Yannis Schumann
| Snapshot Date: 2025-10-13 13:45 -0400 (Mon, 13 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 2025-10-14 12:04 -0400 (Tue, 14 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" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
| 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 164/2346 | 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: 2025-10-13 20:18:16 -0400 (Mon, 13 Oct 2025) |
| EndedAt: 2025-10-13 20:19:47 -0400 (Mon, 13 Oct 2025) |
| EllapsedTime: 90.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 26.552 1.545 19.072
* 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")
2025-10-13 20:19:19.644268 INFO::Formatting Data.
2025-10-13 20:19:19.648788 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:19.660599 INFO::Removing potential empty rows and columns
2025-10-13 20:19:19.975358 INFO::Found 0 missing values.
2025-10-13 20:19:19.979049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:19.979906 INFO::Done
2025-10-13 20:19:19.980874 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:19.996635 INFO::Starting hierarchical adjustment
2025-10-13 20:19:19.997745 INFO::Found 3 batches.
2025-10-13 20:19:19.998338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:19.999856 INFO::Using default BPPARAM
2025-10-13 20:19:20.00071 INFO::Processing subtree level 1
2025-10-13 20:19:20.162648 INFO::Adjusting the last 1 batches sequentially
2025-10-13 20:19:20.169204 INFO::Done
2025-10-13 20:19:20.170616 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:20.177023 INFO::ASW Batch was -0.025488217662609 prior to batch effect correction and is now -0.025488217662609 .
2025-10-13 20:19:20.178432 INFO::Total function execution time is 0.535218000411987 s and adjustment time is 0.171622037887573 s ( 32.07 )
2025-10-13 20:19:20.199534 INFO::Formatting Data.
2025-10-13 20:19:20.20083 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:20.201982 INFO::Removing potential empty rows and columns
2025-10-13 20:19:20.203084 INFO::Found 0 missing values.
2025-10-13 20:19:20.20496 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.
2025-10-13 20:19:20.217237 INFO::Formatting Data.
2025-10-13 20:19:20.218136 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:20.219456 INFO::Removing potential empty rows and columns
2025-10-13 20:19:20.220645 INFO::Found 0 missing values.
2025-10-13 20:19:20.22155 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.
2025-10-13 20:19:20.243404 INFO::Formatting Data.
2025-10-13 20:19:20.244304 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:20.245391 INFO::Removing potential empty rows and columns
2025-10-13 20:19:20.246414 INFO::Found 0 missing values.
2025-10-13 20:19:20.247523 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.
2025-10-13 20:19:20.253305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:20.254176 INFO::Done
2025-10-13 20:19:20.254902 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:20.257764 INFO::Starting hierarchical adjustment
2025-10-13 20:19:20.258781 INFO::Found 2 batches.
2025-10-13 20:19:20.259537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:20.260432 INFO::Using default BPPARAM
2025-10-13 20:19:20.26115 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:20.262441 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 20:19:20.288129 INFO::Done
2025-10-13 20:19:20.288844 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:20.292087 INFO::ASW Batch was -0.104780666013351 prior to batch effect correction and is now -0.126407810138508 .
2025-10-13 20:19:20.293523 INFO::Total function execution time is 0.049994945526123 s and adjustment time is 0.0295350551605225 s ( 59.08 )
2025-10-13 20:19:20.297917 INFO::Formatting Data.
2025-10-13 20:19:20.298983 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:20.310347 INFO::Formatting Data.
2025-10-13 20:19:20.311452 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:20.312763 INFO::Removing potential empty rows and columns
2025-10-13 20:19:20.313777 INFO::Found 0 missing values.
2025-10-13 20:19:20.31739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:20.318204 INFO::Done
2025-10-13 20:19:20.318855 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:20.321393 INFO::Starting hierarchical adjustment
2025-10-13 20:19:20.322422 INFO::Found 2 batches.
2025-10-13 20:19:20.323228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:20.324099 INFO::Using default BPPARAM
2025-10-13 20:19:20.324792 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:20.325776 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 20:19:20.378401 INFO::Done
2025-10-13 20:19:20.379479 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:20.382437 INFO::ASW Batch was 0.0259894892829828 prior to batch effect correction and is now -0.130289865523493 .
