Yannis Schumann
| Snapshot Date: 2025-09-25 13:40 -0400 (Thu, 25 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 2025-09-29 11:41 -0400 (Mon, 29 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" | 4580 |
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.4.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.4.0.tar.gz |
| StartedAt: 2025-09-26 07:43:24 -0000 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 07:44:50 -0000 (Fri, 26 Sep 2025) |
| EllapsedTime: 86.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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 31.156 1.375 22.327
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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")
2025-09-26 07:44:32.926866 INFO::Formatting Data.
2025-09-26 07:44:32.929437 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:32.953353 INFO::Removing potential empty rows and columns
2025-09-26 07:44:33.574768 INFO::Found 0 missing values.
2025-09-26 07:44:33.579739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:33.580681 INFO::Done
2025-09-26 07:44:33.581539 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:33.598334 INFO::Starting hierarchical adjustment
2025-09-26 07:44:33.599682 INFO::Found 3 batches.
2025-09-26 07:44:33.600521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:33.602229 INFO::Using default BPPARAM
2025-09-26 07:44:33.603053 INFO::Processing subtree level 1
2025-09-26 07:44:33.761468 INFO::Adjusting the last 1 batches sequentially
2025-09-26 07:44:33.764114 INFO::Done
2025-09-26 07:44:33.765139 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:33.769028 INFO::ASW Batch was -0.0722343941370842 prior to batch effect correction and is now -0.0722343941370842 .
2025-09-26 07:44:33.770851 INFO::Total function execution time is 0.845198154449463 s and adjustment time is 0.164702892303467 s ( 19.49 )
2025-09-26 07:44:33.79198 INFO::Formatting Data.
2025-09-26 07:44:33.793125 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:33.794502 INFO::Removing potential empty rows and columns
2025-09-26 07:44:33.796378 INFO::Found 0 missing values.
2025-09-26 07:44:33.797934 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.
2025-09-26 07:44:33.814169 INFO::Formatting Data.
2025-09-26 07:44:33.815201 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:33.816457 INFO::Removing potential empty rows and columns
2025-09-26 07:44:33.817989 INFO::Found 0 missing values.
2025-09-26 07:44:33.819272 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.
2025-09-26 07:44:33.842446 INFO::Formatting Data.
2025-09-26 07:44:33.843489 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:33.844805 INFO::Removing potential empty rows and columns
2025-09-26 07:44:33.846346 INFO::Found 0 missing values.
2025-09-26 07:44:33.84773 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.
2025-09-26 07:44:33.854502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:33.855453 INFO::Done
2025-09-26 07:44:33.856231 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:33.859167 INFO::Starting hierarchical adjustment
2025-09-26 07:44:33.860273 INFO::Found 2 batches.
2025-09-26 07:44:33.861144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:33.862118 INFO::Using default BPPARAM
2025-09-26 07:44:33.862927 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:33.864346 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 07:44:33.896023 INFO::Done
2025-09-26 07:44:33.896992 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:33.89981 INFO::ASW Batch was -0.0726477434288376 prior to batch effect correction and is now -0.120697774301762 .
2025-09-26 07:44:33.900988 INFO::Total function execution time is 0.0586094856262207 s and adjustment time is 0.0359566211700439 s ( 61.35 )
2025-09-26 07:44:33.904663 INFO::Formatting Data.
2025-09-26 07:44:33.905632 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:33.918212 INFO::Formatting Data.
2025-09-26 07:44:33.919233 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:33.920571 INFO::Removing potential empty rows and columns
2025-09-26 07:44:33.922202 INFO::Found 0 missing values.
2025-09-26 07:44:33.967365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:33.968813 INFO::Done
2025-09-26 07:44:33.96959 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:33.972489 INFO::Starting hierarchical adjustment
2025-09-26 07:44:33.973566 INFO::Found 2 batches.
2025-09-26 07:44:33.974336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:33.975209 INFO::Using default BPPARAM
2025-09-26 07:44:33.975975 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:33.977373 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 07:44:33.999613 INFO::Done
2025-09-26 07:44:34.000601 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:34.003484 INFO::ASW Batch was -0.00125023797654874 prior to batch effect correction and is now -0.0945150844707213 .
2025-09-26 07:44:34.004646 INFO::Total function execution time is 0.0864801406860352 s and adjustment time is 0.0262367725372314 s ( 30.34 )
2025-09-26 07:44:34.006211 INFO::Formatting Data.
2025-09-26 07:44:34.007072 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:34.008309 INFO::Removing potential empty rows and columns
2025-09-26 07:44:34.009894 INFO::Found 0 missing values.
2025-09-26 07:44:34.014318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:34.015293 INFO::Done
2025-09-26 07:44:34.016107 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:34.01918 INFO::Starting hierarchical adjustment
2025-09-26 07:44:34.020302 INFO::Found 2 batches.
2025-09-26 07:44:34.021168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:34.02208 INFO::Using default BPPARAM
2025-09-26 07:44:34.022889 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:34.024277 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 07:44:34.046585 INFO::Done
2025-09-26 07:44:34.047541 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:34.05046 INFO::ASW Batch was -0.00125023797654874 prior to batch effect correction and is now -0.0945150844707213 .
2025-09-26 07:44:34.05168 INFO::Total function execution time is 0.0454118251800537 s and adjustment time is 0.0264787673950195 s ( 58.31 )
2025-09-26 07:44:38.223067 INFO::Formatting Data.
2025-09-26 07:44:38.223962 INFO::Recognized SummarizedExperiment
2025-09-26 07:44:38.224689 INFO::Typecasting input to dataframe.
2025-09-26 07:44:38.264309 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:38.265823 INFO::Removing potential empty rows and columns
2025-09-26 07:44:38.270684 INFO::Found 0 missing values.
2025-09-26 07:44:38.280784 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:38.281722 INFO::Done
2025-09-26 07:44:38.282489 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:38.287432 INFO::Starting hierarchical adjustment
2025-09-26 07:44:38.288646 INFO::Found 2 batches.
2025-09-26 07:44:38.289433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:38.290916 INFO::Using default BPPARAM
2025-09-26 07:44:38.291829 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:38.293406 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 07:44:38.372013 INFO::Done
2025-09-26 07:44:38.372983 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:38.377962 INFO::ASW Batch was -0.0231988151215545 prior to batch effect correction and is now -0.0965343114736022 .
2025-09-26 07:44:38.379226 INFO::Total function execution time is 0.156533479690552 s and adjustment time is 0.0836255550384521 s ( 53.42 )
2025-09-26 07:44:38.404469 INFO::Formatting Data.
2025-09-26 07:44:38.405455 INFO::Recognized SummarizedExperiment
2025-09-26 07:44:38.406184 INFO::Typecasting input to dataframe.
2025-09-26 07:44:38.418798 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:38.420356 INFO::Removing potential empty rows and columns
2025-09-26 07:44:38.425534 INFO::Found 0 missing values.
2025-09-26 07:44:38.435832 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:38.436821 INFO::Done
2025-09-26 07:44:38.437791 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:38.442761 INFO::Starting hierarchical adjustment
2025-09-26 07:44:38.443946 INFO::Found 2 batches.
2025-09-26 07:44:38.444794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:38.445662 INFO::Using default BPPARAM
2025-09-26 07:44:38.446414 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:38.447794 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 07:44:38.483038 INFO::Done
2025-09-26 07:44:38.483952 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:38.488894 INFO::ASW Batch was 0.00510847810558299 prior to batch effect correction and is now 0.00510847810558299 .
2025-09-26 07:44:38.490126 INFO::Total function execution time is 0.0856592655181885 s and adjustment time is 0.0393078327178955 s ( 45.89 )
2025-09-26 07:44:38.514556 INFO::Formatting Data.
2025-09-26 07:44:38.515553 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:38.516785 INFO::Removing potential empty rows and columns
2025-09-26 07:44:38.518201 INFO::Found 0 missing values.
2025-09-26 07:44:38.522499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:38.523417 INFO::Done
2025-09-26 07:44:38.524171 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:38.526996 INFO::Starting hierarchical adjustment
2025-09-26 07:44:38.52807 INFO::Found 3 batches.
2025-09-26 07:44:38.52889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:38.52973 INFO::Using default BPPARAM
2025-09-26 07:44:38.530483 INFO::Processing subtree level 1
2025-09-26 07:44:38.831699 INFO::Adjusting the last 1 batches sequentially
2025-09-26 07:44:38.83411 INFO::Done
2025-09-26 07:44:38.834956 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:38.838294 INFO::ASW Batch was -0.0996207440452302 prior to batch effect correction and is now -0.154367751683618 .
2025-09-26 07:44:38.839582 INFO::Total function execution time is 0.325058937072754 s and adjustment time is 0.306255578994751 s ( 94.22 )
2025-09-26 07:44:38.928347 INFO::Skipping initial DF formatting
2025-09-26 07:44:38.929372 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:38.93513 INFO::Starting hierarchical adjustment
2025-09-26 07:44:38.936316 INFO::Found 5 batches.
2025-09-26 07:44:38.937164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:38.938042 INFO::Using default BPPARAM
2025-09-26 07:44:38.938819 INFO::Processing subtree level 1
2025-09-26 07:44:39.143315 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:39.146048 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 07:44:39.194245 INFO::Done
2025-09-26 07:44:39.195492 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:39.202707 INFO::ASW Batch was 0.519761199374625 prior to batch effect correction and is now 0.519761199374625 .
2025-09-26 07:44:39.203735 INFO::ASW Label was 0.374267098836789 prior to batch effect correction and is now 0.374267098836789 .
2025-09-26 07:44:39.205194 INFO::Total function execution time is 0.276883840560913 s and adjustment time is 0.258083820343018 s ( 93.21 )
2025-09-26 07:44:39.235402 INFO::Formatting Data.
2025-09-26 07:44:39.236518 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:39.237963 INFO::Removing potential empty rows and columns
2025-09-26 07:44:39.239606 INFO::Found 0 missing values.
2025-09-26 07:44:39.246524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:39.247476 INFO::Done
2025-09-26 07:44:39.248311 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:39.253205 INFO::Starting hierarchical adjustment
2025-09-26 07:44:39.254411 INFO::Found 5 batches.
2025-09-26 07:44:39.255289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:39.256248 INFO::Using default BPPARAM
2025-09-26 07:44:39.257121 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.
2025-09-26 07:44:39.422641 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:39.424973 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 07:44:39.450659 INFO::Done
2025-09-26 07:44:39.451661 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:39.456669 INFO::ASW Batch was 0.308375350055388 prior to batch effect correction and is now -0.0510847059179558 .
2025-09-26 07:44:39.457683 INFO::ASW Label was 0.491986226527229 prior to batch effect correction and is now 0.804821932482345 .
2025-09-26 07:44:39.458989 INFO::Total function execution time is 0.223648548126221 s and adjustment time is 0.196485996246338 s ( 87.85 )
2025-09-26 07:44:39.460295 INFO::Formatting Data.
2025-09-26 07:44:39.46127 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:39.462663 INFO::Removing potential empty rows and columns
2025-09-26 07:44:39.464286 INFO::Found 0 missing values.
2025-09-26 07:44:39.471018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:39.472073 INFO::Done
2025-09-26 07:44:39.472947 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:39.477497 INFO::Starting hierarchical adjustment
2025-09-26 07:44:39.478756 INFO::Found 5 batches.
2025-09-26 07:44:39.479604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:39.480629 INFO::Using default BPPARAM
2025-09-26 07:44:39.481467 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.
2025-09-26 07:44:39.649016 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:39.651365 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 07:44:39.675806 INFO::Done
2025-09-26 07:44:39.676881 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:39.681878 INFO::ASW Batch was 0.308375350055388 prior to batch effect correction and is now -0.0510847059179558 .
2025-09-26 07:44:39.682938 INFO::ASW Label was 0.491986226527229 prior to batch effect correction and is now 0.804821932482345 .
2025-09-26 07:44:39.684235 INFO::Total function execution time is 0.223875999450684 s and adjustment time is 0.197259902954102 s ( 88.11 )
2025-09-26 07:44:39.70571 INFO::Formatting Data.
2025-09-26 07:44:39.706903 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:39.708371 INFO::Removing potential empty rows and columns
2025-09-26 07:44:39.710186 INFO::Found 0 missing values.
2025-09-26 07:44:39.717572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:39.718635 INFO::Done
2025-09-26 07:44:39.719628 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:39.724618 INFO::Starting hierarchical adjustment
2025-09-26 07:44:39.72606 INFO::Found 5 batches.
2025-09-26 07:44:39.727064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:39.728287 INFO::Using default BPPARAM
2025-09-26 07:44:39.729418 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.
2025-09-26 07:44:39.892533 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:39.895111 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 07:44:39.919113 INFO::Done
2025-09-26 07:44:39.920187 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:39.925215 INFO::ASW Batch was 0.383267759687682 prior to batch effect correction and is now -0.0289042684228746 .
2025-09-26 07:44:39.926252 INFO::ASW Label was 0.329434471910135 prior to batch effect correction and is now 0.807180886786276 .
2025-09-26 07:44:39.927552 INFO::Total function execution time is 0.22187876701355 s and adjustment time is 0.193331956863403 s ( 87.13 )
2025-09-26 07:44:39.928911 INFO::Formatting Data.
2025-09-26 07:44:39.929916 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:39.9313 INFO::Removing potential empty rows and columns
2025-09-26 07:44:39.932858 INFO::Found 0 missing values.
2025-09-26 07:44:39.939196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:39.940144 INFO::Done
2025-09-26 07:44:39.941011 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:39.945301 INFO::Starting hierarchical adjustment
2025-09-26 07:44:39.94643 INFO::Found 5 batches.
2025-09-26 07:44:39.947248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:39.948183 INFO::Using default BPPARAM
2025-09-26 07:44:39.949026 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.
2025-09-26 07:44:40.100499 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:40.103038 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 07:44:40.125922 INFO::Done
2025-09-26 07:44:40.126882 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:40.131479 INFO::ASW Batch was 0.383267759687682 prior to batch effect correction and is now -0.0289042684228746 .
2025-09-26 07:44:40.132481 INFO::ASW Label was 0.329434471910135 prior to batch effect correction and is now 0.807180886786276 .
2025-09-26 07:44:40.133741 INFO::Total function execution time is 0.204843044281006 s and adjustment time is 0.17969536781311 s ( 87.72 )
2025-09-26 07:44:40.153507 INFO::Formatting Data.
2025-09-26 07:44:40.154574 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:40.15587 INFO::Removing potential empty rows and columns
2025-09-26 07:44:40.157393 INFO::Found 0 missing values.
2025-09-26 07:44:40.161446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:40.162295 INFO::Done
2025-09-26 07:44:40.163058 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:40.16716 INFO::Starting hierarchical adjustment
2025-09-26 07:44:40.168249 INFO::Found 2 batches.
2025-09-26 07:44:40.169081 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:40.169987 INFO::Using default BPPARAM
2025-09-26 07:44:40.170761 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:40.172079 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 07:44:40.193612 INFO::Done
2025-09-26 07:44:40.194538 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:40.19873 INFO::ASW Batch was 0.502770402258289 prior to batch effect correction and is now -0.00812729879499293 .
2025-09-26 07:44:40.199671 INFO::ASW Label was 0.421980249181985 prior to batch effect correction and is now 0.889383875247753 .
2025-09-26 07:44:40.200843 INFO::Total function execution time is 0.0474190711975098 s and adjustment time is 0.0255424976348877 s ( 53.87 )
2025-09-26 07:44:40.20194 INFO::Formatting Data.
2025-09-26 07:44:40.202793 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:40.204023 INFO::Removing potential empty rows and columns
2025-09-26 07:44:40.205468 INFO::Found 0 missing values.
2025-09-26 07:44:40.209735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:40.210718 INFO::Done
2025-09-26 07:44:40.211575 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:40.216045 INFO::Starting hierarchical adjustment
2025-09-26 07:44:40.217316 INFO::Found 2 batches.
2025-09-26 07:44:40.218146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:40.219039 INFO::Using default BPPARAM
2025-09-26 07:44:40.219824 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:40.221221 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 07:44:40.242648 INFO::Done
2025-09-26 07:44:40.243579 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:40.247714 INFO::ASW Batch was 0.502770402258289 prior to batch effect correction and is now -0.00812729879499293 .
2025-09-26 07:44:40.248692 INFO::ASW Label was 0.421980249181985 prior to batch effect correction and is now 0.889383875247753 .
2025-09-26 07:44:40.249853 INFO::Total function execution time is 0.0478999614715576 s and adjustment time is 0.0255739688873291 s ( 53.39 )
2025-09-26 07:44:40.266102 INFO::Formatting Data.
2025-09-26 07:44:40.267116 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:40.268339 INFO::Removing potential empty rows and columns
2025-09-26 07:44:40.269714 INFO::Found 0 missing values.
2025-09-26 07:44:40.272857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:40.273734 INFO::Done
2025-09-26 07:44:40.274507 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:40.277262 INFO::Starting hierarchical adjustment
2025-09-26 07:44:40.278354 INFO::Found 2 batches.
2025-09-26 07:44:40.27912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:40.279981 INFO::Using default BPPARAM
2025-09-26 07:44:40.280802 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:40.282204 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 07:44:40.32757 INFO::Done
2025-09-26 07:44:40.328516 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:40.331209 INFO::ASW Batch was 0.169030033638465 prior to batch effect correction and is now -0.133795173246201 .
2025-09-26 07:44:40.332342 INFO::Total function execution time is 0.0663077831268311 s and adjustment time is 0.0494065284729004 s ( 74.51 )
2025-09-26 07:44:40.349079 INFO::Formatting Data.
2025-09-26 07:44:40.350088 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:40.351289 INFO::Removing potential empty rows and columns
2025-09-26 07:44:40.352734 INFO::Found 0 missing values.
2025-09-26 07:44:40.354287 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.
2025-09-26 07:44:40.360963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:40.361865 INFO::Done
2025-09-26 07:44:40.362647 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:40.366688 INFO::Starting hierarchical adjustment
2025-09-26 07:44:40.367753 INFO::Found 2 batches.
2025-09-26 07:44:40.368535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:40.369408 INFO::Using default BPPARAM
2025-09-26 07:44:40.370159 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:40.371499 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 07:44:40.394822 INFO::Done
2025-09-26 07:44:40.395743 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:40.399818 INFO::ASW Batch was 0.471772006224888 prior to batch effect correction and is now -0.0278086888296158 .
2025-09-26 07:44:40.40076 INFO::ASW Label was 0.591861460913104 prior to batch effect correction and is now 0.919235886538642 .
2025-09-26 07:44:40.401831 INFO::Total function execution time is 0.0528326034545898 s and adjustment time is 0.0272574424743652 s ( 51.59 )
2025-09-26 07:44:40.402906 INFO::Formatting Data.
2025-09-26 07:44:40.403733 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:40.405059 INFO::Removing potential empty rows and columns
2025-09-26 07:44:40.406453 INFO::Found 0 missing values.
2025-09-26 07:44:40.407719 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.
2025-09-26 07:44:40.414352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:40.415249 INFO::Done
2025-09-26 07:44:40.416014 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:40.42005 INFO::Starting hierarchical adjustment
2025-09-26 07:44:40.421184 INFO::Found 2 batches.
2025-09-26 07:44:40.421934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:40.422745 INFO::Using default BPPARAM
2025-09-26 07:44:40.423457 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:40.424786 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 07:44:40.447369 INFO::Done
2025-09-26 07:44:40.448256 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:40.452165 INFO::ASW Batch was 0.471772006224888 prior to batch effect correction and is now -0.0278086888296158 .
2025-09-26 07:44:40.453034 INFO::ASW Label was 0.591861460913104 prior to batch effect correction and is now 0.919235886538642 .
2025-09-26 07:44:40.454118 INFO::Total function execution time is 0.0512139797210693 s and adjustment time is 0.0263805389404297 s ( 51.51 )
2025-09-26 07:44:40.759409 INFO::Formatting Data.
2025-09-26 07:44:40.760592 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:40.761865 INFO::Removing potential empty rows and columns
2025-09-26 07:44:40.76335 INFO::Found 0 missing values.
2025-09-26 07:44:40.767986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:40.768996 INFO::Done
2025-09-26 07:44:40.769833 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:40.772971 INFO::Starting hierarchical adjustment
2025-09-26 07:44:40.77423 INFO::Found 3 batches.
2025-09-26 07:44:40.774995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:40.775876 INFO::Using default BPPARAM
2025-09-26 07:44:40.776687 INFO::Processing subtree level 1
2025-09-26 07:44:40.89163 INFO::Adjusting the last 1 batches sequentially
2025-09-26 07:44:40.894369 INFO::Done
2025-09-26 07:44:40.895357 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:40.899291 INFO::ASW Batch was -0.123389571919985 prior to batch effect correction and is now -0.123389571919985 .
2025-09-26 07:44:40.900986 INFO::Total function execution time is 0.1415855884552 s and adjustment time is 0.120346069335938 s ( 85 )
2025-09-26 07:44:40.902718 INFO::Formatting Data.
2025-09-26 07:44:40.903813 INFO::Typecasting input to dataframe.
2025-09-26 07:44:40.905101 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:40.906533 INFO::Removing potential empty rows and columns
2025-09-26 07:44:40.90819 INFO::Found 0 missing values.
2025-09-26 07:44:40.913064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:40.914069 INFO::Done
2025-09-26 07:44:40.914923 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:40.918068 INFO::Starting hierarchical adjustment
2025-09-26 07:44:40.919317 INFO::Found 3 batches.
2025-09-26 07:44:40.920207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:40.921264 INFO::Using default BPPARAM
2025-09-26 07:44:40.922112 INFO::Processing subtree level 1
2025-09-26 07:44:41.031292 INFO::Adjusting the last 1 batches sequentially
2025-09-26 07:44:41.033952 INFO::Done
2025-09-26 07:44:41.034927 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:41.038625 INFO::ASW Batch was -0.123389571919985 prior to batch effect correction and is now -0.123389571919985 .
2025-09-26 07:44:41.040169 INFO::Total function execution time is 0.137410163879395 s and adjustment time is 0.114881277084351 s ( 83.6 )
2025-09-26 07:44:41.059413 INFO::Formatting Data.
2025-09-26 07:44:41.060514 INFO::Typecasting input to dataframe.
2025-09-26 07:44:41.061748 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:41.063054 INFO::Removing potential empty rows and columns
2025-09-26 07:44:41.064903 INFO::Found 0 missing values.
2025-09-26 07:44:41.06984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:41.070824 INFO::Done
2025-09-26 07:44:41.071701 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:41.0748 INFO::Starting hierarchical adjustment
2025-09-26 07:44:41.076047 INFO::Found 3 batches.
2025-09-26 07:44:41.076991 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:41.077976 INFO::Using default BPPARAM
2025-09-26 07:44:41.078818 INFO::Processing subtree level 1
2025-09-26 07:44:41.187976 INFO::Adjusting the last 1 batches sequentially
2025-09-26 07:44:41.190581 INFO::Done
2025-09-26 07:44:41.191546 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:41.195264 INFO::ASW Batch was -0.0750270191174205 prior to batch effect correction and is now -0.0750270191174205 .
2025-09-26 07:44:41.196793 INFO::Total function execution time is 0.137416124343872 s and adjustment time is 0.114763259887695 s ( 83.52 )
2025-09-26 07:44:41.38042 INFO::Formatting Data.
2025-09-26 07:44:41.381707 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:41.383362 INFO::Removing potential empty rows and columns
2025-09-26 07:44:41.387674 INFO::Found 1000 missing values.
2025-09-26 07:44:41.416924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:41.417925 INFO::Done
2025-09-26 07:44:41.418754 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:41.42664 INFO::Starting hierarchical adjustment
2025-09-26 07:44:41.42787 INFO::Found 10 batches.
2025-09-26 07:44:41.42873 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:41.429643 INFO::Using default BPPARAM
2025-09-26 07:44:41.430439 INFO::Processing subtree level 1
2025-09-26 07:44:41.609717 INFO::Processing subtree level 2
2025-09-26 07:44:41.798397 INFO::Adjusting the last 1 batches sequentially
2025-09-26 07:44:41.801089 INFO::Done
2025-09-26 07:44:41.801977 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:41.810093 INFO::ASW Batch was 0.494560624035295 prior to batch effect correction and is now 0.494560624035295 .
2025-09-26 07:44:41.811093 INFO::ASW Label was 0.338511590802307 prior to batch effect correction and is now 0.338511590802307 .
2025-09-26 07:44:41.812463 INFO::Total function execution time is 0.432058572769165 s and adjustment time is 0.373470067977905 s ( 86.44 )
2025-09-26 07:44:41.813742 INFO::Formatting Data.
2025-09-26 07:44:41.814653 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:41.816506 INFO::Removing potential empty rows and columns
2025-09-26 07:44:41.820832 INFO::Found 1000 missing values.
2025-09-26 07:44:41.84872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:41.849647 INFO::Done
2025-09-26 07:44:41.850422 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:41.858099 INFO::Starting hierarchical adjustment
2025-09-26 07:44:41.859287 INFO::Found 10 batches.
2025-09-26 07:44:43.263676 INFO::Set up parallel execution backend with 2 workers
2025-09-26 07:44:43.266062 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-26 07:44:44.969378 INFO::Adjusting the last 2 batches sequentially
2025-09-26 07:44:44.972583 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 07:44:45.000089 INFO::Done
2025-09-26 07:44:45.000998 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:45.008289 INFO::ASW Batch was 0.494560624035295 prior to batch effect correction and is now 0.494560624035295 .
2025-09-26 07:44:45.009225 INFO::ASW Label was 0.338511590802307 prior to batch effect correction and is now 0.338511590802307 .
2025-09-26 07:44:45.010494 INFO::Total function execution time is 3.19672417640686 s and adjustment time is 3.14101314544678 s ( 98.26 )
2025-09-26 07:44:45.215822 INFO::Formatting Data.
2025-09-26 07:44:45.21706 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:45.218476 INFO::Removing potential empty rows and columns
2025-09-26 07:44:45.220224 INFO::Found 0 missing values.
2025-09-26 07:44:45.226664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:45.227644 INFO::Done
2025-09-26 07:44:45.22849 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 07:44:45.232835 INFO::Starting hierarchical adjustment
2025-09-26 07:44:45.234069 INFO::Found 3 batches.
2025-09-26 07:44:45.234921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 07:44:45.235886 INFO::Using default BPPARAM
2025-09-26 07:44:45.236763 INFO::Processing subtree level 1
2025-09-26 07:44:45.377645 INFO::Adjusting the last 1 batches sequentially
2025-09-26 07:44:45.380299 INFO::Done
2025-09-26 07:44:45.38139 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 07:44:45.386561 INFO::ASW Batch was 0.195822194932394 prior to batch effect correction and is now -0.142504811461179 .
2025-09-26 07:44:45.387699 INFO::ASW Label was -0.175227077981031 prior to batch effect correction and is now -0.0494374799605118 .
2025-09-26 07:44:45.389171 INFO::Total function execution time is 0.173354148864746 s and adjustment time is 0.146451473236084 s ( 84.48 )
2025-09-26 07:44:45.582586 INFO::Formatting Data.
2025-09-26 07:44:45.583841 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:45.585515 INFO::Removing potential empty rows and columns
2025-09-26 07:44:45.587418 INFO::Found 2 missing values.
2025-09-26 07:44:45.592758 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:45.593815 INFO::Done
2025-09-26 07:44:45.642524 INFO::Found NA in Reference column
2025-09-26 07:44:45.660087 INFO::Require at least two references per batch.
2025-09-26 07:44:45.697623 INFO::Formatting Data.
2025-09-26 07:44:45.698801 INFO::Recognized SummarizedExperiment
2025-09-26 07:44:45.699772 INFO::Typecasting input to dataframe.
2025-09-26 07:44:45.720105 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:45.7222 INFO::Removing potential empty rows and columns
2025-09-26 07:44:45.728862 INFO::Found 0 missing values.
2025-09-26 07:44:45.741906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:45.743062 INFO::Done
2025-09-26 07:44:45.766381 INFO::Formatting Data.
2025-09-26 07:44:45.767408 INFO::Recognized SummarizedExperiment
2025-09-26 07:44:45.768182 INFO::Typecasting input to dataframe.
2025-09-26 07:44:45.79505 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:45.796797 INFO::Removing potential empty rows and columns
2025-09-26 07:44:45.802759 INFO::Found 0 missing values.
2025-09-26 07:44:45.821522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:45.822468 INFO::Done
2025-09-26 07:44:45.844731 INFO::Formatting Data.
2025-09-26 07:44:45.845722 INFO::Recognized SummarizedExperiment
2025-09-26 07:44:45.846451 INFO::Typecasting input to dataframe.
2025-09-26 07:44:45.882509 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:45.884443 INFO::Removing potential empty rows and columns
2025-09-26 07:44:45.886346 INFO::Found 0 missing values.
2025-09-26 07:44:45.887734 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.
2025-09-26 07:44:45.89489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:45.895828 INFO::Done
2025-09-26 07:44:45.91106 INFO::Formatting Data.
2025-09-26 07:44:45.912167 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:45.913454 INFO::Removing potential empty rows and columns
2025-09-26 07:44:45.914909 INFO::Found 0 missing values.
2025-09-26 07:44:45.919235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:45.92015 INFO::Done
2025-09-26 07:44:45.938915 INFO::Formatting Data.
2025-09-26 07:44:45.940021 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:45.941386 INFO::Removing potential empty rows and columns
2025-09-26 07:44:45.942915 INFO::Found 0 missing values.
2025-09-26 07:44:45.947494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:45.948461 INFO::Done
2025-09-26 07:44:46.000618 INFO::Formatting Data.
2025-09-26 07:44:46.001952 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:46.003767 INFO::Removing potential empty rows and columns
2025-09-26 07:44:46.006153 INFO::Found 1 missing values.
2025-09-26 07:44:46.011916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:46.013542 INFO::Done
2025-09-26 07:44:46.052397 INFO::Formatting Data.
2025-09-26 07:44:46.053883 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:46.055482 INFO::Removing potential empty rows and columns
2025-09-26 07:44:46.057681 INFO::Found 2 missing values.
2025-09-26 07:44:46.059399 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.
2025-09-26 07:44:46.064027 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:46.06571 INFO::Done
2025-09-26 07:44:46.085248 INFO::Formatting Data.
2025-09-26 07:44:46.086554 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:46.088099 INFO::Removing potential empty rows and columns
2025-09-26 07:44:46.089915 INFO::Found 2 missing values.
2025-09-26 07:44:46.093114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:46.094209 INFO::Done
2025-09-26 07:44:46.117313 INFO::Formatting Data.
2025-09-26 07:44:46.118706 INFO::Typecasting input to dataframe.
2025-09-26 07:44:46.120496 INFO::Replacing NaNs with NAs.
2025-09-26 07:44:46.122159 INFO::Removing potential empty rows and columns
2025-09-26 07:44:46.124153 INFO::Found 0 missing values.
2025-09-26 07:44:46.130114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 07:44:46.131308 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
23.025 5.043 27.866
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.156 | 1.375 | 22.327 | |
| compute_asw | 0.037 | 0.000 | 0.037 | |
| count_existing | 0.019 | 0.000 | 0.019 | |
| generate_data_covariables | 0.016 | 0.000 | 0.016 | |
| generate_dataset | 0.015 | 0.000 | 0.015 | |