Yannis Schumann
| Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 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 2025-09-03 12:06 -0400 (Wed, 03 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4826 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 163/2321 | 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: 2025-09-02 18:18:18 -0400 (Tue, 02 Sep 2025) |
| EndedAt: 2025-09-02 18:18:48 -0400 (Tue, 02 Sep 2025) |
| EllapsedTime: 30.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.653 0.404 6.932
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-09-02 18:18:41.304837 INFO::Formatting Data.
2025-09-02 18:18:41.306262 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:41.310234 INFO::Removing potential empty rows and columns
2025-09-02 18:18:41.413634 INFO::Found 0 missing values.
2025-09-02 18:18:41.414798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:41.415026 INFO::Done
2025-09-02 18:18:41.415199 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:41.421027 INFO::Starting hierarchical adjustment
2025-09-02 18:18:41.421367 INFO::Found 3 batches.
2025-09-02 18:18:41.421554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:41.422011 INFO::Using default BPPARAM
2025-09-02 18:18:41.422198 INFO::Processing subtree level 1
2025-09-02 18:18:41.470221 INFO::Adjusting the last 1 batches sequentially
2025-09-02 18:18:41.471639 INFO::Done
2025-09-02 18:18:41.471919 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:41.473819 INFO::ASW Batch was 0.0659749243086896 prior to batch effect correction and is now 0.0659749243086896 .
2025-09-02 18:18:41.474437 INFO::Total function execution time is 0.169822216033936 s and adjustment time is 0.0503320693969727 s ( 29.64 )
2025-09-02 18:18:41.481714 INFO::Formatting Data.
2025-09-02 18:18:41.481965 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:41.482256 INFO::Removing potential empty rows and columns
2025-09-02 18:18:41.482647 INFO::Found 0 missing values.
2025-09-02 18:18:41.482956 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.
2025-09-02 18:18:41.486991 INFO::Formatting Data.
2025-09-02 18:18:41.487242 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:41.487525 INFO::Removing potential empty rows and columns
2025-09-02 18:18:41.487853 INFO::Found 0 missing values.
2025-09-02 18:18:41.488137 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.
2025-09-02 18:18:41.493711 INFO::Formatting Data.
2025-09-02 18:18:41.493956 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:41.494231 INFO::Removing potential empty rows and columns
2025-09-02 18:18:41.494553 INFO::Found 0 missing values.
2025-09-02 18:18:41.494822 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.
2025-09-02 18:18:41.496211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:41.496388 INFO::Done
2025-09-02 18:18:41.496566 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:41.497865 INFO::Starting hierarchical adjustment
2025-09-02 18:18:41.498133 INFO::Found 2 batches.
2025-09-02 18:18:41.498334 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:41.500268 INFO::Using default BPPARAM
2025-09-02 18:18:41.500516 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:41.500866 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 18:18:41.510789 INFO::Done
2025-09-02 18:18:41.511043 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:41.511765 INFO::ASW Batch was -0.035051990357704 prior to batch effect correction and is now -0.129692613553313 .
2025-09-02 18:18:41.51203 INFO::Total function execution time is 0.0183329582214355 s and adjustment time is 0.0126960277557373 s ( 69.25 )
2025-09-02 18:18:41.513147 INFO::Formatting Data.
2025-09-02 18:18:41.513354 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:41.517559 INFO::Formatting Data.
2025-09-02 18:18:41.517828 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:41.518112 INFO::Removing potential empty rows and columns
2025-09-02 18:18:41.518508 INFO::Found 0 missing values.
2025-09-02 18:18:41.519444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:41.519618 INFO::Done
2025-09-02 18:18:41.519786 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:41.520582 INFO::Starting hierarchical adjustment
2025-09-02 18:18:41.520815 INFO::Found 2 batches.
2025-09-02 18:18:41.521004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:41.521195 INFO::Using default BPPARAM
2025-09-02 18:18:41.521426 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:41.521725 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 18:18:41.543752 INFO::Done
2025-09-02 18:18:41.544011 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:41.544689 INFO::ASW Batch was 0.0294531699701434 prior to batch effect correction and is now -0.101256057676579 .
2025-09-02 18:18:41.544949 INFO::Total function execution time is 0.0274059772491455 s and adjustment time is 0.0229649543762207 s ( 83.8 )
2025-09-02 18:18:41.545282 INFO::Formatting Data.
2025-09-02 18:18:41.545453 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:41.54571 INFO::Removing potential empty rows and columns
2025-09-02 18:18:41.546048 INFO::Found 0 missing values.
2025-09-02 18:18:41.546879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:41.547057 INFO::Done
2025-09-02 18:18:41.547218 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:41.547806 INFO::Starting hierarchical adjustment
2025-09-02 18:18:41.54802 INFO::Found 2 batches.
2025-09-02 18:18:41.548185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:41.54837 INFO::Using default BPPARAM
2025-09-02 18:18:41.548519 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:41.548803 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 18:18:41.553915 INFO::Done
2025-09-02 18:18:41.554131 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:41.554816 INFO::ASW Batch was 0.0294531699701434 prior to batch effect correction and is now -0.101256057676579 .
2025-09-02 18:18:41.555059 INFO::Total function execution time is 0.00977182388305664 s and adjustment time is 0.00593209266662598 s ( 60.71 )
2025-09-02 18:18:42.702256 INFO::Formatting Data.
2025-09-02 18:18:42.702542 INFO::Recognized SummarizedExperiment
2025-09-02 18:18:42.702716 INFO::Typecasting input to dataframe.
2025-09-02 18:18:42.71327 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:42.713751 INFO::Removing potential empty rows and columns
2025-09-02 18:18:42.714955 INFO::Found 0 missing values.
2025-09-02 18:18:42.71704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:42.717224 INFO::Done
2025-09-02 18:18:42.717373 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:42.718544 INFO::Starting hierarchical adjustment
2025-09-02 18:18:42.718751 INFO::Found 2 batches.
2025-09-02 18:18:42.718903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:42.719216 INFO::Using default BPPARAM
2025-09-02 18:18:42.719363 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:42.719642 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 18:18:42.7361 INFO::Done
2025-09-02 18:18:42.73629 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:42.737369 INFO::ASW Batch was -0.0170486016782666 prior to batch effect correction and is now -0.0958154547360296 .
2025-09-02 18:18:42.737623 INFO::Total function execution time is 0.0354688167572021 s and adjustment time is 0.0173912048339844 s ( 49.03 )
2025-09-02 18:18:42.74356 INFO::Formatting Data.
2025-09-02 18:18:42.743757 INFO::Recognized SummarizedExperiment
2025-09-02 18:18:42.743913 INFO::Typecasting input to dataframe.
2025-09-02 18:18:42.746686 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:42.747012 INFO::Removing potential empty rows and columns
2025-09-02 18:18:42.748075 INFO::Found 0 missing values.
2025-09-02 18:18:42.750132 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:42.750296 INFO::Done
2025-09-02 18:18:42.750448 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:42.751558 INFO::Starting hierarchical adjustment
2025-09-02 18:18:42.751765 INFO::Found 2 batches.
2025-09-02 18:18:42.751912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:42.752098 INFO::Using default BPPARAM
2025-09-02 18:18:42.752239 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:42.752518 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 18:18:42.760056 INFO::Done
2025-09-02 18:18:42.76026 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:42.761376 INFO::ASW Batch was -0.00332316865432238 prior to batch effect correction and is now -0.00332316865432238 .
2025-09-02 18:18:42.761634 INFO::Total function execution time is 0.0180609226226807 s and adjustment time is 0.00833010673522949 s ( 46.12 )
2025-09-02 18:18:42.767887 INFO::Formatting Data.
2025-09-02 18:18:42.768099 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:42.768357 INFO::Removing potential empty rows and columns
2025-09-02 18:18:42.768648 INFO::Found 0 missing values.
2025-09-02 18:18:42.769469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:42.769621 INFO::Done
2025-09-02 18:18:42.769762 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:42.77032 INFO::Starting hierarchical adjustment
2025-09-02 18:18:42.770513 INFO::Found 3 batches.
2025-09-02 18:18:42.770658 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:42.770827 INFO::Using default BPPARAM
2025-09-02 18:18:42.770967 INFO::Processing subtree level 1
2025-09-02 18:18:42.841694 INFO::Adjusting the last 1 batches sequentially
2025-09-02 18:18:42.842975 INFO::Done
2025-09-02 18:18:42.843269 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:42.844873 INFO::ASW Batch was 0.0154986032121162 prior to batch effect correction and is now -0.153323719049225 .
2025-09-02 18:18:42.845883 INFO::Total function execution time is 0.0778899192810059 s and adjustment time is 0.0724859237670898 s ( 93.06 )
2025-09-02 18:18:42.853301 INFO::Skipping initial DF formatting
2025-09-02 18:18:42.853563 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:42.854902 INFO::Starting hierarchical adjustment
2025-09-02 18:18:42.855174 INFO::Found 5 batches.
2025-09-02 18:18:42.855364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:42.855744 INFO::Using default BPPARAM
2025-09-02 18:18:42.855917 INFO::Processing subtree level 1
2025-09-02 18:18:42.966961 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:42.970581 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 18:18:42.98044 INFO::Done
2025-09-02 18:18:42.980673 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:42.98306 INFO::ASW Batch was 0.544784680192087 prior to batch effect correction and is now 0.544784680192087 .
2025-09-02 18:18:42.983431 INFO::ASW Label was 0.393425933548266 prior to batch effect correction and is now 0.393425933548266 .
2025-09-02 18:18:42.984453 INFO::Total function execution time is 0.13102388381958 s and adjustment time is 0.125320911407471 s ( 95.65 )
2025-09-02 18:18:43.015705 INFO::Formatting Data.
2025-09-02 18:18:43.015956 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.016257 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.016561 INFO::Found 0 missing values.
2025-09-02 18:18:43.017752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.017961 INFO::Done
2025-09-02 18:18:43.018124 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.01915 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.019481 INFO::Found 5 batches.
2025-09-02 18:18:43.01968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.01988 INFO::Using default BPPARAM
2025-09-02 18:18:43.020029 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.
2025-09-02 18:18:43.081431 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.083069 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 18:18:43.09286 INFO::Done
2025-09-02 18:18:43.093189 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.095 INFO::ASW Batch was 0.553054166824449 prior to batch effect correction and is now 0.0257459889577173 .
2025-09-02 18:18:43.095247 INFO::ASW Label was 0.218945320086754 prior to batch effect correction and is now 0.709370306937443 .
2025-09-02 18:18:43.09592 INFO::Total function execution time is 0.0802090167999268 s and adjustment time is 0.0733129978179932 s ( 91.4 )
2025-09-02 18:18:43.096411 INFO::Formatting Data.
2025-09-02 18:18:43.096639 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.097035 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.097537 INFO::Found 0 missing values.
2025-09-02 18:18:43.099394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.099631 INFO::Done
2025-09-02 18:18:43.099821 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.10095 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.101381 INFO::Found 5 batches.
2025-09-02 18:18:43.101572 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.101993 INFO::Using default BPPARAM
2025-09-02 18:18:43.102294 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.
2025-09-02 18:18:43.163002 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.164828 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 18:18:43.174836 INFO::Done
2025-09-02 18:18:43.175106 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.176446 INFO::ASW Batch was 0.553054166824449 prior to batch effect correction and is now 0.0257459889577173 .
2025-09-02 18:18:43.176647 INFO::ASW Label was 0.218945320086754 prior to batch effect correction and is now 0.709370306937443 .
2025-09-02 18:18:43.178375 INFO::Total function execution time is 0.0814440250396729 s and adjustment time is 0.0736210346221924 s ( 90.39 )
2025-09-02 18:18:43.185792 INFO::Formatting Data.
2025-09-02 18:18:43.186057 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.186365 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.186761 INFO::Found 0 missing values.
2025-09-02 18:18:43.188123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.18832 INFO::Done
2025-09-02 18:18:43.188523 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.189624 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.189889 INFO::Found 5 batches.
2025-09-02 18:18:43.190249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.19049 INFO::Using default BPPARAM
2025-09-02 18:18:43.190762 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.
2025-09-02 18:18:43.256933 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.259235 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 18:18:43.269538 INFO::Done
2025-09-02 18:18:43.269846 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.271454 INFO::ASW Batch was 0.319408052687251 prior to batch effect correction and is now -0.0402929285812777 .
2025-09-02 18:18:43.271673 INFO::ASW Label was 0.472383692233109 prior to batch effect correction and is now 0.736908274556248 .
2025-09-02 18:18:43.272196 INFO::Total function execution time is 0.0864119529724121 s and adjustment time is 0.0796890258789062 s ( 92.22 )
2025-09-02 18:18:43.27253 INFO::Formatting Data.
2025-09-02 18:18:43.272875 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.273219 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.273579 INFO::Found 0 missing values.
2025-09-02 18:18:43.275006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.27523 INFO::Done
2025-09-02 18:18:43.275403 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.276432 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.27674 INFO::Found 5 batches.
2025-09-02 18:18:43.276937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.277329 INFO::Using default BPPARAM
2025-09-02 18:18:43.277659 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.
2025-09-02 18:18:43.338219 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.339337 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 18:18:43.349201 INFO::Done
2025-09-02 18:18:43.349522 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.351631 INFO::ASW Batch was 0.319408052687251 prior to batch effect correction and is now -0.0402929285812777 .
2025-09-02 18:18:43.351915 INFO::ASW Label was 0.472383692233109 prior to batch effect correction and is now 0.736908274556248 .
2025-09-02 18:18:43.352591 INFO::Total function execution time is 0.0800139904022217 s and adjustment time is 0.0725131034851074 s ( 90.63 )
2025-09-02 18:18:43.35923 INFO::Formatting Data.
2025-09-02 18:18:43.35949 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.359939 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.36033 INFO::Found 0 missing values.
2025-09-02 18:18:43.361282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.361473 INFO::Done
2025-09-02 18:18:43.361647 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.362876 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.363143 INFO::Found 2 batches.
2025-09-02 18:18:43.363343 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.36359 INFO::Using default BPPARAM
2025-09-02 18:18:43.363789 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.364102 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 18:18:43.369538 INFO::Done
2025-09-02 18:18:43.369744 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.370704 INFO::ASW Batch was 0.685242672308691 prior to batch effect correction and is now -0.00117714408331089 .
2025-09-02 18:18:43.370898 INFO::ASW Label was 0.398361985979395 prior to batch effect correction and is now 0.903239856144137 .
2025-09-02 18:18:43.371168 INFO::Total function execution time is 0.0119619369506836 s and adjustment time is 0.00644612312316895 s ( 53.89 )
2025-09-02 18:18:43.371406 INFO::Formatting Data.
2025-09-02 18:18:43.371587 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.371857 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.372147 INFO::Found 0 missing values.
2025-09-02 18:18:43.372994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.373299 INFO::Done
2025-09-02 18:18:43.373478 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.374391 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.37462 INFO::Found 2 batches.
2025-09-02 18:18:43.374779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.374968 INFO::Using default BPPARAM
2025-09-02 18:18:43.375134 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.375394 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 18:18:43.380451 INFO::Done
2025-09-02 18:18:43.380673 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.38163 INFO::ASW Batch was 0.685242672308691 prior to batch effect correction and is now -0.00117714408331089 .
2025-09-02 18:18:43.381825 INFO::ASW Label was 0.398361985979395 prior to batch effect correction and is now 0.903239856144137 .
2025-09-02 18:18:43.382085 INFO::Total function execution time is 0.0106699466705322 s and adjustment time is 0.00586295127868652 s ( 54.95 )
2025-09-02 18:18:43.386722 INFO::Formatting Data.
2025-09-02 18:18:43.386953 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.38724 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.387541 INFO::Found 0 missing values.
2025-09-02 18:18:43.388269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.388441 INFO::Done
2025-09-02 18:18:43.388611 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.389211 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.389436 INFO::Found 2 batches.
2025-09-02 18:18:43.389599 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.389803 INFO::Using default BPPARAM
2025-09-02 18:18:43.389985 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.39024 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 18:18:43.401129 INFO::Done
2025-09-02 18:18:43.401352 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.401965 INFO::ASW Batch was 0.110892020629575 prior to batch effect correction and is now -0.143509311147147 .
2025-09-02 18:18:43.402214 INFO::Total function execution time is 0.0155019760131836 s and adjustment time is 0.0117340087890625 s ( 75.69 )
2025-09-02 18:18:43.406721 INFO::Formatting Data.
2025-09-02 18:18:43.406961 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.407225 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.407545 INFO::Found 0 missing values.
2025-09-02 18:18:43.407987 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.
2025-09-02 18:18:43.409476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.409664 INFO::Done
2025-09-02 18:18:43.409828 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.410752 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.410981 INFO::Found 2 batches.
2025-09-02 18:18:43.41115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.411342 INFO::Using default BPPARAM
2025-09-02 18:18:43.411515 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.411799 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 18:18:43.417457 INFO::Done
2025-09-02 18:18:43.417675 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.418598 INFO::ASW Batch was 0.506920017857036 prior to batch effect correction and is now 0.0177491466644829 .
2025-09-02 18:18:43.418792 INFO::ASW Label was 0.561095140916902 prior to batch effect correction and is now 0.911773241867368 .
2025-09-02 18:18:43.419052 INFO::Total function execution time is 0.0123331546783447 s and adjustment time is 0.00650691986083984 s ( 52.76 )
2025-09-02 18:18:43.419309 INFO::Formatting Data.
2025-09-02 18:18:43.419483 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.41977 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.42007 INFO::Found 0 missing values.
2025-09-02 18:18:43.420346 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.
2025-09-02 18:18:43.421732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.421918 INFO::Done
2025-09-02 18:18:43.422099 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.422978 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.423205 INFO::Found 2 batches.
2025-09-02 18:18:43.423368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.423575 INFO::Using default BPPARAM
2025-09-02 18:18:43.423742 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:43.424056 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 18:18:43.429631 INFO::Done
2025-09-02 18:18:43.429852 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.430784 INFO::ASW Batch was 0.506920017857036 prior to batch effect correction and is now 0.0177491466644829 .
2025-09-02 18:18:43.430977 INFO::ASW Label was 0.561095140916902 prior to batch effect correction and is now 0.911773241867368 .
2025-09-02 18:18:43.431233 INFO::Total function execution time is 0.0119199752807617 s and adjustment time is 0.00646686553955078 s ( 54.25 )
2025-09-02 18:18:43.497593 INFO::Formatting Data.
2025-09-02 18:18:43.497885 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.498195 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.498525 INFO::Found 0 missing values.
2025-09-02 18:18:43.499432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.499612 INFO::Done
2025-09-02 18:18:43.499762 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.500403 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.500608 INFO::Found 3 batches.
2025-09-02 18:18:43.500761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.500941 INFO::Using default BPPARAM
2025-09-02 18:18:43.501097 INFO::Processing subtree level 1
2025-09-02 18:18:43.543412 INFO::Adjusting the last 1 batches sequentially
2025-09-02 18:18:43.544536 INFO::Done
2025-09-02 18:18:43.544935 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.546368 INFO::ASW Batch was 0.116169313155887 prior to batch effect correction and is now 0.116169313155887 .
2025-09-02 18:18:43.546948 INFO::Total function execution time is 0.0493948459625244 s and adjustment time is 0.0439670085906982 s ( 89.01 )
2025-09-02 18:18:43.547312 INFO::Formatting Data.
2025-09-02 18:18:43.547516 INFO::Typecasting input to dataframe.
2025-09-02 18:18:43.547749 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.548054 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.548576 INFO::Found 0 missing values.
2025-09-02 18:18:43.549519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.549683 INFO::Done
2025-09-02 18:18:43.549828 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.550426 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.550645 INFO::Found 3 batches.
2025-09-02 18:18:43.550908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.551214 INFO::Using default BPPARAM
2025-09-02 18:18:43.551373 INFO::Processing subtree level 1
2025-09-02 18:18:43.589468 INFO::Adjusting the last 1 batches sequentially
2025-09-02 18:18:43.590378 INFO::Done
2025-09-02 18:18:43.590675 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.592052 INFO::ASW Batch was 0.116169313155887 prior to batch effect correction and is now 0.116169313155887 .
2025-09-02 18:18:43.592744 INFO::Total function execution time is 0.0454170703887939 s and adjustment time is 0.0397739410400391 s ( 87.57 )
2025-09-02 18:18:43.598009 INFO::Formatting Data.
2025-09-02 18:18:43.598232 INFO::Typecasting input to dataframe.
2025-09-02 18:18:43.598479 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.59876 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.599121 INFO::Found 0 missing values.
2025-09-02 18:18:43.599995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.600162 INFO::Done
2025-09-02 18:18:43.600316 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.600898 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.601103 INFO::Found 3 batches.
2025-09-02 18:18:43.601252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.601449 INFO::Using default BPPARAM
2025-09-02 18:18:43.601602 INFO::Processing subtree level 1
2025-09-02 18:18:43.635049 INFO::Adjusting the last 1 batches sequentially
2025-09-02 18:18:43.635996 INFO::Done
2025-09-02 18:18:43.636202 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.63758 INFO::ASW Batch was -0.130179762763263 prior to batch effect correction and is now -0.130179762763263 .
2025-09-02 18:18:43.638161 INFO::Total function execution time is 0.0401568412780762 s and adjustment time is 0.0349321365356445 s ( 86.99 )
2025-09-02 18:18:43.69543 INFO::Formatting Data.
2025-09-02 18:18:43.695686 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.696044 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.696929 INFO::Found 1000 missing values.
2025-09-02 18:18:43.702606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.702848 INFO::Done
2025-09-02 18:18:43.703026 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.705074 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.705346 INFO::Found 10 batches.
2025-09-02 18:18:43.705521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:43.705747 INFO::Using default BPPARAM
2025-09-02 18:18:43.705907 INFO::Processing subtree level 1
2025-09-02 18:18:43.756276 INFO::Processing subtree level 2
2025-09-02 18:18:43.810961 INFO::Adjusting the last 1 batches sequentially
2025-09-02 18:18:43.812208 INFO::Done
2025-09-02 18:18:43.812403 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:43.814883 INFO::ASW Batch was 0.440359713957561 prior to batch effect correction and is now 0.440359713957561 .
2025-09-02 18:18:43.815085 INFO::ASW Label was 0.389363858494381 prior to batch effect correction and is now 0.389363858494381 .
2025-09-02 18:18:43.816357 INFO::Total function execution time is 0.120929002761841 s and adjustment time is 0.106915950775146 s ( 88.41 )
2025-09-02 18:18:43.816631 INFO::Formatting Data.
2025-09-02 18:18:43.816818 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:43.817186 INFO::Removing potential empty rows and columns
2025-09-02 18:18:43.818075 INFO::Found 1000 missing values.
2025-09-02 18:18:43.823562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:43.823947 INFO::Done
2025-09-02 18:18:43.824118 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:43.82597 INFO::Starting hierarchical adjustment
2025-09-02 18:18:43.826222 INFO::Found 10 batches.
2025-09-02 18:18:44.222104 INFO::Set up parallel execution backend with 2 workers
2025-09-02 18:18:44.222375 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-02 18:18:44.732268 INFO::Adjusting the last 2 batches sequentially
2025-09-02 18:18:44.732915 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 18:18:44.73882 INFO::Done
2025-09-02 18:18:44.739075 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:44.741121 INFO::ASW Batch was 0.440359713957561 prior to batch effect correction and is now 0.440359713957561 .
2025-09-02 18:18:44.741329 INFO::ASW Label was 0.389363858494381 prior to batch effect correction and is now 0.389363858494381 .
2025-09-02 18:18:44.741563 INFO::Total function execution time is 0.924936056137085 s and adjustment time is 0.912636995315552 s ( 98.67 )
2025-09-02 18:18:44.804525 INFO::Formatting Data.
2025-09-02 18:18:44.80483 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:44.805198 INFO::Removing potential empty rows and columns
2025-09-02 18:18:44.805636 INFO::Found 0 missing values.
2025-09-02 18:18:44.807135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:44.807321 INFO::Done
2025-09-02 18:18:44.807518 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 18:18:44.808545 INFO::Starting hierarchical adjustment
2025-09-02 18:18:44.808833 INFO::Found 3 batches.
2025-09-02 18:18:44.809003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 18:18:44.809263 INFO::Using default BPPARAM
2025-09-02 18:18:44.80945 INFO::Processing subtree level 1
2025-09-02 18:18:44.857984 INFO::Adjusting the last 1 batches sequentially
2025-09-02 18:18:44.859386 INFO::Done
2025-09-02 18:18:44.859616 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 18:18:44.862353 INFO::ASW Batch was 0.222627171574447 prior to batch effect correction and is now -0.161670798904031 .
2025-09-02 18:18:44.862582 INFO::ASW Label was -0.214059486590522 prior to batch effect correction and is now -0.131133900711258 .
2025-09-02 18:18:44.863585 INFO::Total function execution time is 0.0590507984161377 s and adjustment time is 0.0506038665771484 s ( 85.7 )
2025-09-02 18:18:44.915018 INFO::Formatting Data.
2025-09-02 18:18:44.915388 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:44.915754 INFO::Removing potential empty rows and columns
2025-09-02 18:18:44.916254 INFO::Found 2 missing values.
2025-09-02 18:18:44.917393 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:44.91761 INFO::Done
2025-09-02 18:18:44.92854 INFO::Found NA in Reference column
2025-09-02 18:18:44.932252 INFO::Require at least two references per batch.
2025-09-02 18:18:44.941099 INFO::Formatting Data.
2025-09-02 18:18:44.941379 INFO::Recognized SummarizedExperiment
2025-09-02 18:18:44.941569 INFO::Typecasting input to dataframe.
2025-09-02 18:18:44.945801 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:44.946212 INFO::Removing potential empty rows and columns
2025-09-02 18:18:44.947559 INFO::Found 0 missing values.
2025-09-02 18:18:44.950095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:44.95031 INFO::Done
2025-09-02 18:18:44.956225 INFO::Formatting Data.
2025-09-02 18:18:44.956461 INFO::Recognized SummarizedExperiment
2025-09-02 18:18:44.956634 INFO::Typecasting input to dataframe.
2025-09-02 18:18:44.962951 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:44.963415 INFO::Removing potential empty rows and columns
2025-09-02 18:18:44.964814 INFO::Found 0 missing values.
2025-09-02 18:18:44.969004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:44.969215 INFO::Done
2025-09-02 18:18:44.974931 INFO::Formatting Data.
2025-09-02 18:18:44.975173 INFO::Recognized SummarizedExperiment
2025-09-02 18:18:44.97535 INFO::Typecasting input to dataframe.
2025-09-02 18:18:44.98067 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:44.981002 INFO::Removing potential empty rows and columns
2025-09-02 18:18:44.981379 INFO::Found 0 missing values.
2025-09-02 18:18:44.981688 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.
2025-09-02 18:18:44.983125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:44.983305 INFO::Done
2025-09-02 18:18:44.98758 INFO::Formatting Data.
2025-09-02 18:18:44.987839 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:44.988126 INFO::Removing potential empty rows and columns
2025-09-02 18:18:44.98845 INFO::Found 0 missing values.
2025-09-02 18:18:44.989399 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:44.989583 INFO::Done
2025-09-02 18:18:44.993976 INFO::Formatting Data.
2025-09-02 18:18:44.994209 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:44.994473 INFO::Removing potential empty rows and columns
2025-09-02 18:18:44.994822 INFO::Found 0 missing values.
2025-09-02 18:18:44.995764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:44.995955 INFO::Done
2025-09-02 18:18:45.007279 INFO::Formatting Data.
2025-09-02 18:18:45.007628 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:45.008007 INFO::Removing potential empty rows and columns
2025-09-02 18:18:45.008465 INFO::Found 1 missing values.
2025-09-02 18:18:45.009448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:45.009652 INFO::Done
2025-09-02 18:18:45.017838 INFO::Formatting Data.
2025-09-02 18:18:45.018125 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:45.018426 INFO::Removing potential empty rows and columns
2025-09-02 18:18:45.01878 INFO::Found 2 missing values.
2025-09-02 18:18:45.019079 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.
2025-09-02 18:18:45.019936 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:45.020145 INFO::Done
2025-09-02 18:18:45.024817 INFO::Formatting Data.
2025-09-02 18:18:45.025077 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:45.025376 INFO::Removing potential empty rows and columns
2025-09-02 18:18:45.025701 INFO::Found 2 missing values.
2025-09-02 18:18:45.026267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:45.026458 INFO::Done
2025-09-02 18:18:45.031444 INFO::Formatting Data.
2025-09-02 18:18:45.031739 INFO::Typecasting input to dataframe.
2025-09-02 18:18:45.032049 INFO::Replacing NaNs with NAs.
2025-09-02 18:18:45.032361 INFO::Removing potential empty rows and columns
2025-09-02 18:18:45.03277 INFO::Found 0 missing values.
2025-09-02 18:18:45.033723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 18:18:45.033894 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.648 1.480 8.354
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.653 | 0.404 | 6.932 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.028 | |