Yannis Schumann
| Snapshot Date: 2025-11-30 13:40 -0500 (Sun, 30 Nov 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 2025-12-01 11:35 -0500 (Mon, 01 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: 2025-11-30 18:40:13 -0500 (Sun, 30 Nov 2025) |
| EndedAt: 2025-11-30 18:40:48 -0500 (Sun, 30 Nov 2025) |
| EllapsedTime: 35.5 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 10.386 0.405 7.833
* 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")
2025-11-30 18:40:39.927027 INFO::Formatting Data.
2025-11-30 18:40:39.928579 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:39.932644 INFO::Removing potential empty rows and columns
2025-11-30 18:40:40.046619 INFO::Found 0 missing values.
2025-11-30 18:40:40.048057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:40.048319 INFO::Done
2025-11-30 18:40:40.048532 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:40.055183 INFO::Starting hierarchical adjustment
2025-11-30 18:40:40.055596 INFO::Found 3 batches.
2025-11-30 18:40:40.055864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:40.056355 INFO::Using default BPPARAM
2025-11-30 18:40:40.056556 INFO::Processing subtree level 1
2025-11-30 18:40:40.117808 INFO::Adjusting the last 1 batches sequentially
2025-11-30 18:40:40.119597 INFO::Done
2025-11-30 18:40:40.119884 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:40.121774 INFO::ASW Batch was 0.0417175817771946 prior to batch effect correction and is now 0.0417175817771946 .
2025-11-30 18:40:40.122636 INFO::Total function execution time is 0.195799112319946 s and adjustment time is 0.0640771389007568 s ( 32.73 )
2025-11-30 18:40:40.130354 INFO::Formatting Data.
2025-11-30 18:40:40.130661 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:40.131076 INFO::Removing potential empty rows and columns
2025-11-30 18:40:40.131668 INFO::Found 0 missing values.
2025-11-30 18:40:40.132171 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.
2025-11-30 18:40:40.145564 INFO::Formatting Data.
2025-11-30 18:40:40.145933 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:40.146331 INFO::Removing potential empty rows and columns
2025-11-30 18:40:40.147092 INFO::Found 0 missing values.
2025-11-30 18:40:40.147497 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.
2025-11-30 18:40:40.155511 INFO::Formatting Data.
2025-11-30 18:40:40.155909 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:40.156337 INFO::Removing potential empty rows and columns
2025-11-30 18:40:40.156802 INFO::Found 0 missing values.
2025-11-30 18:40:40.157167 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.
2025-11-30 18:40:40.159031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:40.159268 INFO::Done
2025-11-30 18:40:40.160182 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:40.161149 INFO::Starting hierarchical adjustment
2025-11-30 18:40:40.161448 INFO::Found 2 batches.
2025-11-30 18:40:40.161659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:40.161977 INFO::Using default BPPARAM
2025-11-30 18:40:40.162202 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:40.162666 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-30 18:40:40.173823 INFO::Done
2025-11-30 18:40:40.174163 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:40.174964 INFO::ASW Batch was -0.0140699777176162 prior to batch effect correction and is now -0.123901125489102 .
2025-11-30 18:40:40.17524 INFO::Total function execution time is 0.0197911262512207 s and adjustment time is 0.0124168395996094 s ( 62.74 )
2025-11-30 18:40:40.176404 INFO::Formatting Data.
2025-11-30 18:40:40.176782 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:40.180807 INFO::Formatting Data.
2025-11-30 18:40:40.181043 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:40.181348 INFO::Removing potential empty rows and columns
2025-11-30 18:40:40.18174 INFO::Found 0 missing values.
2025-11-30 18:40:40.182911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:40.183115 INFO::Done
2025-11-30 18:40:40.183296 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:40.184104 INFO::Starting hierarchical adjustment
2025-11-30 18:40:40.184344 INFO::Found 2 batches.
2025-11-30 18:40:40.184533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:40.184759 INFO::Using default BPPARAM
2025-11-30 18:40:40.184945 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:40.185256 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-30 18:40:40.21137 INFO::Done
2025-11-30 18:40:40.211618 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:40.212256 INFO::ASW Batch was 0.019100488666825 prior to batch effect correction and is now -0.104318230758357 .
