Yannis Schumann
| Snapshot Date: 2026-05-06 13:40 -0400 (Wed, 06 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_23 |
| git_last_commit: 0c9135c |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-07 11:36 -0400 (Thu, 07 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4990 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4723 |
| 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 172/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.8.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2026-05-06 19:02:43 -0400 (Wed, 06 May 2026) |
| EndedAt: 2026-05-06 19:03:15 -0400 (Wed, 06 May 2026) |
| EllapsedTime: 32.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-06 23:02:43 UTC
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.588 0.448 6.82
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.8.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-05-06 19:03:07.426816 INFO::Formatting Data.
2026-05-06 19:03:07.428495 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:07.432867 INFO::Removing potential empty rows and columns
2026-05-06 19:03:07.542599 INFO::Found 0 missing values.
2026-05-06 19:03:07.544649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:07.545036 INFO::Done
2026-05-06 19:03:07.545369 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:07.552404 INFO::Starting hierarchical adjustment
2026-05-06 19:03:07.552919 INFO::Found 3 batches.
2026-05-06 19:03:07.55323 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:07.553862 INFO::Using default BPPARAM
2026-05-06 19:03:07.554172 INFO::Processing subtree level 1
2026-05-06 19:03:07.627875 INFO::Adjusting the last 1 batches sequentially
2026-05-06 19:03:07.629048 INFO::Done
2026-05-06 19:03:07.629423 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:07.630674 INFO::ASW Batch was -0.114168941648813 prior to batch effect correction and is now -0.114168941648813 .
2026-05-06 19:03:07.631272 INFO::Total function execution time is 0.204785823822021 s and adjustment time is 0.0762100219726562 s ( 37.21 )
2026-05-06 19:03:07.638566 INFO::Formatting Data.
2026-05-06 19:03:07.639003 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:07.639525 INFO::Removing potential empty rows and columns
2026-05-06 19:03:07.640152 INFO::Found 0 missing values.
2026-05-06 19:03:07.640631 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 19:03:07.645602 INFO::Formatting Data.
2026-05-06 19:03:07.646062 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:07.646576 INFO::Removing potential empty rows and columns
2026-05-06 19:03:07.647321 INFO::Found 0 missing values.
2026-05-06 19:03:07.648053 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 19:03:07.655821 INFO::Formatting Data.
2026-05-06 19:03:07.656291 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:07.656769 INFO::Removing potential empty rows and columns
2026-05-06 19:03:07.657578 INFO::Found 0 missing values.
2026-05-06 19:03:07.658149 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 19:03:07.659917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:07.660271 INFO::Done
2026-05-06 19:03:07.660587 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:07.661512 INFO::Starting hierarchical adjustment
2026-05-06 19:03:07.661913 INFO::Found 2 batches.
2026-05-06 19:03:07.662224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:07.662595 INFO::Using default BPPARAM
2026-05-06 19:03:07.662892 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:07.663333 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 19:03:07.6719 INFO::Done
2026-05-06 19:03:07.672286 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:07.6731 INFO::ASW Batch was -0.0304863994783715 prior to batch effect correction and is now -0.129776685257722 .
2026-05-06 19:03:07.673464 INFO::Total function execution time is 0.0176889896392822 s and adjustment time is 0.0100359916687012 s ( 56.74 )
2026-05-06 19:03:07.674653 INFO::Formatting Data.
2026-05-06 19:03:07.674987 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:07.678116 INFO::Formatting Data.
2026-05-06 19:03:07.678437 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:07.678815 INFO::Removing potential empty rows and columns
2026-05-06 19:03:07.679268 INFO::Found 0 missing values.
2026-05-06 19:03:07.680383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:07.680782 INFO::Done
2026-05-06 19:03:07.681095 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:07.681923 INFO::Starting hierarchical adjustment
2026-05-06 19:03:07.682295 INFO::Found 2 batches.
2026-05-06 19:03:07.682643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:07.682957 INFO::Using default BPPARAM
2026-05-06 19:03:07.683219 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:07.683684 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:07.689584 INFO::Done
2026-05-06 19:03:07.689957 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:07.690707 INFO::ASW Batch was -0.0688100244356126 prior to batch effect correction and is now -0.130653907059657 .
2026-05-06 19:03:07.691173 INFO::Total function execution time is 0.0130391120910645 s and adjustment time is 0.00733518600463867 s ( 56.26 )
2026-05-06 19:03:07.691757 INFO::Formatting Data.
2026-05-06 19:03:07.692104 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:07.692486 INFO::Removing potential empty rows and columns
2026-05-06 19:03:07.692977 INFO::Found 0 missing values.
2026-05-06 19:03:07.694139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:07.694434 INFO::Done
2026-05-06 19:03:07.69475 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:07.695601 INFO::Starting hierarchical adjustment
2026-05-06 19:03:07.696003 INFO::Found 2 batches.
2026-05-06 19:03:07.69636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:07.696707 INFO::Using default BPPARAM
2026-05-06 19:03:07.697024 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:07.697417 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:07.702211 INFO::Done
2026-05-06 19:03:07.702539 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:07.703237 INFO::ASW Batch was -0.0688100244356126 prior to batch effect correction and is now -0.130653907059657 .
2026-05-06 19:03:07.703572 INFO::Total function execution time is 0.0118098258972168 s and adjustment time is 0.00625109672546387 s ( 52.93 )
2026-05-06 19:03:08.943325 INFO::Formatting Data.
2026-05-06 19:03:08.943868 INFO::Recognized SummarizedExperiment
2026-05-06 19:03:08.944223 INFO::Typecasting input to dataframe.
2026-05-06 19:03:08.955069 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:08.955693 INFO::Removing potential empty rows and columns
2026-05-06 19:03:08.957009 INFO::Found 0 missing values.
2026-05-06 19:03:08.95929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:08.959624 INFO::Done
2026-05-06 19:03:08.959891 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:08.961221 INFO::Starting hierarchical adjustment
2026-05-06 19:03:08.961579 INFO::Found 2 batches.
2026-05-06 19:03:08.961887 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:08.962353 INFO::Using default BPPARAM
2026-05-06 19:03:08.962639 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:08.963042 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 19:03:08.981368 INFO::Done
2026-05-06 19:03:08.981898 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:08.983675 INFO::ASW Batch was 0.0139335307124917 prior to batch effect correction and is now -0.0902721248357421 .
2026-05-06 19:03:08.984164 INFO::Total function execution time is 0.040942907333374 s and adjustment time is 0.0198068618774414 s ( 48.38 )
2026-05-06 19:03:08.991262 INFO::Formatting Data.
2026-05-06 19:03:08.991701 INFO::Recognized SummarizedExperiment
2026-05-06 19:03:08.992033 INFO::Typecasting input to dataframe.
2026-05-06 19:03:08.995558 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:08.996146 INFO::Removing potential empty rows and columns
2026-05-06 19:03:08.997453 INFO::Found 0 missing values.
2026-05-06 19:03:08.999838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.0002 INFO::Done
2026-05-06 19:03:09.000538 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.00232 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.002743 INFO::Found 2 batches.
2026-05-06 19:03:09.003079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.003454 INFO::Using default BPPARAM
2026-05-06 19:03:09.003829 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.004396 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 19:03:09.013066 INFO::Done
2026-05-06 19:03:09.013501 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.014955 INFO::ASW Batch was 0.00680072660055235 prior to batch effect correction and is now 0.00680072660055235 .
2026-05-06 19:03:09.015395 INFO::Total function execution time is 0.0241310596466064 s and adjustment time is 0.010357141494751 s ( 42.92 )
2026-05-06 19:03:09.023 INFO::Formatting Data.
2026-05-06 19:03:09.023456 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.023926 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.024411 INFO::Found 0 missing values.
2026-05-06 19:03:09.025702 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.026096 INFO::Done
2026-05-06 19:03:09.026584 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.027546 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.027929 INFO::Found 3 batches.
2026-05-06 19:03:09.028199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.028518 INFO::Using default BPPARAM
2026-05-06 19:03:09.028791 INFO::Processing subtree level 1
2026-05-06 19:03:09.188034 INFO::Adjusting the last 1 batches sequentially
2026-05-06 19:03:09.189288 INFO::Done
2026-05-06 19:03:09.189643 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.191082 INFO::ASW Batch was -0.0900131279594286 prior to batch effect correction and is now -0.173635501663721 .
2026-05-06 19:03:09.191656 INFO::Total function execution time is 0.168664932250977 s and adjustment time is 0.161403894424438 s ( 95.69 )
2026-05-06 19:03:09.199625 INFO::Skipping initial DF formatting
2026-05-06 19:03:09.200062 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.202557 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.203073 INFO::Found 5 batches.
2026-05-06 19:03:09.203448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.203843 INFO::Using default BPPARAM
2026-05-06 19:03:09.20419 INFO::Processing subtree level 1
2026-05-06 19:03:09.267533 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.268754 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 19:03:09.27637 INFO::Done
2026-05-06 19:03:09.276794 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.278742 INFO::ASW Batch was 0.524324856589096 prior to batch effect correction and is now 0.524324856589096 .
2026-05-06 19:03:09.279088 INFO::ASW Label was 0.376682881171435 prior to batch effect correction and is now 0.376682881171435 .
2026-05-06 19:03:09.279682 INFO::Total function execution time is 0.0800321102142334 s and adjustment time is 0.0733628273010254 s ( 91.67 )
2026-05-06 19:03:09.287794 INFO::Formatting Data.
2026-05-06 19:03:09.288212 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.288688 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.289188 INFO::Found 0 missing values.
2026-05-06 19:03:09.290525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.29086 INFO::Done
2026-05-06 19:03:09.291149 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.292311 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.292669 INFO::Found 5 batches.
2026-05-06 19:03:09.292938 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.29327 INFO::Using default BPPARAM
2026-05-06 19:03:09.293547 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.353973 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.35555 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.362723 INFO::Done
2026-05-06 19:03:09.363148 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.364501 INFO::ASW Batch was 0.20032385589402 prior to batch effect correction and is now -0.0792508790692311 .
2026-05-06 19:03:09.364853 INFO::ASW Label was 0.433491381130212 prior to batch effect correction and is now 0.892253765124332 .
2026-05-06 19:03:09.365277 INFO::Total function execution time is 0.0774948596954346 s and adjustment time is 0.0701000690460205 s ( 90.46 )
2026-05-06 19:03:09.365689 INFO::Formatting Data.
2026-05-06 19:03:09.365999 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.366411 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.366863 INFO::Found 0 missing values.
2026-05-06 19:03:09.368139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.368471 INFO::Done
2026-05-06 19:03:09.368779 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.369789 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.370152 INFO::Found 5 batches.
2026-05-06 19:03:09.370465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.37079 INFO::Using default BPPARAM
2026-05-06 19:03:09.371083 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.432296 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.433738 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.44387 INFO::Done
2026-05-06 19:03:09.444426 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.446109 INFO::ASW Batch was 0.20032385589402 prior to batch effect correction and is now -0.0792508790692311 .
2026-05-06 19:03:09.446484 INFO::ASW Label was 0.433491381130212 prior to batch effect correction and is now 0.892253765124332 .
2026-05-06 19:03:09.44695 INFO::Total function execution time is 0.0811958312988281 s and adjustment time is 0.0737409591674805 s ( 90.82 )
2026-05-06 19:03:09.454906 INFO::Formatting Data.
2026-05-06 19:03:09.455348 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.455801 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.456304 INFO::Found 0 missing values.
2026-05-06 19:03:09.457789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.458196 INFO::Done
2026-05-06 19:03:09.458602 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.459828 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.460213 INFO::Found 5 batches.
2026-05-06 19:03:09.460531 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.460907 INFO::Using default BPPARAM
2026-05-06 19:03:09.461223 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.518343 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.519817 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.528002 INFO::Done
2026-05-06 19:03:09.528511 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.530119 INFO::ASW Batch was 0.297295166389887 prior to batch effect correction and is now -0.0158748583355806 .
2026-05-06 19:03:09.530518 INFO::ASW Label was 0.385858881747824 prior to batch effect correction and is now 0.818919716569839 .
2026-05-06 19:03:09.53108 INFO::Total function execution time is 0.0761299133300781 s and adjustment time is 0.0678360462188721 s ( 89.11 )
2026-05-06 19:03:09.53153 INFO::Formatting Data.
2026-05-06 19:03:09.53184 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.532321 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.532904 INFO::Found 0 missing values.
2026-05-06 19:03:09.534407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.534779 INFO::Done
2026-05-06 19:03:09.535082 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.536328 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.536775 INFO::Found 5 batches.
2026-05-06 19:03:09.537108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.5375 INFO::Using default BPPARAM
2026-05-06 19:03:09.537811 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.599704 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.600871 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.608271 INFO::Done
2026-05-06 19:03:09.6087 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.610259 INFO::ASW Batch was 0.297295166389887 prior to batch effect correction and is now -0.0158748583355806 .
2026-05-06 19:03:09.610654 INFO::ASW Label was 0.385858881747824 prior to batch effect correction and is now 0.818919716569839 .
2026-05-06 19:03:09.611628 INFO::Total function execution time is 0.0799939632415771 s and adjustment time is 0.0715699195861816 s ( 89.47 )
2026-05-06 19:03:09.619092 INFO::Formatting Data.
2026-05-06 19:03:09.619549 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.620016 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.620603 INFO::Found 0 missing values.
2026-05-06 19:03:09.621592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.621887 INFO::Done
2026-05-06 19:03:09.622173 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.62334 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.623716 INFO::Found 2 batches.
2026-05-06 19:03:09.623984 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.624335 INFO::Using default BPPARAM
2026-05-06 19:03:09.624669 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.625081 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.629968 INFO::Done
2026-05-06 19:03:09.630306 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.631316 INFO::ASW Batch was 0.328619853061278 prior to batch effect correction and is now 0.00315667071220253 .
2026-05-06 19:03:09.631611 INFO::ASW Label was 0.665062684789612 prior to batch effect correction and is now 0.922623118140821 .
2026-05-06 19:03:09.631963 INFO::Total function execution time is 0.0129139423370361 s and adjustment time is 0.00630998611450195 s ( 48.86 )
2026-05-06 19:03:09.63246 INFO::Formatting Data.
2026-05-06 19:03:09.632762 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.633164 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.633603 INFO::Found 0 missing values.
2026-05-06 19:03:09.634629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.634943 INFO::Done
2026-05-06 19:03:09.63525 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.636737 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.637353 INFO::Found 2 batches.
2026-05-06 19:03:09.637743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.638103 INFO::Using default BPPARAM
2026-05-06 19:03:09.638384 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.638759 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 19:03:09.643345 INFO::Done
2026-05-06 19:03:09.643682 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.644702 INFO::ASW Batch was 0.328619853061278 prior to batch effect correction and is now 0.00315667071220253 .
2026-05-06 19:03:09.645035 INFO::ASW Label was 0.665062684789612 prior to batch effect correction and is now 0.922623118140821 .
2026-05-06 19:03:09.645408 INFO::Total function execution time is 0.0129408836364746 s and adjustment time is 0.00607109069824219 s ( 46.91 )
2026-05-06 19:03:09.650612 INFO::Formatting Data.
2026-05-06 19:03:09.651016 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.651413 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.651811 INFO::Found 0 missing values.
2026-05-06 19:03:09.652572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.652917 INFO::Done
2026-05-06 19:03:09.653209 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.653911 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.654221 INFO::Found 2 batches.
2026-05-06 19:03:09.654515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.654824 INFO::Using default BPPARAM
2026-05-06 19:03:09.655092 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.655507 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 19:03:09.667947 INFO::Done
2026-05-06 19:03:09.66836 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.669455 INFO::ASW Batch was -0.0122239205921904 prior to batch effect correction and is now -0.151524763686025 .
2026-05-06 19:03:09.670093 INFO::Total function execution time is 0.0192689895629883 s and adjustment time is 0.0137510299682617 s ( 71.36 )
2026-05-06 19:03:09.675669 INFO::Formatting Data.
2026-05-06 19:03:09.676118 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.676604 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.677089 INFO::Found 0 missing values.
2026-05-06 19:03:09.678133 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 19:03:09.680488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.681012 INFO::Done
2026-05-06 19:03:09.681391 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.682644 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.683109 INFO::Found 2 batches.
2026-05-06 19:03:09.68346 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.683823 INFO::Using default BPPARAM
2026-05-06 19:03:09.684107 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.684823 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 19:03:09.690655 INFO::Done
2026-05-06 19:03:09.691098 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.692503 INFO::ASW Batch was 0.60591310990344 prior to batch effect correction and is now -0.00798513196232433 .
2026-05-06 19:03:09.693203 INFO::ASW Label was 0.445516447650724 prior to batch effect correction and is now 0.869885770450782 .
2026-05-06 19:03:09.693817 INFO::Total function execution time is 0.0181479454040527 s and adjustment time is 0.0075991153717041 s ( 41.87 )
2026-05-06 19:03:09.694205 INFO::Formatting Data.
2026-05-06 19:03:09.694497 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.694948 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.695371 INFO::Found 0 missing values.
2026-05-06 19:03:09.695762 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 19:03:09.697269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.697665 INFO::Done
2026-05-06 19:03:09.697948 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.699018 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.699369 INFO::Found 2 batches.
2026-05-06 19:03:09.699658 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.69997 INFO::Using default BPPARAM
2026-05-06 19:03:09.700237 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:09.700651 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 19:03:09.706096 INFO::Done
2026-05-06 19:03:09.706548 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.707774 INFO::ASW Batch was 0.60591310990344 prior to batch effect correction and is now -0.00798513196232433 .
2026-05-06 19:03:09.708143 INFO::ASW Label was 0.445516447650724 prior to batch effect correction and is now 0.869885770450782 .
2026-05-06 19:03:09.708594 INFO::Total function execution time is 0.0143740177154541 s and adjustment time is 0.00676298141479492 s ( 47.05 )
2026-05-06 19:03:09.778583 INFO::Formatting Data.
2026-05-06 19:03:09.779291 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.779826 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.780323 INFO::Found 0 missing values.
2026-05-06 19:03:09.781387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.781696 INFO::Done
2026-05-06 19:03:09.781997 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.782845 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.783181 INFO::Found 3 batches.
2026-05-06 19:03:09.783485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.783775 INFO::Using default BPPARAM
2026-05-06 19:03:09.784064 INFO::Processing subtree level 1
2026-05-06 19:03:09.848319 INFO::Adjusting the last 1 batches sequentially
2026-05-06 19:03:09.850115 INFO::Done
2026-05-06 19:03:09.850569 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.851928 INFO::ASW Batch was -0.0338981557645181 prior to batch effect correction and is now -0.0338981557645181 .
2026-05-06 19:03:09.852682 INFO::Total function execution time is 0.0740962028503418 s and adjustment time is 0.0669808387756348 s ( 90.4 )
2026-05-06 19:03:09.853181 INFO::Formatting Data.
2026-05-06 19:03:09.853517 INFO::Typecasting input to dataframe.
2026-05-06 19:03:09.853894 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.854367 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.854908 INFO::Found 0 missing values.
2026-05-06 19:03:09.856021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.856395 INFO::Done
2026-05-06 19:03:09.856729 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.857565 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.857979 INFO::Found 3 batches.
2026-05-06 19:03:09.858363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.858764 INFO::Using default BPPARAM
2026-05-06 19:03:09.859122 INFO::Processing subtree level 1
2026-05-06 19:03:09.906572 INFO::Adjusting the last 1 batches sequentially
2026-05-06 19:03:09.908699 INFO::Done
2026-05-06 19:03:09.90914 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.910753 INFO::ASW Batch was -0.0338981557645181 prior to batch effect correction and is now -0.0338981557645181 .
2026-05-06 19:03:09.911556 INFO::Total function execution time is 0.0582451820373535 s and adjustment time is 0.0507421493530273 s ( 87.12 )
2026-05-06 19:03:09.918768 INFO::Formatting Data.
2026-05-06 19:03:09.919151 INFO::Typecasting input to dataframe.
2026-05-06 19:03:09.919543 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:09.920043 INFO::Removing potential empty rows and columns
2026-05-06 19:03:09.920607 INFO::Found 0 missing values.
2026-05-06 19:03:09.922126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:09.922518 INFO::Done
2026-05-06 19:03:09.922853 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:09.92373 INFO::Starting hierarchical adjustment
2026-05-06 19:03:09.924119 INFO::Found 3 batches.
2026-05-06 19:03:09.924395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:09.92478 INFO::Using default BPPARAM
2026-05-06 19:03:09.925136 INFO::Processing subtree level 1
2026-05-06 19:03:09.975181 INFO::Adjusting the last 1 batches sequentially
2026-05-06 19:03:09.976736 INFO::Done
2026-05-06 19:03:09.977158 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:09.978692 INFO::ASW Batch was -0.0818239209421145 prior to batch effect correction and is now -0.0818239209421145 .
2026-05-06 19:03:09.979351 INFO::Total function execution time is 0.0605762004852295 s and adjustment time is 0.0526759624481201 s ( 86.96 )
2026-05-06 19:03:10.057765 INFO::Formatting Data.
2026-05-06 19:03:10.058263 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:10.058857 INFO::Removing potential empty rows and columns
2026-05-06 19:03:10.060219 INFO::Found 1000 missing values.
2026-05-06 19:03:10.067619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:10.068122 INFO::Done
2026-05-06 19:03:10.068465 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:10.070864 INFO::Starting hierarchical adjustment
2026-05-06 19:03:10.071871 INFO::Found 10 batches.
2026-05-06 19:03:10.072306 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:10.072722 INFO::Using default BPPARAM
2026-05-06 19:03:10.073079 INFO::Processing subtree level 1
2026-05-06 19:03:10.150352 INFO::Processing subtree level 2
2026-05-06 19:03:10.213181 INFO::Adjusting the last 1 batches sequentially
2026-05-06 19:03:10.215295 INFO::Done
2026-05-06 19:03:10.215716 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:10.218962 INFO::ASW Batch was 0.520133719116375 prior to batch effect correction and is now 0.520133719116375 .
2026-05-06 19:03:10.21937 INFO::ASW Label was 0.297696031225044 prior to batch effect correction and is now 0.297696031225044 .
2026-05-06 19:03:10.220237 INFO::Total function execution time is 0.162414073944092 s and adjustment time is 0.143534898757935 s ( 88.38 )
2026-05-06 19:03:10.220796 INFO::Formatting Data.
2026-05-06 19:03:10.221185 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:10.223877 INFO::Removing potential empty rows and columns
2026-05-06 19:03:10.225312 INFO::Found 1000 missing values.
2026-05-06 19:03:10.232672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:10.233087 INFO::Done
2026-05-06 19:03:10.233419 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:10.235657 INFO::Starting hierarchical adjustment
2026-05-06 19:03:10.236124 INFO::Found 10 batches.
2026-05-06 19:03:10.846178 INFO::Set up parallel execution backend with 2 workers
2026-05-06 19:03:10.846759 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-06 19:03:11.44436 INFO::Adjusting the last 2 batches sequentially
2026-05-06 19:03:11.445184 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 19:03:11.450833 INFO::Done
2026-05-06 19:03:11.451171 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:11.453126 INFO::ASW Batch was 0.520133719116375 prior to batch effect correction and is now 0.520133719116375 .
2026-05-06 19:03:11.453421 INFO::ASW Label was 0.297696031225044 prior to batch effect correction and is now 0.297696031225044 .
2026-05-06 19:03:11.453758 INFO::Total function execution time is 1.23300099372864 s and adjustment time is 1.21477198600769 s ( 98.52 )
2026-05-06 19:03:11.581986 INFO::Formatting Data.
2026-05-06 19:03:11.582385 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.58345 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.584173 INFO::Found 0 missing values.
2026-05-06 19:03:11.585714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.58607 INFO::Done
2026-05-06 19:03:11.586414 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 19:03:11.587581 INFO::Starting hierarchical adjustment
2026-05-06 19:03:11.587993 INFO::Found 3 batches.
2026-05-06 19:03:11.588312 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 19:03:11.588648 INFO::Using default BPPARAM
2026-05-06 19:03:11.588944 INFO::Processing subtree level 1
2026-05-06 19:03:11.652601 INFO::Adjusting the last 1 batches sequentially
2026-05-06 19:03:11.654548 INFO::Done
2026-05-06 19:03:11.654942 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 19:03:11.656688 INFO::ASW Batch was 0.20898945467665 prior to batch effect correction and is now -0.132760883111438 .
2026-05-06 19:03:11.657074 INFO::ASW Label was -0.202237877433525 prior to batch effect correction and is now 0.0385957724685851 .
2026-05-06 19:03:11.657666 INFO::Total function execution time is 0.0756590366363525 s and adjustment time is 0.0665950775146484 s ( 88.02 )
2026-05-06 19:03:11.706472 INFO::Formatting Data.
2026-05-06 19:03:11.706925 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.707336 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.707831 INFO::Found 2 missing values.
2026-05-06 19:03:11.708852 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.709124 INFO::Done
2026-05-06 19:03:11.71968 INFO::Found NA in Reference column
2026-05-06 19:03:11.723304 INFO::Require at least two references per batch.
2026-05-06 19:03:11.732871 INFO::Formatting Data.
2026-05-06 19:03:11.733429 INFO::Recognized SummarizedExperiment
2026-05-06 19:03:11.733736 INFO::Typecasting input to dataframe.
2026-05-06 19:03:11.737902 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.73849 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.739888 INFO::Found 0 missing values.
2026-05-06 19:03:11.742329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.742644 INFO::Done
2026-05-06 19:03:11.74836 INFO::Formatting Data.
2026-05-06 19:03:11.74876 INFO::Recognized SummarizedExperiment
2026-05-06 19:03:11.749077 INFO::Typecasting input to dataframe.
2026-05-06 19:03:11.755435 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.756074 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.757492 INFO::Found 0 missing values.
2026-05-06 19:03:11.761748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.762173 INFO::Done
2026-05-06 19:03:11.768077 INFO::Formatting Data.
2026-05-06 19:03:11.768471 INFO::Recognized SummarizedExperiment
2026-05-06 19:03:11.768788 INFO::Typecasting input to dataframe.
2026-05-06 19:03:11.774269 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.774795 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.775276 INFO::Found 0 missing values.
2026-05-06 19:03:11.775686 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 19:03:11.777302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.77761 INFO::Done
2026-05-06 19:03:11.781823 INFO::Formatting Data.
2026-05-06 19:03:11.782191 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.782593 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.783016 INFO::Found 0 missing values.
2026-05-06 19:03:11.784037 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.784345 INFO::Done
2026-05-06 19:03:11.789289 INFO::Formatting Data.
2026-05-06 19:03:11.789705 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.790148 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.790646 INFO::Found 0 missing values.
2026-05-06 19:03:11.791662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.791984 INFO::Done
2026-05-06 19:03:11.80606 INFO::Formatting Data.
2026-05-06 19:03:11.80675 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.80734 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.807883 INFO::Found 1 missing values.
2026-05-06 19:03:11.808878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.809172 INFO::Done
2026-05-06 19:03:11.817207 INFO::Formatting Data.
2026-05-06 19:03:11.817696 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.818133 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.818601 INFO::Found 2 missing values.
2026-05-06 19:03:11.819023 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 19:03:11.819848 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.820145 INFO::Done
2026-05-06 19:03:11.824586 INFO::Formatting Data.
2026-05-06 19:03:11.824969 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.8254 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.82594 INFO::Found 2 missing values.
2026-05-06 19:03:11.826786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.82711 INFO::Done
2026-05-06 19:03:11.831935 INFO::Formatting Data.
2026-05-06 19:03:11.832391 INFO::Typecasting input to dataframe.
2026-05-06 19:03:11.832773 INFO::Replacing NaNs with NAs.
2026-05-06 19:03:11.83318 INFO::Removing potential empty rows and columns
2026-05-06 19:03:11.833615 INFO::Found 0 missing values.
2026-05-06 19:03:11.834861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 19:03:11.835169 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.065 2.125 9.364
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.588 | 0.448 | 6.820 | |
| compute_asw | 0.01 | 0.00 | 0.01 | |
| count_existing | 0.005 | 0.000 | 0.006 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.005 | 0.001 | 0.004 | |