Yannis Schumann
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:05 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-11-18 03:04:23 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 03:04:58 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 35.3 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 Patched (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 ‘1.6.0’
* 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 10.187 0.356 8.204
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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")
2025-11-18 03:04:48.679187 INFO::Formatting Data.
2025-11-18 03:04:48.680601 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:48.684932 INFO::Removing potential empty rows and columns
2025-11-18 03:04:48.796981 INFO::Found 0 missing values.
2025-11-18 03:04:48.798177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:48.79841 INFO::Done
2025-11-18 03:04:48.798592 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:48.80424 INFO::Starting hierarchical adjustment
2025-11-18 03:04:48.804604 INFO::Found 3 batches.
2025-11-18 03:04:48.804805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:48.805265 INFO::Using default BPPARAM
2025-11-18 03:04:48.805468 INFO::Processing subtree level 1
2025-11-18 03:04:48.849167 INFO::Adjusting the last 1 batches sequentially
2025-11-18 03:04:48.853245 INFO::Done
2025-11-18 03:04:48.853815 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:48.855967 INFO::ASW Batch was 0.0124920977006259 prior to batch effect correction and is now 0.0124920977006259 .
2025-11-18 03:04:48.856991 INFO::Total function execution time is 0.177949905395508 s and adjustment time is 0.0485649108886719 s ( 27.29 )
2025-11-18 03:04:48.864548 INFO::Formatting Data.
2025-11-18 03:04:48.865012 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:48.866352 INFO::Removing potential empty rows and columns
2025-11-18 03:04:48.866989 INFO::Found 0 missing values.
2025-11-18 03:04:48.867446 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.
2025-11-18 03:04:48.872811 INFO::Formatting Data.
2025-11-18 03:04:48.873312 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:48.873687 INFO::Removing potential empty rows and columns
2025-11-18 03:04:48.87411 INFO::Found 0 missing values.
2025-11-18 03:04:48.874499 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.
2025-11-18 03:04:48.88172 INFO::Formatting Data.
2025-11-18 03:04:48.882054 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:48.882407 INFO::Removing potential empty rows and columns
2025-11-18 03:04:48.882827 INFO::Found 0 missing values.
2025-11-18 03:04:48.883224 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.
2025-11-18 03:04:48.889075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:48.889424 INFO::Done
2025-11-18 03:04:48.889644 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:48.890916 INFO::Starting hierarchical adjustment
2025-11-18 03:04:48.891252 INFO::Found 2 batches.
2025-11-18 03:04:48.891467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:48.89173 INFO::Using default BPPARAM
2025-11-18 03:04:48.891906 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:48.89226 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 03:04:48.901067 INFO::Done
2025-11-18 03:04:48.901365 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:48.90218 INFO::ASW Batch was 0.0243587972797925 prior to batch effect correction and is now -0.07671663638179 .
2025-11-18 03:04:48.902554 INFO::Total function execution time is 0.0208699703216553 s and adjustment time is 0.00983190536499023 s ( 47.11 )
2025-11-18 03:04:48.903794 INFO::Formatting Data.
2025-11-18 03:04:48.90405 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:48.907531 INFO::Formatting Data.
2025-11-18 03:04:48.907884 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:48.908193 INFO::Removing potential empty rows and columns
2025-11-18 03:04:48.908561 INFO::Found 0 missing values.
2025-11-18 03:04:48.909578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:48.909781 INFO::Done
2025-11-18 03:04:48.909953 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:48.9107 INFO::Starting hierarchical adjustment
2025-11-18 03:04:48.923075 INFO::Found 2 batches.
2025-11-18 03:04:48.923317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:48.923512 INFO::Using default BPPARAM
2025-11-18 03:04:48.923658 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:48.923947 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 03:04:48.929184 INFO::Done
2025-11-18 03:04:48.929487 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:48.930218 INFO::ASW Batch was -0.0705919338153547 prior to batch effect correction and is now -0.121187219950727 .
2025-11-18 03:04:48.930505 INFO::Total function execution time is 0.0230228900909424 s and adjustment time is 0.00617218017578125 s ( 26.81 )
2025-11-18 03:04:48.930836 INFO::Formatting Data.
2025-11-18 03:04:48.93101 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:48.931296 INFO::Removing potential empty rows and columns
2025-11-18 03:04:48.93162 INFO::Found 0 missing values.
2025-11-18 03:04:48.932534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:48.932718 INFO::Done
2025-11-18 03:04:48.932886 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:48.933596 INFO::Starting hierarchical adjustment
2025-11-18 03:04:48.93383 INFO::Found 2 batches.
2025-11-18 03:04:48.933992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:48.934173 INFO::Using default BPPARAM
2025-11-18 03:04:48.934329 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:48.934609 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 03:04:48.941452 INFO::Done
2025-11-18 03:04:48.941729 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:48.942469 INFO::ASW Batch was -0.0705919338153547 prior to batch effect correction and is now -0.121187219950727 .
2025-11-18 03:04:48.942731 INFO::Total function execution time is 0.0118770599365234 s and adjustment time is 0.00764298439025879 s ( 64.35 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-18 03:04:50.296399 INFO::Formatting Data.
2025-11-18 03:04:50.296725 INFO::Recognized SummarizedExperiment
2025-11-18 03:04:50.296931 INFO::Typecasting input to dataframe.
2025-11-18 03:04:50.310197 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:50.310657 INFO::Removing potential empty rows and columns
2025-11-18 03:04:50.311919 INFO::Found 0 missing values.
2025-11-18 03:04:50.314553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:50.314819 INFO::Done
2025-11-18 03:04:50.314986 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:50.317892 INFO::Starting hierarchical adjustment
2025-11-18 03:04:50.318216 INFO::Found 2 batches.
2025-11-18 03:04:50.318404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:50.318832 INFO::Using default BPPARAM
2025-11-18 03:04:50.319016 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:50.319385 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 03:04:50.343048 INFO::Done
2025-11-18 03:04:50.343405 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:50.345022 INFO::ASW Batch was -0.00456104945310885 prior to batch effect correction and is now -0.0933294195236835 .
2025-11-18 03:04:50.345408 INFO::Total function execution time is 0.0491559505462646 s and adjustment time is 0.0248658657073975 s ( 50.59 )
Warning: stack imbalance in '{', 73 then 74
2025-11-18 03:04:50.353666 INFO::Formatting Data.
2025-11-18 03:04:50.353943 INFO::Recognized SummarizedExperiment
2025-11-18 03:04:50.354113 INFO::Typecasting input to dataframe.
2025-11-18 03:04:50.357398 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:50.35786 INFO::Removing potential empty rows and columns
2025-11-18 03:04:50.359074 INFO::Found 0 missing values.
2025-11-18 03:04:50.36141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:50.361628 INFO::Done
2025-11-18 03:04:50.361797 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:50.363238 INFO::Starting hierarchical adjustment
2025-11-18 03:04:50.364152 INFO::Found 2 batches.
2025-11-18 03:04:50.36433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:50.364527 INFO::Using default BPPARAM
2025-11-18 03:04:50.364691 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:50.365004 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 03:04:50.373901 INFO::Done
2025-11-18 03:04:50.374192 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:50.37554 INFO::ASW Batch was -0.00536684834812377 prior to batch effect correction and is now -0.00536684834812377 .
2025-11-18 03:04:50.375873 INFO::Total function execution time is 0.022212028503418 s and adjustment time is 0.00978899002075195 s ( 44.07 )
2025-11-18 03:04:50.383349 INFO::Formatting Data.
2025-11-18 03:04:50.383651 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:50.38397 INFO::Removing potential empty rows and columns
2025-11-18 03:04:50.384329 INFO::Found 0 missing values.
2025-11-18 03:04:50.38663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:50.387334 INFO::Done
2025-11-18 03:04:50.387824 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:50.392267 INFO::Starting hierarchical adjustment
2025-11-18 03:04:50.392585 INFO::Found 3 batches.
2025-11-18 03:04:50.392771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:50.392981 INFO::Using default BPPARAM
2025-11-18 03:04:50.393147 INFO::Processing subtree level 1
2025-11-18 03:04:50.452968 INFO::Adjusting the last 1 batches sequentially
2025-11-18 03:04:50.454457 INFO::Done
2025-11-18 03:04:50.454735 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:50.456723 INFO::ASW Batch was -0.123970484302158 prior to batch effect correction and is now -0.17613935235271 .
2025-11-18 03:04:50.457581 INFO::Total function execution time is 0.0742111206054688 s and adjustment time is 0.0619208812713623 s ( 83.44 )
2025-11-18 03:04:50.467287 INFO::Skipping initial DF formatting
2025-11-18 03:04:50.467711 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:50.469589 INFO::Starting hierarchical adjustment
2025-11-18 03:04:50.470064 INFO::Found 5 batches.
2025-11-18 03:04:50.470342 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:50.470635 INFO::Using default BPPARAM
2025-11-18 03:04:50.470856 INFO::Processing subtree level 1
2025-11-18 03:04:50.59069 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:50.595854 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 03:04:50.604976 INFO::Done
2025-11-18 03:04:50.605488 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:50.608107 INFO::ASW Batch was 0.52323416084331 prior to batch effect correction and is now 0.52323416084331 .
2025-11-18 03:04:50.608382 INFO::ASW Label was 0.380299315964846 prior to batch effect correction and is now 0.380299315964846 .
2025-11-18 03:04:50.608887 INFO::Total function execution time is 0.141645193099976 s and adjustment time is 0.134994983673096 s ( 95.31 )
2025-11-18 03:04:50.643456 INFO::Formatting Data.
2025-11-18 03:04:50.643778 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:50.644138 INFO::Removing potential empty rows and columns
2025-11-18 03:04:50.644506 INFO::Found 0 missing values.
2025-11-18 03:04:50.645812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:50.646046 INFO::Done
2025-11-18 03:04:50.646214 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:50.647365 INFO::Starting hierarchical adjustment
2025-11-18 03:04:50.647684 INFO::Found 5 batches.
2025-11-18 03:04:50.647871 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:50.648099 INFO::Using default BPPARAM
2025-11-18 03:04:50.648273 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.
2025-11-18 03:04:50.71952 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:50.721462 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 03:04:50.731936 INFO::Done
2025-11-18 03:04:50.732292 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:50.734207 INFO::ASW Batch was 0.473344358617788 prior to batch effect correction and is now -0.0097911473139176 .
2025-11-18 03:04:50.734498 INFO::ASW Label was 0.306677347621179 prior to batch effect correction and is now 0.759753107087002 .
2025-11-18 03:04:50.734939 INFO::Total function execution time is 0.0914909839630127 s and adjustment time is 0.0842869281768799 s ( 92.13 )
2025-11-18 03:04:50.735385 INFO::Formatting Data.
2025-11-18 03:04:50.735616 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:50.735988 INFO::Removing potential empty rows and columns
2025-11-18 03:04:50.736513 INFO::Found 0 missing values.
2025-11-18 03:04:50.738231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:50.738502 INFO::Done
2025-11-18 03:04:50.738731 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:50.739896 INFO::Starting hierarchical adjustment
2025-11-18 03:04:50.7402 INFO::Found 5 batches.
2025-11-18 03:04:50.740397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:50.740648 INFO::Using default BPPARAM
2025-11-18 03:04:50.740834 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.
2025-11-18 03:04:50.790571 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:50.791959 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 03:04:50.807662 INFO::Done
2025-11-18 03:04:50.80829 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:50.810279 INFO::ASW Batch was 0.473344358617788 prior to batch effect correction and is now -0.0097911473139176 .
2025-11-18 03:04:50.810531 INFO::ASW Label was 0.306677347621179 prior to batch effect correction and is now 0.759753107087002 .
2025-11-18 03:04:50.811062 INFO::Total function execution time is 0.0755529403686523 s and adjustment time is 0.0674951076507568 s ( 89.33 )
2025-11-18 03:04:50.818592 INFO::Formatting Data.
2025-11-18 03:04:50.81893 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:50.819302 INFO::Removing potential empty rows and columns
2025-11-18 03:04:50.819711 INFO::Found 0 missing values.
2025-11-18 03:04:50.821111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:50.821353 INFO::Done
2025-11-18 03:04:50.821538 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:50.823597 INFO::Starting hierarchical adjustment
2025-11-18 03:04:50.823936 INFO::Found 5 batches.
2025-11-18 03:04:50.824132 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:50.824373 INFO::Using default BPPARAM
2025-11-18 03:04:50.824574 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.
2025-11-18 03:04:50.906379 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:50.911634 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 03:04:50.922911 INFO::Done
2025-11-18 03:04:50.923556 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:50.925305 INFO::ASW Batch was 0.377756267200201 prior to batch effect correction and is now -0.11214176279845 .
2025-11-18 03:04:50.92559 INFO::ASW Label was 0.294645527183392 prior to batch effect correction and is now 0.900368226724525 .
2025-11-18 03:04:50.926066 INFO::Total function execution time is 0.107390880584717 s and adjustment time is 0.0990250110626221 s ( 92.21 )
2025-11-18 03:04:50.926428 INFO::Formatting Data.
2025-11-18 03:04:50.926664 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:50.927015 INFO::Removing potential empty rows and columns
2025-11-18 03:04:50.927486 INFO::Found 0 missing values.
2025-11-18 03:04:50.929366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:50.929702 INFO::Done
2025-11-18 03:04:50.92995 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:50.931291 INFO::Starting hierarchical adjustment
2025-11-18 03:04:50.931655 INFO::Found 5 batches.
2025-11-18 03:04:50.931884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:50.932187 INFO::Using default BPPARAM
2025-11-18 03:04:50.932451 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.
2025-11-18 03:04:50.996742 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:50.998248 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 03:04:51.016284 INFO::Done
2025-11-18 03:04:51.016914 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.018908 INFO::ASW Batch was 0.377756267200201 prior to batch effect correction and is now -0.11214176279845 .
2025-11-18 03:04:51.01928 INFO::ASW Label was 0.294645527183392 prior to batch effect correction and is now 0.900368226724525 .
2025-11-18 03:04:51.019804 INFO::Total function execution time is 0.0933620929718018 s and adjustment time is 0.08467698097229 s ( 90.7 )
2025-11-18 03:04:51.026176 INFO::Formatting Data.
2025-11-18 03:04:51.026472 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.026807 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.027177 INFO::Found 0 missing values.
2025-11-18 03:04:51.028097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.0283 INFO::Done
2025-11-18 03:04:51.028474 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.029539 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.029826 INFO::Found 2 batches.
2025-11-18 03:04:51.030002 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.030228 INFO::Using default BPPARAM
2025-11-18 03:04:51.030402 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:51.03069 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 03:04:51.036101 INFO::Done
2025-11-18 03:04:51.036364 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.037423 INFO::ASW Batch was 0.695186524467485 prior to batch effect correction and is now -0.0227088157980635 .
2025-11-18 03:04:51.037674 INFO::ASW Label was 0.325803007939965 prior to batch effect correction and is now 0.876244049762525 .
2025-11-18 03:04:51.037948 INFO::Total function execution time is 0.0118241310119629 s and adjustment time is 0.0063169002532959 s ( 53.42 )
2025-11-18 03:04:51.038195 INFO::Formatting Data.
2025-11-18 03:04:51.038379 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.038663 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.038993 INFO::Found 0 missing values.
2025-11-18 03:04:51.039873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.040066 INFO::Done
2025-11-18 03:04:51.040232 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.041268 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.041546 INFO::Found 2 batches.
2025-11-18 03:04:51.041726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.041935 INFO::Using default BPPARAM
2025-11-18 03:04:51.042103 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:51.0424 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 03:04:51.04761 INFO::Done
2025-11-18 03:04:51.047891 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.048915 INFO::ASW Batch was 0.695186524467485 prior to batch effect correction and is now -0.0227088157980635 .
2025-11-18 03:04:51.049132 INFO::ASW Label was 0.325803007939965 prior to batch effect correction and is now 0.876244049762525 .
2025-11-18 03:04:51.049406 INFO::Total function execution time is 0.0111970901489258 s and adjustment time is 0.00610709190368652 s ( 54.54 )
2025-11-18 03:04:51.05435 INFO::Formatting Data.
2025-11-18 03:04:51.054645 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.054934 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.05524 INFO::Found 0 missing values.
2025-11-18 03:04:51.055935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.056124 INFO::Done
2025-11-18 03:04:51.056292 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.05698 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.057217 INFO::Found 2 batches.
2025-11-18 03:04:51.05738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.057573 INFO::Using default BPPARAM
2025-11-18 03:04:51.057746 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:51.058025 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 03:04:51.069324 INFO::Done
2025-11-18 03:04:51.069603 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.070312 INFO::ASW Batch was -0.103247093163717 prior to batch effect correction and is now -0.152793765427827 .
2025-11-18 03:04:51.070588 INFO::Total function execution time is 0.0162980556488037 s and adjustment time is 0.0121359825134277 s ( 74.46 )
2025-11-18 03:04:51.075625 INFO::Formatting Data.
2025-11-18 03:04:51.07591 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.076209 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.07655 INFO::Found 0 missing values.
2025-11-18 03:04:51.076971 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.
2025-11-18 03:04:51.078506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.078723 INFO::Done
2025-11-18 03:04:51.078893 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.079915 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.080174 INFO::Found 2 batches.
2025-11-18 03:04:51.080339 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.08054 INFO::Using default BPPARAM
2025-11-18 03:04:51.080701 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:51.080997 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 03:04:51.086781 INFO::Done
2025-11-18 03:04:51.087045 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.088058 INFO::ASW Batch was 0.507556712970988 prior to batch effect correction and is now 0.0842272559521411 .
2025-11-18 03:04:51.088266 INFO::ASW Label was 0.389318447249624 prior to batch effect correction and is now 0.810583386860279 .
2025-11-18 03:04:51.088521 INFO::Total function execution time is 0.0129449367523193 s and adjustment time is 0.00663590431213379 s ( 51.26 )
2025-11-18 03:04:51.088775 INFO::Formatting Data.
2025-11-18 03:04:51.088975 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.089283 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.0896 INFO::Found 0 missing values.
2025-11-18 03:04:51.089911 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.
2025-11-18 03:04:51.091349 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.091566 INFO::Done
2025-11-18 03:04:51.091743 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.09275 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.093003 INFO::Found 2 batches.
2025-11-18 03:04:51.093172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.093373 INFO::Using default BPPARAM
2025-11-18 03:04:51.093536 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:51.093859 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 03:04:51.099801 INFO::Done
2025-11-18 03:04:51.100081 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.101314 INFO::ASW Batch was 0.507556712970988 prior to batch effect correction and is now 0.0842272559521411 .
2025-11-18 03:04:51.105872 INFO::ASW Label was 0.389318447249624 prior to batch effect correction and is now 0.810583386860279 .
2025-11-18 03:04:51.106193 INFO::Total function execution time is 0.0174129009246826 s and adjustment time is 0.00682210922241211 s ( 39.18 )
2025-11-18 03:04:51.192156 INFO::Formatting Data.
2025-11-18 03:04:51.192456 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.19277 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.193139 INFO::Found 0 missing values.
2025-11-18 03:04:51.194124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.194345 INFO::Done
2025-11-18 03:04:51.194515 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.19526 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.195523 INFO::Found 3 batches.
2025-11-18 03:04:51.195699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.195899 INFO::Using default BPPARAM
2025-11-18 03:04:51.19606 INFO::Processing subtree level 1
2025-11-18 03:04:51.239717 INFO::Adjusting the last 1 batches sequentially
2025-11-18 03:04:51.240582 INFO::Done
2025-11-18 03:04:51.241151 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.242786 INFO::ASW Batch was -0.105406607959488 prior to batch effect correction and is now -0.105406607959488 .
2025-11-18 03:04:51.243418 INFO::Total function execution time is 0.0512940883636475 s and adjustment time is 0.0451138019561768 s ( 87.95 )
2025-11-18 03:04:51.243803 INFO::Formatting Data.
2025-11-18 03:04:51.244012 INFO::Typecasting input to dataframe.
2025-11-18 03:04:51.244276 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.24462 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.245018 INFO::Found 0 missing values.
2025-11-18 03:04:51.245977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.246179 INFO::Done
2025-11-18 03:04:51.246346 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.247041 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.247292 INFO::Found 3 batches.
2025-11-18 03:04:51.247596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.247831 INFO::Using default BPPARAM
2025-11-18 03:04:51.247996 INFO::Processing subtree level 1
2025-11-18 03:04:51.284562 INFO::Adjusting the last 1 batches sequentially
2025-11-18 03:04:51.293689 INFO::Done
2025-11-18 03:04:51.294385 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.296171 INFO::ASW Batch was -0.105406607959488 prior to batch effect correction and is now -0.105406607959488 .
2025-11-18 03:04:51.296975 INFO::Total function execution time is 0.0531249046325684 s and adjustment time is 0.0464060306549072 s ( 87.35 )
2025-11-18 03:04:51.303965 INFO::Formatting Data.
2025-11-18 03:04:51.304262 INFO::Typecasting input to dataframe.
2025-11-18 03:04:51.30457 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.304928 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.305369 INFO::Found 0 missing values.
2025-11-18 03:04:51.306355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.306569 INFO::Done
2025-11-18 03:04:51.306736 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.307454 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.307696 INFO::Found 3 batches.
2025-11-18 03:04:51.307865 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.308282 INFO::Using default BPPARAM
2025-11-18 03:04:51.308453 INFO::Processing subtree level 1
2025-11-18 03:04:51.34665 INFO::Adjusting the last 1 batches sequentially
2025-11-18 03:04:51.348042 INFO::Done
2025-11-18 03:04:51.348373 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.352942 INFO::ASW Batch was -0.0884259679253696 prior to batch effect correction and is now -0.0884259679253696 .
2025-11-18 03:04:51.354764 INFO::Total function execution time is 0.0504360198974609 s and adjustment time is 0.0403749942779541 s ( 80.05 )
2025-11-18 03:04:51.430097 INFO::Formatting Data.
2025-11-18 03:04:51.430593 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.431193 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.432171 INFO::Found 1000 missing values.
2025-11-18 03:04:51.438722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.43905 INFO::Done
2025-11-18 03:04:51.439243 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.44147 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.441946 INFO::Found 10 batches.
2025-11-18 03:04:51.442136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:51.442478 INFO::Using default BPPARAM
2025-11-18 03:04:51.44277 INFO::Processing subtree level 1
2025-11-18 03:04:51.515431 INFO::Processing subtree level 2
2025-11-18 03:04:51.575176 INFO::Adjusting the last 1 batches sequentially
2025-11-18 03:04:51.576443 INFO::Done
2025-11-18 03:04:51.576698 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:51.583946 INFO::ASW Batch was 0.481794281094136 prior to batch effect correction and is now 0.481794281094136 .
2025-11-18 03:04:51.584578 INFO::ASW Label was 0.347812567822146 prior to batch effect correction and is now 0.347812567822146 .
2025-11-18 03:04:51.586016 INFO::Total function execution time is 0.15574312210083 s and adjustment time is 0.134552955627441 s ( 86.39 )
2025-11-18 03:04:51.586585 INFO::Formatting Data.
2025-11-18 03:04:51.587059 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:51.588181 INFO::Removing potential empty rows and columns
2025-11-18 03:04:51.589205 INFO::Found 1000 missing values.
2025-11-18 03:04:51.598278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:51.598836 INFO::Done
2025-11-18 03:04:51.599046 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:51.601241 INFO::Starting hierarchical adjustment
2025-11-18 03:04:51.6016 INFO::Found 10 batches.
2025-11-18 03:04:52.063833 INFO::Set up parallel execution backend with 2 workers
2025-11-18 03:04:52.064159 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-18 03:04:52.565621 INFO::Adjusting the last 2 batches sequentially
2025-11-18 03:04:52.566161 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 03:04:52.571873 INFO::Done
2025-11-18 03:04:52.572139 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:52.574144 INFO::ASW Batch was 0.481794281094136 prior to batch effect correction and is now 0.481794281094136 .
2025-11-18 03:04:52.574376 INFO::ASW Label was 0.347812567822146 prior to batch effect correction and is now 0.347812567822146 .
2025-11-18 03:04:52.574636 INFO::Total function execution time is 0.988113880157471 s and adjustment time is 0.970326900482178 s ( 98.2 )
2025-11-18 03:04:52.646241 INFO::Formatting Data.
2025-11-18 03:04:52.646572 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.647061 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.647483 INFO::Found 0 missing values.
2025-11-18 03:04:52.648738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.648967 INFO::Done
2025-11-18 03:04:52.649785 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 03:04:52.650876 INFO::Starting hierarchical adjustment
2025-11-18 03:04:52.651178 INFO::Found 3 batches.
2025-11-18 03:04:52.651366 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 03:04:52.651601 INFO::Using default BPPARAM
2025-11-18 03:04:52.65178 INFO::Processing subtree level 1
2025-11-18 03:04:52.716325 INFO::Adjusting the last 1 batches sequentially
2025-11-18 03:04:52.719038 INFO::Done
2025-11-18 03:04:52.719496 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 03:04:52.721889 INFO::ASW Batch was 0.214419366982706 prior to batch effect correction and is now -0.153715839957344 .
2025-11-18 03:04:52.722157 INFO::ASW Label was -0.129039016114186 prior to batch effect correction and is now 0.117246974734008 .
2025-11-18 03:04:52.722963 INFO::Total function execution time is 0.0767529010772705 s and adjustment time is 0.0678911209106445 s ( 88.45 )
2025-11-18 03:04:52.78213 INFO::Formatting Data.
2025-11-18 03:04:52.782506 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.78289 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.783337 INFO::Found 2 missing values.
2025-11-18 03:04:52.784395 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.784621 INFO::Done
2025-11-18 03:04:52.805892 INFO::Found NA in Reference column
2025-11-18 03:04:52.810482 INFO::Require at least two references per batch.
2025-11-18 03:04:52.820566 INFO::Formatting Data.
2025-11-18 03:04:52.820906 INFO::Recognized SummarizedExperiment
2025-11-18 03:04:52.821109 INFO::Typecasting input to dataframe.
2025-11-18 03:04:52.826061 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.826631 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.828188 INFO::Found 0 missing values.
2025-11-18 03:04:52.830943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.831232 INFO::Done
2025-11-18 03:04:52.842069 INFO::Formatting Data.
2025-11-18 03:04:52.842409 INFO::Recognized SummarizedExperiment
2025-11-18 03:04:52.842609 INFO::Typecasting input to dataframe.
2025-11-18 03:04:52.849485 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.85002 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.851369 INFO::Found 0 missing values.
2025-11-18 03:04:52.855736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.856035 INFO::Done
2025-11-18 03:04:52.862143 INFO::Formatting Data.
2025-11-18 03:04:52.862436 INFO::Recognized SummarizedExperiment
2025-11-18 03:04:52.86262 INFO::Typecasting input to dataframe.
2025-11-18 03:04:52.869102 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.869527 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.869916 INFO::Found 0 missing values.
2025-11-18 03:04:52.87027 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.
2025-11-18 03:04:52.871906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.872152 INFO::Done
2025-11-18 03:04:52.876668 INFO::Formatting Data.
2025-11-18 03:04:52.876994 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.877292 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.877623 INFO::Found 0 missing values.
2025-11-18 03:04:52.878519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.878697 INFO::Done
2025-11-18 03:04:52.88905 INFO::Formatting Data.
2025-11-18 03:04:52.889471 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.889843 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.890302 INFO::Found 0 missing values.
2025-11-18 03:04:52.891481 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.891731 INFO::Done
2025-11-18 03:04:52.907289 INFO::Formatting Data.
2025-11-18 03:04:52.907651 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.908122 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.908583 INFO::Found 1 missing values.
2025-11-18 03:04:52.909702 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.909986 INFO::Done
2025-11-18 03:04:52.924051 INFO::Formatting Data.
2025-11-18 03:04:52.924401 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.92474 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.925161 INFO::Found 2 missing values.
2025-11-18 03:04:52.925521 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.
2025-11-18 03:04:52.926438 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.926661 INFO::Done
2025-11-18 03:04:52.931361 INFO::Formatting Data.
2025-11-18 03:04:52.931713 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.932086 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.932467 INFO::Found 2 missing values.
2025-11-18 03:04:52.933091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.933312 INFO::Done
2025-11-18 03:04:52.938088 INFO::Formatting Data.
2025-11-18 03:04:52.938386 INFO::Typecasting input to dataframe.
2025-11-18 03:04:52.938651 INFO::Replacing NaNs with NAs.
2025-11-18 03:04:52.938939 INFO::Removing potential empty rows and columns
2025-11-18 03:04:52.939269 INFO::Found 0 missing values.
2025-11-18 03:04:52.940221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 03:04:52.940446 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.260 1.408 9.757
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.187 | 0.356 | 8.204 | |
| compute_asw | 0.010 | 0.000 | 0.011 | |
| count_existing | 0.006 | 0.001 | 0.006 | |
| generate_data_covariables | 0.005 | 0.000 | 0.005 | |
| generate_dataset | 0.005 | 0.001 | 0.005 | |