Yannis Schumann
| Snapshot Date: 2025-12-04 13:45 -0500 (Thu, 04 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-08 12:01 -0500 (Mon, 08 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4668 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-12-05 01:05:48 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 01:08:31 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 162.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 43.779 2.722 41.665
* 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-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-12-05 01:07:50.153308 INFO::Formatting Data.
2025-12-05 01:07:50.161421 INFO::Replacing NaNs with NAs.
2025-12-05 01:07:50.200022 INFO::Removing potential empty rows and columns
2025-12-05 01:07:51.379356 INFO::Found 0 missing values.
2025-12-05 01:07:51.387626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:07:51.389149 INFO::Done
2025-12-05 01:07:51.390481 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:07:51.420911 INFO::Starting hierarchical adjustment
2025-12-05 01:07:51.422817 INFO::Found 3 batches.
2025-12-05 01:07:51.424159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:07:51.428069 INFO::Using default BPPARAM
2025-12-05 01:07:51.429455 INFO::Processing subtree level 1
2025-12-05 01:07:51.70788 INFO::Adjusting the last 1 batches sequentially
2025-12-05 01:07:51.714211 INFO::Done
2025-12-05 01:07:51.715824 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:07:51.723708 INFO::ASW Batch was -0.127298245149029 prior to batch effect correction and is now -0.127298245149029 .
2025-12-05 01:07:51.726067 INFO::Total function execution time is 1.57411003112793 s and adjustment time is 0.291747093200684 s ( 18.53 )
2025-12-05 01:07:51.763417 INFO::Formatting Data.
2025-12-05 01:07:51.765161 INFO::Replacing NaNs with NAs.
2025-12-05 01:07:51.767499 INFO::Removing potential empty rows and columns
2025-12-05 01:07:51.771111 INFO::Found 0 missing values.
2025-12-05 01:07:51.773573 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-05 01:07:51.803784 INFO::Formatting Data.
2025-12-05 01:07:51.805524 INFO::Replacing NaNs with NAs.
2025-12-05 01:07:51.807787 INFO::Removing potential empty rows and columns
2025-12-05 01:07:51.8118 INFO::Found 0 missing values.
2025-12-05 01:07:51.814308 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-05 01:07:51.880351 INFO::Formatting Data.
2025-12-05 01:07:51.882097 INFO::Replacing NaNs with NAs.
2025-12-05 01:07:51.884314 INFO::Removing potential empty rows and columns
2025-12-05 01:07:51.886911 INFO::Found 0 missing values.
2025-12-05 01:07:51.8897 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-05 01:07:51.967691 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:07:51.989526 INFO::Done
2025-12-05 01:07:51.991128 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:07:52.006446 INFO::Starting hierarchical adjustment
2025-12-05 01:07:52.009708 INFO::Found 2 batches.
2025-12-05 01:07:52.011096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:07:52.012769 INFO::Using default BPPARAM
2025-12-05 01:07:52.014131 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:07:52.016484 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 01:07:52.089946 INFO::Done
2025-12-05 01:07:52.091702 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:07:52.099773 INFO::ASW Batch was -0.0112902832810787 prior to batch effect correction and is now -0.0945343688260607 .
2025-12-05 01:07:52.102247 INFO::Total function execution time is 0.221932888031006 s and adjustment time is 0.0806300640106201 s ( 36.33 )
2025-12-05 01:07:52.114568 INFO::Formatting Data.
2025-12-05 01:07:52.116361 INFO::Replacing NaNs with NAs.
2025-12-05 01:07:52.145328 INFO::Formatting Data.
2025-12-05 01:07:52.148094 INFO::Replacing NaNs with NAs.
2025-12-05 01:07:52.150305 INFO::Removing potential empty rows and columns
2025-12-05 01:07:52.152916 INFO::Found 0 missing values.
2025-12-05 01:07:52.163485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:07:52.165547 INFO::Done
2025-12-05 01:07:52.166921 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:07:52.2328 INFO::Starting hierarchical adjustment
2025-12-05 01:07:52.234817 INFO::Found 2 batches.
2025-12-05 01:07:52.236204 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:07:52.237668 INFO::Using default BPPARAM
2025-12-05 01:07:52.238956 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:07:52.241089 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:07:52.275619 INFO::Done
2025-12-05 01:07:52.277147 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:07:52.281746 INFO::ASW Batch was 0.0354602281397187 prior to batch effect correction and is now -0.0976408322465303 .
2025-12-05 01:07:52.283932 INFO::Total function execution time is 0.138678789138794 s and adjustment time is 0.0411760807037354 s ( 29.69 )
2025-12-05 01:07:52.286702 INFO::Formatting Data.
2025-12-05 01:07:52.288274 INFO::Replacing NaNs with NAs.
2025-12-05 01:07:52.290345 INFO::Removing potential empty rows and columns
2025-12-05 01:07:52.293025 INFO::Found 0 missing values.
2025-12-05 01:07:52.301018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:07:52.302456 INFO::Done
2025-12-05 01:07:52.304456 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:07:52.309181 INFO::Starting hierarchical adjustment
2025-12-05 01:07:52.311022 INFO::Found 2 batches.
2025-12-05 01:07:52.312338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:07:52.313858 INFO::Using default BPPARAM
2025-12-05 01:07:52.315159 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:07:52.317379 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:07:52.356178 INFO::Done
2025-12-05 01:07:52.357654 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:07:52.362378 INFO::ASW Batch was 0.0354602281397187 prior to batch effect correction and is now -0.0976408322465303 .
2025-12-05 01:07:52.364298 INFO::Total function execution time is 0.0776140689849854 s and adjustment time is 0.0454649925231934 s ( 58.58 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-05 01:08:01.506682 INFO::Formatting Data.
2025-12-05 01:08:01.508239 INFO::Recognized SummarizedExperiment
2025-12-05 01:08:01.509505 INFO::Typecasting input to dataframe.
2025-12-05 01:08:01.661929 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:01.665186 INFO::Removing potential empty rows and columns
2025-12-05 01:08:01.679238 INFO::Found 0 missing values.
2025-12-05 01:08:01.786208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:01.787739 INFO::Done
2025-12-05 01:08:01.789285 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:01.799414 INFO::Starting hierarchical adjustment
2025-12-05 01:08:01.801647 INFO::Found 2 batches.
2025-12-05 01:08:01.803252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:01.80593 INFO::Using default BPPARAM
2025-12-05 01:08:01.807471 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:01.810606 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 01:08:02.078776 INFO::Done
2025-12-05 01:08:02.080361 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:02.10296 INFO::ASW Batch was -0.011921932656294 prior to batch effect correction and is now -0.0932297669127645 .
2025-12-05 01:08:02.104964 INFO::Total function execution time is 0.598963975906372 s and adjustment time is 0.277682065963745 s ( 46.36 )
Warning: stack imbalance in '{', 73 then 75
2025-12-05 01:08:02.226289 INFO::Formatting Data.
2025-12-05 01:08:02.22797 INFO::Recognized SummarizedExperiment
2025-12-05 01:08:02.229294 INFO::Typecasting input to dataframe.
2025-12-05 01:08:02.293177 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:02.295725 INFO::Removing potential empty rows and columns
2025-12-05 01:08:02.306656 INFO::Found 0 missing values.
2025-12-05 01:08:02.333047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:02.396134 INFO::Done
2025-12-05 01:08:02.397678 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:02.406654 INFO::Starting hierarchical adjustment
2025-12-05 01:08:02.408459 INFO::Found 2 batches.
2025-12-05 01:08:02.409733 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:02.411083 INFO::Using default BPPARAM
2025-12-05 01:08:02.412411 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:02.414846 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 01:08:02.563188 INFO::Done
2025-12-05 01:08:02.564743 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:02.580744 INFO::ASW Batch was -0.0175723810429814 prior to batch effect correction and is now -0.0175723810429814 .
2025-12-05 01:08:02.582814 INFO::Total function execution time is 0.356478929519653 s and adjustment time is 0.155035972595215 s ( 43.49 )
2025-12-05 01:08:02.693217 INFO::Formatting Data.
2025-12-05 01:08:02.70068 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:02.703098 INFO::Removing potential empty rows and columns
2025-12-05 01:08:02.705921 INFO::Found 0 missing values.
2025-12-05 01:08:02.714846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:02.71636 INFO::Done
2025-12-05 01:08:02.717711 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:02.76201 INFO::Starting hierarchical adjustment
2025-12-05 01:08:02.765028 INFO::Found 3 batches.
2025-12-05 01:08:02.770967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:02.772585 INFO::Using default BPPARAM
2025-12-05 01:08:02.773975 INFO::Processing subtree level 1
2025-12-05 01:08:03.136824 INFO::Adjusting the last 1 batches sequentially
2025-12-05 01:08:03.148269 INFO::Done
2025-12-05 01:08:03.15016 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:03.162675 INFO::ASW Batch was -0.0558259556325532 prior to batch effect correction and is now -0.161858634463309 .
2025-12-05 01:08:03.166171 INFO::Total function execution time is 0.472898006439209 s and adjustment time is 0.383659839630127 s ( 81.13 )
2025-12-05 01:08:03.206879 INFO::Skipping initial DF formatting
2025-12-05 01:08:03.208399 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:03.218066 INFO::Starting hierarchical adjustment
2025-12-05 01:08:03.221012 INFO::Found 5 batches.
2025-12-05 01:08:03.222576 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:03.224172 INFO::Using default BPPARAM
2025-12-05 01:08:03.225562 INFO::Processing subtree level 1
2025-12-05 01:08:04.058768 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:04.069409 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 01:08:04.152643 INFO::Done
2025-12-05 01:08:04.155489 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:04.171803 INFO::ASW Batch was 0.572440118394726 prior to batch effect correction and is now 0.572440118394726 .
2025-12-05 01:08:04.174088 INFO::ASW Label was 0.296741571787111 prior to batch effect correction and is now 0.296741571787111 .
2025-12-05 01:08:04.17861 INFO::Total function execution time is 0.970513820648193 s and adjustment time is 0.932104110717773 s ( 96.04 )
2025-12-05 01:08:04.394138 INFO::Formatting Data.
2025-12-05 01:08:04.397818 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:04.401288 INFO::Removing potential empty rows and columns
2025-12-05 01:08:04.404173 INFO::Found 0 missing values.
2025-12-05 01:08:04.415852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:04.417293 INFO::Done
2025-12-05 01:08:04.418738 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:04.428944 INFO::Starting hierarchical adjustment
2025-12-05 01:08:04.430884 INFO::Found 5 batches.
2025-12-05 01:08:04.439559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:04.441225 INFO::Using default BPPARAM
2025-12-05 01:08:04.442572 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:04.891687 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:04.907884 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:04.966993 INFO::Done
2025-12-05 01:08:04.969094 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:04.977514 INFO::ASW Batch was 0.524869486157407 prior to batch effect correction and is now -0.00539941444351676 .
2025-12-05 01:08:04.979963 INFO::ASW Label was 0.237822111259186 prior to batch effect correction and is now 0.744114870336915 .
2025-12-05 01:08:04.982313 INFO::Total function execution time is 0.588587999343872 s and adjustment time is 0.536443948745728 s ( 91.14 )
2025-12-05 01:08:04.984826 INFO::Formatting Data.
2025-12-05 01:08:04.986656 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:04.989011 INFO::Removing potential empty rows and columns
2025-12-05 01:08:04.992365 INFO::Found 0 missing values.
2025-12-05 01:08:05.00473 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:05.006352 INFO::Done
2025-12-05 01:08:05.0079 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:05.015631 INFO::Starting hierarchical adjustment
2025-12-05 01:08:05.017783 INFO::Found 5 batches.
2025-12-05 01:08:05.019318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:05.021004 INFO::Using default BPPARAM
2025-12-05 01:08:05.023801 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:05.327794 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:05.334206 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:05.414996 INFO::Done
2025-12-05 01:08:05.422831 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:05.444431 INFO::ASW Batch was 0.524869486157407 prior to batch effect correction and is now -0.00539941444351676 .
2025-12-05 01:08:05.447362 INFO::ASW Label was 0.237822111259186 prior to batch effect correction and is now 0.744114870336915 .
2025-12-05 01:08:05.452318 INFO::Total function execution time is 0.466398954391479 s and adjustment time is 0.397630929946899 s ( 85.26 )
2025-12-05 01:08:05.501732 INFO::Formatting Data.
2025-12-05 01:08:05.50632 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:05.509578 INFO::Removing potential empty rows and columns
2025-12-05 01:08:05.512746 INFO::Found 0 missing values.
2025-12-05 01:08:05.533493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:05.535148 INFO::Done
2025-12-05 01:08:05.536646 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:05.545058 INFO::Starting hierarchical adjustment
2025-12-05 01:08:05.547641 INFO::Found 5 batches.
2025-12-05 01:08:05.549631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:05.551431 INFO::Using default BPPARAM
2025-12-05 01:08:05.553949 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:05.917173 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:05.931598 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:05.994156 INFO::Done
2025-12-05 01:08:05.995815 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:06.003798 INFO::ASW Batch was 0.419310281307037 prior to batch effect correction and is now -0.0463137165701702 .
2025-12-05 01:08:06.005394 INFO::ASW Label was 0.379686992400347 prior to batch effect correction and is now 0.720907665815401 .
2025-12-05 01:08:06.007393 INFO::Total function execution time is 0.505933046340942 s and adjustment time is 0.446939945220947 s ( 88.34 )
2025-12-05 01:08:06.009698 INFO::Formatting Data.
2025-12-05 01:08:06.011374 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:06.014043 INFO::Removing potential empty rows and columns
2025-12-05 01:08:06.017244 INFO::Found 0 missing values.
2025-12-05 01:08:06.0313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:06.032874 INFO::Done
2025-12-05 01:08:06.034294 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:06.04177 INFO::Starting hierarchical adjustment
2025-12-05 01:08:06.043802 INFO::Found 5 batches.
2025-12-05 01:08:06.04527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:06.046924 INFO::Using default BPPARAM
2025-12-05 01:08:06.048363 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:06.377718 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:06.391025 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:06.456078 INFO::Done
2025-12-05 01:08:06.458104 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:06.467987 INFO::ASW Batch was 0.419310281307037 prior to batch effect correction and is now -0.0463137165701702 .
2025-12-05 01:08:06.469491 INFO::ASW Label was 0.379686992400347 prior to batch effect correction and is now 0.720907665815401 .
2025-12-05 01:08:06.471987 INFO::Total function execution time is 0.462267875671387 s and adjustment time is 0.41264009475708 s ( 89.26 )
2025-12-05 01:08:06.537327 INFO::Formatting Data.
2025-12-05 01:08:06.539201 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:06.541793 INFO::Removing potential empty rows and columns
2025-12-05 01:08:06.544484 INFO::Found 0 missing values.
2025-12-05 01:08:06.560299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:06.562388 INFO::Done
2025-12-05 01:08:06.564347 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:06.576598 INFO::Starting hierarchical adjustment
2025-12-05 01:08:06.578408 INFO::Found 2 batches.
2025-12-05 01:08:06.588907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:06.592084 INFO::Using default BPPARAM
2025-12-05 01:08:06.593693 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:06.597039 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:06.668743 INFO::Done
2025-12-05 01:08:06.672515 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:06.679885 INFO::ASW Batch was 0.568365331994458 prior to batch effect correction and is now 0.0931411264653453 .
2025-12-05 01:08:06.681479 INFO::ASW Label was 0.552979471685885 prior to batch effect correction and is now 0.854110498499992 .
2025-12-05 01:08:06.693053 INFO::Total function execution time is 0.155807018280029 s and adjustment time is 0.0906281471252441 s ( 58.17 )
2025-12-05 01:08:06.695356 INFO::Formatting Data.
2025-12-05 01:08:06.69712 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:06.699488 INFO::Removing potential empty rows and columns
2025-12-05 01:08:06.703457 INFO::Found 0 missing values.
2025-12-05 01:08:06.711056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:06.712569 INFO::Done
2025-12-05 01:08:06.715541 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:06.723436 INFO::Starting hierarchical adjustment
2025-12-05 01:08:06.727793 INFO::Found 2 batches.
2025-12-05 01:08:06.729299 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:06.730934 INFO::Using default BPPARAM
2025-12-05 01:08:06.732362 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:06.734735 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 01:08:06.774849 INFO::Done
2025-12-05 01:08:06.7764 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:06.783396 INFO::ASW Batch was 0.568365331994458 prior to batch effect correction and is now 0.0931411264653453 .
2025-12-05 01:08:06.78485 INFO::ASW Label was 0.552979471685885 prior to batch effect correction and is now 0.854110498499992 .
2025-12-05 01:08:06.786644 INFO::Total function execution time is 0.0913939476013184 s and adjustment time is 0.0475130081176758 s ( 51.99 )
2025-12-05 01:08:06.819309 INFO::Formatting Data.
2025-12-05 01:08:06.820996 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:06.823035 INFO::Removing potential empty rows and columns
2025-12-05 01:08:06.825223 INFO::Found 0 missing values.
2025-12-05 01:08:06.831117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:06.832627 INFO::Done
2025-12-05 01:08:06.834064 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:06.839094 INFO::Starting hierarchical adjustment
2025-12-05 01:08:06.841436 INFO::Found 2 batches.
2025-12-05 01:08:06.842911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:06.844414 INFO::Using default BPPARAM
2025-12-05 01:08:06.845739 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:06.84809 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 01:08:06.945912 INFO::Done
2025-12-05 01:08:06.947386 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:06.953824 INFO::ASW Batch was -0.0285343885582331 prior to batch effect correction and is now -0.136420332842205 .
2025-12-05 01:08:06.962451 INFO::Total function execution time is 0.136785984039307 s and adjustment time is 0.104950904846191 s ( 76.73 )
2025-12-05 01:08:07.013681 INFO::Formatting Data.
2025-12-05 01:08:07.015515 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:07.017734 INFO::Removing potential empty rows and columns
2025-12-05 01:08:07.036899 INFO::Found 0 missing values.
2025-12-05 01:08:07.039911 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-05 01:08:07.058699 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:07.060181 INFO::Done
2025-12-05 01:08:07.0662 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:07.073642 INFO::Starting hierarchical adjustment
2025-12-05 01:08:07.079475 INFO::Found 2 batches.
2025-12-05 01:08:07.082089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:07.083592 INFO::Using default BPPARAM
2025-12-05 01:08:07.084852 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:07.087107 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 01:08:07.14498 INFO::Done
2025-12-05 01:08:07.146465 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:07.152922 INFO::ASW Batch was 0.371853169293931 prior to batch effect correction and is now 0.230761872532011 .
2025-12-05 01:08:07.154857 INFO::ASW Label was 0.643283933350912 prior to batch effect correction and is now 0.782108810573038 .
2025-12-05 01:08:07.156821 INFO::Total function execution time is 0.143255949020386 s and adjustment time is 0.0660040378570557 s ( 46.07 )
2025-12-05 01:08:07.158599 INFO::Formatting Data.
2025-12-05 01:08:07.16014 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:07.162386 INFO::Removing potential empty rows and columns
2025-12-05 01:08:07.165598 INFO::Found 0 missing values.
2025-12-05 01:08:07.167904 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-05 01:08:07.181323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:07.182968 INFO::Done
2025-12-05 01:08:07.184232 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:07.192622 INFO::Starting hierarchical adjustment
2025-12-05 01:08:07.194553 INFO::Found 2 batches.
2025-12-05 01:08:07.195891 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:07.198371 INFO::Using default BPPARAM
2025-12-05 01:08:07.19983 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:07.202218 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 01:08:07.248533 INFO::Done
2025-12-05 01:08:07.250642 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:07.261317 INFO::ASW Batch was 0.371853169293931 prior to batch effect correction and is now 0.230761872532011 .
2025-12-05 01:08:07.262859 INFO::ASW Label was 0.643283933350912 prior to batch effect correction and is now 0.782108810573038 .
2025-12-05 01:08:07.267826 INFO::Total function execution time is 0.109174013137817 s and adjustment time is 0.0543191432952881 s ( 49.75 )
2025-12-05 01:08:07.948311 INFO::Formatting Data.
2025-12-05 01:08:07.95187 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:07.954254 INFO::Removing potential empty rows and columns
2025-12-05 01:08:07.958079 INFO::Found 0 missing values.
2025-12-05 01:08:07.965536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:07.967789 INFO::Done
2025-12-05 01:08:07.969166 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:07.973804 INFO::Starting hierarchical adjustment
2025-12-05 01:08:07.975541 INFO::Found 3 batches.
2025-12-05 01:08:07.977734 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:07.979281 INFO::Using default BPPARAM
2025-12-05 01:08:07.980634 INFO::Processing subtree level 1
2025-12-05 01:08:08.200005 INFO::Adjusting the last 1 batches sequentially
2025-12-05 01:08:08.211111 INFO::Done
2025-12-05 01:08:08.212591 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:08.22367 INFO::ASW Batch was -0.0223898204945674 prior to batch effect correction and is now -0.0223898204945674 .
2025-12-05 01:08:08.226251 INFO::Total function execution time is 0.27934193611145 s and adjustment time is 0.23584508895874 s ( 84.43 )
2025-12-05 01:08:08.231686 INFO::Formatting Data.
2025-12-05 01:08:08.234509 INFO::Typecasting input to dataframe.
2025-12-05 01:08:08.236584 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:08.244229 INFO::Removing potential empty rows and columns
2025-12-05 01:08:08.247538 INFO::Found 0 missing values.
2025-12-05 01:08:08.258073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:08.259797 INFO::Done
2025-12-05 01:08:08.261121 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:08.268032 INFO::Starting hierarchical adjustment
2025-12-05 01:08:08.270893 INFO::Found 3 batches.
2025-12-05 01:08:08.272338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:08.27485 INFO::Using default BPPARAM
2025-12-05 01:08:08.276465 INFO::Processing subtree level 1
2025-12-05 01:08:08.504721 INFO::Adjusting the last 1 batches sequentially
2025-12-05 01:08:08.5209 INFO::Done
2025-12-05 01:08:08.522442 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:08.533509 INFO::ASW Batch was -0.0223898204945674 prior to batch effect correction and is now -0.0223898204945674 .
2025-12-05 01:08:08.536365 INFO::Total function execution time is 0.305323839187622 s and adjustment time is 0.25080680847168 s ( 82.14 )
2025-12-05 01:08:08.576006 INFO::Formatting Data.
2025-12-05 01:08:08.57779 INFO::Typecasting input to dataframe.
2025-12-05 01:08:08.579968 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:08.582234 INFO::Removing potential empty rows and columns
2025-12-05 01:08:08.586011 INFO::Found 0 missing values.
2025-12-05 01:08:08.59397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:08.596014 INFO::Done
2025-12-05 01:08:08.597387 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:08.602256 INFO::Starting hierarchical adjustment
2025-12-05 01:08:08.605464 INFO::Found 3 batches.
2025-12-05 01:08:08.607022 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:08.608509 INFO::Using default BPPARAM
2025-12-05 01:08:08.609796 INFO::Processing subtree level 1
2025-12-05 01:08:08.840035 INFO::Adjusting the last 1 batches sequentially
2025-12-05 01:08:08.850818 INFO::Done
2025-12-05 01:08:08.85282 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:08.864351 INFO::ASW Batch was -0.108310530446913 prior to batch effect correction and is now -0.108310530446913 .
2025-12-05 01:08:08.869902 INFO::Total function execution time is 0.292176961898804 s and adjustment time is 0.245753049850464 s ( 84.11 )
2025-12-05 01:08:09.27358 INFO::Formatting Data.
2025-12-05 01:08:09.275429 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:09.278471 INFO::Removing potential empty rows and columns
2025-12-05 01:08:09.287679 INFO::Found 1000 missing values.
2025-12-05 01:08:09.354068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:09.355743 INFO::Done
2025-12-05 01:08:09.357477 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:09.373768 INFO::Starting hierarchical adjustment
2025-12-05 01:08:09.376027 INFO::Found 10 batches.
2025-12-05 01:08:09.377738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:09.379789 INFO::Using default BPPARAM
2025-12-05 01:08:09.382804 INFO::Processing subtree level 1
2025-12-05 01:08:09.710297 INFO::Processing subtree level 2
2025-12-05 01:08:10.15531 INFO::Adjusting the last 1 batches sequentially
2025-12-05 01:08:10.168161 INFO::Done
2025-12-05 01:08:10.172276 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:10.193943 INFO::ASW Batch was 0.500458317846087 prior to batch effect correction and is now 0.500458317846087 .
2025-12-05 01:08:10.19632 INFO::ASW Label was 0.330372085088857 prior to batch effect correction and is now 0.330372085088857 .
2025-12-05 01:08:10.200102 INFO::Total function execution time is 0.926548957824707 s and adjustment time is 0.792646169662476 s ( 85.55 )
2025-12-05 01:08:10.202412 INFO::Formatting Data.
2025-12-05 01:08:10.206977 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:10.211264 INFO::Removing potential empty rows and columns
2025-12-05 01:08:10.220416 INFO::Found 1000 missing values.
2025-12-05 01:08:10.279101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:10.282053 INFO::Done
2025-12-05 01:08:10.283492 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:10.299849 INFO::Starting hierarchical adjustment
2025-12-05 01:08:10.302884 INFO::Found 10 batches.
2025-12-05 01:08:11.718753 INFO::Set up parallel execution backend with 2 workers
2025-12-05 01:08:11.720627 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-05 01:08:13.56322 INFO::Adjusting the last 2 batches sequentially
2025-12-05 01:08:13.565805 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 01:08:13.612825 INFO::Done
2025-12-05 01:08:13.614164 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:13.626254 INFO::ASW Batch was 0.500458317846087 prior to batch effect correction and is now 0.500458317846087 .
2025-12-05 01:08:13.627565 INFO::ASW Label was 0.330372085088857 prior to batch effect correction and is now 0.330372085088857 .
2025-12-05 01:08:13.629228 INFO::Total function execution time is 3.42698788642883 s and adjustment time is 3.31048107147217 s ( 96.6 )
2025-12-05 01:08:14.040813 INFO::Formatting Data.
2025-12-05 01:08:14.042687 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:14.044929 INFO::Removing potential empty rows and columns
2025-12-05 01:08:14.047718 INFO::Found 0 missing values.
2025-12-05 01:08:14.058428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:14.059908 INFO::Done
2025-12-05 01:08:14.061221 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 01:08:14.067664 INFO::Starting hierarchical adjustment
2025-12-05 01:08:14.069531 INFO::Found 3 batches.
2025-12-05 01:08:14.07088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 01:08:14.072609 INFO::Using default BPPARAM
2025-12-05 01:08:14.07397 INFO::Processing subtree level 1
2025-12-05 01:08:14.369216 INFO::Adjusting the last 1 batches sequentially
2025-12-05 01:08:14.380456 INFO::Done
2025-12-05 01:08:14.383231 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 01:08:14.400739 INFO::ASW Batch was 0.240891765206549 prior to batch effect correction and is now -0.127761442412069 .
2025-12-05 01:08:14.407925 INFO::ASW Label was -0.221110481824613 prior to batch effect correction and is now -0.0409260601823264 .
2025-12-05 01:08:14.414843 INFO::Total function execution time is 0.372894048690796 s and adjustment time is 0.310656785964966 s ( 83.31 )
2025-12-05 01:08:14.805858 INFO::Formatting Data.
2025-12-05 01:08:14.807628 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:14.811265 INFO::Removing potential empty rows and columns
2025-12-05 01:08:14.814308 INFO::Found 2 missing values.
2025-12-05 01:08:14.823656 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:14.825142 INFO::Done
2025-12-05 01:08:14.913372 INFO::Found NA in Reference column
2025-12-05 01:08:14.945078 INFO::Require at least two references per batch.
2025-12-05 01:08:15.006697 INFO::Formatting Data.
2025-12-05 01:08:15.008145 INFO::Recognized SummarizedExperiment
2025-12-05 01:08:15.009321 INFO::Typecasting input to dataframe.
2025-12-05 01:08:15.038058 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.040789 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.053003 INFO::Found 0 missing values.
2025-12-05 01:08:15.076749 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.078195 INFO::Done
2025-12-05 01:08:15.120491 INFO::Formatting Data.
2025-12-05 01:08:15.12218 INFO::Recognized SummarizedExperiment
2025-12-05 01:08:15.123508 INFO::Typecasting input to dataframe.
2025-12-05 01:08:15.174838 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.177741 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.189167 INFO::Found 0 missing values.
2025-12-05 01:08:15.232758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.234271 INFO::Done
2025-12-05 01:08:15.282435 INFO::Formatting Data.
2025-12-05 01:08:15.286302 INFO::Recognized SummarizedExperiment
2025-12-05 01:08:15.287733 INFO::Typecasting input to dataframe.
2025-12-05 01:08:15.336131 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.338483 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.341416 INFO::Found 0 missing values.
2025-12-05 01:08:15.343754 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-05 01:08:15.357307 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.358766 INFO::Done
2025-12-05 01:08:15.388292 INFO::Formatting Data.
2025-12-05 01:08:15.390258 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.39301 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.395786 INFO::Found 0 missing values.
2025-12-05 01:08:15.404106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.405682 INFO::Done
2025-12-05 01:08:15.440777 INFO::Formatting Data.
2025-12-05 01:08:15.443535 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.445928 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.452629 INFO::Found 0 missing values.
2025-12-05 01:08:15.4618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.463295 INFO::Done
2025-12-05 01:08:15.553285 INFO::Formatting Data.
2025-12-05 01:08:15.555158 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.560796 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.564492 INFO::Found 1 missing values.
2025-12-05 01:08:15.575998 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.577606 INFO::Done
2025-12-05 01:08:15.640695 INFO::Formatting Data.
2025-12-05 01:08:15.642574 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.644711 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.647033 INFO::Found 2 missing values.
2025-12-05 01:08:15.649358 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-05 01:08:15.657245 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.658762 INFO::Done
2025-12-05 01:08:15.708921 INFO::Formatting Data.
2025-12-05 01:08:15.710593 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.712638 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.71671 INFO::Found 2 missing values.
2025-12-05 01:08:15.720873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.722396 INFO::Done
2025-12-05 01:08:15.757702 INFO::Formatting Data.
2025-12-05 01:08:15.759379 INFO::Typecasting input to dataframe.
2025-12-05 01:08:15.762318 INFO::Replacing NaNs with NAs.
2025-12-05 01:08:15.764637 INFO::Removing potential empty rows and columns
2025-12-05 01:08:15.767246 INFO::Found 0 missing values.
2025-12-05 01:08:15.776434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 01:08:15.777907 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.402 6.824 52.486
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.779 | 2.722 | 41.665 | |
| compute_asw | 0.055 | 0.004 | 0.066 | |
| count_existing | 0.028 | 0.001 | 0.038 | |
| generate_data_covariables | 0.025 | 0.003 | 0.030 | |
| generate_dataset | 0.024 | 0.002 | 0.041 | |