Yannis Schumann
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_21 |
| git_last_commit: dedce04 |
| git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:40 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2025-09-23 13:45:00 -0400 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 13:46:28 -0400 (Tue, 23 Sep 2025) |
| EllapsedTime: 87.2 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* 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 29.031 1.466 21.224
* 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 ‘1.4.0’ ** 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")
2025-09-23 13:46:03.477115 INFO::Formatting Data.
2025-09-23 13:46:03.482428 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:03.490575 INFO::Removing potential empty rows and columns
2025-09-23 13:46:03.781577 INFO::Found 0 missing values.
2025-09-23 13:46:03.783584 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:03.783862 INFO::Done
2025-09-23 13:46:03.784159 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:03.804855 INFO::Starting hierarchical adjustment
2025-09-23 13:46:03.805955 INFO::Found 3 batches.
2025-09-23 13:46:03.806568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:03.808025 INFO::Using default BPPARAM
2025-09-23 13:46:03.808571 INFO::Processing subtree level 1
2025-09-23 13:46:03.955708 INFO::Adjusting the last 1 batches sequentially
2025-09-23 13:46:03.959459 INFO::Done
2025-09-23 13:46:03.960141 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:03.964051 INFO::ASW Batch was 0.00265263685300458 prior to batch effect correction and is now 0.00265263685300458 .
2025-09-23 13:46:03.967617 INFO::Total function execution time is 0.491113901138306 s and adjustment time is 0.153701066970825 s ( 31.3 )
2025-09-23 13:46:03.996984 INFO::Formatting Data.
2025-09-23 13:46:03.998159 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:03.999301 INFO::Removing potential empty rows and columns
2025-09-23 13:46:04.001267 INFO::Found 0 missing values.
2025-09-23 13:46:04.002618 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.
2025-09-23 13:46:04.017083 INFO::Formatting Data.
2025-09-23 13:46:04.018009 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:04.018966 INFO::Removing potential empty rows and columns
2025-09-23 13:46:04.020021 INFO::Found 0 missing values.
2025-09-23 13:46:04.021805 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.
2025-09-23 13:46:04.044325 INFO::Formatting Data.
2025-09-23 13:46:04.045048 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:04.046194 INFO::Removing potential empty rows and columns
2025-09-23 13:46:04.048354 INFO::Found 0 missing values.
2025-09-23 13:46:04.050259 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.
2025-09-23 13:46:04.053443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:04.05386 INFO::Done
2025-09-23 13:46:04.054162 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:04.056019 INFO::Starting hierarchical adjustment
2025-09-23 13:46:04.056522 INFO::Found 2 batches.
2025-09-23 13:46:04.056921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:04.057388 INFO::Using default BPPARAM
2025-09-23 13:46:04.057588 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:04.058044 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-23 13:46:04.079697 INFO::Done
2025-09-23 13:46:04.080354 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:04.082815 INFO::ASW Batch was -0.0305447002525304 prior to batch effect correction and is now -0.117508165793783 .
2025-09-23 13:46:04.083309 INFO::Total function execution time is 0.039201021194458 s and adjustment time is 0.0231559276580811 s ( 59.07 )
2025-09-23 13:46:04.086143 INFO::Formatting Data.
2025-09-23 13:46:04.086592 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:04.096609 INFO::Formatting Data.
2025-09-23 13:46:04.097999 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:04.159462 INFO::Removing potential empty rows and columns
2025-09-23 13:46:04.16003 INFO::Found 0 missing values.
2025-09-23 13:46:04.161286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:04.161627 INFO::Done
2025-09-23 13:46:04.161844 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:04.163236 INFO::Starting hierarchical adjustment
2025-09-23 13:46:04.163621 INFO::Found 2 batches.
2025-09-23 13:46:04.163937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:04.164274 INFO::Using default BPPARAM
2025-09-23 13:46:04.165294 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:04.166767 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-23 13:46:04.183558 INFO::Done
2025-09-23 13:46:04.184427 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:04.186773 INFO::ASW Batch was 0.0161805871032727 prior to batch effect correction and is now -0.119672206687239 .
2025-09-23 13:46:04.187638 INFO::Total function execution time is 0.0911469459533691 s and adjustment time is 0.0198898315429688 s ( 21.82 )
2025-09-23 13:46:04.188666 INFO::Formatting Data.
2025-09-23 13:46:04.189281 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:04.190112 INFO::Removing potential empty rows and columns
2025-09-23 13:46:04.191253 INFO::Found 0 missing values.
2025-09-23 13:46:04.194393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:04.195178 INFO::Done
2025-09-23 13:46:04.195749 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:04.198145 INFO::Starting hierarchical adjustment
2025-09-23 13:46:04.199062 INFO::Found 2 batches.
2025-09-23 13:46:04.199744 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:04.201427 INFO::Using default BPPARAM
2025-09-23 13:46:04.202491 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:04.204013 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-23 13:46:04.217617 INFO::Done
2025-09-23 13:46:04.218889 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:04.221413 INFO::ASW Batch was 0.0161805871032727 prior to batch effect correction and is now -0.119672206687239 .
2025-09-23 13:46:04.222354 INFO::Total function execution time is 0.0336768627166748 s and adjustment time is 0.0185918807983398 s ( 55.21 )
2025-09-23 13:46:07.935267 INFO::Formatting Data.
2025-09-23 13:46:07.936155 INFO::Recognized SummarizedExperiment
2025-09-23 13:46:07.936646 INFO::Typecasting input to dataframe.
2025-09-23 13:46:07.977944 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:07.980384 INFO::Removing potential empty rows and columns
2025-09-23 13:46:07.984085 INFO::Found 0 missing values.
2025-09-23 13:46:07.991138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:07.991946 INFO::Done
2025-09-23 13:46:07.99248 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:07.99645 INFO::Starting hierarchical adjustment
2025-09-23 13:46:07.997272 INFO::Found 2 batches.
2025-09-23 13:46:07.99777 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:07.998909 INFO::Using default BPPARAM
2025-09-23 13:46:07.999389 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:08.000305 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-23 13:46:08.059708 INFO::Done
2025-09-23 13:46:08.060585 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:08.064663 INFO::ASW Batch was 0.00250851465345951 prior to batch effect correction and is now -0.0947979952374979 .
2025-09-23 13:46:08.065675 INFO::Total function execution time is 0.130763053894043 s and adjustment time is 0.0625209808349609 s ( 47.81 )
2025-09-23 13:46:08.090226 INFO::Formatting Data.
2025-09-23 13:46:08.091116 INFO::Recognized SummarizedExperiment
2025-09-23 13:46:08.091643 INFO::Typecasting input to dataframe.
2025-09-23 13:46:08.101005 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:08.102396 INFO::Removing potential empty rows and columns
2025-09-23 13:46:08.106079 INFO::Found 0 missing values.
2025-09-23 13:46:08.113458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:08.114439 INFO::Done
2025-09-23 13:46:08.114985 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:08.119204 INFO::Starting hierarchical adjustment
2025-09-23 13:46:08.120172 INFO::Found 2 batches.
2025-09-23 13:46:08.120694 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:08.121269 INFO::Using default BPPARAM
2025-09-23 13:46:08.121733 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:08.12267 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-23 13:46:08.148897 INFO::Done
2025-09-23 13:46:08.149746 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:08.153614 INFO::ASW Batch was -0.00939933484450714 prior to batch effect correction and is now -0.00939933484450714 .
2025-09-23 13:46:08.154524 INFO::Total function execution time is 0.0643308162689209 s and adjustment time is 0.0288081169128418 s ( 44.78 )
2025-09-23 13:46:08.180064 INFO::Formatting Data.
2025-09-23 13:46:08.180962 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:08.181982 INFO::Removing potential empty rows and columns
2025-09-23 13:46:08.182974 INFO::Found 0 missing values.
2025-09-23 13:46:08.185603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:08.186184 INFO::Done
2025-09-23 13:46:08.186669 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:08.188919 INFO::Starting hierarchical adjustment
2025-09-23 13:46:08.189714 INFO::Found 3 batches.
2025-09-23 13:46:08.19019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:08.190743 INFO::Using default BPPARAM
2025-09-23 13:46:08.191189 INFO::Processing subtree level 1
2025-09-23 13:46:08.638748 INFO::Adjusting the last 1 batches sequentially
2025-09-23 13:46:08.646946 INFO::Done
2025-09-23 13:46:08.649198 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:08.659355 INFO::ASW Batch was 0.026216890107631 prior to batch effect correction and is now -0.13154082258511 .
2025-09-23 13:46:08.663046 INFO::Total function execution time is 0.482396841049194 s and adjustment time is 0.457305908203125 s ( 94.8 )
2025-09-23 13:46:08.824777 INFO::Skipping initial DF formatting
2025-09-23 13:46:08.825774 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:08.830266 INFO::Starting hierarchical adjustment
2025-09-23 13:46:08.831189 INFO::Found 5 batches.
2025-09-23 13:46:08.831794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:08.832505 INFO::Using default BPPARAM
2025-09-23 13:46:08.833023 INFO::Processing subtree level 1
2025-09-23 13:46:09.12235 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:09.128295 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-23 13:46:09.176225 INFO::Done
2025-09-23 13:46:09.177987 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:09.18649 INFO::ASW Batch was 0.509714853778557 prior to batch effect correction and is now 0.509714853778557 .
2025-09-23 13:46:09.187635 INFO::ASW Label was 0.396156699666595 prior to batch effect correction and is now 0.396156699666595 .
2025-09-23 13:46:09.18942 INFO::Total function execution time is 0.364586114883423 s and adjustment time is 0.345082998275757 s ( 94.65 )
2025-09-23 13:46:09.22168 INFO::Formatting Data.
2025-09-23 13:46:09.222772 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:09.224048 INFO::Removing potential empty rows and columns
2025-09-23 13:46:09.225611 INFO::Found 0 missing values.
2025-09-23 13:46:09.231728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:09.232649 INFO::Done
2025-09-23 13:46:09.233438 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:09.238203 INFO::Starting hierarchical adjustment
2025-09-23 13:46:09.239728 INFO::Found 5 batches.
2025-09-23 13:46:09.240607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:09.242334 INFO::Using default BPPARAM
2025-09-23 13:46:09.24314 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.
2025-09-23 13:46:09.462277 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:09.469561 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-23 13:46:09.50946 INFO::Done
2025-09-23 13:46:09.511461 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:09.519069 INFO::ASW Batch was 0.485684023095182 prior to batch effect correction and is now -0.0953400237309907 .
2025-09-23 13:46:09.520289 INFO::ASW Label was 0.301833977817787 prior to batch effect correction and is now 0.834901128472325 .
2025-09-23 13:46:09.521645 INFO::Total function execution time is 0.300106048583984 s and adjustment time is 0.270003080368042 s ( 89.97 )
2025-09-23 13:46:09.522863 INFO::Formatting Data.
2025-09-23 13:46:09.523775 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:09.525152 INFO::Removing potential empty rows and columns
2025-09-23 13:46:09.526768 INFO::Found 0 missing values.
2025-09-23 13:46:09.532509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:09.533368 INFO::Done
2025-09-23 13:46:09.534047 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:09.537986 INFO::Starting hierarchical adjustment
2025-09-23 13:46:09.538976 INFO::Found 5 batches.
2025-09-23 13:46:09.53971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:09.54067 INFO::Using default BPPARAM
2025-09-23 13:46:09.541968 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.
2025-09-23 13:46:09.841676 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:09.849691 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-23 13:46:09.880281 INFO::Done
2025-09-23 13:46:09.881751 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:09.888577 INFO::ASW Batch was 0.485684023095182 prior to batch effect correction and is now -0.0953400237309907 .
2025-09-23 13:46:09.889499 INFO::ASW Label was 0.301833977817787 prior to batch effect correction and is now 0.834901128472325 .
2025-09-23 13:46:09.890808 INFO::Total function execution time is 0.367781162261963 s and adjustment time is 0.341418981552124 s ( 92.83 )
2025-09-23 13:46:09.919028 INFO::Formatting Data.
2025-09-23 13:46:09.919931 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:09.920932 INFO::Removing potential empty rows and columns
2025-09-23 13:46:09.922493 INFO::Found 0 missing values.
2025-09-23 13:46:09.928461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:09.929301 INFO::Done
2025-09-23 13:46:09.930042 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:09.933955 INFO::Starting hierarchical adjustment
2025-09-23 13:46:09.935524 INFO::Found 5 batches.
2025-09-23 13:46:09.936453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:09.937595 INFO::Using default BPPARAM
2025-09-23 13:46:09.938467 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.
2025-09-23 13:46:10.15595 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:10.162632 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-23 13:46:10.197393 INFO::Done
2025-09-23 13:46:10.198926 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:10.206629 INFO::ASW Batch was 0.358664626916838 prior to batch effect correction and is now -0.00860802459230311 .
2025-09-23 13:46:10.208836 INFO::ASW Label was 0.355733278802837 prior to batch effect correction and is now 0.826021331298057 .
2025-09-23 13:46:10.210413 INFO::Total function execution time is 0.290947914123535 s and adjustment time is 0.262573003768921 s ( 90.25 )
2025-09-23 13:46:10.211514 INFO::Formatting Data.
2025-09-23 13:46:10.212275 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:10.21484 INFO::Removing potential empty rows and columns
2025-09-23 13:46:10.216634 INFO::Found 0 missing values.
2025-09-23 13:46:10.223986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:10.22572 INFO::Done
2025-09-23 13:46:10.226509 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:10.230837 INFO::Starting hierarchical adjustment
2025-09-23 13:46:10.231919 INFO::Found 5 batches.
2025-09-23 13:46:10.232604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:10.233415 INFO::Using default BPPARAM
2025-09-23 13:46:10.234047 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.
2025-09-23 13:46:10.418448 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:10.425049 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-23 13:46:10.457228 INFO::Done
2025-09-23 13:46:10.458793 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:10.464823 INFO::ASW Batch was 0.358664626916838 prior to batch effect correction and is now -0.00860802459230311 .
2025-09-23 13:46:10.465623 INFO::ASW Label was 0.355733278802837 prior to batch effect correction and is now 0.826021331298057 .
2025-09-23 13:46:10.466811 INFO::Total function execution time is 0.255133152008057 s and adjustment time is 0.225427150726318 s ( 88.36 )
2025-09-23 13:46:10.491925 INFO::Formatting Data.
2025-09-23 13:46:10.493004 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:10.494266 INFO::Removing potential empty rows and columns
2025-09-23 13:46:10.496582 INFO::Found 0 missing values.
2025-09-23 13:46:10.500007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:10.500712 INFO::Done
2025-09-23 13:46:10.501314 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:10.504853 INFO::Starting hierarchical adjustment
2025-09-23 13:46:10.505765 INFO::Found 2 batches.
2025-09-23 13:46:10.506337 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:10.507263 INFO::Using default BPPARAM
2025-09-23 13:46:10.507804 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:10.508826 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-23 13:46:10.527996 INFO::Done
2025-09-23 13:46:10.528847 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:10.532312 INFO::ASW Batch was 0.417514578751645 prior to batch effect correction and is now -0.0374124485083911 .
2025-09-23 13:46:10.533134 INFO::ASW Label was 0.6114427197401 prior to batch effect correction and is now 0.957976314680924 .
2025-09-23 13:46:10.534075 INFO::Total function execution time is 0.042323112487793 s and adjustment time is 0.0223510265350342 s ( 52.81 )
2025-09-23 13:46:10.5349 INFO::Formatting Data.
2025-09-23 13:46:10.535508 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:10.536498 INFO::Removing potential empty rows and columns
2025-09-23 13:46:10.53753 INFO::Found 0 missing values.
2025-09-23 13:46:10.54064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:10.541271 INFO::Done
2025-09-23 13:46:10.541843 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:10.545161 INFO::Starting hierarchical adjustment
2025-09-23 13:46:10.546026 INFO::Found 2 batches.
2025-09-23 13:46:10.546573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:10.547255 INFO::Using default BPPARAM
2025-09-23 13:46:10.54786 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:10.548835 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-23 13:46:10.568348 INFO::Done
2025-09-23 13:46:10.569235 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:10.572661 INFO::ASW Batch was 0.417514578751645 prior to batch effect correction and is now -0.0374124485083911 .
2025-09-23 13:46:10.573339 INFO::ASW Label was 0.6114427197401 prior to batch effect correction and is now 0.957976314680924 .
2025-09-23 13:46:10.574305 INFO::Total function execution time is 0.039341926574707 s and adjustment time is 0.0224809646606445 s ( 57.14 )
2025-09-23 13:46:10.593961 INFO::Formatting Data.
2025-09-23 13:46:10.595147 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:10.596328 INFO::Removing potential empty rows and columns
2025-09-23 13:46:10.597512 INFO::Found 0 missing values.
2025-09-23 13:46:10.601181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:10.60245 INFO::Done
2025-09-23 13:46:10.603103 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:10.605839 INFO::Starting hierarchical adjustment
2025-09-23 13:46:10.606732 INFO::Found 2 batches.
2025-09-23 13:46:10.607318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:10.608097 INFO::Using default BPPARAM
2025-09-23 13:46:10.608736 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:10.609731 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-23 13:46:10.659506 INFO::Done
2025-09-23 13:46:10.660668 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:10.663445 INFO::ASW Batch was -0.00940701520508491 prior to batch effect correction and is now -0.0804603021644795 .
2025-09-23 13:46:10.664496 INFO::Total function execution time is 0.0707299709320068 s and adjustment time is 0.0529379844665527 s ( 74.85 )
2025-09-23 13:46:10.681448 INFO::Formatting Data.
2025-09-23 13:46:10.68246 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:10.683576 INFO::Removing potential empty rows and columns
2025-09-23 13:46:10.684858 INFO::Found 0 missing values.
2025-09-23 13:46:10.686406 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.
2025-09-23 13:46:10.691703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:10.692529 INFO::Done
2025-09-23 13:46:10.693175 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:10.69679 INFO::Starting hierarchical adjustment
2025-09-23 13:46:10.697667 INFO::Found 2 batches.
2025-09-23 13:46:10.698251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:10.698968 INFO::Using default BPPARAM
2025-09-23 13:46:10.700399 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:10.701665 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-23 13:46:10.721331 INFO::Done
2025-09-23 13:46:10.722693 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:10.728126 INFO::ASW Batch was 0.675921138820877 prior to batch effect correction and is now 0.0390080293334718 .
2025-09-23 13:46:10.729265 INFO::ASW Label was 0.37545732243766 prior to batch effect correction and is now 0.86177009354965 .
2025-09-23 13:46:10.730447 INFO::Total function execution time is 0.0491020679473877 s and adjustment time is 0.0237410068511963 s ( 48.35 )
2025-09-23 13:46:10.731457 INFO::Formatting Data.
2025-09-23 13:46:10.732089 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:10.73309 INFO::Removing potential empty rows and columns
2025-09-23 13:46:10.734255 INFO::Found 0 missing values.
2025-09-23 13:46:10.735946 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.
2025-09-23 13:46:10.74242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:10.743255 INFO::Done
2025-09-23 13:46:10.743853 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:10.747271 INFO::Starting hierarchical adjustment
2025-09-23 13:46:10.748233 INFO::Found 2 batches.
2025-09-23 13:46:10.748837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:10.749558 INFO::Using default BPPARAM
2025-09-23 13:46:10.750142 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:10.751252 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-23 13:46:10.772931 INFO::Done
2025-09-23 13:46:10.773826 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:10.776806 INFO::ASW Batch was 0.675921138820877 prior to batch effect correction and is now 0.0390080293334718 .
2025-09-23 13:46:10.777618 INFO::ASW Label was 0.37545732243766 prior to batch effect correction and is now 0.86177009354965 .
2025-09-23 13:46:10.781153 INFO::Total function execution time is 0.0475809574127197 s and adjustment time is 0.0247809886932373 s ( 52.08 )
2025-09-23 13:46:11.033192 INFO::Formatting Data.
2025-09-23 13:46:11.034101 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:11.035085 INFO::Removing potential empty rows and columns
2025-09-23 13:46:11.03613 INFO::Found 0 missing values.
2025-09-23 13:46:11.039196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:11.039956 INFO::Done
2025-09-23 13:46:11.040454 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:11.042835 INFO::Starting hierarchical adjustment
2025-09-23 13:46:11.043733 INFO::Found 3 batches.
2025-09-23 13:46:11.04424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:11.044832 INFO::Using default BPPARAM
2025-09-23 13:46:11.045303 INFO::Processing subtree level 1
2025-09-23 13:46:11.180257 INFO::Adjusting the last 1 batches sequentially
2025-09-23 13:46:11.186743 INFO::Done
2025-09-23 13:46:11.18826 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:11.194995 INFO::ASW Batch was -0.0650775809272757 prior to batch effect correction and is now -0.0650775809272757 .
2025-09-23 13:46:11.198321 INFO::Total function execution time is 0.164933919906616 s and adjustment time is 0.143064022064209 s ( 86.74 )
2025-09-23 13:46:11.200344 INFO::Formatting Data.
2025-09-23 13:46:11.201105 INFO::Typecasting input to dataframe.
2025-09-23 13:46:11.201915 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:11.203418 INFO::Removing potential empty rows and columns
2025-09-23 13:46:11.205617 INFO::Found 0 missing values.
2025-09-23 13:46:11.208767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:11.209595 INFO::Done
2025-09-23 13:46:11.210237 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:11.213354 INFO::Starting hierarchical adjustment
2025-09-23 13:46:11.214499 INFO::Found 3 batches.
2025-09-23 13:46:11.215055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:11.215831 INFO::Using default BPPARAM
2025-09-23 13:46:11.216335 INFO::Processing subtree level 1
2025-09-23 13:46:11.355186 INFO::Adjusting the last 1 batches sequentially
2025-09-23 13:46:11.360825 INFO::Done
2025-09-23 13:46:11.3619 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:11.366894 INFO::ASW Batch was -0.0650775809272757 prior to batch effect correction and is now -0.0650775809272757 .
2025-09-23 13:46:11.369327 INFO::Total function execution time is 0.168927192687988 s and adjustment time is 0.146405935287476 s ( 86.67 )
2025-09-23 13:46:11.387895 INFO::Formatting Data.
2025-09-23 13:46:11.388838 INFO::Typecasting input to dataframe.
2025-09-23 13:46:11.389675 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:11.390655 INFO::Removing potential empty rows and columns
2025-09-23 13:46:11.39232 INFO::Found 0 missing values.
2025-09-23 13:46:11.395151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:11.39567 INFO::Done
2025-09-23 13:46:11.396823 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:11.399787 INFO::Starting hierarchical adjustment
2025-09-23 13:46:11.400544 INFO::Found 3 batches.
2025-09-23 13:46:11.401066 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:11.401758 INFO::Using default BPPARAM
2025-09-23 13:46:11.402257 INFO::Processing subtree level 1
2025-09-23 13:46:11.542753 INFO::Adjusting the last 1 batches sequentially
2025-09-23 13:46:11.548585 INFO::Done
2025-09-23 13:46:11.549453 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:11.555979 INFO::ASW Batch was -0.0351354361936723 prior to batch effect correction and is now -0.0351354361936723 .
2025-09-23 13:46:11.558492 INFO::Total function execution time is 0.170512914657593 s and adjustment time is 0.148119926452637 s ( 86.87 )
2025-09-23 13:46:11.78862 INFO::Formatting Data.
2025-09-23 13:46:11.789734 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:11.791462 INFO::Removing potential empty rows and columns
2025-09-23 13:46:11.795132 INFO::Found 1000 missing values.
2025-09-23 13:46:11.814661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:11.815581 INFO::Done
2025-09-23 13:46:11.816786 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:11.823903 INFO::Starting hierarchical adjustment
2025-09-23 13:46:11.82501 INFO::Found 10 batches.
2025-09-23 13:46:11.825613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:11.826411 INFO::Using default BPPARAM
2025-09-23 13:46:11.827189 INFO::Processing subtree level 1
2025-09-23 13:46:12.010489 INFO::Processing subtree level 2
2025-09-23 13:46:12.206985 INFO::Adjusting the last 1 batches sequentially
2025-09-23 13:46:12.213149 INFO::Done
2025-09-23 13:46:12.214281 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:12.223909 INFO::ASW Batch was 0.491745356821721 prior to batch effect correction and is now 0.491745356821721 .
2025-09-23 13:46:12.224886 INFO::ASW Label was 0.330176587605437 prior to batch effect correction and is now 0.330176587605437 .
2025-09-23 13:46:12.226605 INFO::Total function execution time is 0.437780857086182 s and adjustment time is 0.388315916061401 s ( 88.7 )
2025-09-23 13:46:12.227593 INFO::Formatting Data.
2025-09-23 13:46:12.228193 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:12.230286 INFO::Removing potential empty rows and columns
2025-09-23 13:46:12.233703 INFO::Found 1000 missing values.
2025-09-23 13:46:12.254683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:12.25588 INFO::Done
2025-09-23 13:46:12.256503 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:12.263497 INFO::Starting hierarchical adjustment
2025-09-23 13:46:12.264458 INFO::Found 10 batches.
2025-09-23 13:46:13.680361 INFO::Set up parallel execution backend with 2 workers
2025-09-23 13:46:13.681261 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-23 13:46:15.148827 INFO::Adjusting the last 2 batches sequentially
2025-09-23 13:46:15.150955 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-23 13:46:15.169979 INFO::Done
2025-09-23 13:46:15.170833 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:15.176533 INFO::ASW Batch was 0.491745356821721 prior to batch effect correction and is now 0.491745356821721 .
2025-09-23 13:46:15.177181 INFO::ASW Label was 0.330176587605437 prior to batch effect correction and is now 0.330176587605437 .
2025-09-23 13:46:15.17793 INFO::Total function execution time is 2.95038199424744 s and adjustment time is 2.9056670665741 s ( 98.48 )
2025-09-23 13:46:15.39434 INFO::Formatting Data.
2025-09-23 13:46:15.395655 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:15.397566 INFO::Removing potential empty rows and columns
2025-09-23 13:46:15.400557 INFO::Found 0 missing values.
2025-09-23 13:46:15.405526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:15.406302 INFO::Done
2025-09-23 13:46:15.406937 INFO::Acquiring quality metrics before batch effect correction.
2025-09-23 13:46:15.410393 INFO::Starting hierarchical adjustment
2025-09-23 13:46:15.412375 INFO::Found 3 batches.
2025-09-23 13:46:15.413422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-23 13:46:15.414423 INFO::Using default BPPARAM
2025-09-23 13:46:15.415811 INFO::Processing subtree level 1
2025-09-23 13:46:15.616905 INFO::Adjusting the last 1 batches sequentially
2025-09-23 13:46:15.624844 INFO::Done
2025-09-23 13:46:15.626968 INFO::Acquiring quality metrics after batch effect correction.
2025-09-23 13:46:15.636056 INFO::ASW Batch was 0.181874753031977 prior to batch effect correction and is now -0.131505047746297 .
2025-09-23 13:46:15.638182 INFO::ASW Label was -0.230611055361216 prior to batch effect correction and is now -0.0887500606231418 .
2025-09-23 13:46:15.640504 INFO::Total function execution time is 0.246084928512573 s and adjustment time is 0.212820053100586 s ( 86.48 )
2025-09-23 13:46:15.844307 INFO::Formatting Data.
2025-09-23 13:46:15.84555 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:15.846911 INFO::Removing potential empty rows and columns
2025-09-23 13:46:15.848485 INFO::Found 2 missing values.
2025-09-23 13:46:15.851779 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:15.852474 INFO::Done
2025-09-23 13:46:15.893688 INFO::Found NA in Reference column
2025-09-23 13:46:15.906912 INFO::Require at least two references per batch.
2025-09-23 13:46:15.93969 INFO::Formatting Data.
2025-09-23 13:46:15.940783 INFO::Recognized SummarizedExperiment
2025-09-23 13:46:15.942855 INFO::Typecasting input to dataframe.
2025-09-23 13:46:15.958732 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:15.960568 INFO::Removing potential empty rows and columns
2025-09-23 13:46:15.965593 INFO::Found 0 missing values.
2025-09-23 13:46:15.974989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:15.976585 INFO::Done
2025-09-23 13:46:15.999381 INFO::Formatting Data.
2025-09-23 13:46:16.000574 INFO::Recognized SummarizedExperiment
2025-09-23 13:46:16.001283 INFO::Typecasting input to dataframe.
2025-09-23 13:46:16.027599 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:16.029621 INFO::Removing potential empty rows and columns
2025-09-23 13:46:16.034237 INFO::Found 0 missing values.
2025-09-23 13:46:16.04613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:16.047009 INFO::Done
2025-09-23 13:46:16.066438 INFO::Formatting Data.
2025-09-23 13:46:16.067438 INFO::Recognized SummarizedExperiment
2025-09-23 13:46:16.06804 INFO::Typecasting input to dataframe.
2025-09-23 13:46:16.089452 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:16.090794 INFO::Removing potential empty rows and columns
2025-09-23 13:46:16.092011 INFO::Found 0 missing values.
2025-09-23 13:46:16.093008 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.
2025-09-23 13:46:16.09763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:16.098318 INFO::Done
2025-09-23 13:46:16.111804 INFO::Formatting Data.
2025-09-23 13:46:16.112802 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:16.113822 INFO::Removing potential empty rows and columns
2025-09-23 13:46:16.114933 INFO::Found 0 missing values.
2025-09-23 13:46:16.118025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:16.118714 INFO::Done
2025-09-23 13:46:16.135848 INFO::Formatting Data.
2025-09-23 13:46:16.136812 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:16.137792 INFO::Removing potential empty rows and columns
2025-09-23 13:46:16.138901 INFO::Found 0 missing values.
2025-09-23 13:46:16.142196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:16.142923 INFO::Done
2025-09-23 13:46:16.184957 INFO::Formatting Data.
2025-09-23 13:46:16.18654 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:16.18859 INFO::Removing potential empty rows and columns
2025-09-23 13:46:16.192016 INFO::Found 1 missing values.
2025-09-23 13:46:16.196437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:16.197509 INFO::Done
2025-09-23 13:46:16.225848 INFO::Formatting Data.
2025-09-23 13:46:16.227047 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:16.228141 INFO::Removing potential empty rows and columns
2025-09-23 13:46:16.229333 INFO::Found 2 missing values.
2025-09-23 13:46:16.230579 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.
2025-09-23 13:46:16.233685 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:16.234465 INFO::Done
2025-09-23 13:46:16.247629 INFO::Formatting Data.
2025-09-23 13:46:16.248763 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:16.249814 INFO::Removing potential empty rows and columns
2025-09-23 13:46:16.250895 INFO::Found 2 missing values.
2025-09-23 13:46:16.253178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:16.254285 INFO::Done
2025-09-23 13:46:16.272516 INFO::Formatting Data.
2025-09-23 13:46:16.27351 INFO::Typecasting input to dataframe.
2025-09-23 13:46:16.274514 INFO::Replacing NaNs with NAs.
2025-09-23 13:46:16.275553 INFO::Removing potential empty rows and columns
2025-09-23 13:46:16.276727 INFO::Found 0 missing values.
2025-09-23 13:46:16.280282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-23 13:46:16.281003 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.513 5.834 27.219
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.031 | 1.466 | 21.224 | |
| compute_asw | 0.030 | 0.001 | 0.031 | |
| count_existing | 0.016 | 0.000 | 0.017 | |
| generate_data_covariables | 0.014 | 0.001 | 0.015 | |
| generate_dataset | 0.014 | 0.002 | 0.015 | |