Yannis Schumann
| Snapshot Date: 2026-02-24 13:45 -0500 (Tue, 24 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 2026-02-25 11:57 -0500 (Wed, 25 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: 2026-02-24 21:33:11 -0500 (Tue, 24 Feb 2026) |
| EndedAt: 2026-02-24 21:34:41 -0500 (Tue, 24 Feb 2026) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 25.601 1.495 18.657
* 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")
2026-02-24 21:34:04.353988 INFO::Formatting Data.
2026-02-24 21:34:04.355309 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:04.366211 INFO::Removing potential empty rows and columns
2026-02-24 21:34:04.607578 INFO::Found 0 missing values.
2026-02-24 21:34:04.610861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:04.611527 INFO::Done
2026-02-24 21:34:04.612059 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:04.623473 INFO::Starting hierarchical adjustment
2026-02-24 21:34:04.62441 INFO::Found 3 batches.
2026-02-24 21:34:04.624999 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:04.626148 INFO::Using default BPPARAM
2026-02-24 21:34:04.626698 INFO::Processing subtree level 1
2026-02-24 21:34:04.722394 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:34:04.724192 INFO::Done
2026-02-24 21:34:04.724846 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:04.727364 INFO::ASW Batch was -0.156030479357095 prior to batch effect correction and is now -0.156030479357095 .
2026-02-24 21:34:04.728429 INFO::Total function execution time is 0.375146865844727 s and adjustment time is 0.0999965667724609 s ( 26.66 )
2026-02-24 21:34:04.742913 INFO::Formatting Data.
2026-02-24 21:34:04.743737 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:04.74474 INFO::Removing potential empty rows and columns
2026-02-24 21:34:04.745918 INFO::Found 0 missing values.
2026-02-24 21:34:04.746881 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.
2026-02-24 21:34:04.757995 INFO::Formatting Data.
2026-02-24 21:34:04.758839 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:04.759815 INFO::Removing potential empty rows and columns
2026-02-24 21:34:04.760885 INFO::Found 0 missing values.
2026-02-24 21:34:04.761829 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.
2026-02-24 21:34:04.778834 INFO::Formatting Data.
2026-02-24 21:34:04.779626 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:04.780559 INFO::Removing potential empty rows and columns
2026-02-24 21:34:04.781629 INFO::Found 0 missing values.
2026-02-24 21:34:04.782583 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.
2026-02-24 21:34:04.787004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:04.787619 INFO::Done
2026-02-24 21:34:04.788133 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:04.790164 INFO::Starting hierarchical adjustment
2026-02-24 21:34:04.790895 INFO::Found 2 batches.
2026-02-24 21:34:04.791409 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:04.792034 INFO::Using default BPPARAM
2026-02-24 21:34:04.792553 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:04.793493 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:34:04.814977 INFO::Done
2026-02-24 21:34:04.815721 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:04.81804 INFO::ASW Batch was 0.0250881736474109 prior to batch effect correction and is now -0.0857739319310373 .
2026-02-24 21:34:04.81896 INFO::Total function execution time is 0.0402305126190186 s and adjustment time is 0.0241935253143311 s ( 60.14 )
2026-02-24 21:34:04.822102 INFO::Formatting Data.
2026-02-24 21:34:04.822787 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:04.83215 INFO::Formatting Data.
2026-02-24 21:34:04.83297 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:04.833917 INFO::Removing potential empty rows and columns
2026-02-24 21:34:04.835015 INFO::Found 0 missing values.
2026-02-24 21:34:04.838028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:04.838595 INFO::Done
2026-02-24 21:34:04.839126 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:04.864437 INFO::Starting hierarchical adjustment
2026-02-24 21:34:04.867213 INFO::Found 2 batches.
2026-02-24 21:34:04.867791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:04.868344 INFO::Using default BPPARAM
2026-02-24 21:34:04.868844 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:04.869767 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:34:04.884095 INFO::Done
2026-02-24 21:34:04.88478 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:04.886727 INFO::ASW Batch was -0.0706701864690464 prior to batch effect correction and is now -0.119905253940569 .
2026-02-24 21:34:04.887493 INFO::Total function execution time is 0.0554540157318115 s and adjustment time is 0.0170655250549316 s ( 30.77 )
2026-02-24 21:34:04.888476 INFO::Formatting Data.
2026-02-24 21:34:04.889064 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:04.889877 INFO::Removing potential empty rows and columns
2026-02-24 21:34:04.890832 INFO::Found 0 missing values.
2026-02-24 21:34:04.893431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:04.893942 INFO::Done
2026-02-24 21:34:04.894417 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:04.896373 INFO::Starting hierarchical adjustment
2026-02-24 21:34:04.897062 INFO::Found 2 batches.
2026-02-24 21:34:04.897556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:04.898132 INFO::Using default BPPARAM
2026-02-24 21:34:04.898638 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:04.899498 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:34:04.913936 INFO::Done
2026-02-24 21:34:04.914617 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:04.916564 INFO::ASW Batch was -0.0706701864690464 prior to batch effect correction and is now -0.119905253940569 .
2026-02-24 21:34:04.917331 INFO::Total function execution time is 0.0288639068603516 s and adjustment time is 0.016991138458252 s ( 58.87 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-24 21:34:08.007682 INFO::Formatting Data.
2026-02-24 21:34:08.008377 INFO::Recognized SummarizedExperiment
2026-02-24 21:34:08.00889 INFO::Typecasting input to dataframe.
2026-02-24 21:34:08.039536 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:08.040846 INFO::Removing potential empty rows and columns
2026-02-24 21:34:08.044961 INFO::Found 0 missing values.
2026-02-24 21:34:08.052463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:08.053168 INFO::Done
2026-02-24 21:34:08.05373 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:08.057442 INFO::Starting hierarchical adjustment
2026-02-24 21:34:08.058194 INFO::Found 2 batches.
2026-02-24 21:34:08.058752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:08.059841 INFO::Using default BPPARAM
2026-02-24 21:34:08.060384 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:08.06139 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:34:08.118218 INFO::Done
2026-02-24 21:34:08.118945 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:08.122596 INFO::ASW Batch was -0.00408509561662697 prior to batch effect correction and is now -0.0931230460307073 .
2026-02-24 21:34:08.123453 INFO::Total function execution time is 0.116044282913208 s and adjustment time is 0.0601444244384766 s ( 51.83 )
Warning: stack imbalance in '{', 73 then 75
2026-02-24 21:34:08.142754 INFO::Formatting Data.
2026-02-24 21:34:08.143546 INFO::Recognized SummarizedExperiment
2026-02-24 21:34:08.144097 INFO::Typecasting input to dataframe.
2026-02-24 21:34:08.153532 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:08.154777 INFO::Removing potential empty rows and columns
2026-02-24 21:34:08.158565 INFO::Found 0 missing values.
2026-02-24 21:34:08.16578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:08.166438 INFO::Done
2026-02-24 21:34:08.16715 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:08.170766 INFO::Starting hierarchical adjustment
2026-02-24 21:34:08.171485 INFO::Found 2 batches.
2026-02-24 21:34:08.172035 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:08.17263 INFO::Using default BPPARAM
2026-02-24 21:34:08.173155 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:08.174149 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:34:08.199433 INFO::Done
2026-02-24 21:34:08.200146 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:08.203793 INFO::ASW Batch was 0.0183633478715082 prior to batch effect correction and is now 0.0183633478715082 .
2026-02-24 21:34:08.204668 INFO::Total function execution time is 0.0618996620178223 s and adjustment time is 0.0280575752258301 s ( 45.33 )
2026-02-24 21:34:08.223186 INFO::Formatting Data.
2026-02-24 21:34:08.223987 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:08.224894 INFO::Removing potential empty rows and columns
2026-02-24 21:34:08.226057 INFO::Found 0 missing values.
2026-02-24 21:34:08.229572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:08.230133 INFO::Done
2026-02-24 21:34:08.230672 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:08.232724 INFO::Starting hierarchical adjustment
2026-02-24 21:34:08.233417 INFO::Found 3 batches.
2026-02-24 21:34:08.233961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:08.234569 INFO::Using default BPPARAM
2026-02-24 21:34:08.235097 INFO::Processing subtree level 1
2026-02-24 21:34:08.372025 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:34:08.374206 INFO::Done
2026-02-24 21:34:08.374976 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:08.377831 INFO::ASW Batch was -0.0808013322796955 prior to batch effect correction and is now -0.185505395769364 .
2026-02-24 21:34:08.378872 INFO::Total function execution time is 0.155698776245117 s and adjustment time is 0.140882253646851 s ( 90.48 )
2026-02-24 21:34:08.395136 INFO::Skipping initial DF formatting
2026-02-24 21:34:08.396007 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:08.400444 INFO::Starting hierarchical adjustment
2026-02-24 21:34:08.401307 INFO::Found 5 batches.
2026-02-24 21:34:08.401906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:08.402566 INFO::Using default BPPARAM
2026-02-24 21:34:08.403111 INFO::Processing subtree level 1
2026-02-24 21:34:08.637939 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:08.639604 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:34:08.659376 INFO::Done
2026-02-24 21:34:08.660139 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:08.664459 INFO::ASW Batch was 0.564695470405358 prior to batch effect correction and is now 0.564695470405358 .
2026-02-24 21:34:08.665145 INFO::ASW Label was 0.317666884268293 prior to batch effect correction and is now 0.317666884268293 .
2026-02-24 21:34:08.666019 INFO::Total function execution time is 0.271023273468018 s and adjustment time is 0.258226156234741 s ( 95.28 )
2026-02-24 21:34:08.73813 INFO::Formatting Data.
2026-02-24 21:34:08.739004 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:08.739983 INFO::Removing potential empty rows and columns
2026-02-24 21:34:08.74109 INFO::Found 0 missing values.
2026-02-24 21:34:08.74536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:08.745933 INFO::Done
2026-02-24 21:34:08.746449 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:08.749483 INFO::Starting hierarchical adjustment
2026-02-24 21:34:08.750201 INFO::Found 5 batches.
2026-02-24 21:34:08.750727 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:08.751343 INFO::Using default BPPARAM
2026-02-24 21:34:08.751887 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.
2026-02-24 21:34:08.904671 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:08.906555 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:34:08.925703 INFO::Done
2026-02-24 21:34:08.926615 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:08.93043 INFO::ASW Batch was 0.658570414511471 prior to batch effect correction and is now -0.0762006700782667 .
2026-02-24 21:34:08.931119 INFO::ASW Label was 0.154834377774753 prior to batch effect correction and is now 0.792851771657412 .
2026-02-24 21:34:08.932027 INFO::Total function execution time is 0.193974494934082 s and adjustment time is 0.175604104995728 s ( 90.53 )
2026-02-24 21:34:08.933001 INFO::Formatting Data.
2026-02-24 21:34:08.933731 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:08.934723 INFO::Removing potential empty rows and columns
2026-02-24 21:34:08.935884 INFO::Found 0 missing values.
2026-02-24 21:34:08.940781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:08.94149 INFO::Done
2026-02-24 21:34:08.942139 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:08.945417 INFO::Starting hierarchical adjustment
2026-02-24 21:34:08.9462 INFO::Found 5 batches.
2026-02-24 21:34:08.946782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:08.947441 INFO::Using default BPPARAM
2026-02-24 21:34:08.948036 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.
2026-02-24 21:34:09.073073 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:09.074681 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:34:09.09121 INFO::Done
2026-02-24 21:34:09.092016 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.095468 INFO::ASW Batch was 0.658570414511471 prior to batch effect correction and is now -0.0762006700782667 .
2026-02-24 21:34:09.096109 INFO::ASW Label was 0.154834377774753 prior to batch effect correction and is now 0.792851771657412 .
2026-02-24 21:34:09.096934 INFO::Total function execution time is 0.16395092010498 s and adjustment time is 0.145138740539551 s ( 88.53 )
2026-02-24 21:34:09.110551 INFO::Formatting Data.
2026-02-24 21:34:09.111278 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.112155 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.113133 INFO::Found 0 missing values.
2026-02-24 21:34:09.117079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.117623 INFO::Done
2026-02-24 21:34:09.118124 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.12108 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.121774 INFO::Found 5 batches.
2026-02-24 21:34:09.122276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:09.122892 INFO::Using default BPPARAM
2026-02-24 21:34:09.12341 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.
2026-02-24 21:34:09.239967 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:09.241479 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:34:09.263433 INFO::Done
2026-02-24 21:34:09.264354 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.267972 INFO::ASW Batch was 0.452445135270958 prior to batch effect correction and is now -0.0345128494852516 .
2026-02-24 21:34:09.268553 INFO::ASW Label was 0.333293857223136 prior to batch effect correction and is now 0.779613706251492 .
2026-02-24 21:34:09.269433 INFO::Total function execution time is 0.158948421478271 s and adjustment time is 0.141622543334961 s ( 89.1 )
2026-02-24 21:34:09.270254 INFO::Formatting Data.
2026-02-24 21:34:09.270863 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.271735 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.272785 INFO::Found 0 missing values.
2026-02-24 21:34:09.27676 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.277281 INFO::Done
2026-02-24 21:34:09.277786 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.280712 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.281407 INFO::Found 5 batches.
2026-02-24 21:34:09.281921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:09.282548 INFO::Using default BPPARAM
2026-02-24 21:34:09.283066 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.
2026-02-24 21:34:09.404853 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:09.406657 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:34:09.426036 INFO::Done
2026-02-24 21:34:09.426822 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.430665 INFO::ASW Batch was 0.452445135270958 prior to batch effect correction and is now -0.0345128494852516 .
2026-02-24 21:34:09.431427 INFO::ASW Label was 0.333293857223136 prior to batch effect correction and is now 0.779613706251492 .
2026-02-24 21:34:09.432738 INFO::Total function execution time is 0.162381410598755 s and adjustment time is 0.14469838142395 s ( 89.11 )
2026-02-24 21:34:09.44874 INFO::Formatting Data.
2026-02-24 21:34:09.449569 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.450561 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.451638 INFO::Found 0 missing values.
2026-02-24 21:34:09.454574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.455154 INFO::Done
2026-02-24 21:34:09.455746 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.458991 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.459755 INFO::Found 2 batches.
2026-02-24 21:34:09.460314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:09.460968 INFO::Using default BPPARAM
2026-02-24 21:34:09.461541 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:09.462537 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:34:09.477773 INFO::Done
2026-02-24 21:34:09.478504 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.48166 INFO::ASW Batch was 0.2199076061924 prior to batch effect correction and is now 0.0533365565577426 .
2026-02-24 21:34:09.482285 INFO::ASW Label was 0.786361372562142 prior to batch effect correction and is now 0.871834892500043 .
2026-02-24 21:34:09.483089 INFO::Total function execution time is 0.0344624519348145 s and adjustment time is 0.0181536674499512 s ( 52.68 )
2026-02-24 21:34:09.483904 INFO::Formatting Data.
2026-02-24 21:34:09.484527 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.485388 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.486425 INFO::Found 0 missing values.
2026-02-24 21:34:09.489148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.489698 INFO::Done
2026-02-24 21:34:09.490202 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.493196 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.493927 INFO::Found 2 batches.
2026-02-24 21:34:09.494472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:09.49511 INFO::Using default BPPARAM
2026-02-24 21:34:09.495654 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:09.496587 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:34:09.511377 INFO::Done
2026-02-24 21:34:09.512072 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.515082 INFO::ASW Batch was 0.2199076061924 prior to batch effect correction and is now 0.0533365565577426 .
2026-02-24 21:34:09.515683 INFO::ASW Label was 0.786361372562142 prior to batch effect correction and is now 0.871834892500043 .
2026-02-24 21:34:09.516427 INFO::Total function execution time is 0.0325593948364258 s and adjustment time is 0.0175731182098389 s ( 53.97 )
2026-02-24 21:34:09.52772 INFO::Formatting Data.
2026-02-24 21:34:09.528461 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.529326 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.53023 INFO::Found 0 missing values.
2026-02-24 21:34:09.532315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.532842 INFO::Done
2026-02-24 21:34:09.533333 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.535233 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.535933 INFO::Found 2 batches.
2026-02-24 21:34:09.536434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:09.537042 INFO::Using default BPPARAM
2026-02-24 21:34:09.537578 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:09.53846 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:34:09.569775 INFO::Done
2026-02-24 21:34:09.570491 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.572579 INFO::ASW Batch was -0.148007780592982 prior to batch effect correction and is now -0.171184282888227 .
2026-02-24 21:34:09.573438 INFO::Total function execution time is 0.0458614826202393 s and adjustment time is 0.0339524745941162 s ( 74.03 )
2026-02-24 21:34:09.586171 INFO::Formatting Data.
2026-02-24 21:34:09.58706 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.587992 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.589016 INFO::Found 0 missing values.
2026-02-24 21:34:09.59019 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.
2026-02-24 21:34:09.594821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.59539 INFO::Done
2026-02-24 21:34:09.595926 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.598899 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.599617 INFO::Found 2 batches.
2026-02-24 21:34:09.600154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:09.600759 INFO::Using default BPPARAM
2026-02-24 21:34:09.601272 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:09.602186 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:34:09.618486 INFO::Done
2026-02-24 21:34:09.619198 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.622153 INFO::ASW Batch was 0.503222747198938 prior to batch effect correction and is now 0.116071727096458 .
2026-02-24 21:34:09.622769 INFO::ASW Label was 0.627488258678229 prior to batch effect correction and is now 0.872087235539763 .
2026-02-24 21:34:09.623583 INFO::Total function execution time is 0.0374796390533447 s and adjustment time is 0.0189981460571289 s ( 50.69 )
2026-02-24 21:34:09.624403 INFO::Formatting Data.
2026-02-24 21:34:09.625064 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.625998 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.626997 INFO::Found 0 missing values.
2026-02-24 21:34:09.627928 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.
2026-02-24 21:34:09.632462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.633041 INFO::Done
2026-02-24 21:34:09.633592 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.636523 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.637215 INFO::Found 2 batches.
2026-02-24 21:34:09.637741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:09.638319 INFO::Using default BPPARAM
2026-02-24 21:34:09.638833 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:09.639771 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:34:09.656502 INFO::Done
2026-02-24 21:34:09.657236 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.660333 INFO::ASW Batch was 0.503222747198938 prior to batch effect correction and is now 0.116071727096458 .
2026-02-24 21:34:09.660998 INFO::ASW Label was 0.627488258678229 prior to batch effect correction and is now 0.872087235539763 .
2026-02-24 21:34:09.661848 INFO::Total function execution time is 0.0374705791473389 s and adjustment time is 0.0193822383880615 s ( 51.73 )
2026-02-24 21:34:09.878429 INFO::Formatting Data.
2026-02-24 21:34:09.879257 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.880283 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.881346 INFO::Found 0 missing values.
2026-02-24 21:34:09.88443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.88499 INFO::Done
2026-02-24 21:34:09.885502 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.887601 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.888298 INFO::Found 3 batches.
2026-02-24 21:34:09.888829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:09.889419 INFO::Using default BPPARAM
2026-02-24 21:34:09.889942 INFO::Processing subtree level 1
2026-02-24 21:34:09.981639 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:34:09.983565 INFO::Done
2026-02-24 21:34:09.984261 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:09.98686 INFO::ASW Batch was -0.0895369484548985 prior to batch effect correction and is now -0.0895369484548985 .
2026-02-24 21:34:09.987899 INFO::Total function execution time is 0.109485387802124 s and adjustment time is 0.0953648090362549 s ( 87.1 )
2026-02-24 21:34:09.989023 INFO::Formatting Data.
2026-02-24 21:34:09.989705 INFO::Typecasting input to dataframe.
2026-02-24 21:34:09.990488 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:09.991454 INFO::Removing potential empty rows and columns
2026-02-24 21:34:09.992568 INFO::Found 0 missing values.
2026-02-24 21:34:09.995804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:09.99635 INFO::Done
2026-02-24 21:34:09.996905 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:09.99905 INFO::Starting hierarchical adjustment
2026-02-24 21:34:09.999804 INFO::Found 3 batches.
2026-02-24 21:34:10.000356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:10.001015 INFO::Using default BPPARAM
2026-02-24 21:34:10.001563 INFO::Processing subtree level 1
2026-02-24 21:34:10.086667 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:34:10.08854 INFO::Done
2026-02-24 21:34:10.08919 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:10.091653 INFO::ASW Batch was -0.0895369484548985 prior to batch effect correction and is now -0.0895369484548985 .
2026-02-24 21:34:10.092582 INFO::Total function execution time is 0.103542566299438 s and adjustment time is 0.0888657569885254 s ( 85.83 )
2026-02-24 21:34:10.105412 INFO::Formatting Data.
2026-02-24 21:34:10.106307 INFO::Typecasting input to dataframe.
2026-02-24 21:34:10.10717 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:10.108101 INFO::Removing potential empty rows and columns
2026-02-24 21:34:10.10921 INFO::Found 0 missing values.
2026-02-24 21:34:10.112239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:10.112788 INFO::Done
2026-02-24 21:34:10.113303 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:10.11531 INFO::Starting hierarchical adjustment
2026-02-24 21:34:10.11602 INFO::Found 3 batches.
2026-02-24 21:34:10.116547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:10.117173 INFO::Using default BPPARAM
2026-02-24 21:34:10.117735 INFO::Processing subtree level 1
2026-02-24 21:34:10.200234 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:34:10.202165 INFO::Done
2026-02-24 21:34:10.202817 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:10.205345 INFO::ASW Batch was -0.0980737175985251 prior to batch effect correction and is now -0.0980737175985251 .
2026-02-24 21:34:10.206298 INFO::Total function execution time is 0.100950479507446 s and adjustment time is 0.0862557888031006 s ( 85.44 )
2026-02-24 21:34:10.340446 INFO::Formatting Data.
2026-02-24 21:34:10.341222 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:10.34229 INFO::Removing potential empty rows and columns
2026-02-24 21:34:10.34499 INFO::Found 1000 missing values.
2026-02-24 21:34:10.363537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:10.364264 INFO::Done
2026-02-24 21:34:10.36483 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:10.370238 INFO::Starting hierarchical adjustment
2026-02-24 21:34:10.371053 INFO::Found 10 batches.
2026-02-24 21:34:10.371595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:10.372208 INFO::Using default BPPARAM
2026-02-24 21:34:10.372743 INFO::Processing subtree level 1
2026-02-24 21:34:10.500844 INFO::Processing subtree level 2
2026-02-24 21:34:10.634481 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:34:10.636356 INFO::Done
2026-02-24 21:34:10.637006 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:10.642479 INFO::ASW Batch was 0.506995219961324 prior to batch effect correction and is now 0.506995219961324 .
2026-02-24 21:34:10.643137 INFO::ASW Label was 0.337108218942191 prior to batch effect correction and is now 0.337108218942191 .
2026-02-24 21:34:10.644056 INFO::Total function execution time is 0.303658246994019 s and adjustment time is 0.265443086624146 s ( 87.42 )
2026-02-24 21:34:10.644925 INFO::Formatting Data.
2026-02-24 21:34:10.645577 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:10.646815 INFO::Removing potential empty rows and columns
2026-02-24 21:34:10.649615 INFO::Found 1000 missing values.
2026-02-24 21:34:10.668839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:10.669575 INFO::Done
2026-02-24 21:34:10.670151 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:10.675723 INFO::Starting hierarchical adjustment
2026-02-24 21:34:10.676485 INFO::Found 10 batches.
2026-02-24 21:34:11.670234 INFO::Set up parallel execution backend with 2 workers
2026-02-24 21:34:11.672279 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-24 21:34:12.675106 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:34:12.676795 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:34:12.692068 INFO::Done
2026-02-24 21:34:12.692681 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:12.696918 INFO::ASW Batch was 0.506995219961324 prior to batch effect correction and is now 0.506995219961324 .
2026-02-24 21:34:12.697444 INFO::ASW Label was 0.337108218942191 prior to batch effect correction and is now 0.337108218942191 .
2026-02-24 21:34:12.698133 INFO::Total function execution time is 2.05325841903687 s and adjustment time is 2.01572203636169 s ( 98.17 )
2026-02-24 21:34:12.835057 INFO::Formatting Data.
2026-02-24 21:34:12.8358 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:12.836683 INFO::Removing potential empty rows and columns
2026-02-24 21:34:12.837708 INFO::Found 0 missing values.
2026-02-24 21:34:12.841181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:12.84171 INFO::Done
2026-02-24 21:34:12.842201 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:34:12.844943 INFO::Starting hierarchical adjustment
2026-02-24 21:34:12.845641 INFO::Found 3 batches.
2026-02-24 21:34:12.846135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:34:12.846739 INFO::Using default BPPARAM
2026-02-24 21:34:12.847237 INFO::Processing subtree level 1
2026-02-24 21:34:12.949167 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:34:12.951616 INFO::Done
2026-02-24 21:34:12.952563 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:34:12.957124 INFO::ASW Batch was 0.125507116519662 prior to batch effect correction and is now -0.147699841873536 .
2026-02-24 21:34:12.958079 INFO::ASW Label was -0.173885045325845 prior to batch effect correction and is now 0.110318444045005 .
2026-02-24 21:34:12.959369 INFO::Total function execution time is 0.12427830696106 s and adjustment time is 0.106051445007324 s ( 85.33 )
2026-02-24 21:34:13.10272 INFO::Formatting Data.
2026-02-24 21:34:13.103449 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.104306 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.105279 INFO::Found 2 missing values.
2026-02-24 21:34:13.107965 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.108474 INFO::Done
2026-02-24 21:34:13.134737 INFO::Found NA in Reference column
2026-02-24 21:34:13.143772 INFO::Require at least two references per batch.
2026-02-24 21:34:13.16299 INFO::Formatting Data.
2026-02-24 21:34:13.16369 INFO::Recognized SummarizedExperiment
2026-02-24 21:34:13.164184 INFO::Typecasting input to dataframe.
2026-02-24 21:34:13.173278 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.174413 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.177797 INFO::Found 0 missing values.
2026-02-24 21:34:13.184128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.184751 INFO::Done
2026-02-24 21:34:13.199665 INFO::Formatting Data.
2026-02-24 21:34:13.200352 INFO::Recognized SummarizedExperiment
2026-02-24 21:34:13.200871 INFO::Typecasting input to dataframe.
2026-02-24 21:34:13.217276 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.218432 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.221694 INFO::Found 0 missing values.
2026-02-24 21:34:13.231595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.2322 INFO::Done
2026-02-24 21:34:13.246639 INFO::Formatting Data.
2026-02-24 21:34:13.247313 INFO::Recognized SummarizedExperiment
2026-02-24 21:34:13.247819 INFO::Typecasting input to dataframe.
2026-02-24 21:34:13.263437 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.26439 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.265381 INFO::Found 0 missing values.
2026-02-24 21:34:13.266237 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.
2026-02-24 21:34:13.270229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.270736 INFO::Done
2026-02-24 21:34:13.279933 INFO::Formatting Data.
2026-02-24 21:34:13.280641 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.281441 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.28237 INFO::Found 0 missing values.
2026-02-24 21:34:13.285024 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.285524 INFO::Done
2026-02-24 21:34:13.295905 INFO::Formatting Data.
2026-02-24 21:34:13.296666 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.29766 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.298617 INFO::Found 0 missing values.
2026-02-24 21:34:13.301308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.301826 INFO::Done
2026-02-24 21:34:13.329587 INFO::Formatting Data.
2026-02-24 21:34:13.330365 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.331383 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.332527 INFO::Found 1 missing values.
2026-02-24 21:34:13.335078 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.335607 INFO::Done
2026-02-24 21:34:13.353828 INFO::Formatting Data.
2026-02-24 21:34:13.354645 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.355483 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.356393 INFO::Found 2 missing values.
2026-02-24 21:34:13.357273 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.
2026-02-24 21:34:13.359405 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.35993 INFO::Done
2026-02-24 21:34:13.36929 INFO::Formatting Data.
2026-02-24 21:34:13.370012 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.370849 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.371803 INFO::Found 2 missing values.
2026-02-24 21:34:13.373327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.373836 INFO::Done
2026-02-24 21:34:13.38341 INFO::Formatting Data.
2026-02-24 21:34:13.384104 INFO::Typecasting input to dataframe.
2026-02-24 21:34:13.384859 INFO::Replacing NaNs with NAs.
2026-02-24 21:34:13.385658 INFO::Removing potential empty rows and columns
2026-02-24 21:34:13.38666 INFO::Found 0 missing values.
2026-02-24 21:34:13.389351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:34:13.389863 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.103 3.311 20.170
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.601 | 1.495 | 18.657 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.014 | 0.000 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.010 | 0.002 | 0.012 | |