Yannis Schumann
| Snapshot Date: 2026-04-12 13:40 -0400 (Sun, 12 Apr 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 2026-04-13 11:35 -0400 (Mon, 13 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4919 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4632 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 170/2390 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.7.0 |
| 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: 2026-04-12 22:16:27 -0400 (Sun, 12 Apr 2026) |
| EndedAt: 2026-04-12 22:18:00 -0400 (Sun, 12 Apr 2026) |
| EllapsedTime: 93.1 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 version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-13 02:16:27 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 23.762 1.146 17.219
* 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 version 4.6.0 alpha (2026-04-05 r89794)
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")
2026-04-12 22:17:19.452959 INFO::Formatting Data.
2026-04-12 22:17:19.454273 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:19.465029 INFO::Removing potential empty rows and columns
2026-04-12 22:17:19.711135 INFO::Found 0 missing values.
2026-04-12 22:17:19.714683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:19.715431 INFO::Done
2026-04-12 22:17:19.716064 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:19.728505 INFO::Starting hierarchical adjustment
2026-04-12 22:17:19.729373 INFO::Found 3 batches.
2026-04-12 22:17:19.729932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:19.731015 INFO::Using default BPPARAM
2026-04-12 22:17:19.731595 INFO::Processing subtree level 1
2026-04-12 22:17:19.829473 INFO::Adjusting the last 1 batches sequentially
2026-04-12 22:17:19.831334 INFO::Done
2026-04-12 22:17:19.832014 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:19.83457 INFO::ASW Batch was -0.0854480718456814 prior to batch effect correction and is now -0.0854480718456814 .
2026-04-12 22:17:19.835655 INFO::Total function execution time is 0.383297204971313 s and adjustment time is 0.102112531661987 s ( 26.64 )
2026-04-12 22:17:19.849457 INFO::Formatting Data.
2026-04-12 22:17:19.850303 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:19.851264 INFO::Removing potential empty rows and columns
2026-04-12 22:17:19.852372 INFO::Found 0 missing values.
2026-04-12 22:17:19.853358 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.
2026-04-12 22:17:19.864105 INFO::Formatting Data.
2026-04-12 22:17:19.864947 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:19.86589 INFO::Removing potential empty rows and columns
2026-04-12 22:17:19.867032 INFO::Found 0 missing values.
2026-04-12 22:17:19.867984 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.
2026-04-12 22:17:19.883674 INFO::Formatting Data.
2026-04-12 22:17:19.884507 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:19.885439 INFO::Removing potential empty rows and columns
2026-04-12 22:17:19.886511 INFO::Found 0 missing values.
2026-04-12 22:17:19.887449 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.
2026-04-12 22:17:19.891952 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:19.892598 INFO::Done
2026-04-12 22:17:19.893166 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:19.895249 INFO::Starting hierarchical adjustment
2026-04-12 22:17:19.896008 INFO::Found 2 batches.
2026-04-12 22:17:19.896584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:19.897241 INFO::Using default BPPARAM
2026-04-12 22:17:19.897812 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:19.898806 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-12 22:17:19.919869 INFO::Done
2026-04-12 22:17:19.920697 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:19.922931 INFO::ASW Batch was -0.0297464415820412 prior to batch effect correction and is now -0.120603401683688 .
2026-04-12 22:17:19.923828 INFO::Total function execution time is 0.0402171611785889 s and adjustment time is 0.0239694118499756 s ( 59.6 )
2026-04-12 22:17:19.926711 INFO::Formatting Data.
2026-04-12 22:17:19.927428 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:19.936337 INFO::Formatting Data.
2026-04-12 22:17:19.937152 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:19.938108 INFO::Removing potential empty rows and columns
2026-04-12 22:17:19.939348 INFO::Found 0 missing values.
2026-04-12 22:17:19.942322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:19.942916 INFO::Done
2026-04-12 22:17:19.943491 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:19.945543 INFO::Starting hierarchical adjustment
2026-04-12 22:17:19.946301 INFO::Found 2 batches.
2026-04-12 22:17:19.946868 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:19.947524 INFO::Using default BPPARAM
2026-04-12 22:17:19.948096 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:19.949064 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-12 22:17:19.965012 INFO::Done
2026-04-12 22:17:19.965868 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:19.968045 INFO::ASW Batch was 0.0587440775476795 prior to batch effect correction and is now -0.122301817092796 .
2026-04-12 22:17:19.968978 INFO::Total function execution time is 0.0327050685882568 s and adjustment time is 0.0188324451446533 s ( 57.58 )
2026-04-12 22:17:19.970099 INFO::Formatting Data.
2026-04-12 22:17:19.97078 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:19.971735 INFO::Removing potential empty rows and columns
2026-04-12 22:17:19.972835 INFO::Found 0 missing values.
2026-04-12 22:17:19.975951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:19.97661 INFO::Done
2026-04-12 22:17:19.977196 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:19.979375 INFO::Starting hierarchical adjustment
2026-04-12 22:17:19.980158 INFO::Found 2 batches.
2026-04-12 22:17:19.98075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:19.981446 INFO::Using default BPPARAM
2026-04-12 22:17:19.982014 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:19.982996 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-12 22:17:19.998293 INFO::Done
2026-04-12 22:17:19.999087 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:20.001213 INFO::ASW Batch was 0.0587440775476795 prior to batch effect correction and is now -0.122301817092796 .
2026-04-12 22:17:20.002069 INFO::Total function execution time is 0.0319766998291016 s and adjustment time is 0.0182631015777588 s ( 57.11 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-12 22:17:23.072147 INFO::Formatting Data.
2026-04-12 22:17:23.072956 INFO::Recognized SummarizedExperiment
2026-04-12 22:17:23.073509 INFO::Typecasting input to dataframe.
2026-04-12 22:17:23.103936 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:23.105204 INFO::Removing potential empty rows and columns
2026-04-12 22:17:23.108584 INFO::Found 0 missing values.
2026-04-12 22:17:23.114875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:23.115464 INFO::Done
2026-04-12 22:17:23.11598 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:23.119209 INFO::Starting hierarchical adjustment
2026-04-12 22:17:23.119908 INFO::Found 2 batches.
2026-04-12 22:17:23.120428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:23.121487 INFO::Using default BPPARAM
2026-04-12 22:17:23.122034 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:23.122971 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-12 22:17:23.17172 INFO::Done
2026-04-12 22:17:23.172451 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:23.175786 INFO::ASW Batch was 0.0150476994169147 prior to batch effect correction and is now -0.092278842604081 .
2026-04-12 22:17:23.176611 INFO::Total function execution time is 0.104754686355591 s and adjustment time is 0.0519213676452637 s ( 49.56 )
Warning: stack imbalance in '{', 73 then 75
2026-04-12 22:17:23.193135 INFO::Formatting Data.
2026-04-12 22:17:23.193869 INFO::Recognized SummarizedExperiment
2026-04-12 22:17:23.194391 INFO::Typecasting input to dataframe.
2026-04-12 22:17:23.202525 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:23.203627 INFO::Removing potential empty rows and columns
2026-04-12 22:17:23.206866 INFO::Found 0 missing values.
2026-04-12 22:17:23.213083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:23.213696 INFO::Done
2026-04-12 22:17:23.21421 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:23.217455 INFO::Starting hierarchical adjustment
2026-04-12 22:17:23.218144 INFO::Found 2 batches.
2026-04-12 22:17:23.218687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:23.219286 INFO::Using default BPPARAM
2026-04-12 22:17:23.21982 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:23.220757 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-12 22:17:23.245844 INFO::Done
2026-04-12 22:17:23.246743 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:23.250585 INFO::ASW Batch was -0.00504475435523401 prior to batch effect correction and is now -0.00504475435523401 .
2026-04-12 22:17:23.251518 INFO::Total function execution time is 0.0583453178405762 s and adjustment time is 0.0277926921844482 s ( 47.63 )
2026-04-12 22:17:23.271365 INFO::Formatting Data.
2026-04-12 22:17:23.272235 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:23.273237 INFO::Removing potential empty rows and columns
2026-04-12 22:17:23.274351 INFO::Found 0 missing values.
2026-04-12 22:17:23.277488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:23.278066 INFO::Done
2026-04-12 22:17:23.278639 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:23.280826 INFO::Starting hierarchical adjustment
2026-04-12 22:17:23.281592 INFO::Found 3 batches.
2026-04-12 22:17:23.282143 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:23.282797 INFO::Using default BPPARAM
2026-04-12 22:17:23.283379 INFO::Processing subtree level 1
2026-04-12 22:17:23.426957 INFO::Adjusting the last 1 batches sequentially
2026-04-12 22:17:23.429141 INFO::Done
2026-04-12 22:17:23.429974 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:23.432859 INFO::ASW Batch was -0.0475145621431801 prior to batch effect correction and is now -0.16011564002247 .
2026-04-12 22:17:23.43394 INFO::Total function execution time is 0.16291356086731 s and adjustment time is 0.147653341293335 s ( 90.63 )
2026-04-12 22:17:23.449721 INFO::Skipping initial DF formatting
2026-04-12 22:17:23.450604 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:23.455026 INFO::Starting hierarchical adjustment
2026-04-12 22:17:23.455946 INFO::Found 5 batches.
2026-04-12 22:17:23.456566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:23.457265 INFO::Using default BPPARAM
2026-04-12 22:17:23.457846 INFO::Processing subtree level 1
2026-04-12 22:17:23.591188 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:23.593208 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-12 22:17:23.614359 INFO::Done
2026-04-12 22:17:23.615315 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:23.619986 INFO::ASW Batch was 0.520931327904951 prior to batch effect correction and is now 0.520931327904951 .
2026-04-12 22:17:23.620757 INFO::ASW Label was 0.353960098966416 prior to batch effect correction and is now 0.353960098966416 .
2026-04-12 22:17:23.62177 INFO::Total function execution time is 0.172177791595459 s and adjustment time is 0.158533811569214 s ( 92.08 )
2026-04-12 22:17:23.641023 INFO::Formatting Data.
2026-04-12 22:17:23.642023 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:23.64315 INFO::Removing potential empty rows and columns
2026-04-12 22:17:23.64429 INFO::Found 0 missing values.
2026-04-12 22:17:23.648666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:23.649335 INFO::Done
2026-04-12 22:17:23.649927 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:23.653238 INFO::Starting hierarchical adjustment
2026-04-12 22:17:23.654051 INFO::Found 5 batches.
2026-04-12 22:17:23.654646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:23.655339 INFO::Using default BPPARAM
2026-04-12 22:17:23.655915 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.
2026-04-12 22:17:23.778919 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:23.780977 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-12 22:17:23.799084 INFO::Done
2026-04-12 22:17:23.80005 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:23.803862 INFO::ASW Batch was 0.119042139984176 prior to batch effect correction and is now -0.085410031463264 .
2026-04-12 22:17:23.804663 INFO::ASW Label was 0.582532468305841 prior to batch effect correction and is now 0.849368454798403 .
2026-04-12 22:17:23.805605 INFO::Total function execution time is 0.16471791267395 s and adjustment time is 0.145110368728638 s ( 88.1 )
2026-04-12 22:17:23.80654 INFO::Formatting Data.
2026-04-12 22:17:23.807228 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:23.808249 INFO::Removing potential empty rows and columns
2026-04-12 22:17:23.809404 INFO::Found 0 missing values.
2026-04-12 22:17:23.813819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:23.814464 INFO::Done
2026-04-12 22:17:23.815048 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:23.818377 INFO::Starting hierarchical adjustment
2026-04-12 22:17:23.819167 INFO::Found 5 batches.
2026-04-12 22:17:23.819759 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:23.820465 INFO::Using default BPPARAM
2026-04-12 22:17:23.82105 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.
2026-04-12 22:17:23.949416 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:23.951569 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-12 22:17:23.968978 INFO::Done
2026-04-12 22:17:23.97003 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:23.974056 INFO::ASW Batch was 0.119042139984176 prior to batch effect correction and is now -0.085410031463264 .
2026-04-12 22:17:23.974897 INFO::ASW Label was 0.582532468305841 prior to batch effect correction and is now 0.849368454798403 .
2026-04-12 22:17:23.975902 INFO::Total function execution time is 0.169347524642944 s and adjustment time is 0.149903774261475 s ( 88.52 )
2026-04-12 22:17:23.992492 INFO::Formatting Data.
2026-04-12 22:17:23.993525 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:23.994669 INFO::Removing potential empty rows and columns
2026-04-12 22:17:23.995858 INFO::Found 0 missing values.
2026-04-12 22:17:24.000369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.001131 INFO::Done
2026-04-12 22:17:24.001794 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.005233 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.006102 INFO::Found 5 batches.
2026-04-12 22:17:24.006716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.00741 INFO::Using default BPPARAM
2026-04-12 22:17:24.00799 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.
2026-04-12 22:17:24.1227 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:24.124483 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-12 22:17:24.140483 INFO::Done
2026-04-12 22:17:24.141307 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:24.14481 INFO::ASW Batch was 0.519464284074341 prior to batch effect correction and is now -0.0546662430666206 .
2026-04-12 22:17:24.14555 INFO::ASW Label was 0.331099008927481 prior to batch effect correction and is now 0.822538808032981 .
2026-04-12 22:17:24.146437 INFO::Total function execution time is 0.154090881347656 s and adjustment time is 0.134543180465698 s ( 87.31 )
2026-04-12 22:17:24.147343 INFO::Formatting Data.
2026-04-12 22:17:24.148019 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:24.148974 INFO::Removing potential empty rows and columns
2026-04-12 22:17:24.150008 INFO::Found 0 missing values.
2026-04-12 22:17:24.15415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.154753 INFO::Done
2026-04-12 22:17:24.155328 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.158406 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.15916 INFO::Found 5 batches.
2026-04-12 22:17:24.159756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.160437 INFO::Using default BPPARAM
2026-04-12 22:17:24.161001 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.
2026-04-12 22:17:24.279878 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:24.282883 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-12 22:17:24.302301 INFO::Done
2026-04-12 22:17:24.303341 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:24.307181 INFO::ASW Batch was 0.519464284074341 prior to batch effect correction and is now -0.0546662430666206 .
2026-04-12 22:17:24.307974 INFO::ASW Label was 0.331099008927481 prior to batch effect correction and is now 0.822538808032981 .
2026-04-12 22:17:24.30897 INFO::Total function execution time is 0.161633253097534 s and adjustment time is 0.143181085586548 s ( 88.58 )
2026-04-12 22:17:24.324455 INFO::Formatting Data.
2026-04-12 22:17:24.325513 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:24.326682 INFO::Removing potential empty rows and columns
2026-04-12 22:17:24.327919 INFO::Found 0 missing values.
2026-04-12 22:17:24.331075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.331728 INFO::Done
2026-04-12 22:17:24.332323 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.33593 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.336819 INFO::Found 2 batches.
2026-04-12 22:17:24.337425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.338115 INFO::Using default BPPARAM
2026-04-12 22:17:24.338705 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:24.339817 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-12 22:17:24.357172 INFO::Done
2026-04-12 22:17:24.358145 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:24.361629 INFO::ASW Batch was 0.487848152208132 prior to batch effect correction and is now -0.0239424981197932 .
2026-04-12 22:17:24.36235 INFO::ASW Label was 0.559940382843073 prior to batch effect correction and is now 0.925544337553601 .
2026-04-12 22:17:24.363367 INFO::Total function execution time is 0.0390937328338623 s and adjustment time is 0.0204513072967529 s ( 52.31 )
2026-04-12 22:17:24.364293 INFO::Formatting Data.
2026-04-12 22:17:24.364993 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:24.366008 INFO::Removing potential empty rows and columns
2026-04-12 22:17:24.367131 INFO::Found 0 missing values.
2026-04-12 22:17:24.370158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.370798 INFO::Done
2026-04-12 22:17:24.371379 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.37482 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.375673 INFO::Found 2 batches.
2026-04-12 22:17:24.37627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.376941 INFO::Using default BPPARAM
2026-04-12 22:17:24.377517 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:24.378603 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-12 22:17:24.395211 INFO::Done
2026-04-12 22:17:24.396128 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:24.399619 INFO::ASW Batch was 0.487848152208132 prior to batch effect correction and is now -0.0239424981197932 .
2026-04-12 22:17:24.400344 INFO::ASW Label was 0.559940382843073 prior to batch effect correction and is now 0.925544337553601 .
2026-04-12 22:17:24.401276 INFO::Total function execution time is 0.0370256900787354 s and adjustment time is 0.0196602344512939 s ( 53.1 )
2026-04-12 22:17:24.414304 INFO::Formatting Data.
2026-04-12 22:17:24.415344 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:24.416407 INFO::Removing potential empty rows and columns
2026-04-12 22:17:24.417442 INFO::Found 0 missing values.
2026-04-12 22:17:24.419809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.420441 INFO::Done
2026-04-12 22:17:24.421003 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.423205 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.423987 INFO::Found 2 batches.
2026-04-12 22:17:24.424568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.425226 INFO::Using default BPPARAM
2026-04-12 22:17:24.425827 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:24.426835 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-12 22:17:24.4604 INFO::Done
2026-04-12 22:17:24.461329 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:24.463628 INFO::ASW Batch was -0.0565775589462125 prior to batch effect correction and is now -0.169353761002018 .
2026-04-12 22:17:24.464562 INFO::Total function execution time is 0.0504393577575684 s and adjustment time is 0.0364978313446045 s ( 72.36 )
2026-04-12 22:17:24.477859 INFO::Formatting Data.
2026-04-12 22:17:24.478873 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:24.479915 INFO::Removing potential empty rows and columns
2026-04-12 22:17:24.481033 INFO::Found 0 missing values.
2026-04-12 22:17:24.482356 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.
2026-04-12 22:17:24.487406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.488191 INFO::Done
2026-04-12 22:17:24.488811 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.492074 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.492908 INFO::Found 2 batches.
2026-04-12 22:17:24.493506 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.494169 INFO::Using default BPPARAM
2026-04-12 22:17:24.494781 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:24.495809 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-12 22:17:24.513812 INFO::Done
2026-04-12 22:17:24.514718 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:24.518125 INFO::ASW Batch was 0.497562032454928 prior to batch effect correction and is now 0.0383538357507065 .
2026-04-12 22:17:24.518867 INFO::ASW Label was 0.595541510179734 prior to batch effect correction and is now 0.921253313951784 .
2026-04-12 22:17:24.519804 INFO::Total function execution time is 0.0420923233032227 s and adjustment time is 0.0210177898406982 s ( 49.93 )
2026-04-12 22:17:24.520696 INFO::Formatting Data.
2026-04-12 22:17:24.521379 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:24.522434 INFO::Removing potential empty rows and columns
2026-04-12 22:17:24.523545 INFO::Found 0 missing values.
2026-04-12 22:17:24.524577 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.
2026-04-12 22:17:24.529628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.530391 INFO::Done
2026-04-12 22:17:24.530987 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.534322 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.535165 INFO::Found 2 batches.
2026-04-12 22:17:24.535775 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.536491 INFO::Using default BPPARAM
2026-04-12 22:17:24.53706 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:24.538142 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-12 22:17:24.55601 INFO::Done
2026-04-12 22:17:24.556881 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:24.560164 INFO::ASW Batch was 0.497562032454928 prior to batch effect correction and is now 0.0383538357507065 .
2026-04-12 22:17:24.560937 INFO::ASW Label was 0.595541510179734 prior to batch effect correction and is now 0.921253313951784 .
2026-04-12 22:17:24.561842 INFO::Total function execution time is 0.0411579608917236 s and adjustment time is 0.0209536552429199 s ( 50.91 )
2026-04-12 22:17:24.791841 INFO::Formatting Data.
2026-04-12 22:17:24.79283 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:24.793983 INFO::Removing potential empty rows and columns
2026-04-12 22:17:24.795192 INFO::Found 0 missing values.
2026-04-12 22:17:24.798457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.799084 INFO::Done
2026-04-12 22:17:24.79968 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.801948 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.802715 INFO::Found 3 batches.
2026-04-12 22:17:24.803299 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.803985 INFO::Using default BPPARAM
2026-04-12 22:17:24.804575 INFO::Processing subtree level 1
2026-04-12 22:17:24.89802 INFO::Adjusting the last 1 batches sequentially
2026-04-12 22:17:24.900186 INFO::Done
2026-04-12 22:17:24.901028 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:24.903924 INFO::ASW Batch was -0.0476687662519521 prior to batch effect correction and is now -0.0476687662519521 .
2026-04-12 22:17:24.905112 INFO::Total function execution time is 0.113338708877563 s and adjustment time is 0.0975723266601562 s ( 86.09 )
2026-04-12 22:17:24.906401 INFO::Formatting Data.
2026-04-12 22:17:24.907169 INFO::Typecasting input to dataframe.
2026-04-12 22:17:24.908047 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:24.909117 INFO::Removing potential empty rows and columns
2026-04-12 22:17:24.910346 INFO::Found 0 missing values.
2026-04-12 22:17:24.913744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:24.914433 INFO::Done
2026-04-12 22:17:24.915093 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:24.917449 INFO::Starting hierarchical adjustment
2026-04-12 22:17:24.918265 INFO::Found 3 batches.
2026-04-12 22:17:24.918852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:24.919561 INFO::Using default BPPARAM
2026-04-12 22:17:24.920152 INFO::Processing subtree level 1
2026-04-12 22:17:25.014885 INFO::Adjusting the last 1 batches sequentially
2026-04-12 22:17:25.017026 INFO::Done
2026-04-12 22:17:25.017805 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:25.020623 INFO::ASW Batch was -0.0476687662519521 prior to batch effect correction and is now -0.0476687662519521 .
2026-04-12 22:17:25.02174 INFO::Total function execution time is 0.115395307540894 s and adjustment time is 0.0989251136779785 s ( 85.73 )
2026-04-12 22:17:25.035827 INFO::Formatting Data.
2026-04-12 22:17:25.036746 INFO::Typecasting input to dataframe.
2026-04-12 22:17:25.037704 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:25.038731 INFO::Removing potential empty rows and columns
2026-04-12 22:17:25.039906 INFO::Found 0 missing values.
2026-04-12 22:17:25.043038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:25.043684 INFO::Done
2026-04-12 22:17:25.044279 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:25.046401 INFO::Starting hierarchical adjustment
2026-04-12 22:17:25.04718 INFO::Found 3 batches.
2026-04-12 22:17:25.047768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:25.048462 INFO::Using default BPPARAM
2026-04-12 22:17:25.049034 INFO::Processing subtree level 1
2026-04-12 22:17:25.136069 INFO::Adjusting the last 1 batches sequentially
2026-04-12 22:17:25.138056 INFO::Done
2026-04-12 22:17:25.138833 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:25.141481 INFO::ASW Batch was -0.0736686101610344 prior to batch effect correction and is now -0.0736686101610344 .
2026-04-12 22:17:25.142553 INFO::Total function execution time is 0.106781244277954 s and adjustment time is 0.0910103321075439 s ( 85.23 )
2026-04-12 22:17:25.294208 INFO::Formatting Data.
2026-04-12 22:17:25.295562 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:25.297393 INFO::Removing potential empty rows and columns
2026-04-12 22:17:25.302082 INFO::Found 1000 missing values.
2026-04-12 22:17:25.334895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:25.336229 INFO::Done
2026-04-12 22:17:25.337225 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:25.346128 INFO::Starting hierarchical adjustment
2026-04-12 22:17:25.347378 INFO::Found 10 batches.
2026-04-12 22:17:25.348246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:25.349277 INFO::Using default BPPARAM
2026-04-12 22:17:25.350124 INFO::Processing subtree level 1
2026-04-12 22:17:25.52564 INFO::Processing subtree level 2
2026-04-12 22:17:25.705736 INFO::Adjusting the last 1 batches sequentially
2026-04-12 22:17:25.708962 INFO::Done
2026-04-12 22:17:25.710239 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:25.719543 INFO::ASW Batch was 0.459240458303652 prior to batch effect correction and is now 0.459240458303652 .
2026-04-12 22:17:25.720934 INFO::ASW Label was 0.345237541172587 prior to batch effect correction and is now 0.345237541172587 .
2026-04-12 22:17:25.722661 INFO::Total function execution time is 0.428480863571167 s and adjustment time is 0.361779689788818 s ( 84.43 )
2026-04-12 22:17:25.724175 INFO::Formatting Data.
2026-04-12 22:17:25.72534 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:25.727341 INFO::Removing potential empty rows and columns
2026-04-12 22:17:25.732226 INFO::Found 1000 missing values.
2026-04-12 22:17:25.783946 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:25.787283 INFO::Done
2026-04-12 22:17:25.788413 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:25.800498 INFO::Starting hierarchical adjustment
2026-04-12 22:17:25.801696 INFO::Found 10 batches.
2026-04-12 22:17:27.550467 INFO::Set up parallel execution backend with 2 workers
2026-04-12 22:17:27.563238 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-12 22:17:29.085797 INFO::Adjusting the last 2 batches sequentially
2026-04-12 22:17:29.089147 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-12 22:17:29.10606 INFO::Done
2026-04-12 22:17:29.106866 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:29.11164 INFO::ASW Batch was 0.459240458303652 prior to batch effect correction and is now 0.459240458303652 .
2026-04-12 22:17:29.112401 INFO::ASW Label was 0.345237541172587 prior to batch effect correction and is now 0.345237541172587 .
2026-04-12 22:17:29.113197 INFO::Total function execution time is 3.38920450210571 s and adjustment time is 3.3046293258667 s ( 97.5 )
2026-04-12 22:17:29.267629 INFO::Formatting Data.
2026-04-12 22:17:29.268827 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.270041 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.27139 INFO::Found 0 missing values.
2026-04-12 22:17:29.275593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.276277 INFO::Done
2026-04-12 22:17:29.2769 INFO::Acquiring quality metrics before batch effect correction.
2026-04-12 22:17:29.280042 INFO::Starting hierarchical adjustment
2026-04-12 22:17:29.280979 INFO::Found 3 batches.
2026-04-12 22:17:29.281638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-12 22:17:29.282387 INFO::Using default BPPARAM
2026-04-12 22:17:29.283068 INFO::Processing subtree level 1
2026-04-12 22:17:29.398023 INFO::Adjusting the last 1 batches sequentially
2026-04-12 22:17:29.400085 INFO::Done
2026-04-12 22:17:29.400848 INFO::Acquiring quality metrics after batch effect correction.
2026-04-12 22:17:29.404371 INFO::ASW Batch was 0.175042591151229 prior to batch effect correction and is now -0.156461865924864 .
2026-04-12 22:17:29.405066 INFO::ASW Label was -0.188183787422582 prior to batch effect correction and is now -0.0726657468433008 .
2026-04-12 22:17:29.406109 INFO::Total function execution time is 0.138626337051392 s and adjustment time is 0.119260549545288 s ( 86.03 )
2026-04-12 22:17:29.539664 INFO::Formatting Data.
2026-04-12 22:17:29.54072 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.541759 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.542914 INFO::Found 2 missing values.
2026-04-12 22:17:29.546004 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.546691 INFO::Done
2026-04-12 22:17:29.576125 INFO::Found NA in Reference column
2026-04-12 22:17:29.586176 INFO::Require at least two references per batch.
2026-04-12 22:17:29.60809 INFO::Formatting Data.
2026-04-12 22:17:29.609015 INFO::Recognized SummarizedExperiment
2026-04-12 22:17:29.609663 INFO::Typecasting input to dataframe.
2026-04-12 22:17:29.619862 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.621175 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.625072 INFO::Found 0 missing values.
2026-04-12 22:17:29.63254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.633246 INFO::Done
2026-04-12 22:17:29.650035 INFO::Formatting Data.
2026-04-12 22:17:29.650903 INFO::Recognized SummarizedExperiment
2026-04-12 22:17:29.651563 INFO::Typecasting input to dataframe.
2026-04-12 22:17:29.67074 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.672176 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.676329 INFO::Found 0 missing values.
2026-04-12 22:17:29.688321 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.689102 INFO::Done
2026-04-12 22:17:29.705205 INFO::Formatting Data.
2026-04-12 22:17:29.706075 INFO::Recognized SummarizedExperiment
2026-04-12 22:17:29.706694 INFO::Typecasting input to dataframe.
2026-04-12 22:17:29.724167 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.725435 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.726664 INFO::Found 0 missing values.
2026-04-12 22:17:29.727665 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.
2026-04-12 22:17:29.732177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.732796 INFO::Done
2026-04-12 22:17:29.743483 INFO::Formatting Data.
2026-04-12 22:17:29.744435 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.745443 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.746552 INFO::Found 0 missing values.
2026-04-12 22:17:29.749726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.750334 INFO::Done
2026-04-12 22:17:29.762352 INFO::Formatting Data.
2026-04-12 22:17:29.763228 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.764159 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.76518 INFO::Found 0 missing values.
2026-04-12 22:17:29.768194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.768806 INFO::Done
2026-04-12 22:17:29.798821 INFO::Formatting Data.
2026-04-12 22:17:29.799721 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.800887 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.802131 INFO::Found 1 missing values.
2026-04-12 22:17:29.804893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.805532 INFO::Done
2026-04-12 22:17:29.825327 INFO::Formatting Data.
2026-04-12 22:17:29.82621 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.827159 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.828169 INFO::Found 2 missing values.
2026-04-12 22:17:29.829153 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.
2026-04-12 22:17:29.831637 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.832212 INFO::Done
2026-04-12 22:17:29.843012 INFO::Formatting Data.
2026-04-12 22:17:29.843915 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.84496 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.845984 INFO::Found 2 missing values.
2026-04-12 22:17:29.84772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.848329 INFO::Done
2026-04-12 22:17:29.8596 INFO::Formatting Data.
2026-04-12 22:17:29.860489 INFO::Typecasting input to dataframe.
2026-04-12 22:17:29.861387 INFO::Replacing NaNs with NAs.
2026-04-12 22:17:29.862324 INFO::Removing potential empty rows and columns
2026-04-12 22:17:29.863441 INFO::Found 0 missing values.
2026-04-12 22:17:29.866562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-12 22:17:29.867147 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.131 4.259 22.012
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.762 | 1.146 | 17.219 | |
| compute_asw | 0.025 | 0.001 | 0.024 | |
| count_existing | 0.014 | 0.000 | 0.013 | |
| generate_data_covariables | 0.012 | 0.001 | 0.012 | |
| generate_dataset | 0.010 | 0.002 | 0.011 | |