Yannis Schumann
| Snapshot Date: 2026-02-05 13:45 -0500 (Thu, 05 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-09 11:57 -0500 (Mon, 09 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4888 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-02-05 21:27:36 -0500 (Thu, 05 Feb 2026) |
| EndedAt: 2026-02-05 21:29:04 -0500 (Thu, 05 Feb 2026) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.145 1.607 17.546
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
2026-02-05 21:28:27.933275 INFO::Formatting Data.
2026-02-05 21:28:27.934641 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:27.946273 INFO::Removing potential empty rows and columns
2026-02-05 21:28:28.200702 INFO::Found 0 missing values.
2026-02-05 21:28:28.204254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:28.20495 INFO::Done
2026-02-05 21:28:28.205518 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:28.217029 INFO::Starting hierarchical adjustment
2026-02-05 21:28:28.217893 INFO::Found 3 batches.
2026-02-05 21:28:28.218446 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:28.219624 INFO::Using default BPPARAM
2026-02-05 21:28:28.220195 INFO::Processing subtree level 1
2026-02-05 21:28:28.323045 INFO::Adjusting the last 1 batches sequentially
2026-02-05 21:28:28.324786 INFO::Done
2026-02-05 21:28:28.325431 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:28.327981 INFO::ASW Batch was -0.0798439093934295 prior to batch effect correction and is now -0.0798439093934295 .
2026-02-05 21:28:28.329041 INFO::Total function execution time is 0.396413087844849 s and adjustment time is 0.107062101364136 s ( 27.01 )
2026-02-05 21:28:28.34328 INFO::Formatting Data.
2026-02-05 21:28:28.344179 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:28.345205 INFO::Removing potential empty rows and columns
2026-02-05 21:28:28.346451 INFO::Found 0 missing values.
2026-02-05 21:28:28.347467 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.
2026-02-05 21:28:28.358753 INFO::Formatting Data.
2026-02-05 21:28:28.359513 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:28.360456 INFO::Removing potential empty rows and columns
2026-02-05 21:28:28.361528 INFO::Found 0 missing values.
2026-02-05 21:28:28.362484 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.
2026-02-05 21:28:28.37895 INFO::Formatting Data.
2026-02-05 21:28:28.379735 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:28.380637 INFO::Removing potential empty rows and columns
2026-02-05 21:28:28.381713 INFO::Found 0 missing values.
2026-02-05 21:28:28.382678 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.
2026-02-05 21:28:28.387219 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:28.387809 INFO::Done
2026-02-05 21:28:28.388329 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:28.390332 INFO::Starting hierarchical adjustment
2026-02-05 21:28:28.391051 INFO::Found 2 batches.
2026-02-05 21:28:28.391599 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:28.39224 INFO::Using default BPPARAM
2026-02-05 21:28:28.392776 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:28.393706 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-05 21:28:28.414916 INFO::Done
2026-02-05 21:28:28.41575 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:28.418031 INFO::ASW Batch was 0.0328552737760971 prior to batch effect correction and is now -0.111689226201751 .
2026-02-05 21:28:28.419036 INFO::Total function execution time is 0.0401430130004883 s and adjustment time is 0.0239686965942383 s ( 59.71 )
2026-02-05 21:28:28.422087 INFO::Formatting Data.
2026-02-05 21:28:28.42281 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:28.431838 INFO::Formatting Data.
2026-02-05 21:28:28.432582 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:28.43352 INFO::Removing potential empty rows and columns
2026-02-05 21:28:28.434584 INFO::Found 0 missing values.
2026-02-05 21:28:28.437611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:28.438174 INFO::Done
2026-02-05 21:28:28.438713 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:28.463771 INFO::Starting hierarchical adjustment
2026-02-05 21:28:28.465034 INFO::Found 2 batches.
2026-02-05 21:28:28.465556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:28.466104 INFO::Using default BPPARAM
2026-02-05 21:28:28.466596 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:28.467445 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-05 21:28:28.481134 INFO::Done
2026-02-05 21:28:28.481783 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:28.483668 INFO::ASW Batch was -0.0320385954283052 prior to batch effect correction and is now -0.111512382513493 .
2026-02-05 21:28:28.4844 INFO::Total function execution time is 0.0526397228240967 s and adjustment time is 0.0162427425384521 s ( 30.86 )
2026-02-05 21:28:28.485349 INFO::Formatting Data.
2026-02-05 21:28:28.485906 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:28.486684 INFO::Removing potential empty rows and columns
2026-02-05 21:28:28.487615 INFO::Found 0 missing values.
2026-02-05 21:28:28.490182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:28.490701 INFO::Done
2026-02-05 21:28:28.491178 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:28.493116 INFO::Starting hierarchical adjustment
2026-02-05 21:28:28.493799 INFO::Found 2 batches.
2026-02-05 21:28:28.494287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:28.49489 INFO::Using default BPPARAM
2026-02-05 21:28:28.495381 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:28.49626 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-05 21:28:28.510681 INFO::Done
2026-02-05 21:28:28.511357 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:28.5134 INFO::ASW Batch was -0.0320385954283052 prior to batch effect correction and is now -0.111512382513493 .
2026-02-05 21:28:28.514184 INFO::Total function execution time is 0.0288290977478027 s and adjustment time is 0.0169773101806641 s ( 58.89 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-05 21:28:31.455967 INFO::Formatting Data.
2026-02-05 21:28:31.45667 INFO::Recognized SummarizedExperiment
2026-02-05 21:28:31.45714 INFO::Typecasting input to dataframe.
2026-02-05 21:28:31.48928 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:31.490643 INFO::Removing potential empty rows and columns
2026-02-05 21:28:31.494516 INFO::Found 0 missing values.
2026-02-05 21:28:31.501832 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:31.502471 INFO::Done
2026-02-05 21:28:31.50303 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:31.506763 INFO::Starting hierarchical adjustment
2026-02-05 21:28:31.507499 INFO::Found 2 batches.
2026-02-05 21:28:31.508039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:31.509448 INFO::Using default BPPARAM
2026-02-05 21:28:31.510012 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:31.511014 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-05 21:28:31.569984 INFO::Done
2026-02-05 21:28:31.570772 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:31.574455 INFO::ASW Batch was -0.0108043887112443 prior to batch effect correction and is now -0.0926531935606218 .
2026-02-05 21:28:31.575344 INFO::Total function execution time is 0.119685173034668 s and adjustment time is 0.062589168548584 s ( 52.29 )
Warning: stack imbalance in '{', 73 then 75
2026-02-05 21:28:31.595701 INFO::Formatting Data.
2026-02-05 21:28:31.596487 INFO::Recognized SummarizedExperiment
2026-02-05 21:28:31.597048 INFO::Typecasting input to dataframe.
2026-02-05 21:28:31.613643 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:31.615023 INFO::Removing potential empty rows and columns
2026-02-05 21:28:31.618911 INFO::Found 0 missing values.
2026-02-05 21:28:31.626431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:31.627091 INFO::Done
2026-02-05 21:28:31.627639 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:31.631529 INFO::Starting hierarchical adjustment
2026-02-05 21:28:31.632279 INFO::Found 2 batches.
2026-02-05 21:28:31.63282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:31.633435 INFO::Using default BPPARAM
2026-02-05 21:28:31.633961 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:31.63493 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-05 21:28:31.661074 INFO::Done
2026-02-05 21:28:31.661906 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:31.665942 INFO::ASW Batch was 0.000587205313612856 prior to batch effect correction and is now 0.000587205313612856 .
2026-02-05 21:28:31.667002 INFO::Total function execution time is 0.0712459087371826 s and adjustment time is 0.0288901329040527 s ( 40.55 )
2026-02-05 21:28:31.687874 INFO::Formatting Data.
2026-02-05 21:28:31.688723 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:31.689655 INFO::Removing potential empty rows and columns
2026-02-05 21:28:31.690714 INFO::Found 0 missing values.
2026-02-05 21:28:31.693684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:31.694223 INFO::Done
2026-02-05 21:28:31.694739 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:31.696817 INFO::Starting hierarchical adjustment
2026-02-05 21:28:31.697528 INFO::Found 3 batches.
2026-02-05 21:28:31.698053 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:31.698645 INFO::Using default BPPARAM
2026-02-05 21:28:31.699172 INFO::Processing subtree level 1
2026-02-05 21:28:31.845134 INFO::Adjusting the last 1 batches sequentially
2026-02-05 21:28:31.847101 INFO::Done
2026-02-05 21:28:31.847845 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:31.850528 INFO::ASW Batch was -0.0875215283286971 prior to batch effect correction and is now -0.149503114786561 .
2026-02-05 21:28:31.85154 INFO::Total function execution time is 0.163676500320435 s and adjustment time is 0.149703502655029 s ( 91.46 )
2026-02-05 21:28:31.867319 INFO::Skipping initial DF formatting
2026-02-05 21:28:31.868086 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:31.872354 INFO::Starting hierarchical adjustment
2026-02-05 21:28:31.873186 INFO::Found 5 batches.
2026-02-05 21:28:31.873762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:31.874381 INFO::Using default BPPARAM
2026-02-05 21:28:31.874922 INFO::Processing subtree level 1
2026-02-05 21:28:32.110082 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:32.111719 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-05 21:28:32.131154 INFO::Done
2026-02-05 21:28:32.131871 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:32.136219 INFO::ASW Batch was 0.531185993343052 prior to batch effect correction and is now 0.531185993343052 .
2026-02-05 21:28:32.136841 INFO::ASW Label was 0.367792421288535 prior to batch effect correction and is now 0.367792421288535 .
2026-02-05 21:28:32.137708 INFO::Total function execution time is 0.270504474639893 s and adjustment time is 0.258141756057739 s ( 95.43 )
2026-02-05 21:28:32.209904 INFO::Formatting Data.
2026-02-05 21:28:32.210645 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:32.211543 INFO::Removing potential empty rows and columns
2026-02-05 21:28:32.21248 INFO::Found 0 missing values.
2026-02-05 21:28:32.216325 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:32.216842 INFO::Done
2026-02-05 21:28:32.21734 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:32.220206 INFO::Starting hierarchical adjustment
2026-02-05 21:28:32.220927 INFO::Found 5 batches.
2026-02-05 21:28:32.221439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:32.222055 INFO::Using default BPPARAM
2026-02-05 21:28:32.222578 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.
2026-02-05 21:28:32.399349 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:32.402015 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-05 21:28:32.421718 INFO::Done
2026-02-05 21:28:32.422534 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:32.426388 INFO::ASW Batch was 0.29884033331366 prior to batch effect correction and is now -0.0739432501768165 .
2026-02-05 21:28:32.427112 INFO::ASW Label was 0.395658176343546 prior to batch effect correction and is now 0.856375697727636 .
2026-02-05 21:28:32.428005 INFO::Total function execution time is 0.21814751625061 s and adjustment time is 0.200895547866821 s ( 92.09 )
2026-02-05 21:28:32.428975 INFO::Formatting Data.
2026-02-05 21:28:32.42969 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:32.430729 INFO::Removing potential empty rows and columns
2026-02-05 21:28:32.43191 INFO::Found 0 missing values.
2026-02-05 21:28:32.436762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:32.437475 INFO::Done
2026-02-05 21:28:32.438072 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:32.441585 INFO::Starting hierarchical adjustment
2026-02-05 21:28:32.442358 INFO::Found 5 batches.
2026-02-05 21:28:32.442936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:32.443627 INFO::Using default BPPARAM
2026-02-05 21:28:32.444201 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.
2026-02-05 21:28:32.568336 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:32.57007 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-05 21:28:32.587984 INFO::Done
2026-02-05 21:28:32.588793 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:32.59253 INFO::ASW Batch was 0.29884033331366 prior to batch effect correction and is now -0.0739432501768165 .
2026-02-05 21:28:32.593271 INFO::ASW Label was 0.395658176343546 prior to batch effect correction and is now 0.856375697727636 .
2026-02-05 21:28:32.594238 INFO::Total function execution time is 0.165231227874756 s and adjustment time is 0.145760536193848 s ( 88.22 )
2026-02-05 21:28:32.609773 INFO::Formatting Data.
2026-02-05 21:28:32.610591 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:32.611544 INFO::Removing potential empty rows and columns
2026-02-05 21:28:32.612586 INFO::Found 0 missing values.
2026-02-05 21:28:32.616972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:32.617555 INFO::Done
2026-02-05 21:28:32.618091 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:32.621252 INFO::Starting hierarchical adjustment
2026-02-05 21:28:32.628264 INFO::Found 5 batches.
2026-02-05 21:28:32.628996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:32.629681 INFO::Using default BPPARAM
2026-02-05 21:28:32.630309 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.
2026-02-05 21:28:32.759074 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:32.760928 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-05 21:28:32.779155 INFO::Done
2026-02-05 21:28:32.779986 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:32.7841 INFO::ASW Batch was 0.364598277355812 prior to batch effect correction and is now -0.0873083906816376 .
2026-02-05 21:28:32.784851 INFO::ASW Label was 0.363548946058342 prior to batch effect correction and is now 0.896180692212879 .
2026-02-05 21:28:32.785802 INFO::Total function execution time is 0.176074266433716 s and adjustment time is 0.151095628738403 s ( 85.81 )
2026-02-05 21:28:32.786752 INFO::Formatting Data.
2026-02-05 21:28:32.787454 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:32.788484 INFO::Removing potential empty rows and columns
2026-02-05 21:28:32.789656 INFO::Found 0 missing values.
2026-02-05 21:28:32.794182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:32.794826 INFO::Done
2026-02-05 21:28:32.795404 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:32.798747 INFO::Starting hierarchical adjustment
2026-02-05 21:28:32.799537 INFO::Found 5 batches.
2026-02-05 21:28:32.800142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:32.800845 INFO::Using default BPPARAM
2026-02-05 21:28:32.801413 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.
2026-02-05 21:28:32.922542 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:32.924171 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-05 21:28:32.941434 INFO::Done
2026-02-05 21:28:32.942171 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:32.945502 INFO::ASW Batch was 0.364598277355812 prior to batch effect correction and is now -0.0873083906816376 .
2026-02-05 21:28:32.94617 INFO::ASW Label was 0.363548946058342 prior to batch effect correction and is now 0.896180692212879 .
2026-02-05 21:28:32.94706 INFO::Total function execution time is 0.160332202911377 s and adjustment time is 0.142043828964233 s ( 88.59 )
2026-02-05 21:28:32.961575 INFO::Formatting Data.
2026-02-05 21:28:32.962381 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:32.963341 INFO::Removing potential empty rows and columns
2026-02-05 21:28:32.964402 INFO::Found 0 missing values.
2026-02-05 21:28:32.967291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:32.967889 INFO::Done
2026-02-05 21:28:32.968433 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:32.971663 INFO::Starting hierarchical adjustment
2026-02-05 21:28:32.97241 INFO::Found 2 batches.
2026-02-05 21:28:32.972987 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:32.973639 INFO::Using default BPPARAM
2026-02-05 21:28:32.974197 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:32.97515 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-05 21:28:32.990653 INFO::Done
2026-02-05 21:28:32.99137 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:32.994541 INFO::ASW Batch was 0.271053237636773 prior to batch effect correction and is now -0.0255478716622639 .
2026-02-05 21:28:32.995174 INFO::ASW Label was 0.74641331832473 prior to batch effect correction and is now 0.936041298622696 .
2026-02-05 21:28:32.995981 INFO::Total function execution time is 0.0344891548156738 s and adjustment time is 0.0183615684509277 s ( 53.24 )
2026-02-05 21:28:32.99679 INFO::Formatting Data.
2026-02-05 21:28:32.997432 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:32.998366 INFO::Removing potential empty rows and columns
2026-02-05 21:28:32.999404 INFO::Found 0 missing values.
2026-02-05 21:28:33.002194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:33.002788 INFO::Done
2026-02-05 21:28:33.003323 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:33.006521 INFO::Starting hierarchical adjustment
2026-02-05 21:28:33.007275 INFO::Found 2 batches.
2026-02-05 21:28:33.007848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:33.00847 INFO::Using default BPPARAM
2026-02-05 21:28:33.009017 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:33.009969 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-05 21:28:33.025723 INFO::Done
2026-02-05 21:28:33.026461 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:33.029713 INFO::ASW Batch was 0.271053237636773 prior to batch effect correction and is now -0.0255478716622639 .
2026-02-05 21:28:33.030371 INFO::ASW Label was 0.74641331832473 prior to batch effect correction and is now 0.936041298622696 .
2026-02-05 21:28:33.031209 INFO::Total function execution time is 0.0344209671020508 s and adjustment time is 0.0185675621032715 s ( 53.94 )
2026-02-05 21:28:33.043455 INFO::Formatting Data.
2026-02-05 21:28:33.044292 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:33.045226 INFO::Removing potential empty rows and columns
2026-02-05 21:28:33.046239 INFO::Found 0 missing values.
2026-02-05 21:28:33.048499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:33.049078 INFO::Done
2026-02-05 21:28:33.04967 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:33.051795 INFO::Starting hierarchical adjustment
2026-02-05 21:28:33.052551 INFO::Found 2 batches.
2026-02-05 21:28:33.053128 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:33.053802 INFO::Using default BPPARAM
2026-02-05 21:28:33.054352 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:33.055309 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-05 21:28:33.093245 INFO::Done
2026-02-05 21:28:33.094265 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:33.097269 INFO::ASW Batch was -0.104814928098631 prior to batch effect correction and is now -0.123434990671264 .
2026-02-05 21:28:33.098475 INFO::Total function execution time is 0.0550537109375 s and adjustment time is 0.0407922267913818 s ( 74.1 )
2026-02-05 21:28:33.115233 INFO::Formatting Data.
2026-02-05 21:28:33.11606 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:33.116997 INFO::Removing potential empty rows and columns
2026-02-05 21:28:33.118057 INFO::Found 0 missing values.
2026-02-05 21:28:33.119244 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.
2026-02-05 21:28:33.124079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:33.124669 INFO::Done
2026-02-05 21:28:33.125205 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:33.128343 INFO::Starting hierarchical adjustment
2026-02-05 21:28:33.129084 INFO::Found 2 batches.
2026-02-05 21:28:33.129642 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:33.130257 INFO::Using default BPPARAM
2026-02-05 21:28:33.130813 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:33.131768 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-05 21:28:33.149295 INFO::Done
2026-02-05 21:28:33.150036 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:33.153167 INFO::ASW Batch was 0.491435198693919 prior to batch effect correction and is now -0.027370181210711 .
2026-02-05 21:28:33.153801 INFO::ASW Label was 0.595982175056147 prior to batch effect correction and is now 0.938215388649005 .
2026-02-05 21:28:33.154619 INFO::Total function execution time is 0.0394701957702637 s and adjustment time is 0.0203189849853516 s ( 51.48 )
2026-02-05 21:28:33.155484 INFO::Formatting Data.
2026-02-05 21:28:33.156152 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:33.157116 INFO::Removing potential empty rows and columns
2026-02-05 21:28:33.158141 INFO::Found 0 missing values.
2026-02-05 21:28:33.159106 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.
2026-02-05 21:28:33.164135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:33.164783 INFO::Done
2026-02-05 21:28:33.165347 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:33.168575 INFO::Starting hierarchical adjustment
2026-02-05 21:28:33.169334 INFO::Found 2 batches.
2026-02-05 21:28:33.169926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:33.170565 INFO::Using default BPPARAM
2026-02-05 21:28:33.171139 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:33.172145 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-05 21:28:33.189867 INFO::Done
2026-02-05 21:28:33.190598 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:33.193797 INFO::ASW Batch was 0.491435198693919 prior to batch effect correction and is now -0.027370181210711 .
2026-02-05 21:28:33.194455 INFO::ASW Label was 0.595982175056147 prior to batch effect correction and is now 0.938215388649005 .
2026-02-05 21:28:33.195377 INFO::Total function execution time is 0.0399322509765625 s and adjustment time is 0.0206623077392578 s ( 51.74 )
2026-02-05 21:28:33.417085 INFO::Formatting Data.
2026-02-05 21:28:33.418026 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:33.41904 INFO::Removing potential empty rows and columns
2026-02-05 21:28:33.420154 INFO::Found 0 missing values.
2026-02-05 21:28:33.423403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:33.424003 INFO::Done
2026-02-05 21:28:33.424534 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:33.426705 INFO::Starting hierarchical adjustment
2026-02-05 21:28:33.427425 INFO::Found 3 batches.
2026-02-05 21:28:33.427976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:33.428594 INFO::Using default BPPARAM
2026-02-05 21:28:33.42913 INFO::Processing subtree level 1
2026-02-05 21:28:33.520313 INFO::Adjusting the last 1 batches sequentially
2026-02-05 21:28:33.522121 INFO::Done
2026-02-05 21:28:33.522806 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:33.525347 INFO::ASW Batch was -0.0909391423565304 prior to batch effect correction and is now -0.0909391423565304 .
2026-02-05 21:28:33.526312 INFO::Total function execution time is 0.109328746795654 s and adjustment time is 0.0948293209075928 s ( 86.74 )
2026-02-05 21:28:33.527379 INFO::Formatting Data.
2026-02-05 21:28:33.528054 INFO::Typecasting input to dataframe.
2026-02-05 21:28:33.528842 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:33.529809 INFO::Removing potential empty rows and columns
2026-02-05 21:28:33.530928 INFO::Found 0 missing values.
2026-02-05 21:28:33.534102 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:33.53471 INFO::Done
2026-02-05 21:28:33.535278 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:33.537352 INFO::Starting hierarchical adjustment
2026-02-05 21:28:33.538108 INFO::Found 3 batches.
2026-02-05 21:28:33.538677 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:33.539305 INFO::Using default BPPARAM
2026-02-05 21:28:33.539874 INFO::Processing subtree level 1
2026-02-05 21:28:33.623959 INFO::Adjusting the last 1 batches sequentially
2026-02-05 21:28:33.625778 INFO::Done
2026-02-05 21:28:33.626459 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:33.629103 INFO::ASW Batch was -0.0909391423565304 prior to batch effect correction and is now -0.0909391423565304 .
2026-02-05 21:28:33.63009 INFO::Total function execution time is 0.10267448425293 s and adjustment time is 0.0878052711486816 s ( 85.52 )
2026-02-05 21:28:33.643573 INFO::Formatting Data.
2026-02-05 21:28:33.644383 INFO::Typecasting input to dataframe.
2026-02-05 21:28:33.645249 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:33.646205 INFO::Removing potential empty rows and columns
2026-02-05 21:28:33.647308 INFO::Found 0 missing values.
2026-02-05 21:28:33.650384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:33.650969 INFO::Done
2026-02-05 21:28:33.651503 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:33.653643 INFO::Starting hierarchical adjustment
2026-02-05 21:28:33.654368 INFO::Found 3 batches.
2026-02-05 21:28:33.654923 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:33.655568 INFO::Using default BPPARAM
2026-02-05 21:28:33.656125 INFO::Processing subtree level 1
2026-02-05 21:28:33.74277 INFO::Adjusting the last 1 batches sequentially
2026-02-05 21:28:33.744879 INFO::Done
2026-02-05 21:28:33.745655 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:33.748327 INFO::ASW Batch was -0.0581018686851829 prior to batch effect correction and is now -0.0581018686851829 .
2026-02-05 21:28:33.749338 INFO::Total function execution time is 0.105817317962646 s and adjustment time is 0.0906400680541992 s ( 85.66 )
2026-02-05 21:28:33.902591 INFO::Formatting Data.
2026-02-05 21:28:33.903438 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:33.904574 INFO::Removing potential empty rows and columns
2026-02-05 21:28:33.907396 INFO::Found 1000 missing values.
2026-02-05 21:28:33.92626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:33.927037 INFO::Done
2026-02-05 21:28:33.927624 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:33.933144 INFO::Starting hierarchical adjustment
2026-02-05 21:28:33.93395 INFO::Found 10 batches.
2026-02-05 21:28:33.934489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:33.935134 INFO::Using default BPPARAM
2026-02-05 21:28:33.935675 INFO::Processing subtree level 1
2026-02-05 21:28:34.06539 INFO::Processing subtree level 2
2026-02-05 21:28:34.203116 INFO::Adjusting the last 1 batches sequentially
2026-02-05 21:28:34.205062 INFO::Done
2026-02-05 21:28:34.205734 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:34.211132 INFO::ASW Batch was 0.474079390081693 prior to batch effect correction and is now 0.474079390081693 .
2026-02-05 21:28:34.211758 INFO::ASW Label was 0.346467670899175 prior to batch effect correction and is now 0.346467670899175 .
2026-02-05 21:28:34.212646 INFO::Total function execution time is 0.310125589370728 s and adjustment time is 0.271251201629639 s ( 87.46 )
2026-02-05 21:28:34.213476 INFO::Formatting Data.
2026-02-05 21:28:34.214124 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:34.215344 INFO::Removing potential empty rows and columns
2026-02-05 21:28:34.218122 INFO::Found 1000 missing values.
2026-02-05 21:28:34.236938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:34.237709 INFO::Done
2026-02-05 21:28:34.238279 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:34.24378 INFO::Starting hierarchical adjustment
2026-02-05 21:28:34.244586 INFO::Found 10 batches.
2026-02-05 21:28:35.40362 INFO::Set up parallel execution backend with 2 workers
2026-02-05 21:28:35.405497 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-05 21:28:36.594317 INFO::Adjusting the last 2 batches sequentially
2026-02-05 21:28:36.59596 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-05 21:28:36.611536 INFO::Done
2026-02-05 21:28:36.612194 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:36.616486 INFO::ASW Batch was 0.474079390081693 prior to batch effect correction and is now 0.474079390081693 .
2026-02-05 21:28:36.617051 INFO::ASW Label was 0.346467670899175 prior to batch effect correction and is now 0.346467670899175 .
2026-02-05 21:28:36.617747 INFO::Total function execution time is 2.40432047843933 s and adjustment time is 2.36707997322083 s ( 98.45 )
2026-02-05 21:28:36.76997 INFO::Formatting Data.
2026-02-05 21:28:36.770796 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:36.771752 INFO::Removing potential empty rows and columns
2026-02-05 21:28:36.772863 INFO::Found 0 missing values.
2026-02-05 21:28:36.776614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:36.777165 INFO::Done
2026-02-05 21:28:36.777705 INFO::Acquiring quality metrics before batch effect correction.
2026-02-05 21:28:36.780529 INFO::Starting hierarchical adjustment
2026-02-05 21:28:36.781262 INFO::Found 3 batches.
2026-02-05 21:28:36.781807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-05 21:28:36.782436 INFO::Using default BPPARAM
2026-02-05 21:28:36.783002 INFO::Processing subtree level 1
2026-02-05 21:28:36.89364 INFO::Adjusting the last 1 batches sequentially
2026-02-05 21:28:36.895561 INFO::Done
2026-02-05 21:28:36.896219 INFO::Acquiring quality metrics after batch effect correction.
2026-02-05 21:28:36.899634 INFO::ASW Batch was 0.207024417992532 prior to batch effect correction and is now -0.153552813839338 .
2026-02-05 21:28:36.900308 INFO::ASW Label was -0.154332906089004 prior to batch effect correction and is now -0.0343577074233369 .
2026-02-05 21:28:36.901264 INFO::Total function execution time is 0.13134765625 s and adjustment time is 0.114422082901001 s ( 87.11 )
2026-02-05 21:28:37.028583 INFO::Formatting Data.
2026-02-05 21:28:37.02942 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.030354 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.031531 INFO::Found 2 missing values.
2026-02-05 21:28:37.034396 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.034948 INFO::Done
2026-02-05 21:28:37.063273 INFO::Found NA in Reference column
2026-02-05 21:28:37.072851 INFO::Require at least two references per batch.
2026-02-05 21:28:37.092905 INFO::Formatting Data.
2026-02-05 21:28:37.093703 INFO::Recognized SummarizedExperiment
2026-02-05 21:28:37.094257 INFO::Typecasting input to dataframe.
2026-02-05 21:28:37.103436 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.104589 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.107891 INFO::Found 0 missing values.
2026-02-05 21:28:37.114248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.114849 INFO::Done
2026-02-05 21:28:37.129815 INFO::Formatting Data.
2026-02-05 21:28:37.130594 INFO::Recognized SummarizedExperiment
2026-02-05 21:28:37.131111 INFO::Typecasting input to dataframe.
2026-02-05 21:28:37.157439 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.158818 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.162725 INFO::Found 0 missing values.
2026-02-05 21:28:37.174687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.175417 INFO::Done
2026-02-05 21:28:37.192036 INFO::Formatting Data.
2026-02-05 21:28:37.192787 INFO::Recognized SummarizedExperiment
2026-02-05 21:28:37.19333 INFO::Typecasting input to dataframe.
2026-02-05 21:28:37.210536 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.211626 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.21275 INFO::Found 0 missing values.
2026-02-05 21:28:37.213711 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.
2026-02-05 21:28:37.218351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.218979 INFO::Done
2026-02-05 21:28:37.229723 INFO::Formatting Data.
2026-02-05 21:28:37.230532 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.231419 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.23255 INFO::Found 0 missing values.
2026-02-05 21:28:37.235517 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.236074 INFO::Done
2026-02-05 21:28:37.247991 INFO::Formatting Data.
2026-02-05 21:28:37.248823 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.24983 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.250854 INFO::Found 0 missing values.
2026-02-05 21:28:37.253735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.254271 INFO::Done
2026-02-05 21:28:37.285191 INFO::Formatting Data.
2026-02-05 21:28:37.28608 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.287163 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.288369 INFO::Found 1 missing values.
2026-02-05 21:28:37.291085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.291645 INFO::Done
2026-02-05 21:28:37.312044 INFO::Formatting Data.
2026-02-05 21:28:37.312907 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.31381 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.31481 INFO::Found 2 missing values.
2026-02-05 21:28:37.315763 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.
2026-02-05 21:28:37.31815 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.318717 INFO::Done
2026-02-05 21:28:37.329186 INFO::Formatting Data.
2026-02-05 21:28:37.329984 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.330973 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.33194 INFO::Found 2 missing values.
2026-02-05 21:28:37.33358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.334136 INFO::Done
2026-02-05 21:28:37.344785 INFO::Formatting Data.
2026-02-05 21:28:37.345651 INFO::Typecasting input to dataframe.
2026-02-05 21:28:37.346465 INFO::Replacing NaNs with NAs.
2026-02-05 21:28:37.347337 INFO::Removing potential empty rows and columns
2026-02-05 21:28:37.348332 INFO::Found 0 missing values.
2026-02-05 21:28:37.351223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-05 21:28:37.351768 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.165 3.627 20.575
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.145 | 1.607 | 17.546 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.015 | 0.001 | 0.015 | |
| generate_data_covariables | 0.010 | 0.004 | 0.013 | |
| generate_dataset | 0.011 | 0.002 | 0.012 | |