Yannis Schumann
| Snapshot Date: 2026-02-26 13:45 -0500 (Thu, 26 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-27 11:57 -0500 (Fri, 27 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-02-26 21:23:42 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 21:25:09 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 87.0 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 24.414 1.112 17.153
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-26 21:24:32.388333 INFO::Formatting Data.
2026-02-26 21:24:32.389617 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:32.400637 INFO::Removing potential empty rows and columns
2026-02-26 21:24:32.645689 INFO::Found 0 missing values.
2026-02-26 21:24:32.649008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:32.649668 INFO::Done
2026-02-26 21:24:32.650193 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:32.661102 INFO::Starting hierarchical adjustment
2026-02-26 21:24:32.661932 INFO::Found 3 batches.
2026-02-26 21:24:32.662452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:32.663593 INFO::Using default BPPARAM
2026-02-26 21:24:32.664129 INFO::Processing subtree level 1
2026-02-26 21:24:32.766749 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:24:32.768631 INFO::Done
2026-02-26 21:24:32.769348 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:32.772093 INFO::ASW Batch was -0.0805848336712818 prior to batch effect correction and is now -0.0805848336712818 .
2026-02-26 21:24:32.773231 INFO::Total function execution time is 0.385610580444336 s and adjustment time is 0.106829166412354 s ( 27.7 )
2026-02-26 21:24:32.787434 INFO::Formatting Data.
2026-02-26 21:24:32.788261 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:32.789237 INFO::Removing potential empty rows and columns
2026-02-26 21:24:32.79045 INFO::Found 0 missing values.
2026-02-26 21:24:32.791448 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-26 21:24:32.802486 INFO::Formatting Data.
2026-02-26 21:24:32.803287 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:32.804209 INFO::Removing potential empty rows and columns
2026-02-26 21:24:32.805296 INFO::Found 0 missing values.
2026-02-26 21:24:32.806267 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-26 21:24:32.8229 INFO::Formatting Data.
2026-02-26 21:24:32.82388 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:32.824924 INFO::Removing potential empty rows and columns
2026-02-26 21:24:32.826061 INFO::Found 0 missing values.
2026-02-26 21:24:32.827077 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-26 21:24:32.831761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:32.832378 INFO::Done
2026-02-26 21:24:32.832937 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:32.835124 INFO::Starting hierarchical adjustment
2026-02-26 21:24:32.835866 INFO::Found 2 batches.
2026-02-26 21:24:32.836395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:32.837064 INFO::Using default BPPARAM
2026-02-26 21:24:32.837602 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:32.838543 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:24:32.860249 INFO::Done
2026-02-26 21:24:32.861004 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:32.863287 INFO::ASW Batch was -0.0538867817706384 prior to batch effect correction and is now -0.117788925186541 .
2026-02-26 21:24:32.864164 INFO::Total function execution time is 0.0413732528686523 s and adjustment time is 0.0245006084442139 s ( 59.22 )
2026-02-26 21:24:32.867215 INFO::Formatting Data.
2026-02-26 21:24:32.867912 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:32.877258 INFO::Formatting Data.
2026-02-26 21:24:32.878052 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:32.878977 INFO::Removing potential empty rows and columns
2026-02-26 21:24:32.880072 INFO::Found 0 missing values.
2026-02-26 21:24:32.883122 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:32.883689 INFO::Done
2026-02-26 21:24:32.88432 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:32.911403 INFO::Starting hierarchical adjustment
2026-02-26 21:24:32.913133 INFO::Found 2 batches.
2026-02-26 21:24:32.913767 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:32.914311 INFO::Using default BPPARAM
2026-02-26 21:24:32.914861 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:32.915873 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:32.930342 INFO::Done
2026-02-26 21:24:32.930979 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:32.93295 INFO::ASW Batch was -0.0130536550345034 prior to batch effect correction and is now -0.119097495113874 .
2026-02-26 21:24:32.9337 INFO::Total function execution time is 0.0565319061279297 s and adjustment time is 0.0174510478973389 s ( 30.87 )
2026-02-26 21:24:32.934757 INFO::Formatting Data.
2026-02-26 21:24:32.935338 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:32.93614 INFO::Removing potential empty rows and columns
2026-02-26 21:24:32.937095 INFO::Found 0 missing values.
2026-02-26 21:24:32.939727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:32.940225 INFO::Done
2026-02-26 21:24:32.940715 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:32.942654 INFO::Starting hierarchical adjustment
2026-02-26 21:24:32.943302 INFO::Found 2 batches.
2026-02-26 21:24:32.943794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:32.944346 INFO::Using default BPPARAM
2026-02-26 21:24:32.944844 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:32.945675 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:32.960022 INFO::Done
2026-02-26 21:24:32.960697 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:32.962628 INFO::ASW Batch was -0.0130536550345034 prior to batch effect correction and is now -0.119097495113874 .
2026-02-26 21:24:32.963435 INFO::Total function execution time is 0.0286831855773926 s and adjustment time is 0.0168344974517822 s ( 58.69 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-26 21:24:35.957939 INFO::Formatting Data.
2026-02-26 21:24:35.958646 INFO::Recognized SummarizedExperiment
2026-02-26 21:24:35.959116 INFO::Typecasting input to dataframe.
2026-02-26 21:24:35.990077 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:35.991323 INFO::Removing potential empty rows and columns
2026-02-26 21:24:35.995134 INFO::Found 0 missing values.
2026-02-26 21:24:36.002478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:36.003186 INFO::Done
2026-02-26 21:24:36.003732 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:36.00745 INFO::Starting hierarchical adjustment
2026-02-26 21:24:36.008262 INFO::Found 2 batches.
2026-02-26 21:24:36.008804 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:36.009951 INFO::Using default BPPARAM
2026-02-26 21:24:36.010497 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:36.011543 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:24:36.068678 INFO::Done
2026-02-26 21:24:36.069379 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:36.072959 INFO::ASW Batch was 0.0194947269481976 prior to batch effect correction and is now -0.0888710691360846 .
2026-02-26 21:24:36.073813 INFO::Total function execution time is 0.116190671920776 s and adjustment time is 0.0605647563934326 s ( 52.13 )
Warning: stack imbalance in '{', 73 then 75
2026-02-26 21:24:36.092311 INFO::Formatting Data.
2026-02-26 21:24:36.093065 INFO::Recognized SummarizedExperiment
2026-02-26 21:24:36.093605 INFO::Typecasting input to dataframe.
2026-02-26 21:24:36.102733 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:36.103927 INFO::Removing potential empty rows and columns
2026-02-26 21:24:36.10777 INFO::Found 0 missing values.
2026-02-26 21:24:36.114937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:36.115594 INFO::Done
2026-02-26 21:24:36.116125 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:36.119658 INFO::Starting hierarchical adjustment
2026-02-26 21:24:36.120377 INFO::Found 2 batches.
2026-02-26 21:24:36.120897 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:36.121483 INFO::Using default BPPARAM
2026-02-26 21:24:36.122003 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:36.122956 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:24:36.148249 INFO::Done
2026-02-26 21:24:36.149035 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:36.152847 INFO::ASW Batch was 0.000365076525182753 prior to batch effect correction and is now 0.000365076525182753 .
2026-02-26 21:24:36.153764 INFO::Total function execution time is 0.0614309310913086 s and adjustment time is 0.0279664993286133 s ( 45.53 )
2026-02-26 21:24:36.172618 INFO::Formatting Data.
2026-02-26 21:24:36.173404 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:36.174378 INFO::Removing potential empty rows and columns
2026-02-26 21:24:36.175416 INFO::Found 0 missing values.
2026-02-26 21:24:36.178397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:36.183888 INFO::Done
2026-02-26 21:24:36.184491 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:36.186648 INFO::Starting hierarchical adjustment
2026-02-26 21:24:36.187358 INFO::Found 3 batches.
2026-02-26 21:24:36.187887 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:36.18848 INFO::Using default BPPARAM
2026-02-26 21:24:36.189013 INFO::Processing subtree level 1
2026-02-26 21:24:36.319867 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:24:36.321577 INFO::Done
2026-02-26 21:24:36.322197 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:36.324605 INFO::ASW Batch was -0.0229609148567492 prior to batch effect correction and is now -0.150076248895045 .
2026-02-26 21:24:36.325527 INFO::Total function execution time is 0.152947664260864 s and adjustment time is 0.134343147277832 s ( 87.84 )
2026-02-26 21:24:36.34013 INFO::Skipping initial DF formatting
2026-02-26 21:24:36.340867 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:36.344856 INFO::Starting hierarchical adjustment
2026-02-26 21:24:36.345632 INFO::Found 5 batches.
2026-02-26 21:24:36.346164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:36.346798 INFO::Using default BPPARAM
2026-02-26 21:24:36.347317 INFO::Processing subtree level 1
2026-02-26 21:24:36.647207 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:36.649221 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:24:36.67045 INFO::Done
2026-02-26 21:24:36.671397 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:36.676336 INFO::ASW Batch was 0.508393490883276 prior to batch effect correction and is now 0.508393490883276 .
2026-02-26 21:24:36.677098 INFO::ASW Label was 0.38734992804541 prior to batch effect correction and is now 0.38734992804541 .
2026-02-26 21:24:36.678064 INFO::Total function execution time is 0.337981700897217 s and adjustment time is 0.324911832809448 s ( 96.13 )
2026-02-26 21:24:36.75866 INFO::Formatting Data.
2026-02-26 21:24:36.759667 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:36.760731 INFO::Removing potential empty rows and columns
2026-02-26 21:24:36.761853 INFO::Found 0 missing values.
2026-02-26 21:24:36.76617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:36.766745 INFO::Done
2026-02-26 21:24:36.767247 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:36.77047 INFO::Starting hierarchical adjustment
2026-02-26 21:24:36.771191 INFO::Found 5 batches.
2026-02-26 21:24:36.77171 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:36.772306 INFO::Using default BPPARAM
2026-02-26 21:24:36.772863 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:36.921131 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:36.922818 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:36.9408 INFO::Done
2026-02-26 21:24:36.941641 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:36.9454 INFO::ASW Batch was 0.382988283859987 prior to batch effect correction and is now -0.0462605576727249 .
2026-02-26 21:24:36.946085 INFO::ASW Label was 0.4403750649637 prior to batch effect correction and is now 0.848953883349448 .
2026-02-26 21:24:36.946959 INFO::Total function execution time is 0.188553333282471 s and adjustment time is 0.169727325439453 s ( 90.02 )
2026-02-26 21:24:36.94789 INFO::Formatting Data.
2026-02-26 21:24:36.948577 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:36.949568 INFO::Removing potential empty rows and columns
2026-02-26 21:24:36.950699 INFO::Found 0 missing values.
2026-02-26 21:24:36.955327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:36.95591 INFO::Done
2026-02-26 21:24:36.956531 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:36.959744 INFO::Starting hierarchical adjustment
2026-02-26 21:24:36.960469 INFO::Found 5 batches.
2026-02-26 21:24:36.961028 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:36.961686 INFO::Using default BPPARAM
2026-02-26 21:24:36.962241 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:37.094565 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:37.096373 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:37.114748 INFO::Done
2026-02-26 21:24:37.115497 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:37.119137 INFO::ASW Batch was 0.382988283859987 prior to batch effect correction and is now -0.0462605576727249 .
2026-02-26 21:24:37.119856 INFO::ASW Label was 0.4403750649637 prior to batch effect correction and is now 0.848953883349448 .
2026-02-26 21:24:37.120757 INFO::Total function execution time is 0.172868251800537 s and adjustment time is 0.154402732849121 s ( 89.32 )
2026-02-26 21:24:37.136098 INFO::Formatting Data.
2026-02-26 21:24:37.136926 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:37.137982 INFO::Removing potential empty rows and columns
2026-02-26 21:24:37.139078 INFO::Found 0 missing values.
2026-02-26 21:24:37.143762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:37.144331 INFO::Done
2026-02-26 21:24:37.144882 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:37.148031 INFO::Starting hierarchical adjustment
2026-02-26 21:24:37.148744 INFO::Found 5 batches.
2026-02-26 21:24:37.14928 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:37.149893 INFO::Using default BPPARAM
2026-02-26 21:24:37.150426 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:37.288316 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:37.290179 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:37.307375 INFO::Done
2026-02-26 21:24:37.308188 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:37.312047 INFO::ASW Batch was 0.392737278748726 prior to batch effect correction and is now -0.0649824605786125 .
2026-02-26 21:24:37.3128 INFO::ASW Label was 0.364043803449507 prior to batch effect correction and is now 0.884203658916611 .
2026-02-26 21:24:37.313763 INFO::Total function execution time is 0.17772388458252 s and adjustment time is 0.15874719619751 s ( 89.32 )
2026-02-26 21:24:37.314765 INFO::Formatting Data.
2026-02-26 21:24:37.315452 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:37.316453 INFO::Removing potential empty rows and columns
2026-02-26 21:24:37.317635 INFO::Found 0 missing values.
2026-02-26 21:24:37.322073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:37.322675 INFO::Done
2026-02-26 21:24:37.323229 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:37.326628 INFO::Starting hierarchical adjustment
2026-02-26 21:24:37.32744 INFO::Found 5 batches.
2026-02-26 21:24:37.328008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:37.328648 INFO::Using default BPPARAM
2026-02-26 21:24:37.329191 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:37.477539 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:37.479611 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:37.499176 INFO::Done
2026-02-26 21:24:37.500035 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:37.504377 INFO::ASW Batch was 0.392737278748726 prior to batch effect correction and is now -0.0649824605786125 .
2026-02-26 21:24:37.505278 INFO::ASW Label was 0.364043803449507 prior to batch effect correction and is now 0.884203658916611 .
2026-02-26 21:24:37.506569 INFO::Total function execution time is 0.191759347915649 s and adjustment time is 0.171866178512573 s ( 89.63 )
2026-02-26 21:24:37.523676 INFO::Formatting Data.
2026-02-26 21:24:37.52462 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:37.525688 INFO::Removing potential empty rows and columns
2026-02-26 21:24:37.526844 INFO::Found 0 missing values.
2026-02-26 21:24:37.529894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:37.530477 INFO::Done
2026-02-26 21:24:37.53104 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:37.534279 INFO::Starting hierarchical adjustment
2026-02-26 21:24:37.535069 INFO::Found 2 batches.
2026-02-26 21:24:37.535644 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:37.536299 INFO::Using default BPPARAM
2026-02-26 21:24:37.536863 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:37.537838 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:37.553962 INFO::Done
2026-02-26 21:24:37.554731 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:37.558083 INFO::ASW Batch was 0.672622634666726 prior to batch effect correction and is now -0.0226460369105352 .
2026-02-26 21:24:37.558789 INFO::ASW Label was 0.424082949683598 prior to batch effect correction and is now 0.943046840688842 .
2026-02-26 21:24:37.559658 INFO::Total function execution time is 0.0360896587371826 s and adjustment time is 0.0190372467041016 s ( 52.75 )
2026-02-26 21:24:37.560534 INFO::Formatting Data.
2026-02-26 21:24:37.561218 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:37.562184 INFO::Removing potential empty rows and columns
2026-02-26 21:24:37.563282 INFO::Found 0 missing values.
2026-02-26 21:24:37.566299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:37.566914 INFO::Done
2026-02-26 21:24:37.567495 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:37.571116 INFO::Starting hierarchical adjustment
2026-02-26 21:24:37.571985 INFO::Found 2 batches.
2026-02-26 21:24:37.572597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:37.573294 INFO::Using default BPPARAM
2026-02-26 21:24:37.573896 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:37.574949 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-26 21:24:37.592801 INFO::Done
2026-02-26 21:24:37.593701 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:37.597033 INFO::ASW Batch was 0.672622634666726 prior to batch effect correction and is now -0.0226460369105352 .
2026-02-26 21:24:37.597697 INFO::ASW Label was 0.424082949683598 prior to batch effect correction and is now 0.943046840688842 .
2026-02-26 21:24:37.598559 INFO::Total function execution time is 0.0380313396453857 s and adjustment time is 0.0209624767303467 s ( 55.12 )
2026-02-26 21:24:37.611157 INFO::Formatting Data.
2026-02-26 21:24:37.612032 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:37.613012 INFO::Removing potential empty rows and columns
2026-02-26 21:24:37.614041 INFO::Found 0 missing values.
2026-02-26 21:24:37.616339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:37.616917 INFO::Done
2026-02-26 21:24:37.617442 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:37.619517 INFO::Starting hierarchical adjustment
2026-02-26 21:24:37.620294 INFO::Found 2 batches.
2026-02-26 21:24:37.62088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:37.621525 INFO::Using default BPPARAM
2026-02-26 21:24:37.622095 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:37.623077 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:24:37.655776 INFO::Done
2026-02-26 21:24:37.656527 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:37.658585 INFO::ASW Batch was -0.0114252351691004 prior to batch effect correction and is now -0.0582941108921219 .
2026-02-26 21:24:37.659449 INFO::Total function execution time is 0.0483772754669189 s and adjustment time is 0.0356204509735107 s ( 73.63 )
2026-02-26 21:24:37.683077 INFO::Formatting Data.
2026-02-26 21:24:37.684101 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:37.68513 INFO::Removing potential empty rows and columns
2026-02-26 21:24:37.686287 INFO::Found 0 missing values.
2026-02-26 21:24:37.6876 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-26 21:24:37.692464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:37.693047 INFO::Done
2026-02-26 21:24:37.693582 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:37.696931 INFO::Starting hierarchical adjustment
2026-02-26 21:24:37.697688 INFO::Found 2 batches.
2026-02-26 21:24:37.698242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:37.698935 INFO::Using default BPPARAM
2026-02-26 21:24:37.699482 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:37.700472 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:24:37.719401 INFO::Done
2026-02-26 21:24:37.720142 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:37.723306 INFO::ASW Batch was 0.698281033054934 prior to batch effect correction and is now 0.142452945121707 .
2026-02-26 21:24:37.723964 INFO::ASW Label was 0.285730492998371 prior to batch effect correction and is now 0.794144851151592 .
2026-02-26 21:24:37.724844 INFO::Total function execution time is 0.0422084331512451 s and adjustment time is 0.0218496322631836 s ( 51.77 )
2026-02-26 21:24:37.725757 INFO::Formatting Data.
2026-02-26 21:24:37.726463 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:37.72745 INFO::Removing potential empty rows and columns
2026-02-26 21:24:37.728559 INFO::Found 0 missing values.
2026-02-26 21:24:37.729563 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-26 21:24:37.734466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:37.735053 INFO::Done
2026-02-26 21:24:37.735595 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:37.738679 INFO::Starting hierarchical adjustment
2026-02-26 21:24:37.739451 INFO::Found 2 batches.
2026-02-26 21:24:37.740024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:37.740674 INFO::Using default BPPARAM
2026-02-26 21:24:37.741226 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:37.742208 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:24:37.759558 INFO::Done
2026-02-26 21:24:37.760296 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:37.763357 INFO::ASW Batch was 0.698281033054934 prior to batch effect correction and is now 0.142452945121707 .
2026-02-26 21:24:37.763988 INFO::ASW Label was 0.285730492998371 prior to batch effect correction and is now 0.794144851151592 .
2026-02-26 21:24:37.764814 INFO::Total function execution time is 0.0390946865081787 s and adjustment time is 0.0202262401580811 s ( 51.74 )
2026-02-26 21:24:37.981347 INFO::Formatting Data.
2026-02-26 21:24:37.982188 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:37.983116 INFO::Removing potential empty rows and columns
2026-02-26 21:24:37.984189 INFO::Found 0 missing values.
2026-02-26 21:24:37.987232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:37.987776 INFO::Done
2026-02-26 21:24:37.988284 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:37.990298 INFO::Starting hierarchical adjustment
2026-02-26 21:24:37.991008 INFO::Found 3 batches.
2026-02-26 21:24:37.991529 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:37.992136 INFO::Using default BPPARAM
2026-02-26 21:24:37.992667 INFO::Processing subtree level 1
2026-02-26 21:24:38.088208 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:24:38.090073 INFO::Done
2026-02-26 21:24:38.090737 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:38.09328 INFO::ASW Batch was -0.0186491686771005 prior to batch effect correction and is now -0.0186491686771005 .
2026-02-26 21:24:38.094291 INFO::Total function execution time is 0.112998247146606 s and adjustment time is 0.099189281463623 s ( 87.78 )
2026-02-26 21:24:38.09545 INFO::Formatting Data.
2026-02-26 21:24:38.096158 INFO::Typecasting input to dataframe.
2026-02-26 21:24:38.096956 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:38.097918 INFO::Removing potential empty rows and columns
2026-02-26 21:24:38.099039 INFO::Found 0 missing values.
2026-02-26 21:24:38.102181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:38.102755 INFO::Done
2026-02-26 21:24:38.103292 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:38.105301 INFO::Starting hierarchical adjustment
2026-02-26 21:24:38.106029 INFO::Found 3 batches.
2026-02-26 21:24:38.106579 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:38.107217 INFO::Using default BPPARAM
2026-02-26 21:24:38.107768 INFO::Processing subtree level 1
2026-02-26 21:24:38.193851 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:24:38.195572 INFO::Done
2026-02-26 21:24:38.196215 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:38.19864 INFO::ASW Batch was -0.0186491686771005 prior to batch effect correction and is now -0.0186491686771005 .
2026-02-26 21:24:38.199562 INFO::Total function execution time is 0.104105949401855 s and adjustment time is 0.0896666049957275 s ( 86.13 )
2026-02-26 21:24:38.212542 INFO::Formatting Data.
2026-02-26 21:24:38.213307 INFO::Typecasting input to dataframe.
2026-02-26 21:24:38.214139 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:38.215059 INFO::Removing potential empty rows and columns
2026-02-26 21:24:38.216128 INFO::Found 0 missing values.
2026-02-26 21:24:38.219142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:38.219693 INFO::Done
2026-02-26 21:24:38.2202 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:38.222206 INFO::Starting hierarchical adjustment
2026-02-26 21:24:38.222918 INFO::Found 3 batches.
2026-02-26 21:24:38.223438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:38.224061 INFO::Using default BPPARAM
2026-02-26 21:24:38.224604 INFO::Processing subtree level 1
2026-02-26 21:24:38.308677 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:24:38.310497 INFO::Done
2026-02-26 21:24:38.311181 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:38.313748 INFO::ASW Batch was -0.129668183208156 prior to batch effect correction and is now -0.129668183208156 .
2026-02-26 21:24:38.314726 INFO::Total function execution time is 0.102203607559204 s and adjustment time is 0.0877039432525635 s ( 85.81 )
2026-02-26 21:24:38.453201 INFO::Formatting Data.
2026-02-26 21:24:38.454026 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:38.455138 INFO::Removing potential empty rows and columns
2026-02-26 21:24:38.457904 INFO::Found 1000 missing values.
2026-02-26 21:24:38.476727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:38.477492 INFO::Done
2026-02-26 21:24:38.478064 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:38.489022 INFO::Starting hierarchical adjustment
2026-02-26 21:24:38.490094 INFO::Found 10 batches.
2026-02-26 21:24:38.490671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:38.491331 INFO::Using default BPPARAM
2026-02-26 21:24:38.49189 INFO::Processing subtree level 1
2026-02-26 21:24:38.643055 INFO::Processing subtree level 2
2026-02-26 21:24:38.787893 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:24:38.789924 INFO::Done
2026-02-26 21:24:38.790607 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:38.7964 INFO::ASW Batch was 0.461170734535015 prior to batch effect correction and is now 0.461170734535015 .
2026-02-26 21:24:38.797132 INFO::ASW Label was 0.351257209346153 prior to batch effect correction and is now 0.351257209346153 .
2026-02-26 21:24:38.798178 INFO::Total function execution time is 0.345013618469238 s and adjustment time is 0.300035238265991 s ( 86.96 )
2026-02-26 21:24:38.799107 INFO::Formatting Data.
2026-02-26 21:24:38.799781 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:38.801067 INFO::Removing potential empty rows and columns
2026-02-26 21:24:38.803942 INFO::Found 1000 missing values.
2026-02-26 21:24:38.823 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:38.823782 INFO::Done
2026-02-26 21:24:38.824325 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:38.829909 INFO::Starting hierarchical adjustment
2026-02-26 21:24:38.830714 INFO::Found 10 batches.
2026-02-26 21:24:39.993634 INFO::Set up parallel execution backend with 2 workers
2026-02-26 21:24:39.995481 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-26 21:24:41.192222 INFO::Adjusting the last 2 batches sequentially
2026-02-26 21:24:41.193893 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-26 21:24:41.209326 INFO::Done
2026-02-26 21:24:41.209956 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:41.214202 INFO::ASW Batch was 0.461170734535015 prior to batch effect correction and is now 0.461170734535015 .
2026-02-26 21:24:41.214735 INFO::ASW Label was 0.351257209346153 prior to batch effect correction and is now 0.351257209346153 .
2026-02-26 21:24:41.215412 INFO::Total function execution time is 2.41635155677795 s and adjustment time is 2.37878203392029 s ( 98.45 )
2026-02-26 21:24:41.353691 INFO::Formatting Data.
2026-02-26 21:24:41.35444 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.355333 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.356376 INFO::Found 0 missing values.
2026-02-26 21:24:41.359829 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.360341 INFO::Done
2026-02-26 21:24:41.360834 INFO::Acquiring quality metrics before batch effect correction.
2026-02-26 21:24:41.363499 INFO::Starting hierarchical adjustment
2026-02-26 21:24:41.364185 INFO::Found 3 batches.
2026-02-26 21:24:41.364696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-26 21:24:41.365282 INFO::Using default BPPARAM
2026-02-26 21:24:41.365797 INFO::Processing subtree level 1
2026-02-26 21:24:41.466462 INFO::Adjusting the last 1 batches sequentially
2026-02-26 21:24:41.468229 INFO::Done
2026-02-26 21:24:41.468877 INFO::Acquiring quality metrics after batch effect correction.
2026-02-26 21:24:41.472305 INFO::ASW Batch was 0.132274040975453 prior to batch effect correction and is now -0.166743711523391 .
2026-02-26 21:24:41.472956 INFO::ASW Label was -0.189857822849518 prior to batch effect correction and is now -0.0235780782870052 .
2026-02-26 21:24:41.473849 INFO::Total function execution time is 0.120219230651855 s and adjustment time is 0.104165315628052 s ( 86.65 )
2026-02-26 21:24:41.590564 INFO::Formatting Data.
2026-02-26 21:24:41.591316 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.59218 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.593176 INFO::Found 2 missing values.
2026-02-26 21:24:41.595869 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.596373 INFO::Done
2026-02-26 21:24:41.622962 INFO::Found NA in Reference column
2026-02-26 21:24:41.632204 INFO::Require at least two references per batch.
2026-02-26 21:24:41.651653 INFO::Formatting Data.
2026-02-26 21:24:41.652355 INFO::Recognized SummarizedExperiment
2026-02-26 21:24:41.652867 INFO::Typecasting input to dataframe.
2026-02-26 21:24:41.661801 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.662896 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.666129 INFO::Found 0 missing values.
2026-02-26 21:24:41.672385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.672995 INFO::Done
2026-02-26 21:24:41.687832 INFO::Formatting Data.
2026-02-26 21:24:41.688555 INFO::Recognized SummarizedExperiment
2026-02-26 21:24:41.689062 INFO::Typecasting input to dataframe.
2026-02-26 21:24:41.705353 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.706519 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.709731 INFO::Found 0 missing values.
2026-02-26 21:24:41.719524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.720135 INFO::Done
2026-02-26 21:24:41.734761 INFO::Formatting Data.
2026-02-26 21:24:41.735447 INFO::Recognized SummarizedExperiment
2026-02-26 21:24:41.73596 INFO::Typecasting input to dataframe.
2026-02-26 21:24:41.751722 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.752713 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.75374 INFO::Found 0 missing values.
2026-02-26 21:24:41.754606 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-26 21:24:41.758691 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.759201 INFO::Done
2026-02-26 21:24:41.768805 INFO::Formatting Data.
2026-02-26 21:24:41.769592 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.77045 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.771406 INFO::Found 0 missing values.
2026-02-26 21:24:41.774138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.774657 INFO::Done
2026-02-26 21:24:41.785462 INFO::Formatting Data.
2026-02-26 21:24:41.786441 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.787423 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.788421 INFO::Found 0 missing values.
2026-02-26 21:24:41.791165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.791689 INFO::Done
2026-02-26 21:24:41.828638 INFO::Formatting Data.
2026-02-26 21:24:41.829457 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.830488 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.831722 INFO::Found 1 missing values.
2026-02-26 21:24:41.834391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.834935 INFO::Done
2026-02-26 21:24:41.854306 INFO::Formatting Data.
2026-02-26 21:24:41.855178 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.85607 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.857031 INFO::Found 2 missing values.
2026-02-26 21:24:41.857935 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-26 21:24:41.860154 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.860694 INFO::Done
2026-02-26 21:24:41.870693 INFO::Formatting Data.
2026-02-26 21:24:41.871413 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.87225 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.873163 INFO::Found 2 missing values.
2026-02-26 21:24:41.874727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.875242 INFO::Done
2026-02-26 21:24:41.885629 INFO::Formatting Data.
2026-02-26 21:24:41.886403 INFO::Typecasting input to dataframe.
2026-02-26 21:24:41.887302 INFO::Replacing NaNs with NAs.
2026-02-26 21:24:41.888199 INFO::Removing potential empty rows and columns
2026-02-26 21:24:41.889244 INFO::Found 0 missing values.
2026-02-26 21:24:41.892271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-26 21:24:41.892813 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.946 3.779 20.363
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.414 | 1.112 | 17.153 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.000 | 0.014 | |
| generate_data_covariables | 0.010 | 0.001 | 0.012 | |
| generate_dataset | 0.011 | 0.000 | 0.012 | |