Yannis Schumann
| Snapshot Date: 2025-12-15 13:40 -0500 (Mon, 15 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-16 11:34 -0500 (Tue, 16 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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 168/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-12-15 21:11:03 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 21:12:30 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 86.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.7.0’
* 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 23.418 1.189 16.598
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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) (2025-10-20 r88955) -- "Unsuffered Consequences"
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")
2025-12-15 21:11:53.83732 INFO::Formatting Data.
2025-12-15 21:11:53.838611 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:53.849577 INFO::Removing potential empty rows and columns
2025-12-15 21:11:54.099078 INFO::Found 0 missing values.
2025-12-15 21:11:54.102489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:54.103188 INFO::Done
2025-12-15 21:11:54.103762 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:54.115915 INFO::Starting hierarchical adjustment
2025-12-15 21:11:54.116905 INFO::Found 3 batches.
2025-12-15 21:11:54.117493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:54.118671 INFO::Using default BPPARAM
2025-12-15 21:11:54.119242 INFO::Processing subtree level 1
2025-12-15 21:11:54.225563 INFO::Adjusting the last 1 batches sequentially
2025-12-15 21:11:54.22746 INFO::Done
2025-12-15 21:11:54.228188 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:54.231143 INFO::ASW Batch was -0.127577553417448 prior to batch effect correction and is now -0.127577553417448 .
2025-12-15 21:11:54.232337 INFO::Total function execution time is 0.395612478256226 s and adjustment time is 0.110753536224365 s ( 28 )
2025-12-15 21:11:54.247919 INFO::Formatting Data.
2025-12-15 21:11:54.248829 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:54.249878 INFO::Removing potential empty rows and columns
2025-12-15 21:11:54.251076 INFO::Found 0 missing values.
2025-12-15 21:11:54.252131 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.
2025-12-15 21:11:54.263941 INFO::Formatting Data.
2025-12-15 21:11:54.264805 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:54.26586 INFO::Removing potential empty rows and columns
2025-12-15 21:11:54.267111 INFO::Found 0 missing values.
2025-12-15 21:11:54.268139 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.
2025-12-15 21:11:54.287172 INFO::Formatting Data.
2025-12-15 21:11:54.288123 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:54.289203 INFO::Removing potential empty rows and columns
2025-12-15 21:11:54.290388 INFO::Found 0 missing values.
2025-12-15 21:11:54.291453 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.
2025-12-15 21:11:54.296683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:54.297335 INFO::Done
2025-12-15 21:11:54.297949 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:54.300318 INFO::Starting hierarchical adjustment
2025-12-15 21:11:54.301085 INFO::Found 2 batches.
2025-12-15 21:11:54.301652 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:54.302383 INFO::Using default BPPARAM
2025-12-15 21:11:54.302974 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:54.304036 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 21:11:54.327333 INFO::Done
2025-12-15 21:11:54.328186 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:54.330542 INFO::ASW Batch was -0.0692432259697335 prior to batch effect correction and is now -0.116250775150203 .
2025-12-15 21:11:54.331479 INFO::Total function execution time is 0.0444154739379883 s and adjustment time is 0.0263476371765137 s ( 59.32 )
2025-12-15 21:11:54.334467 INFO::Formatting Data.
2025-12-15 21:11:54.335254 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:54.344741 INFO::Formatting Data.
2025-12-15 21:11:54.34561 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:54.346606 INFO::Removing potential empty rows and columns
2025-12-15 21:11:54.347742 INFO::Found 0 missing values.
2025-12-15 21:11:54.350768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:54.351355 INFO::Done
2025-12-15 21:11:54.351917 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:54.354295 INFO::Starting hierarchical adjustment
2025-12-15 21:11:54.355045 INFO::Found 2 batches.
2025-12-15 21:11:54.355588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:54.356253 INFO::Using default BPPARAM
2025-12-15 21:11:54.356816 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:54.357798 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 21:11:54.394995 INFO::Done
2025-12-15 21:11:54.395678 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:54.397599 INFO::ASW Batch was 0.0620722830494281 prior to batch effect correction and is now -0.0975992035597045 .
2025-12-15 21:11:54.398391 INFO::Total function execution time is 0.0537457466125488 s and adjustment time is 0.0400919914245605 s ( 74.6 )
2025-12-15 21:11:54.399381 INFO::Formatting Data.
2025-12-15 21:11:54.399953 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:54.400756 INFO::Removing potential empty rows and columns
2025-12-15 21:11:54.401711 INFO::Found 0 missing values.
2025-12-15 21:11:54.404337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:54.404879 INFO::Done
2025-12-15 21:11:54.405364 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:54.407241 INFO::Starting hierarchical adjustment
2025-12-15 21:11:54.407918 INFO::Found 2 batches.
2025-12-15 21:11:54.40841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:54.408983 INFO::Using default BPPARAM
2025-12-15 21:11:54.40947 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:54.41036 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 21:11:54.424259 INFO::Done
2025-12-15 21:11:54.424915 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:54.426805 INFO::ASW Batch was 0.0620722830494281 prior to batch effect correction and is now -0.0975992035597045 .
2025-12-15 21:11:54.427534 INFO::Total function execution time is 0.0281572341918945 s and adjustment time is 0.0164661407470703 s ( 58.48 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-15 21:11:57.197774 INFO::Formatting Data.
2025-12-15 21:11:57.198437 INFO::Recognized SummarizedExperiment
2025-12-15 21:11:57.198916 INFO::Typecasting input to dataframe.
2025-12-15 21:11:57.226488 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:57.227593 INFO::Removing potential empty rows and columns
2025-12-15 21:11:57.23056 INFO::Found 0 missing values.
2025-12-15 21:11:57.236279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:57.236868 INFO::Done
2025-12-15 21:11:57.237337 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:57.240284 INFO::Starting hierarchical adjustment
2025-12-15 21:11:57.240931 INFO::Found 2 batches.
2025-12-15 21:11:57.241396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:57.242364 INFO::Using default BPPARAM
2025-12-15 21:11:57.242846 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:57.243689 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 21:11:57.289556 INFO::Done
2025-12-15 21:11:57.290235 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:57.293327 INFO::ASW Batch was 0.0104700330935898 prior to batch effect correction and is now -0.0860290967403815 .
2025-12-15 21:11:57.294139 INFO::Total function execution time is 0.0966203212738037 s and adjustment time is 0.0487296581268311 s ( 50.43 )
Warning: stack imbalance in '{', 73 then 75
2025-12-15 21:11:57.310269 INFO::Formatting Data.
2025-12-15 21:11:57.310947 INFO::Recognized SummarizedExperiment
2025-12-15 21:11:57.311425 INFO::Typecasting input to dataframe.
2025-12-15 21:11:57.319324 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:57.320363 INFO::Removing potential empty rows and columns
2025-12-15 21:11:57.323322 INFO::Found 0 missing values.
2025-12-15 21:11:57.329077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:57.32964 INFO::Done
2025-12-15 21:11:57.330118 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:57.333263 INFO::Starting hierarchical adjustment
2025-12-15 21:11:57.33398 INFO::Found 2 batches.
2025-12-15 21:11:57.334509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:57.33515 INFO::Using default BPPARAM
2025-12-15 21:11:57.335673 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:57.336642 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 21:11:57.361539 INFO::Done
2025-12-15 21:11:57.362269 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:57.366053 INFO::ASW Batch was -0.00151180193136339 prior to batch effect correction and is now -0.00151180193136339 .
2025-12-15 21:11:57.366915 INFO::Total function execution time is 0.0566167831420898 s and adjustment time is 0.0276691913604736 s ( 48.87 )
2025-12-15 21:11:57.384926 INFO::Formatting Data.
2025-12-15 21:11:57.38571 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:57.386635 INFO::Removing potential empty rows and columns
2025-12-15 21:11:57.38764 INFO::Found 0 missing values.
2025-12-15 21:11:57.390549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:57.391088 INFO::Done
2025-12-15 21:11:57.391602 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:57.393592 INFO::Starting hierarchical adjustment
2025-12-15 21:11:57.394509 INFO::Found 3 batches.
2025-12-15 21:11:57.395047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:57.395641 INFO::Using default BPPARAM
2025-12-15 21:11:57.396169 INFO::Processing subtree level 1
2025-12-15 21:11:57.52942 INFO::Adjusting the last 1 batches sequentially
2025-12-15 21:11:57.531224 INFO::Done
2025-12-15 21:11:57.531873 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:57.534306 INFO::ASW Batch was 0.0145621935886797 prior to batch effect correction and is now -0.172928643027954 .
2025-12-15 21:11:57.535255 INFO::Total function execution time is 0.150372982025146 s and adjustment time is 0.137033224105835 s ( 91.13 )
2025-12-15 21:11:57.549697 INFO::Skipping initial DF formatting
2025-12-15 21:11:57.550443 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:57.554486 INFO::Starting hierarchical adjustment
2025-12-15 21:11:57.555294 INFO::Found 5 batches.
2025-12-15 21:11:57.555859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:57.556492 INFO::Using default BPPARAM
2025-12-15 21:11:57.557067 INFO::Processing subtree level 1
2025-12-15 21:11:57.685863 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:57.687676 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 21:11:57.708274 INFO::Done
2025-12-15 21:11:57.709021 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:57.713223 INFO::ASW Batch was 0.546856906039901 prior to batch effect correction and is now 0.546856906039901 .
2025-12-15 21:11:57.713862 INFO::ASW Label was 0.354988398929566 prior to batch effect correction and is now 0.354988398929566 .
2025-12-15 21:11:57.714712 INFO::Total function execution time is 0.165082454681396 s and adjustment time is 0.153122901916504 s ( 92.76 )
2025-12-15 21:11:57.732663 INFO::Formatting Data.
2025-12-15 21:11:57.733484 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:57.734424 INFO::Removing potential empty rows and columns
2025-12-15 21:11:57.735428 INFO::Found 0 missing values.
2025-12-15 21:11:57.739472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:57.740081 INFO::Done
2025-12-15 21:11:57.740614 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:57.743622 INFO::Starting hierarchical adjustment
2025-12-15 21:11:57.744377 INFO::Found 5 batches.
2025-12-15 21:11:57.744932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:57.745563 INFO::Using default BPPARAM
2025-12-15 21:11:57.746138 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.
2025-12-15 21:11:57.857417 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:57.859191 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 21:11:57.876384 INFO::Done
2025-12-15 21:11:57.877221 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:57.880754 INFO::ASW Batch was 0.630516308581273 prior to batch effect correction and is now -0.0910007626893526 .
2025-12-15 21:11:57.881448 INFO::ASW Label was 0.128697826349523 prior to batch effect correction and is now 0.764260617503095 .
2025-12-15 21:11:57.882349 INFO::Total function execution time is 0.149726152420044 s and adjustment time is 0.132096767425537 s ( 88.23 )
2025-12-15 21:11:57.883248 INFO::Formatting Data.
2025-12-15 21:11:57.8839 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:57.884838 INFO::Removing potential empty rows and columns
2025-12-15 21:11:57.885916 INFO::Found 0 missing values.
2025-12-15 21:11:57.890054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:57.890607 INFO::Done
2025-12-15 21:11:57.891164 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:57.894314 INFO::Starting hierarchical adjustment
2025-12-15 21:11:57.895045 INFO::Found 5 batches.
2025-12-15 21:11:57.895593 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:57.896269 INFO::Using default BPPARAM
2025-12-15 21:11:57.896822 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.
2025-12-15 21:11:58.022437 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:58.025128 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 21:11:58.050726 INFO::Done
2025-12-15 21:11:58.051863 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.057199 INFO::ASW Batch was 0.630516308581273 prior to batch effect correction and is now -0.0910007626893526 .
2025-12-15 21:11:58.058292 INFO::ASW Label was 0.128697826349523 prior to batch effect correction and is now 0.764260617503095 .
2025-12-15 21:11:58.059643 INFO::Total function execution time is 0.176314830780029 s and adjustment time is 0.155753135681152 s ( 88.34 )
2025-12-15 21:11:58.080593 INFO::Formatting Data.
2025-12-15 21:11:58.081847 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.08333 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.084908 INFO::Found 0 missing values.
2025-12-15 21:11:58.091733 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.092756 INFO::Done
2025-12-15 21:11:58.093656 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.107074 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.108113 INFO::Found 5 batches.
2025-12-15 21:11:58.108755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.109699 INFO::Using default BPPARAM
2025-12-15 21:11:58.11046 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.
2025-12-15 21:11:58.219386 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:58.220995 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 21:11:58.237375 INFO::Done
2025-12-15 21:11:58.238117 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.241532 INFO::ASW Batch was 0.443972230934439 prior to batch effect correction and is now 0.011937258005814 .
2025-12-15 21:11:58.242159 INFO::ASW Label was 0.300361423807333 prior to batch effect correction and is now 0.630266043248974 .
2025-12-15 21:11:58.243006 INFO::Total function execution time is 0.162618160247803 s and adjustment time is 0.12944769859314 s ( 79.6 )
2025-12-15 21:11:58.243878 INFO::Formatting Data.
2025-12-15 21:11:58.244546 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.245468 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.246493 INFO::Found 0 missing values.
2025-12-15 21:11:58.250556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.251123 INFO::Done
2025-12-15 21:11:58.251655 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.254706 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.25544 INFO::Found 5 batches.
2025-12-15 21:11:58.256007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.256633 INFO::Using default BPPARAM
2025-12-15 21:11:58.257188 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.
2025-12-15 21:11:58.365262 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:58.366853 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 21:11:58.382504 INFO::Done
2025-12-15 21:11:58.383271 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.386562 INFO::ASW Batch was 0.443972230934439 prior to batch effect correction and is now 0.011937258005814 .
2025-12-15 21:11:58.387185 INFO::ASW Label was 0.300361423807333 prior to batch effect correction and is now 0.630266043248974 .
2025-12-15 21:11:58.388059 INFO::Total function execution time is 0.144191980361938 s and adjustment time is 0.12717604637146 s ( 88.2 )
2025-12-15 21:11:58.402362 INFO::Formatting Data.
2025-12-15 21:11:58.403248 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.404244 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.405287 INFO::Found 0 missing values.
2025-12-15 21:11:58.40811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.4087 INFO::Done
2025-12-15 21:11:58.409262 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.412548 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.413284 INFO::Found 2 batches.
2025-12-15 21:11:58.41384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.414489 INFO::Using default BPPARAM
2025-12-15 21:11:58.415063 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:58.416018 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 21:11:58.430839 INFO::Done
2025-12-15 21:11:58.431528 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.434484 INFO::ASW Batch was 0.448627446561812 prior to batch effect correction and is now -0.0238012860898727 .
2025-12-15 21:11:58.435107 INFO::ASW Label was 0.546975908720188 prior to batch effect correction and is now 0.913986164474089 .
2025-12-15 21:11:58.435942 INFO::Total function execution time is 0.0336897373199463 s and adjustment time is 0.0176689624786377 s ( 52.45 )
2025-12-15 21:11:58.436727 INFO::Formatting Data.
2025-12-15 21:11:58.437357 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.43825 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.439246 INFO::Found 0 missing values.
2025-12-15 21:11:58.441924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.442491 INFO::Done
2025-12-15 21:11:58.44303 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.44615 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.446903 INFO::Found 2 batches.
2025-12-15 21:11:58.447435 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.448069 INFO::Using default BPPARAM
2025-12-15 21:11:58.44862 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:58.449542 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-15 21:11:58.464211 INFO::Done
2025-12-15 21:11:58.464916 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.46791 INFO::ASW Batch was 0.448627446561812 prior to batch effect correction and is now -0.0238012860898727 .
2025-12-15 21:11:58.46853 INFO::ASW Label was 0.546975908720188 prior to batch effect correction and is now 0.913986164474089 .
2025-12-15 21:11:58.469323 INFO::Total function execution time is 0.0325977802276611 s and adjustment time is 0.0174648761749268 s ( 53.58 )
2025-12-15 21:11:58.480898 INFO::Formatting Data.
2025-12-15 21:11:58.481704 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.482615 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.48353 INFO::Found 0 missing values.
2025-12-15 21:11:58.485698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.48625 INFO::Done
2025-12-15 21:11:58.486775 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.48873 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.489438 INFO::Found 2 batches.
2025-12-15 21:11:58.489986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.490609 INFO::Using default BPPARAM
2025-12-15 21:11:58.491172 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:58.492112 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 21:11:58.5239 INFO::Done
2025-12-15 21:11:58.52463 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.526643 INFO::ASW Batch was -0.0410019629381849 prior to batch effect correction and is now -0.173942888879794 .
2025-12-15 21:11:58.527467 INFO::Total function execution time is 0.0466570854187012 s and adjustment time is 0.0345773696899414 s ( 74.11 )
2025-12-15 21:11:58.539637 INFO::Formatting Data.
2025-12-15 21:11:58.540431 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.541341 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.54234 INFO::Found 0 missing values.
2025-12-15 21:11:58.543497 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.
2025-12-15 21:11:58.548146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.548755 INFO::Done
2025-12-15 21:11:58.54931 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.552347 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.553088 INFO::Found 2 batches.
2025-12-15 21:11:58.553622 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.554282 INFO::Using default BPPARAM
2025-12-15 21:11:58.554827 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:58.555791 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 21:11:58.572712 INFO::Done
2025-12-15 21:11:58.573488 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.57656 INFO::ASW Batch was 0.644932975344045 prior to batch effect correction and is now 0.0149738304520432 .
2025-12-15 21:11:58.577193 INFO::ASW Label was 0.321994033184418 prior to batch effect correction and is now 0.855733207355135 .
2025-12-15 21:11:58.578028 INFO::Total function execution time is 0.0384814739227295 s and adjustment time is 0.0197429656982422 s ( 51.31 )
2025-12-15 21:11:58.578831 INFO::Formatting Data.
2025-12-15 21:11:58.579468 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.58043 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.581445 INFO::Found 0 missing values.
2025-12-15 21:11:58.582383 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.
2025-12-15 21:11:58.587002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.587594 INFO::Done
2025-12-15 21:11:58.588143 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.59116 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.591864 INFO::Found 2 batches.
2025-12-15 21:11:58.592431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.593045 INFO::Using default BPPARAM
2025-12-15 21:11:58.593582 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:11:58.594556 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 21:11:58.611413 INFO::Done
2025-12-15 21:11:58.612203 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.61528 INFO::ASW Batch was 0.644932975344045 prior to batch effect correction and is now 0.0149738304520432 .
2025-12-15 21:11:58.615972 INFO::ASW Label was 0.321994033184418 prior to batch effect correction and is now 0.855733207355135 .
2025-12-15 21:11:58.616835 INFO::Total function execution time is 0.0380139350891113 s and adjustment time is 0.0196425914764404 s ( 51.67 )
2025-12-15 21:11:58.841304 INFO::Formatting Data.
2025-12-15 21:11:58.842221 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.843194 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.844277 INFO::Found 0 missing values.
2025-12-15 21:11:58.847272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.847832 INFO::Done
2025-12-15 21:11:58.84837 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.85044 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.851297 INFO::Found 3 batches.
2025-12-15 21:11:58.851843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.852498 INFO::Using default BPPARAM
2025-12-15 21:11:58.853041 INFO::Processing subtree level 1
2025-12-15 21:11:58.940806 INFO::Adjusting the last 1 batches sequentially
2025-12-15 21:11:58.942613 INFO::Done
2025-12-15 21:11:58.943301 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:58.945831 INFO::ASW Batch was -0.0841584903516638 prior to batch effect correction and is now -0.0841584903516638 .
2025-12-15 21:11:58.946834 INFO::Total function execution time is 0.105582714080811 s and adjustment time is 0.0914511680603027 s ( 86.62 )
2025-12-15 21:11:58.947929 INFO::Formatting Data.
2025-12-15 21:11:58.948594 INFO::Typecasting input to dataframe.
2025-12-15 21:11:58.94937 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:58.950291 INFO::Removing potential empty rows and columns
2025-12-15 21:11:58.95138 INFO::Found 0 missing values.
2025-12-15 21:11:58.954426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:58.955051 INFO::Done
2025-12-15 21:11:58.955596 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:58.95765 INFO::Starting hierarchical adjustment
2025-12-15 21:11:58.95838 INFO::Found 3 batches.
2025-12-15 21:11:58.958943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:58.959572 INFO::Using default BPPARAM
2025-12-15 21:11:58.960156 INFO::Processing subtree level 1
2025-12-15 21:11:59.046081 INFO::Adjusting the last 1 batches sequentially
2025-12-15 21:11:59.047842 INFO::Done
2025-12-15 21:11:59.048488 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:59.051091 INFO::ASW Batch was -0.0841584903516638 prior to batch effect correction and is now -0.0841584903516638 .
2025-12-15 21:11:59.052044 INFO::Total function execution time is 0.104105710983276 s and adjustment time is 0.0895671844482422 s ( 86.03 )
2025-12-15 21:11:59.065049 INFO::Formatting Data.
2025-12-15 21:11:59.065855 INFO::Typecasting input to dataframe.
2025-12-15 21:11:59.066725 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:59.06764 INFO::Removing potential empty rows and columns
2025-12-15 21:11:59.068709 INFO::Found 0 missing values.
2025-12-15 21:11:59.071778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:59.072362 INFO::Done
2025-12-15 21:11:59.07291 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:59.074937 INFO::Starting hierarchical adjustment
2025-12-15 21:11:59.075647 INFO::Found 3 batches.
2025-12-15 21:11:59.076191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:59.076823 INFO::Using default BPPARAM
2025-12-15 21:11:59.077369 INFO::Processing subtree level 1
2025-12-15 21:11:59.163018 INFO::Adjusting the last 1 batches sequentially
2025-12-15 21:11:59.164778 INFO::Done
2025-12-15 21:11:59.165482 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:59.167993 INFO::ASW Batch was -0.0845009418852509 prior to batch effect correction and is now -0.0845009418852509 .
2025-12-15 21:11:59.168953 INFO::Total function execution time is 0.103954792022705 s and adjustment time is 0.08925461769104 s ( 85.86 )
2025-12-15 21:11:59.313424 INFO::Formatting Data.
2025-12-15 21:11:59.31439 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:59.315594 INFO::Removing potential empty rows and columns
2025-12-15 21:11:59.318508 INFO::Found 1000 missing values.
2025-12-15 21:11:59.337701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:59.338495 INFO::Done
2025-12-15 21:11:59.33908 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:59.344844 INFO::Starting hierarchical adjustment
2025-12-15 21:11:59.345715 INFO::Found 10 batches.
2025-12-15 21:11:59.346289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:11:59.346974 INFO::Using default BPPARAM
2025-12-15 21:11:59.347533 INFO::Processing subtree level 1
2025-12-15 21:11:59.489025 INFO::Processing subtree level 2
2025-12-15 21:11:59.896019 INFO::Adjusting the last 1 batches sequentially
2025-12-15 21:11:59.898252 INFO::Done
2025-12-15 21:11:59.89902 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:11:59.90506 INFO::ASW Batch was 0.474061971167441 prior to batch effect correction and is now 0.474061971167441 .
2025-12-15 21:11:59.905838 INFO::ASW Label was 0.350836788555466 prior to batch effect correction and is now 0.350836788555466 .
2025-12-15 21:11:59.906828 INFO::Total function execution time is 0.593508958816528 s and adjustment time is 0.552668333053589 s ( 93.12 )
2025-12-15 21:11:59.907701 INFO::Formatting Data.
2025-12-15 21:11:59.908389 INFO::Replacing NaNs with NAs.
2025-12-15 21:11:59.909588 INFO::Removing potential empty rows and columns
2025-12-15 21:11:59.964649 INFO::Found 1000 missing values.
2025-12-15 21:11:59.989976 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:11:59.990946 INFO::Done
2025-12-15 21:11:59.99161 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:11:59.997903 INFO::Starting hierarchical adjustment
2025-12-15 21:11:59.998796 INFO::Found 10 batches.
2025-12-15 21:12:01.099411 INFO::Set up parallel execution backend with 2 workers
2025-12-15 21:12:01.100864 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-15 21:12:02.302313 INFO::Adjusting the last 2 batches sequentially
2025-12-15 21:12:02.305595 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-15 21:12:02.321319 INFO::Done
2025-12-15 21:12:02.321996 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:12:02.326411 INFO::ASW Batch was 0.474061971167441 prior to batch effect correction and is now 0.474061971167441 .
2025-12-15 21:12:02.327005 INFO::ASW Label was 0.350836788555466 prior to batch effect correction and is now 0.350836788555466 .
2025-12-15 21:12:02.327721 INFO::Total function execution time is 2.42007064819336 s and adjustment time is 2.32270860671997 s ( 95.98 )
2025-12-15 21:12:02.475318 INFO::Formatting Data.
2025-12-15 21:12:02.476104 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.477096 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.4782 INFO::Found 0 missing values.
2025-12-15 21:12:02.481825 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.482364 INFO::Done
2025-12-15 21:12:02.482878 INFO::Acquiring quality metrics before batch effect correction.
2025-12-15 21:12:02.485587 INFO::Starting hierarchical adjustment
2025-12-15 21:12:02.486302 INFO::Found 3 batches.
2025-12-15 21:12:02.486836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-15 21:12:02.487462 INFO::Using default BPPARAM
2025-12-15 21:12:02.488002 INFO::Processing subtree level 1
2025-12-15 21:12:02.591995 INFO::Adjusting the last 1 batches sequentially
2025-12-15 21:12:02.593767 INFO::Done
2025-12-15 21:12:02.594431 INFO::Acquiring quality metrics after batch effect correction.
2025-12-15 21:12:02.597592 INFO::ASW Batch was 0.24832223569918 prior to batch effect correction and is now -0.109759205697406 .
2025-12-15 21:12:02.598264 INFO::ASW Label was -0.195946727765572 prior to batch effect correction and is now 0.0231770288694903 .
2025-12-15 21:12:02.599206 INFO::Total function execution time is 0.123909473419189 s and adjustment time is 0.10757851600647 s ( 86.82 )
2025-12-15 21:12:02.712384 INFO::Formatting Data.
2025-12-15 21:12:02.713186 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.714057 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.715024 INFO::Found 2 missing values.
2025-12-15 21:12:02.717656 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.718208 INFO::Done
2025-12-15 21:12:02.743834 INFO::Found NA in Reference column
2025-12-15 21:12:02.752654 INFO::Require at least two references per batch.
2025-12-15 21:12:02.77167 INFO::Formatting Data.
2025-12-15 21:12:02.772388 INFO::Recognized SummarizedExperiment
2025-12-15 21:12:02.772902 INFO::Typecasting input to dataframe.
2025-12-15 21:12:02.781801 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.782885 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.786167 INFO::Found 0 missing values.
2025-12-15 21:12:02.792414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.79303 INFO::Done
2025-12-15 21:12:02.807727 INFO::Formatting Data.
2025-12-15 21:12:02.808427 INFO::Recognized SummarizedExperiment
2025-12-15 21:12:02.808945 INFO::Typecasting input to dataframe.
2025-12-15 21:12:02.825301 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.826465 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.829813 INFO::Found 0 missing values.
2025-12-15 21:12:02.839855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.840469 INFO::Done
2025-12-15 21:12:02.8548 INFO::Formatting Data.
2025-12-15 21:12:02.855479 INFO::Recognized SummarizedExperiment
2025-12-15 21:12:02.856 INFO::Typecasting input to dataframe.
2025-12-15 21:12:02.871485 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.872495 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.87354 INFO::Found 0 missing values.
2025-12-15 21:12:02.874416 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.
2025-12-15 21:12:02.878477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.87901 INFO::Done
2025-12-15 21:12:02.888594 INFO::Formatting Data.
2025-12-15 21:12:02.889361 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.890191 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.891144 INFO::Found 0 missing values.
2025-12-15 21:12:02.893825 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.894338 INFO::Done
2025-12-15 21:12:02.905243 INFO::Formatting Data.
2025-12-15 21:12:02.906054 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.906938 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.908001 INFO::Found 0 missing values.
2025-12-15 21:12:02.910779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.91131 INFO::Done
2025-12-15 21:12:02.949489 INFO::Formatting Data.
2025-12-15 21:12:02.950676 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.951883 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.953094 INFO::Found 1 missing values.
2025-12-15 21:12:02.955638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.956204 INFO::Done
2025-12-15 21:12:02.975271 INFO::Formatting Data.
2025-12-15 21:12:02.976027 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.976864 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.977751 INFO::Found 2 missing values.
2025-12-15 21:12:02.978625 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.
2025-12-15 21:12:02.980855 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.98138 INFO::Done
2025-12-15 21:12:02.991545 INFO::Formatting Data.
2025-12-15 21:12:02.992401 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:02.993358 INFO::Removing potential empty rows and columns
2025-12-15 21:12:02.994281 INFO::Found 2 missing values.
2025-12-15 21:12:02.995864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:02.996405 INFO::Done
2025-12-15 21:12:03.00649 INFO::Formatting Data.
2025-12-15 21:12:03.007231 INFO::Typecasting input to dataframe.
2025-12-15 21:12:03.008015 INFO::Replacing NaNs with NAs.
2025-12-15 21:12:03.008851 INFO::Removing potential empty rows and columns
2025-12-15 21:12:03.009802 INFO::Found 0 missing values.
2025-12-15 21:12:03.012454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-15 21:12:03.012995 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.240 3.707 19.622
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.418 | 1.189 | 16.598 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.000 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.011 | |