2025-11-30 18:40:40.212504 INFO::Total function execution time is 0.0317108631134033 s and adjustment time is 0.0270731449127197 s ( 85.37 )
2025-11-30 18:40:40.212826 INFO::Formatting Data.
2025-11-30 18:40:40.21301 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:40.213266 INFO::Removing potential empty rows and columns
2025-11-30 18:40:40.213575 INFO::Found 0 missing values.
2025-11-30 18:40:40.214443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:40.21461 INFO::Done
2025-11-30 18:40:40.214761 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:40.215334 INFO::Starting hierarchical adjustment
2025-11-30 18:40:40.215593 INFO::Found 2 batches.
2025-11-30 18:40:40.215805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:40.216053 INFO::Using default BPPARAM
2025-11-30 18:40:40.21627 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:40.216618 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-30 18:40:40.221731 INFO::Done
2025-11-30 18:40:40.221937 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:40.222547 INFO::ASW Batch was 0.019100488666825 prior to batch effect correction and is now -0.104318230758357 .
2025-11-30 18:40:40.222799 INFO::Total function execution time is 0.00995588302612305 s and adjustment time is 0.00619816780090332 s ( 62.26 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-30 18:40:41.514241 INFO::Formatting Data.
2025-11-30 18:40:41.514495 INFO::Recognized SummarizedExperiment
2025-11-30 18:40:41.514649 INFO::Typecasting input to dataframe.
2025-11-30 18:40:41.525088 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:41.526117 INFO::Removing potential empty rows and columns
2025-11-30 18:40:41.527282 INFO::Found 0 missing values.
2025-11-30 18:40:41.529338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:41.529512 INFO::Done
2025-11-30 18:40:41.529655 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:41.530819 INFO::Starting hierarchical adjustment
2025-11-30 18:40:41.53103 INFO::Found 2 batches.
2025-11-30 18:40:41.531176 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:41.531534 INFO::Using default BPPARAM
2025-11-30 18:40:41.531677 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:41.531954 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-30 18:40:41.548901 INFO::Done
2025-11-30 18:40:41.549165 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:41.550541 INFO::ASW Batch was 0.018003459601844 prior to batch effect correction and is now -0.0862115462339398 .
2025-11-30 18:40:41.550827 INFO::Total function execution time is 0.0366809368133545 s and adjustment time is 0.0179059505462646 s ( 48.82 )
Warning: stack imbalance in '{', 73 then 75
2025-11-30 18:40:41.562825 INFO::Formatting Data.
2025-11-30 18:40:41.563078 INFO::Recognized SummarizedExperiment
2025-11-30 18:40:41.563242 INFO::Typecasting input to dataframe.
2025-11-30 18:40:41.566234 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:41.566629 INFO::Removing potential empty rows and columns
2025-11-30 18:40:41.567769 INFO::Found 0 missing values.
2025-11-30 18:40:41.571399 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:41.571634 INFO::Done
2025-11-30 18:40:41.571805 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:41.57301 INFO::Starting hierarchical adjustment
2025-11-30 18:40:41.573231 INFO::Found 2 batches.
2025-11-30 18:40:41.573379 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:41.573557 INFO::Using default BPPARAM
2025-11-30 18:40:41.573712 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:41.574015 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-30 18:40:41.582068 INFO::Done
2025-11-30 18:40:41.582296 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:41.583568 INFO::ASW Batch was 0.000877161574568201 prior to batch effect correction and is now 0.000877161574568201 .
2025-11-30 18:40:41.583844 INFO::Total function execution time is 0.021024227142334 s and adjustment time is 0.00887513160705566 s ( 42.21 )
2025-11-30 18:40:41.590473 INFO::Formatting Data.
2025-11-30 18:40:41.590703 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:41.591002 INFO::Removing potential empty rows and columns
2025-11-30 18:40:41.591315 INFO::Found 0 missing values.
2025-11-30 18:40:41.592201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:41.592365 INFO::Done
2025-11-30 18:40:41.592514 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:41.593172 INFO::Starting hierarchical adjustment
2025-11-30 18:40:41.593379 INFO::Found 3 batches.
2025-11-30 18:40:41.593531 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:41.593713 INFO::Using default BPPARAM
2025-11-30 18:40:41.59387 INFO::Processing subtree level 1
2025-11-30 18:40:41.69074 INFO::Adjusting the last 1 batches sequentially
2025-11-30 18:40:41.692373 INFO::Done
2025-11-30 18:40:41.692796 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:41.695972 INFO::ASW Batch was -0.120381754834555 prior to batch effect correction and is now -0.156686143911859 .
2025-11-30 18:40:41.697059 INFO::Total function execution time is 0.106416940689087 s and adjustment time is 0.0990228652954102 s ( 93.05 )
2025-11-30 18:40:41.707094 INFO::Skipping initial DF formatting
2025-11-30 18:40:41.70741 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:41.708969 INFO::Starting hierarchical adjustment
2025-11-30 18:40:41.709254 INFO::Found 5 batches.
2025-11-30 18:40:41.709437 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:41.70968 INFO::Using default BPPARAM
2025-11-30 18:40:41.709856 INFO::Processing subtree level 1
2025-11-30 18:40:41.777521 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:41.780173 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-30 18:40:41.793665 INFO::Done
2025-11-30 18:40:41.794144 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:41.79668 INFO::ASW Batch was 0.48696096321895 prior to batch effect correction and is now 0.48696096321895 .
2025-11-30 18:40:41.796965 INFO::ASW Label was 0.393971320750049 prior to batch effect correction and is now 0.393971320750049 .
2025-11-30 18:40:41.797958 INFO::Total function execution time is 0.090872049331665 s and adjustment time is 0.0844419002532959 s ( 92.92 )
2025-11-30 18:40:41.806824 INFO::Formatting Data.
2025-11-30 18:40:41.807232 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:41.807579 INFO::Removing potential empty rows and columns
2025-11-30 18:40:41.807973 INFO::Found 0 missing values.
2025-11-30 18:40:41.809193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:41.809381 INFO::Done
2025-11-30 18:40:41.809562 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:41.810543 INFO::Starting hierarchical adjustment
2025-11-30 18:40:41.811048 INFO::Found 5 batches.
2025-11-30 18:40:41.811232 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:41.812314 INFO::Using default BPPARAM
2025-11-30 18:40:41.812876 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.
2025-11-30 18:40:41.867486 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:41.869058 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-30 18:40:41.876726 INFO::Done
2025-11-30 18:40:41.877081 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:41.878384 INFO::ASW Batch was 0.323692541707405 prior to batch effect correction and is now -0.045309059429325 .
2025-11-30 18:40:41.878714 INFO::ASW Label was 0.451500575119189 prior to batch effect correction and is now 0.743662667762157 .
2025-11-30 18:40:41.879142 INFO::Total function execution time is 0.0723319053649902 s and adjustment time is 0.0657320022583008 s ( 90.88 )
2025-11-30 18:40:41.879542 INFO::Formatting Data.
2025-11-30 18:40:41.879729 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:41.880018 INFO::Removing potential empty rows and columns
2025-11-30 18:40:41.880346 INFO::Found 0 missing values.
2025-11-30 18:40:41.881528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:41.881696 INFO::Done
2025-11-30 18:40:41.88186 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:41.882753 INFO::Starting hierarchical adjustment
2025-11-30 18:40:41.882989 INFO::Found 5 batches.
2025-11-30 18:40:41.883154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:41.883364 INFO::Using default BPPARAM
2025-11-30 18:40:41.883534 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.
2025-11-30 18:40:41.939433 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:41.941533 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-30 18:40:41.950125 INFO::Done
2025-11-30 18:40:41.950556 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:41.952221 INFO::ASW Batch was 0.323692541707405 prior to batch effect correction and is now -0.045309059429325 .
2025-11-30 18:40:41.952483 INFO::ASW Label was 0.451500575119189 prior to batch effect correction and is now 0.743662667762157 .
2025-11-30 18:40:41.953376 INFO::Total function execution time is 0.0736730098724365 s and adjustment time is 0.0671730041503906 s ( 91.18 )
2025-11-30 18:40:41.961844 INFO::Formatting Data.
2025-11-30 18:40:41.962182 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:41.962569 INFO::Removing potential empty rows and columns
2025-11-30 18:40:41.963008 INFO::Found 0 missing values.
2025-11-30 18:40:41.964508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:41.964729 INFO::Done
2025-11-30 18:40:41.964917 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:41.966132 INFO::Starting hierarchical adjustment
2025-11-30 18:40:41.966427 INFO::Found 5 batches.
2025-11-30 18:40:41.96661 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:41.966872 INFO::Using default BPPARAM
2025-11-30 18:40:41.967084 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.
2025-11-30 18:40:42.018966 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:42.023377 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-30 18:40:42.031585 INFO::Done
2025-11-30 18:40:42.032095 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.033621 INFO::ASW Batch was 0.361322790297563 prior to batch effect correction and is now -0.0803821416834641 .
2025-11-30 18:40:42.033823 INFO::ASW Label was 0.430027775585936 prior to batch effect correction and is now 0.89605458724871 .
2025-11-30 18:40:42.034336 INFO::Total function execution time is 0.0724208354949951 s and adjustment time is 0.0652101039886475 s ( 90.04 )
2025-11-30 18:40:42.034628 INFO::Formatting Data.
2025-11-30 18:40:42.03481 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.035105 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.035432 INFO::Found 0 missing values.
2025-11-30 18:40:42.036581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.036886 INFO::Done
2025-11-30 18:40:42.037048 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.037951 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.038366 INFO::Found 5 batches.
2025-11-30 18:40:42.038528 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.03875 INFO::Using default BPPARAM
2025-11-30 18:40:42.038966 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.
2025-11-30 18:40:42.090745 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:42.095527 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-30 18:40:42.106135 INFO::Done
2025-11-30 18:40:42.106602 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.108523 INFO::ASW Batch was 0.361322790297563 prior to batch effect correction and is now -0.0803821416834641 .
2025-11-30 18:40:42.108788 INFO::ASW Label was 0.430027775585936 prior to batch effect correction and is now 0.89605458724871 .
2025-11-30 18:40:42.109186 INFO::Total function execution time is 0.0745258331298828 s and adjustment time is 0.0677890777587891 s ( 90.96 )
2025-11-30 18:40:42.116383 INFO::Formatting Data.
2025-11-30 18:40:42.116653 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.116989 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.11738 INFO::Found 0 missing values.
2025-11-30 18:40:42.118272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.118455 INFO::Done
2025-11-30 18:40:42.118619 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.119589 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.119832 INFO::Found 2 batches.
2025-11-30 18:40:42.120027 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.120274 INFO::Using default BPPARAM
2025-11-30 18:40:42.12043 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:42.120707 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-30 18:40:42.125971 INFO::Done
2025-11-30 18:40:42.126188 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.127112 INFO::ASW Batch was 0.464435367117067 prior to batch effect correction and is now -0.0369841675740622 .
2025-11-30 18:40:42.127312 INFO::ASW Label was 0.62023759641369 prior to batch effect correction and is now 0.942399972598081 .
2025-11-30 18:40:42.127559 INFO::Total function execution time is 0.0112121105194092 s and adjustment time is 0.00618910789489746 s ( 55.2 )
2025-11-30 18:40:42.127801 INFO::Formatting Data.
2025-11-30 18:40:42.127986 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.128254 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.128559 INFO::Found 0 missing values.
2025-11-30 18:40:42.129414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.129645 INFO::Done
2025-11-30 18:40:42.129849 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.131056 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.131356 INFO::Found 2 batches.
2025-11-30 18:40:42.131564 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.131804 INFO::Using default BPPARAM
2025-11-30 18:40:42.132001 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:42.132344 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-30 18:40:42.137245 INFO::Done
2025-11-30 18:40:42.137473 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.138453 INFO::ASW Batch was 0.464435367117067 prior to batch effect correction and is now -0.0369841675740622 .
2025-11-30 18:40:42.138655 INFO::ASW Label was 0.62023759641369 prior to batch effect correction and is now 0.942399972598081 .
2025-11-30 18:40:42.138907 INFO::Total function execution time is 0.0110960006713867 s and adjustment time is 0.00594592094421387 s ( 53.59 )
2025-11-30 18:40:42.143792 INFO::Formatting Data.
2025-11-30 18:40:42.144206 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.144478 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.144768 INFO::Found 0 missing values.
2025-11-30 18:40:42.145475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.145637 INFO::Done
2025-11-30 18:40:42.14579 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.146361 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.146556 INFO::Found 2 batches.
2025-11-30 18:40:42.146711 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.146924 INFO::Using default BPPARAM
2025-11-30 18:40:42.147085 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:42.147369 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-30 18:40:42.158558 INFO::Done
2025-11-30 18:40:42.158812 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.159434 INFO::ASW Batch was -0.138046260966483 prior to batch effect correction and is now -0.152656811284509 .
2025-11-30 18:40:42.159695 INFO::Total function execution time is 0.0159249305725098 s and adjustment time is 0.0120289325714111 s ( 75.54 )
2025-11-30 18:40:42.164285 INFO::Formatting Data.
2025-11-30 18:40:42.16454 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.164816 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.165144 INFO::Found 0 missing values.
2025-11-30 18:40:42.165567 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.
2025-11-30 18:40:42.167164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.167346 INFO::Done
2025-11-30 18:40:42.167519 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.168505 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.168747 INFO::Found 2 batches.
2025-11-30 18:40:42.168894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.169082 INFO::Using default BPPARAM
2025-11-30 18:40:42.169232 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:42.169502 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-30 18:40:42.174677 INFO::Done
2025-11-30 18:40:42.174874 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.175756 INFO::ASW Batch was 0.548947776871256 prior to batch effect correction and is now 0.0200876036931669 .
2025-11-30 18:40:42.176634 INFO::ASW Label was 0.540346939361776 prior to batch effect correction and is now 0.902195354562776 .
2025-11-30 18:40:42.176881 INFO::Total function execution time is 0.0126159191131592 s and adjustment time is 0.00599098205566406 s ( 47.49 )
2025-11-30 18:40:42.177109 INFO::Formatting Data.
2025-11-30 18:40:42.177277 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.177547 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.177837 INFO::Found 0 missing values.
2025-11-30 18:40:42.17812 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.
2025-11-30 18:40:42.179586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.179768 INFO::Done
2025-11-30 18:40:42.179927 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.180794 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.181009 INFO::Found 2 batches.
2025-11-30 18:40:42.18116 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.181361 INFO::Using default BPPARAM
2025-11-30 18:40:42.181517 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:42.181789 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-30 18:40:42.187039 INFO::Done
2025-11-30 18:40:42.187268 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.188154 INFO::ASW Batch was 0.548947776871256 prior to batch effect correction and is now 0.0200876036931669 .
2025-11-30 18:40:42.188338 INFO::ASW Label was 0.540346939361776 prior to batch effect correction and is now 0.902195354562776 .
2025-11-30 18:40:42.188593 INFO::Total function execution time is 0.0114829540252686 s and adjustment time is 0.00606894493103027 s ( 52.85 )
2025-11-30 18:40:42.259887 INFO::Formatting Data.
2025-11-30 18:40:42.260153 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.260458 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.260776 INFO::Found 0 missing values.
2025-11-30 18:40:42.261705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.261872 INFO::Done
2025-11-30 18:40:42.262024 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.262688 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.2629 INFO::Found 3 batches.
2025-11-30 18:40:42.263049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.263243 INFO::Using default BPPARAM
2025-11-30 18:40:42.263394 INFO::Processing subtree level 1
2025-11-30 18:40:42.304559 INFO::Adjusting the last 1 batches sequentially
2025-11-30 18:40:42.306628 INFO::Done
2025-11-30 18:40:42.306965 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.308833 INFO::ASW Batch was 0.0219643903135798 prior to batch effect correction and is now 0.0219643903135798 .
2025-11-30 18:40:42.309799 INFO::Total function execution time is 0.0499241352081299 s and adjustment time is 0.0437619686126709 s ( 87.66 )
2025-11-30 18:40:42.310183 INFO::Formatting Data.
2025-11-30 18:40:42.310578 INFO::Typecasting input to dataframe.
2025-11-30 18:40:42.310808 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.311107 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.311624 INFO::Found 0 missing values.
2025-11-30 18:40:42.312582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.31276 INFO::Done
2025-11-30 18:40:42.312947 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.313599 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.313823 INFO::Found 3 batches.
2025-11-30 18:40:42.313986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.314204 INFO::Using default BPPARAM
2025-11-30 18:40:42.314555 INFO::Processing subtree level 1
2025-11-30 18:40:42.364666 INFO::Adjusting the last 1 batches sequentially
2025-11-30 18:40:42.366175 INFO::Done
2025-11-30 18:40:42.366675 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.368368 INFO::ASW Batch was 0.0219643903135798 prior to batch effect correction and is now 0.0219643903135798 .
2025-11-30 18:40:42.368933 INFO::Total function execution time is 0.0587079524993896 s and adjustment time is 0.0523879528045654 s ( 89.23 )
2025-11-30 18:40:42.376075 INFO::Formatting Data.
2025-11-30 18:40:42.376324 INFO::Typecasting input to dataframe.
2025-11-30 18:40:42.376597 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.376902 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.377306 INFO::Found 0 missing values.
2025-11-30 18:40:42.378208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.378386 INFO::Done
2025-11-30 18:40:42.379279 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.380007 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.380246 INFO::Found 3 batches.
2025-11-30 18:40:42.38041 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.380648 INFO::Using default BPPARAM
2025-11-30 18:40:42.380817 INFO::Processing subtree level 1
2025-11-30 18:40:42.422403 INFO::Adjusting the last 1 batches sequentially
2025-11-30 18:40:42.424146 INFO::Done
2025-11-30 18:40:42.424735 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.426841 INFO::ASW Batch was -0.0293202187121541 prior to batch effect correction and is now -0.0293202187121541 .
2025-11-30 18:40:42.427863 INFO::Total function execution time is 0.0517880916595459 s and adjustment time is 0.0439438819885254 s ( 84.85 )
2025-11-30 18:40:42.501839 INFO::Formatting Data.
2025-11-30 18:40:42.502118 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.502525 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.503476 INFO::Found 1000 missing values.
2025-11-30 18:40:42.509183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.509473 INFO::Done
2025-11-30 18:40:42.509648 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.511703 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.511993 INFO::Found 10 batches.
2025-11-30 18:40:42.51223 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:42.512518 INFO::Using default BPPARAM
2025-11-30 18:40:42.512737 INFO::Processing subtree level 1
2025-11-30 18:40:42.580035 INFO::Processing subtree level 2
2025-11-30 18:40:42.761411 INFO::Adjusting the last 1 batches sequentially
2025-11-30 18:40:42.764981 INFO::Done
2025-11-30 18:40:42.766498 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:42.772893 INFO::ASW Batch was 0.475677644149281 prior to batch effect correction and is now 0.475677644149281 .
2025-11-30 18:40:42.773548 INFO::ASW Label was 0.367015229535534 prior to batch effect correction and is now 0.367015229535534 .
2025-11-30 18:40:42.774818 INFO::Total function execution time is 0.2727370262146 s and adjustment time is 0.253036975860596 s ( 92.78 )
2025-11-30 18:40:42.775787 INFO::Formatting Data.
2025-11-30 18:40:42.776047 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:42.776711 INFO::Removing potential empty rows and columns
2025-11-30 18:40:42.824744 INFO::Found 1000 missing values.
2025-11-30 18:40:42.833135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:42.833527 INFO::Done
2025-11-30 18:40:42.833918 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:42.841363 INFO::Starting hierarchical adjustment
2025-11-30 18:40:42.841718 INFO::Found 10 batches.
2025-11-30 18:40:43.335079 INFO::Set up parallel execution backend with 2 workers
2025-11-30 18:40:43.335475 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-30 18:40:43.947285 INFO::Adjusting the last 2 batches sequentially
2025-11-30 18:40:43.947879 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-30 18:40:43.953478 INFO::Done
2025-11-30 18:40:43.953693 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:43.955539 INFO::ASW Batch was 0.475677644149281 prior to batch effect correction and is now 0.475677644149281 .
2025-11-30 18:40:43.955718 INFO::ASW Label was 0.367015229535534 prior to batch effect correction and is now 0.367015229535534 .
2025-11-30 18:40:43.955954 INFO::Total function execution time is 1.18021011352539 s and adjustment time is 1.111820936203 s ( 94.21 )
2025-11-30 18:40:44.032447 INFO::Formatting Data.
2025-11-30 18:40:44.032793 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.033181 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.033646 INFO::Found 0 missing values.
2025-11-30 18:40:44.035943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.036232 INFO::Done
2025-11-30 18:40:44.036687 INFO::Acquiring quality metrics before batch effect correction.
2025-11-30 18:40:44.038595 INFO::Starting hierarchical adjustment
2025-11-30 18:40:44.038981 INFO::Found 3 batches.
2025-11-30 18:40:44.03929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-30 18:40:44.039541 INFO::Using default BPPARAM
2025-11-30 18:40:44.039841 INFO::Processing subtree level 1
2025-11-30 18:40:44.096997 INFO::Adjusting the last 1 batches sequentially
2025-11-30 18:40:44.101252 INFO::Done
2025-11-30 18:40:44.101674 INFO::Acquiring quality metrics after batch effect correction.
2025-11-30 18:40:44.104928 INFO::ASW Batch was 0.269238149746288 prior to batch effect correction and is now -0.142286918683011 .
2025-11-30 18:40:44.105167 INFO::ASW Label was -0.190775438675936 prior to batch effect correction and is now -0.00482170737602897 .
2025-11-30 18:40:44.106425 INFO::Total function execution time is 0.073828935623169 s and adjustment time is 0.0623090267181396 s ( 84.4 )
2025-11-30 18:40:44.161977 INFO::Formatting Data.
2025-11-30 18:40:44.162337 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.162672 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.163102 INFO::Found 2 missing values.
2025-11-30 18:40:44.164116 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.164305 INFO::Done
2025-11-30 18:40:44.176164 INFO::Found NA in Reference column
2025-11-30 18:40:44.180174 INFO::Require at least two references per batch.
2025-11-30 18:40:44.188402 INFO::Formatting Data.
2025-11-30 18:40:44.188649 INFO::Recognized SummarizedExperiment
2025-11-30 18:40:44.188827 INFO::Typecasting input to dataframe.
2025-11-30 18:40:44.19279 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.1932 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.194488 INFO::Found 0 missing values.
2025-11-30 18:40:44.197275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.197475 INFO::Done
2025-11-30 18:40:44.204549 INFO::Formatting Data.
2025-11-30 18:40:44.204856 INFO::Recognized SummarizedExperiment
2025-11-30 18:40:44.205089 INFO::Typecasting input to dataframe.
2025-11-30 18:40:44.211802 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.212241 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.213479 INFO::Found 0 missing values.
2025-11-30 18:40:44.217429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.217641 INFO::Done
2025-11-30 18:40:44.224194 INFO::Formatting Data.
2025-11-30 18:40:44.224477 INFO::Recognized SummarizedExperiment
2025-11-30 18:40:44.224688 INFO::Typecasting input to dataframe.
2025-11-30 18:40:44.23152 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.231941 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.232392 INFO::Found 0 missing values.
2025-11-30 18:40:44.232772 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.
2025-11-30 18:40:44.234656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.234912 INFO::Done
2025-11-30 18:40:44.240103 INFO::Formatting Data.
2025-11-30 18:40:44.240398 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.240714 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.241107 INFO::Found 0 missing values.
2025-11-30 18:40:44.242211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.242447 INFO::Done
2025-11-30 18:40:44.251148 INFO::Formatting Data.
2025-11-30 18:40:44.251585 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.251925 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.252331 INFO::Found 0 missing values.
2025-11-30 18:40:44.253439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.253647 INFO::Done
2025-11-30 18:40:44.268023 INFO::Formatting Data.
2025-11-30 18:40:44.268333 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.268697 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.269148 INFO::Found 1 missing values.
2025-11-30 18:40:44.270005 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.270196 INFO::Done
2025-11-30 18:40:44.278459 INFO::Formatting Data.
2025-11-30 18:40:44.278738 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.27902 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.27933 INFO::Found 2 missing values.
2025-11-30 18:40:44.279638 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.
2025-11-30 18:40:44.280442 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.28063 INFO::Done
2025-11-30 18:40:44.285611 INFO::Formatting Data.
2025-11-30 18:40:44.28597 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.286359 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.286713 INFO::Found 2 missing values.
2025-11-30 18:40:44.287315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.28751 INFO::Done
2025-11-30 18:40:44.29268 INFO::Formatting Data.
2025-11-30 18:40:44.292944 INFO::Typecasting input to dataframe.
2025-11-30 18:40:44.293274 INFO::Replacing NaNs with NAs.
2025-11-30 18:40:44.293579 INFO::Removing potential empty rows and columns
2025-11-30 18:40:44.29391 INFO::Found 0 missing values.
2025-11-30 18:40:44.29495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-30 18:40:44.295144 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.307 1.664 9.459
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.386 | 0.405 | 7.833 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.006 | 0.001 | 0.013 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |