Yannis Schumann
| Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026) |
| 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:36 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 170/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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: 2026-04-19 18:32:32 -0400 (Sun, 19 Apr 2026) |
| EndedAt: 2026-04-19 18:33:05 -0400 (Sun, 19 Apr 2026) |
| EllapsedTime: 33.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-19 22:32:32 UTC
* 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 9.702 0.372 6.859
* 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/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 version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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")
2026-04-19 18:32:57.092383 INFO::Formatting Data.
2026-04-19 18:32:57.09489 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:57.100591 INFO::Removing potential empty rows and columns
2026-04-19 18:32:57.238872 INFO::Found 0 missing values.
2026-04-19 18:32:57.240273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:57.240675 INFO::Done
2026-04-19 18:32:57.241002 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:57.24794 INFO::Starting hierarchical adjustment
2026-04-19 18:32:57.248566 INFO::Found 3 batches.
2026-04-19 18:32:57.248953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:57.249563 INFO::Using default BPPARAM
2026-04-19 18:32:57.2499 INFO::Processing subtree level 1
2026-04-19 18:32:57.30678 INFO::Adjusting the last 1 batches sequentially
2026-04-19 18:32:57.30843 INFO::Done
2026-04-19 18:32:57.308848 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:57.310363 INFO::ASW Batch was 0.0568731238991555 prior to batch effect correction and is now 0.0568731238991555 .
2026-04-19 18:32:57.311035 INFO::Total function execution time is 0.219370126724243 s and adjustment time is 0.0599379539489746 s ( 27.32 )
2026-04-19 18:32:57.319586 INFO::Formatting Data.
2026-04-19 18:32:57.32011 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:57.320679 INFO::Removing potential empty rows and columns
2026-04-19 18:32:57.321528 INFO::Found 0 missing values.
2026-04-19 18:32:57.322101 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.
2026-04-19 18:32:57.328272 INFO::Formatting Data.
2026-04-19 18:32:57.328718 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:57.329248 INFO::Removing potential empty rows and columns
2026-04-19 18:32:57.329931 INFO::Found 0 missing values.
2026-04-19 18:32:57.330567 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.
2026-04-19 18:32:57.339013 INFO::Formatting Data.
2026-04-19 18:32:57.339518 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:57.340036 INFO::Removing potential empty rows and columns
2026-04-19 18:32:57.340673 INFO::Found 0 missing values.
2026-04-19 18:32:57.341237 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.
2026-04-19 18:32:57.343344 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:57.343744 INFO::Done
2026-04-19 18:32:57.344142 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:57.345229 INFO::Starting hierarchical adjustment
2026-04-19 18:32:57.345697 INFO::Found 2 batches.
2026-04-19 18:32:57.346033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:57.346465 INFO::Using default BPPARAM
2026-04-19 18:32:57.346846 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:57.347402 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-19 18:32:57.359751 INFO::Done
2026-04-19 18:32:57.36018 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:57.361099 INFO::ASW Batch was 0.0949813035607835 prior to batch effect correction and is now -0.0882750573117386 .
2026-04-19 18:32:57.361537 INFO::Total function execution time is 0.0225598812103271 s and adjustment time is 0.0141010284423828 s ( 62.5 )
2026-04-19 18:32:57.362837 INFO::Formatting Data.
2026-04-19 18:32:57.363222 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:57.367032 INFO::Formatting Data.
2026-04-19 18:32:57.367426 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:57.367897 INFO::Removing potential empty rows and columns
2026-04-19 18:32:57.368466 INFO::Found 0 missing values.
2026-04-19 18:32:57.369712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:57.370048 INFO::Done
2026-04-19 18:32:57.370372 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:57.371248 INFO::Starting hierarchical adjustment
2026-04-19 18:32:57.371666 INFO::Found 2 batches.
2026-04-19 18:32:57.371997 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:57.372345 INFO::Using default BPPARAM
2026-04-19 18:32:57.372648 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:57.373053 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-19 18:32:57.379958 INFO::Done
2026-04-19 18:32:57.380429 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:57.381358 INFO::ASW Batch was -0.036321530776287 prior to batch effect correction and is now -0.113805881597968 .
2026-04-19 18:32:57.381744 INFO::Total function execution time is 0.0147111415863037 s and adjustment time is 0.00831890106201172 s ( 56.55 )
2026-04-19 18:32:57.382222 INFO::Formatting Data.
2026-04-19 18:32:57.382561 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:57.382946 INFO::Removing potential empty rows and columns
2026-04-19 18:32:57.38341 INFO::Found 0 missing values.
2026-04-19 18:32:57.384618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:57.384982 INFO::Done
2026-04-19 18:32:57.385368 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:57.386317 INFO::Starting hierarchical adjustment
2026-04-19 18:32:57.38681 INFO::Found 2 batches.
2026-04-19 18:32:57.387129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:57.387493 INFO::Using default BPPARAM
2026-04-19 18:32:57.387855 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:57.388285 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-19 18:32:57.393014 INFO::Done
2026-04-19 18:32:57.393402 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:57.394183 INFO::ASW Batch was -0.036321530776287 prior to batch effect correction and is now -0.113805881597968 .
2026-04-19 18:32:57.394555 INFO::Total function execution time is 0.0123209953308105 s and adjustment time is 0.00625300407409668 s ( 50.75 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-19 18:32:58.718114 INFO::Formatting Data.
2026-04-19 18:32:58.718588 INFO::Recognized SummarizedExperiment
2026-04-19 18:32:58.71893 INFO::Typecasting input to dataframe.
2026-04-19 18:32:58.729328 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:58.729945 INFO::Removing potential empty rows and columns
2026-04-19 18:32:58.731209 INFO::Found 0 missing values.
2026-04-19 18:32:58.73346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:58.733766 INFO::Done
2026-04-19 18:32:58.734076 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:58.73539 INFO::Starting hierarchical adjustment
2026-04-19 18:32:58.735735 INFO::Found 2 batches.
2026-04-19 18:32:58.736005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:58.736419 INFO::Using default BPPARAM
2026-04-19 18:32:58.736671 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:58.737047 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-19 18:32:58.753592 INFO::Done
2026-04-19 18:32:58.754035 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:58.755341 INFO::ASW Batch was -0.0112256948869883 prior to batch effect correction and is now -0.0950819255301862 .
2026-04-19 18:32:58.755729 INFO::Total function execution time is 0.0377230644226074 s and adjustment time is 0.0178940296173096 s ( 47.44 )
Warning: stack imbalance in '{', 73 then 75
2026-04-19 18:32:58.762276 INFO::Formatting Data.
2026-04-19 18:32:58.762681 INFO::Recognized SummarizedExperiment
2026-04-19 18:32:58.762968 INFO::Typecasting input to dataframe.
2026-04-19 18:32:58.76602 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:58.766496 INFO::Removing potential empty rows and columns
2026-04-19 18:32:58.767798 INFO::Found 0 missing values.
2026-04-19 18:32:58.770092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:58.770444 INFO::Done
2026-04-19 18:32:58.770769 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:58.772089 INFO::Starting hierarchical adjustment
2026-04-19 18:32:58.77242 INFO::Found 2 batches.
2026-04-19 18:32:58.772683 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:58.772998 INFO::Using default BPPARAM
2026-04-19 18:32:58.773292 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:58.773702 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-19 18:32:58.78211 INFO::Done
2026-04-19 18:32:58.782494 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:58.7838 INFO::ASW Batch was 0.00710924125513242 prior to batch effect correction and is now 0.00710924125513242 .
2026-04-19 18:32:58.784211 INFO::Total function execution time is 0.0219268798828125 s and adjustment time is 0.00972986221313477 s ( 44.37 )
2026-04-19 18:32:58.791131 INFO::Formatting Data.
2026-04-19 18:32:58.791517 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:58.791914 INFO::Removing potential empty rows and columns
2026-04-19 18:32:58.792353 INFO::Found 0 missing values.
2026-04-19 18:32:58.79335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:58.793658 INFO::Done
2026-04-19 18:32:58.793943 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:58.794726 INFO::Starting hierarchical adjustment
2026-04-19 18:32:58.795069 INFO::Found 3 batches.
2026-04-19 18:32:58.795351 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:58.795665 INFO::Using default BPPARAM
2026-04-19 18:32:58.795921 INFO::Processing subtree level 1
2026-04-19 18:32:58.908308 INFO::Adjusting the last 1 batches sequentially
2026-04-19 18:32:58.909358 INFO::Done
2026-04-19 18:32:58.909761 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:58.911019 INFO::ASW Batch was -0.0965212737252445 prior to batch effect correction and is now -0.149983080573191 .
2026-04-19 18:32:58.911618 INFO::Total function execution time is 0.120480060577393 s and adjustment time is 0.114331960678101 s ( 94.9 )
2026-04-19 18:32:58.918526 INFO::Skipping initial DF formatting
2026-04-19 18:32:58.918989 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:58.920684 INFO::Starting hierarchical adjustment
2026-04-19 18:32:58.921155 INFO::Found 5 batches.
2026-04-19 18:32:58.921473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:58.921852 INFO::Using default BPPARAM
2026-04-19 18:32:58.922204 INFO::Processing subtree level 1
2026-04-19 18:32:58.985144 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:58.986225 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-19 18:32:58.99334 INFO::Done
2026-04-19 18:32:58.993791 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:58.995588 INFO::ASW Batch was 0.492706126648635 prior to batch effect correction and is now 0.492706126648635 .
2026-04-19 18:32:58.99597 INFO::ASW Label was 0.383820076888353 prior to batch effect correction and is now 0.383820076888353 .
2026-04-19 18:32:58.996459 INFO::Total function execution time is 0.0779609680175781 s and adjustment time is 0.0722460746765137 s ( 92.67 )
2026-04-19 18:32:59.004747 INFO::Formatting Data.
2026-04-19 18:32:59.00523 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.005786 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.006341 INFO::Found 0 missing values.
2026-04-19 18:32:59.007996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.008365 INFO::Done
2026-04-19 18:32:59.008703 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.009989 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.010408 INFO::Found 5 batches.
2026-04-19 18:32:59.010807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.012225 INFO::Using default BPPARAM
2026-04-19 18:32:59.013057 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.
2026-04-19 18:32:59.079915 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.082087 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-19 18:32:59.095699 INFO::Done
2026-04-19 18:32:59.096663 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.098297 INFO::ASW Batch was 0.325607090475379 prior to batch effect correction and is now -0.100733928429489 .
2026-04-19 18:32:59.098738 INFO::ASW Label was 0.334419033734825 prior to batch effect correction and is now 0.908491043730307 .
2026-04-19 18:32:59.09924 INFO::Total function execution time is 0.0945589542388916 s and adjustment time is 0.085299015045166 s ( 90.21 )
2026-04-19 18:32:59.100363 INFO::Formatting Data.
2026-04-19 18:32:59.101235 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.102218 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.103298 INFO::Found 0 missing values.
2026-04-19 18:32:59.106428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.107123 INFO::Done
2026-04-19 18:32:59.107788 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.110255 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.110889 INFO::Found 5 batches.
2026-04-19 18:32:59.111288 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.111725 INFO::Using default BPPARAM
2026-04-19 18:32:59.112035 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.
2026-04-19 18:32:59.178216 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.179984 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-19 18:32:59.186964 INFO::Done
2026-04-19 18:32:59.187498 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.188945 INFO::ASW Batch was 0.325607090475379 prior to batch effect correction and is now -0.100733928429489 .
2026-04-19 18:32:59.189326 INFO::ASW Label was 0.334419033734825 prior to batch effect correction and is now 0.908491043730307 .
2026-04-19 18:32:59.189833 INFO::Total function execution time is 0.0895569324493408 s and adjustment time is 0.0761508941650391 s ( 85.03 )
2026-04-19 18:32:59.196761 INFO::Formatting Data.
2026-04-19 18:32:59.197242 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.197707 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.198199 INFO::Found 0 missing values.
2026-04-19 18:32:59.199538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.199856 INFO::Done
2026-04-19 18:32:59.200138 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.201209 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.201599 INFO::Found 5 batches.
2026-04-19 18:32:59.201918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.20227 INFO::Using default BPPARAM
2026-04-19 18:32:59.202572 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.
2026-04-19 18:32:59.282006 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.283801 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-19 18:32:59.291918 INFO::Done
2026-04-19 18:32:59.292402 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.293818 INFO::ASW Batch was 0.413212994637867 prior to batch effect correction and is now -0.0498025024161163 .
2026-04-19 18:32:59.294213 INFO::ASW Label was 0.416392114039948 prior to batch effect correction and is now 0.745645549185975 .
2026-04-19 18:32:59.295651 INFO::Total function execution time is 0.0988278388977051 s and adjustment time is 0.0903661251068115 s ( 91.44 )
2026-04-19 18:32:59.296462 INFO::Formatting Data.
2026-04-19 18:32:59.297026 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.297594 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.298566 INFO::Found 0 missing values.
2026-04-19 18:32:59.300968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.30137 INFO::Done
2026-04-19 18:32:59.301773 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.303424 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.304324 INFO::Found 5 batches.
2026-04-19 18:32:59.304983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.305529 INFO::Using default BPPARAM
2026-04-19 18:32:59.305904 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.
2026-04-19 18:32:59.378869 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.392551 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-19 18:32:59.404828 INFO::Done
2026-04-19 18:32:59.405272 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.406926 INFO::ASW Batch was 0.413212994637867 prior to batch effect correction and is now -0.0498025024161163 .
2026-04-19 18:32:59.411695 INFO::ASW Label was 0.416392114039948 prior to batch effect correction and is now 0.745645549185975 .
2026-04-19 18:32:59.413278 INFO::Total function execution time is 0.116500854492188 s and adjustment time is 0.100657939910889 s ( 86.4 )
2026-04-19 18:32:59.424592 INFO::Formatting Data.
2026-04-19 18:32:59.425195 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.426231 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.427009 INFO::Found 0 missing values.
2026-04-19 18:32:59.428289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.42868 INFO::Done
2026-04-19 18:32:59.429014 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.430208 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.430857 INFO::Found 2 batches.
2026-04-19 18:32:59.431652 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.432465 INFO::Using default BPPARAM
2026-04-19 18:32:59.432828 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.433411 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-19 18:32:59.44091 INFO::Done
2026-04-19 18:32:59.441596 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.444621 INFO::ASW Batch was 0.75481348652819 prior to batch effect correction and is now -0.0273420575871255 .
2026-04-19 18:32:59.445234 INFO::ASW Label was 0.255555999154997 prior to batch effect correction and is now 0.853016404669097 .
2026-04-19 18:32:59.445672 INFO::Total function execution time is 0.0211589336395264 s and adjustment time is 0.00986409187316895 s ( 46.62 )
2026-04-19 18:32:59.446613 INFO::Formatting Data.
2026-04-19 18:32:59.447151 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.447651 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.44823 INFO::Found 0 missing values.
2026-04-19 18:32:59.449481 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.449822 INFO::Done
2026-04-19 18:32:59.450199 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.451666 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.452532 INFO::Found 2 batches.
2026-04-19 18:32:59.453284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.454033 INFO::Using default BPPARAM
2026-04-19 18:32:59.454396 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.455154 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-19 18:32:59.462181 INFO::Done
2026-04-19 18:32:59.462626 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.46416 INFO::ASW Batch was 0.75481348652819 prior to batch effect correction and is now -0.0273420575871255 .
2026-04-19 18:32:59.464524 INFO::ASW Label was 0.255555999154997 prior to batch effect correction and is now 0.853016404669097 .
2026-04-19 18:32:59.464915 INFO::Total function execution time is 0.0183000564575195 s and adjustment time is 0.00973105430603027 s ( 53.17 )
2026-04-19 18:32:59.473578 INFO::Formatting Data.
2026-04-19 18:32:59.47457 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.475061 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.475553 INFO::Found 0 missing values.
2026-04-19 18:32:59.476965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.477323 INFO::Done
2026-04-19 18:32:59.477662 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.478562 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.479067 INFO::Found 2 batches.
2026-04-19 18:32:59.479465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.482038 INFO::Using default BPPARAM
2026-04-19 18:32:59.483277 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.484298 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-19 18:32:59.49873 INFO::Done
2026-04-19 18:32:59.520504 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.522614 INFO::ASW Batch was -0.0199689949450158 prior to batch effect correction and is now -0.0927710740909732 .
2026-04-19 18:32:59.531043 INFO::Total function execution time is 0.057574987411499 s and adjustment time is 0.0197710990905762 s ( 34.34 )
2026-04-19 18:32:59.541732 INFO::Formatting Data.
2026-04-19 18:32:59.542146 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.542807 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.54329 INFO::Found 0 missing values.
