Yannis Schumann
| Snapshot Date: 2025-12-15 13:40 -0500 (Mon, 15 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 2025-12-16 11:35 -0500 (Tue, 16 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: 2025-12-15 18:35:27 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 18:36:04 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 36.6 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 10.418 0.448 7.645
* 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")
2025-12-15 18:35:54.958699 INFO::Formatting Data.
2025-12-15 18:35:54.960248 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:54.971178 INFO::Removing potential empty rows and columns
2025-12-15 18:35:55.072779 INFO::Found 0 missing values.
2025-12-15 18:35:55.074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:55.074219 INFO::Done
2025-12-15 18:35:55.074401 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:55.081086 INFO::Starting hierarchical adjustment
2025-12-15 18:35:55.081395 INFO::Found 3 batches.
2025-12-15 18:35:55.081584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:55.081974 INFO::Using default BPPARAM
2025-12-15 18:35:55.082127 INFO::Processing subtree level 1
2025-12-15 18:35:55.158296 INFO::Adjusting the last 1 batches sequentially
2025-12-15 18:35:55.161895 INFO::Done
2025-12-15 18:35:55.16223 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:55.164647 INFO::ASW Batch was -0.0680125731807703 prior to batch effect correction and is now -0.0680125731807703 .
2025-12-15 18:35:55.165473 INFO::Total function execution time is 0.206990003585815 s and adjustment time is 0.0805280208587646 s ( 38.9 )
2025-12-15 18:35:55.175809 INFO::Formatting Data.
2025-12-15 18:35:55.176136 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:55.176529 INFO::Removing potential empty rows and columns
2025-12-15 18:35:55.177132 INFO::Found 0 missing values.
2025-12-15 18:35:55.177552 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.
2025-12-15 18:35:55.183937 INFO::Formatting Data.
2025-12-15 18:35:55.18421 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:55.184608 INFO::Removing potential empty rows and columns
2025-12-15 18:35:55.185268 INFO::Found 0 missing values.
2025-12-15 18:35:55.18568 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.
2025-12-15 18:35:55.194288 INFO::Formatting Data.
2025-12-15 18:35:55.194641 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:55.19509 INFO::Removing potential empty rows and columns
2025-12-15 18:35:55.195556 INFO::Found 0 missing values.
2025-12-15 18:35:55.195942 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.
2025-12-15 18:35:55.197846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:55.198091 INFO::Done
2025-12-15 18:35:55.198326 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:55.201267 INFO::Starting hierarchical adjustment
2025-12-15 18:35:55.201694 INFO::Found 2 batches.
2025-12-15 18:35:55.206022 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:55.206487 INFO::Using default BPPARAM
2025-12-15 18:35:55.206775 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:55.207361 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 18:35:55.222224 INFO::Done
2025-12-15 18:35:55.222566 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:55.223427 INFO::ASW Batch was 0.0112399254352491 prior to batch effect correction and is now -0.122712974375967 .
2025-12-15 18:35:55.223735 INFO::Total function execution time is 0.0295000076293945 s and adjustment time is 0.0206129550933838 s ( 69.87 )
2025-12-15 18:35:55.225081 INFO::Formatting Data.
2025-12-15 18:35:55.225489 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:55.229391 INFO::Formatting Data.
2025-12-15 18:35:55.229651 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:55.229969 INFO::Removing potential empty rows and columns
2025-12-15 18:35:55.230351 INFO::Found 0 missing values.
2025-12-15 18:35:55.231473 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:55.231669 INFO::Done
2025-12-15 18:35:55.231836 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:55.232559 INFO::Starting hierarchical adjustment
2025-12-15 18:35:55.232827 INFO::Found 2 batches.
2025-12-15 18:35:55.233012 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:55.233246 INFO::Using default BPPARAM
2025-12-15 18:35:55.233414 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:55.233713 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 18:35:55.263411 INFO::Done
2025-12-15 18:35:55.263651 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:55.264287 INFO::ASW Batch was -0.0759612259430058 prior to batch effect correction and is now -0.117274819539704 .
2025-12-15 18:35:55.264516 INFO::Total function execution time is 0.0351519584655762 s and adjustment time is 0.0306229591369629 s ( 87.12 )
2025-12-15 18:35:55.264819 INFO::Formatting Data.
2025-12-15 18:35:55.264991 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:55.265243 INFO::Removing potential empty rows and columns
2025-12-15 18:35:55.265557 INFO::Found 0 missing values.
2025-12-15 18:35:55.266486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:55.26671 INFO::Done
2025-12-15 18:35:55.266875 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:55.267492 INFO::Starting hierarchical adjustment
2025-12-15 18:35:55.267715 INFO::Found 2 batches.
2025-12-15 18:35:55.267878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:55.268069 INFO::Using default BPPARAM
2025-12-15 18:35:55.268224 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:55.268493 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 18:35:55.273545 INFO::Done
2025-12-15 18:35:55.273818 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:55.27444 INFO::ASW Batch was -0.0759612259430058 prior to batch effect correction and is now -0.117274819539704 .
2025-12-15 18:35:55.274688 INFO::Total function execution time is 0.00985598564147949 s and adjustment time is 0.0058739185333252 s ( 59.6 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-15 18:35:56.568266 INFO::Formatting Data.
2025-12-15 18:35:56.568522 INFO::Recognized SummarizedExperiment
2025-12-15 18:35:56.568681 INFO::Typecasting input to dataframe.
2025-12-15 18:35:56.578965 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:56.579365 INFO::Removing potential empty rows and columns
2025-12-15 18:35:56.580456 INFO::Found 0 missing values.
2025-12-15 18:35:56.582329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:56.582485 INFO::Done
2025-12-15 18:35:56.582621 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:56.583691 INFO::Starting hierarchical adjustment
2025-12-15 18:35:56.583875 INFO::Found 2 batches.
2025-12-15 18:35:56.584007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:56.584286 INFO::Using default BPPARAM
2025-12-15 18:35:56.584681 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:56.584951 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 18:35:56.600935 INFO::Done
2025-12-15 18:35:56.601208 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:56.602515 INFO::ASW Batch was 0.0146273674899209 prior to batch effect correction and is now -0.0851366680529945 .
2025-12-15 18:35:56.602802 INFO::Total function execution time is 0.0346269607543945 s and adjustment time is 0.0170729160308838 s ( 49.31 )
Warning: stack imbalance in '{', 73 then 75
2025-12-15 18:35:56.609531 INFO::Formatting Data.
2025-12-15 18:35:56.609777 INFO::Recognized SummarizedExperiment
2025-12-15 18:35:56.609951 INFO::Typecasting input to dataframe.
2025-12-15 18:35:56.613112 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:56.613519 INFO::Removing potential empty rows and columns
2025-12-15 18:35:56.614749 INFO::Found 0 missing values.
2025-12-15 18:35:56.618915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:56.619182 INFO::Done
2025-12-15 18:35:56.619384 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:56.620802 INFO::Starting hierarchical adjustment
2025-12-15 18:35:56.621083 INFO::Found 2 batches.
2025-12-15 18:35:56.621251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:56.621441 INFO::Using default BPPARAM
2025-12-15 18:35:56.621618 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:56.621981 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 18:35:56.630987 INFO::Done
2025-12-15 18:35:56.631255 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:56.632511 INFO::ASW Batch was 0.0127505433799118 prior to batch effect correction and is now 0.0127505433799118 .
2025-12-15 18:35:56.632785 INFO::Total function execution time is 0.023245096206665 s and adjustment time is 0.00994420051574707 s ( 42.78 )
2025-12-15 18:35:56.642758 INFO::Formatting Data.
2025-12-15 18:35:56.643075 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:56.643412 INFO::Removing potential empty rows and columns
2025-12-15 18:35:56.643764 INFO::Found 0 missing values.
2025-12-15 18:35:56.644697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:56.644884 INFO::Done
2025-12-15 18:35:56.645044 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:56.645761 INFO::Starting hierarchical adjustment
2025-12-15 18:35:56.645968 INFO::Found 3 batches.
2025-12-15 18:35:56.646134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:56.646317 INFO::Using default BPPARAM
2025-12-15 18:35:56.646463 INFO::Processing subtree level 1
2025-12-15 18:35:56.751956 INFO::Adjusting the last 1 batches sequentially
2025-12-15 18:35:56.754303 INFO::Done
2025-12-15 18:35:56.754666 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:56.756966 INFO::ASW Batch was -0.0506859562531342 prior to batch effect correction and is now -0.153158538969843 .
