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.783757 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:51:17.800975 INFO::Done
2026-05-20 21:51:17.801841 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.80543 INFO::ASW Batch was 0.711220260639119 prior to batch effect correction and is now -0.0906861085280693 .
2026-05-20 21:51:17.806175 INFO::ASW Label was 0.138378297460612 prior to batch effect correction and is now 0.695245517024182 .
2026-05-20 21:51:17.807119 INFO::Total function execution time is 0.152797698974609 s and adjustment time is 0.133967638015747 s ( 87.68 )
2026-05-20 21:51:17.821851 INFO::Formatting Data.
2026-05-20 21:51:17.822772 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:17.823808 INFO::Removing potential empty rows and columns
2026-05-20 21:51:17.82491 INFO::Found 0 missing values.
2026-05-20 21:51:17.827835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:17.82863 INFO::Done
2026-05-20 21:51:17.829234 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.832415 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.833215 INFO::Found 2 batches.
2026-05-20 21:51:17.833812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.834485 INFO::Using default BPPARAM
2026-05-20 21:51:17.835068 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.836076 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:51:17.851441 INFO::Done
2026-05-20 21:51:17.852324 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.862835 INFO::ASW Batch was 0.50894310045816 prior to batch effect correction and is now 0.0934327442078093 .
2026-05-20 21:51:17.863778 INFO::ASW Label was 0.636651183891602 prior to batch effect correction and is now 0.888701856166153 .
2026-05-20 21:51:17.864789 INFO::Total function execution time is 0.043043851852417 s and adjustment time is 0.0183291435241699 s ( 42.58 )
2026-05-20 21:51:17.865743 INFO::Formatting Data.
2026-05-20 21:51:17.866431 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:17.867477 INFO::Removing potential empty rows and columns
2026-05-20 21:51:17.868607 INFO::Found 0 missing values.
2026-05-20 21:51:17.871928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:17.87253 INFO::Done
2026-05-20 21:51:17.873127 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.876514 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.87732 INFO::Found 2 batches.
2026-05-20 21:51:17.877911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.878571 INFO::Using default BPPARAM
2026-05-20 21:51:17.879177 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.88022 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-20 21:51:17.896534 INFO::Done
2026-05-20 21:51:17.897439 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.900721 INFO::ASW Batch was 0.50894310045816 prior to batch effect correction and is now 0.0934327442078093 .
2026-05-20 21:51:17.901415 INFO::ASW Label was 0.636651183891602 prior to batch effect correction and is now 0.888701856166153 .
2026-05-20 21:51:17.902308 INFO::Total function execution time is 0.0366024971008301 s and adjustment time is 0.0193386077880859 s ( 52.83 )
2026-05-20 21:51:17.915415 INFO::Formatting Data.
2026-05-20 21:51:17.916389 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:17.917427 INFO::Removing potential empty rows and columns
2026-05-20 21:51:17.918461 INFO::Found 0 missing values.
2026-05-20 21:51:17.920792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:17.921384 INFO::Done
2026-05-20 21:51:17.921975 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.924141 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.924915 INFO::Found 2 batches.
2026-05-20 21:51:17.925499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.926171 INFO::Using default BPPARAM
2026-05-20 21:51:17.926754 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.927756 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:51:17.960111 INFO::Done
2026-05-20 21:51:17.96094 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:17.963057 INFO::ASW Batch was 0.139284767462662 prior to batch effect correction and is now -0.144219301481899 .
2026-05-20 21:51:17.963954 INFO::Total function execution time is 0.0486555099487305 s and adjustment time is 0.0353379249572754 s ( 72.63 )
2026-05-20 21:51:17.976482 INFO::Formatting Data.
2026-05-20 21:51:17.977389 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:17.97842 INFO::Removing potential empty rows and columns
2026-05-20 21:51:17.979492 INFO::Found 0 missing values.
2026-05-20 21:51:17.980748 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.
2026-05-20 21:51:17.985511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:17.98621 INFO::Done
2026-05-20 21:51:17.986838 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:17.989927 INFO::Starting hierarchical adjustment
2026-05-20 21:51:17.990707 INFO::Found 2 batches.
2026-05-20 21:51:17.991289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:17.991946 INFO::Using default BPPARAM
2026-05-20 21:51:17.992535 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:17.993556 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:51:18.010923 INFO::Done
2026-05-20 21:51:18.011753 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:18.014939 INFO::ASW Batch was 0.695961340260418 prior to batch effect correction and is now -0.035612164722137 .
2026-05-20 21:51:18.015638 INFO::ASW Label was 0.348930170854087 prior to batch effect correction and is now 0.907697347606275 .
2026-05-20 21:51:18.016512 INFO::Total function execution time is 0.0401051044464111 s and adjustment time is 0.0203490257263184 s ( 50.74 )
2026-05-20 21:51:18.017403 INFO::Formatting Data.
2026-05-20 21:51:18.018092 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:18.019079 INFO::Removing potential empty rows and columns
2026-05-20 21:51:18.020133 INFO::Found 0 missing values.
2026-05-20 21:51:18.021117 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.
2026-05-20 21:51:18.025843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:18.026491 INFO::Done
2026-05-20 21:51:18.027083 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:18.030112 INFO::Starting hierarchical adjustment
2026-05-20 21:51:18.03093 INFO::Found 2 batches.
2026-05-20 21:51:18.031513 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:18.032182 INFO::Using default BPPARAM
2026-05-20 21:51:18.032805 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:18.033844 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:51:18.050836 INFO::Done
2026-05-20 21:51:18.051632 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:18.054742 INFO::ASW Batch was 0.695961340260418 prior to batch effect correction and is now -0.035612164722137 .
2026-05-20 21:51:18.055428 INFO::ASW Label was 0.348930170854087 prior to batch effect correction and is now 0.907697347606275 .
2026-05-20 21:51:18.056322 INFO::Total function execution time is 0.038947582244873 s and adjustment time is 0.0200588703155518 s ( 51.5 )
2026-05-20 21:51:18.279919 INFO::Formatting Data.
2026-05-20 21:51:18.280842 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:18.28186 INFO::Removing potential empty rows and columns
2026-05-20 21:51:18.282959 INFO::Found 0 missing values.
2026-05-20 21:51:18.286145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:18.286786 INFO::Done
2026-05-20 21:51:18.287353 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:18.289511 INFO::Starting hierarchical adjustment
2026-05-20 21:51:18.290298 INFO::Found 3 batches.
2026-05-20 21:51:18.290882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:18.291543 INFO::Using default BPPARAM
2026-05-20 21:51:18.292129 INFO::Processing subtree level 1
2026-05-20 21:51:18.380749 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:51:18.382727 INFO::Done
2026-05-20 21:51:18.383476 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:18.386167 INFO::ASW Batch was -0.0966926916473592 prior to batch effect correction and is now -0.0966926916473592 .
2026-05-20 21:51:18.387221 INFO::Total function execution time is 0.107365846633911 s and adjustment time is 0.092540979385376 s ( 86.19 )
2026-05-20 21:51:18.388357 INFO::Formatting Data.
2026-05-20 21:51:18.389081 INFO::Typecasting input to dataframe.
2026-05-20 21:51:18.389895 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:18.390892 INFO::Removing potential empty rows and columns
2026-05-20 21:51:18.392029 INFO::Found 0 missing values.
2026-05-20 21:51:18.395251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:18.395882 INFO::Done
2026-05-20 21:51:18.396473 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:18.398828 INFO::Starting hierarchical adjustment
2026-05-20 21:51:18.399598 INFO::Found 3 batches.
2026-05-20 21:51:18.400187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:18.400855 INFO::Using default BPPARAM
2026-05-20 21:51:18.401428 INFO::Processing subtree level 1
2026-05-20 21:51:18.485159 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:51:18.487192 INFO::Done
2026-05-20 21:51:18.488023 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:18.490782 INFO::ASW Batch was -0.0966926916473592 prior to batch effect correction and is now -0.0966926916473592 .
2026-05-20 21:51:18.491868 INFO::Total function execution time is 0.103470087051392 s and adjustment time is 0.0877170562744141 s ( 84.78 )
2026-05-20 21:51:18.506092 INFO::Formatting Data.
2026-05-20 21:51:18.507076 INFO::Typecasting input to dataframe.
2026-05-20 21:51:18.508058 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:18.509079 INFO::Removing potential empty rows and columns
2026-05-20 21:51:18.510224 INFO::Found 0 missing values.
2026-05-20 21:51:18.5134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:18.514028 INFO::Done
2026-05-20 21:51:18.514605 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:18.516881 INFO::Starting hierarchical adjustment
2026-05-20 21:51:18.517652 INFO::Found 3 batches.
2026-05-20 21:51:18.518276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:18.518978 INFO::Using default BPPARAM
2026-05-20 21:51:18.51957 INFO::Processing subtree level 1
2026-05-20 21:51:18.602608 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:51:18.604583 INFO::Done
2026-05-20 21:51:18.605362 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:18.608087 INFO::ASW Batch was -0.0477309394052876 prior to batch effect correction and is now -0.0477309394052876 .
2026-05-20 21:51:18.609184 INFO::Total function execution time is 0.103192806243896 s and adjustment time is 0.0870673656463623 s ( 84.37 )
2026-05-20 21:51:18.746242 INFO::Formatting Data.
2026-05-20 21:51:18.747207 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:18.748476 INFO::Removing potential empty rows and columns
2026-05-20 21:51:18.751452 INFO::Found 1000 missing values.
2026-05-20 21:51:18.771731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:18.772702 INFO::Done
2026-05-20 21:51:18.773361 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:18.779153 INFO::Starting hierarchical adjustment
2026-05-20 21:51:18.780077 INFO::Found 10 batches.
2026-05-20 21:51:18.78071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:18.781394 INFO::Using default BPPARAM
2026-05-20 21:51:18.782026 INFO::Processing subtree level 1
2026-05-20 21:51:18.92221 INFO::Processing subtree level 2
2026-05-20 21:51:19.066528 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:51:19.068816 INFO::Done
2026-05-20 21:51:19.06967 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:19.075538 INFO::ASW Batch was 0.501236733710615 prior to batch effect correction and is now 0.501236733710615 .
2026-05-20 21:51:19.076379 INFO::ASW Label was 0.344304015635293 prior to batch effect correction and is now 0.344304015635293 .
2026-05-20 21:51:19.077469 INFO::Total function execution time is 0.331298351287842 s and adjustment time is 0.288893938064575 s ( 87.2 )
2026-05-20 21:51:19.078452 INFO::Formatting Data.
2026-05-20 21:51:19.079213 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:19.080574 INFO::Removing potential empty rows and columns
2026-05-20 21:51:19.083776 INFO::Found 1000 missing values.
2026-05-20 21:51:19.105249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:19.106355 INFO::Done
2026-05-20 21:51:19.107086 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:19.113562 INFO::Starting hierarchical adjustment
2026-05-20 21:51:19.114592 INFO::Found 10 batches.
2026-05-20 21:51:20.346472 INFO::Set up parallel execution backend with 2 workers
2026-05-20 21:51:20.354144 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-20 21:51:21.452871 INFO::Adjusting the last 2 batches sequentially
2026-05-20 21:51:21.455616 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-20 21:51:21.48054 INFO::Done
2026-05-20 21:51:21.481529 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:21.48642 INFO::ASW Batch was 0.501236733710615 prior to batch effect correction and is now 0.501236733710615 .
2026-05-20 21:51:21.487041 INFO::ASW Label was 0.344304015635293 prior to batch effect correction and is now 0.344304015635293 .
2026-05-20 21:51:21.487957 INFO::Total function execution time is 2.40957260131836 s and adjustment time is 2.36610531806946 s ( 98.2 )
2026-05-20 21:51:21.631047 INFO::Formatting Data.
2026-05-20 21:51:21.631909 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:21.632882 INFO::Removing potential empty rows and columns
2026-05-20 21:51:21.633989 INFO::Found 0 missing values.
2026-05-20 21:51:21.637626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:21.638205 INFO::Done
2026-05-20 21:51:21.638805 INFO::Acquiring quality metrics before batch effect correction.
2026-05-20 21:51:21.641597 INFO::Starting hierarchical adjustment
2026-05-20 21:51:21.642334 INFO::Found 3 batches.
2026-05-20 21:51:21.64292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-20 21:51:21.64357 INFO::Using default BPPARAM
2026-05-20 21:51:21.644161 INFO::Processing subtree level 1
2026-05-20 21:51:21.746567 INFO::Adjusting the last 1 batches sequentially
2026-05-20 21:51:21.74853 INFO::Done
2026-05-20 21:51:21.749212 INFO::Acquiring quality metrics after batch effect correction.
2026-05-20 21:51:21.75245 INFO::ASW Batch was 0.249792938640229 prior to batch effect correction and is now -0.162142557597596 .
2026-05-20 21:51:21.75309 INFO::ASW Label was -0.180858086946222 prior to batch effect correction and is now 0.0878008712579098 .
2026-05-20 21:51:21.753998 INFO::Total function execution time is 0.123015403747559 s and adjustment time is 0.106313467025757 s ( 86.42 )
2026-05-20 21:51:21.870359 INFO::Formatting Data.
2026-05-20 21:51:21.871233 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:21.872189 INFO::Removing potential empty rows and columns
2026-05-20 21:51:21.87326 INFO::Found 2 missing values.
2026-05-20 21:51:21.876073 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:21.876623 INFO::Done
2026-05-20 21:51:21.903241 INFO::Found NA in Reference column
2026-05-20 21:51:21.912457 INFO::Require at least two references per batch.
2026-05-20 21:51:21.934046 INFO::Formatting Data.
2026-05-20 21:51:21.934859 INFO::Recognized SummarizedExperiment
2026-05-20 21:51:21.935427 INFO::Typecasting input to dataframe.
2026-05-20 21:51:21.945512 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:21.946709 INFO::Removing potential empty rows and columns
2026-05-20 21:51:21.950233 INFO::Found 0 missing values.
2026-05-20 21:51:21.95696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:21.957596 INFO::Done
2026-05-20 21:51:21.973235 INFO::Formatting Data.
2026-05-20 21:51:21.974038 INFO::Recognized SummarizedExperiment
2026-05-20 21:51:21.974604 INFO::Typecasting input to dataframe.
2026-05-20 21:51:21.992026 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:21.993309 INFO::Removing potential empty rows and columns
2026-05-20 21:51:21.996963 INFO::Found 0 missing values.
2026-05-20 21:51:22.007929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:22.008602 INFO::Done
2026-05-20 21:51:22.024211 INFO::Formatting Data.
2026-05-20 21:51:22.025059 INFO::Recognized SummarizedExperiment
2026-05-20 21:51:22.025658 INFO::Typecasting input to dataframe.
2026-05-20 21:51:22.04338 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:22.044568 INFO::Removing potential empty rows and columns
2026-05-20 21:51:22.045805 INFO::Found 0 missing values.
2026-05-20 21:51:22.046787 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.
2026-05-20 21:51:22.051615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:22.052236 INFO::Done
2026-05-20 21:51:22.063223 INFO::Formatting Data.
2026-05-20 21:51:22.06412 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:22.065105 INFO::Removing potential empty rows and columns
2026-05-20 21:51:22.066193 INFO::Found 0 missing values.
2026-05-20 21:51:22.069234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:22.069843 INFO::Done
2026-05-20 21:51:22.082112 INFO::Formatting Data.
2026-05-20 21:51:22.083014 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:22.083974 INFO::Removing potential empty rows and columns
2026-05-20 21:51:22.085071 INFO::Found 0 missing values.
2026-05-20 21:51:22.088236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:22.08887 INFO::Done
2026-05-20 21:51:22.126173 INFO::Formatting Data.
2026-05-20 21:51:22.127234 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:22.12839 INFO::Removing potential empty rows and columns
2026-05-20 21:51:22.12969 INFO::Found 1 missing values.
2026-05-20 21:51:22.132526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:22.133148 INFO::Done
2026-05-20 21:51:22.153952 INFO::Formatting Data.
2026-05-20 21:51:22.154896 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:22.155969 INFO::Removing potential empty rows and columns
2026-05-20 21:51:22.157029 INFO::Found 2 missing values.
2026-05-20 21:51:22.158052 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.
2026-05-20 21:51:22.160536 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:22.161162 INFO::Done
2026-05-20 21:51:22.172343 INFO::Formatting Data.
2026-05-20 21:51:22.173208 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:22.174205 INFO::Removing potential empty rows and columns
2026-05-20 21:51:22.175291 INFO::Found 2 missing values.
2026-05-20 21:51:22.177378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:22.178073 INFO::Done
2026-05-20 21:51:22.190619 INFO::Formatting Data.
2026-05-20 21:51:22.191629 INFO::Typecasting input to dataframe.
2026-05-20 21:51:22.192696 INFO::Replacing NaNs with NAs.
2026-05-20 21:51:22.193816 INFO::Removing potential empty rows and columns
2026-05-20 21:51:22.195001 INFO::Found 0 missing values.
2026-05-20 21:51:22.198293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-20 21:51:22.198966 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.342 3.214 20.359
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.979 | 1.400 | 18.760 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.013 | 0.000 | 0.013 | |