Yannis Schumann
| Snapshot Date: 2026-05-18 13:45 -0400 (Mon, 18 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-19 12:54 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4898 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4617 |
| 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 174/2377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2026-05-18 20:27:51 -0400 (Mon, 18 May 2026) |
| EndedAt: 2026-05-18 20:28:23 -0400 (Mon, 18 May 2026) |
| EllapsedTime: 32.4 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* 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: 2026-05-19 00:27:51 UTC
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 9.549 0.366 6.784
* 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 ‘1.9.0’ ** 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 Patched (2026-05-01 r89994) -- "Because it was There"
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")
2026-05-18 20:28:15.389213 INFO::Formatting Data.
2026-05-18 20:28:15.390929 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:15.395852 INFO::Removing potential empty rows and columns
2026-05-18 20:28:15.500451 INFO::Found 0 missing values.
2026-05-18 20:28:15.501789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:15.502149 INFO::Done
2026-05-18 20:28:15.50254 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:15.508617 INFO::Starting hierarchical adjustment
2026-05-18 20:28:15.509087 INFO::Found 3 batches.
2026-05-18 20:28:15.5094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:15.509889 INFO::Using default BPPARAM
2026-05-18 20:28:15.5102 INFO::Processing subtree level 1
2026-05-18 20:28:15.568183 INFO::Adjusting the last 1 batches sequentially
2026-05-18 20:28:15.56928 INFO::Done
2026-05-18 20:28:15.569787 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:15.570943 INFO::ASW Batch was -0.0430477376281203 prior to batch effect correction and is now -0.0430477376281203 .
2026-05-18 20:28:15.571501 INFO::Total function execution time is 0.182703018188477 s and adjustment time is 0.0602211952209473 s ( 32.96 )
2026-05-18 20:28:15.578245 INFO::Formatting Data.
2026-05-18 20:28:15.578709 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:15.579178 INFO::Removing potential empty rows and columns
2026-05-18 20:28:15.57987 INFO::Found 0 missing values.
2026-05-18 20:28:15.580588 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.
2026-05-18 20:28:15.585378 INFO::Formatting Data.
2026-05-18 20:28:15.585892 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:15.58638 INFO::Removing potential empty rows and columns
2026-05-18 20:28:15.586931 INFO::Found 0 missing values.
2026-05-18 20:28:15.587371 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.
2026-05-18 20:28:15.594499 INFO::Formatting Data.
2026-05-18 20:28:15.594957 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:15.595444 INFO::Removing potential empty rows and columns
2026-05-18 20:28:15.596014 INFO::Found 0 missing values.
2026-05-18 20:28:15.59646 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.
2026-05-18 20:28:15.598041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:15.598436 INFO::Done
2026-05-18 20:28:15.598814 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:15.599718 INFO::Starting hierarchical adjustment
2026-05-18 20:28:15.600136 INFO::Found 2 batches.
2026-05-18 20:28:15.60051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:15.600962 INFO::Using default BPPARAM
2026-05-18 20:28:15.601304 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:15.601799 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-18 20:28:15.611278 INFO::Done
2026-05-18 20:28:15.611749 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:15.612626 INFO::ASW Batch was -0.0615467277060113 prior to batch effect correction and is now -0.127703362598693 .
2026-05-18 20:28:15.613091 INFO::Total function execution time is 0.018596887588501 s and adjustment time is 0.0111801624298096 s ( 60.12 )
2026-05-18 20:28:15.614395 INFO::Formatting Data.
2026-05-18 20:28:15.614851 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:15.6193 INFO::Formatting Data.
2026-05-18 20:28:15.620007 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:15.62066 INFO::Removing potential empty rows and columns
2026-05-18 20:28:15.621295 INFO::Found 0 missing values.
2026-05-18 20:28:15.6228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:15.623174 INFO::Done
2026-05-18 20:28:15.623487 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:15.624649 INFO::Starting hierarchical adjustment
2026-05-18 20:28:15.62516 INFO::Found 2 batches.
2026-05-18 20:28:15.625486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:15.625855 INFO::Using default BPPARAM
2026-05-18 20:28:15.626176 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:15.626683 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-18 20:28:15.632972 INFO::Done
2026-05-18 20:28:15.633446 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:15.634396 INFO::ASW Batch was -0.0360409999116835 prior to batch effect correction and is now -0.120183589852341 .
2026-05-18 20:28:15.63486 INFO::Total function execution time is 0.0156168937683105 s and adjustment time is 0.00786900520324707 s ( 50.39 )
2026-05-18 20:28:15.635412 INFO::Formatting Data.
2026-05-18 20:28:15.635816 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:15.636316 INFO::Removing potential empty rows and columns
2026-05-18 20:28:15.636891 INFO::Found 0 missing values.
2026-05-18 20:28:15.638097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:15.638431 INFO::Done
2026-05-18 20:28:15.638762 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:15.639598 INFO::Starting hierarchical adjustment
2026-05-18 20:28:15.64012 INFO::Found 2 batches.
2026-05-18 20:28:15.640432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:15.640796 INFO::Using default BPPARAM
2026-05-18 20:28:15.641378 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:15.642069 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-18 20:28:15.647313 INFO::Done
2026-05-18 20:28:15.647709 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:15.648479 INFO::ASW Batch was -0.0360409999116835 prior to batch effect correction and is now -0.120183589852341 .
2026-05-18 20:28:15.64886 INFO::Total function execution time is 0.0134658813476562 s and adjustment time is 0.00728487968444824 s ( 54.1 )
2026-05-18 20:28:16.851637 INFO::Formatting Data.
2026-05-18 20:28:16.852072 INFO::Recognized SummarizedExperiment
2026-05-18 20:28:16.852367 INFO::Typecasting input to dataframe.
2026-05-18 20:28:16.863065 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:16.863704 INFO::Removing potential empty rows and columns
2026-05-18 20:28:16.865073 INFO::Found 0 missing values.
2026-05-18 20:28:16.867309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:16.86762 INFO::Done
2026-05-18 20:28:16.867876 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:16.869093 INFO::Starting hierarchical adjustment
2026-05-18 20:28:16.869403 INFO::Found 2 batches.
2026-05-18 20:28:16.869643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:16.870075 INFO::Using default BPPARAM
2026-05-18 20:28:16.870341 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:16.870744 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-18 20:28:16.887244 INFO::Done
2026-05-18 20:28:16.887608 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:16.888907 INFO::ASW Batch was 0.00530276589482923 prior to batch effect correction and is now -0.0913513720323063 .
2026-05-18 20:28:16.889652 INFO::Total function execution time is 0.0380749702453613 s and adjustment time is 0.0178749561309814 s ( 46.95 )
2026-05-18 20:28:16.896498 INFO::Formatting Data.
2026-05-18 20:28:16.896989 INFO::Recognized SummarizedExperiment
2026-05-18 20:28:16.897293 INFO::Typecasting input to dataframe.
2026-05-18 20:28:16.900403 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:16.90091 INFO::Removing potential empty rows and columns
2026-05-18 20:28:16.902145 INFO::Found 0 missing values.
2026-05-18 20:28:16.904368 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:16.904681 INFO::Done
2026-05-18 20:28:16.904956 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:16.906295 INFO::Starting hierarchical adjustment
2026-05-18 20:28:16.907067 INFO::Found 2 batches.
2026-05-18 20:28:16.907419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:16.907739 INFO::Using default BPPARAM
2026-05-18 20:28:16.908007 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:16.908455 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-18 20:28:16.916847 INFO::Done
2026-05-18 20:28:16.917293 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:16.91868 INFO::ASW Batch was -0.00697392335727756 prior to batch effect correction and is now -0.00697392335727756 .
2026-05-18 20:28:16.919096 INFO::Total function execution time is 0.0226080417633057 s and adjustment time is 0.00986695289611816 s ( 43.64 )
2026-05-18 20:28:16.926821 INFO::Formatting Data.
2026-05-18 20:28:16.927216 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:16.927607 INFO::Removing potential empty rows and columns
2026-05-18 20:28:16.928053 INFO::Found 0 missing values.
2026-05-18 20:28:16.92905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:16.929374 INFO::Done
2026-05-18 20:28:16.929644 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:16.930458 INFO::Starting hierarchical adjustment
2026-05-18 20:28:16.930812 INFO::Found 3 batches.
2026-05-18 20:28:16.931102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:16.931432 INFO::Using default BPPARAM
2026-05-18 20:28:16.93173 INFO::Processing subtree level 1
2026-05-18 20:28:17.060098 INFO::Adjusting the last 1 batches sequentially
2026-05-18 20:28:17.06168 INFO::Done
2026-05-18 20:28:17.062117 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.063451 INFO::ASW Batch was -0.0749276514614495 prior to batch effect correction and is now -0.159013022195749 .
2026-05-18 20:28:17.064135 INFO::Total function execution time is 0.137298822402954 s and adjustment time is 0.130911111831665 s ( 95.35 )
2026-05-18 20:28:17.072167 INFO::Skipping initial DF formatting
2026-05-18 20:28:17.072687 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.074421 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.074979 INFO::Found 5 batches.
2026-05-18 20:28:17.075353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.075726 INFO::Using default BPPARAM
2026-05-18 20:28:17.076392 INFO::Processing subtree level 1
2026-05-18 20:28:17.141722 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.143761 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-18 20:28:17.152563 INFO::Done
2026-05-18 20:28:17.153063 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.15537 INFO::ASW Batch was 0.513231920124548 prior to batch effect correction and is now 0.513231920124548 .
2026-05-18 20:28:17.155822 INFO::ASW Label was 0.348871390865138 prior to batch effect correction and is now 0.348871390865138 .
2026-05-18 20:28:17.156561 INFO::Total function execution time is 0.0843830108642578 s and adjustment time is 0.0776419639587402 s ( 92.01 )
2026-05-18 20:28:17.165807 INFO::Formatting Data.
2026-05-18 20:28:17.166295 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.166819 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.16737 INFO::Found 0 missing values.
2026-05-18 20:28:17.168782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.169159 INFO::Done
2026-05-18 20:28:17.16952 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.17068 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.171096 INFO::Found 5 batches.
2026-05-18 20:28:17.171443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.171937 INFO::Using default BPPARAM
2026-05-18 20:28:17.172277 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.
2026-05-18 20:28:17.239616 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.241291 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-18 20:28:17.25025 INFO::Done
2026-05-18 20:28:17.250861 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.252695 INFO::ASW Batch was 0.23018274975853 prior to batch effect correction and is now -0.104877923086093 .
2026-05-18 20:28:17.253216 INFO::ASW Label was 0.545185696639898 prior to batch effect correction and is now 0.92574655364167 .
2026-05-18 20:28:17.253742 INFO::Total function execution time is 0.0879368782043457 s and adjustment time is 0.0791869163513184 s ( 90.05 )
2026-05-18 20:28:17.254242 INFO::Formatting Data.
2026-05-18 20:28:17.254592 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.25504 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.255548 INFO::Found 0 missing values.
2026-05-18 20:28:17.257097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.257441 INFO::Done
2026-05-18 20:28:17.257786 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.258854 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.259257 INFO::Found 5 batches.
2026-05-18 20:28:17.259547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.259902 INFO::Using default BPPARAM
2026-05-18 20:28:17.260173 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.
2026-05-18 20:28:17.308739 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.310145 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-18 20:28:17.317463 INFO::Done
2026-05-18 20:28:17.317963 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.319536 INFO::ASW Batch was 0.23018274975853 prior to batch effect correction and is now -0.104877923086093 .
2026-05-18 20:28:17.319895 INFO::ASW Label was 0.545185696639898 prior to batch effect correction and is now 0.92574655364167 .
2026-05-18 20:28:17.320409 INFO::Total function execution time is 0.0661139488220215 s and adjustment time is 0.058264970779419 s ( 88.13 )
2026-05-18 20:28:17.326931 INFO::Formatting Data.
2026-05-18 20:28:17.327414 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.32787 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.328344 INFO::Found 0 missing values.
2026-05-18 20:28:17.329622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.329971 INFO::Done
2026-05-18 20:28:17.330262 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.331295 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.331704 INFO::Found 5 batches.
2026-05-18 20:28:17.332018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.332391 INFO::Using default BPPARAM
2026-05-18 20:28:17.332702 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.
2026-05-18 20:28:17.388507 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.390143 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-18 20:28:17.398306 INFO::Done
2026-05-18 20:28:17.398768 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.400333 INFO::ASW Batch was 0.382896084153015 prior to batch effect correction and is now -0.069931111837546 .
2026-05-18 20:28:17.400706 INFO::ASW Label was 0.386392555683395 prior to batch effect correction and is now 0.786517333526154 .
2026-05-18 20:28:17.401193 INFO::Total function execution time is 0.074242115020752 s and adjustment time is 0.0666439533233643 s ( 89.77 )
2026-05-18 20:28:17.401667 INFO::Formatting Data.
2026-05-18 20:28:17.402004 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.402454 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.402965 INFO::Found 0 missing values.
2026-05-18 20:28:17.404343 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.404619 INFO::Done
2026-05-18 20:28:17.404938 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.406006 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.406386 INFO::Found 5 batches.
2026-05-18 20:28:17.406664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.40704 INFO::Using default BPPARAM
2026-05-18 20:28:17.407359 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.
2026-05-18 20:28:17.486149 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.492295 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-18 20:28:17.501331 INFO::Done
2026-05-18 20:28:17.501821 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.503375 INFO::ASW Batch was 0.382896084153015 prior to batch effect correction and is now -0.069931111837546 .
2026-05-18 20:28:17.503747 INFO::ASW Label was 0.386392555683395 prior to batch effect correction and is now 0.786517333526154 .
2026-05-18 20:28:17.504235 INFO::Total function execution time is 0.102517127990723 s and adjustment time is 0.0949828624725342 s ( 92.65 )
2026-05-18 20:28:17.511575 INFO::Formatting Data.
2026-05-18 20:28:17.512132 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.512674 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.513223 INFO::Found 0 missing values.
2026-05-18 20:28:17.51434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.51466 INFO::Done
2026-05-18 20:28:17.514972 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.516053 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.516436 INFO::Found 2 batches.
2026-05-18 20:28:17.516728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.517065 INFO::Using default BPPARAM
2026-05-18 20:28:17.517347 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.517734 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-18 20:28:17.522852 INFO::Done
2026-05-18 20:28:17.523239 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.524806 INFO::ASW Batch was 0.26142636405022 prior to batch effect correction and is now -0.0361107569691614 .
2026-05-18 20:28:17.525278 INFO::ASW Label was 0.742315017647774 prior to batch effect correction and is now 0.921521346802816 .
2026-05-18 20:28:17.525754 INFO::Total function execution time is 0.0142288208007812 s and adjustment time is 0.0064551830291748 s ( 45.37 )
2026-05-18 20:28:17.526151 INFO::Formatting Data.
2026-05-18 20:28:17.526471 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.52691 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.527459 INFO::Found 0 missing values.
2026-05-18 20:28:17.528679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.529059 INFO::Done
2026-05-18 20:28:17.529386 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.530581 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.531023 INFO::Found 2 batches.
2026-05-18 20:28:17.531323 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.53165 INFO::Using default BPPARAM
2026-05-18 20:28:17.531963 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.532384 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-18 20:28:17.538497 INFO::Done
2026-05-18 20:28:17.538969 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.540159 INFO::ASW Batch was 0.26142636405022 prior to batch effect correction and is now -0.0361107569691614 .
2026-05-18 20:28:17.540511 INFO::ASW Label was 0.742315017647774 prior to batch effect correction and is now 0.921521346802816 .
2026-05-18 20:28:17.540951 INFO::Total function execution time is 0.0147898197174072 s and adjustment time is 0.00751709938049316 s ( 50.83 )
2026-05-18 20:28:17.546108 INFO::Formatting Data.
2026-05-18 20:28:17.546508 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.546931 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.547346 INFO::Found 0 missing values.
2026-05-18 20:28:17.548107 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.54838 INFO::Done
2026-05-18 20:28:17.548668 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.549437 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.549818 INFO::Found 2 batches.
2026-05-18 20:28:17.550108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.550424 INFO::Using default BPPARAM
2026-05-18 20:28:17.550736 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.551125 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-18 20:28:17.562818 INFO::Done
2026-05-18 20:28:17.563271 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.564055 INFO::ASW Batch was -0.0305883874233521 prior to batch effect correction and is now -0.148035242946549 .
2026-05-18 20:28:17.564484 INFO::Total function execution time is 0.0184080600738525 s and adjustment time is 0.0130279064178467 s ( 70.77 )
2026-05-18 20:28:17.569535 INFO::Formatting Data.
2026-05-18 20:28:17.569919 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.57036 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.57086 INFO::Found 0 missing values.
2026-05-18 20:28:17.571488 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.
2026-05-18 20:28:17.573157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.573503 INFO::Done
2026-05-18 20:28:17.573822 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.574856 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.575226 INFO::Found 2 batches.
2026-05-18 20:28:17.575497 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.575842 INFO::Using default BPPARAM
2026-05-18 20:28:17.576189 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.576614 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-18 20:28:17.582235 INFO::Done
2026-05-18 20:28:17.582697 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.583816 INFO::ASW Batch was 0.627614352813087 prior to batch effect correction and is now 0.0925224314671391 .
2026-05-18 20:28:17.584145 INFO::ASW Label was 0.423162185536408 prior to batch effect correction and is now 0.850421678561786 .
2026-05-18 20:28:17.584528 INFO::Total function execution time is 0.0149948596954346 s and adjustment time is 0.00703597068786621 s ( 46.92 )
2026-05-18 20:28:17.584906 INFO::Formatting Data.
2026-05-18 20:28:17.585258 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.585666 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.586116 INFO::Found 0 missing values.
2026-05-18 20:28:17.58654 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.
2026-05-18 20:28:17.587972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.588272 INFO::Done
2026-05-18 20:28:17.58854 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.589528 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.589929 INFO::Found 2 batches.
2026-05-18 20:28:17.590224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.590568 INFO::Using default BPPARAM
2026-05-18 20:28:17.590875 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:17.591294 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-18 20:28:17.596612 INFO::Done
2026-05-18 20:28:17.596993 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.598034 INFO::ASW Batch was 0.627614352813087 prior to batch effect correction and is now 0.0925224314671391 .
2026-05-18 20:28:17.598345 INFO::ASW Label was 0.423162185536408 prior to batch effect correction and is now 0.850421678561786 .
2026-05-18 20:28:17.598726 INFO::Total function execution time is 0.0138111114501953 s and adjustment time is 0.00671792030334473 s ( 48.64 )
2026-05-18 20:28:17.667598 INFO::Formatting Data.
2026-05-18 20:28:17.668066 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.668486 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.66899 INFO::Found 0 missing values.
2026-05-18 20:28:17.670047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.6704 INFO::Done
2026-05-18 20:28:17.670695 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.671525 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.671899 INFO::Found 3 batches.
2026-05-18 20:28:17.672225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.672574 INFO::Using default BPPARAM
2026-05-18 20:28:17.672872 INFO::Processing subtree level 1
2026-05-18 20:28:17.74949 INFO::Adjusting the last 1 batches sequentially
2026-05-18 20:28:17.751482 INFO::Done
2026-05-18 20:28:17.751913 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.753679 INFO::ASW Batch was -0.113013225869811 prior to batch effect correction and is now -0.113013225869811 .
2026-05-18 20:28:17.754491 INFO::Total function execution time is 0.0868701934814453 s and adjustment time is 0.079617977142334 s ( 91.65 )
2026-05-18 20:28:17.755084 INFO::Formatting Data.
2026-05-18 20:28:17.755443 INFO::Typecasting input to dataframe.
2026-05-18 20:28:17.755852 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.756336 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.75689 INFO::Found 0 missing values.
2026-05-18 20:28:17.758029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.758362 INFO::Done
2026-05-18 20:28:17.758636 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.759399 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.759758 INFO::Found 3 batches.
2026-05-18 20:28:17.76008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.760455 INFO::Using default BPPARAM
2026-05-18 20:28:17.760719 INFO::Processing subtree level 1
2026-05-18 20:28:17.806136 INFO::Adjusting the last 1 batches sequentially
2026-05-18 20:28:17.807481 INFO::Done
2026-05-18 20:28:17.807845 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.809177 INFO::ASW Batch was -0.113013225869811 prior to batch effect correction and is now -0.113013225869811 .
2026-05-18 20:28:17.809817 INFO::Total function execution time is 0.0547010898590088 s and adjustment time is 0.0477678775787354 s ( 87.33 )
2026-05-18 20:28:17.818424 INFO::Formatting Data.
2026-05-18 20:28:17.818902 INFO::Typecasting input to dataframe.
2026-05-18 20:28:17.819335 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.819806 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.8204 INFO::Found 0 missing values.
2026-05-18 20:28:17.821561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.821921 INFO::Done
2026-05-18 20:28:17.822277 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.823111 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.82351 INFO::Found 3 batches.
2026-05-18 20:28:17.823835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.824175 INFO::Using default BPPARAM
2026-05-18 20:28:17.824503 INFO::Processing subtree level 1
2026-05-18 20:28:17.875257 INFO::Adjusting the last 1 batches sequentially
2026-05-18 20:28:17.876637 INFO::Done
2026-05-18 20:28:17.877222 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:17.878955 INFO::ASW Batch was -0.113195246690646 prior to batch effect correction and is now -0.113195246690646 .
2026-05-18 20:28:17.879683 INFO::Total function execution time is 0.061237096786499 s and adjustment time is 0.0531721115112305 s ( 86.83 )
2026-05-18 20:28:17.964961 INFO::Formatting Data.
2026-05-18 20:28:17.965409 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:17.965973 INFO::Removing potential empty rows and columns
2026-05-18 20:28:17.967093 INFO::Found 1000 missing values.
2026-05-18 20:28:17.972888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:17.973293 INFO::Done
2026-05-18 20:28:17.973614 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:17.975767 INFO::Starting hierarchical adjustment
2026-05-18 20:28:17.976167 INFO::Found 10 batches.
2026-05-18 20:28:17.976501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:17.976871 INFO::Using default BPPARAM
2026-05-18 20:28:17.977154 INFO::Processing subtree level 1
2026-05-18 20:28:18.052923 INFO::Processing subtree level 2
2026-05-18 20:28:18.118611 INFO::Adjusting the last 1 batches sequentially
2026-05-18 20:28:18.120289 INFO::Done
2026-05-18 20:28:18.120693 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:18.123619 INFO::ASW Batch was 0.562891496174876 prior to batch effect correction and is now 0.562891496174876 .
2026-05-18 20:28:18.124029 INFO::ASW Label was 0.280700208507454 prior to batch effect correction and is now 0.280700208507454 .
2026-05-18 20:28:18.12467 INFO::Total function execution time is 0.159693002700806 s and adjustment time is 0.144161939620972 s ( 90.27 )
2026-05-18 20:28:18.12515 INFO::Formatting Data.
2026-05-18 20:28:18.125481 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:18.126073 INFO::Removing potential empty rows and columns
2026-05-18 20:28:18.127237 INFO::Found 1000 missing values.
2026-05-18 20:28:18.133477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:18.133932 INFO::Done
2026-05-18 20:28:18.134248 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:18.136652 INFO::Starting hierarchical adjustment
2026-05-18 20:28:18.137105 INFO::Found 10 batches.
2026-05-18 20:28:18.564853 INFO::Set up parallel execution backend with 2 workers
2026-05-18 20:28:18.565363 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-18 20:28:19.169643 INFO::Adjusting the last 2 batches sequentially
2026-05-18 20:28:19.17053 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-18 20:28:19.176538 INFO::Done
2026-05-18 20:28:19.177303 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:19.180094 INFO::ASW Batch was 0.562891496174876 prior to batch effect correction and is now 0.562891496174876 .
2026-05-18 20:28:19.180584 INFO::ASW Label was 0.280700208507454 prior to batch effect correction and is now 0.280700208507454 .
2026-05-18 20:28:19.181011 INFO::Total function execution time is 1.05586886405945 s and adjustment time is 1.03948307037354 s ( 98.45 )
2026-05-18 20:28:19.350697 INFO::Formatting Data.
2026-05-18 20:28:19.351137 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.351646 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.352593 INFO::Found 0 missing values.
2026-05-18 20:28:19.356662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.357138 INFO::Done
2026-05-18 20:28:19.357461 INFO::Acquiring quality metrics before batch effect correction.
2026-05-18 20:28:19.358666 INFO::Starting hierarchical adjustment
2026-05-18 20:28:19.359095 INFO::Found 3 batches.
2026-05-18 20:28:19.359438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-18 20:28:19.359803 INFO::Using default BPPARAM
2026-05-18 20:28:19.360085 INFO::Processing subtree level 1
2026-05-18 20:28:19.430318 INFO::Adjusting the last 1 batches sequentially
2026-05-18 20:28:19.432419 INFO::Done
2026-05-18 20:28:19.432946 INFO::Acquiring quality metrics after batch effect correction.
2026-05-18 20:28:19.434885 INFO::ASW Batch was 0.238082053176639 prior to batch effect correction and is now -0.163911059909673 .
2026-05-18 20:28:19.435287 INFO::ASW Label was -0.182718594430523 prior to batch effect correction and is now 0.0356138499298344 .
2026-05-18 20:28:19.435942 INFO::Total function execution time is 0.0852410793304443 s and adjustment time is 0.0733339786529541 s ( 86.03 )
2026-05-18 20:28:19.494724 INFO::Formatting Data.
2026-05-18 20:28:19.495312 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.49589 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.496492 INFO::Found 2 missing values.
2026-05-18 20:28:19.497754 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.498124 INFO::Done
2026-05-18 20:28:19.511316 INFO::Found NA in Reference column
2026-05-18 20:28:19.515787 INFO::Require at least two references per batch.
2026-05-18 20:28:19.52563 INFO::Formatting Data.
2026-05-18 20:28:19.526097 INFO::Recognized SummarizedExperiment
2026-05-18 20:28:19.526437 INFO::Typecasting input to dataframe.
2026-05-18 20:28:19.531504 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.532138 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.533891 INFO::Found 0 missing values.
2026-05-18 20:28:19.537364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.538395 INFO::Done
2026-05-18 20:28:19.54582 INFO::Formatting Data.
2026-05-18 20:28:19.546363 INFO::Recognized SummarizedExperiment
2026-05-18 20:28:19.546727 INFO::Typecasting input to dataframe.
2026-05-18 20:28:19.553445 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.554112 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.555811 INFO::Found 0 missing values.
2026-05-18 20:28:19.560687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.561116 INFO::Done
2026-05-18 20:28:19.567603 INFO::Formatting Data.
2026-05-18 20:28:19.568096 INFO::Recognized SummarizedExperiment
2026-05-18 20:28:19.568414 INFO::Typecasting input to dataframe.
2026-05-18 20:28:19.574246 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.574816 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.575462 INFO::Found 0 missing values.
2026-05-18 20:28:19.575972 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.
2026-05-18 20:28:19.577814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.578225 INFO::Done
2026-05-18 20:28:19.583298 INFO::Formatting Data.
2026-05-18 20:28:19.583763 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.584213 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.584666 INFO::Found 0 missing values.
2026-05-18 20:28:19.585763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.586173 INFO::Done
2026-05-18 20:28:19.591871 INFO::Formatting Data.
2026-05-18 20:28:19.592394 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.592842 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.593353 INFO::Found 0 missing values.
2026-05-18 20:28:19.594524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.594853 INFO::Done
2026-05-18 20:28:19.61031 INFO::Formatting Data.
2026-05-18 20:28:19.610814 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.611356 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.612001 INFO::Found 1 missing values.
2026-05-18 20:28:19.613081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.613447 INFO::Done
2026-05-18 20:28:19.623391 INFO::Formatting Data.
2026-05-18 20:28:19.623903 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.624398 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.624881 INFO::Found 2 missing values.
2026-05-18 20:28:19.625368 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.
2026-05-18 20:28:19.626306 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.626664 INFO::Done
2026-05-18 20:28:19.631136 INFO::Formatting Data.
2026-05-18 20:28:19.631585 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.632022 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.632517 INFO::Found 2 missing values.
2026-05-18 20:28:19.633243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.633568 INFO::Done
2026-05-18 20:28:19.63828 INFO::Formatting Data.
2026-05-18 20:28:19.638683 INFO::Typecasting input to dataframe.
2026-05-18 20:28:19.639042 INFO::Replacing NaNs with NAs.
2026-05-18 20:28:19.639433 INFO::Removing potential empty rows and columns
2026-05-18 20:28:19.639961 INFO::Found 0 missing values.
2026-05-18 20:28:19.641385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-18 20:28:19.641802 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.957 1.796 8.991
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.549 | 0.366 | 6.784 | |
| compute_asw | 0.010 | 0.001 | 0.027 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.004 | |
| generate_dataset | 0.005 | 0.000 | 0.005 | |