2025-12-15 18:35:56.757603 INFO::Total function execution time is 0.114792108535767 s and adjustment time is 0.108375072479248 s ( 94.41 )
2025-12-15 18:35:56.765536 INFO::Skipping initial DF formatting
2025-12-15 18:35:56.7658 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:56.767274 INFO::Starting hierarchical adjustment
2025-12-15 18:35:56.767547 INFO::Found 5 batches.
2025-12-15 18:35:56.767756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:56.767976 INFO::Using default BPPARAM
2025-12-15 18:35:56.768154 INFO::Processing subtree level 1
2025-12-15 18:35:56.845765 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:56.847652 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 18:35:56.85831 INFO::Done
2025-12-15 18:35:56.858725 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:56.861451 INFO::ASW Batch was 0.487899243951767 prior to batch effect correction and is now 0.487899243951767 .
2025-12-15 18:35:56.861686 INFO::ASW Label was 0.352369801044178 prior to batch effect correction and is now 0.352369801044178 .
2025-12-15 18:35:56.862295 INFO::Total function execution time is 0.0966150760650635 s and adjustment time is 0.0907797813415527 s ( 93.96 )
2025-12-15 18:35:56.871349 INFO::Formatting Data.
2025-12-15 18:35:56.871657 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:56.872017 INFO::Removing potential empty rows and columns
2025-12-15 18:35:56.872444 INFO::Found 0 missing values.
2025-12-15 18:35:56.873837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:56.874033 INFO::Done
2025-12-15 18:35:56.874234 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:56.87567 INFO::Starting hierarchical adjustment
2025-12-15 18:35:56.875943 INFO::Found 5 batches.
2025-12-15 18:35:56.876153 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:56.876427 INFO::Using default BPPARAM
2025-12-15 18:35:56.87661 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.
2025-12-15 18:35:56.948399 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:56.950133 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 18:35:56.959587 INFO::Done
2025-12-15 18:35:56.960058 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:56.962012 INFO::ASW Batch was 0.392826900129533 prior to batch effect correction and is now -0.0809697937889529 .
2025-12-15 18:35:56.962235 INFO::ASW Label was 0.309569692532021 prior to batch effect correction and is now 0.90250672236324 .
2025-12-15 18:35:56.962673 INFO::Total function execution time is 0.0912561416625977 s and adjustment time is 0.0836780071258545 s ( 91.7 )
2025-12-15 18:35:56.963045 INFO::Formatting Data.
2025-12-15 18:35:56.96329 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:56.963679 INFO::Removing potential empty rows and columns
2025-12-15 18:35:56.964076 INFO::Found 0 missing values.
2025-12-15 18:35:56.965578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:56.965792 INFO::Done
2025-12-15 18:35:56.965987 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:56.967218 INFO::Starting hierarchical adjustment
2025-12-15 18:35:56.96752 INFO::Found 5 batches.
2025-12-15 18:35:56.967716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:56.967973 INFO::Using default BPPARAM
2025-12-15 18:35:56.968147 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.
2025-12-15 18:35:57.03551 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:57.042573 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 18:35:57.061136 INFO::Done
2025-12-15 18:35:57.061701 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.063183 INFO::ASW Batch was 0.392826900129533 prior to batch effect correction and is now -0.0809697937889529 .
2025-12-15 18:35:57.063386 INFO::ASW Label was 0.309569692532021 prior to batch effect correction and is now 0.90250672236324 .
2025-12-15 18:35:57.063887 INFO::Total function execution time is 0.100684881210327 s and adjustment time is 0.0936589241027832 s ( 93.02 )
2025-12-15 18:35:57.070167 INFO::Formatting Data.
2025-12-15 18:35:57.07064 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.070965 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.071366 INFO::Found 0 missing values.
2025-12-15 18:35:57.072641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.072827 INFO::Done
2025-12-15 18:35:57.072996 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.074015 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.074262 INFO::Found 5 batches.
2025-12-15 18:35:57.074429 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.074665 INFO::Using default BPPARAM
2025-12-15 18:35:57.074842 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.
2025-12-15 18:35:57.154096 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:57.158449 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 18:35:57.168838 INFO::Done
2025-12-15 18:35:57.169453 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.171163 INFO::ASW Batch was 0.188096470054231 prior to batch effect correction and is now -0.0584383230231137 .
2025-12-15 18:35:57.171402 INFO::ASW Label was 0.544166967957577 prior to batch effect correction and is now 0.8698320352478 .
2025-12-15 18:35:57.171766 INFO::Total function execution time is 0.10159707069397 s and adjustment time is 0.0946109294891357 s ( 93.12 )
2025-12-15 18:35:57.17208 INFO::Formatting Data.
2025-12-15 18:35:57.172299 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.172632 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.173011 INFO::Found 0 missing values.
2025-12-15 18:35:57.181675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.181926 INFO::Done
2025-12-15 18:35:57.182145 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.183542 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.183833 INFO::Found 5 batches.
2025-12-15 18:35:57.184014 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.184271 INFO::Using default BPPARAM
2025-12-15 18:35:57.184434 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.
2025-12-15 18:35:57.259675 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:57.262123 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 18:35:57.271556 INFO::Done
2025-12-15 18:35:57.271838 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.273445 INFO::ASW Batch was 0.188096470054231 prior to batch effect correction and is now -0.0584383230231137 .
2025-12-15 18:35:57.273655 INFO::ASW Label was 0.544166967957577 prior to batch effect correction and is now 0.8698320352478 .
2025-12-15 18:35:57.274148 INFO::Total function execution time is 0.101912975311279 s and adjustment time is 0.0877559185028076 s ( 86.11 )
2025-12-15 18:35:57.28121 INFO::Formatting Data.
2025-12-15 18:35:57.281481 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.282125 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.282505 INFO::Found 0 missing values.
2025-12-15 18:35:57.28337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.283722 INFO::Done
2025-12-15 18:35:57.283895 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.284892 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.28513 INFO::Found 2 batches.
2025-12-15 18:35:57.2853 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.285519 INFO::Using default BPPARAM
2025-12-15 18:35:57.285688 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:57.285959 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 18:35:57.291596 INFO::Done
2025-12-15 18:35:57.291891 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.293033 INFO::ASW Batch was 0.605775401596205 prior to batch effect correction and is now -0.0328825742899983 .
2025-12-15 18:35:57.293266 INFO::ASW Label was 0.449906226336957 prior to batch effect correction and is now 0.917997094586016 .
2025-12-15 18:35:57.293567 INFO::Total function execution time is 0.0124030113220215 s and adjustment time is 0.00650691986083984 s ( 52.46 )
2025-12-15 18:35:57.293861 INFO::Formatting Data.
2025-12-15 18:35:57.294075 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.294643 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.29506 INFO::Found 0 missing values.
2025-12-15 18:35:57.296016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.296198 INFO::Done
2025-12-15 18:35:57.296383 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.297453 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.297717 INFO::Found 2 batches.
2025-12-15 18:35:57.298024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.298235 INFO::Using default BPPARAM
2025-12-15 18:35:57.298385 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:57.298679 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 18:35:57.303994 INFO::Done
2025-12-15 18:35:57.304349 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.305581 INFO::ASW Batch was 0.605775401596205 prior to batch effect correction and is now -0.0328825742899983 .
2025-12-15 18:35:57.305801 INFO::ASW Label was 0.449906226336957 prior to batch effect correction and is now 0.917997094586016 .
2025-12-15 18:35:57.306073 INFO::Total function execution time is 0.0122060775756836 s and adjustment time is 0.00633907318115234 s ( 51.93 )
2025-12-15 18:35:57.310641 INFO::Formatting Data.
2025-12-15 18:35:57.310907 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.311212 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.311533 INFO::Found 0 missing values.
2025-12-15 18:35:57.312267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.312479 INFO::Done
2025-12-15 18:35:57.312668 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.31334 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.313562 INFO::Found 2 batches.
2025-12-15 18:35:57.313727 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.313931 INFO::Using default BPPARAM
2025-12-15 18:35:57.314083 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:57.319904 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 18:35:57.333003 INFO::Done
2025-12-15 18:35:57.333356 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.33423 INFO::ASW Batch was -0.0606883388643309 prior to batch effect correction and is now -0.108213037683412 .
2025-12-15 18:35:57.334581 INFO::Total function execution time is 0.0239710807800293 s and adjustment time is 0.0194611549377441 s ( 81.19 )
2025-12-15 18:35:57.339885 INFO::Formatting Data.
2025-12-15 18:35:57.340282 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.340592 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.340919 INFO::Found 0 missing values.
2025-12-15 18:35:57.341467 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.
2025-12-15 18:35:57.343216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.343437 INFO::Done
2025-12-15 18:35:57.34367 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.344845 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.345116 INFO::Found 2 batches.
2025-12-15 18:35:57.345297 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.345534 INFO::Using default BPPARAM
2025-12-15 18:35:57.345717 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:57.346062 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 18:35:57.351692 INFO::Done
2025-12-15 18:35:57.351918 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.352821 INFO::ASW Batch was 0.65865499830216 prior to batch effect correction and is now -0.0342800304914201 .
2025-12-15 18:35:57.353077 INFO::ASW Label was 0.40251190227139 prior to batch effect correction and is now 0.90613150253537 .
2025-12-15 18:35:57.35343 INFO::Total function execution time is 0.0135550498962402 s and adjustment time is 0.00661683082580566 s ( 48.81 )
2025-12-15 18:35:57.353718 INFO::Formatting Data.
2025-12-15 18:35:57.353919 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.354241 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.354614 INFO::Found 0 missing values.
2025-12-15 18:35:57.354959 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.
2025-12-15 18:35:57.356583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.356814 INFO::Done
2025-12-15 18:35:57.357021 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.358079 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.358338 INFO::Found 2 batches.
2025-12-15 18:35:57.358508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.358773 INFO::Using default BPPARAM
2025-12-15 18:35:57.358966 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:57.359317 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 18:35:57.365779 INFO::Done
2025-12-15 18:35:57.366034 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.367009 INFO::ASW Batch was 0.65865499830216 prior to batch effect correction and is now -0.0342800304914201 .
2025-12-15 18:35:57.367195 INFO::ASW Label was 0.40251190227139 prior to batch effect correction and is now 0.90613150253537 .
2025-12-15 18:35:57.367466 INFO::Total function execution time is 0.0137310028076172 s and adjustment time is 0.00747108459472656 s ( 54.41 )
2025-12-15 18:35:57.447441 INFO::Formatting Data.
2025-12-15 18:35:57.447801 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.448153 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.448564 INFO::Found 0 missing values.
2025-12-15 18:35:57.449659 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.449886 INFO::Done
2025-12-15 18:35:57.450088 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.450938 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.451209 INFO::Found 3 batches.
2025-12-15 18:35:57.451416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.451653 INFO::Using default BPPARAM
2025-12-15 18:35:57.45184 INFO::Processing subtree level 1
2025-12-15 18:35:57.571179 INFO::Adjusting the last 1 batches sequentially
2025-12-15 18:35:57.574291 INFO::Done
2025-12-15 18:35:57.574656 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.576764 INFO::ASW Batch was -0.0988732549521045 prior to batch effect correction and is now -0.0988732549521045 .
2025-12-15 18:35:57.57727 INFO::Total function execution time is 0.129781007766724 s and adjustment time is 0.123131036758423 s ( 94.88 )
2025-12-15 18:35:57.577637 INFO::Formatting Data.
2025-12-15 18:35:57.577952 INFO::Typecasting input to dataframe.
2025-12-15 18:35:57.578188 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.578596 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.57896 INFO::Found 0 missing values.
2025-12-15 18:35:57.580085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.580262 INFO::Done
2025-12-15 18:35:57.580449 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.581098 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.582049 INFO::Found 3 batches.
2025-12-15 18:35:57.582374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.582653 INFO::Using default BPPARAM
2025-12-15 18:35:57.582843 INFO::Processing subtree level 1
2025-12-15 18:35:57.683918 INFO::Adjusting the last 1 batches sequentially
2025-12-15 18:35:57.685787 INFO::Done
2025-12-15 18:35:57.686089 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.697228 INFO::ASW Batch was -0.0988732549521045 prior to batch effect correction and is now -0.0988732549521045 .
2025-12-15 18:35:57.698825 INFO::Total function execution time is 0.120775938034058 s and adjustment time is 0.103868007659912 s ( 86 )
2025-12-15 18:35:57.707439 INFO::Formatting Data.
2025-12-15 18:35:57.707754 INFO::Typecasting input to dataframe.
2025-12-15 18:35:57.708054 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.70843 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.708873 INFO::Found 0 missing values.
2025-12-15 18:35:57.709939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.710144 INFO::Done
2025-12-15 18:35:57.729145 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.730627 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.731009 INFO::Found 3 batches.
2025-12-15 18:35:57.731266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.731595 INFO::Using default BPPARAM
2025-12-15 18:35:57.731879 INFO::Processing subtree level 1
2025-12-15 18:35:57.817889 INFO::Adjusting the last 1 batches sequentially
2025-12-15 18:35:57.821717 INFO::Done
2025-12-15 18:35:57.822345 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:57.826351 INFO::ASW Batch was -0.0243379972206641 prior to batch effect correction and is now -0.0243379972206641 .
2025-12-15 18:35:57.827798 INFO::Total function execution time is 0.120175838470459 s and adjustment time is 0.0907509326934814 s ( 75.52 )
2025-12-15 18:35:57.94319 INFO::Formatting Data.
2025-12-15 18:35:57.944158 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:57.948874 INFO::Removing potential empty rows and columns
2025-12-15 18:35:57.950524 INFO::Found 1000 missing values.
2025-12-15 18:35:57.964073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:57.964438 INFO::Done
2025-12-15 18:35:57.964672 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:57.967084 INFO::Starting hierarchical adjustment
2025-12-15 18:35:57.96738 INFO::Found 10 batches.
2025-12-15 18:35:57.967655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:57.967915 INFO::Using default BPPARAM
2025-12-15 18:35:57.968192 INFO::Processing subtree level 1
2025-12-15 18:35:58.058537 INFO::Processing subtree level 2
2025-12-15 18:35:58.160601 INFO::Adjusting the last 1 batches sequentially
2025-12-15 18:35:58.162979 INFO::Done
2025-12-15 18:35:58.163555 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:58.167592 INFO::ASW Batch was 0.496327682250526 prior to batch effect correction and is now 0.496327682250526 .
2025-12-15 18:35:58.167967 INFO::ASW Label was 0.330562506990788 prior to batch effect correction and is now 0.330562506990788 .
2025-12-15 18:35:58.168772 INFO::Total function execution time is 0.225634098052979 s and adjustment time is 0.195643901824951 s ( 86.71 )
2025-12-15 18:35:58.169124 INFO::Formatting Data.
2025-12-15 18:35:58.169343 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:58.169799 INFO::Removing potential empty rows and columns
2025-12-15 18:35:58.170817 INFO::Found 1000 missing values.
2025-12-15 18:35:58.178408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:58.178703 INFO::Done
2025-12-15 18:35:58.1789 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:58.18105 INFO::Starting hierarchical adjustment
2025-12-15 18:35:58.181352 INFO::Found 10 batches.
2025-12-15 18:35:58.670016 INFO::Set up parallel execution backend with 2 workers
2025-12-15 18:35:58.670387 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-15 18:35:59.26255 INFO::Adjusting the last 2 batches sequentially
2025-12-15 18:35:59.263121 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 18:35:59.270071 INFO::Done
2025-12-15 18:35:59.270335 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:59.272437 INFO::ASW Batch was 0.496327682250526 prior to batch effect correction and is now 0.496327682250526 .
2025-12-15 18:35:59.272624 INFO::ASW Label was 0.330562506990788 prior to batch effect correction and is now 0.330562506990788 .
2025-12-15 18:35:59.27289 INFO::Total function execution time is 1.10377192497253 s and adjustment time is 1.08877682685852 s ( 98.64 )
2025-12-15 18:35:59.348802 INFO::Formatting Data.
2025-12-15 18:35:59.349126 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.349512 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.349985 INFO::Found 0 missing values.
2025-12-15 18:35:59.351363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.351563 INFO::Done
2025-12-15 18:35:59.351738 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 18:35:59.352781 INFO::Starting hierarchical adjustment
2025-12-15 18:35:59.358525 INFO::Found 3 batches.
2025-12-15 18:35:59.358919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 18:35:59.359279 INFO::Using default BPPARAM
2025-12-15 18:35:59.359536 INFO::Processing subtree level 1
2025-12-15 18:35:59.421804 INFO::Adjusting the last 1 batches sequentially
2025-12-15 18:35:59.425415 INFO::Done
2025-12-15 18:35:59.425815 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 18:35:59.42839 INFO::ASW Batch was 0.192040654772607 prior to batch effect correction and is now -0.147903327076485 .
2025-12-15 18:35:59.428798 INFO::ASW Label was -0.190550481971294 prior to batch effect correction and is now -0.135149101744305 .
2025-12-15 18:35:59.429322 INFO::Total function execution time is 0.0805518627166748 s and adjustment time is 0.0723838806152344 s ( 89.86 )
2025-12-15 18:35:59.488487 INFO::Formatting Data.
2025-12-15 18:35:59.48884 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.489192 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.489581 INFO::Found 2 missing values.
2025-12-15 18:35:59.490545 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.490723 INFO::Done
2025-12-15 18:35:59.502359 INFO::Found NA in Reference column
2025-12-15 18:35:59.506786 INFO::Require at least two references per batch.
2025-12-15 18:35:59.515749 INFO::Formatting Data.
2025-12-15 18:35:59.516033 INFO::Recognized SummarizedExperiment
2025-12-15 18:35:59.516233 INFO::Typecasting input to dataframe.
2025-12-15 18:35:59.521134 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.5216 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.523132 INFO::Found 0 missing values.
2025-12-15 18:35:59.525728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.525946 INFO::Done
2025-12-15 18:35:59.532104 INFO::Formatting Data.
2025-12-15 18:35:59.532319 INFO::Recognized SummarizedExperiment
2025-12-15 18:35:59.532485 INFO::Typecasting input to dataframe.
2025-12-15 18:35:59.538047 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.538426 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.539706 INFO::Found 0 missing values.
2025-12-15 18:35:59.543397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.543586 INFO::Done
2025-12-15 18:35:59.549355 INFO::Formatting Data.
2025-12-15 18:35:59.549596 INFO::Recognized SummarizedExperiment
2025-12-15 18:35:59.549787 INFO::Typecasting input to dataframe.
2025-12-15 18:35:59.555259 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.555607 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.555956 INFO::Found 0 missing values.
2025-12-15 18:35:59.556275 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.
2025-12-15 18:35:59.557731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.55791 INFO::Done
2025-12-15 18:35:59.562342 INFO::Formatting Data.
2025-12-15 18:35:59.562586 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.562862 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.563228 INFO::Found 0 missing values.
2025-12-15 18:35:59.564458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.564633 INFO::Done
2025-12-15 18:35:59.570388 INFO::Formatting Data.
2025-12-15 18:35:59.570738 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.57108 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.571515 INFO::Found 0 missing values.
2025-12-15 18:35:59.57256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.572737 INFO::Done
2025-12-15 18:35:59.58436 INFO::Formatting Data.
2025-12-15 18:35:59.584665 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.584967 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.585326 INFO::Found 1 missing values.
2025-12-15 18:35:59.586114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.586272 INFO::Done
2025-12-15 18:35:59.593145 INFO::Formatting Data.
2025-12-15 18:35:59.593392 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.593661 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.59395 INFO::Found 2 missing values.
2025-12-15 18:35:59.594225 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.
2025-12-15 18:35:59.595022 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.595266 INFO::Done
2025-12-15 18:35:59.599532 INFO::Formatting Data.
2025-12-15 18:35:59.599781 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.600072 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.600355 INFO::Found 2 missing values.
2025-12-15 18:35:59.600876 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.601041 INFO::Done
2025-12-15 18:35:59.604962 INFO::Formatting Data.
2025-12-15 18:35:59.605228 INFO::Typecasting input to dataframe.
2025-12-15 18:35:59.605501 INFO::Replacing NaNs with NAs.
2025-12-15 18:35:59.60577 INFO::Removing potential empty rows and columns
2025-12-15 18:35:59.60611 INFO::Found 0 missing values.
2025-12-15 18:35:59.607088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 18:35:59.60727 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.465 1.877 9.845
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.418 | 0.448 | 7.645 | |
| compute_asw | 0.009 | 0.001 | 0.011 | |
| count_existing | 0.006 | 0.000 | 0.007 | |
| generate_data_covariables | 0.004 | 0.000 | 0.004 | |
| generate_dataset | 0.005 | 0.000 | 0.005 | |