2026-04-19 18:32:59.544201 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.
2026-04-19 18:32:59.547185 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.5477 INFO::Done
2026-04-19 18:32:59.548033 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.54924 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.549663 INFO::Found 2 batches.
2026-04-19 18:32:59.549967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.550324 INFO::Using default BPPARAM
2026-04-19 18:32:59.551309 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.552321 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-19 18:32:59.558509 INFO::Done
2026-04-19 18:32:59.558956 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.560103 INFO::ASW Batch was 0.546549311065751 prior to batch effect correction and is now 0.00308574458534821 .
2026-04-19 18:32:59.560474 INFO::ASW Label was 0.535864611545964 prior to batch effect correction and is now 0.906587053985676 .
2026-04-19 18:32:59.56086 INFO::Total function execution time is 0.0191700458526611 s and adjustment time is 0.00888705253601074 s ( 46.36 )
2026-04-19 18:32:59.56123 INFO::Formatting Data.
2026-04-19 18:32:59.561737 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.562892 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.563548 INFO::Found 0 missing values.
2026-04-19 18:32:59.564699 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.
2026-04-19 18:32:59.566735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.567085 INFO::Done
2026-04-19 18:32:59.567603 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.569258 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.569647 INFO::Found 2 batches.
2026-04-19 18:32:59.569958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.570671 INFO::Using default BPPARAM
2026-04-19 18:32:59.571013 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:32:59.571452 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-19 18:32:59.579379 INFO::Done
2026-04-19 18:32:59.579969 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.581931 INFO::ASW Batch was 0.546549311065751 prior to batch effect correction and is now 0.00308574458534821 .
2026-04-19 18:32:59.582595 INFO::ASW Label was 0.535864611545964 prior to batch effect correction and is now 0.906587053985676 .
2026-04-19 18:32:59.583081 INFO::Total function execution time is 0.0218381881713867 s and adjustment time is 0.00977587699890137 s ( 44.77 )
2026-04-19 18:32:59.69003 INFO::Formatting Data.
2026-04-19 18:32:59.690564 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.691098 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.691671 INFO::Found 0 missing values.
2026-04-19 18:32:59.692815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.693178 INFO::Done
2026-04-19 18:32:59.693481 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.694477 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.694903 INFO::Found 3 batches.
2026-04-19 18:32:59.695248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.695616 INFO::Using default BPPARAM
2026-04-19 18:32:59.695932 INFO::Processing subtree level 1
2026-04-19 18:32:59.779697 INFO::Adjusting the last 1 batches sequentially
2026-04-19 18:32:59.781721 INFO::Done
2026-04-19 18:32:59.782499 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.784828 INFO::ASW Batch was -0.0259694129694228 prior to batch effect correction and is now -0.0259694129694228 .
2026-04-19 18:32:59.785749 INFO::Total function execution time is 0.0957019329071045 s and adjustment time is 0.0868020057678223 s ( 90.7 )
2026-04-19 18:32:59.791614 INFO::Formatting Data.
2026-04-19 18:32:59.792387 INFO::Typecasting input to dataframe.
2026-04-19 18:32:59.793491 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.794622 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.796664 INFO::Found 0 missing values.
2026-04-19 18:32:59.799497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.799886 INFO::Done
2026-04-19 18:32:59.800248 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.801421 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.801877 INFO::Found 3 batches.
2026-04-19 18:32:59.802224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.802678 INFO::Using default BPPARAM
2026-04-19 18:32:59.803033 INFO::Processing subtree level 1
2026-04-19 18:32:59.877436 INFO::Adjusting the last 1 batches sequentially
2026-04-19 18:32:59.878665 INFO::Done
2026-04-19 18:32:59.879105 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.880467 INFO::ASW Batch was -0.0259694129694228 prior to batch effect correction and is now -0.0259694129694228 .
2026-04-19 18:32:59.881083 INFO::Total function execution time is 0.0895369052886963 s and adjustment time is 0.0768508911132812 s ( 85.83 )
2026-04-19 18:32:59.889041 INFO::Formatting Data.
2026-04-19 18:32:59.88957 INFO::Typecasting input to dataframe.
2026-04-19 18:32:59.890138 INFO::Replacing NaNs with NAs.