2025-10-13 20:19:20.383614 INFO::Total function execution time is 0.0733070373535156 s and adjustment time is 0.0561380386352539 s ( 76.58 )
2025-10-13 20:19:20.384925 INFO::Formatting Data.
2025-10-13 20:19:20.385516 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:20.386304 INFO::Removing potential empty rows and columns
2025-10-13 20:19:20.387182 INFO::Found 0 missing values.
2025-10-13 20:19:20.390054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:20.390543 INFO::Done
2025-10-13 20:19:20.391004 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:20.393792 INFO::Starting hierarchical adjustment
2025-10-13 20:19:20.394879 INFO::Found 2 batches.
2025-10-13 20:19:20.395507 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:20.396049 INFO::Using default BPPARAM
2025-10-13 20:19:20.396513 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:20.397326 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 20:19:20.416988 INFO::Done
2025-10-13 20:19:20.417968 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:20.420898 INFO::ASW Batch was 0.0259894892829828 prior to batch effect correction and is now -0.130289865523493 .
2025-10-13 20:19:20.422085 INFO::Total function execution time is 0.0370960235595703 s and adjustment time is 0.0223121643066406 s ( 60.15 )
2025-10-13 20:19:23.754001 INFO::Formatting Data.
2025-10-13 20:19:23.754672 INFO::Recognized SummarizedExperiment
2025-10-13 20:19:23.755137 INFO::Typecasting input to dataframe.
2025-10-13 20:19:23.792708 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:23.793982 INFO::Removing potential empty rows and columns
2025-10-13 20:19:23.799256 INFO::Found 0 missing values.
2025-10-13 20:19:23.808125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:23.809089 INFO::Done
2025-10-13 20:19:23.809985 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:23.813649 INFO::Starting hierarchical adjustment
2025-10-13 20:19:23.814621 INFO::Found 2 batches.
2025-10-13 20:19:23.815222 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:23.816524 INFO::Using default BPPARAM
2025-10-13 20:19:23.817044 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:23.818152 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 20:19:23.886601 INFO::Done
2025-10-13 20:19:23.887619 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:23.893276 INFO::ASW Batch was 0.00865565807502339 prior to batch effect correction and is now -0.0863509744480882 .
2025-10-13 20:19:23.894691 INFO::Total function execution time is 0.140841960906982 s and adjustment time is 0.0721430778503418 s ( 51.22 )
2025-10-13 20:19:23.934021 INFO::Formatting Data.
2025-10-13 20:19:23.93485 INFO::Recognized SummarizedExperiment
2025-10-13 20:19:23.935391 INFO::Typecasting input to dataframe.
2025-10-13 20:19:23.94582 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:23.946954 INFO::Removing potential empty rows and columns
2025-10-13 20:19:23.95071 INFO::Found 0 missing values.
2025-10-13 20:19:24.06353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:24.067696 INFO::Done
2025-10-13 20:19:24.068476 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:24.083801 INFO::Starting hierarchical adjustment
2025-10-13 20:19:24.085238 INFO::Found 2 batches.
2025-10-13 20:19:24.086161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:24.087054 INFO::Using default BPPARAM
2025-10-13 20:19:24.087834 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:24.089513 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 20:19:24.440959 INFO::Done
2025-10-13 20:19:24.441677 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:24.450227 INFO::ASW Batch was 0.0152233171170377 prior to batch effect correction and is now 0.0152233171170377 .
2025-10-13 20:19:24.451152 INFO::Total function execution time is 0.517125844955444 s and adjustment time is 0.355998992919922 s ( 68.84 )
2025-10-13 20:19:25.470027 INFO::Formatting Data.
2025-10-13 20:19:25.470943 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:25.47235 INFO::Removing potential empty rows and columns
2025-10-13 20:19:25.473643 INFO::Found 0 missing values.
2025-10-13 20:19:25.476912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:25.477457 INFO::Done
2025-10-13 20:19:25.477942 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:25.501381 INFO::Starting hierarchical adjustment
2025-10-13 20:19:25.502661 INFO::Found 3 batches.
2025-10-13 20:19:25.503348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:25.503932 INFO::Using default BPPARAM
2025-10-13 20:19:25.515633 INFO::Processing subtree level 1
2025-10-13 20:19:27.565969 INFO::Adjusting the last 1 batches sequentially
2025-10-13 20:19:27.606198 INFO::Done
2025-10-13 20:19:27.608786 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:27.622678 INFO::ASW Batch was -0.0550430934258215 prior to batch effect correction and is now -0.149374718905523 .
2025-10-13 20:19:27.627878 INFO::Total function execution time is 2.1578221321106 s and adjustment time is 2.10354018211365 s ( 97.48 )
2025-10-13 20:19:27.656558 INFO::Skipping initial DF formatting
2025-10-13 20:19:27.657465 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:27.662809 INFO::Starting hierarchical adjustment
2025-10-13 20:19:27.664197 INFO::Found 5 batches.
2025-10-13 20:19:27.665174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:27.665904 INFO::Using default BPPARAM
2025-10-13 20:19:27.666411 INFO::Processing subtree level 1
2025-10-13 20:19:28.119341 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:28.122891 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 20:19:28.2019 INFO::Done
2025-10-13 20:19:28.204217 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:28.217276 INFO::ASW Batch was 0.551907170951909 prior to batch effect correction and is now 0.551907170951909 .
2025-10-13 20:19:28.218551 INFO::ASW Label was 0.387004005733712 prior to batch effect correction and is now 0.387004005733712 .
2025-10-13 20:19:28.224884 INFO::Total function execution time is 0.566635847091675 s and adjustment time is 0.538240909576416 s ( 94.99 )
2025-10-13 20:19:28.349403 INFO::Formatting Data.
2025-10-13 20:19:28.350668 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:28.352161 INFO::Removing potential empty rows and columns
2025-10-13 20:19:28.353743 INFO::Found 0 missing values.
2025-10-13 20:19:28.358527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:28.359353 INFO::Done
2025-10-13 20:19:28.360138 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:28.364449 INFO::Starting hierarchical adjustment
2025-10-13 20:19:28.365336 INFO::Found 5 batches.
2025-10-13 20:19:28.365905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:28.366517 INFO::Using default BPPARAM
2025-10-13 20:19:28.367065 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.
2025-10-13 20:19:28.648759 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:28.666456 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 20:19:28.735259 INFO::Done
2025-10-13 20:19:28.73623 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:28.744783 INFO::ASW Batch was 0.423201612951715 prior to batch effect correction and is now -0.0436100473771259 .
2025-10-13 20:19:28.746137 INFO::ASW Label was 0.31630661582234 prior to batch effect correction and is now 0.854317613323484 .
2025-10-13 20:19:28.747564 INFO::Total function execution time is 0.39824104309082 s and adjustment time is 0.370070934295654 s ( 92.93 )
2025-10-13 20:19:28.749906 INFO::Formatting Data.
2025-10-13 20:19:28.751163 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:28.752594 INFO::Removing potential empty rows and columns
2025-10-13 20:19:28.754688 INFO::Found 0 missing values.
2025-10-13 20:19:28.760335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:28.761002 INFO::Done
2025-10-13 20:19:28.761784 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:28.775562 INFO::Starting hierarchical adjustment
2025-10-13 20:19:28.776827 INFO::Found 5 batches.
2025-10-13 20:19:28.777454 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:28.780555 INFO::Using default BPPARAM
2025-10-13 20:19:28.782968 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.
2025-10-13 20:19:29.281114 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:29.299164 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 20:19:29.350508 INFO::Done
2025-10-13 20:19:29.351747 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:29.357091 INFO::ASW Batch was 0.423201612951715 prior to batch effect correction and is now -0.0436100473771259 .
2025-10-13 20:19:29.358378 INFO::ASW Label was 0.31630661582234 prior to batch effect correction and is now 0.854317613323484 .
2025-10-13 20:19:29.359836 INFO::Total function execution time is 0.610503911972046 s and adjustment time is 0.573831796646118 s ( 93.99 )
2025-10-13 20:19:29.383602 INFO::Formatting Data.
2025-10-13 20:19:29.38503 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:29.386576 INFO::Removing potential empty rows and columns
2025-10-13 20:19:29.388165 INFO::Found 0 missing values.
2025-10-13 20:19:29.393651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:29.394379 INFO::Done
2025-10-13 20:19:29.394954 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:29.398138 INFO::Starting hierarchical adjustment
2025-10-13 20:19:29.399169 INFO::Found 5 batches.
2025-10-13 20:19:29.39974 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:29.400357 INFO::Using default BPPARAM
2025-10-13 20:19:29.40104 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.
2025-10-13 20:19:29.584289 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:29.618608 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 20:19:29.659284 INFO::Done
2025-10-13 20:19:29.660512 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:29.66687 INFO::ASW Batch was 0.426755512554496 prior to batch effect correction and is now -0.0810002142625877 .
2025-10-13 20:19:29.66868 INFO::ASW Label was 0.209729430972078 prior to batch effect correction and is now 0.844242870847643 .
2025-10-13 20:19:29.670528 INFO::Total function execution time is 0.287165880203247 s and adjustment time is 0.260398149490356 s ( 90.68 )
2025-10-13 20:19:29.671763 INFO::Formatting Data.
2025-10-13 20:19:29.672903 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:29.674497 INFO::Removing potential empty rows and columns
2025-10-13 20:19:29.675621 INFO::Found 0 missing values.
2025-10-13 20:19:29.680649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:29.681298 INFO::Done
2025-10-13 20:19:29.682391 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:29.687018 INFO::Starting hierarchical adjustment
2025-10-13 20:19:29.688218 INFO::Found 5 batches.
2025-10-13 20:19:29.689076 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:29.689988 INFO::Using default BPPARAM
2025-10-13 20:19:29.690757 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.
2025-10-13 20:19:29.902485 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:29.916731 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 20:19:29.952988 INFO::Done
2025-10-13 20:19:29.954227 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:29.959956 INFO::ASW Batch was 0.426755512554496 prior to batch effect correction and is now -0.0810002142625877 .
2025-10-13 20:19:29.960682 INFO::ASW Label was 0.209729430972078 prior to batch effect correction and is now 0.844242870847643 .
2025-10-13 20:19:29.963233 INFO::Total function execution time is 0.291424036026001 s and adjustment time is 0.265007019042969 s ( 90.94 )
2025-10-13 20:19:29.983954 INFO::Formatting Data.
2025-10-13 20:19:29.985188 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:29.986841 INFO::Removing potential empty rows and columns
2025-10-13 20:19:29.98797 INFO::Found 0 missing values.
2025-10-13 20:19:29.991925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:29.992591 INFO::Done
2025-10-13 20:19:29.993418 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:29.998031 INFO::Starting hierarchical adjustment
2025-10-13 20:19:29.999257 INFO::Found 2 batches.
2025-10-13 20:19:30.000152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:30.00111 INFO::Using default BPPARAM
2025-10-13 20:19:30.001924 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:30.003373 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 20:19:30.02095 INFO::Done
2025-10-13 20:19:30.02192 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:30.026338 INFO::ASW Batch was 0.756547081692626 prior to batch effect correction and is now -0.0119418471367956 .
2025-10-13 20:19:30.027355 INFO::ASW Label was 0.27841988035469 prior to batch effect correction and is now 0.828331428624508 .
2025-10-13 20:19:30.028779 INFO::Total function execution time is 0.0447251796722412 s and adjustment time is 0.0219709873199463 s ( 49.12 )
2025-10-13 20:19:30.029819 INFO::Formatting Data.
2025-10-13 20:19:30.030461 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:30.03151 INFO::Removing potential empty rows and columns
2025-10-13 20:19:30.032966 INFO::Found 0 missing values.
2025-10-13 20:19:30.037358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:30.038275 INFO::Done
2025-10-13 20:19:30.038868 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:30.042623 INFO::Starting hierarchical adjustment
2025-10-13 20:19:30.043389 INFO::Found 2 batches.
2025-10-13 20:19:30.043912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:30.044488 INFO::Using default BPPARAM
2025-10-13 20:19:30.045262 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:30.046183 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 20:19:30.063571 INFO::Done
2025-10-13 20:19:30.064736 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:30.068972 INFO::ASW Batch was 0.756547081692626 prior to batch effect correction and is now -0.0119418471367956 .
2025-10-13 20:19:30.069924 INFO::ASW Label was 0.27841988035469 prior to batch effect correction and is now 0.828331428624508 .
2025-10-13 20:19:30.07091 INFO::Total function execution time is 0.0411269664764404 s and adjustment time is 0.0202789306640625 s ( 49.31 )
2025-10-13 20:19:30.090072 INFO::Formatting Data.
2025-10-13 20:19:30.091196 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:30.092471 INFO::Removing potential empty rows and columns
2025-10-13 20:19:30.093432 INFO::Found 0 missing values.
2025-10-13 20:19:30.096578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:30.097165 INFO::Done
2025-10-13 20:19:30.097749 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:30.100279 INFO::Starting hierarchical adjustment
2025-10-13 20:19:30.100977 INFO::Found 2 batches.
2025-10-13 20:19:30.101967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:30.103038 INFO::Using default BPPARAM
2025-10-13 20:19:30.103837 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:30.105192 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 20:19:30.145204 INFO::Done
2025-10-13 20:19:30.145894 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:30.148586 INFO::ASW Batch was 0.00129011153845258 prior to batch effect correction and is now -0.1067351892164 .
2025-10-13 20:19:30.149798 INFO::Total function execution time is 0.0598170757293701 s and adjustment time is 0.0443220138549805 s ( 74.1 )
2025-10-13 20:19:30.167057 INFO::Formatting Data.
2025-10-13 20:19:30.167898 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:30.168748 INFO::Removing potential empty rows and columns
2025-10-13 20:19:30.170294 INFO::Found 0 missing values.
2025-10-13 20:19:30.171727 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.
2025-10-13 20:19:30.17811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:30.178853 INFO::Done
2025-10-13 20:19:30.179843 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:30.184337 INFO::Starting hierarchical adjustment
2025-10-13 20:19:30.18556 INFO::Found 2 batches.
2025-10-13 20:19:30.186425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:30.187317 INFO::Using default BPPARAM
2025-10-13 20:19:30.188091 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:30.189492 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 20:19:30.211813 INFO::Done
2025-10-13 20:19:30.212831 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:30.216617 INFO::ASW Batch was 0.569886277258243 prior to batch effect correction and is now -0.021268790042934 .
2025-10-13 20:19:30.217466 INFO::ASW Label was 0.362208211139268 prior to batch effect correction and is now 0.906032132258707 .
2025-10-13 20:19:30.218421 INFO::Total function execution time is 0.0515141487121582 s and adjustment time is 0.0265178680419922 s ( 51.48 )
2025-10-13 20:19:30.219214 INFO::Formatting Data.
2025-10-13 20:19:30.219806 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:30.220701 INFO::Removing potential empty rows and columns
2025-10-13 20:19:30.22163 INFO::Found 0 missing values.
2025-10-13 20:19:30.222521 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.
2025-10-13 20:19:30.227635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:30.228289 INFO::Done
2025-10-13 20:19:30.229046 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:30.233146 INFO::Starting hierarchical adjustment
2025-10-13 20:19:30.23426 INFO::Found 2 batches.
2025-10-13 20:19:30.235043 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:30.235937 INFO::Using default BPPARAM
2025-10-13 20:19:30.236674 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:30.23796 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 20:19:30.255926 INFO::Done
2025-10-13 20:19:30.256941 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:30.261158 INFO::ASW Batch was 0.569886277258243 prior to batch effect correction and is now -0.021268790042934 .
2025-10-13 20:19:30.262095 INFO::ASW Label was 0.362208211139268 prior to batch effect correction and is now 0.906032132258707 .
2025-10-13 20:19:30.263242 INFO::Total function execution time is 0.0439789295196533 s and adjustment time is 0.0218648910522461 s ( 49.72 )
2025-10-13 20:19:30.562556 INFO::Formatting Data.
2025-10-13 20:19:30.563859 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:30.565239 INFO::Removing potential empty rows and columns
2025-10-13 20:19:30.566571 INFO::Found 0 missing values.
2025-10-13 20:19:30.570051 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:30.570655 INFO::Done
2025-10-13 20:19:30.571164 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:30.573438 INFO::Starting hierarchical adjustment
2025-10-13 20:19:30.574273 INFO::Found 3 batches.
2025-10-13 20:19:30.574769 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:30.575509 INFO::Using default BPPARAM
2025-10-13 20:19:30.576246 INFO::Processing subtree level 1
2025-10-13 20:19:30.7328 INFO::Adjusting the last 1 batches sequentially
2025-10-13 20:19:30.747552 INFO::Done
2025-10-13 20:19:30.749721 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:30.765417 INFO::ASW Batch was 0.0191658285851763 prior to batch effect correction and is now 0.0191658285851763 .
2025-10-13 20:19:30.77146 INFO::Total function execution time is 0.208910226821899 s and adjustment time is 0.173369884490967 s ( 82.99 )
2025-10-13 20:19:30.773246 INFO::Formatting Data.
2025-10-13 20:19:30.774599 INFO::Typecasting input to dataframe.
2025-10-13 20:19:30.775805 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:30.779063 INFO::Removing potential empty rows and columns
2025-10-13 20:19:30.781071 INFO::Found 0 missing values.
2025-10-13 20:19:30.786269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:30.787168 INFO::Done
2025-10-13 20:19:30.787934 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:30.790654 INFO::Starting hierarchical adjustment
2025-10-13 20:19:30.791574 INFO::Found 3 batches.
2025-10-13 20:19:30.792222 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:30.793496 INFO::Using default BPPARAM
2025-10-13 20:19:30.794847 INFO::Processing subtree level 1
2025-10-13 20:19:31.038252 INFO::Adjusting the last 1 batches sequentially
2025-10-13 20:19:31.283227 INFO::Done
2025-10-13 20:19:31.286681 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:31.300173 INFO::ASW Batch was 0.0191658285851763 prior to batch effect correction and is now 0.0191658285851763 .
2025-10-13 20:19:31.306745 INFO::Total function execution time is 0.533667802810669 s and adjustment time is 0.491691112518311 s ( 92.13 )
2025-10-13 20:19:31.329853 INFO::Formatting Data.
2025-10-13 20:19:31.330786 INFO::Typecasting input to dataframe.
2025-10-13 20:19:31.332116 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:31.333506 INFO::Removing potential empty rows and columns
2025-10-13 20:19:31.335678 INFO::Found 0 missing values.
2025-10-13 20:19:31.339786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:31.340432 INFO::Done
2025-10-13 20:19:31.340967 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:31.34307 INFO::Starting hierarchical adjustment
2025-10-13 20:19:31.344304 INFO::Found 3 batches.
2025-10-13 20:19:31.34485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:31.345826 INFO::Using default BPPARAM
2025-10-13 20:19:31.346355 INFO::Processing subtree level 1
2025-10-13 20:19:31.496136 INFO::Adjusting the last 1 batches sequentially
2025-10-13 20:19:31.508752 INFO::Done
2025-10-13 20:19:31.5095 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:31.521233 INFO::ASW Batch was -0.0234756287553902 prior to batch effect correction and is now -0.0234756287553902 .
2025-10-13 20:19:31.524851 INFO::Total function execution time is 0.195593118667603 s and adjustment time is 0.164561986923218 s ( 84.13 )
2025-10-13 20:19:31.846376 INFO::Formatting Data.
2025-10-13 20:19:31.847195 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:31.848917 INFO::Removing potential empty rows and columns
2025-10-13 20:19:31.852873 INFO::Found 1000 missing values.
2025-10-13 20:19:31.877826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:31.878624 INFO::Done
2025-10-13 20:19:31.879294 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:31.88596 INFO::Starting hierarchical adjustment
2025-10-13 20:19:31.886965 INFO::Found 10 batches.
2025-10-13 20:19:31.887773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:31.888649 INFO::Using default BPPARAM
2025-10-13 20:19:31.889389 INFO::Processing subtree level 1
2025-10-13 20:19:32.07075 INFO::Processing subtree level 2
2025-10-13 20:19:32.32076 INFO::Adjusting the last 1 batches sequentially
2025-10-13 20:19:32.356017 INFO::Done
2025-10-13 20:19:32.359023 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:32.379279 INFO::ASW Batch was 0.498717002757114 prior to batch effect correction and is now 0.498717002757114 .
2025-10-13 20:19:32.380129 INFO::ASW Label was 0.315697647230721 prior to batch effect correction and is now 0.315697647230721 .
2025-10-13 20:19:32.386364 INFO::Total function execution time is 0.538653135299683 s and adjustment time is 0.469280958175659 s ( 87.12 )
2025-10-13 20:19:32.388459 INFO::Formatting Data.
2025-10-13 20:19:32.389666 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:32.391472 INFO::Removing potential empty rows and columns
2025-10-13 20:19:32.394283 INFO::Found 1000 missing values.
2025-10-13 20:19:32.425676 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:32.42693 INFO::Done
2025-10-13 20:19:32.427791 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:32.447811 INFO::Starting hierarchical adjustment
2025-10-13 20:19:32.449942 INFO::Found 10 batches.
2025-10-13 20:19:33.602247 INFO::Set up parallel execution backend with 2 workers
2025-10-13 20:19:33.60316 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-13 20:19:34.977772 INFO::Adjusting the last 2 batches sequentially
2025-10-13 20:19:34.978947 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 20:19:34.996748 INFO::Done
2025-10-13 20:19:34.997362 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:35.002996 INFO::ASW Batch was 0.498717002757114 prior to batch effect correction and is now 0.498717002757114 .
2025-10-13 20:19:35.003863 INFO::ASW Label was 0.315697647230721 prior to batch effect correction and is now 0.315697647230721 .
2025-10-13 20:19:35.004889 INFO::Total function execution time is 2.61654496192932 s and adjustment time is 2.54739308357239 s ( 97.36 )
2025-10-13 20:19:35.235694 INFO::Formatting Data.
2025-10-13 20:19:35.237021 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:35.238661 INFO::Removing potential empty rows and columns
2025-10-13 20:19:35.240589 INFO::Found 0 missing values.
2025-10-13 20:19:35.247499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:35.248798 INFO::Done
2025-10-13 20:19:35.249848 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 20:19:35.254421 INFO::Starting hierarchical adjustment
2025-10-13 20:19:35.255416 INFO::Found 3 batches.
2025-10-13 20:19:35.25638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 20:19:35.257659 INFO::Using default BPPARAM
2025-10-13 20:19:35.258592 INFO::Processing subtree level 1
2025-10-13 20:19:35.419398 INFO::Adjusting the last 1 batches sequentially
2025-10-13 20:19:35.425879 INFO::Done
2025-10-13 20:19:35.427013 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 20:19:35.432479 INFO::ASW Batch was 0.109779835151646 prior to batch effect correction and is now -0.105470362649033 .
2025-10-13 20:19:35.433599 INFO::ASW Label was -0.186951365280988 prior to batch effect correction and is now 0.0499283891198144 .
2025-10-13 20:19:35.435331 INFO::Total function execution time is 0.1995849609375 s and adjustment time is 0.170639038085938 s ( 85.5 )
2025-10-13 20:19:35.672618 INFO::Formatting Data.
2025-10-13 20:19:35.673981 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:35.675468 INFO::Removing potential empty rows and columns
2025-10-13 20:19:35.677483 INFO::Found 2 missing values.
2025-10-13 20:19:35.683008 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:35.684135 INFO::Done
2025-10-13 20:19:35.745922 INFO::Found NA in Reference column
2025-10-13 20:19:35.76423 INFO::Require at least two references per batch.
2025-10-13 20:19:35.804939 INFO::Formatting Data.
2025-10-13 20:19:35.806329 INFO::Recognized SummarizedExperiment
2025-10-13 20:19:35.807489 INFO::Typecasting input to dataframe.
2025-10-13 20:19:35.825367 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:35.827486 INFO::Removing potential empty rows and columns
2025-10-13 20:19:35.834521 INFO::Found 0 missing values.
2025-10-13 20:19:35.846835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:35.848024 INFO::Done
2025-10-13 20:19:35.876757 INFO::Formatting Data.
2025-10-13 20:19:35.878034 INFO::Recognized SummarizedExperiment
2025-10-13 20:19:35.879144 INFO::Typecasting input to dataframe.
2025-10-13 20:19:35.908795 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:35.911068 INFO::Removing potential empty rows and columns
2025-10-13 20:19:35.921085 INFO::Found 0 missing values.
2025-10-13 20:19:35.940197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:35.9414 INFO::Done
2025-10-13 20:19:35.967539 INFO::Formatting Data.
2025-10-13 20:19:35.968875 INFO::Recognized SummarizedExperiment
2025-10-13 20:19:35.970024 INFO::Typecasting input to dataframe.
2025-10-13 20:19:36.000241 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:36.00167 INFO::Removing potential empty rows and columns
2025-10-13 20:19:36.0035 INFO::Found 0 missing values.
2025-10-13 20:19:36.004819 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.
2025-10-13 20:19:36.012301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:36.013399 INFO::Done
2025-10-13 20:19:36.033148 INFO::Formatting Data.
2025-10-13 20:19:36.034483 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:36.036041 INFO::Removing potential empty rows and columns
2025-10-13 20:19:36.03782 INFO::Found 0 missing values.
2025-10-13 20:19:36.042896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:36.044064 INFO::Done
2025-10-13 20:19:36.06652 INFO::Formatting Data.
2025-10-13 20:19:36.067894 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:36.0695 INFO::Removing potential empty rows and columns
2025-10-13 20:19:36.071423 INFO::Found 0 missing values.
2025-10-13 20:19:36.077213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:36.078363 INFO::Done
2025-10-13 20:19:36.140425 INFO::Formatting Data.
2025-10-13 20:19:36.141751 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:36.143676 INFO::Removing potential empty rows and columns
2025-10-13 20:19:36.145862 INFO::Found 1 missing values.
2025-10-13 20:19:36.15095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:36.152142 INFO::Done
2025-10-13 20:19:36.192242 INFO::Formatting Data.
2025-10-13 20:19:36.193497 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:36.195178 INFO::Removing potential empty rows and columns
2025-10-13 20:19:36.197056 INFO::Found 2 missing values.
2025-10-13 20:19:36.198811 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.
2025-10-13 20:19:36.203203 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:36.204072 INFO::Done
2025-10-13 20:19:36.223467 INFO::Formatting Data.
2025-10-13 20:19:36.224803 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:36.226506 INFO::Removing potential empty rows and columns
2025-10-13 20:19:36.228511 INFO::Found 2 missing values.
2025-10-13 20:19:36.231533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:36.232709 INFO::Done
2025-10-13 20:19:36.255468 INFO::Formatting Data.
2025-10-13 20:19:36.256875 INFO::Typecasting input to dataframe.
2025-10-13 20:19:36.258763 INFO::Replacing NaNs with NAs.
2025-10-13 20:19:36.26058 INFO::Removing potential empty rows and columns
2025-10-13 20:19:36.262849 INFO::Found 0 missing values.
2025-10-13 20:19:36.268048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 20:19:36.269124 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.876 5.277 30.180
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.552 | 1.545 | 19.072 | |
| compute_asw | 0.030 | 0.002 | 0.032 | |
| count_existing | 0.017 | 0.002 | 0.019 | |
| generate_data_covariables | 0.015 | 0.002 | 0.017 | |
| generate_dataset | 0.014 | 0.001 | 0.015 | |