Yannis Schumann
| Snapshot Date: 2025-12-01 13:40 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-02 11:35 -0500 (Tue, 02 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 167/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-12-01 18:42:56 -0500 (Mon, 01 Dec 2025) |
| EndedAt: 2025-12-01 18:43:32 -0500 (Mon, 01 Dec 2025) |
| EllapsedTime: 36.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 10.3 0.442 7.753
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-12-01 18:43:23.806362 INFO::Formatting Data.
2025-12-01 18:43:23.808281 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:23.812798 INFO::Removing potential empty rows and columns
2025-12-01 18:43:23.928756 INFO::Found 0 missing values.
2025-12-01 18:43:23.929896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:23.930107 INFO::Done
2025-12-01 18:43:23.930281 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:23.935308 INFO::Starting hierarchical adjustment
2025-12-01 18:43:23.935652 INFO::Found 3 batches.
2025-12-01 18:43:23.935895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:23.936349 INFO::Using default BPPARAM
2025-12-01 18:43:23.93662 INFO::Processing subtree level 1
2025-12-01 18:43:24.00969 INFO::Adjusting the last 1 batches sequentially
2025-12-01 18:43:24.011161 INFO::Done
2025-12-01 18:43:24.011483 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:24.013948 INFO::ASW Batch was -0.0855199548418321 prior to batch effect correction and is now -0.0855199548418321 .
2025-12-01 18:43:24.014976 INFO::Total function execution time is 0.208843946456909 s and adjustment time is 0.0755949020385742 s ( 36.2 )
2025-12-01 18:43:24.023787 INFO::Formatting Data.
2025-12-01 18:43:24.024087 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:24.024452 INFO::Removing potential empty rows and columns
2025-12-01 18:43:24.024928 INFO::Found 0 missing values.
2025-12-01 18:43:24.025266 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-01 18:43:24.030099 INFO::Formatting Data.
2025-12-01 18:43:24.030402 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:24.030791 INFO::Removing potential empty rows and columns
2025-12-01 18:43:24.032808 INFO::Found 0 missing values.
2025-12-01 18:43:24.033317 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-01 18:43:24.04325 INFO::Formatting Data.
2025-12-01 18:43:24.043815 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:24.044358 INFO::Removing potential empty rows and columns
2025-12-01 18:43:24.044909 INFO::Found 0 missing values.
2025-12-01 18:43:24.045317 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-01 18:43:24.047381 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:24.047614 INFO::Done
2025-12-01 18:43:24.047846 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:24.048943 INFO::Starting hierarchical adjustment
2025-12-01 18:43:24.049311 INFO::Found 2 batches.
2025-12-01 18:43:24.049578 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:24.049922 INFO::Using default BPPARAM
2025-12-01 18:43:24.05017 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:24.050681 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 18:43:24.061117 INFO::Done
2025-12-01 18:43:24.061362 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:24.062074 INFO::ASW Batch was 0.102753648390854 prior to batch effect correction and is now -0.045518870993756 .
2025-12-01 18:43:24.062348 INFO::Total function execution time is 0.0197799205780029 s and adjustment time is 0.0118811130523682 s ( 60.07 )
2025-12-01 18:43:24.063636 INFO::Formatting Data.
2025-12-01 18:43:24.064021 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:24.067609 INFO::Formatting Data.
2025-12-01 18:43:24.067863 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:24.068191 INFO::Removing potential empty rows and columns
2025-12-01 18:43:24.068581 INFO::Found 0 missing values.
2025-12-01 18:43:24.069655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:24.069842 INFO::Done
2025-12-01 18:43:24.070008 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:24.070726 INFO::Starting hierarchical adjustment
2025-12-01 18:43:24.07096 INFO::Found 2 batches.
2025-12-01 18:43:24.071139 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:24.071351 INFO::Using default BPPARAM
2025-12-01 18:43:24.071521 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:24.071819 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:24.099491 INFO::Done
2025-12-01 18:43:24.099765 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:24.100469 INFO::ASW Batch was 0.0326914019166982 prior to batch effect correction and is now -0.129137517229546 .
2025-12-01 18:43:24.100739 INFO::Total function execution time is 0.0331459045410156 s and adjustment time is 0.0285689830780029 s ( 86.19 )
2025-12-01 18:43:24.101082 INFO::Formatting Data.
2025-12-01 18:43:24.10127 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:24.101542 INFO::Removing potential empty rows and columns
2025-12-01 18:43:24.101854 INFO::Found 0 missing values.
2025-12-01 18:43:24.103056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:24.103251 INFO::Done
2025-12-01 18:43:24.103413 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:24.104018 INFO::Starting hierarchical adjustment
2025-12-01 18:43:24.10425 INFO::Found 2 batches.
2025-12-01 18:43:24.104433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:24.104673 INFO::Using default BPPARAM
2025-12-01 18:43:24.104881 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:24.105231 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:24.111054 INFO::Done
2025-12-01 18:43:24.111306 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:24.112039 INFO::ASW Batch was 0.0326914019166982 prior to batch effect correction and is now -0.129137517229546 .
2025-12-01 18:43:24.11235 INFO::Total function execution time is 0.0112390518188477 s and adjustment time is 0.00683999061584473 s ( 60.86 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-01 18:43:25.408927 INFO::Formatting Data.
2025-12-01 18:43:25.409186 INFO::Recognized SummarizedExperiment
2025-12-01 18:43:25.40934 INFO::Typecasting input to dataframe.
2025-12-01 18:43:25.420287 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:25.420672 INFO::Removing potential empty rows and columns
2025-12-01 18:43:25.421931 INFO::Found 0 missing values.
2025-12-01 18:43:25.424186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:25.424388 INFO::Done
2025-12-01 18:43:25.424575 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:25.425918 INFO::Starting hierarchical adjustment
2025-12-01 18:43:25.426172 INFO::Found 2 batches.
2025-12-01 18:43:25.426324 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:25.426685 INFO::Using default BPPARAM
2025-12-01 18:43:25.426864 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:25.427205 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 18:43:25.450165 INFO::Done
2025-12-01 18:43:25.450479 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:25.451899 INFO::ASW Batch was 0.0188429957936834 prior to batch effect correction and is now -0.0945182445274286 .
2025-12-01 18:43:25.452193 INFO::Total function execution time is 0.0433609485626221 s and adjustment time is 0.0240209102630615 s ( 55.4 )
Warning: stack imbalance in '{', 73 then 75
2025-12-01 18:43:25.459108 INFO::Formatting Data.
2025-12-01 18:43:25.45935 INFO::Recognized SummarizedExperiment
2025-12-01 18:43:25.459516 INFO::Typecasting input to dataframe.
2025-12-01 18:43:25.462561 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:25.462921 INFO::Removing potential empty rows and columns
2025-12-01 18:43:25.464056 INFO::Found 0 missing values.
2025-12-01 18:43:25.466177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:25.466341 INFO::Done
2025-12-01 18:43:25.466495 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:25.467656 INFO::Starting hierarchical adjustment
2025-12-01 18:43:25.46786 INFO::Found 2 batches.
2025-12-01 18:43:25.468008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:25.468187 INFO::Using default BPPARAM
2025-12-01 18:43:25.468334 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:25.468611 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 18:43:25.476941 INFO::Done
2025-12-01 18:43:25.477166 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:25.478349 INFO::ASW Batch was 0.0035300525516856 prior to batch effect correction and is now 0.0035300525516856 .
2025-12-01 18:43:25.478618 INFO::Total function execution time is 0.0194990634918213 s and adjustment time is 0.00911521911621094 s ( 46.75 )
2025-12-01 18:43:25.48548 INFO::Formatting Data.
2025-12-01 18:43:25.485717 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:25.485987 INFO::Removing potential empty rows and columns
2025-12-01 18:43:25.486315 INFO::Found 0 missing values.
2025-12-01 18:43:25.487182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:25.487343 INFO::Done
2025-12-01 18:43:25.487494 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:25.488142 INFO::Starting hierarchical adjustment
2025-12-01 18:43:25.488345 INFO::Found 3 batches.
2025-12-01 18:43:25.488502 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:25.488685 INFO::Using default BPPARAM
2025-12-01 18:43:25.488843 INFO::Processing subtree level 1
2025-12-01 18:43:25.566744 INFO::Adjusting the last 1 batches sequentially
2025-12-01 18:43:25.568142 INFO::Done
2025-12-01 18:43:25.568543 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:25.570432 INFO::ASW Batch was -0.0784721189845587 prior to batch effect correction and is now -0.166067447359412 .
2025-12-01 18:43:25.57115 INFO::Total function execution time is 0.0856409072875977 s and adjustment time is 0.0798261165618896 s ( 93.21 )
2025-12-01 18:43:25.578732 INFO::Skipping initial DF formatting
2025-12-01 18:43:25.579015 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:25.580441 INFO::Starting hierarchical adjustment
2025-12-01 18:43:25.580727 INFO::Found 5 batches.
2025-12-01 18:43:25.580899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:25.581126 INFO::Using default BPPARAM
2025-12-01 18:43:25.581492 INFO::Processing subtree level 1
2025-12-01 18:43:25.638856 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:25.64145 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 18:43:25.651182 INFO::Done
2025-12-01 18:43:25.651638 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:25.654545 INFO::ASW Batch was 0.606762709619244 prior to batch effect correction and is now 0.606762709619244 .
2025-12-01 18:43:25.654989 INFO::ASW Label was 0.372852996407996 prior to batch effect correction and is now 0.372852996407996 .
2025-12-01 18:43:25.655778 INFO::Total function execution time is 0.0770478248596191 s and adjustment time is 0.0704989433288574 s ( 91.5 )
2025-12-01 18:43:25.665329 INFO::Formatting Data.
2025-12-01 18:43:25.665605 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:25.666074 INFO::Removing potential empty rows and columns
2025-12-01 18:43:25.666441 INFO::Found 0 missing values.
2025-12-01 18:43:25.67065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:25.670986 INFO::Done
2025-12-01 18:43:25.671225 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:25.672555 INFO::Starting hierarchical adjustment
2025-12-01 18:43:25.672817 INFO::Found 5 batches.
2025-12-01 18:43:25.67301 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:25.673264 INFO::Using default BPPARAM
2025-12-01 18:43:25.673449 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:25.73536 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:25.738932 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:25.75825 INFO::Done
2025-12-01 18:43:25.758746 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:25.760699 INFO::ASW Batch was 0.373059679416556 prior to batch effect correction and is now 0.00398379308719279 .
2025-12-01 18:43:25.761148 INFO::ASW Label was 0.44010294224231 prior to batch effect correction and is now 0.741039525267199 .
2025-12-01 18:43:25.761746 INFO::Total function execution time is 0.0963459014892578 s and adjustment time is 0.0854620933532715 s ( 88.7 )
2025-12-01 18:43:25.762122 INFO::Formatting Data.
2025-12-01 18:43:25.762409 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:25.7628 INFO::Removing potential empty rows and columns
2025-12-01 18:43:25.763251 INFO::Found 0 missing values.
2025-12-01 18:43:25.764968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:25.765191 INFO::Done
2025-12-01 18:43:25.765407 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:25.766611 INFO::Starting hierarchical adjustment
2025-12-01 18:43:25.767023 INFO::Found 5 batches.
2025-12-01 18:43:25.767214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:25.767444 INFO::Using default BPPARAM
2025-12-01 18:43:25.767616 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:25.835664 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:25.837488 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:25.845694 INFO::Done
2025-12-01 18:43:25.846074 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:25.847495 INFO::ASW Batch was 0.373059679416556 prior to batch effect correction and is now 0.00398379308719279 .
2025-12-01 18:43:25.847697 INFO::ASW Label was 0.44010294224231 prior to batch effect correction and is now 0.741039525267199 .
2025-12-01 18:43:25.848327 INFO::Total function execution time is 0.0861730575561523 s and adjustment time is 0.0788500308990479 s ( 91.5 )
2025-12-01 18:43:25.857185 INFO::Formatting Data.
2025-12-01 18:43:25.857481 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:25.857819 INFO::Removing potential empty rows and columns
2025-12-01 18:43:25.858209 INFO::Found 0 missing values.
2025-12-01 18:43:25.859444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:25.859621 INFO::Done
2025-12-01 18:43:25.859788 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:25.860875 INFO::Starting hierarchical adjustment
2025-12-01 18:43:25.861115 INFO::Found 5 batches.
2025-12-01 18:43:25.861279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:25.861485 INFO::Using default BPPARAM
2025-12-01 18:43:25.861649 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:25.921424 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:25.927087 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:25.937864 INFO::Done
2025-12-01 18:43:25.938361 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:25.940574 INFO::ASW Batch was 0.344062550903439 prior to batch effect correction and is now -0.0112622283219296 .
2025-12-01 18:43:25.941085 INFO::ASW Label was 0.425317461869804 prior to batch effect correction and is now 0.812639429990478 .
2025-12-01 18:43:25.941759 INFO::Total function execution time is 0.0843188762664795 s and adjustment time is 0.0767779350280762 s ( 91.06 )
2025-12-01 18:43:25.942303 INFO::Formatting Data.
2025-12-01 18:43:25.942527 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:25.942893 INFO::Removing potential empty rows and columns
2025-12-01 18:43:25.943304 INFO::Found 0 missing values.
2025-12-01 18:43:25.944762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:25.944951 INFO::Done
2025-12-01 18:43:25.945171 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:25.946318 INFO::Starting hierarchical adjustment
2025-12-01 18:43:25.946854 INFO::Found 5 batches.
2025-12-01 18:43:25.947248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:25.94752 INFO::Using default BPPARAM
2025-12-01 18:43:25.947723 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:26.013 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:26.03087 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:26.039932 INFO::Done
2025-12-01 18:43:26.040348 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.042384 INFO::ASW Batch was 0.344062550903439 prior to batch effect correction and is now -0.0112622283219296 .
2025-12-01 18:43:26.042604 INFO::ASW Label was 0.425317461869804 prior to batch effect correction and is now 0.812639429990478 .
2025-12-01 18:43:26.043251 INFO::Total function execution time is 0.100780963897705 s and adjustment time is 0.0933680534362793 s ( 92.64 )
2025-12-01 18:43:26.051838 INFO::Formatting Data.
2025-12-01 18:43:26.052173 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.052541 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.052964 INFO::Found 0 missing values.
2025-12-01 18:43:26.054017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.054302 INFO::Done
2025-12-01 18:43:26.054512 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.055579 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.055871 INFO::Found 2 batches.
2025-12-01 18:43:26.056087 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.056361 INFO::Using default BPPARAM
2025-12-01 18:43:26.056563 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:26.056892 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:26.063003 INFO::Done
2025-12-01 18:43:26.063215 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.065875 INFO::ASW Batch was 0.792098371676845 prior to batch effect correction and is now -0.00555338570492453 .
2025-12-01 18:43:26.066145 INFO::ASW Label was 0.259713210394887 prior to batch effect correction and is now 0.861161673724062 .
2025-12-01 18:43:26.066475 INFO::Total function execution time is 0.0147089958190918 s and adjustment time is 0.00718593597412109 s ( 48.85 )
2025-12-01 18:43:26.067007 INFO::Formatting Data.
2025-12-01 18:43:26.06719 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.067498 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.067803 INFO::Found 0 missing values.
2025-12-01 18:43:26.068746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.068944 INFO::Done
2025-12-01 18:43:26.069148 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.070239 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.070614 INFO::Found 2 batches.
2025-12-01 18:43:26.070845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.071106 INFO::Using default BPPARAM
2025-12-01 18:43:26.071347 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:26.071736 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 18:43:26.079854 INFO::Done
2025-12-01 18:43:26.080314 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.081272 INFO::ASW Batch was 0.792098371676845 prior to batch effect correction and is now -0.00555338570492453 .
2025-12-01 18:43:26.081474 INFO::ASW Label was 0.259713210394887 prior to batch effect correction and is now 0.861161673724062 .
2025-12-01 18:43:26.081751 INFO::Total function execution time is 0.0147697925567627 s and adjustment time is 0.00934004783630371 s ( 63.24 )
2025-12-01 18:43:26.087731 INFO::Formatting Data.
2025-12-01 18:43:26.087969 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.088246 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.088537 INFO::Found 0 missing values.
2025-12-01 18:43:26.089191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.08936 INFO::Done
2025-12-01 18:43:26.089524 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.091223 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.091465 INFO::Found 2 batches.
2025-12-01 18:43:26.091764 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.092768 INFO::Using default BPPARAM
2025-12-01 18:43:26.093071 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:26.093896 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 18:43:26.106583 INFO::Done
2025-12-01 18:43:26.106872 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.107716 INFO::ASW Batch was 0.180361522942422 prior to batch effect correction and is now -0.130538209411662 .
2025-12-01 18:43:26.108034 INFO::Total function execution time is 0.0203068256378174 s and adjustment time is 0.0151300430297852 s ( 74.51 )
2025-12-01 18:43:26.113517 INFO::Formatting Data.
2025-12-01 18:43:26.113764 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.114058 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.114437 INFO::Found 0 missing values.
2025-12-01 18:43:26.114906 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-01 18:43:26.116476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.116692 INFO::Done
2025-12-01 18:43:26.116883 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.11787 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.118104 INFO::Found 2 batches.
2025-12-01 18:43:26.118274 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.118476 INFO::Using default BPPARAM
2025-12-01 18:43:26.118636 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:26.11892 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 18:43:26.124491 INFO::Done
2025-12-01 18:43:26.124727 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.125704 INFO::ASW Batch was 0.852767369533894 prior to batch effect correction and is now -0.0269845932843706 .
2025-12-01 18:43:26.125889 INFO::ASW Label was 0.158617693559494 prior to batch effect correction and is now 0.890717773347059 .
2025-12-01 18:43:26.126138 INFO::Total function execution time is 0.0126481056213379 s and adjustment time is 0.00641703605651855 s ( 50.74 )
2025-12-01 18:43:26.126377 INFO::Formatting Data.
2025-12-01 18:43:26.126553 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.126831 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.127123 INFO::Found 0 missing values.
2025-12-01 18:43:26.127398 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-01 18:43:26.128693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.12887 INFO::Done
2025-12-01 18:43:26.129029 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.129879 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.13012 INFO::Found 2 batches.
2025-12-01 18:43:26.130298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.130527 INFO::Using default BPPARAM
2025-12-01 18:43:26.130709 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:26.130992 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 18:43:26.1361 INFO::Done
2025-12-01 18:43:26.136301 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.137192 INFO::ASW Batch was 0.852767369533894 prior to batch effect correction and is now -0.0269845932843706 .
2025-12-01 18:43:26.137433 INFO::ASW Label was 0.158617693559494 prior to batch effect correction and is now 0.890717773347059 .
2025-12-01 18:43:26.137736 INFO::Total function execution time is 0.0113468170166016 s and adjustment time is 0.00602221488952637 s ( 53.07 )
2025-12-01 18:43:26.216198 INFO::Formatting Data.
2025-12-01 18:43:26.216619 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.217035 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.217481 INFO::Found 0 missing values.
2025-12-01 18:43:26.218693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.218957 INFO::Done
2025-12-01 18:43:26.219161 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.220143 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.220415 INFO::Found 3 batches.
2025-12-01 18:43:26.220606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.220841 INFO::Using default BPPARAM
2025-12-01 18:43:26.221043 INFO::Processing subtree level 1
2025-12-01 18:43:26.26788 INFO::Adjusting the last 1 batches sequentially
2025-12-01 18:43:26.269521 INFO::Done
2025-12-01 18:43:26.269738 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.2717 INFO::ASW Batch was -0.131539672833231 prior to batch effect correction and is now -0.131539672833231 .
2025-12-01 18:43:26.272431 INFO::Total function execution time is 0.0563218593597412 s and adjustment time is 0.0491728782653809 s ( 87.31 )
2025-12-01 18:43:26.273006 INFO::Formatting Data.
2025-12-01 18:43:26.273213 INFO::Typecasting input to dataframe.
2025-12-01 18:43:26.273459 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.273771 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.274169 INFO::Found 0 missing values.
2025-12-01 18:43:26.275131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.275326 INFO::Done
2025-12-01 18:43:26.275496 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.276163 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.276395 INFO::Found 3 batches.
2025-12-01 18:43:26.276554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.276764 INFO::Using default BPPARAM
2025-12-01 18:43:26.276924 INFO::Processing subtree level 1
2025-12-01 18:43:26.321243 INFO::Adjusting the last 1 batches sequentially
2025-12-01 18:43:26.323248 INFO::Done
2025-12-01 18:43:26.323837 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.326492 INFO::ASW Batch was -0.131539672833231 prior to batch effect correction and is now -0.131539672833231 .
2025-12-01 18:43:26.327827 INFO::Total function execution time is 0.0549468994140625 s and adjustment time is 0.0468900203704834 s ( 85.34 )
2025-12-01 18:43:26.336212 INFO::Formatting Data.
2025-12-01 18:43:26.336536 INFO::Typecasting input to dataframe.
2025-12-01 18:43:26.336847 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.337299 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.337831 INFO::Found 0 missing values.
2025-12-01 18:43:26.338753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.338928 INFO::Done
2025-12-01 18:43:26.339095 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.33997 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.340225 INFO::Found 3 batches.
2025-12-01 18:43:26.340388 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.340619 INFO::Using default BPPARAM
2025-12-01 18:43:26.340778 INFO::Processing subtree level 1
2025-12-01 18:43:26.381568 INFO::Adjusting the last 1 batches sequentially
2025-12-01 18:43:26.383088 INFO::Done
2025-12-01 18:43:26.383324 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.385475 INFO::ASW Batch was -0.110135497848645 prior to batch effect correction and is now -0.110135497848645 .
2025-12-01 18:43:26.38613 INFO::Total function execution time is 0.0500640869140625 s and adjustment time is 0.0429298877716064 s ( 85.75 )
2025-12-01 18:43:26.459073 INFO::Formatting Data.
2025-12-01 18:43:26.459378 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.459864 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.460891 INFO::Found 1000 missing values.
2025-12-01 18:43:26.466916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.467169 INFO::Done
2025-12-01 18:43:26.467345 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.46971 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.470042 INFO::Found 10 batches.
2025-12-01 18:43:26.470273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:26.470613 INFO::Using default BPPARAM
2025-12-01 18:43:26.470887 INFO::Processing subtree level 1
2025-12-01 18:43:26.533947 INFO::Processing subtree level 2
2025-12-01 18:43:26.692833 INFO::Adjusting the last 1 batches sequentially
2025-12-01 18:43:26.694522 INFO::Done
2025-12-01 18:43:26.694818 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:26.705388 INFO::ASW Batch was 0.494434574773868 prior to batch effect correction and is now 0.494434574773868 .
2025-12-01 18:43:26.705914 INFO::ASW Label was 0.353819095566223 prior to batch effect correction and is now 0.353819095566223 .
2025-12-01 18:43:26.70968 INFO::Total function execution time is 0.250201940536499 s and adjustment time is 0.22454309463501 s ( 89.74 )
2025-12-01 18:43:26.710988 INFO::Formatting Data.
2025-12-01 18:43:26.71142 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:26.712228 INFO::Removing potential empty rows and columns
2025-12-01 18:43:26.748042 INFO::Found 1000 missing values.
2025-12-01 18:43:26.75813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:26.758494 INFO::Done
2025-12-01 18:43:26.758793 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:26.761396 INFO::Starting hierarchical adjustment
2025-12-01 18:43:26.761729 INFO::Found 10 batches.
2025-12-01 18:43:27.228814 INFO::Set up parallel execution backend with 2 workers
2025-12-01 18:43:27.229143 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-01 18:43:27.832552 INFO::Adjusting the last 2 batches sequentially
2025-12-01 18:43:27.833182 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 18:43:27.839689 INFO::Done
2025-12-01 18:43:27.839949 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:27.842047 INFO::ASW Batch was 0.494434574773868 prior to batch effect correction and is now 0.494434574773868 .
2025-12-01 18:43:27.842248 INFO::ASW Label was 0.353819095566223 prior to batch effect correction and is now 0.353819095566223 .
2025-12-01 18:43:27.842531 INFO::Total function execution time is 1.13155388832092 s and adjustment time is 1.07801008224487 s ( 95.27 )
2025-12-01 18:43:27.926307 INFO::Formatting Data.
2025-12-01 18:43:27.926636 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:27.927017 INFO::Removing potential empty rows and columns
2025-12-01 18:43:27.927511 INFO::Found 0 missing values.
2025-12-01 18:43:27.929061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:27.929269 INFO::Done
2025-12-01 18:43:27.929487 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 18:43:27.930673 INFO::Starting hierarchical adjustment
2025-12-01 18:43:27.930972 INFO::Found 3 batches.
2025-12-01 18:43:27.931199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 18:43:27.931685 INFO::Using default BPPARAM
2025-12-01 18:43:27.931884 INFO::Processing subtree level 1
2025-12-01 18:43:27.996069 INFO::Adjusting the last 1 batches sequentially
2025-12-01 18:43:27.997584 INFO::Done
2025-12-01 18:43:27.997824 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 18:43:28.000327 INFO::ASW Batch was 0.109567413431265 prior to batch effect correction and is now -0.171100780198163 .
2025-12-01 18:43:28.000711 INFO::ASW Label was -0.196615422364265 prior to batch effect correction and is now -0.0232984331846309 .
2025-12-01 18:43:28.001478 INFO::Total function execution time is 0.0751700401306152 s and adjustment time is 0.0666701793670654 s ( 88.69 )
2025-12-01 18:43:28.06336 INFO::Formatting Data.
2025-12-01 18:43:28.063751 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.064149 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.064671 INFO::Found 2 missing values.
2025-12-01 18:43:28.065799 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.065987 INFO::Done
2025-12-01 18:43:28.078431 INFO::Found NA in Reference column
2025-12-01 18:43:28.082726 INFO::Require at least two references per batch.
2025-12-01 18:43:28.094549 INFO::Formatting Data.
2025-12-01 18:43:28.09495 INFO::Recognized SummarizedExperiment
2025-12-01 18:43:28.095187 INFO::Typecasting input to dataframe.
2025-12-01 18:43:28.101025 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.101719 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.103776 INFO::Found 0 missing values.
2025-12-01 18:43:28.106895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.107167 INFO::Done
2025-12-01 18:43:28.116061 INFO::Formatting Data.
2025-12-01 18:43:28.116418 INFO::Recognized SummarizedExperiment
2025-12-01 18:43:28.116639 INFO::Typecasting input to dataframe.
2025-12-01 18:43:28.123494 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.123962 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.125242 INFO::Found 0 missing values.
2025-12-01 18:43:28.129084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.129294 INFO::Done
2025-12-01 18:43:28.135669 INFO::Formatting Data.
2025-12-01 18:43:28.135976 INFO::Recognized SummarizedExperiment
2025-12-01 18:43:28.136162 INFO::Typecasting input to dataframe.
2025-12-01 18:43:28.141716 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.142061 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.14243 INFO::Found 0 missing values.
2025-12-01 18:43:28.142743 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-01 18:43:28.14437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.144587 INFO::Done
2025-12-01 18:43:28.149308 INFO::Formatting Data.
2025-12-01 18:43:28.150025 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.150629 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.151064 INFO::Found 0 missing values.
2025-12-01 18:43:28.152182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.152396 INFO::Done
2025-12-01 18:43:28.158256 INFO::Formatting Data.
2025-12-01 18:43:28.158702 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.159074 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.159444 INFO::Found 0 missing values.
2025-12-01 18:43:28.160496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.160684 INFO::Done
2025-12-01 18:43:28.173863 INFO::Formatting Data.
2025-12-01 18:43:28.174262 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.174725 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.175212 INFO::Found 1 missing values.
2025-12-01 18:43:28.176107 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.176272 INFO::Done
2025-12-01 18:43:28.184134 INFO::Formatting Data.
2025-12-01 18:43:28.184454 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.184757 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.185127 INFO::Found 2 missing values.
2025-12-01 18:43:28.185484 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-01 18:43:28.18639 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.186615 INFO::Done
2025-12-01 18:43:28.191981 INFO::Formatting Data.
2025-12-01 18:43:28.192335 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.192716 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.193081 INFO::Found 2 missing values.
2025-12-01 18:43:28.193713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.193921 INFO::Done
2025-12-01 18:43:28.19838 INFO::Formatting Data.
2025-12-01 18:43:28.198634 INFO::Typecasting input to dataframe.
2025-12-01 18:43:28.198903 INFO::Replacing NaNs with NAs.
2025-12-01 18:43:28.199196 INFO::Removing potential empty rows and columns
2025-12-01 18:43:28.199532 INFO::Found 0 missing values.
2025-12-01 18:43:28.200501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 18:43:28.200683 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.247 1.687 9.570
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.300 | 0.442 | 7.753 | |
| compute_asw | 0.010 | 0.001 | 0.011 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |