Yannis Schumann
| Snapshot Date: 2026-03-12 13:40 -0400 (Thu, 12 Mar 2026) |
| 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-13 11:33 -0400 (Fri, 13 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4819 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4049 |
| 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 170/2360 | 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 | ERROR | ERROR | skipped | skipped | |||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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: 2026-03-12 21:18:42 -0400 (Thu, 12 Mar 2026) |
| EndedAt: 2026-03-12 21:20:26 -0400 (Thu, 12 Mar 2026) |
| EllapsedTime: 104.3 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) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-13 01:18:42 UTC
* 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 34.022 2.064 23.636
* 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) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 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")
2026-03-12 21:19:47.990901 INFO::Formatting Data.
2026-03-12 21:19:47.992299 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:48.003877 INFO::Removing potential empty rows and columns
2026-03-12 21:19:48.25476 INFO::Found 0 missing values.
2026-03-12 21:19:48.258496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:48.259344 INFO::Done
2026-03-12 21:19:48.260008 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:48.274809 INFO::Starting hierarchical adjustment
2026-03-12 21:19:48.275999 INFO::Found 3 batches.
2026-03-12 21:19:48.276658 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:48.277997 INFO::Using default BPPARAM
2026-03-12 21:19:48.278626 INFO::Processing subtree level 1
2026-03-12 21:19:48.385569 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:19:48.387607 INFO::Done
2026-03-12 21:19:48.388334 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:48.39112 INFO::ASW Batch was -0.0641632686947458 prior to batch effect correction and is now -0.0641632686947458 .
2026-03-12 21:19:48.392268 INFO::Total function execution time is 0.40202522277832 s and adjustment time is 0.111814260482788 s ( 27.81 )
2026-03-12 21:19:48.407585 INFO::Formatting Data.
2026-03-12 21:19:48.408569 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:48.409656 INFO::Removing potential empty rows and columns
2026-03-12 21:19:48.410953 INFO::Found 0 missing values.
2026-03-12 21:19:48.412054 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.
2026-03-12 21:19:48.423765 INFO::Formatting Data.
2026-03-12 21:19:48.424744 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:48.425835 INFO::Removing potential empty rows and columns
2026-03-12 21:19:48.427109 INFO::Found 0 missing values.
2026-03-12 21:19:48.428163 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.
2026-03-12 21:19:48.445576 INFO::Formatting Data.
2026-03-12 21:19:48.446591 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:48.447694 INFO::Removing potential empty rows and columns
2026-03-12 21:19:48.448973 INFO::Found 0 missing values.
2026-03-12 21:19:48.45009 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.
2026-03-12 21:19:48.45528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:48.456054 INFO::Done
2026-03-12 21:19:48.456693 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:48.459247 INFO::Starting hierarchical adjustment
2026-03-12 21:19:48.460142 INFO::Found 2 batches.
2026-03-12 21:19:48.460779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:48.461556 INFO::Using default BPPARAM
2026-03-12 21:19:48.462182 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:48.463317 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:19:48.486426 INFO::Done
2026-03-12 21:19:48.487301 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:48.489652 INFO::ASW Batch was -0.0842477349713721 prior to batch effect correction and is now -0.130836326335363 .
2026-03-12 21:19:48.490574 INFO::Total function execution time is 0.0451014041900635 s and adjustment time is 0.0264263153076172 s ( 58.59 )
2026-03-12 21:19:48.493591 INFO::Formatting Data.
2026-03-12 21:19:48.494298 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:48.503889 INFO::Formatting Data.
2026-03-12 21:19:48.504775 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:48.505767 INFO::Removing potential empty rows and columns
2026-03-12 21:19:48.506906 INFO::Found 0 missing values.
2026-03-12 21:19:48.510034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:48.510666 INFO::Done
2026-03-12 21:19:48.511245 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:48.513559 INFO::Starting hierarchical adjustment
2026-03-12 21:19:48.514335 INFO::Found 2 batches.
2026-03-12 21:19:48.514935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:48.515635 INFO::Using default BPPARAM
2026-03-12 21:19:48.516231 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:48.51724 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:19:48.561504 INFO::Done
2026-03-12 21:19:48.56233 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:48.564505 INFO::ASW Batch was -0.0334175591444908 prior to batch effect correction and is now -0.120819329029028 .
2026-03-12 21:19:48.565377 INFO::Total function execution time is 0.0615742206573486 s and adjustment time is 0.0472774505615234 s ( 76.78 )
2026-03-12 21:19:48.566489 INFO::Formatting Data.
2026-03-12 21:19:48.567137 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:48.56804 INFO::Removing potential empty rows and columns
2026-03-12 21:19:48.569088 INFO::Found 0 missing values.
2026-03-12 21:19:48.571921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:48.572531 INFO::Done
2026-03-12 21:19:48.573092 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:48.575177 INFO::Starting hierarchical adjustment
2026-03-12 21:19:48.575908 INFO::Found 2 batches.
2026-03-12 21:19:48.576444 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:48.57708 INFO::Using default BPPARAM
2026-03-12 21:19:48.577632 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:48.578587 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:19:48.593537 INFO::Done
2026-03-12 21:19:48.594368 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:48.596576 INFO::ASW Batch was -0.0334175591444908 prior to batch effect correction and is now -0.120819329029028 .
2026-03-12 21:19:48.597425 INFO::Total function execution time is 0.0309288501739502 s and adjustment time is 0.0177164077758789 s ( 57.28 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-12 21:19:51.904843 INFO::Formatting Data.
2026-03-12 21:19:51.905644 INFO::Recognized SummarizedExperiment
2026-03-12 21:19:51.906212 INFO::Typecasting input to dataframe.
2026-03-12 21:19:51.935638 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:51.936889 INFO::Removing potential empty rows and columns
2026-03-12 21:19:51.940128 INFO::Found 0 missing values.
2026-03-12 21:19:51.946375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:51.946986 INFO::Done
2026-03-12 21:19:51.947493 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:51.950626 INFO::Starting hierarchical adjustment
2026-03-12 21:19:51.951299 INFO::Found 2 batches.
2026-03-12 21:19:51.951819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:51.952843 INFO::Using default BPPARAM
2026-03-12 21:19:51.953347 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:51.954264 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:19:52.001271 INFO::Done
2026-03-12 21:19:52.002003 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:52.005196 INFO::ASW Batch was 0.00121617522953182 prior to batch effect correction and is now -0.0913961711970682 .
2026-03-12 21:19:52.006024 INFO::Total function execution time is 0.101472854614258 s and adjustment time is 0.0500705242156982 s ( 49.34 )
Warning: stack imbalance in '{', 73 then 75
2026-03-12 21:19:52.022367 INFO::Formatting Data.
2026-03-12 21:19:52.023192 INFO::Recognized SummarizedExperiment
2026-03-12 21:19:52.023752 INFO::Typecasting input to dataframe.
2026-03-12 21:19:52.032366 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:52.033557 INFO::Removing potential empty rows and columns
2026-03-12 21:19:52.036977 INFO::Found 0 missing values.
2026-03-12 21:19:52.04355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:52.044199 INFO::Done
2026-03-12 21:19:52.044755 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:52.048157 INFO::Starting hierarchical adjustment
2026-03-12 21:19:52.048883 INFO::Found 2 batches.
2026-03-12 21:19:52.049411 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:52.050045 INFO::Using default BPPARAM
2026-03-12 21:19:52.050583 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:52.05156 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:19:52.080301 INFO::Done
2026-03-12 21:19:52.081258 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:52.085522 INFO::ASW Batch was -0.00256563635433248 prior to batch effect correction and is now -0.00256563635433248 .
2026-03-12 21:19:52.086599 INFO::Total function execution time is 0.0641744136810303 s and adjustment time is 0.0314807891845703 s ( 49.06 )
2026-03-12 21:19:52.120042 INFO::Formatting Data.
2026-03-12 21:19:52.121138 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:52.12221 INFO::Removing potential empty rows and columns
2026-03-12 21:19:52.123412 INFO::Found 0 missing values.
2026-03-12 21:19:52.126858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:52.127501 INFO::Done
2026-03-12 21:19:52.128154 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:52.130866 INFO::Starting hierarchical adjustment
2026-03-12 21:19:52.131676 INFO::Found 3 batches.
2026-03-12 21:19:52.132289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:52.133023 INFO::Using default BPPARAM
2026-03-12 21:19:52.133654 INFO::Processing subtree level 1
2026-03-12 21:19:52.297561 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:19:52.29959 INFO::Done
2026-03-12 21:19:52.300329 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:52.303107 INFO::ASW Batch was -0.113278756702429 prior to batch effect correction and is now -0.183405435897811 .
2026-03-12 21:19:52.304154 INFO::Total function execution time is 0.184198617935181 s and adjustment time is 0.168085813522339 s ( 91.25 )
2026-03-12 21:19:52.319753 INFO::Skipping initial DF formatting
2026-03-12 21:19:52.320585 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:52.324837 INFO::Starting hierarchical adjustment
2026-03-12 21:19:52.325718 INFO::Found 5 batches.
2026-03-12 21:19:52.326325 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:52.327013 INFO::Using default BPPARAM
2026-03-12 21:19:52.327599 INFO::Processing subtree level 1
2026-03-12 21:19:52.465629 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:52.467649 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:19:52.489451 INFO::Done
2026-03-12 21:19:52.49032 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:52.495239 INFO::ASW Batch was 0.512795852800317 prior to batch effect correction and is now 0.512795852800317 .
2026-03-12 21:19:52.49595 INFO::ASW Label was 0.355086901558254 prior to batch effect correction and is now 0.355086901558254 .
2026-03-12 21:19:52.496932 INFO::Total function execution time is 0.177271604537964 s and adjustment time is 0.163886070251465 s ( 92.45 )
2026-03-12 21:19:52.51621 INFO::Formatting Data.
2026-03-12 21:19:52.517156 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:52.518191 INFO::Removing potential empty rows and columns
2026-03-12 21:19:52.519284 INFO::Found 0 missing values.
2026-03-12 21:19:52.523569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:52.524168 INFO::Done
2026-03-12 21:19:52.524756 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:52.527977 INFO::Starting hierarchical adjustment
2026-03-12 21:19:52.52876 INFO::Found 5 batches.
2026-03-12 21:19:52.529332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:52.530017 INFO::Using default BPPARAM
2026-03-12 21:19:52.530601 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.
2026-03-12 21:19:52.65306 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:52.655596 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:19:52.67515 INFO::Done
2026-03-12 21:19:52.676212 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:52.680278 INFO::ASW Batch was 0.165712112606566 prior to batch effect correction and is now -0.061557250345616 .
2026-03-12 21:19:52.681098 INFO::ASW Label was 0.49032467468983 prior to batch effect correction and is now 0.867081626216268 .
2026-03-12 21:19:52.682102 INFO::Total function execution time is 0.165990591049194 s and adjustment time is 0.146491527557373 s ( 88.25 )
2026-03-12 21:19:52.683083 INFO::Formatting Data.
2026-03-12 21:19:52.683808 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:52.684995 INFO::Removing potential empty rows and columns
2026-03-12 21:19:52.686305 INFO::Found 0 missing values.
2026-03-12 21:19:52.691115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:52.691913 INFO::Done
2026-03-12 21:19:52.692852 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:52.696671 INFO::Starting hierarchical adjustment
2026-03-12 21:19:52.697523 INFO::Found 5 batches.
2026-03-12 21:19:52.698146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:52.698926 INFO::Using default BPPARAM
2026-03-12 21:19:52.699551 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.
2026-03-12 21:19:52.825889 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:52.82795 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:19:52.84736 INFO::Done
2026-03-12 21:19:52.848379 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:52.852219 INFO::ASW Batch was 0.165712112606566 prior to batch effect correction and is now -0.061557250345616 .
2026-03-12 21:19:52.853038 INFO::ASW Label was 0.49032467468983 prior to batch effect correction and is now 0.867081626216268 .
2026-03-12 21:19:52.854061 INFO::Total function execution time is 0.170977592468262 s and adjustment time is 0.1499342918396 s ( 87.69 )
2026-03-12 21:19:52.869978 INFO::Formatting Data.
2026-03-12 21:19:52.871057 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:52.872212 INFO::Removing potential empty rows and columns
2026-03-12 21:19:52.873444 INFO::Found 0 missing values.
2026-03-12 21:19:52.87826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:52.879029 INFO::Done
2026-03-12 21:19:52.879679 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:52.883052 INFO::Starting hierarchical adjustment
2026-03-12 21:19:52.883888 INFO::Found 5 batches.
2026-03-12 21:19:52.884451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:52.885142 INFO::Using default BPPARAM
2026-03-12 21:19:52.885727 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.
2026-03-12 21:19:53.002873 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:53.005029 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:19:53.022036 INFO::Done
2026-03-12 21:19:53.022896 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.026284 INFO::ASW Batch was 0.562840436672015 prior to batch effect correction and is now -0.104216794020609 .
2026-03-12 21:19:53.026969 INFO::ASW Label was 0.281647032897458 prior to batch effect correction and is now 0.752055006535435 .
2026-03-12 21:19:53.027837 INFO::Total function execution time is 0.157971620559692 s and adjustment time is 0.138271570205688 s ( 87.53 )
2026-03-12 21:19:53.02875 INFO::Formatting Data.
2026-03-12 21:19:53.029445 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.030437 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.031554 INFO::Found 0 missing values.
2026-03-12 21:19:53.036243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.036917 INFO::Done
2026-03-12 21:19:53.037534 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.040868 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.041711 INFO::Found 5 batches.
2026-03-12 21:19:53.04236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.043095 INFO::Using default BPPARAM
2026-03-12 21:19:53.043727 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.
2026-03-12 21:19:53.1606 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:53.162294 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:19:53.178088 INFO::Done
2026-03-12 21:19:53.17889 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.182218 INFO::ASW Batch was 0.562840436672015 prior to batch effect correction and is now -0.104216794020609 .
2026-03-12 21:19:53.182867 INFO::ASW Label was 0.281647032897458 prior to batch effect correction and is now 0.752055006535435 .
2026-03-12 21:19:53.183744 INFO::Total function execution time is 0.155006408691406 s and adjustment time is 0.136538028717041 s ( 88.09 )
2026-03-12 21:19:53.197682 INFO::Formatting Data.
2026-03-12 21:19:53.198525 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.1995 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.200577 INFO::Found 0 missing values.
2026-03-12 21:19:53.203402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.204028 INFO::Done
2026-03-12 21:19:53.204593 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.207685 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.208435 INFO::Found 2 batches.
2026-03-12 21:19:53.209018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.209705 INFO::Using default BPPARAM
2026-03-12 21:19:53.210304 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:53.211273 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:19:53.226756 INFO::Done
2026-03-12 21:19:53.227562 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.230678 INFO::ASW Batch was 0.509582453163477 prior to batch effect correction and is now 0.0649417168223324 .
2026-03-12 21:19:53.231317 INFO::ASW Label was 0.467309482603626 prior to batch effect correction and is now 0.880581075097159 .
2026-03-12 21:19:53.232197 INFO::Total function execution time is 0.0346243381500244 s and adjustment time is 0.018435001373291 s ( 53.24 )
2026-03-12 21:19:53.233039 INFO::Formatting Data.
2026-03-12 21:19:53.233716 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.234646 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.235678 INFO::Found 0 missing values.
2026-03-12 21:19:53.23845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.239072 INFO::Done
2026-03-12 21:19:53.239648 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.242676 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.243455 INFO::Found 2 batches.
2026-03-12 21:19:53.244027 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.244685 INFO::Using default BPPARAM
2026-03-12 21:19:53.24527 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:53.246241 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:19:53.270056 INFO::Done
2026-03-12 21:19:53.270869 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.274069 INFO::ASW Batch was 0.509582453163477 prior to batch effect correction and is now 0.0649417168223324 .
2026-03-12 21:19:53.27476 INFO::ASW Label was 0.467309482603626 prior to batch effect correction and is now 0.880581075097159 .
2026-03-12 21:19:53.275664 INFO::Total function execution time is 0.0426084995269775 s and adjustment time is 0.0267000198364258 s ( 62.66 )
2026-03-12 21:19:53.287935 INFO::Formatting Data.
2026-03-12 21:19:53.288856 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.289843 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.290857 INFO::Found 0 missing values.
2026-03-12 21:19:53.293281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.293889 INFO::Done
2026-03-12 21:19:53.294457 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.296559 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.297323 INFO::Found 2 batches.
2026-03-12 21:19:53.297914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.298579 INFO::Using default BPPARAM
2026-03-12 21:19:53.299166 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:53.300161 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:19:53.333583 INFO::Done
2026-03-12 21:19:53.334379 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.336512 INFO::ASW Batch was -0.0783157453589596 prior to batch effect correction and is now -0.156178432135669 .
2026-03-12 21:19:53.337395 INFO::Total function execution time is 0.0495615005493164 s and adjustment time is 0.0363705158233643 s ( 73.38 )
2026-03-12 21:19:53.349995 INFO::Formatting Data.
2026-03-12 21:19:53.350866 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.35185 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.352911 INFO::Found 0 missing values.
2026-03-12 21:19:53.354157 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.
2026-03-12 21:19:53.35908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.359725 INFO::Done
2026-03-12 21:19:53.360302 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.363288 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.364073 INFO::Found 2 batches.
2026-03-12 21:19:53.364675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.36534 INFO::Using default BPPARAM
2026-03-12 21:19:53.36591 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:53.366912 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:19:53.383662 INFO::Done
2026-03-12 21:19:53.384415 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.387582 INFO::ASW Batch was 0.57867721320137 prior to batch effect correction and is now -0.0371636476323069 .
2026-03-12 21:19:53.388237 INFO::ASW Label was 0.50055831064111 prior to batch effect correction and is now 0.93569950557289 .
2026-03-12 21:19:53.389112 INFO::Total function execution time is 0.0392153263092041 s and adjustment time is 0.019697904586792 s ( 50.23 )
2026-03-12 21:19:53.389958 INFO::Formatting Data.
2026-03-12 21:19:53.390621 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.391591 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.392628 INFO::Found 0 missing values.
2026-03-12 21:19:53.393605 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.
2026-03-12 21:19:53.398284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.398939 INFO::Done
2026-03-12 21:19:53.399521 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.402517 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.403288 INFO::Found 2 batches.
2026-03-12 21:19:53.403884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.40455 INFO::Using default BPPARAM
2026-03-12 21:19:53.405116 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:53.406117 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:19:53.422967 INFO::Done
2026-03-12 21:19:53.42374 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.426789 INFO::ASW Batch was 0.57867721320137 prior to batch effect correction and is now -0.0371636476323069 .
2026-03-12 21:19:53.427465 INFO::ASW Label was 0.50055831064111 prior to batch effect correction and is now 0.93569950557289 .
2026-03-12 21:19:53.428333 INFO::Total function execution time is 0.0383775234222412 s and adjustment time is 0.0197961330413818 s ( 51.58 )
2026-03-12 21:19:53.644806 INFO::Formatting Data.
2026-03-12 21:19:53.645696 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.646694 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.64785 INFO::Found 0 missing values.
2026-03-12 21:19:53.651083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.651695 INFO::Done
2026-03-12 21:19:53.652282 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.654483 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.655253 INFO::Found 3 batches.
2026-03-12 21:19:53.655864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.656572 INFO::Using default BPPARAM
2026-03-12 21:19:53.657175 INFO::Processing subtree level 1
2026-03-12 21:19:53.750182 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:19:53.752228 INFO::Done
2026-03-12 21:19:53.752966 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.755797 INFO::ASW Batch was -0.0482813350822975 prior to batch effect correction and is now -0.0482813350822975 .
2026-03-12 21:19:53.756966 INFO::Total function execution time is 0.112155675888062 s and adjustment time is 0.0971088409423828 s ( 86.58 )
2026-03-12 21:19:53.758278 INFO::Formatting Data.
2026-03-12 21:19:53.759108 INFO::Typecasting input to dataframe.
2026-03-12 21:19:53.759979 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.761054 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.762316 INFO::Found 0 missing values.
2026-03-12 21:19:53.765889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.7666 INFO::Done
2026-03-12 21:19:53.767226 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.769523 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.770349 INFO::Found 3 batches.
2026-03-12 21:19:53.770975 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.771719 INFO::Using default BPPARAM
2026-03-12 21:19:53.772573 INFO::Processing subtree level 1
2026-03-12 21:19:53.870937 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:19:53.873259 INFO::Done
2026-03-12 21:19:53.874032 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:53.876789 INFO::ASW Batch was -0.0482813350822975 prior to batch effect correction and is now -0.0482813350822975 .
2026-03-12 21:19:53.877862 INFO::Total function execution time is 0.119567632675171 s and adjustment time is 0.103009939193726 s ( 86.15 )
2026-03-12 21:19:53.891438 INFO::Formatting Data.
2026-03-12 21:19:53.892365 INFO::Typecasting input to dataframe.
2026-03-12 21:19:53.893297 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:53.894284 INFO::Removing potential empty rows and columns
2026-03-12 21:19:53.895547 INFO::Found 0 missing values.
2026-03-12 21:19:53.898663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:53.899244 INFO::Done
2026-03-12 21:19:53.899825 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:53.901988 INFO::Starting hierarchical adjustment
2026-03-12 21:19:53.902749 INFO::Found 3 batches.
2026-03-12 21:19:53.903312 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:53.904006 INFO::Using default BPPARAM
2026-03-12 21:19:53.904574 INFO::Processing subtree level 1
2026-03-12 21:19:53.999066 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:19:54.001056 INFO::Done
2026-03-12 21:19:54.001735 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:54.004298 INFO::ASW Batch was -0.110148731577664 prior to batch effect correction and is now -0.110148731577664 .
2026-03-12 21:19:54.005288 INFO::Total function execution time is 0.113916158676147 s and adjustment time is 0.0984570980072021 s ( 86.43 )
2026-03-12 21:19:54.145597 INFO::Formatting Data.
2026-03-12 21:19:54.146505 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:54.147716 INFO::Removing potential empty rows and columns
2026-03-12 21:19:54.15063 INFO::Found 1000 missing values.
2026-03-12 21:19:54.17052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:54.171352 INFO::Done
2026-03-12 21:19:54.171963 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:54.177552 INFO::Starting hierarchical adjustment
2026-03-12 21:19:54.178384 INFO::Found 10 batches.
2026-03-12 21:19:54.178992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:54.179684 INFO::Using default BPPARAM
2026-03-12 21:19:54.18027 INFO::Processing subtree level 1
2026-03-12 21:19:54.335919 INFO::Processing subtree level 2
2026-03-12 21:19:54.669565 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:19:54.672127 INFO::Done
2026-03-12 21:19:54.673078 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:54.680659 INFO::ASW Batch was 0.499067905035911 prior to batch effect correction and is now 0.499067905035911 .
2026-03-12 21:19:54.681656 INFO::ASW Label was 0.338194871877755 prior to batch effect correction and is now 0.338194871877755 .
2026-03-12 21:19:54.682924 INFO::Total function execution time is 0.537335634231567 s and adjustment time is 0.493867635726929 s ( 91.91 )
2026-03-12 21:19:54.684095 INFO::Formatting Data.
2026-03-12 21:19:54.685131 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:54.686777 INFO::Removing potential empty rows and columns
2026-03-12 21:19:54.690852 INFO::Found 1000 missing values.
2026-03-12 21:19:54.779827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:54.78081 INFO::Done
2026-03-12 21:19:54.781507 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:54.787596 INFO::Starting hierarchical adjustment
2026-03-12 21:19:54.78846 INFO::Found 10 batches.
2026-03-12 21:19:56.082433 INFO::Set up parallel execution backend with 2 workers
2026-03-12 21:19:56.083651 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-12 21:19:57.379235 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:19:57.386062 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:19:57.403617 INFO::Done
2026-03-12 21:19:57.404435 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:57.409412 INFO::ASW Batch was 0.499067905035911 prior to batch effect correction and is now 0.499067905035911 .
2026-03-12 21:19:57.410141 INFO::ASW Label was 0.338194871877755 prior to batch effect correction and is now 0.338194871877755 .
2026-03-12 21:19:57.411023 INFO::Total function execution time is 2.72699570655823 s and adjustment time is 2.61528301239014 s ( 95.9 )
2026-03-12 21:19:57.577335 INFO::Formatting Data.
2026-03-12 21:19:57.578371 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:57.57951 INFO::Removing potential empty rows and columns
2026-03-12 21:19:57.580748 INFO::Found 0 missing values.
2026-03-12 21:19:57.584802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:57.585608 INFO::Done
2026-03-12 21:19:57.58628 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:19:57.589556 INFO::Starting hierarchical adjustment
2026-03-12 21:19:57.590419 INFO::Found 3 batches.
2026-03-12 21:19:57.591071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:19:57.591862 INFO::Using default BPPARAM
2026-03-12 21:19:57.592464 INFO::Processing subtree level 1
2026-03-12 21:19:57.722559 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:19:57.724785 INFO::Done
2026-03-12 21:19:57.725621 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:19:57.72932 INFO::ASW Batch was 0.10480650708667 prior to batch effect correction and is now -0.135672730949351 .
2026-03-12 21:19:57.730072 INFO::ASW Label was -0.168752001949701 prior to batch effect correction and is now 0.018389532220369 .
2026-03-12 21:19:57.731199 INFO::Total function execution time is 0.153911590576172 s and adjustment time is 0.1345055103302 s ( 87.39 )
2026-03-12 21:19:57.857811 INFO::Formatting Data.
2026-03-12 21:19:57.858727 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:57.85971 INFO::Removing potential empty rows and columns
2026-03-12 21:19:57.860819 INFO::Found 2 missing values.
2026-03-12 21:19:57.863604 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:57.864203 INFO::Done
2026-03-12 21:19:57.890949 INFO::Found NA in Reference column
2026-03-12 21:19:57.900254 INFO::Require at least two references per batch.
2026-03-12 21:19:57.920495 INFO::Formatting Data.
2026-03-12 21:19:57.921372 INFO::Recognized SummarizedExperiment
2026-03-12 21:19:57.921985 INFO::Typecasting input to dataframe.
2026-03-12 21:19:57.931461 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:57.932757 INFO::Removing potential empty rows and columns
2026-03-12 21:19:57.936439 INFO::Found 0 missing values.
2026-03-12 21:19:57.943391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:57.94411 INFO::Done
2026-03-12 21:19:57.960292 INFO::Formatting Data.
2026-03-12 21:19:57.961228 INFO::Recognized SummarizedExperiment
2026-03-12 21:19:57.961874 INFO::Typecasting input to dataframe.
2026-03-12 21:19:57.980568 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:57.981972 INFO::Removing potential empty rows and columns
2026-03-12 21:19:57.985849 INFO::Found 0 missing values.
2026-03-12 21:19:57.997386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:57.998256 INFO::Done
2026-03-12 21:19:58.013935 INFO::Formatting Data.
2026-03-12 21:19:58.014766 INFO::Recognized SummarizedExperiment
2026-03-12 21:19:58.015329 INFO::Typecasting input to dataframe.
2026-03-12 21:19:58.031513 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:58.032656 INFO::Removing potential empty rows and columns
2026-03-12 21:19:58.033801 INFO::Found 0 missing values.
2026-03-12 21:19:58.034769 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.
2026-03-12 21:19:58.039222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:58.039863 INFO::Done
2026-03-12 21:19:58.049802 INFO::Formatting Data.
2026-03-12 21:19:58.050722 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:58.051641 INFO::Removing potential empty rows and columns
2026-03-12 21:19:58.052671 INFO::Found 0 missing values.
2026-03-12 21:19:58.055588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:58.056174 INFO::Done
2026-03-12 21:19:58.068347 INFO::Formatting Data.
2026-03-12 21:19:58.069241 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:58.070214 INFO::Removing potential empty rows and columns
2026-03-12 21:19:58.071325 INFO::Found 0 missing values.
2026-03-12 21:19:58.074322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:58.074983 INFO::Done
2026-03-12 21:19:58.105495 INFO::Formatting Data.
2026-03-12 21:19:58.106408 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:58.107563 INFO::Removing potential empty rows and columns
2026-03-12 21:19:58.108865 INFO::Found 1 missing values.
2026-03-12 21:19:58.111515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:58.112138 INFO::Done
2026-03-12 21:19:58.131553 INFO::Formatting Data.
2026-03-12 21:19:58.13249 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:58.133736 INFO::Removing potential empty rows and columns
2026-03-12 21:19:58.13488 INFO::Found 2 missing values.
2026-03-12 21:19:58.13602 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.
2026-03-12 21:19:58.138447 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:58.13922 INFO::Done
2026-03-12 21:19:58.149397 INFO::Formatting Data.
2026-03-12 21:19:58.150264 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:58.151179 INFO::Removing potential empty rows and columns
2026-03-12 21:19:58.152152 INFO::Found 2 missing values.
2026-03-12 21:19:58.153749 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:58.15434 INFO::Done
2026-03-12 21:19:58.164538 INFO::Formatting Data.
2026-03-12 21:19:58.165499 INFO::Typecasting input to dataframe.
2026-03-12 21:19:58.166421 INFO::Replacing NaNs with NAs.
2026-03-12 21:19:58.16739 INFO::Removing potential empty rows and columns
2026-03-12 21:19:58.168533 INFO::Found 0 missing values.
2026-03-12 21:19:58.1716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:19:58.172203 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.526 4.300 23.487
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 34.022 | 2.064 | 23.636 | |
| compute_asw | 0.024 | 0.001 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.015 | |
| generate_data_covariables | 0.012 | 0.001 | 0.012 | |
| generate_dataset | 0.011 | 0.002 | 0.012 | |