Yannis Schumann
| Snapshot Date: 2026-01-19 13:45 -0500 (Mon, 19 Jan 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 2026-01-22 11:57 -0500 (Thu, 22 Jan 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" | 4886 |
| 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 | | ||||||||
|
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: 2026-01-19 21:31:55 -0500 (Mon, 19 Jan 2026) |
| EndedAt: 2026-01-19 21:33:27 -0500 (Mon, 19 Jan 2026) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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 22.946 1.159 16.358
* 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")
2026-01-19 21:32:45.920355 INFO::Formatting Data.
2026-01-19 21:32:45.921575 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:45.932446 INFO::Removing potential empty rows and columns
2026-01-19 21:32:46.204752 INFO::Found 0 missing values.
2026-01-19 21:32:46.208246 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:46.208901 INFO::Done
2026-01-19 21:32:46.209441 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:46.221071 INFO::Starting hierarchical adjustment
2026-01-19 21:32:46.22196 INFO::Found 3 batches.
2026-01-19 21:32:46.222544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:46.223693 INFO::Using default BPPARAM
2026-01-19 21:32:46.224265 INFO::Processing subtree level 1
2026-01-19 21:32:46.351724 INFO::Adjusting the last 1 batches sequentially
2026-01-19 21:32:46.353695 INFO::Done
2026-01-19 21:32:46.354353 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:46.357219 INFO::ASW Batch was -0.130557658634965 prior to batch effect correction and is now -0.130557658634965 .
2026-01-19 21:32:46.358331 INFO::Total function execution time is 0.438539981842041 s and adjustment time is 0.131918907165527 s ( 30.08 )
2026-01-19 21:32:46.373337 INFO::Formatting Data.
2026-01-19 21:32:46.374156 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:46.375161 INFO::Removing potential empty rows and columns
2026-01-19 21:32:46.376409 INFO::Found 0 missing values.
2026-01-19 21:32:46.3774 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.
2026-01-19 21:32:46.389143 INFO::Formatting Data.
2026-01-19 21:32:46.389847 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:46.39076 INFO::Removing potential empty rows and columns
2026-01-19 21:32:46.39179 INFO::Found 0 missing values.
2026-01-19 21:32:46.392721 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.
2026-01-19 21:32:46.409523 INFO::Formatting Data.
2026-01-19 21:32:46.41023 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:46.4111 INFO::Removing potential empty rows and columns
2026-01-19 21:32:46.412186 INFO::Found 0 missing values.
2026-01-19 21:32:46.413142 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.
2026-01-19 21:32:46.417879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:46.418443 INFO::Done
2026-01-19 21:32:46.418995 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:46.421118 INFO::Starting hierarchical adjustment
2026-01-19 21:32:46.421841 INFO::Found 2 batches.
2026-01-19 21:32:46.422371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:46.423026 INFO::Using default BPPARAM
2026-01-19 21:32:46.423566 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:46.424552 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-19 21:32:46.446445 INFO::Done
2026-01-19 21:32:46.447163 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:46.449291 INFO::ASW Batch was 0.00150609740172171 prior to batch effect correction and is now -0.0936278621859088 .
2026-01-19 21:32:46.450206 INFO::Total function execution time is 0.0407264232635498 s and adjustment time is 0.0247259140014648 s ( 60.71 )
2026-01-19 21:32:46.453102 INFO::Formatting Data.
2026-01-19 21:32:46.453751 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:46.462782 INFO::Formatting Data.
2026-01-19 21:32:46.463477 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:46.464378 INFO::Removing potential empty rows and columns
2026-01-19 21:32:46.465438 INFO::Found 0 missing values.
2026-01-19 21:32:46.468439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:46.469008 INFO::Done
2026-01-19 21:32:46.469537 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:46.499487 INFO::Starting hierarchical adjustment
2026-01-19 21:32:46.502272 INFO::Found 2 batches.
2026-01-19 21:32:46.502893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:46.503466 INFO::Using default BPPARAM
2026-01-19 21:32:46.503991 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:46.504934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-19 21:32:46.519362 INFO::Done
2026-01-19 21:32:46.519964 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:46.521931 INFO::ASW Batch was -0.00398361763063973 prior to batch effect correction and is now -0.127105090143498 .
2026-01-19 21:32:46.522653 INFO::Total function execution time is 0.0599119663238525 s and adjustment time is 0.0173215866088867 s ( 28.91 )
2026-01-19 21:32:46.52368 INFO::Formatting Data.
2026-01-19 21:32:46.524273 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:46.525087 INFO::Removing potential empty rows and columns
2026-01-19 21:32:46.526023 INFO::Found 0 missing values.
2026-01-19 21:32:46.528672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:46.529177 INFO::Done
2026-01-19 21:32:46.529674 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:46.531614 INFO::Starting hierarchical adjustment
2026-01-19 21:32:46.532286 INFO::Found 2 batches.
2026-01-19 21:32:46.532793 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:46.533363 INFO::Using default BPPARAM
2026-01-19 21:32:46.53388 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:46.534768 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-19 21:32:46.54942 INFO::Done
2026-01-19 21:32:46.550067 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:46.551987 INFO::ASW Batch was -0.00398361763063973 prior to batch effect correction and is now -0.127105090143498 .
2026-01-19 21:32:46.552736 INFO::Total function execution time is 0.0290539264678955 s and adjustment time is 0.0172576904296875 s ( 59.4 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-19 21:32:49.523853 INFO::Formatting Data.
2026-01-19 21:32:49.524573 INFO::Recognized SummarizedExperiment
2026-01-19 21:32:49.525053 INFO::Typecasting input to dataframe.
2026-01-19 21:32:49.554588 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:49.55583 INFO::Removing potential empty rows and columns
2026-01-19 21:32:49.559648 INFO::Found 0 missing values.
2026-01-19 21:32:49.566707 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:49.567327 INFO::Done
2026-01-19 21:32:49.567854 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:49.57146 INFO::Starting hierarchical adjustment
2026-01-19 21:32:49.572198 INFO::Found 2 batches.
2026-01-19 21:32:49.57273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:49.573777 INFO::Using default BPPARAM
2026-01-19 21:32:49.574306 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:49.57526 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-19 21:32:49.640019 INFO::Done
2026-01-19 21:32:49.640973 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:49.645005 INFO::ASW Batch was -0.00710976954227418 prior to batch effect correction and is now -0.0888189588205932 .
2026-01-19 21:32:49.645941 INFO::Total function execution time is 0.122354030609131 s and adjustment time is 0.0678162574768066 s ( 55.43 )
Warning: stack imbalance in '{', 73 then 75
2026-01-19 21:32:49.666979 INFO::Formatting Data.
2026-01-19 21:32:49.667729 INFO::Recognized SummarizedExperiment
2026-01-19 21:32:49.668262 INFO::Typecasting input to dataframe.
2026-01-19 21:32:49.678328 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:49.679468 INFO::Removing potential empty rows and columns
2026-01-19 21:32:49.683209 INFO::Found 0 missing values.
2026-01-19 21:32:49.690229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:49.690831 INFO::Done
2026-01-19 21:32:49.691349 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:49.694832 INFO::Starting hierarchical adjustment
2026-01-19 21:32:49.695543 INFO::Found 2 batches.
2026-01-19 21:32:49.696064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:49.696668 INFO::Using default BPPARAM
2026-01-19 21:32:49.697175 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:49.698138 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-19 21:32:49.7234 INFO::Done
2026-01-19 21:32:49.72413 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:49.727657 INFO::ASW Batch was -0.00045319821396515 prior to batch effect correction and is now -0.00045319821396515 .
2026-01-19 21:32:49.728492 INFO::Total function execution time is 0.0614943504333496 s and adjustment time is 0.0279710292816162 s ( 45.49 )
2026-01-19 21:32:49.7472 INFO::Formatting Data.
2026-01-19 21:32:49.748118 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:49.749052 INFO::Removing potential empty rows and columns
2026-01-19 21:32:49.750062 INFO::Found 0 missing values.
2026-01-19 21:32:49.753026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:49.75356 INFO::Done
2026-01-19 21:32:49.754073 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:49.756051 INFO::Starting hierarchical adjustment
2026-01-19 21:32:49.756754 INFO::Found 3 batches.
2026-01-19 21:32:49.757272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:49.757868 INFO::Using default BPPARAM
2026-01-19 21:32:49.758376 INFO::Processing subtree level 1
2026-01-19 21:32:49.896358 INFO::Adjusting the last 1 batches sequentially
2026-01-19 21:32:49.898123 INFO::Done
2026-01-19 21:32:49.898797 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:49.901205 INFO::ASW Batch was 0.0112242195392412 prior to batch effect correction and is now -0.1603452787719 .
2026-01-19 21:32:49.902107 INFO::Total function execution time is 0.154952049255371 s and adjustment time is 0.141491889953613 s ( 91.31 )
2026-01-19 21:32:49.916987 INFO::Skipping initial DF formatting
2026-01-19 21:32:49.917709 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:49.922079 INFO::Starting hierarchical adjustment
2026-01-19 21:32:49.922933 INFO::Found 5 batches.
2026-01-19 21:32:49.923525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:49.924178 INFO::Using default BPPARAM
2026-01-19 21:32:49.924767 INFO::Processing subtree level 1
2026-01-19 21:32:50.197742 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:50.20029 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-19 21:32:50.230464 INFO::Done
2026-01-19 21:32:50.231528 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:50.237616 INFO::ASW Batch was 0.505144101198214 prior to batch effect correction and is now 0.505144101198214 .
2026-01-19 21:32:50.238554 INFO::ASW Label was 0.380369908805993 prior to batch effect correction and is now 0.380369908805993 .
2026-01-19 21:32:50.239751 INFO::Total function execution time is 0.322752475738525 s and adjustment time is 0.307636976242065 s ( 95.32 )
2026-01-19 21:32:50.334857 INFO::Formatting Data.
2026-01-19 21:32:50.335783 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:50.336715 INFO::Removing potential empty rows and columns
2026-01-19 21:32:50.337687 INFO::Found 0 missing values.
2026-01-19 21:32:50.341534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:50.342063 INFO::Done
2026-01-19 21:32:50.342546 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:50.345412 INFO::Starting hierarchical adjustment
2026-01-19 21:32:50.346144 INFO::Found 5 batches.
2026-01-19 21:32:50.346689 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:50.347287 INFO::Using default BPPARAM
2026-01-19 21:32:50.347807 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.
2026-01-19 21:32:50.494025 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:50.496092 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-19 21:32:50.516159 INFO::Done
2026-01-19 21:32:50.517023 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:50.521131 INFO::ASW Batch was 0.588935482075571 prior to batch effect correction and is now -0.0474680923088234 .
2026-01-19 21:32:50.521934 INFO::ASW Label was 0.266186595123495 prior to batch effect correction and is now 0.715183053676312 .
2026-01-19 21:32:50.522899 INFO::Total function execution time is 0.188192367553711 s and adjustment time is 0.17008113861084 s ( 90.38 )
2026-01-19 21:32:50.523912 INFO::Formatting Data.
2026-01-19 21:32:50.524608 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:50.525653 INFO::Removing potential empty rows and columns
2026-01-19 21:32:50.5269 INFO::Found 0 missing values.
2026-01-19 21:32:50.531733 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:50.53234 INFO::Done
2026-01-19 21:32:50.532916 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:50.536469 INFO::Starting hierarchical adjustment
2026-01-19 21:32:50.53724 INFO::Found 5 batches.
2026-01-19 21:32:50.537819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:50.538461 INFO::Using default BPPARAM
2026-01-19 21:32:50.539041 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.
2026-01-19 21:32:50.673345 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:50.675044 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-19 21:32:50.698738 INFO::Done
2026-01-19 21:32:50.69964 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:50.703476 INFO::ASW Batch was 0.588935482075571 prior to batch effect correction and is now -0.0474680923088234 .
2026-01-19 21:32:50.704172 INFO::ASW Label was 0.266186595123495 prior to batch effect correction and is now 0.715183053676312 .
2026-01-19 21:32:50.705042 INFO::Total function execution time is 0.181154012680054 s and adjustment time is 0.161605834960938 s ( 89.21 )
2026-01-19 21:32:50.723325 INFO::Formatting Data.
2026-01-19 21:32:50.724236 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:50.725291 INFO::Removing potential empty rows and columns
2026-01-19 21:32:50.726439 INFO::Found 0 missing values.
2026-01-19 21:32:50.730926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:50.731526 INFO::Done
2026-01-19 21:32:50.732073 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:50.735339 INFO::Starting hierarchical adjustment
2026-01-19 21:32:50.736098 INFO::Found 5 batches.
2026-01-19 21:32:50.736684 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:50.737376 INFO::Using default BPPARAM
2026-01-19 21:32:50.73797 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.
2026-01-19 21:32:50.867343 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:50.868983 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-19 21:32:50.885623 INFO::Done
2026-01-19 21:32:50.886343 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:50.889777 INFO::ASW Batch was 0.50013811079653 prior to batch effect correction and is now -0.0750615985820018 .
2026-01-19 21:32:50.890379 INFO::ASW Label was 0.21158331973896 prior to batch effect correction and is now 0.776680613950519 .
2026-01-19 21:32:50.891216 INFO::Total function execution time is 0.167957782745361 s and adjustment time is 0.149627447128296 s ( 89.09 )
2026-01-19 21:32:50.892064 INFO::Formatting Data.
2026-01-19 21:32:50.892735 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:50.893643 INFO::Removing potential empty rows and columns
2026-01-19 21:32:50.8947 INFO::Found 0 missing values.
2026-01-19 21:32:50.8989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:50.899453 INFO::Done
2026-01-19 21:32:50.899996 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:50.903012 INFO::Starting hierarchical adjustment
2026-01-19 21:32:50.903726 INFO::Found 5 batches.
2026-01-19 21:32:50.904286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:50.90494 INFO::Using default BPPARAM
2026-01-19 21:32:50.905487 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.
2026-01-19 21:32:51.028113 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:51.029804 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-19 21:32:51.048266 INFO::Done
2026-01-19 21:32:51.049047 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.053264 INFO::ASW Batch was 0.50013811079653 prior to batch effect correction and is now -0.0750615985820018 .
2026-01-19 21:32:51.053895 INFO::ASW Label was 0.21158331973896 prior to batch effect correction and is now 0.776680613950519 .
2026-01-19 21:32:51.054737 INFO::Total function execution time is 0.162661552429199 s and adjustment time is 0.144660949707031 s ( 88.93 )
2026-01-19 21:32:51.068652 INFO::Formatting Data.
2026-01-19 21:32:51.069358 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.070256 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.071248 INFO::Found 0 missing values.
2026-01-19 21:32:51.073855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.074364 INFO::Done
2026-01-19 21:32:51.074874 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.077685 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.078362 INFO::Found 2 batches.
2026-01-19 21:32:51.078883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.079468 INFO::Using default BPPARAM
2026-01-19 21:32:51.079987 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:51.080863 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-19 21:32:51.094633 INFO::Done
2026-01-19 21:32:51.095209 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.097993 INFO::ASW Batch was 0.308745904292867 prior to batch effect correction and is now -0.0233373773930614 .
2026-01-19 21:32:51.09857 INFO::ASW Label was 0.746896288683725 prior to batch effect correction and is now 0.94538420077242 .
2026-01-19 21:32:51.099301 INFO::Total function execution time is 0.03072190284729 s and adjustment time is 0.0164127349853516 s ( 53.42 )
2026-01-19 21:32:51.100038 INFO::Formatting Data.
2026-01-19 21:32:51.100625 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.101418 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.102348 INFO::Found 0 missing values.
2026-01-19 21:32:51.104832 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.105336 INFO::Done
2026-01-19 21:32:51.10583 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.108516 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.109172 INFO::Found 2 batches.
2026-01-19 21:32:51.109676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.110249 INFO::Using default BPPARAM
2026-01-19 21:32:51.110751 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:51.111592 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-19 21:32:51.125191 INFO::Done
2026-01-19 21:32:51.12579 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.128532 INFO::ASW Batch was 0.308745904292867 prior to batch effect correction and is now -0.0233373773930614 .
2026-01-19 21:32:51.129063 INFO::ASW Label was 0.746896288683725 prior to batch effect correction and is now 0.94538420077242 .
2026-01-19 21:32:51.129791 INFO::Total function execution time is 0.0297615528106689 s and adjustment time is 0.0161490440368652 s ( 54.26 )
2026-01-19 21:32:51.140274 INFO::Formatting Data.
2026-01-19 21:32:51.140945 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.14175 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.142689 INFO::Found 0 missing values.
2026-01-19 21:32:51.144656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.145162 INFO::Done
2026-01-19 21:32:51.145665 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.147419 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.148093 INFO::Found 2 batches.
2026-01-19 21:32:51.148597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.149163 INFO::Using default BPPARAM
2026-01-19 21:32:51.149689 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:51.150531 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-19 21:32:51.180113 INFO::Done
2026-01-19 21:32:51.180769 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.182613 INFO::ASW Batch was 0.075820945112391 prior to batch effect correction and is now -0.162184483130691 .
2026-01-19 21:32:51.183378 INFO::Total function execution time is 0.0431408882141113 s and adjustment time is 0.0321307182312012 s ( 74.48 )
2026-01-19 21:32:51.194849 INFO::Formatting Data.
2026-01-19 21:32:51.195607 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.196434 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.197372 INFO::Found 0 missing values.
2026-01-19 21:32:51.198468 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.
2026-01-19 21:32:51.202755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.203261 INFO::Done
2026-01-19 21:32:51.203761 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.206549 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.207201 INFO::Found 2 batches.
2026-01-19 21:32:51.207712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.208267 INFO::Using default BPPARAM
2026-01-19 21:32:51.208773 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:51.209675 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-19 21:32:51.225113 INFO::Done
2026-01-19 21:32:51.225776 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.228588 INFO::ASW Batch was 0.470120951103808 prior to batch effect correction and is now 0.0401952211086196 .
2026-01-19 21:32:51.229146 INFO::ASW Label was 0.623959595417817 prior to batch effect correction and is now 0.903308508119229 .
2026-01-19 21:32:51.229893 INFO::Total function execution time is 0.0351154804229736 s and adjustment time is 0.0180232524871826 s ( 51.33 )
2026-01-19 21:32:51.230652 INFO::Formatting Data.
2026-01-19 21:32:51.231236 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.232125 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.233076 INFO::Found 0 missing values.
2026-01-19 21:32:51.233934 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.
2026-01-19 21:32:51.238176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.238724 INFO::Done
2026-01-19 21:32:51.239212 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.241993 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.242664 INFO::Found 2 batches.
2026-01-19 21:32:51.243152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.243718 INFO::Using default BPPARAM
2026-01-19 21:32:51.244206 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:51.245082 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-19 21:32:51.260475 INFO::Done
2026-01-19 21:32:51.261123 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.263877 INFO::ASW Batch was 0.470120951103808 prior to batch effect correction and is now 0.0401952211086196 .
2026-01-19 21:32:51.264407 INFO::ASW Label was 0.623959595417817 prior to batch effect correction and is now 0.903308508119229 .
2026-01-19 21:32:51.26516 INFO::Total function execution time is 0.0345277786254883 s and adjustment time is 0.0179483890533447 s ( 51.98 )
2026-01-19 21:32:51.481923 INFO::Formatting Data.
2026-01-19 21:32:51.48278 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.483797 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.484923 INFO::Found 0 missing values.
2026-01-19 21:32:51.488083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.488649 INFO::Done
2026-01-19 21:32:51.489157 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.491188 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.491894 INFO::Found 3 batches.
2026-01-19 21:32:51.492413 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.493043 INFO::Using default BPPARAM
2026-01-19 21:32:51.493578 INFO::Processing subtree level 1
2026-01-19 21:32:51.578493 INFO::Adjusting the last 1 batches sequentially
2026-01-19 21:32:51.580381 INFO::Done
2026-01-19 21:32:51.581068 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.583596 INFO::ASW Batch was -0.0806625069044518 prior to batch effect correction and is now -0.0806625069044518 .
2026-01-19 21:32:51.584538 INFO::Total function execution time is 0.102648973464966 s and adjustment time is 0.0886034965515137 s ( 86.32 )
2026-01-19 21:32:51.585616 INFO::Formatting Data.
2026-01-19 21:32:51.586276 INFO::Typecasting input to dataframe.
2026-01-19 21:32:51.587063 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.587973 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.589103 INFO::Found 0 missing values.
2026-01-19 21:32:51.59226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.592844 INFO::Done
2026-01-19 21:32:51.593363 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.595463 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.596214 INFO::Found 3 batches.
2026-01-19 21:32:51.596813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.597501 INFO::Using default BPPARAM
2026-01-19 21:32:51.598044 INFO::Processing subtree level 1
2026-01-19 21:32:51.683851 INFO::Adjusting the last 1 batches sequentially
2026-01-19 21:32:51.68563 INFO::Done
2026-01-19 21:32:51.686285 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.688724 INFO::ASW Batch was -0.0806625069044518 prior to batch effect correction and is now -0.0806625069044518 .
2026-01-19 21:32:51.689655 INFO::Total function execution time is 0.104019641876221 s and adjustment time is 0.0895538330078125 s ( 86.09 )
2026-01-19 21:32:51.703014 INFO::Formatting Data.
2026-01-19 21:32:51.703839 INFO::Typecasting input to dataframe.
2026-01-19 21:32:51.704762 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.705703 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.706786 INFO::Found 0 missing values.
2026-01-19 21:32:51.709842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.710402 INFO::Done
2026-01-19 21:32:51.710949 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.712947 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.713657 INFO::Found 3 batches.
2026-01-19 21:32:51.714178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.714801 INFO::Using default BPPARAM
2026-01-19 21:32:51.715355 INFO::Processing subtree level 1
2026-01-19 21:32:51.800854 INFO::Adjusting the last 1 batches sequentially
2026-01-19 21:32:51.802744 INFO::Done
2026-01-19 21:32:51.803437 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:51.806062 INFO::ASW Batch was -0.0165501212877497 prior to batch effect correction and is now -0.0165501212877497 .
2026-01-19 21:32:51.807067 INFO::Total function execution time is 0.104104995727539 s and adjustment time is 0.0892114639282227 s ( 85.69 )
2026-01-19 21:32:51.94944 INFO::Formatting Data.
2026-01-19 21:32:51.950319 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:51.951443 INFO::Removing potential empty rows and columns
2026-01-19 21:32:51.954245 INFO::Found 1000 missing values.
2026-01-19 21:32:51.973434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:51.974329 INFO::Done
2026-01-19 21:32:51.97496 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:51.980549 INFO::Starting hierarchical adjustment
2026-01-19 21:32:51.981374 INFO::Found 10 batches.
2026-01-19 21:32:51.981944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:51.982572 INFO::Using default BPPARAM
2026-01-19 21:32:51.983112 INFO::Processing subtree level 1
2026-01-19 21:32:52.123629 INFO::Processing subtree level 2
2026-01-19 21:32:52.272086 INFO::Adjusting the last 1 batches sequentially
2026-01-19 21:32:52.274239 INFO::Done
2026-01-19 21:32:52.274978 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:52.280827 INFO::ASW Batch was 0.499193379271521 prior to batch effect correction and is now 0.499193379271521 .
2026-01-19 21:32:52.281571 INFO::ASW Label was 0.32348695673717 prior to batch effect correction and is now 0.32348695673717 .
2026-01-19 21:32:52.282542 INFO::Total function execution time is 0.333165407180786 s and adjustment time is 0.292996168136597 s ( 87.94 )
2026-01-19 21:32:52.283395 INFO::Formatting Data.
2026-01-19 21:32:52.284061 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:52.285396 INFO::Removing potential empty rows and columns
2026-01-19 21:32:52.288269 INFO::Found 1000 missing values.
2026-01-19 21:32:52.308219 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:52.309127 INFO::Done
2026-01-19 21:32:52.309738 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:52.315702 INFO::Starting hierarchical adjustment
2026-01-19 21:32:52.316623 INFO::Found 10 batches.
2026-01-19 21:32:53.47313 INFO::Set up parallel execution backend with 2 workers
2026-01-19 21:32:53.474985 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-19 21:32:54.538323 INFO::Adjusting the last 2 batches sequentially
2026-01-19 21:32:54.540129 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-19 21:32:54.556093 INFO::Done
2026-01-19 21:32:54.556771 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:54.56115 INFO::ASW Batch was 0.499193379271521 prior to batch effect correction and is now 0.499193379271521 .
2026-01-19 21:32:54.561717 INFO::ASW Label was 0.32348695673717 prior to batch effect correction and is now 0.32348695673717 .
2026-01-19 21:32:54.562409 INFO::Total function execution time is 2.27904939651489 s and adjustment time is 2.23966002464294 s ( 98.27 )
2026-01-19 21:32:54.726769 INFO::Formatting Data.
2026-01-19 21:32:54.727569 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:54.728487 INFO::Removing potential empty rows and columns
2026-01-19 21:32:54.729516 INFO::Found 0 missing values.
2026-01-19 21:32:54.732957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:54.733463 INFO::Done
2026-01-19 21:32:54.733951 INFO::Acquiring quality metrics before batch effect correction.
2026-01-19 21:32:54.73655 INFO::Starting hierarchical adjustment
2026-01-19 21:32:54.737217 INFO::Found 3 batches.
2026-01-19 21:32:54.737723 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-19 21:32:54.738298 INFO::Using default BPPARAM
2026-01-19 21:32:54.738803 INFO::Processing subtree level 1
2026-01-19 21:32:54.871731 INFO::Adjusting the last 1 batches sequentially
2026-01-19 21:32:54.873967 INFO::Done
2026-01-19 21:32:54.874646 INFO::Acquiring quality metrics after batch effect correction.
2026-01-19 21:32:54.878295 INFO::ASW Batch was 0.17627340581797 prior to batch effect correction and is now -0.146352360828181 .
2026-01-19 21:32:54.878939 INFO::ASW Label was -0.170872175455757 prior to batch effect correction and is now 0.142490931316139 .
2026-01-19 21:32:54.879966 INFO::Total function execution time is 0.153224229812622 s and adjustment time is 0.136852025985718 s ( 89.31 )
2026-01-19 21:32:55.005687 INFO::Formatting Data.
2026-01-19 21:32:55.006547 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.007436 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.008485 INFO::Found 2 missing values.
2026-01-19 21:32:55.011231 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.011759 INFO::Done
2026-01-19 21:32:55.038298 INFO::Found NA in Reference column
2026-01-19 21:32:55.04735 INFO::Require at least two references per batch.
2026-01-19 21:32:55.067803 INFO::Formatting Data.
2026-01-19 21:32:55.068584 INFO::Recognized SummarizedExperiment
2026-01-19 21:32:55.069106 INFO::Typecasting input to dataframe.
2026-01-19 21:32:55.07921 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.080422 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.083713 INFO::Found 0 missing values.
2026-01-19 21:32:55.090034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.090672 INFO::Done
2026-01-19 21:32:55.105797 INFO::Formatting Data.
2026-01-19 21:32:55.106574 INFO::Recognized SummarizedExperiment
2026-01-19 21:32:55.10709 INFO::Typecasting input to dataframe.
2026-01-19 21:32:55.12383 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.125098 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.128438 INFO::Found 0 missing values.
2026-01-19 21:32:55.13871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.139481 INFO::Done
2026-01-19 21:32:55.15456 INFO::Formatting Data.
2026-01-19 21:32:55.155327 INFO::Recognized SummarizedExperiment
2026-01-19 21:32:55.155856 INFO::Typecasting input to dataframe.
2026-01-19 21:32:55.172385 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.17348 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.174562 INFO::Found 0 missing values.
2026-01-19 21:32:55.175474 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.
2026-01-19 21:32:55.179705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.180288 INFO::Done
2026-01-19 21:32:55.19024 INFO::Formatting Data.
2026-01-19 21:32:55.191113 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.192058 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.193005 INFO::Found 0 missing values.
2026-01-19 21:32:55.195767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.196277 INFO::Done
2026-01-19 21:32:55.207518 INFO::Formatting Data.
2026-01-19 21:32:55.208411 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.209526 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.210521 INFO::Found 0 missing values.
2026-01-19 21:32:55.213268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.213818 INFO::Done
2026-01-19 21:32:55.243067 INFO::Formatting Data.
2026-01-19 21:32:55.243925 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.244964 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.246106 INFO::Found 1 missing values.
2026-01-19 21:32:55.248689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.249203 INFO::Done
2026-01-19 21:32:55.268292 INFO::Formatting Data.
2026-01-19 21:32:55.269191 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.270112 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.271088 INFO::Found 2 missing values.
2026-01-19 21:32:55.271985 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.
2026-01-19 21:32:55.274186 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.274719 INFO::Done
2026-01-19 21:32:55.28459 INFO::Formatting Data.
2026-01-19 21:32:55.285398 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.286268 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.287263 INFO::Found 2 missing values.
2026-01-19 21:32:55.28886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.289376 INFO::Done
2026-01-19 21:32:55.299366 INFO::Formatting Data.
2026-01-19 21:32:55.300251 INFO::Typecasting input to dataframe.
2026-01-19 21:32:55.301032 INFO::Replacing NaNs with NAs.
2026-01-19 21:32:55.301849 INFO::Removing potential empty rows and columns
2026-01-19 21:32:55.302791 INFO::Found 0 missing values.
2026-01-19 21:32:55.305516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-19 21:32:55.306021 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.811 3.786 21.284
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 22.946 | 1.159 | 16.358 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.015 | 0.000 | 0.014 | |
| generate_data_covariables | 0.012 | 0.001 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |