Yannis Schumann
| Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-18 12:03 -0400 (Sat, 18 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 165/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-10-17 21:22:52 -0400 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 21:24:19 -0400 (Fri, 17 Oct 2025) |
| EllapsedTime: 87.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 24.416 1.792 18.101
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
2025-10-17 21:23:43.983247 INFO::Formatting Data.
2025-10-17 21:23:43.98455 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:43.995558 INFO::Removing potential empty rows and columns
2025-10-17 21:23:44.23582 INFO::Found 0 missing values.
2025-10-17 21:23:44.23924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:44.239956 INFO::Done
2025-10-17 21:23:44.240541 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:44.253509 INFO::Starting hierarchical adjustment
2025-10-17 21:23:44.254617 INFO::Found 3 batches.
2025-10-17 21:23:44.255209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:44.256416 INFO::Using default BPPARAM
2025-10-17 21:23:44.256994 INFO::Processing subtree level 1
2025-10-17 21:23:44.358989 INFO::Adjusting the last 1 batches sequentially
2025-10-17 21:23:44.361086 INFO::Done
2025-10-17 21:23:44.361986 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:44.365239 INFO::ASW Batch was -0.0806050151736926 prior to batch effect correction and is now -0.0806050151736926 .
2025-10-17 21:23:44.366465 INFO::Total function execution time is 0.383808851242065 s and adjustment time is 0.106649875640869 s ( 27.79 )
2025-10-17 21:23:44.380363 INFO::Formatting Data.
2025-10-17 21:23:44.381185 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:44.382154 INFO::Removing potential empty rows and columns
2025-10-17 21:23:44.383393 INFO::Found 0 missing values.
2025-10-17 21:23:44.384398 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-17 21:23:44.395816 INFO::Formatting Data.
2025-10-17 21:23:44.396725 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:44.397753 INFO::Removing potential empty rows and columns
2025-10-17 21:23:44.39889 INFO::Found 0 missing values.
2025-10-17 21:23:44.399887 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-17 21:23:44.416195 INFO::Formatting Data.
2025-10-17 21:23:44.417003 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:44.417907 INFO::Removing potential empty rows and columns
2025-10-17 21:23:44.418958 INFO::Found 0 missing values.
2025-10-17 21:23:44.419896 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-17 21:23:44.424272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:44.424813 INFO::Done
2025-10-17 21:23:44.425323 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:44.427289 INFO::Starting hierarchical adjustment
2025-10-17 21:23:44.427995 INFO::Found 2 batches.
2025-10-17 21:23:44.428516 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:44.429142 INFO::Using default BPPARAM
2025-10-17 21:23:44.429662 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:44.430603 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 21:23:44.454287 INFO::Done
2025-10-17 21:23:44.455067 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:44.457347 INFO::ASW Batch was -0.0244445103325848 prior to batch effect correction and is now -0.118446786262704 .
2025-10-17 21:23:44.458215 INFO::Total function execution time is 0.0420982837677002 s and adjustment time is 0.0263957977294922 s ( 62.7 )
2025-10-17 21:23:44.461142 INFO::Formatting Data.
2025-10-17 21:23:44.461799 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:44.471152 INFO::Formatting Data.
2025-10-17 21:23:44.471959 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:44.472925 INFO::Removing potential empty rows and columns
2025-10-17 21:23:44.474012 INFO::Found 0 missing values.
2025-10-17 21:23:44.477041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:44.477605 INFO::Done
2025-10-17 21:23:44.478139 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:44.480359 INFO::Starting hierarchical adjustment
2025-10-17 21:23:44.481127 INFO::Found 2 batches.
2025-10-17 21:23:44.481669 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:44.482325 INFO::Using default BPPARAM
2025-10-17 21:23:44.482908 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:44.483915 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:44.526029 INFO::Done
2025-10-17 21:23:44.526714 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:44.528645 INFO::ASW Batch was -0.0688729135030028 prior to batch effect correction and is now -0.115777174502129 .
2025-10-17 21:23:44.529419 INFO::Total function execution time is 0.0583639144897461 s and adjustment time is 0.0450665950775146 s ( 77.22 )
2025-10-17 21:23:44.53044 INFO::Formatting Data.
2025-10-17 21:23:44.530998 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:44.531823 INFO::Removing potential empty rows and columns
2025-10-17 21:23:44.532794 INFO::Found 0 missing values.
2025-10-17 21:23:44.53538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:44.535877 INFO::Done
2025-10-17 21:23:44.536368 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:44.53825 INFO::Starting hierarchical adjustment
2025-10-17 21:23:44.538917 INFO::Found 2 batches.
2025-10-17 21:23:44.539428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:44.539985 INFO::Using default BPPARAM
2025-10-17 21:23:44.54048 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:44.541316 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:44.555435 INFO::Done
2025-10-17 21:23:44.556142 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:44.558107 INFO::ASW Batch was -0.0688729135030028 prior to batch effect correction and is now -0.115777174502129 .
2025-10-17 21:23:44.558883 INFO::Total function execution time is 0.0284414291381836 s and adjustment time is 0.0166277885437012 s ( 58.46 )
2025-10-17 21:23:47.39869 INFO::Formatting Data.
2025-10-17 21:23:47.39938 INFO::Recognized SummarizedExperiment
2025-10-17 21:23:47.399847 INFO::Typecasting input to dataframe.
2025-10-17 21:23:47.429248 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:47.430468 INFO::Removing potential empty rows and columns
2025-10-17 21:23:47.434214 INFO::Found 0 missing values.
2025-10-17 21:23:47.441365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:47.442083 INFO::Done
2025-10-17 21:23:47.442622 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:47.446171 INFO::Starting hierarchical adjustment
2025-10-17 21:23:47.446939 INFO::Found 2 batches.
2025-10-17 21:23:47.447471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:47.448522 INFO::Using default BPPARAM
2025-10-17 21:23:47.449066 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:47.450044 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 21:23:47.505386 INFO::Done
2025-10-17 21:23:47.506089 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:47.509742 INFO::ASW Batch was -0.016836471631737 prior to batch effect correction and is now -0.0982200809226489 .
2025-10-17 21:23:47.510597 INFO::Total function execution time is 0.11218523979187 s and adjustment time is 0.0585763454437256 s ( 52.21 )
2025-10-17 21:23:47.528728 INFO::Formatting Data.
2025-10-17 21:23:47.52949 INFO::Recognized SummarizedExperiment
2025-10-17 21:23:47.530005 INFO::Typecasting input to dataframe.
2025-10-17 21:23:47.539346 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:47.540546 INFO::Removing potential empty rows and columns
2025-10-17 21:23:47.544222 INFO::Found 0 missing values.
2025-10-17 21:23:47.551293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:47.551967 INFO::Done
2025-10-17 21:23:47.552514 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:47.556072 INFO::Starting hierarchical adjustment
2025-10-17 21:23:47.556835 INFO::Found 2 batches.
2025-10-17 21:23:47.557367 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:47.557957 INFO::Using default BPPARAM
2025-10-17 21:23:47.55849 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:47.559479 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 21:23:47.58465 INFO::Done
2025-10-17 21:23:47.585417 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:47.58904 INFO::ASW Batch was 0.0054548218052503 prior to batch effect correction and is now 0.0054548218052503 .
2025-10-17 21:23:47.589928 INFO::Total function execution time is 0.0611720085144043 s and adjustment time is 0.0279214382171631 s ( 45.64 )
2025-10-17 21:23:47.608678 INFO::Formatting Data.
2025-10-17 21:23:47.609526 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:47.610443 INFO::Removing potential empty rows and columns
2025-10-17 21:23:47.611608 INFO::Found 0 missing values.
2025-10-17 21:23:47.614597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:47.615146 INFO::Done
2025-10-17 21:23:47.615662 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:47.617684 INFO::Starting hierarchical adjustment
2025-10-17 21:23:47.618399 INFO::Found 3 batches.
2025-10-17 21:23:47.618919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:47.619534 INFO::Using default BPPARAM
2025-10-17 21:23:47.620043 INFO::Processing subtree level 1
2025-10-17 21:23:47.753559 INFO::Adjusting the last 1 batches sequentially
2025-10-17 21:23:47.755303 INFO::Done
2025-10-17 21:23:47.755948 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:47.758391 INFO::ASW Batch was -0.106280937178649 prior to batch effect correction and is now -0.162891926502499 .
2025-10-17 21:23:47.7593 INFO::Total function execution time is 0.150678396224976 s and adjustment time is 0.137042760848999 s ( 90.95 )
2025-10-17 21:23:47.773176 INFO::Skipping initial DF formatting
2025-10-17 21:23:47.773887 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:47.777908 INFO::Starting hierarchical adjustment
2025-10-17 21:23:47.778717 INFO::Found 5 batches.
2025-10-17 21:23:47.77929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:47.779902 INFO::Using default BPPARAM
2025-10-17 21:23:47.78045 INFO::Processing subtree level 1
2025-10-17 21:23:47.994842 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:47.996469 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 21:23:48.016267 INFO::Done
2025-10-17 21:23:48.017035 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.021456 INFO::ASW Batch was 0.507178336403747 prior to batch effect correction and is now 0.507178336403747 .
2025-10-17 21:23:48.022142 INFO::ASW Label was 0.370822654123326 prior to batch effect correction and is now 0.370822654123326 .
2025-10-17 21:23:48.023012 INFO::Total function execution time is 0.249914169311523 s and adjustment time is 0.237670183181763 s ( 95.1 )
2025-10-17 21:23:48.08997 INFO::Formatting Data.
2025-10-17 21:23:48.090851 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.091845 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.092866 INFO::Found 0 missing values.
2025-10-17 21:23:48.09707 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:48.097734 INFO::Done
2025-10-17 21:23:48.098304 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:48.101604 INFO::Starting hierarchical adjustment
2025-10-17 21:23:48.102387 INFO::Found 5 batches.
2025-10-17 21:23:48.102906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:48.103621 INFO::Using default BPPARAM
2025-10-17 21:23:48.104267 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.248492 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:48.250563 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.271835 INFO::Done
2025-10-17 21:23:48.272711 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.276829 INFO::ASW Batch was 0.448948677295334 prior to batch effect correction and is now -0.0847266509046842 .
2025-10-17 21:23:48.277552 INFO::ASW Label was 0.282693451759029 prior to batch effect correction and is now 0.842145944503745 .
2025-10-17 21:23:48.278537 INFO::Total function execution time is 0.188636064529419 s and adjustment time is 0.169550657272339 s ( 89.88 )
2025-10-17 21:23:48.27958 INFO::Formatting Data.
2025-10-17 21:23:48.280304 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.281415 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.282711 INFO::Found 0 missing values.
2025-10-17 21:23:48.287826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:48.288502 INFO::Done
2025-10-17 21:23:48.289055 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:48.292607 INFO::Starting hierarchical adjustment
2025-10-17 21:23:48.293438 INFO::Found 5 batches.
2025-10-17 21:23:48.294024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:48.294714 INFO::Using default BPPARAM
2025-10-17 21:23:48.295317 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.440923 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:48.442774 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.461552 INFO::Done
2025-10-17 21:23:48.462417 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.466552 INFO::ASW Batch was 0.448948677295334 prior to batch effect correction and is now -0.0847266509046842 .
2025-10-17 21:23:48.467317 INFO::ASW Label was 0.282693451759029 prior to batch effect correction and is now 0.842145944503745 .
2025-10-17 21:23:48.468295 INFO::Total function execution time is 0.188717365264893 s and adjustment time is 0.168239116668701 s ( 89.15 )
2025-10-17 21:23:48.483832 INFO::Formatting Data.
2025-10-17 21:23:48.484738 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.485779 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.486884 INFO::Found 0 missing values.
2025-10-17 21:23:48.491202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:48.49182 INFO::Done
2025-10-17 21:23:48.492382 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:48.495694 INFO::Starting hierarchical adjustment
2025-10-17 21:23:48.496435 INFO::Found 5 batches.
2025-10-17 21:23:48.496974 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:48.497614 INFO::Using default BPPARAM
2025-10-17 21:23:48.498143 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.6278 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:48.629632 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.646152 INFO::Done
2025-10-17 21:23:48.646884 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.650306 INFO::ASW Batch was 0.349838553851992 prior to batch effect correction and is now -0.111385679104575 .
2025-10-17 21:23:48.650969 INFO::ASW Label was 0.360637414750848 prior to batch effect correction and is now 0.916217126900629 .
2025-10-17 21:23:48.651803 INFO::Total function execution time is 0.168081521987915 s and adjustment time is 0.14983057975769 s ( 89.14 )
2025-10-17 21:23:48.652662 INFO::Formatting Data.
2025-10-17 21:23:48.653311 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.654243 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.655265 INFO::Found 0 missing values.
2025-10-17 21:23:48.659474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:48.660095 INFO::Done
2025-10-17 21:23:48.660682 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:48.663892 INFO::Starting hierarchical adjustment
2025-10-17 21:23:48.664623 INFO::Found 5 batches.
2025-10-17 21:23:48.665173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:48.665788 INFO::Using default BPPARAM
2025-10-17 21:23:48.666328 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.791623 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:48.79325 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.809867 INFO::Done
2025-10-17 21:23:48.810603 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.813941 INFO::ASW Batch was 0.349838553851992 prior to batch effect correction and is now -0.111385679104575 .
2025-10-17 21:23:48.814625 INFO::ASW Label was 0.360637414750848 prior to batch effect correction and is now 0.916217126900629 .
2025-10-17 21:23:48.815513 INFO::Total function execution time is 0.162859439849854 s and adjustment time is 0.145351648330688 s ( 89.25 )
2025-10-17 21:23:48.828832 INFO::Formatting Data.
2025-10-17 21:23:48.829625 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.830547 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.831576 INFO::Found 0 missing values.
2025-10-17 21:23:48.834268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:48.834811 INFO::Done
2025-10-17 21:23:48.835326 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:48.838297 INFO::Starting hierarchical adjustment
2025-10-17 21:23:48.839048 INFO::Found 2 batches.
2025-10-17 21:23:48.839595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:48.840213 INFO::Using default BPPARAM
2025-10-17 21:23:48.840739 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:48.841668 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.856105 INFO::Done
2025-10-17 21:23:48.856833 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.859886 INFO::ASW Batch was 0.589665839439261 prior to batch effect correction and is now -0.0217007807374605 .
2025-10-17 21:23:48.86054 INFO::ASW Label was 0.480183045800813 prior to batch effect correction and is now 0.942845035247222 .
2025-10-17 21:23:48.861325 INFO::Total function execution time is 0.0325865745544434 s and adjustment time is 0.0171694755554199 s ( 52.69 )
2025-10-17 21:23:48.862098 INFO::Formatting Data.
2025-10-17 21:23:48.862724 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.863607 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.864623 INFO::Found 0 missing values.
2025-10-17 21:23:48.867288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:48.867814 INFO::Done
2025-10-17 21:23:48.868335 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:48.871219 INFO::Starting hierarchical adjustment
2025-10-17 21:23:48.871929 INFO::Found 2 batches.
2025-10-17 21:23:48.872457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:48.873029 INFO::Using default BPPARAM
2025-10-17 21:23:48.873557 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:48.874482 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 21:23:48.888751 INFO::Done
2025-10-17 21:23:48.889466 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.892479 INFO::ASW Batch was 0.589665839439261 prior to batch effect correction and is now -0.0217007807374605 .
2025-10-17 21:23:48.893092 INFO::ASW Label was 0.480183045800813 prior to batch effect correction and is now 0.942845035247222 .
2025-10-17 21:23:48.893867 INFO::Total function execution time is 0.0317838191986084 s and adjustment time is 0.0169363021850586 s ( 53.29 )
2025-10-17 21:23:48.90471 INFO::Formatting Data.
2025-10-17 21:23:48.905484 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.90637 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.907255 INFO::Found 0 missing values.
2025-10-17 21:23:48.909281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:48.909808 INFO::Done
2025-10-17 21:23:48.910322 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:48.912219 INFO::Starting hierarchical adjustment
2025-10-17 21:23:48.912893 INFO::Found 2 batches.
2025-10-17 21:23:48.913418 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:48.913992 INFO::Using default BPPARAM
2025-10-17 21:23:48.914495 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:48.9154 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 21:23:48.945455 INFO::Done
2025-10-17 21:23:48.946157 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.948133 INFO::ASW Batch was -0.0226439266687608 prior to batch effect correction and is now -0.196438529441035 .
2025-10-17 21:23:48.948952 INFO::Total function execution time is 0.0443196296691895 s and adjustment time is 0.0326693058013916 s ( 73.71 )
2025-10-17 21:23:48.960594 INFO::Formatting Data.
2025-10-17 21:23:48.96142 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.962328 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.963324 INFO::Found 0 missing values.
2025-10-17 21:23:48.964478 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-17 21:23:48.968928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:48.969532 INFO::Done
2025-10-17 21:23:48.970046 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:48.972923 INFO::Starting hierarchical adjustment
2025-10-17 21:23:48.973626 INFO::Found 2 batches.
2025-10-17 21:23:48.974138 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:48.97472 INFO::Using default BPPARAM
2025-10-17 21:23:48.975236 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:48.97615 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 21:23:48.991794 INFO::Done
2025-10-17 21:23:48.992453 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:48.995257 INFO::ASW Batch was 0.580861659298034 prior to batch effect correction and is now 0.232263422727934 .
2025-10-17 21:23:48.995842 INFO::ASW Label was 0.621906412755707 prior to batch effect correction and is now 0.840182237282807 .
2025-10-17 21:23:48.996583 INFO::Total function execution time is 0.0360915660858154 s and adjustment time is 0.0182864665985107 s ( 50.67 )
2025-10-17 21:23:48.997333 INFO::Formatting Data.
2025-10-17 21:23:48.997917 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:48.998818 INFO::Removing potential empty rows and columns
2025-10-17 21:23:48.999792 INFO::Found 0 missing values.
2025-10-17 21:23:49.000692 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-17 21:23:49.005017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:49.005597 INFO::Done
2025-10-17 21:23:49.006077 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:49.008984 INFO::Starting hierarchical adjustment
2025-10-17 21:23:49.009678 INFO::Found 2 batches.
2025-10-17 21:23:49.010185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:49.010754 INFO::Using default BPPARAM
2025-10-17 21:23:49.011255 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:49.012136 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 21:23:49.027519 INFO::Done
2025-10-17 21:23:49.028195 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:49.031035 INFO::ASW Batch was 0.580861659298034 prior to batch effect correction and is now 0.232263422727934 .
2025-10-17 21:23:49.031634 INFO::ASW Label was 0.621906412755707 prior to batch effect correction and is now 0.840182237282807 .
2025-10-17 21:23:49.032407 INFO::Total function execution time is 0.0350842475891113 s and adjustment time is 0.0179495811462402 s ( 51.16 )
2025-10-17 21:23:49.227661 INFO::Formatting Data.
2025-10-17 21:23:49.228432 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:49.229312 INFO::Removing potential empty rows and columns
2025-10-17 21:23:49.230397 INFO::Found 0 missing values.
2025-10-17 21:23:49.233367 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:49.233917 INFO::Done
2025-10-17 21:23:49.234425 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:49.236433 INFO::Starting hierarchical adjustment
2025-10-17 21:23:49.237136 INFO::Found 3 batches.
2025-10-17 21:23:49.237655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:49.23827 INFO::Using default BPPARAM
2025-10-17 21:23:49.238779 INFO::Processing subtree level 1
2025-10-17 21:23:49.320864 INFO::Adjusting the last 1 batches sequentially
2025-10-17 21:23:49.322572 INFO::Done
2025-10-17 21:23:49.323246 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:49.325675 INFO::ASW Batch was -0.090293008445171 prior to batch effect correction and is now -0.090293008445171 .
2025-10-17 21:23:49.326617 INFO::Total function execution time is 0.0989854335784912 s and adjustment time is 0.0855717658996582 s ( 86.45 )
2025-10-17 21:23:49.327638 INFO::Formatting Data.
2025-10-17 21:23:49.328293 INFO::Typecasting input to dataframe.
2025-10-17 21:23:49.329039 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:49.329952 INFO::Removing potential empty rows and columns
2025-10-17 21:23:49.331031 INFO::Found 0 missing values.
2025-10-17 21:23:49.334097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:49.33469 INFO::Done
2025-10-17 21:23:49.335243 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:49.337367 INFO::Starting hierarchical adjustment
2025-10-17 21:23:49.338077 INFO::Found 3 batches.
2025-10-17 21:23:49.338614 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:49.339227 INFO::Using default BPPARAM
2025-10-17 21:23:49.339757 INFO::Processing subtree level 1
2025-10-17 21:23:49.420636 INFO::Adjusting the last 1 batches sequentially
2025-10-17 21:23:49.422351 INFO::Done
2025-10-17 21:23:49.423018 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:49.425509 INFO::ASW Batch was -0.090293008445171 prior to batch effect correction and is now -0.090293008445171 .
2025-10-17 21:23:49.426447 INFO::Total function execution time is 0.0987927913665771 s and adjustment time is 0.0844094753265381 s ( 85.44 )
2025-10-17 21:23:49.438974 INFO::Formatting Data.
2025-10-17 21:23:49.439852 INFO::Typecasting input to dataframe.
2025-10-17 21:23:49.440692 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:49.441603 INFO::Removing potential empty rows and columns
2025-10-17 21:23:49.442647 INFO::Found 0 missing values.
2025-10-17 21:23:49.445619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:49.446172 INFO::Done
2025-10-17 21:23:49.446681 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:49.448642 INFO::Starting hierarchical adjustment
2025-10-17 21:23:49.449365 INFO::Found 3 batches.
2025-10-17 21:23:49.449886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:49.450502 INFO::Using default BPPARAM
2025-10-17 21:23:49.451022 INFO::Processing subtree level 1
2025-10-17 21:23:49.532497 INFO::Adjusting the last 1 batches sequentially
2025-10-17 21:23:49.534354 INFO::Done
2025-10-17 21:23:49.535062 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:49.537677 INFO::ASW Batch was 0.00474479092259085 prior to batch effect correction and is now 0.00474479092259085 .
2025-10-17 21:23:49.538606 INFO::Total function execution time is 0.0996901988983154 s and adjustment time is 0.0851304531097412 s ( 85.4 )
2025-10-17 21:23:49.688756 INFO::Formatting Data.
2025-10-17 21:23:49.689656 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:49.690858 INFO::Removing potential empty rows and columns
2025-10-17 21:23:49.693714 INFO::Found 1000 missing values.
2025-10-17 21:23:49.712719 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:49.713577 INFO::Done
2025-10-17 21:23:49.714211 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:49.720043 INFO::Starting hierarchical adjustment
2025-10-17 21:23:49.720875 INFO::Found 10 batches.
2025-10-17 21:23:49.721422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:49.722047 INFO::Using default BPPARAM
2025-10-17 21:23:49.722605 INFO::Processing subtree level 1
2025-10-17 21:23:49.87174 INFO::Processing subtree level 2
2025-10-17 21:23:50.013488 INFO::Adjusting the last 1 batches sequentially
2025-10-17 21:23:50.015433 INFO::Done
2025-10-17 21:23:50.016108 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:50.021647 INFO::ASW Batch was 0.542264693899582 prior to batch effect correction and is now 0.542264693899582 .
2025-10-17 21:23:50.022315 INFO::ASW Label was 0.330736196156891 prior to batch effect correction and is now 0.330736196156891 .
2025-10-17 21:23:50.02323 INFO::Total function execution time is 0.334561824798584 s and adjustment time is 0.29471492767334 s ( 88.09 )
2025-10-17 21:23:50.024076 INFO::Formatting Data.
2025-10-17 21:23:50.02475 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:50.026003 INFO::Removing potential empty rows and columns
2025-10-17 21:23:50.028814 INFO::Found 1000 missing values.
2025-10-17 21:23:50.048053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:50.048831 INFO::Done
2025-10-17 21:23:50.049413 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:50.055094 INFO::Starting hierarchical adjustment
2025-10-17 21:23:50.055934 INFO::Found 10 batches.
2025-10-17 21:23:51.140475 INFO::Set up parallel execution backend with 2 workers
2025-10-17 21:23:51.143679 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-17 21:23:52.220815 INFO::Adjusting the last 2 batches sequentially
2025-10-17 21:23:52.222528 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 21:23:52.238858 INFO::Done
2025-10-17 21:23:52.239524 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:52.24395 INFO::ASW Batch was 0.542264693899582 prior to batch effect correction and is now 0.542264693899582 .
2025-10-17 21:23:52.244515 INFO::ASW Label was 0.330736196156891 prior to batch effect correction and is now 0.330736196156891 .
2025-10-17 21:23:52.245229 INFO::Total function execution time is 2.22118043899536 s and adjustment time is 2.18308854103088 s ( 98.29 )
2025-10-17 21:23:52.404524 INFO::Formatting Data.
2025-10-17 21:23:52.405273 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.406136 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.407145 INFO::Found 0 missing values.
2025-10-17 21:23:52.410583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.41109 INFO::Done
2025-10-17 21:23:52.411577 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 21:23:52.414245 INFO::Starting hierarchical adjustment
2025-10-17 21:23:52.414917 INFO::Found 3 batches.
2025-10-17 21:23:52.415429 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 21:23:52.416002 INFO::Using default BPPARAM
2025-10-17 21:23:52.416506 INFO::Processing subtree level 1
2025-10-17 21:23:52.529141 INFO::Adjusting the last 1 batches sequentially
2025-10-17 21:23:52.530843 INFO::Done
2025-10-17 21:23:52.531461 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 21:23:52.534528 INFO::ASW Batch was 0.122719269036313 prior to batch effect correction and is now -0.122386056063388 .
2025-10-17 21:23:52.535134 INFO::ASW Label was -0.19888696205095 prior to batch effect correction and is now -0.0749073552486481 .
2025-10-17 21:23:52.536005 INFO::Total function execution time is 0.131531000137329 s and adjustment time is 0.116047382354736 s ( 88.23 )
2025-10-17 21:23:52.648829 INFO::Formatting Data.
2025-10-17 21:23:52.649611 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.650554 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.651598 INFO::Found 2 missing values.
2025-10-17 21:23:52.654406 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.654932 INFO::Done
2025-10-17 21:23:52.681036 INFO::Found NA in Reference column
2025-10-17 21:23:52.690167 INFO::Require at least two references per batch.
2025-10-17 21:23:52.710315 INFO::Formatting Data.
2025-10-17 21:23:52.711015 INFO::Recognized SummarizedExperiment
2025-10-17 21:23:52.711526 INFO::Typecasting input to dataframe.
2025-10-17 21:23:52.721255 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.722383 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.725661 INFO::Found 0 missing values.
2025-10-17 21:23:52.731959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.732563 INFO::Done
2025-10-17 21:23:52.7475 INFO::Formatting Data.
2025-10-17 21:23:52.748238 INFO::Recognized SummarizedExperiment
2025-10-17 21:23:52.748743 INFO::Typecasting input to dataframe.
2025-10-17 21:23:52.766065 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.767271 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.770568 INFO::Found 0 missing values.
2025-10-17 21:23:52.780742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.781457 INFO::Done
2025-10-17 21:23:52.797349 INFO::Formatting Data.
2025-10-17 21:23:52.798066 INFO::Recognized SummarizedExperiment
2025-10-17 21:23:52.79859 INFO::Typecasting input to dataframe.
2025-10-17 21:23:52.815023 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.816025 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.817041 INFO::Found 0 missing values.
2025-10-17 21:23:52.817907 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-17 21:23:52.821983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.822503 INFO::Done
2025-10-17 21:23:52.831895 INFO::Formatting Data.
2025-10-17 21:23:52.832698 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.833519 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.834458 INFO::Found 0 missing values.
2025-10-17 21:23:52.837148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.837651 INFO::Done
2025-10-17 21:23:52.847975 INFO::Formatting Data.
2025-10-17 21:23:52.848785 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.849666 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.850643 INFO::Found 0 missing values.
2025-10-17 21:23:52.853436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.853995 INFO::Done
2025-10-17 21:23:52.882944 INFO::Formatting Data.
2025-10-17 21:23:52.88382 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.88499 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.886151 INFO::Found 1 missing values.
2025-10-17 21:23:52.888779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.889329 INFO::Done
2025-10-17 21:23:52.908417 INFO::Formatting Data.
2025-10-17 21:23:52.909262 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.910148 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.911137 INFO::Found 2 missing values.
2025-10-17 21:23:52.911997 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-17 21:23:52.914174 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.914702 INFO::Done
2025-10-17 21:23:52.923971 INFO::Formatting Data.
2025-10-17 21:23:52.92479 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.925653 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.92658 INFO::Found 2 missing values.
2025-10-17 21:23:52.928168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.928697 INFO::Done
2025-10-17 21:23:52.938846 INFO::Formatting Data.
2025-10-17 21:23:52.939606 INFO::Typecasting input to dataframe.
2025-10-17 21:23:52.940463 INFO::Replacing NaNs with NAs.
2025-10-17 21:23:52.941327 INFO::Removing potential empty rows and columns
2025-10-17 21:23:52.942344 INFO::Found 0 missing values.
2025-10-17 21:23:52.94518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 21:23:52.945713 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.370 3.300 20.387
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.416 | 1.792 | 18.101 | |
| compute_asw | 0.024 | 0.002 | 0.025 | |
| count_existing | 0.012 | 0.002 | 0.014 | |
| generate_data_covariables | 0.011 | 0.002 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.013 | |