2026-04-19 18:32:59.890662 INFO::Removing potential empty rows and columns
2026-04-19 18:32:59.891241 INFO::Found 0 missing values.
2026-04-19 18:32:59.892374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:32:59.892686 INFO::Done
2026-04-19 18:32:59.892996 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:32:59.893867 INFO::Starting hierarchical adjustment
2026-04-19 18:32:59.894248 INFO::Found 3 batches.
2026-04-19 18:32:59.894566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:32:59.894915 INFO::Using default BPPARAM
2026-04-19 18:32:59.89526 INFO::Processing subtree level 1
2026-04-19 18:32:59.949921 INFO::Adjusting the last 1 batches sequentially
2026-04-19 18:32:59.951451 INFO::Done
2026-04-19 18:32:59.951918 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:32:59.953194 INFO::ASW Batch was -0.0908758770829417 prior to batch effect correction and is now -0.0908758770829417 .
2026-04-19 18:32:59.953828 INFO::Total function execution time is 0.0648059844970703 s and adjustment time is 0.0572509765625 s ( 88.34 )
2026-04-19 18:33:00.045981 INFO::Formatting Data.
2026-04-19 18:33:00.046501 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:00.047201 INFO::Removing potential empty rows and columns
2026-04-19 18:33:00.048824 INFO::Found 1000 missing values.
2026-04-19 18:33:00.058854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:00.059325 INFO::Done
2026-04-19 18:33:00.059768 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:33:00.062491 INFO::Starting hierarchical adjustment
2026-04-19 18:33:00.063008 INFO::Found 10 batches.
2026-04-19 18:33:00.063419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:33:00.063884 INFO::Using default BPPARAM
2026-04-19 18:33:00.064384 INFO::Processing subtree level 1
2026-04-19 18:33:00.170704 INFO::Processing subtree level 2
2026-04-19 18:33:00.250121 INFO::Adjusting the last 1 batches sequentially
2026-04-19 18:33:00.251641 INFO::Done
2026-04-19 18:33:00.252092 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:33:00.254631 INFO::ASW Batch was 0.506227957734138 prior to batch effect correction and is now 0.506227957734138 .
2026-04-19 18:33:00.255061 INFO::ASW Label was 0.323240720338119 prior to batch effect correction and is now 0.323240720338119 .
2026-04-19 18:33:00.255631 INFO::Total function execution time is 0.209658861160278 s and adjustment time is 0.188668966293335 s ( 89.99 )
2026-04-19 18:33:00.256117 INFO::Formatting Data.
2026-04-19 18:33:00.256487 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:00.257082 INFO::Removing potential empty rows and columns
2026-04-19 18:33:00.258306 INFO::Found 1000 missing values.
2026-04-19 18:33:00.267145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:00.267647 INFO::Done
2026-04-19 18:33:00.267997 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:33:00.27022 INFO::Starting hierarchical adjustment
2026-04-19 18:33:00.270692 INFO::Found 10 batches.
2026-04-19 18:33:00.682734 INFO::Set up parallel execution backend with 2 workers
2026-04-19 18:33:00.68326 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-19 18:33:01.31883 INFO::Adjusting the last 2 batches sequentially
2026-04-19 18:33:01.320208 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-19 18:33:01.327279 INFO::Done
2026-04-19 18:33:01.327876 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:33:01.33013 INFO::ASW Batch was 0.506227957734138 prior to batch effect correction and is now 0.506227957734138 .
2026-04-19 18:33:01.330487 INFO::ASW Label was 0.323240720338119 prior to batch effect correction and is now 0.323240720338119 .
2026-04-19 18:33:01.330892 INFO::Total function execution time is 1.07478499412537 s and adjustment time is 1.05661201477051 s ( 98.31 )
2026-04-19 18:33:01.501633 INFO::Formatting Data.
2026-04-19 18:33:01.502215 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.502815 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.503641 INFO::Found 0 missing values.
2026-04-19 18:33:01.50538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.505813 INFO::Done
2026-04-19 18:33:01.506288 INFO::Acquiring quality metrics before batch effect correction.
2026-04-19 18:33:01.507802 INFO::Starting hierarchical adjustment
2026-04-19 18:33:01.508347 INFO::Found 3 batches.
2026-04-19 18:33:01.5087 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-19 18:33:01.509126 INFO::Using default BPPARAM
2026-04-19 18:33:01.509524 INFO::Processing subtree level 1
2026-04-19 18:33:01.576812 INFO::Adjusting the last 1 batches sequentially
2026-04-19 18:33:01.578622 INFO::Done
2026-04-19 18:33:01.579022 INFO::Acquiring quality metrics after batch effect correction.
2026-04-19 18:33:01.581234 INFO::ASW Batch was 0.0628539434093212 prior to batch effect correction and is now -0.146493647373683 .
2026-04-19 18:33:01.581686 INFO::ASW Label was -0.167342701666845 prior to batch effect correction and is now 0.0596532539587002 .
2026-04-19 18:33:01.582462 INFO::Total function execution time is 0.0808191299438477 s and adjustment time is 0.070336103439331 s ( 87.03 )
2026-04-19 18:33:01.640539 INFO::Formatting Data.
2026-04-19 18:33:01.641089 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.64157 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.64217 INFO::Found 2 missing values.
2026-04-19 18:33:01.64325 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.643595 INFO::Done
2026-04-19 18:33:01.655663 INFO::Found NA in Reference column
2026-04-19 18:33:01.662093 INFO::Require at least two references per batch.
2026-04-19 18:33:01.673433 INFO::Formatting Data.
2026-04-19 18:33:01.673981 INFO::Recognized SummarizedExperiment
2026-04-19 18:33:01.674403 INFO::Typecasting input to dataframe.
2026-04-19 18:33:01.679879 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.680637 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.682282 INFO::Found 0 missing values.
2026-04-19 18:33:01.685264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.685699 INFO::Done
2026-04-19 18:33:01.692754 INFO::Formatting Data.
2026-04-19 18:33:01.693261 INFO::Recognized SummarizedExperiment
2026-04-19 18:33:01.693632 INFO::Typecasting input to dataframe.
2026-04-19 18:33:01.702836 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.703574 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.705405 INFO::Found 0 missing values.
2026-04-19 18:33:01.711283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.711671 INFO::Done
2026-04-19 18:33:01.717775 INFO::Formatting Data.
2026-04-19 18:33:01.718238 INFO::Recognized SummarizedExperiment
2026-04-19 18:33:01.718547 INFO::Typecasting input to dataframe.
2026-04-19 18:33:01.724223 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.724793 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.725329 INFO::Found 0 missing values.
2026-04-19 18:33:01.725871 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.
2026-04-19 18:33:01.727629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.728023 INFO::Done
2026-04-19 18:33:01.73256 INFO::Formatting Data.
2026-04-19 18:33:01.732962 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.733426 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.733891 INFO::Found 0 missing values.
2026-04-19 18:33:01.734977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.735287 INFO::Done
2026-04-19 18:33:01.740438 INFO::Formatting Data.
2026-04-19 18:33:01.740865 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.741314 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.741836 INFO::Found 0 missing values.
2026-04-19 18:33:01.742861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.743177 INFO::Done
2026-04-19 18:33:01.75622 INFO::Formatting Data.
2026-04-19 18:33:01.756696 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.757161 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.757731 INFO::Found 1 missing values.
2026-04-19 18:33:01.758685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.758999 INFO::Done
2026-04-19 18:33:01.769691 INFO::Formatting Data.
2026-04-19 18:33:01.770224 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.770749 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.771304 INFO::Found 2 missing values.
2026-04-19 18:33:01.771853 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.
2026-04-19 18:33:01.772932 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.773292 INFO::Done
2026-04-19 18:33:01.785419 INFO::Formatting Data.
2026-04-19 18:33:01.786133 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.786755 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.787335 INFO::Found 2 missing values.
2026-04-19 18:33:01.788296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.788703 INFO::Done
2026-04-19 18:33:01.794896 INFO::Formatting Data.
2026-04-19 18:33:01.795648 INFO::Typecasting input to dataframe.
2026-04-19 18:33:01.796312 INFO::Replacing NaNs with NAs.
2026-04-19 18:33:01.796961 INFO::Removing potential empty rows and columns
2026-04-19 18:33:01.797466 INFO::Found 0 missing values.
2026-04-19 18:33:01.798681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-19 18:33:01.799056 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.254 2.047 9.638
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.702 | 0.372 | 6.859 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.004 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |