Yannis Schumann
| Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-04 12:05 -0400 (Sat, 04 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 164/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2025-10-03 18:21:50 -0400 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 18:22:23 -0400 (Fri, 03 Oct 2025) |
| 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 10.001 0.423 7.258
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-10-03 18:22:14.601877 INFO::Formatting Data.
2025-10-03 18:22:14.60334 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:14.607366 INFO::Removing potential empty rows and columns
2025-10-03 18:22:14.69762 INFO::Found 0 missing values.
2025-10-03 18:22:14.698767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:14.698969 INFO::Done
2025-10-03 18:22:14.699144 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:14.704282 INFO::Starting hierarchical adjustment
2025-10-03 18:22:14.70459 INFO::Found 3 batches.
2025-10-03 18:22:14.704785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:14.705205 INFO::Using default BPPARAM
2025-10-03 18:22:14.705385 INFO::Processing subtree level 1
2025-10-03 18:22:14.756408 INFO::Adjusting the last 1 batches sequentially
2025-10-03 18:22:14.757682 INFO::Done
2025-10-03 18:22:14.757987 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:14.75955 INFO::ASW Batch was -0.0561382479749048 prior to batch effect correction and is now -0.0561382479749048 .
2025-10-03 18:22:14.760265 INFO::Total function execution time is 0.158560037612915 s and adjustment time is 0.0531549453735352 s ( 33.52 )
2025-10-03 18:22:14.767501 INFO::Formatting Data.
2025-10-03 18:22:14.767743 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:14.768023 INFO::Removing potential empty rows and columns
2025-10-03 18:22:14.768386 INFO::Found 0 missing values.
2025-10-03 18:22:14.768686 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-03 18:22:14.772994 INFO::Formatting Data.
2025-10-03 18:22:14.773361 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:14.773815 INFO::Removing potential empty rows and columns
2025-10-03 18:22:14.7743 INFO::Found 0 missing values.
2025-10-03 18:22:14.774671 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-03 18:22:14.780254 INFO::Formatting Data.
2025-10-03 18:22:14.78048 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:14.780753 INFO::Removing potential empty rows and columns
2025-10-03 18:22:14.781075 INFO::Found 0 missing values.
2025-10-03 18:22:14.78136 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-03 18:22:14.783135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:14.783326 INFO::Done
2025-10-03 18:22:14.783506 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:14.784237 INFO::Starting hierarchical adjustment
2025-10-03 18:22:14.784469 INFO::Found 2 batches.
2025-10-03 18:22:14.784654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:14.784882 INFO::Using default BPPARAM
2025-10-03 18:22:14.785119 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:14.785459 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 18:22:14.79882 INFO::Done
2025-10-03 18:22:14.799171 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:14.799954 INFO::ASW Batch was 0.022876774501489 prior to batch effect correction and is now -0.110236473811906 .
2025-10-03 18:22:14.800259 INFO::Total function execution time is 0.0199990272521973 s and adjustment time is 0.0143749713897705 s ( 71.88 )
2025-10-03 18:22:14.801334 INFO::Formatting Data.
2025-10-03 18:22:14.801548 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:14.804953 INFO::Formatting Data.
2025-10-03 18:22:14.8052 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:14.805544 INFO::Removing potential empty rows and columns
2025-10-03 18:22:14.80595 INFO::Found 0 missing values.
2025-10-03 18:22:14.807084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:14.807335 INFO::Done
2025-10-03 18:22:14.807546 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:14.808364 INFO::Starting hierarchical adjustment
2025-10-03 18:22:14.808619 INFO::Found 2 batches.
2025-10-03 18:22:14.808778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:14.808981 INFO::Using default BPPARAM
2025-10-03 18:22:14.809162 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:14.80945 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:14.833785 INFO::Done
2025-10-03 18:22:14.834073 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:14.834838 INFO::ASW Batch was -0.0241408980372051 prior to batch effect correction and is now -0.115271631205912 .
2025-10-03 18:22:14.835129 INFO::Total function execution time is 0.0301740169525146 s and adjustment time is 0.0251941680908203 s ( 83.5 )
2025-10-03 18:22:14.83547 INFO::Formatting Data.
2025-10-03 18:22:14.835649 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:14.835911 INFO::Removing potential empty rows and columns
2025-10-03 18:22:14.83623 INFO::Found 0 missing values.
2025-10-03 18:22:14.837082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:14.837248 INFO::Done
2025-10-03 18:22:14.837394 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:14.83801 INFO::Starting hierarchical adjustment
2025-10-03 18:22:14.838229 INFO::Found 2 batches.
2025-10-03 18:22:14.838391 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:14.838594 INFO::Using default BPPARAM
2025-10-03 18:22:14.838767 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:14.839034 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:14.844652 INFO::Done
2025-10-03 18:22:14.844883 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:14.845563 INFO::ASW Batch was -0.0241408980372051 prior to batch effect correction and is now -0.115271631205912 .
2025-10-03 18:22:14.8458 INFO::Total function execution time is 0.010329008102417 s and adjustment time is 0.00646209716796875 s ( 62.56 )
2025-10-03 18:22:16.040759 INFO::Formatting Data.
2025-10-03 18:22:16.041028 INFO::Recognized SummarizedExperiment
2025-10-03 18:22:16.041191 INFO::Typecasting input to dataframe.
2025-10-03 18:22:16.051421 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.051876 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.053056 INFO::Found 0 missing values.
2025-10-03 18:22:16.055205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.055391 INFO::Done
2025-10-03 18:22:16.055544 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.056798 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.057026 INFO::Found 2 batches.
2025-10-03 18:22:16.057189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.057533 INFO::Using default BPPARAM
2025-10-03 18:22:16.057695 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.057994 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 18:22:16.076109 INFO::Done
2025-10-03 18:22:16.076361 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.077606 INFO::ASW Batch was 0.0372535853498341 prior to batch effect correction and is now -0.102978655822227 .
2025-10-03 18:22:16.077868 INFO::Total function execution time is 0.0372099876403809 s and adjustment time is 0.0191059112548828 s ( 51.35 )
2025-10-03 18:22:16.084255 INFO::Formatting Data.
2025-10-03 18:22:16.084469 INFO::Recognized SummarizedExperiment
2025-10-03 18:22:16.084627 INFO::Typecasting input to dataframe.
2025-10-03 18:22:16.087746 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.088138 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.0893 INFO::Found 0 missing values.
2025-10-03 18:22:16.09149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.091658 INFO::Done
2025-10-03 18:22:16.091816 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.093028 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.093239 INFO::Found 2 batches.
2025-10-03 18:22:16.093392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.093567 INFO::Using default BPPARAM
2025-10-03 18:22:16.093712 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.093988 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 18:22:16.10198 INFO::Done
2025-10-03 18:22:16.102204 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.103373 INFO::ASW Batch was -0.0107191631257558 prior to batch effect correction and is now -0.0107191631257558 .
2025-10-03 18:22:16.103636 INFO::Total function execution time is 0.0193741321563721 s and adjustment time is 0.00877499580383301 s ( 45.29 )
2025-10-03 18:22:16.110664 INFO::Formatting Data.
2025-10-03 18:22:16.110911 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.111178 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.111475 INFO::Found 0 missing values.
2025-10-03 18:22:16.112285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.112436 INFO::Done
2025-10-03 18:22:16.112579 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.11318 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.113367 INFO::Found 3 batches.
2025-10-03 18:22:16.113507 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.113674 INFO::Using default BPPARAM
2025-10-03 18:22:16.11381 INFO::Processing subtree level 1
2025-10-03 18:22:16.179712 INFO::Adjusting the last 1 batches sequentially
2025-10-03 18:22:16.181557 INFO::Done
2025-10-03 18:22:16.182042 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.184484 INFO::ASW Batch was -0.0819005196819156 prior to batch effect correction and is now -0.169377365919214 .
2025-10-03 18:22:16.185221 INFO::Total function execution time is 0.0745398998260498 s and adjustment time is 0.0682189464569092 s ( 91.52 )
2025-10-03 18:22:16.192668 INFO::Skipping initial DF formatting
2025-10-03 18:22:16.192914 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.194295 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.194561 INFO::Found 5 batches.
2025-10-03 18:22:16.194736 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.194984 INFO::Using default BPPARAM
2025-10-03 18:22:16.195152 INFO::Processing subtree level 1
2025-10-03 18:22:16.318141 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.320046 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 18:22:16.327721 INFO::Done
2025-10-03 18:22:16.328067 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.36697 INFO::ASW Batch was 0.544494545642479 prior to batch effect correction and is now 0.544494545642479 .
2025-10-03 18:22:16.367268 INFO::ASW Label was 0.353480037427954 prior to batch effect correction and is now 0.353480037427954 .
2025-10-03 18:22:16.367671 INFO::Total function execution time is 0.175005912780762 s and adjustment time is 0.133219957351685 s ( 76.12 )
2025-10-03 18:22:16.374944 INFO::Formatting Data.
2025-10-03 18:22:16.375194 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.375541 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.375955 INFO::Found 0 missing values.
2025-10-03 18:22:16.377599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.377806 INFO::Done
2025-10-03 18:22:16.378005 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.379121 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.379378 INFO::Found 5 batches.
2025-10-03 18:22:16.379572 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.379839 INFO::Using default BPPARAM
2025-10-03 18:22:16.380022 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.457704 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.459696 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.470176 INFO::Done
2025-10-03 18:22:16.470619 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.472618 INFO::ASW Batch was 0.267227618516859 prior to batch effect correction and is now -0.0901223011176342 .
2025-10-03 18:22:16.472904 INFO::ASW Label was 0.444651971744147 prior to batch effect correction and is now 0.892266876024565 .
2025-10-03 18:22:16.473479 INFO::Total function execution time is 0.0984361171722412 s and adjustment time is 0.0908350944519043 s ( 92.28 )
2025-10-03 18:22:16.473836 INFO::Formatting Data.
2025-10-03 18:22:16.474095 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.474454 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.474933 INFO::Found 0 missing values.
2025-10-03 18:22:16.476639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.47684 INFO::Done
2025-10-03 18:22:16.477014 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.478108 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.478383 INFO::Found 5 batches.
2025-10-03 18:22:16.478576 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.478851 INFO::Using default BPPARAM
2025-10-03 18:22:16.479053 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.53813 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.544664 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.568062 INFO::Done
2025-10-03 18:22:16.568578 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.572549 INFO::ASW Batch was 0.267227618516859 prior to batch effect correction and is now -0.0901223011176342 .
2025-10-03 18:22:16.572892 INFO::ASW Label was 0.444651971744147 prior to batch effect correction and is now 0.892266876024565 .
2025-10-03 18:22:16.573684 INFO::Total function execution time is 0.0996150970458984 s and adjustment time is 0.0897190570831299 s ( 90.07 )
2025-10-03 18:22:16.582666 INFO::Formatting Data.
2025-10-03 18:22:16.583024 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.583543 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.584071 INFO::Found 0 missing values.
2025-10-03 18:22:16.585924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.586185 INFO::Done
2025-10-03 18:22:16.586402 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.587759 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.588311 INFO::Found 5 batches.
2025-10-03 18:22:16.58856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.588859 INFO::Using default BPPARAM
2025-10-03 18:22:16.589095 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.668294 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.673149 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.683112 INFO::Done
2025-10-03 18:22:16.683509 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.685775 INFO::ASW Batch was 0.394397420391834 prior to batch effect correction and is now -0.0465968990001022 .
2025-10-03 18:22:16.686164 INFO::ASW Label was 0.396995253118296 prior to batch effect correction and is now 0.734063838363098 .
2025-10-03 18:22:16.686601 INFO::Total function execution time is 0.104727029800415 s and adjustment time is 0.0950589179992676 s ( 90.77 )
2025-10-03 18:22:16.686932 INFO::Formatting Data.
2025-10-03 18:22:16.687157 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.687478 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.687888 INFO::Found 0 missing values.
2025-10-03 18:22:16.689436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.689638 INFO::Done
2025-10-03 18:22:16.689829 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.690905 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.691336 INFO::Found 5 batches.
2025-10-03 18:22:16.691533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.691802 INFO::Using default BPPARAM
2025-10-03 18:22:16.692012 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.759304 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.760628 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.784351 INFO::Done
2025-10-03 18:22:16.784854 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.786906 INFO::ASW Batch was 0.394397420391834 prior to batch effect correction and is now -0.0465968990001022 .
2025-10-03 18:22:16.78715 INFO::ASW Label was 0.396995253118296 prior to batch effect correction and is now 0.734063838363098 .
2025-10-03 18:22:16.787827 INFO::Total function execution time is 0.100849866867065 s and adjustment time is 0.0931940078735352 s ( 92.41 )
2025-10-03 18:22:16.798694 INFO::Formatting Data.
2025-10-03 18:22:16.798997 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.799362 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.799889 INFO::Found 0 missing values.
2025-10-03 18:22:16.800939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.801138 INFO::Done
2025-10-03 18:22:16.801321 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.802483 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.802756 INFO::Found 2 batches.
2025-10-03 18:22:16.802933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.803171 INFO::Using default BPPARAM
2025-10-03 18:22:16.803366 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.8037 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.814914 INFO::Done
2025-10-03 18:22:16.815203 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.816255 INFO::ASW Batch was 0.365485570112876 prior to batch effect correction and is now 0.0658745671129673 .
2025-10-03 18:22:16.81646 INFO::ASW Label was 0.527415436564891 prior to batch effect correction and is now 0.885053446049801 .
2025-10-03 18:22:16.816921 INFO::Total function execution time is 0.0180900096893311 s and adjustment time is 0.0122110843658447 s ( 67.5 )
2025-10-03 18:22:16.817177 INFO::Formatting Data.
2025-10-03 18:22:16.817369 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.817669 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.817999 INFO::Found 0 missing values.
2025-10-03 18:22:16.818968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.819146 INFO::Done
2025-10-03 18:22:16.819307 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.820252 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.820506 INFO::Found 2 batches.
2025-10-03 18:22:16.820662 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.820859 INFO::Using default BPPARAM
2025-10-03 18:22:16.821023 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.821314 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 18:22:16.827651 INFO::Done
2025-10-03 18:22:16.827892 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.82887 INFO::ASW Batch was 0.365485570112876 prior to batch effect correction and is now 0.0658745671129673 .
2025-10-03 18:22:16.829058 INFO::ASW Label was 0.527415436564891 prior to batch effect correction and is now 0.885053446049801 .
2025-10-03 18:22:16.829302 INFO::Total function execution time is 0.0121250152587891 s and adjustment time is 0.00718808174133301 s ( 59.28 )
2025-10-03 18:22:16.838578 INFO::Formatting Data.
2025-10-03 18:22:16.838844 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.839155 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.839473 INFO::Found 0 missing values.
2025-10-03 18:22:16.840169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.84036 INFO::Done
2025-10-03 18:22:16.840548 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.841195 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.841432 INFO::Found 2 batches.
2025-10-03 18:22:16.841591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.841807 INFO::Using default BPPARAM
2025-10-03 18:22:16.841995 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.842267 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 18:22:16.859881 INFO::Done
2025-10-03 18:22:16.860162 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.860907 INFO::ASW Batch was 0.101676416599167 prior to batch effect correction and is now -0.134803793338302 .
2025-10-03 18:22:16.861182 INFO::Total function execution time is 0.0226459503173828 s and adjustment time is 0.0184588432312012 s ( 81.51 )
2025-10-03 18:22:16.866985 INFO::Formatting Data.
2025-10-03 18:22:16.867254 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.867563 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.867935 INFO::Found 0 missing values.
2025-10-03 18:22:16.868424 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-03 18:22:16.870149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.870352 INFO::Done
2025-10-03 18:22:16.870538 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.871545 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.871785 INFO::Found 2 batches.
2025-10-03 18:22:16.871978 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.872189 INFO::Using default BPPARAM
2025-10-03 18:22:16.872369 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.872672 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 18:22:16.879091 INFO::Done
2025-10-03 18:22:16.879376 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.880441 INFO::ASW Batch was 0.468204721291403 prior to batch effect correction and is now 0.117077291619505 .
2025-10-03 18:22:16.88065 INFO::ASW Label was 0.657460801026605 prior to batch effect correction and is now 0.865402527050518 .
2025-10-03 18:22:16.880928 INFO::Total function execution time is 0.0139820575714111 s and adjustment time is 0.00733518600463867 s ( 52.46 )
2025-10-03 18:22:16.881194 INFO::Formatting Data.
2025-10-03 18:22:16.881387 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.881664 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.881989 INFO::Found 0 missing values.
2025-10-03 18:22:16.882262 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-03 18:22:16.883741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.883941 INFO::Done
2025-10-03 18:22:16.884103 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.885111 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.885349 INFO::Found 2 batches.
2025-10-03 18:22:16.88552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.885719 INFO::Using default BPPARAM
2025-10-03 18:22:16.885888 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:16.886203 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 18:22:16.893281 INFO::Done
2025-10-03 18:22:16.893586 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:16.895718 INFO::ASW Batch was 0.468204721291403 prior to batch effect correction and is now 0.117077291619505 .
2025-10-03 18:22:16.89601 INFO::ASW Label was 0.657460801026605 prior to batch effect correction and is now 0.865402527050518 .
2025-10-03 18:22:16.896366 INFO::Total function execution time is 0.0151550769805908 s and adjustment time is 0.00794386863708496 s ( 52.42 )
2025-10-03 18:22:16.994848 INFO::Formatting Data.
2025-10-03 18:22:16.995145 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:16.995453 INFO::Removing potential empty rows and columns
2025-10-03 18:22:16.995794 INFO::Found 0 missing values.
2025-10-03 18:22:16.996696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:16.996873 INFO::Done
2025-10-03 18:22:16.997034 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:16.997731 INFO::Starting hierarchical adjustment
2025-10-03 18:22:16.998308 INFO::Found 3 batches.
2025-10-03 18:22:16.998511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:16.998743 INFO::Using default BPPARAM
2025-10-03 18:22:16.998917 INFO::Processing subtree level 1
2025-10-03 18:22:17.041075 INFO::Adjusting the last 1 batches sequentially
2025-10-03 18:22:17.042591 INFO::Done
2025-10-03 18:22:17.043011 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:17.044893 INFO::ASW Batch was -0.0131271059991944 prior to batch effect correction and is now -0.0131271059991944 .
2025-10-03 18:22:17.047256 INFO::Total function execution time is 0.0517089366912842 s and adjustment time is 0.0443530082702637 s ( 85.77 )
2025-10-03 18:22:17.048348 INFO::Formatting Data.
2025-10-03 18:22:17.048897 INFO::Typecasting input to dataframe.
2025-10-03 18:22:17.049148 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:17.049781 INFO::Removing potential empty rows and columns
2025-10-03 18:22:17.050476 INFO::Found 0 missing values.
2025-10-03 18:22:17.051423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:17.051583 INFO::Done
2025-10-03 18:22:17.05191 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:17.052584 INFO::Starting hierarchical adjustment
2025-10-03 18:22:17.052798 INFO::Found 3 batches.
2025-10-03 18:22:17.052954 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:17.053165 INFO::Using default BPPARAM
2025-10-03 18:22:17.053315 INFO::Processing subtree level 1
2025-10-03 18:22:17.108256 INFO::Adjusting the last 1 batches sequentially
2025-10-03 18:22:17.114656 INFO::Done
2025-10-03 18:22:17.115221 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:17.117592 INFO::ASW Batch was -0.0131271059991944 prior to batch effect correction and is now -0.0131271059991944 .
2025-10-03 18:22:17.11837 INFO::Total function execution time is 0.070127010345459 s and adjustment time is 0.0618798732757568 s ( 88.24 )
2025-10-03 18:22:17.128734 INFO::Formatting Data.
2025-10-03 18:22:17.129101 INFO::Typecasting input to dataframe.
2025-10-03 18:22:17.129467 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:17.12983 INFO::Removing potential empty rows and columns
2025-10-03 18:22:17.130258 INFO::Found 0 missing values.
2025-10-03 18:22:17.131279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:17.13145 INFO::Done
2025-10-03 18:22:17.131618 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:17.132275 INFO::Starting hierarchical adjustment
2025-10-03 18:22:17.132507 INFO::Found 3 batches.
2025-10-03 18:22:17.132674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:17.132886 INFO::Using default BPPARAM
2025-10-03 18:22:17.133047 INFO::Processing subtree level 1
2025-10-03 18:22:17.191586 INFO::Adjusting the last 1 batches sequentially
2025-10-03 18:22:17.194745 INFO::Done
2025-10-03 18:22:17.195104 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:17.197974 INFO::ASW Batch was 0.0288481968830913 prior to batch effect correction and is now 0.0288481968830913 .
2025-10-03 18:22:17.198908 INFO::Total function execution time is 0.0701959133148193 s and adjustment time is 0.0622751712799072 s ( 88.72 )
2025-10-03 18:22:17.268405 INFO::Formatting Data.
2025-10-03 18:22:17.268794 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:17.269174 INFO::Removing potential empty rows and columns
2025-10-03 18:22:17.2701 INFO::Found 1000 missing values.
2025-10-03 18:22:17.275776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:17.276013 INFO::Done
2025-10-03 18:22:17.276198 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:17.278148 INFO::Starting hierarchical adjustment
2025-10-03 18:22:17.278395 INFO::Found 10 batches.
2025-10-03 18:22:17.278563 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:17.278787 INFO::Using default BPPARAM
2025-10-03 18:22:17.278951 INFO::Processing subtree level 1
2025-10-03 18:22:17.348309 INFO::Processing subtree level 2
2025-10-03 18:22:17.416674 INFO::Adjusting the last 1 batches sequentially
2025-10-03 18:22:17.419114 INFO::Done
2025-10-03 18:22:17.419357 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:17.422943 INFO::ASW Batch was 0.551774754968806 prior to batch effect correction and is now 0.551774754968806 .
2025-10-03 18:22:17.423333 INFO::ASW Label was 0.315519482295953 prior to batch effect correction and is now 0.315519482295953 .
2025-10-03 18:22:17.4242 INFO::Total function execution time is 0.155771970748901 s and adjustment time is 0.140763998031616 s ( 90.37 )
2025-10-03 18:22:17.424583 INFO::Formatting Data.
2025-10-03 18:22:17.424787 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:17.425254 INFO::Removing potential empty rows and columns
2025-10-03 18:22:17.426268 INFO::Found 1000 missing values.
2025-10-03 18:22:17.431974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:17.432203 INFO::Done
2025-10-03 18:22:17.432384 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:17.434282 INFO::Starting hierarchical adjustment
2025-10-03 18:22:17.434558 INFO::Found 10 batches.
2025-10-03 18:22:17.920454 INFO::Set up parallel execution backend with 2 workers
2025-10-03 18:22:17.92079 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-03 18:22:18.525089 INFO::Adjusting the last 2 batches sequentially
2025-10-03 18:22:18.525664 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 18:22:18.531135 INFO::Done
2025-10-03 18:22:18.531353 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:18.533133 INFO::ASW Batch was 0.551774754968806 prior to batch effect correction and is now 0.551774754968806 .
2025-10-03 18:22:18.533309 INFO::ASW Label was 0.315519482295953 prior to batch effect correction and is now 0.315519482295953 .
2025-10-03 18:22:18.53355 INFO::Total function execution time is 1.10896706581116 s and adjustment time is 1.0966329574585 s ( 98.89 )
2025-10-03 18:22:18.600884 INFO::Formatting Data.
2025-10-03 18:22:18.601222 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.601602 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.602094 INFO::Found 0 missing values.
2025-10-03 18:22:18.603622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.603824 INFO::Done
2025-10-03 18:22:18.604013 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 18:22:18.605074 INFO::Starting hierarchical adjustment
2025-10-03 18:22:18.605325 INFO::Found 3 batches.
2025-10-03 18:22:18.605501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 18:22:18.60575 INFO::Using default BPPARAM
2025-10-03 18:22:18.60593 INFO::Processing subtree level 1
2025-10-03 18:22:18.665216 INFO::Adjusting the last 1 batches sequentially
2025-10-03 18:22:18.666809 INFO::Done
2025-10-03 18:22:18.667072 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 18:22:18.669403 INFO::ASW Batch was 0.231878985382185 prior to batch effect correction and is now -0.15448283487626 .
2025-10-03 18:22:18.669733 INFO::ASW Label was -0.171073645176138 prior to batch effect correction and is now 0.0315742094637592 .
2025-10-03 18:22:18.670346 INFO::Total function execution time is 0.0694899559020996 s and adjustment time is 0.0615370273590088 s ( 88.56 )
2025-10-03 18:22:18.71909 INFO::Formatting Data.
2025-10-03 18:22:18.719469 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.719832 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.720317 INFO::Found 2 missing values.
2025-10-03 18:22:18.7217 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.721959 INFO::Done
2025-10-03 18:22:18.733665 INFO::Found NA in Reference column
2025-10-03 18:22:18.738628 INFO::Require at least two references per batch.
2025-10-03 18:22:18.747914 INFO::Formatting Data.
2025-10-03 18:22:18.748225 INFO::Recognized SummarizedExperiment
2025-10-03 18:22:18.748428 INFO::Typecasting input to dataframe.
2025-10-03 18:22:18.753198 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.753678 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.755213 INFO::Found 0 missing values.
2025-10-03 18:22:18.757947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.758212 INFO::Done
2025-10-03 18:22:18.764721 INFO::Formatting Data.
2025-10-03 18:22:18.765024 INFO::Recognized SummarizedExperiment
2025-10-03 18:22:18.765237 INFO::Typecasting input to dataframe.
2025-10-03 18:22:18.771426 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.771892 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.773237 INFO::Found 0 missing values.
2025-10-03 18:22:18.777306 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.777504 INFO::Done
2025-10-03 18:22:18.783251 INFO::Formatting Data.
2025-10-03 18:22:18.78488 INFO::Recognized SummarizedExperiment
2025-10-03 18:22:18.785102 INFO::Typecasting input to dataframe.
2025-10-03 18:22:18.790877 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.791263 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.791656 INFO::Found 0 missing values.
2025-10-03 18:22:18.791975 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-03 18:22:18.793508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.793695 INFO::Done
2025-10-03 18:22:18.797823 INFO::Formatting Data.
2025-10-03 18:22:18.798072 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.798342 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.798673 INFO::Found 0 missing values.
2025-10-03 18:22:18.799536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.799747 INFO::Done
2025-10-03 18:22:18.804445 INFO::Formatting Data.
2025-10-03 18:22:18.804692 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.804955 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.805293 INFO::Found 0 missing values.
2025-10-03 18:22:18.806313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.806488 INFO::Done
2025-10-03 18:22:18.817868 INFO::Formatting Data.
2025-10-03 18:22:18.818173 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.818543 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.818987 INFO::Found 1 missing values.
2025-10-03 18:22:18.819935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.820153 INFO::Done
2025-10-03 18:22:18.828149 INFO::Formatting Data.
2025-10-03 18:22:18.828473 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.828775 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.829112 INFO::Found 2 missing values.
2025-10-03 18:22:18.829416 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-03 18:22:18.830237 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.830461 INFO::Done
2025-10-03 18:22:18.837399 INFO::Formatting Data.
2025-10-03 18:22:18.837688 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.838001 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.838368 INFO::Found 2 missing values.
2025-10-03 18:22:18.839599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.839806 INFO::Done
2025-10-03 18:22:18.844929 INFO::Formatting Data.
2025-10-03 18:22:18.845204 INFO::Typecasting input to dataframe.
2025-10-03 18:22:18.845506 INFO::Replacing NaNs with NAs.
2025-10-03 18:22:18.845776 INFO::Removing potential empty rows and columns
2025-10-03 18:22:18.84773 INFO::Found 0 missing values.
2025-10-03 18:22:18.848874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 18:22:18.849085 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.925 1.764 9.127
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.001 | 0.423 | 7.258 | |
| compute_asw | 0.010 | 0.001 | 0.016 | |
| count_existing | 0.005 | 0.001 | 0.006 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |