Yannis Schumann
| Snapshot Date: 2026-05-04 13:45 -0400 (Mon, 04 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-05 11:33 -0400 (Tue, 05 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4844 |
| 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 167/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz |
| StartedAt: 2026-05-04 21:29:09 -0400 (Mon, 04 May 2026) |
| EndedAt: 2026-05-04 21:30:43 -0400 (Mon, 04 May 2026) |
| EllapsedTime: 94.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* 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: 2026-05-05 01:29:09 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 25.986 1.223 19.356
* 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-3.24-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.9.0’ ** 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 RC (2026-04-17 r89917) -- "Because it was There"
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")
2026-05-04 21:30:04.979351 INFO::Formatting Data.
2026-05-04 21:30:04.981271 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:04.99454 INFO::Removing potential empty rows and columns
2026-05-04 21:30:05.288182 INFO::Found 0 missing values.
2026-05-04 21:30:05.292337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:05.293264 INFO::Done
2026-05-04 21:30:05.293953 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:05.308809 INFO::Starting hierarchical adjustment
2026-05-04 21:30:05.309915 INFO::Found 3 batches.
2026-05-04 21:30:05.310595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:05.311947 INFO::Using default BPPARAM
2026-05-04 21:30:05.312599 INFO::Processing subtree level 1
2026-05-04 21:30:05.438251 INFO::Adjusting the last 1 batches sequentially
2026-05-04 21:30:05.440854 INFO::Done
2026-05-04 21:30:05.441963 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:05.445476 INFO::ASW Batch was -0.0329754271675802 prior to batch effect correction and is now -0.0329754271675802 .
2026-05-04 21:30:05.446954 INFO::Total function execution time is 0.468414783477783 s and adjustment time is 0.131103992462158 s ( 27.99 )
2026-05-04 21:30:05.465842 INFO::Formatting Data.
2026-05-04 21:30:05.467056 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:05.468314 INFO::Removing potential empty rows and columns
2026-05-04 21:30:05.469766 INFO::Found 0 missing values.
2026-05-04 21:30:05.470986 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.
2026-05-04 21:30:05.484749 INFO::Formatting Data.
2026-05-04 21:30:05.485887 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:05.487073 INFO::Removing potential empty rows and columns
2026-05-04 21:30:05.48853 INFO::Found 0 missing values.
2026-05-04 21:30:05.489699 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.
2026-05-04 21:30:05.509992 INFO::Formatting Data.
2026-05-04 21:30:05.5111 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:05.512293 INFO::Removing potential empty rows and columns
2026-05-04 21:30:05.513605 INFO::Found 0 missing values.
2026-05-04 21:30:05.514815 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.
2026-05-04 21:30:05.520182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:05.5209 INFO::Done
2026-05-04 21:30:05.521558 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:05.524112 INFO::Starting hierarchical adjustment
2026-05-04 21:30:05.52501 INFO::Found 2 batches.
2026-05-04 21:30:05.525705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:05.526498 INFO::Using default BPPARAM
2026-05-04 21:30:05.527141 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:05.528403 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-04 21:30:05.554842 INFO::Done
2026-05-04 21:30:05.555836 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:05.558513 INFO::ASW Batch was -0.0418341075561994 prior to batch effect correction and is now -0.101317073650146 .
2026-05-04 21:30:05.559505 INFO::Total function execution time is 0.0496339797973633 s and adjustment time is 0.0299530029296875 s ( 60.35 )
2026-05-04 21:30:05.562937 INFO::Formatting Data.
2026-05-04 21:30:05.563723 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:05.573391 INFO::Formatting Data.
2026-05-04 21:30:05.574257 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:05.575296 INFO::Removing potential empty rows and columns
2026-05-04 21:30:05.576527 INFO::Found 0 missing values.
2026-05-04 21:30:05.579793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:05.580397 INFO::Done
2026-05-04 21:30:05.580971 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:05.583286 INFO::Starting hierarchical adjustment
2026-05-04 21:30:05.584085 INFO::Found 2 batches.
2026-05-04 21:30:05.584679 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:05.585353 INFO::Using default BPPARAM
2026-05-04 21:30:05.585963 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:05.58699 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-04 21:30:05.605043 INFO::Done
2026-05-04 21:30:05.605999 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:05.608689 INFO::ASW Batch was -0.0345925516339469 prior to batch effect correction and is now -0.0949344870820539 .
2026-05-04 21:30:05.609778 INFO::Total function execution time is 0.0364015102386475 s and adjustment time is 0.0210652351379395 s ( 57.87 )
2026-05-04 21:30:05.611121 INFO::Formatting Data.
2026-05-04 21:30:05.611855 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:05.612885 INFO::Removing potential empty rows and columns
2026-05-04 21:30:05.614087 INFO::Found 0 missing values.
2026-05-04 21:30:05.617245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:05.617842 INFO::Done
2026-05-04 21:30:05.61843 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:05.620677 INFO::Starting hierarchical adjustment
2026-05-04 21:30:05.62155 INFO::Found 2 batches.
2026-05-04 21:30:05.622137 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:05.622835 INFO::Using default BPPARAM
2026-05-04 21:30:05.623453 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:05.624429 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-04 21:30:05.640217 INFO::Done
2026-05-04 21:30:05.640999 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:05.643232 INFO::ASW Batch was -0.0345925516339469 prior to batch effect correction and is now -0.0949344870820539 .
2026-05-04 21:30:05.644108 INFO::Total function execution time is 0.0330109596252441 s and adjustment time is 0.0188195705413818 s ( 57.01 )
2026-05-04 21:30:09.105364 INFO::Formatting Data.
2026-05-04 21:30:09.106393 INFO::Recognized SummarizedExperiment
2026-05-04 21:30:09.106959 INFO::Typecasting input to dataframe.
2026-05-04 21:30:09.138895 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:09.140141 INFO::Removing potential empty rows and columns
2026-05-04 21:30:09.143486 INFO::Found 0 missing values.
2026-05-04 21:30:09.149786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:09.150464 INFO::Done
2026-05-04 21:30:09.150989 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:09.154309 INFO::Starting hierarchical adjustment
2026-05-04 21:30:09.155065 INFO::Found 2 batches.
2026-05-04 21:30:09.155608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:09.156769 INFO::Using default BPPARAM
2026-05-04 21:30:09.1573 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:09.158294 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-04 21:30:09.212221 INFO::Done
2026-05-04 21:30:09.213241 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:09.217587 INFO::ASW Batch was -0.0142423697132389 prior to batch effect correction and is now -0.0874715056897601 .
2026-05-04 21:30:09.218655 INFO::Total function execution time is 0.113572835922241 s and adjustment time is 0.0572104454040527 s ( 50.37 )
2026-05-04 21:30:09.238236 INFO::Formatting Data.
2026-05-04 21:30:09.239095 INFO::Recognized SummarizedExperiment
2026-05-04 21:30:09.239663 INFO::Typecasting input to dataframe.
2026-05-04 21:30:09.248294 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:09.249524 INFO::Removing potential empty rows and columns
2026-05-04 21:30:09.25291 INFO::Found 0 missing values.
2026-05-04 21:30:09.259423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:09.26009 INFO::Done
2026-05-04 21:30:09.260645 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:09.263964 INFO::Starting hierarchical adjustment
2026-05-04 21:30:09.264739 INFO::Found 2 batches.
2026-05-04 21:30:09.265268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:09.265876 INFO::Using default BPPARAM
2026-05-04 21:30:09.266398 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:09.267392 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-04 21:30:09.292791 INFO::Done
2026-05-04 21:30:09.293652 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:09.297517 INFO::ASW Batch was 0.0063050390612384 prior to batch effect correction and is now 0.0063050390612384 .
2026-05-04 21:30:09.298495 INFO::Total function execution time is 0.0602388381958008 s and adjustment time is 0.0281462669372559 s ( 46.72 )
2026-05-04 21:30:09.318608 INFO::Formatting Data.
2026-05-04 21:30:09.319512 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:09.320498 INFO::Removing potential empty rows and columns
2026-05-04 21:30:09.321616 INFO::Found 0 missing values.
2026-05-04 21:30:09.324809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:09.325415 INFO::Done
2026-05-04 21:30:09.32598 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:09.328215 INFO::Starting hierarchical adjustment
2026-05-04 21:30:09.32899 INFO::Found 3 batches.
2026-05-04 21:30:09.329568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:09.330215 INFO::Using default BPPARAM
2026-05-04 21:30:09.330801 INFO::Processing subtree level 1
2026-05-04 21:30:09.474332 INFO::Adjusting the last 1 batches sequentially
2026-05-04 21:30:09.476409 INFO::Done
2026-05-04 21:30:09.477205 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:09.479975 INFO::ASW Batch was -0.0625352852881167 prior to batch effect correction and is now -0.172124890771032 .
2026-05-04 21:30:09.481078 INFO::Total function execution time is 0.162549495697021 s and adjustment time is 0.147529602050781 s ( 90.76 )
2026-05-04 21:30:09.496569 INFO::Skipping initial DF formatting
2026-05-04 21:30:09.497457 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:09.50193 INFO::Starting hierarchical adjustment
2026-05-04 21:30:09.502827 INFO::Found 5 batches.
2026-05-04 21:30:09.503466 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:09.504145 INFO::Using default BPPARAM
2026-05-04 21:30:09.50475 INFO::Processing subtree level 1
2026-05-04 21:30:09.641673 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:09.643879 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-04 21:30:09.666617 INFO::Done
2026-05-04 21:30:09.667679 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:09.672741 INFO::ASW Batch was 0.4829104730129 prior to batch effect correction and is now 0.4829104730129 .
2026-05-04 21:30:09.673601 INFO::ASW Label was 0.40789328811923 prior to batch effect correction and is now 0.40789328811923 .
2026-05-04 21:30:09.674644 INFO::Total function execution time is 0.17816948890686 s and adjustment time is 0.163896322250366 s ( 91.99 )
2026-05-04 21:30:09.695629 INFO::Formatting Data.
2026-05-04 21:30:09.696668 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:09.697746 INFO::Removing potential empty rows and columns
2026-05-04 21:30:09.698866 INFO::Found 0 missing values.
2026-05-04 21:30:09.703298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:09.703954 INFO::Done
2026-05-04 21:30:09.704573 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:09.708005 INFO::Starting hierarchical adjustment
2026-05-04 21:30:09.708834 INFO::Found 5 batches.
2026-05-04 21:30:09.709589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:09.710261 INFO::Using default BPPARAM
2026-05-04 21:30:09.710862 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.
2026-05-04 21:30:09.829795 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:09.831849 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-04 21:30:09.850477 INFO::Done
2026-05-04 21:30:09.851422 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:09.855143 INFO::ASW Batch was 0.380872492630459 prior to batch effect correction and is now -0.105516404765147 .
2026-05-04 21:30:09.855904 INFO::ASW Label was 0.383660015301114 prior to batch effect correction and is now 0.79484521973917 .
2026-05-04 21:30:09.856862 INFO::Total function execution time is 0.161431312561035 s and adjustment time is 0.141714334487915 s ( 87.79 )
2026-05-04 21:30:09.857802 INFO::Formatting Data.
2026-05-04 21:30:09.858511 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:09.859531 INFO::Removing potential empty rows and columns
2026-05-04 21:30:09.860651 INFO::Found 0 missing values.
2026-05-04 21:30:09.865102 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:09.865809 INFO::Done
2026-05-04 21:30:09.866413 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:09.869847 INFO::Starting hierarchical adjustment
2026-05-04 21:30:09.870677 INFO::Found 5 batches.
2026-05-04 21:30:09.871262 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:09.871965 INFO::Using default BPPARAM
2026-05-04 21:30:09.872559 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.
2026-05-04 21:30:09.99578 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:09.997764 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-04 21:30:10.016186 INFO::Done
2026-05-04 21:30:10.017132 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.020903 INFO::ASW Batch was 0.380872492630459 prior to batch effect correction and is now -0.105516404765147 .
2026-05-04 21:30:10.021631 INFO::ASW Label was 0.383660015301114 prior to batch effect correction and is now 0.79484521973917 .
2026-05-04 21:30:10.022557 INFO::Total function execution time is 0.164753675460815 s and adjustment time is 0.145609140396118 s ( 88.38 )
2026-05-04 21:30:10.038116 INFO::Formatting Data.
2026-05-04 21:30:10.039156 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.040255 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.041596 INFO::Found 0 missing values.
2026-05-04 21:30:10.046167 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.047033 INFO::Done
2026-05-04 21:30:10.047667 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.051119 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.051936 INFO::Found 5 batches.
2026-05-04 21:30:10.052554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.053228 INFO::Using default BPPARAM
2026-05-04 21:30:10.053825 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.
2026-05-04 21:30:10.174823 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:10.17678 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-04 21:30:10.193425 INFO::Done
2026-05-04 21:30:10.194195 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.197784 INFO::ASW Batch was 0.293946496403473 prior to batch effect correction and is now -0.0936524015759942 .
2026-05-04 21:30:10.19852 INFO::ASW Label was 0.404717521996164 prior to batch effect correction and is now 0.875480344176049 .
2026-05-04 21:30:10.199451 INFO::Total function execution time is 0.161451578140259 s and adjustment time is 0.141595363616943 s ( 87.7 )
2026-05-04 21:30:10.200342 INFO::Formatting Data.
2026-05-04 21:30:10.201052 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.202096 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.203183 INFO::Found 0 missing values.
2026-05-04 21:30:10.207732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.208464 INFO::Done
2026-05-04 21:30:10.209064 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.212891 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.213821 INFO::Found 5 batches.
2026-05-04 21:30:10.214525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.215284 INFO::Using default BPPARAM
2026-05-04 21:30:10.215926 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.
2026-05-04 21:30:10.333318 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:10.335407 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-04 21:30:10.35325 INFO::Done
2026-05-04 21:30:10.354146 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.357926 INFO::ASW Batch was 0.293946496403473 prior to batch effect correction and is now -0.0936524015759942 .
2026-05-04 21:30:10.358674 INFO::ASW Label was 0.404717521996164 prior to batch effect correction and is now 0.875480344176049 .
2026-05-04 21:30:10.359619 INFO::Total function execution time is 0.159268379211426 s and adjustment time is 0.139535665512085 s ( 87.61 )
2026-05-04 21:30:10.3752 INFO::Formatting Data.
2026-05-04 21:30:10.376216 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.377279 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.37846 INFO::Found 0 missing values.
2026-05-04 21:30:10.381556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.382199 INFO::Done
2026-05-04 21:30:10.382817 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.386083 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.386911 INFO::Found 2 batches.
2026-05-04 21:30:10.387521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.388186 INFO::Using default BPPARAM
2026-05-04 21:30:10.3888 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:10.389849 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-04 21:30:10.406062 INFO::Done
2026-05-04 21:30:10.406924 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.410413 INFO::ASW Batch was 0.380971974041223 prior to batch effect correction and is now 0.0654234202554293 .
2026-05-04 21:30:10.411156 INFO::ASW Label was 0.608105452828543 prior to batch effect correction and is now 0.882847612491304 .
2026-05-04 21:30:10.412066 INFO::Total function execution time is 0.0370383262634277 s and adjustment time is 0.0192646980285645 s ( 52.01 )
2026-05-04 21:30:10.412961 INFO::Formatting Data.
2026-05-04 21:30:10.413668 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.414654 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.415787 INFO::Found 0 missing values.
2026-05-04 21:30:10.418848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.419474 INFO::Done
2026-05-04 21:30:10.420054 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.423365 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.424185 INFO::Found 2 batches.
2026-05-04 21:30:10.424794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.42551 INFO::Using default BPPARAM
2026-05-04 21:30:10.426085 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:10.427125 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-04 21:30:10.443256 INFO::Done
2026-05-04 21:30:10.44417 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.447804 INFO::ASW Batch was 0.380971974041223 prior to batch effect correction and is now 0.0654234202554293 .
2026-05-04 21:30:10.448526 INFO::ASW Label was 0.608105452828543 prior to batch effect correction and is now 0.882847612491304 .
2026-05-04 21:30:10.449413 INFO::Total function execution time is 0.0364573001861572 s and adjustment time is 0.0191919803619385 s ( 52.64 )
2026-05-04 21:30:10.462849 INFO::Formatting Data.
2026-05-04 21:30:10.463929 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.465065 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.466188 INFO::Found 0 missing values.
2026-05-04 21:30:10.468778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.469428 INFO::Done
2026-05-04 21:30:10.470039 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.472386 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.473185 INFO::Found 2 batches.
2026-05-04 21:30:10.473803 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.474501 INFO::Using default BPPARAM
2026-05-04 21:30:10.475091 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:10.476148 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-04 21:30:10.511037 INFO::Done
2026-05-04 21:30:10.511871 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.514075 INFO::ASW Batch was 0.132061636649921 prior to batch effect correction and is now -0.141854279474968 .
2026-05-04 21:30:10.514992 INFO::Total function execution time is 0.052314281463623 s and adjustment time is 0.0379776954650879 s ( 72.6 )
2026-05-04 21:30:10.528448 INFO::Formatting Data.
2026-05-04 21:30:10.529403 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.530458 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.53158 INFO::Found 0 missing values.
2026-05-04 21:30:10.532841 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.
2026-05-04 21:30:10.537859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.538508 INFO::Done
2026-05-04 21:30:10.539085 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.542319 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.54311 INFO::Found 2 batches.
2026-05-04 21:30:10.543693 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.544327 INFO::Using default BPPARAM
2026-05-04 21:30:10.544914 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:10.545919 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-04 21:30:10.563303 INFO::Done
2026-05-04 21:30:10.564107 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.567332 INFO::ASW Batch was 0.504214375994091 prior to batch effect correction and is now -0.0281546507873403 .
2026-05-04 21:30:10.568025 INFO::ASW Label was 0.371663530635068 prior to batch effect correction and is now 0.926175649335183 .
2026-05-04 21:30:10.568877 INFO::Total function execution time is 0.0405800342559814 s and adjustment time is 0.0203042030334473 s ( 50.03 )
2026-05-04 21:30:10.56973 INFO::Formatting Data.
2026-05-04 21:30:10.570408 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.571436 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.572551 INFO::Found 0 missing values.
2026-05-04 21:30:10.57358 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.
2026-05-04 21:30:10.578663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.579444 INFO::Done
2026-05-04 21:30:10.58006 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.583304 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.584114 INFO::Found 2 batches.
2026-05-04 21:30:10.584837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.585521 INFO::Using default BPPARAM
2026-05-04 21:30:10.58609 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:10.58715 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-04 21:30:10.604941 INFO::Done
2026-05-04 21:30:10.605739 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.608955 INFO::ASW Batch was 0.504214375994091 prior to batch effect correction and is now -0.0281546507873403 .
2026-05-04 21:30:10.609675 INFO::ASW Label was 0.371663530635068 prior to batch effect correction and is now 0.926175649335183 .
2026-05-04 21:30:10.610594 INFO::Total function execution time is 0.0408720970153809 s and adjustment time is 0.0209536552429199 s ( 51.27 )
2026-05-04 21:30:10.85139 INFO::Formatting Data.
2026-05-04 21:30:10.852365 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.853402 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.854874 INFO::Found 0 missing values.
2026-05-04 21:30:10.858252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.858905 INFO::Done
2026-05-04 21:30:10.8595 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.861801 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.862598 INFO::Found 3 batches.
2026-05-04 21:30:10.863172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.863851 INFO::Using default BPPARAM
2026-05-04 21:30:10.864437 INFO::Processing subtree level 1
2026-05-04 21:30:10.954647 INFO::Adjusting the last 1 batches sequentially
2026-05-04 21:30:10.956534 INFO::Done
2026-05-04 21:30:10.957259 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:10.960002 INFO::ASW Batch was -0.00117318702732901 prior to batch effect correction and is now -0.00117318702732901 .
2026-05-04 21:30:10.961078 INFO::Total function execution time is 0.109782695770264 s and adjustment time is 0.0940990447998047 s ( 85.71 )
2026-05-04 21:30:10.962236 INFO::Formatting Data.
2026-05-04 21:30:10.962965 INFO::Typecasting input to dataframe.
2026-05-04 21:30:10.963841 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:10.964854 INFO::Removing potential empty rows and columns
2026-05-04 21:30:10.966042 INFO::Found 0 missing values.
2026-05-04 21:30:10.969422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:10.970033 INFO::Done
2026-05-04 21:30:10.97065 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:10.972919 INFO::Starting hierarchical adjustment
2026-05-04 21:30:10.973756 INFO::Found 3 batches.
2026-05-04 21:30:10.974353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:10.975091 INFO::Using default BPPARAM
2026-05-04 21:30:10.975708 INFO::Processing subtree level 1
2026-05-04 21:30:11.06714 INFO::Adjusting the last 1 batches sequentially
2026-05-04 21:30:11.070065 INFO::Done
2026-05-04 21:30:11.07129 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:11.07531 INFO::ASW Batch was -0.00117318702732901 prior to batch effect correction and is now -0.00117318702732901 .
2026-05-04 21:30:11.077036 INFO::Total function execution time is 0.114652156829834 s and adjustment time is 0.0963835716247559 s ( 84.07 )
2026-05-04 21:30:11.098183 INFO::Formatting Data.
2026-05-04 21:30:11.099512 INFO::Typecasting input to dataframe.
2026-05-04 21:30:11.100865 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:11.102235 INFO::Removing potential empty rows and columns
2026-05-04 21:30:11.103863 INFO::Found 0 missing values.
2026-05-04 21:30:11.108214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:11.108884 INFO::Done
2026-05-04 21:30:11.109478 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:11.111713 INFO::Starting hierarchical adjustment
2026-05-04 21:30:11.112544 INFO::Found 3 batches.
2026-05-04 21:30:11.113316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:11.11401 INFO::Using default BPPARAM
2026-05-04 21:30:11.114621 INFO::Processing subtree level 1
2026-05-04 21:30:11.205709 INFO::Adjusting the last 1 batches sequentially
2026-05-04 21:30:11.207769 INFO::Done
2026-05-04 21:30:11.208563 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:11.211383 INFO::ASW Batch was -0.181360524413822 prior to batch effect correction and is now -0.181360524413822 .
2026-05-04 21:30:11.212479 INFO::Total function execution time is 0.114443778991699 s and adjustment time is 0.0954225063323975 s ( 83.38 )
2026-05-04 21:30:11.363259 INFO::Formatting Data.
2026-05-04 21:30:11.364411 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:11.365779 INFO::Removing potential empty rows and columns
2026-05-04 21:30:11.369108 INFO::Found 1000 missing values.
2026-05-04 21:30:11.389968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:11.390859 INFO::Done
2026-05-04 21:30:11.391517 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:11.397672 INFO::Starting hierarchical adjustment
2026-05-04 21:30:11.398649 INFO::Found 10 batches.
2026-05-04 21:30:11.399268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:11.399952 INFO::Using default BPPARAM
2026-05-04 21:30:11.400555 INFO::Processing subtree level 1
2026-05-04 21:30:11.545047 INFO::Processing subtree level 2
2026-05-04 21:30:11.700309 INFO::Adjusting the last 1 batches sequentially
2026-05-04 21:30:11.702832 INFO::Done
2026-05-04 21:30:11.703948 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:11.710939 INFO::ASW Batch was 0.515286199113725 prior to batch effect correction and is now 0.515286199113725 .
2026-05-04 21:30:11.711902 INFO::ASW Label was 0.32497600491371 prior to batch effect correction and is now 0.32497600491371 .
2026-05-04 21:30:11.713064 INFO::Total function execution time is 0.349884033203125 s and adjustment time is 0.304343461990356 s ( 86.98 )
2026-05-04 21:30:11.714139 INFO::Formatting Data.
2026-05-04 21:30:11.714957 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:11.716531 INFO::Removing potential empty rows and columns
2026-05-04 21:30:11.720092 INFO::Found 1000 missing values.
2026-05-04 21:30:11.743243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:11.744269 INFO::Done
2026-05-04 21:30:11.745092 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:11.751612 INFO::Starting hierarchical adjustment
2026-05-04 21:30:11.752615 INFO::Found 10 batches.
2026-05-04 21:30:13.018399 INFO::Set up parallel execution backend with 2 workers
2026-05-04 21:30:13.025814 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-04 21:30:14.367513 INFO::Adjusting the last 2 batches sequentially
2026-05-04 21:30:14.370833 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-04 21:30:14.38851 INFO::Done
2026-05-04 21:30:14.389279 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:14.394139 INFO::ASW Batch was 0.515286199113725 prior to batch effect correction and is now 0.515286199113725 .
2026-05-04 21:30:14.394794 INFO::ASW Label was 0.32497600491371 prior to batch effect correction and is now 0.32497600491371 .
2026-05-04 21:30:14.395582 INFO::Total function execution time is 2.68153238296509 s and adjustment time is 2.63607358932495 s ( 98.3 )
2026-05-04 21:30:14.549513 INFO::Formatting Data.
2026-05-04 21:30:14.550663 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:14.551888 INFO::Removing potential empty rows and columns
2026-05-04 21:30:14.553113 INFO::Found 0 missing values.
2026-05-04 21:30:14.557123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:14.557736 INFO::Done
2026-05-04 21:30:14.558294 INFO::Acquiring quality metrics before batch effect correction.
2026-05-04 21:30:14.561644 INFO::Starting hierarchical adjustment
2026-05-04 21:30:14.562398 INFO::Found 3 batches.
2026-05-04 21:30:14.562953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-04 21:30:14.56361 INFO::Using default BPPARAM
2026-05-04 21:30:14.564164 INFO::Processing subtree level 1
2026-05-04 21:30:14.6747 INFO::Adjusting the last 1 batches sequentially
2026-05-04 21:30:14.676672 INFO::Done
2026-05-04 21:30:14.677425 INFO::Acquiring quality metrics after batch effect correction.
2026-05-04 21:30:14.680844 INFO::ASW Batch was 0.160959436071681 prior to batch effect correction and is now -0.155979002567604 .
2026-05-04 21:30:14.681587 INFO::ASW Label was -0.127764684430236 prior to batch effect correction and is now 0.190021400303346 .
2026-05-04 21:30:14.682564 INFO::Total function execution time is 0.133204460144043 s and adjustment time is 0.114391088485718 s ( 85.88 )
2026-05-04 21:30:14.814815 INFO::Formatting Data.
2026-05-04 21:30:14.815708 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:14.81666 INFO::Removing potential empty rows and columns
2026-05-04 21:30:14.817763 INFO::Found 2 missing values.
2026-05-04 21:30:14.820661 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:14.821227 INFO::Done
2026-05-04 21:30:14.849477 INFO::Found NA in Reference column
2026-05-04 21:30:14.858936 INFO::Require at least two references per batch.
2026-05-04 21:30:14.887735 INFO::Formatting Data.
2026-05-04 21:30:14.888645 INFO::Recognized SummarizedExperiment
2026-05-04 21:30:14.889257 INFO::Typecasting input to dataframe.
2026-05-04 21:30:14.89974 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:14.901092 INFO::Removing potential empty rows and columns
2026-05-04 21:30:14.905068 INFO::Found 0 missing values.
2026-05-04 21:30:14.912647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:14.913412 INFO::Done
2026-05-04 21:30:14.931229 INFO::Formatting Data.
2026-05-04 21:30:14.932085 INFO::Recognized SummarizedExperiment
2026-05-04 21:30:14.93271 INFO::Typecasting input to dataframe.
2026-05-04 21:30:14.951729 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:14.953035 INFO::Removing potential empty rows and columns
2026-05-04 21:30:14.957155 INFO::Found 0 missing values.
2026-05-04 21:30:14.969515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:14.970357 INFO::Done
2026-05-04 21:30:14.98734 INFO::Formatting Data.
2026-05-04 21:30:14.988183 INFO::Recognized SummarizedExperiment
2026-05-04 21:30:14.988788 INFO::Typecasting input to dataframe.
2026-05-04 21:30:15.006264 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:15.00742 INFO::Removing potential empty rows and columns
2026-05-04 21:30:15.008569 INFO::Found 0 missing values.
2026-05-04 21:30:15.009546 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.
2026-05-04 21:30:15.014093 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:15.014708 INFO::Done
2026-05-04 21:30:15.02519 INFO::Formatting Data.
2026-05-04 21:30:15.026082 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:15.027008 INFO::Removing potential empty rows and columns
2026-05-04 21:30:15.028056 INFO::Found 0 missing values.
2026-05-04 21:30:15.030965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:15.031542 INFO::Done
2026-05-04 21:30:15.043157 INFO::Formatting Data.
2026-05-04 21:30:15.044077 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:15.045045 INFO::Removing potential empty rows and columns
2026-05-04 21:30:15.046101 INFO::Found 0 missing values.
2026-05-04 21:30:15.049074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:15.049696 INFO::Done
2026-05-04 21:30:15.081153 INFO::Formatting Data.
2026-05-04 21:30:15.082097 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:15.083215 INFO::Removing potential empty rows and columns
2026-05-04 21:30:15.084511 INFO::Found 1 missing values.
2026-05-04 21:30:15.087267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:15.087873 INFO::Done
2026-05-04 21:30:15.10815 INFO::Formatting Data.
2026-05-04 21:30:15.109124 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:15.110073 INFO::Removing potential empty rows and columns
2026-05-04 21:30:15.111087 INFO::Found 2 missing values.
2026-05-04 21:30:15.11233 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.
2026-05-04 21:30:15.114654 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:15.115241 INFO::Done
2026-05-04 21:30:15.125571 INFO::Formatting Data.
2026-05-04 21:30:15.126448 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:15.127396 INFO::Removing potential empty rows and columns
2026-05-04 21:30:15.128358 INFO::Found 2 missing values.
2026-05-04 21:30:15.129977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:15.130536 INFO::Done
2026-05-04 21:30:15.141297 INFO::Formatting Data.
2026-05-04 21:30:15.142204 INFO::Typecasting input to dataframe.
2026-05-04 21:30:15.14306 INFO::Replacing NaNs with NAs.
2026-05-04 21:30:15.143961 INFO::Removing potential empty rows and columns
2026-05-04 21:30:15.145031 INFO::Found 0 missing values.
2026-05-04 21:30:15.148081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-04 21:30:15.148647 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.603 3.817 23.091
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.986 | 1.223 | 19.356 | |
| compute_asw | 0.027 | 0.000 | 0.027 | |
| count_existing | 0.014 | 0.000 | 0.015 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.013 | 0.000 | 0.013 | |