Yannis Schumann
| Snapshot Date: 2025-12-14 13:40 -0500 (Sun, 14 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 2025-12-15 11:35 -0500 (Mon, 15 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" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 168/2332 | 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: 2025-12-14 18:39:03 -0500 (Sun, 14 Dec 2025) |
| EndedAt: 2025-12-14 18:39:39 -0500 (Sun, 14 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 10.238 0.403 7.703
* 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")
2025-12-14 18:39:31.219441 INFO::Formatting Data.
2025-12-14 18:39:31.221119 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:31.226267 INFO::Removing potential empty rows and columns
2025-12-14 18:39:31.345616 INFO::Found 0 missing values.
2025-12-14 18:39:31.348083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:31.348296 INFO::Done
2025-12-14 18:39:31.348465 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:31.354064 INFO::Starting hierarchical adjustment
2025-12-14 18:39:31.35459 INFO::Found 3 batches.
2025-12-14 18:39:31.354767 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:31.355212 INFO::Using default BPPARAM
2025-12-14 18:39:31.355383 INFO::Processing subtree level 1
2025-12-14 18:39:31.42987 INFO::Adjusting the last 1 batches sequentially
2025-12-14 18:39:31.431198 INFO::Done
2025-12-14 18:39:31.431453 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:31.433137 INFO::ASW Batch was -0.0991294156245052 prior to batch effect correction and is now -0.0991294156245052 .
2025-12-14 18:39:31.43373 INFO::Total function execution time is 0.21464204788208 s and adjustment time is 0.0766699314117432 s ( 35.72 )
2025-12-14 18:39:31.441123 INFO::Formatting Data.
2025-12-14 18:39:31.441389 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:31.44186 INFO::Removing potential empty rows and columns
2025-12-14 18:39:31.442349 INFO::Found 0 missing values.
2025-12-14 18:39:31.442698 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.
2025-12-14 18:39:31.44739 INFO::Formatting Data.
2025-12-14 18:39:31.447635 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:31.447971 INFO::Removing potential empty rows and columns
2025-12-14 18:39:31.448489 INFO::Found 0 missing values.
2025-12-14 18:39:31.448853 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.
2025-12-14 18:39:31.45639 INFO::Formatting Data.
2025-12-14 18:39:31.456676 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:31.457007 INFO::Removing potential empty rows and columns
2025-12-14 18:39:31.457385 INFO::Found 0 missing values.
2025-12-14 18:39:31.457672 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.
2025-12-14 18:39:31.459097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:31.459293 INFO::Done
2025-12-14 18:39:31.459485 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:31.460316 INFO::Starting hierarchical adjustment
2025-12-14 18:39:31.460603 INFO::Found 2 batches.
2025-12-14 18:39:31.460807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:31.461063 INFO::Using default BPPARAM
2025-12-14 18:39:31.46126 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:31.461731 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-14 18:39:31.470315 INFO::Done
2025-12-14 18:39:31.470551 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:31.471205 INFO::ASW Batch was -0.0822712873917191 prior to batch effect correction and is now -0.115606834561291 .
2025-12-14 18:39:31.471466 INFO::Total function execution time is 0.0150940418243408 s and adjustment time is 0.00976300239562988 s ( 64.68 )
2025-12-14 18:39:31.473905 INFO::Formatting Data.
2025-12-14 18:39:31.474569 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:31.479248 INFO::Formatting Data.
2025-12-14 18:39:31.47955 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:31.479938 INFO::Removing potential empty rows and columns
2025-12-14 18:39:31.480368 INFO::Found 0 missing values.
2025-12-14 18:39:31.481588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:31.481825 INFO::Done
2025-12-14 18:39:31.482041 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:31.482764 INFO::Starting hierarchical adjustment
2025-12-14 18:39:31.482979 INFO::Found 2 batches.
2025-12-14 18:39:31.48314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:31.483329 INFO::Using default BPPARAM
2025-12-14 18:39:31.483492 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:31.48375 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-14 18:39:31.5131 INFO::Done
2025-12-14 18:39:31.513375 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:31.514054 INFO::ASW Batch was -0.0852623823307096 prior to batch effect correction and is now -0.119267180704869 .
2025-12-14 18:39:31.514296 INFO::Total function execution time is 0.0350720882415771 s and adjustment time is 0.0301330089569092 s ( 85.92 )
2025-12-14 18:39:31.514642 INFO::Formatting Data.
2025-12-14 18:39:31.514828 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:31.515107 INFO::Removing potential empty rows and columns
2025-12-14 18:39:31.515429 INFO::Found 0 missing values.
2025-12-14 18:39:31.516326 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:31.51651 INFO::Done
2025-12-14 18:39:31.516674 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:31.517336 INFO::Starting hierarchical adjustment
2025-12-14 18:39:31.517552 INFO::Found 2 batches.
2025-12-14 18:39:31.517712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:31.517902 INFO::Using default BPPARAM
2025-12-14 18:39:31.518055 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:31.518326 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-14 18:39:31.523434 INFO::Done
2025-12-14 18:39:31.523649 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:31.52426 INFO::ASW Batch was -0.0852623823307096 prior to batch effect correction and is now -0.119267180704869 .
2025-12-14 18:39:31.524502 INFO::Total function execution time is 0.00984907150268555 s and adjustment time is 0.0059211254119873 s ( 60.12 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-14 18:39:32.805737 INFO::Formatting Data.
2025-12-14 18:39:32.806008 INFO::Recognized SummarizedExperiment
2025-12-14 18:39:32.80617 INFO::Typecasting input to dataframe.
2025-12-14 18:39:32.816383 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:32.816796 INFO::Removing potential empty rows and columns
2025-12-14 18:39:32.817885 INFO::Found 0 missing values.
2025-12-14 18:39:32.819856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:32.820014 INFO::Done
2025-12-14 18:39:32.820154 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:32.821283 INFO::Starting hierarchical adjustment
2025-12-14 18:39:32.821491 INFO::Found 2 batches.
2025-12-14 18:39:32.821632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:32.821932 INFO::Using default BPPARAM
2025-12-14 18:39:32.822075 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:32.822342 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-14 18:39:32.839781 INFO::Done
2025-12-14 18:39:32.840032 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:32.84143 INFO::ASW Batch was -0.00365492877757018 prior to batch effect correction and is now -0.0862320938279372 .
2025-12-14 18:39:32.841749 INFO::Total function execution time is 0.0361490249633789 s and adjustment time is 0.0183150768280029 s ( 50.67 )
Warning: stack imbalance in '{', 73 then 75
2025-12-14 18:39:32.849343 INFO::Formatting Data.
2025-12-14 18:39:32.849633 INFO::Recognized SummarizedExperiment
2025-12-14 18:39:32.84984 INFO::Typecasting input to dataframe.
2025-12-14 18:39:32.853628 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:32.854337 INFO::Removing potential empty rows and columns
2025-12-14 18:39:32.856015 INFO::Found 0 missing values.
2025-12-14 18:39:32.858468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:32.858667 INFO::Done
2025-12-14 18:39:32.858839 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:32.860207 INFO::Starting hierarchical adjustment
2025-12-14 18:39:32.860443 INFO::Found 2 batches.
2025-12-14 18:39:32.860608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:32.860787 INFO::Using default BPPARAM
2025-12-14 18:39:32.860929 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:32.861216 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-14 18:39:32.868972 INFO::Done
2025-12-14 18:39:32.869179 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:32.870319 INFO::ASW Batch was -0.021449791510576 prior to batch effect correction and is now -0.021449791510576 .
2025-12-14 18:39:32.870584 INFO::Total function execution time is 0.0212490558624268 s and adjustment time is 0.00858807563781738 s ( 40.42 )
2025-12-14 18:39:32.877074 INFO::Formatting Data.
2025-12-14 18:39:32.877289 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:32.877553 INFO::Removing potential empty rows and columns
2025-12-14 18:39:32.877873 INFO::Found 0 missing values.
2025-12-14 18:39:32.878684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:32.878848 INFO::Done
2025-12-14 18:39:32.879001 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:32.879589 INFO::Starting hierarchical adjustment
2025-12-14 18:39:32.879787 INFO::Found 3 batches.
2025-12-14 18:39:32.879931 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:32.880104 INFO::Using default BPPARAM
2025-12-14 18:39:32.880246 INFO::Processing subtree level 1
2025-12-14 18:39:32.957341 INFO::Adjusting the last 1 batches sequentially
2025-12-14 18:39:32.958645 INFO::Done
2025-12-14 18:39:32.958998 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:32.963382 INFO::ASW Batch was -0.0604808770617445 prior to batch effect correction and is now -0.18553067884355 .
2025-12-14 18:39:32.964254 INFO::Total function execution time is 0.0870158672332764 s and adjustment time is 0.0788908004760742 s ( 90.66 )
2025-12-14 18:39:32.974055 INFO::Skipping initial DF formatting
2025-12-14 18:39:32.974381 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:32.975881 INFO::Starting hierarchical adjustment
2025-12-14 18:39:32.976147 INFO::Found 5 batches.
2025-12-14 18:39:32.976347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:32.976581 INFO::Using default BPPARAM
2025-12-14 18:39:32.976738 INFO::Processing subtree level 1
2025-12-14 18:39:33.043989 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.050261 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-14 18:39:33.058744 INFO::Done
2025-12-14 18:39:33.059158 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.063058 INFO::ASW Batch was 0.558821835048505 prior to batch effect correction and is now 0.558821835048505 .
2025-12-14 18:39:33.063319 INFO::ASW Label was 0.356091539183051 prior to batch effect correction and is now 0.356091539183051 .
2025-12-14 18:39:33.063868 INFO::Total function execution time is 0.089832067489624 s and adjustment time is 0.0826418399810791 s ( 92 )
2025-12-14 18:39:33.074265 INFO::Formatting Data.
2025-12-14 18:39:33.074606 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.075014 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.075527 INFO::Found 0 missing values.
2025-12-14 18:39:33.076997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.077242 INFO::Done
2025-12-14 18:39:33.077457 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.07858 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.078868 INFO::Found 5 batches.
2025-12-14 18:39:33.079086 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.079372 INFO::Using default BPPARAM
2025-12-14 18:39:33.079567 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.
2025-12-14 18:39:33.141911 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.14605 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-14 18:39:33.158575 INFO::Done
2025-12-14 18:39:33.159043 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.161023 INFO::ASW Batch was 0.242800491317663 prior to batch effect correction and is now -0.0771132899864528 .
2025-12-14 18:39:33.161451 INFO::ASW Label was 0.521072782063091 prior to batch effect correction and is now 0.85222370842816 .
2025-12-14 18:39:33.162192 INFO::Total function execution time is 0.0875639915466309 s and adjustment time is 0.0797350406646729 s ( 91.06 )
2025-12-14 18:39:33.162649 INFO::Formatting Data.
2025-12-14 18:39:33.162866 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.16317 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.163567 INFO::Found 0 missing values.
2025-12-14 18:39:33.164865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.165044 INFO::Done
2025-12-14 18:39:33.165214 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.166197 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.166558 INFO::Found 5 batches.
2025-12-14 18:39:33.166747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.166994 INFO::Using default BPPARAM
2025-12-14 18:39:33.167161 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.
2025-12-14 18:39:33.219041 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.22471 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-14 18:39:33.232389 INFO::Done
2025-12-14 18:39:33.232873 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.234383 INFO::ASW Batch was 0.242800491317663 prior to batch effect correction and is now -0.0771132899864528 .
2025-12-14 18:39:33.234694 INFO::ASW Label was 0.521072782063091 prior to batch effect correction and is now 0.85222370842816 .
2025-12-14 18:39:33.235516 INFO::Total function execution time is 0.072566032409668 s and adjustment time is 0.0659811496734619 s ( 90.93 )
2025-12-14 18:39:33.242463 INFO::Formatting Data.
2025-12-14 18:39:33.242711 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.243012 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.243342 INFO::Found 0 missing values.
2025-12-14 18:39:33.244536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.244716 INFO::Done
2025-12-14 18:39:33.244888 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.245834 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.246063 INFO::Found 5 batches.
2025-12-14 18:39:33.24625 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.246495 INFO::Using default BPPARAM
2025-12-14 18:39:33.246658 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.
2025-12-14 18:39:33.301429 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.306617 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-14 18:39:33.315931 INFO::Done
2025-12-14 18:39:33.316476 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.317832 INFO::ASW Batch was 0.406508598941673 prior to batch effect correction and is now -0.0483864294108916 .
2025-12-14 18:39:33.31819 INFO::ASW Label was 0.3670622685072 prior to batch effect correction and is now 0.841420323466467 .
2025-12-14 18:39:33.318869 INFO::Total function execution time is 0.0761959552764893 s and adjustment time is 0.0699028968811035 s ( 91.74 )
2025-12-14 18:39:33.319255 INFO::Formatting Data.
2025-12-14 18:39:33.319432 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.319729 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.32008 INFO::Found 0 missing values.
2025-12-14 18:39:33.321406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.321644 INFO::Done
2025-12-14 18:39:33.321833 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.322802 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.323063 INFO::Found 5 batches.
2025-12-14 18:39:33.323249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.323485 INFO::Using default BPPARAM
2025-12-14 18:39:33.323718 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.
2025-12-14 18:39:33.382953 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.387038 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-14 18:39:33.396446 INFO::Done
2025-12-14 18:39:33.396751 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.399073 INFO::ASW Batch was 0.406508598941673 prior to batch effect correction and is now -0.0483864294108916 .
2025-12-14 18:39:33.399455 INFO::ASW Label was 0.3670622685072 prior to batch effect correction and is now 0.841420323466467 .
2025-12-14 18:39:33.400108 INFO::Total function execution time is 0.0806410312652588 s and adjustment time is 0.0734128952026367 s ( 91.04 )
2025-12-14 18:39:33.414099 INFO::Formatting Data.
2025-12-14 18:39:33.414455 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.41485 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.415272 INFO::Found 0 missing values.
2025-12-14 18:39:33.417366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.418119 INFO::Done
2025-12-14 18:39:33.418329 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.420148 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.420543 INFO::Found 2 batches.
2025-12-14 18:39:33.420783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.421057 INFO::Using default BPPARAM
2025-12-14 18:39:33.421261 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.421636 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-14 18:39:33.427462 INFO::Done
2025-12-14 18:39:33.42769 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.428691 INFO::ASW Batch was 0.674312963462878 prior to batch effect correction and is now -0.0269260403207672 .
2025-12-14 18:39:33.428891 INFO::ASW Label was 0.274390219566125 prior to batch effect correction and is now 0.898424171064138 .
2025-12-14 18:39:33.429155 INFO::Total function execution time is 0.015172004699707 s and adjustment time is 0.00700211524963379 s ( 46.15 )
2025-12-14 18:39:33.429427 INFO::Formatting Data.
2025-12-14 18:39:33.429608 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.429878 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.430187 INFO::Found 0 missing values.
2025-12-14 18:39:33.430979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.431143 INFO::Done
2025-12-14 18:39:33.431304 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.432194 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.432437 INFO::Found 2 batches.
2025-12-14 18:39:33.432603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.432802 INFO::Using default BPPARAM
2025-12-14 18:39:33.432953 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.433218 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-14 18:39:33.437975 INFO::Done
2025-12-14 18:39:33.438179 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.439079 INFO::ASW Batch was 0.674312963462878 prior to batch effect correction and is now -0.0269260403207672 .
2025-12-14 18:39:33.439269 INFO::ASW Label was 0.274390219566125 prior to batch effect correction and is now 0.898424171064138 .
2025-12-14 18:39:33.439517 INFO::Total function execution time is 0.0100672245025635 s and adjustment time is 0.00557684898376465 s ( 55.4 )
2025-12-14 18:39:33.444725 INFO::Formatting Data.
2025-12-14 18:39:33.444997 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.445296 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.44559 INFO::Found 0 missing values.
2025-12-14 18:39:33.446238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.446412 INFO::Done
2025-12-14 18:39:33.446572 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.447235 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.447456 INFO::Found 2 batches.
2025-12-14 18:39:33.447616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.447833 INFO::Using default BPPARAM
2025-12-14 18:39:33.447981 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.448239 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-14 18:39:33.465359 INFO::Done
2025-12-14 18:39:33.465653 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.466381 INFO::ASW Batch was 0.232023660609194 prior to batch effect correction and is now -0.164433965298316 .
2025-12-14 18:39:33.466654 INFO::Total function execution time is 0.021975040435791 s and adjustment time is 0.0179300308227539 s ( 81.59 )
2025-12-14 18:39:33.471788 INFO::Formatting Data.
2025-12-14 18:39:33.472069 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.472559 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.472982 INFO::Found 0 missing values.
2025-12-14 18:39:33.473522 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.
2025-12-14 18:39:33.475218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.47541 INFO::Done
2025-12-14 18:39:33.475624 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.476794 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.477048 INFO::Found 2 batches.
2025-12-14 18:39:33.477253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.477457 INFO::Using default BPPARAM
2025-12-14 18:39:33.477611 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.477888 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-14 18:39:33.485431 INFO::Done
2025-12-14 18:39:33.485779 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.486966 INFO::ASW Batch was 0.526392802098799 prior to batch effect correction and is now -0.00599097181465766 .
2025-12-14 18:39:33.48721 INFO::ASW Label was 0.547373251997823 prior to batch effect correction and is now 0.90923739035289 .
2025-12-14 18:39:33.48751 INFO::Total function execution time is 0.0157420635223389 s and adjustment time is 0.00840401649475098 s ( 53.39 )
2025-12-14 18:39:33.487776 INFO::Formatting Data.
2025-12-14 18:39:33.487966 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.488284 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.488609 INFO::Found 0 missing values.
2025-12-14 18:39:33.488911 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.
2025-12-14 18:39:33.490339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.490514 INFO::Done
2025-12-14 18:39:33.490683 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.491609 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.49184 INFO::Found 2 batches.
2025-12-14 18:39:33.492004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.492198 INFO::Using default BPPARAM
2025-12-14 18:39:33.492347 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:33.492644 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-14 18:39:33.498242 INFO::Done
2025-12-14 18:39:33.498463 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.49943 INFO::ASW Batch was 0.526392802098799 prior to batch effect correction and is now -0.00599097181465766 .
2025-12-14 18:39:33.499639 INFO::ASW Label was 0.547373251997823 prior to batch effect correction and is now 0.90923739035289 .
2025-12-14 18:39:33.499925 INFO::Total function execution time is 0.0121390819549561 s and adjustment time is 0.00643801689147949 s ( 53.04 )
2025-12-14 18:39:33.579598 INFO::Formatting Data.
2025-12-14 18:39:33.579918 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.580262 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.58067 INFO::Found 0 missing values.
2025-12-14 18:39:33.581796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.582012 INFO::Done
2025-12-14 18:39:33.582223 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.583025 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.583295 INFO::Found 3 batches.
2025-12-14 18:39:33.583509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.583735 INFO::Using default BPPARAM
2025-12-14 18:39:33.583901 INFO::Processing subtree level 1
2025-12-14 18:39:33.631397 INFO::Adjusting the last 1 batches sequentially
2025-12-14 18:39:33.633005 INFO::Done
2025-12-14 18:39:33.633228 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.634829 INFO::ASW Batch was -0.00965406169726367 prior to batch effect correction and is now -0.00965406169726367 .
2025-12-14 18:39:33.63576 INFO::Total function execution time is 0.0560691356658936 s and adjustment time is 0.0497632026672363 s ( 88.75 )
2025-12-14 18:39:33.636133 INFO::Formatting Data.
2025-12-14 18:39:33.636338 INFO::Typecasting input to dataframe.
2025-12-14 18:39:33.636578 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.636883 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.637267 INFO::Found 0 missing values.
2025-12-14 18:39:33.638478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.638713 INFO::Done
2025-12-14 18:39:33.638905 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.639571 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.639802 INFO::Found 3 batches.
2025-12-14 18:39:33.639962 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.640206 INFO::Using default BPPARAM
2025-12-14 18:39:33.640368 INFO::Processing subtree level 1
2025-12-14 18:39:33.686341 INFO::Adjusting the last 1 batches sequentially
2025-12-14 18:39:33.688682 INFO::Done
2025-12-14 18:39:33.688995 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.691957 INFO::ASW Batch was -0.00965406169726367 prior to batch effect correction and is now -0.00965406169726367 .
2025-12-14 18:39:33.693131 INFO::Total function execution time is 0.0567870140075684 s and adjustment time is 0.0489068031311035 s ( 86.12 )
2025-12-14 18:39:33.699597 INFO::Formatting Data.
2025-12-14 18:39:33.699867 INFO::Typecasting input to dataframe.
2025-12-14 18:39:33.700178 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.700531 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.70097 INFO::Found 0 missing values.
2025-12-14 18:39:33.701986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.702184 INFO::Done
2025-12-14 18:39:33.702378 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.703113 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.703347 INFO::Found 3 batches.
2025-12-14 18:39:33.703508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.703713 INFO::Using default BPPARAM
2025-12-14 18:39:33.703874 INFO::Processing subtree level 1
2025-12-14 18:39:33.750008 INFO::Adjusting the last 1 batches sequentially
2025-12-14 18:39:33.751924 INFO::Done
2025-12-14 18:39:33.752157 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:33.754532 INFO::ASW Batch was 0.0114458729128053 prior to batch effect correction and is now 0.0114458729128053 .
2025-12-14 18:39:33.755716 INFO::Total function execution time is 0.0559420585632324 s and adjustment time is 0.0486187934875488 s ( 86.91 )
2025-12-14 18:39:33.836709 INFO::Formatting Data.
2025-12-14 18:39:33.837024 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:33.83744 INFO::Removing potential empty rows and columns
2025-12-14 18:39:33.838427 INFO::Found 1000 missing values.
2025-12-14 18:39:33.844197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:33.844456 INFO::Done
2025-12-14 18:39:33.844638 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:33.846785 INFO::Starting hierarchical adjustment
2025-12-14 18:39:33.847055 INFO::Found 10 batches.
2025-12-14 18:39:33.847235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:33.847475 INFO::Using default BPPARAM
2025-12-14 18:39:33.847657 INFO::Processing subtree level 1
2025-12-14 18:39:33.91768 INFO::Processing subtree level 2
2025-12-14 18:39:34.080975 INFO::Adjusting the last 1 batches sequentially
2025-12-14 18:39:34.085061 INFO::Done
2025-12-14 18:39:34.08685 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:34.09305 INFO::ASW Batch was 0.511394492613635 prior to batch effect correction and is now 0.511394492613635 .
2025-12-14 18:39:34.093808 INFO::ASW Label was 0.332439773231427 prior to batch effect correction and is now 0.332439773231427 .
2025-12-14 18:39:34.095661 INFO::Total function execution time is 0.258440017700195 s and adjustment time is 0.238022089004517 s ( 92.1 )
2025-12-14 18:39:34.096441 INFO::Formatting Data.
2025-12-14 18:39:34.096666 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:34.155151 INFO::Removing potential empty rows and columns
2025-12-14 18:39:34.15677 INFO::Found 1000 missing values.
2025-12-14 18:39:34.165967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:34.166279 INFO::Done
2025-12-14 18:39:34.166529 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:34.1692 INFO::Starting hierarchical adjustment
2025-12-14 18:39:34.169529 INFO::Found 10 batches.
2025-12-14 18:39:34.692983 INFO::Set up parallel execution backend with 2 workers
2025-12-14 18:39:34.693284 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-14 18:39:35.319144 INFO::Adjusting the last 2 batches sequentially
2025-12-14 18:39:35.319661 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-14 18:39:35.325273 INFO::Done
2025-12-14 18:39:35.325496 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:35.327518 INFO::ASW Batch was 0.511394492613635 prior to batch effect correction and is now 0.511394492613635 .
2025-12-14 18:39:35.327729 INFO::ASW Label was 0.332439773231427 prior to batch effect correction and is now 0.332439773231427 .
2025-12-14 18:39:35.327985 INFO::Total function execution time is 1.23156094551086 s and adjustment time is 1.15580987930298 s ( 93.85 )
2025-12-14 18:39:35.394428 INFO::Formatting Data.
2025-12-14 18:39:35.394668 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.394959 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.396435 INFO::Found 0 missing values.
2025-12-14 18:39:35.397804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.398011 INFO::Done
2025-12-14 18:39:35.398227 INFO::Acquiring quality metrics before batch effect correction.
2025-12-14 18:39:35.399191 INFO::Starting hierarchical adjustment
2025-12-14 18:39:35.399446 INFO::Found 3 batches.
2025-12-14 18:39:35.399611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-14 18:39:35.399956 INFO::Using default BPPARAM
2025-12-14 18:39:35.400239 INFO::Processing subtree level 1
2025-12-14 18:39:35.458831 INFO::Adjusting the last 1 batches sequentially
2025-12-14 18:39:35.461956 INFO::Done
2025-12-14 18:39:35.462456 INFO::Acquiring quality metrics after batch effect correction.
2025-12-14 18:39:35.465021 INFO::ASW Batch was 0.141395897867557 prior to batch effect correction and is now -0.150355481370177 .
2025-12-14 18:39:35.465385 INFO::ASW Label was -0.188367668787766 prior to batch effect correction and is now -0.0735694234967369 .
2025-12-14 18:39:35.466325 INFO::Total function execution time is 0.071782112121582 s and adjustment time is 0.0625481605529785 s ( 87.14 )
2025-12-14 18:39:35.529178 INFO::Formatting Data.
2025-12-14 18:39:35.529568 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.529963 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.530425 INFO::Found 2 missing values.
2025-12-14 18:39:35.531458 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.531644 INFO::Done
2025-12-14 18:39:35.544263 INFO::Found NA in Reference column
2025-12-14 18:39:35.550368 INFO::Require at least two references per batch.
2025-12-14 18:39:35.560823 INFO::Formatting Data.
2025-12-14 18:39:35.561112 INFO::Recognized SummarizedExperiment
2025-12-14 18:39:35.561309 INFO::Typecasting input to dataframe.
2025-12-14 18:39:35.566847 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.56739 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.569054 INFO::Found 0 missing values.
2025-12-14 18:39:35.572365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.572615 INFO::Done
2025-12-14 18:39:35.579767 INFO::Formatting Data.
2025-12-14 18:39:35.580118 INFO::Recognized SummarizedExperiment
2025-12-14 18:39:35.580334 INFO::Typecasting input to dataframe.
2025-12-14 18:39:35.587746 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.588246 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.589875 INFO::Found 0 missing values.
2025-12-14 18:39:35.598843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.599127 INFO::Done
2025-12-14 18:39:35.607578 INFO::Formatting Data.
2025-12-14 18:39:35.607867 INFO::Recognized SummarizedExperiment
2025-12-14 18:39:35.608052 INFO::Typecasting input to dataframe.
2025-12-14 18:39:35.614224 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.61465 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.615074 INFO::Found 0 missing values.
2025-12-14 18:39:35.615443 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.
2025-12-14 18:39:35.617354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.617603 INFO::Done
2025-12-14 18:39:35.624717 INFO::Formatting Data.
2025-12-14 18:39:35.625127 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.62558 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.626034 INFO::Found 0 missing values.
2025-12-14 18:39:35.627191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.627394 INFO::Done
2025-12-14 18:39:35.633152 INFO::Formatting Data.
2025-12-14 18:39:35.633582 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.633971 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.63442 INFO::Found 0 missing values.
2025-12-14 18:39:35.635761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.636001 INFO::Done
2025-12-14 18:39:35.654261 INFO::Formatting Data.
2025-12-14 18:39:35.654667 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.655128 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.6556 INFO::Found 1 missing values.
2025-12-14 18:39:35.656649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.656867 INFO::Done
2025-12-14 18:39:35.670044 INFO::Formatting Data.
2025-12-14 18:39:35.670419 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.670778 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.671141 INFO::Found 2 missing values.
2025-12-14 18:39:35.671485 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.
2025-12-14 18:39:35.673078 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.673628 INFO::Done
2025-12-14 18:39:35.68052 INFO::Formatting Data.
2025-12-14 18:39:35.681166 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.681747 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.682266 INFO::Found 2 missing values.
2025-12-14 18:39:35.683024 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.683275 INFO::Done
2025-12-14 18:39:35.689166 INFO::Formatting Data.
2025-12-14 18:39:35.689439 INFO::Typecasting input to dataframe.
2025-12-14 18:39:35.689743 INFO::Replacing NaNs with NAs.
2025-12-14 18:39:35.690087 INFO::Removing potential empty rows and columns
2025-12-14 18:39:35.690505 INFO::Found 0 missing values.
2025-12-14 18:39:35.691603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-14 18:39:35.691828 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.435 1.696 9.704
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.238 | 0.403 | 7.703 | |
| compute_asw | 0.010 | 0.000 | 0.012 | |
| count_existing | 0.005 | 0.000 | 0.007 | |
| generate_data_covariables | 0.005 | 0.001 | 0.007 | |
| generate_dataset | 0.006 | 0.000 | 0.005 | |