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 12:04 -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 19:56:46 -0400 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 19:58:15 -0400 (Fri, 03 Oct 2025) |
| EllapsedTime: 88.9 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_1.5.0.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: 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 ‘1.5.0’
* 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 26.806 1.579 19.422
* 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 ‘1.5.0’ ** 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: 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")
2025-10-03 19:57:53.371827 INFO::Formatting Data.
2025-10-03 19:57:53.37786 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:53.39476 INFO::Removing potential empty rows and columns
2025-10-03 19:57:53.752416 INFO::Found 0 missing values.
2025-10-03 19:57:53.757151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:53.758208 INFO::Done
2025-10-03 19:57:53.759329 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:53.779367 INFO::Starting hierarchical adjustment
2025-10-03 19:57:53.780737 INFO::Found 3 batches.
2025-10-03 19:57:53.781717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:53.783576 INFO::Using default BPPARAM
2025-10-03 19:57:53.784438 INFO::Processing subtree level 1
2025-10-03 19:57:53.97416 INFO::Adjusting the last 1 batches sequentially
2025-10-03 19:57:53.982948 INFO::Done
2025-10-03 19:57:53.984929 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:53.99062 INFO::ASW Batch was -0.0593229354044208 prior to batch effect correction and is now -0.0593229354044208 .
2025-10-03 19:57:53.992486 INFO::Total function execution time is 0.621762990951538 s and adjustment time is 0.202489137649536 s ( 32.57 )
2025-10-03 19:57:54.01435 INFO::Formatting Data.
2025-10-03 19:57:54.015415 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:54.016679 INFO::Removing potential empty rows and columns
2025-10-03 19:57:54.018472 INFO::Found 0 missing values.
2025-10-03 19:57:54.019834 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 19:57:54.032799 INFO::Formatting Data.
2025-10-03 19:57:54.033942 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:54.035307 INFO::Removing potential empty rows and columns
2025-10-03 19:57:54.036845 INFO::Found 0 missing values.
2025-10-03 19:57:54.03818 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 19:57:54.062448 INFO::Formatting Data.
2025-10-03 19:57:54.063371 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:54.06426 INFO::Removing potential empty rows and columns
2025-10-03 19:57:54.066161 INFO::Found 0 missing values.
2025-10-03 19:57:54.067589 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 19:57:54.072822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:54.074029 INFO::Done
2025-10-03 19:57:54.074941 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:54.07828 INFO::Starting hierarchical adjustment
2025-10-03 19:57:54.079311 INFO::Found 2 batches.
2025-10-03 19:57:54.08008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:54.080937 INFO::Using default BPPARAM
2025-10-03 19:57:54.081628 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:54.082949 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 19:57:54.112449 INFO::Done
2025-10-03 19:57:54.113466 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:54.116305 INFO::ASW Batch was -0.0763707722228081 prior to batch effect correction and is now -0.130445892167058 .
2025-10-03 19:57:54.117388 INFO::Total function execution time is 0.0550940036773682 s and adjustment time is 0.0332460403442383 s ( 60.34 )
2025-10-03 19:57:54.121379 INFO::Formatting Data.
2025-10-03 19:57:54.122345 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:54.134879 INFO::Formatting Data.
2025-10-03 19:57:54.136045 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:54.137385 INFO::Removing potential empty rows and columns
2025-10-03 19:57:54.138896 INFO::Found 0 missing values.
2025-10-03 19:57:54.142536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:54.143232 INFO::Done
2025-10-03 19:57:54.144086 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:54.146749 INFO::Starting hierarchical adjustment
2025-10-03 19:57:54.147424 INFO::Found 2 batches.
2025-10-03 19:57:54.147916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:54.148466 INFO::Using default BPPARAM
2025-10-03 19:57:54.148957 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:54.150091 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 19:57:54.208898 INFO::Done
2025-10-03 19:57:54.20987 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:54.212662 INFO::ASW Batch was 0.0100243292640987 prior to batch effect correction and is now -0.117885378654033 .
2025-10-03 19:57:54.213787 INFO::Total function execution time is 0.0790050029754639 s and adjustment time is 0.0615320205688477 s ( 77.88 )
2025-10-03 19:57:54.215256 INFO::Formatting Data.
2025-10-03 19:57:54.216091 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:54.217352 INFO::Removing potential empty rows and columns
2025-10-03 19:57:54.218651 INFO::Found 0 missing values.
2025-10-03 19:57:54.222283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:54.223058 INFO::Done
2025-10-03 19:57:54.223776 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:54.226305 INFO::Starting hierarchical adjustment
2025-10-03 19:57:54.227328 INFO::Found 2 batches.
2025-10-03 19:57:54.228036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:54.228971 INFO::Using default BPPARAM
2025-10-03 19:57:54.22963 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:54.230574 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 19:57:54.248511 INFO::Done
2025-10-03 19:57:54.249456 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:54.252217 INFO::ASW Batch was 0.0100243292640987 prior to batch effect correction and is now -0.117885378654033 .
2025-10-03 19:57:54.253319 INFO::Total function execution time is 0.0380549430847168 s and adjustment time is 0.0213279724121094 s ( 56.05 )
2025-10-03 19:57:57.728343 INFO::Formatting Data.
2025-10-03 19:57:57.729336 INFO::Recognized SummarizedExperiment
2025-10-03 19:57:57.730071 INFO::Typecasting input to dataframe.
2025-10-03 19:57:57.768095 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:57.769863 INFO::Removing potential empty rows and columns
2025-10-03 19:57:57.77502 INFO::Found 0 missing values.
2025-10-03 19:57:57.783086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:57.78425 INFO::Done
2025-10-03 19:57:57.785104 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:57.789291 INFO::Starting hierarchical adjustment
2025-10-03 19:57:57.790587 INFO::Found 2 batches.
2025-10-03 19:57:57.791489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:57.793134 INFO::Using default BPPARAM
2025-10-03 19:57:57.794057 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:57.795727 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 19:57:57.866227 INFO::Done
2025-10-03 19:57:57.867238 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:57.87178 INFO::ASW Batch was -0.0082486973133697 prior to batch effect correction and is now -0.0942555213435287 .
2025-10-03 19:57:57.872662 INFO::Total function execution time is 0.144790887832642 s and adjustment time is 0.0758388042449951 s ( 52.38 )
2025-10-03 19:57:57.896275 INFO::Formatting Data.
2025-10-03 19:57:57.897267 INFO::Recognized SummarizedExperiment
2025-10-03 19:57:57.89814 INFO::Typecasting input to dataframe.
2025-10-03 19:57:57.911159 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:57.913112 INFO::Removing potential empty rows and columns
2025-10-03 19:57:57.917678 INFO::Found 0 missing values.
2025-10-03 19:57:57.926992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:57.928056 INFO::Done
2025-10-03 19:57:57.92867 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:57.933439 INFO::Starting hierarchical adjustment
2025-10-03 19:57:57.934644 INFO::Found 2 batches.
2025-10-03 19:57:57.935255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:57.935924 INFO::Using default BPPARAM
2025-10-03 19:57:57.936647 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:57.937996 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 19:57:57.965005 INFO::Done
2025-10-03 19:57:57.965675 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:57.968921 INFO::ASW Batch was 0.0150568952045899 prior to batch effect correction and is now 0.0150568952045899 .
2025-10-03 19:57:57.969724 INFO::Total function execution time is 0.0734498500823975 s and adjustment time is 0.0305991172790527 s ( 41.66 )
2025-10-03 19:57:57.991735 INFO::Formatting Data.
2025-10-03 19:57:57.992478 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:57.993317 INFO::Removing potential empty rows and columns
2025-10-03 19:57:57.994457 INFO::Found 0 missing values.
2025-10-03 19:57:57.997464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:57.997987 INFO::Done
2025-10-03 19:57:57.998498 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:58.000376 INFO::Starting hierarchical adjustment
2025-10-03 19:57:58.001328 INFO::Found 3 batches.
2025-10-03 19:57:58.002105 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:58.00297 INFO::Using default BPPARAM
2025-10-03 19:57:58.003673 INFO::Processing subtree level 1
2025-10-03 19:57:58.195688 INFO::Adjusting the last 1 batches sequentially
2025-10-03 19:57:58.225438 INFO::Done
2025-10-03 19:57:58.227054 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:58.246282 INFO::ASW Batch was -0.0367374829538193 prior to batch effect correction and is now -0.179041317799552 .
2025-10-03 19:57:58.253259 INFO::Total function execution time is 0.259027004241943 s and adjustment time is 0.224225044250488 s ( 86.56 )
2025-10-03 19:57:58.280823 INFO::Skipping initial DF formatting
2025-10-03 19:57:58.281852 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:58.287424 INFO::Starting hierarchical adjustment
2025-10-03 19:57:58.288292 INFO::Found 5 batches.
2025-10-03 19:57:58.289013 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:58.290043 INFO::Using default BPPARAM
2025-10-03 19:57:58.291002 INFO::Processing subtree level 1
2025-10-03 19:57:58.678543 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:58.681812 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 19:57:58.752829 INFO::Done
2025-10-03 19:57:58.754286 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:58.771032 INFO::ASW Batch was 0.54253951176881 prior to batch effect correction and is now 0.54253951176881 .
2025-10-03 19:57:58.77209 INFO::ASW Label was 0.373303944696388 prior to batch effect correction and is now 0.373303944696388 .
2025-10-03 19:57:58.776385 INFO::Total function execution time is 0.495081186294556 s and adjustment time is 0.46466588973999 s ( 93.86 )
2025-10-03 19:57:58.884917 INFO::Formatting Data.
2025-10-03 19:57:58.885725 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:58.886753 INFO::Removing potential empty rows and columns
2025-10-03 19:57:58.888023 INFO::Found 0 missing values.
2025-10-03 19:57:58.896751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:58.897869 INFO::Done
2025-10-03 19:57:58.899426 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:58.902864 INFO::Starting hierarchical adjustment
2025-10-03 19:57:58.90365 INFO::Found 5 batches.
2025-10-03 19:57:58.904244 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:58.905246 INFO::Using default BPPARAM
2025-10-03 19:57:58.906163 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 19:57:59.147445 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:59.161081 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 19:57:59.20231 INFO::Done
2025-10-03 19:57:59.203538 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:59.208384 INFO::ASW Batch was 0.475390421530435 prior to batch effect correction and is now -0.0557030470085387 .
2025-10-03 19:57:59.209263 INFO::ASW Label was 0.290531242214337 prior to batch effect correction and is now 0.78105515411635 .
2025-10-03 19:57:59.210427 INFO::Total function execution time is 0.32543683052063 s and adjustment time is 0.298719167709351 s ( 91.79 )
2025-10-03 19:57:59.211796 INFO::Formatting Data.
2025-10-03 19:57:59.212714 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:59.213649 INFO::Removing potential empty rows and columns
2025-10-03 19:57:59.214727 INFO::Found 0 missing values.
2025-10-03 19:57:59.22133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:59.222295 INFO::Done
2025-10-03 19:57:59.223057 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:59.227817 INFO::Starting hierarchical adjustment
2025-10-03 19:57:59.229082 INFO::Found 5 batches.
2025-10-03 19:57:59.229972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:59.230949 INFO::Using default BPPARAM
2025-10-03 19:57:59.23175 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 19:57:59.439545 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:59.455128 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 19:57:59.492676 INFO::Done
2025-10-03 19:57:59.494303 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:59.500686 INFO::ASW Batch was 0.475390421530435 prior to batch effect correction and is now -0.0557030470085387 .
2025-10-03 19:57:59.501867 INFO::ASW Label was 0.290531242214337 prior to batch effect correction and is now 0.78105515411635 .
2025-10-03 19:57:59.503146 INFO::Total function execution time is 0.291328907012939 s and adjustment time is 0.263787031173706 s ( 90.55 )
2025-10-03 19:57:59.527905 INFO::Formatting Data.
2025-10-03 19:57:59.529182 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:59.53063 INFO::Removing potential empty rows and columns
2025-10-03 19:57:59.53179 INFO::Found 0 missing values.
2025-10-03 19:57:59.53674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:59.537698 INFO::Done
2025-10-03 19:57:59.538533 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:59.543087 INFO::Starting hierarchical adjustment
2025-10-03 19:57:59.544203 INFO::Found 5 batches.
2025-10-03 19:57:59.545193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:59.546067 INFO::Using default BPPARAM
2025-10-03 19:57:59.546864 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 19:57:59.767132 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:57:59.785999 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 19:57:59.8259 INFO::Done
2025-10-03 19:57:59.827139 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:57:59.837511 INFO::ASW Batch was 0.630144630607326 prior to batch effect correction and is now -0.0860377726508904 .
2025-10-03 19:57:59.838564 INFO::ASW Label was 0.186005934076805 prior to batch effect correction and is now 0.822256665508414 .
2025-10-03 19:57:59.839808 INFO::Total function execution time is 0.31200098991394 s and adjustment time is 0.281915903091431 s ( 90.36 )
2025-10-03 19:57:59.840743 INFO::Formatting Data.
2025-10-03 19:57:59.841334 INFO::Replacing NaNs with NAs.
2025-10-03 19:57:59.842195 INFO::Removing potential empty rows and columns
2025-10-03 19:57:59.843217 INFO::Found 0 missing values.
2025-10-03 19:57:59.849011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:57:59.849619 INFO::Done
2025-10-03 19:57:59.850183 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:57:59.854512 INFO::Starting hierarchical adjustment
2025-10-03 19:57:59.85553 INFO::Found 5 batches.
2025-10-03 19:57:59.856384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:57:59.857186 INFO::Using default BPPARAM
2025-10-03 19:57:59.85784 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 19:58:00.113047 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:58:00.123339 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 19:58:00.158403 INFO::Done
2025-10-03 19:58:00.159402 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:00.164474 INFO::ASW Batch was 0.630144630607326 prior to batch effect correction and is now -0.0860377726508904 .
2025-10-03 19:58:00.165543 INFO::ASW Label was 0.186005934076805 prior to batch effect correction and is now 0.822256665508414 .
2025-10-03 19:58:00.167593 INFO::Total function execution time is 0.326747894287109 s and adjustment time is 0.303053855895996 s ( 92.75 )
2025-10-03 19:58:00.189817 INFO::Formatting Data.
2025-10-03 19:58:00.19088 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:00.192361 INFO::Removing potential empty rows and columns
2025-10-03 19:58:00.194037 INFO::Found 0 missing values.
2025-10-03 19:58:00.197196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:00.19807 INFO::Done
2025-10-03 19:58:00.198897 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:00.203268 INFO::Starting hierarchical adjustment
2025-10-03 19:58:00.204543 INFO::Found 2 batches.
2025-10-03 19:58:00.205347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:00.206247 INFO::Using default BPPARAM
2025-10-03 19:58:00.207022 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:58:00.208375 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 19:58:00.227456 INFO::Done
2025-10-03 19:58:00.22815 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:00.231269 INFO::ASW Batch was 0.560733240563245 prior to batch effect correction and is now 0.000198207389481553 .
2025-10-03 19:58:00.231994 INFO::ASW Label was 0.53375004309807 prior to batch effect correction and is now 0.913463915850247 .
2025-10-03 19:58:00.232909 INFO::Total function execution time is 0.043212890625 s and adjustment time is 0.0231499671936035 s ( 53.57 )
2025-10-03 19:58:00.234283 INFO::Formatting Data.
2025-10-03 19:58:00.235 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:00.236229 INFO::Removing potential empty rows and columns
2025-10-03 19:58:00.237576 INFO::Found 0 missing values.
2025-10-03 19:58:00.240894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:00.241442 INFO::Done
2025-10-03 19:58:00.242142 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:00.246214 INFO::Starting hierarchical adjustment
2025-10-03 19:58:00.247327 INFO::Found 2 batches.
2025-10-03 19:58:00.248146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:00.24919 INFO::Using default BPPARAM
2025-10-03 19:58:00.249732 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:58:00.250638 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 19:58:00.270616 INFO::Done
2025-10-03 19:58:00.27164 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:00.276189 INFO::ASW Batch was 0.560733240563245 prior to batch effect correction and is now 0.000198207389481553 .
2025-10-03 19:58:00.276951 INFO::ASW Label was 0.53375004309807 prior to batch effect correction and is now 0.913463915850247 .
2025-10-03 19:58:00.2782 INFO::Total function execution time is 0.0441548824310303 s and adjustment time is 0.0234739780426025 s ( 53.16 )
2025-10-03 19:58:00.298787 INFO::Formatting Data.
2025-10-03 19:58:00.299935 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:00.301192 INFO::Removing potential empty rows and columns
2025-10-03 19:58:00.302613 INFO::Found 0 missing values.
2025-10-03 19:58:00.305272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:00.30583 INFO::Done
2025-10-03 19:58:00.306341 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:00.309559 INFO::Starting hierarchical adjustment
2025-10-03 19:58:00.310594 INFO::Found 2 batches.
2025-10-03 19:58:00.311363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:00.312208 INFO::Using default BPPARAM
2025-10-03 19:58:00.312996 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:58:00.314355 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 19:58:00.354722 INFO::Done
2025-10-03 19:58:00.355389 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:00.357713 INFO::ASW Batch was -0.0986928456234557 prior to batch effect correction and is now -0.153404434298117 .
2025-10-03 19:58:00.358859 INFO::Total function execution time is 0.060107946395874 s and adjustment time is 0.0443470478057861 s ( 73.78 )
2025-10-03 19:58:00.379083 INFO::Formatting Data.
2025-10-03 19:58:00.380209 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:00.381516 INFO::Removing potential empty rows and columns
2025-10-03 19:58:00.382827 INFO::Found 0 missing values.
2025-10-03 19:58:00.384436 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 19:58:00.390961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:00.391606 INFO::Done
2025-10-03 19:58:00.392129 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:00.396179 INFO::Starting hierarchical adjustment
2025-10-03 19:58:00.397343 INFO::Found 2 batches.
2025-10-03 19:58:00.398175 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:00.399074 INFO::Using default BPPARAM
2025-10-03 19:58:00.399858 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:58:00.401272 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 19:58:00.424251 INFO::Done
2025-10-03 19:58:00.424914 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:00.428037 INFO::ASW Batch was 0.576337629816722 prior to batch effect correction and is now -0.00203243244621644 .
2025-10-03 19:58:00.428915 INFO::ASW Label was 0.424299799679763 prior to batch effect correction and is now 0.906613699450535 .
2025-10-03 19:58:00.429988 INFO::Total function execution time is 0.0510280132293701 s and adjustment time is 0.0271620750427246 s ( 53.23 )
2025-10-03 19:58:00.431103 INFO::Formatting Data.
2025-10-03 19:58:00.431995 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:00.433312 INFO::Removing potential empty rows and columns
2025-10-03 19:58:00.434688 INFO::Found 0 missing values.
2025-10-03 19:58:00.435935 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 19:58:00.440885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:00.44175 INFO::Done
2025-10-03 19:58:00.442716 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:00.4465 INFO::Starting hierarchical adjustment
2025-10-03 19:58:00.447295 INFO::Found 2 batches.
2025-10-03 19:58:00.448236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:00.448975 INFO::Using default BPPARAM
2025-10-03 19:58:00.449523 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:58:00.45044 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 19:58:00.469798 INFO::Done
2025-10-03 19:58:00.470581 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:00.474007 INFO::ASW Batch was 0.576337629816722 prior to batch effect correction and is now -0.00203243244621644 .
2025-10-03 19:58:00.474765 INFO::ASW Label was 0.424299799679763 prior to batch effect correction and is now 0.906613699450535 .
2025-10-03 19:58:00.475831 INFO::Total function execution time is 0.0447700023651123 s and adjustment time is 0.0225880146026611 s ( 50.45 )
2025-10-03 19:58:00.746437 INFO::Formatting Data.
2025-10-03 19:58:00.747726 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:00.749179 INFO::Removing potential empty rows and columns
2025-10-03 19:58:00.750697 INFO::Found 0 missing values.
2025-10-03 19:58:00.754786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:00.755551 INFO::Done
2025-10-03 19:58:00.756254 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:00.758627 INFO::Starting hierarchical adjustment
2025-10-03 19:58:00.75948 INFO::Found 3 batches.
2025-10-03 19:58:00.760088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:00.760792 INFO::Using default BPPARAM
2025-10-03 19:58:00.761395 INFO::Processing subtree level 1
2025-10-03 19:58:00.898731 INFO::Adjusting the last 1 batches sequentially
2025-10-03 19:58:00.917542 INFO::Done
2025-10-03 19:58:00.919187 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:00.930548 INFO::ASW Batch was -0.0702844272518784 prior to batch effect correction and is now -0.0702844272518784 .
2025-10-03 19:58:00.934347 INFO::Total function execution time is 0.187978982925415 s and adjustment time is 0.158217906951904 s ( 84.17 )
2025-10-03 19:58:00.936565 INFO::Formatting Data.
2025-10-03 19:58:00.937749 INFO::Typecasting input to dataframe.
2025-10-03 19:58:00.939954 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:00.941775 INFO::Removing potential empty rows and columns
2025-10-03 19:58:00.943567 INFO::Found 0 missing values.
2025-10-03 19:58:00.947153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:00.947875 INFO::Done
2025-10-03 19:58:00.948889 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:00.951696 INFO::Starting hierarchical adjustment
2025-10-03 19:58:00.952601 INFO::Found 3 batches.
2025-10-03 19:58:00.953269 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:00.954379 INFO::Using default BPPARAM
2025-10-03 19:58:00.955146 INFO::Processing subtree level 1
2025-10-03 19:58:01.108284 INFO::Adjusting the last 1 batches sequentially
2025-10-03 19:58:01.119942 INFO::Done
2025-10-03 19:58:01.121999 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:01.130987 INFO::ASW Batch was -0.0702844272518784 prior to batch effect correction and is now -0.0702844272518784 .
2025-10-03 19:58:01.134127 INFO::Total function execution time is 0.198015928268433 s and adjustment time is 0.167524099349976 s ( 84.6 )
2025-10-03 19:58:01.159222 INFO::Formatting Data.
2025-10-03 19:58:01.16004 INFO::Typecasting input to dataframe.
2025-10-03 19:58:01.16107 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:01.161935 INFO::Removing potential empty rows and columns
2025-10-03 19:58:01.163072 INFO::Found 0 missing values.
2025-10-03 19:58:01.170612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:01.171239 INFO::Done
2025-10-03 19:58:01.171835 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:01.17427 INFO::Starting hierarchical adjustment
2025-10-03 19:58:01.175266 INFO::Found 3 batches.
2025-10-03 19:58:01.175998 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:01.177081 INFO::Using default BPPARAM
2025-10-03 19:58:01.178184 INFO::Processing subtree level 1
2025-10-03 19:58:01.313541 INFO::Adjusting the last 1 batches sequentially
2025-10-03 19:58:01.324355 INFO::Done
2025-10-03 19:58:01.32532 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:01.336394 INFO::ASW Batch was -0.0407626363047281 prior to batch effect correction and is now -0.0407626363047281 .
2025-10-03 19:58:01.339695 INFO::Total function execution time is 0.180877208709717 s and adjustment time is 0.149250030517578 s ( 82.51 )
2025-10-03 19:58:01.599259 INFO::Formatting Data.
2025-10-03 19:58:01.600431 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:01.601754 INFO::Removing potential empty rows and columns
2025-10-03 19:58:01.605416 INFO::Found 1000 missing values.
2025-10-03 19:58:01.631648 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:01.632649 INFO::Done
2025-10-03 19:58:01.633448 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:01.640404 INFO::Starting hierarchical adjustment
2025-10-03 19:58:01.641686 INFO::Found 10 batches.
2025-10-03 19:58:01.642397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:01.643245 INFO::Using default BPPARAM
2025-10-03 19:58:01.644007 INFO::Processing subtree level 1
2025-10-03 19:58:01.833571 INFO::Processing subtree level 2
2025-10-03 19:58:02.075416 INFO::Adjusting the last 1 batches sequentially
2025-10-03 19:58:02.12552 INFO::Done
2025-10-03 19:58:02.127512 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:02.144279 INFO::ASW Batch was 0.523688811465347 prior to batch effect correction and is now 0.523688811465347 .
2025-10-03 19:58:02.146682 INFO::ASW Label was 0.287736431580311 prior to batch effect correction and is now 0.287736431580311 .
2025-10-03 19:58:02.149809 INFO::Total function execution time is 0.550657033920288 s and adjustment time is 0.48393702507019 s ( 87.88 )
2025-10-03 19:58:02.151085 INFO::Formatting Data.
2025-10-03 19:58:02.152433 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:02.153762 INFO::Removing potential empty rows and columns
2025-10-03 19:58:02.15723 INFO::Found 1000 missing values.
2025-10-03 19:58:02.181922 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:02.182983 INFO::Done
2025-10-03 19:58:02.183821 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:02.191378 INFO::Starting hierarchical adjustment
2025-10-03 19:58:02.19313 INFO::Found 10 batches.
2025-10-03 19:58:03.315226 INFO::Set up parallel execution backend with 2 workers
2025-10-03 19:58:03.316157 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-03 19:58:04.642617 INFO::Adjusting the last 2 batches sequentially
2025-10-03 19:58:04.643767 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 19:58:04.663815 INFO::Done
2025-10-03 19:58:04.664757 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:04.670356 INFO::ASW Batch was 0.523688811465347 prior to batch effect correction and is now 0.523688811465347 .
2025-10-03 19:58:04.670998 INFO::ASW Label was 0.287736431580311 prior to batch effect correction and is now 0.287736431580311 .
2025-10-03 19:58:04.671674 INFO::Total function execution time is 2.52072596549988 s and adjustment time is 2.47096586227417 s ( 98.03 )
2025-10-03 19:58:04.975177 INFO::Formatting Data.
2025-10-03 19:58:04.977051 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:04.978388 INFO::Removing potential empty rows and columns
2025-10-03 19:58:04.979829 INFO::Found 0 missing values.
2025-10-03 19:58:04.98553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:04.986478 INFO::Done
2025-10-03 19:58:04.987302 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 19:58:04.991162 INFO::Starting hierarchical adjustment
2025-10-03 19:58:04.992202 INFO::Found 3 batches.
2025-10-03 19:58:04.992961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 19:58:04.993603 INFO::Using default BPPARAM
2025-10-03 19:58:04.99411 INFO::Processing subtree level 1
2025-10-03 19:58:05.167693 INFO::Adjusting the last 1 batches sequentially
2025-10-03 19:58:05.178889 INFO::Done
2025-10-03 19:58:05.180354 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 19:58:05.189978 INFO::ASW Batch was 0.219395776660295 prior to batch effect correction and is now -0.160059041630905 .
2025-10-03 19:58:05.191126 INFO::ASW Label was -0.182563466135437 prior to batch effect correction and is now 0.100138129203352 .
2025-10-03 19:58:05.194377 INFO::Total function execution time is 0.218530178070068 s and adjustment time is 0.186647176742554 s ( 85.41 )
2025-10-03 19:58:05.369207 INFO::Formatting Data.
2025-10-03 19:58:05.370284 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.371381 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.372345 INFO::Found 2 missing values.
2025-10-03 19:58:05.374848 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.375355 INFO::Done
2025-10-03 19:58:05.416673 INFO::Found NA in Reference column
2025-10-03 19:58:05.431693 INFO::Require at least two references per batch.
2025-10-03 19:58:05.459758 INFO::Formatting Data.
2025-10-03 19:58:05.460765 INFO::Recognized SummarizedExperiment
2025-10-03 19:58:05.461574 INFO::Typecasting input to dataframe.
2025-10-03 19:58:05.47269 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.474292 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.477539 INFO::Found 0 missing values.
2025-10-03 19:58:05.483905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.484574 INFO::Done
2025-10-03 19:58:05.504433 INFO::Formatting Data.
2025-10-03 19:58:05.505126 INFO::Recognized SummarizedExperiment
2025-10-03 19:58:05.505617 INFO::Typecasting input to dataframe.
2025-10-03 19:58:05.527637 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.529424 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.534327 INFO::Found 0 missing values.
2025-10-03 19:58:05.545672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.546366 INFO::Done
2025-10-03 19:58:05.56315 INFO::Formatting Data.
2025-10-03 19:58:05.564087 INFO::Recognized SummarizedExperiment
2025-10-03 19:58:05.56489 INFO::Typecasting input to dataframe.
2025-10-03 19:58:05.582223 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.583685 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.585278 INFO::Found 0 missing values.
2025-10-03 19:58:05.586632 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 19:58:05.592453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.593367 INFO::Done
2025-10-03 19:58:05.60755 INFO::Formatting Data.
2025-10-03 19:58:05.608322 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.609152 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.610023 INFO::Found 0 missing values.
2025-10-03 19:58:05.613106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.613822 INFO::Done
2025-10-03 19:58:05.632605 INFO::Formatting Data.
2025-10-03 19:58:05.633839 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.635192 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.636628 INFO::Found 0 missing values.
2025-10-03 19:58:05.641031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.641947 INFO::Done
2025-10-03 19:58:05.687375 INFO::Formatting Data.
2025-10-03 19:58:05.688728 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.689848 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.690993 INFO::Found 1 missing values.
2025-10-03 19:58:05.694026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.69458 INFO::Done
2025-10-03 19:58:05.727352 INFO::Formatting Data.
2025-10-03 19:58:05.728526 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.729878 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.731254 INFO::Found 2 missing values.
2025-10-03 19:58:05.732578 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 19:58:05.736059 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.73694 INFO::Done
2025-10-03 19:58:05.752253 INFO::Formatting Data.
2025-10-03 19:58:05.753222 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.754857 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.75602 INFO::Found 2 missing values.
2025-10-03 19:58:05.758456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.759053 INFO::Done
2025-10-03 19:58:05.77485 INFO::Formatting Data.
2025-10-03 19:58:05.776049 INFO::Typecasting input to dataframe.
2025-10-03 19:58:05.777369 INFO::Replacing NaNs with NAs.
2025-10-03 19:58:05.778702 INFO::Removing potential empty rows and columns
2025-10-03 19:58:05.779977 INFO::Found 0 missing values.
2025-10-03 19:58:05.783271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 19:58:05.784034 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.509 4.638 26.793
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.806 | 1.579 | 19.422 | |
| compute_asw | 0.032 | 0.001 | 0.034 | |
| count_existing | 0.016 | 0.002 | 0.018 | |
| generate_data_covariables | 0.012 | 0.001 | 0.014 | |
| generate_dataset | 0.012 | 0.001 | 0.013 | |