Yannis Schumann
| Snapshot Date: 2026-02-18 13:45 -0500 (Wed, 18 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 2026-02-19 11:57 -0500 (Thu, 19 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" | 4890 |
| 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: 2026-02-18 21:42:47 -0500 (Wed, 18 Feb 2026) |
| EndedAt: 2026-02-18 21:44:17 -0500 (Wed, 18 Feb 2026) |
| EllapsedTime: 89.7 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 24.758 1.319 18.312
* 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")
2026-02-18 21:43:39.807041 INFO::Formatting Data.
2026-02-18 21:43:39.808385 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:39.819139 INFO::Removing potential empty rows and columns
2026-02-18 21:43:40.050527 INFO::Found 0 missing values.
2026-02-18 21:43:40.053644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:40.054228 INFO::Done
2026-02-18 21:43:40.054739 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:40.065114 INFO::Starting hierarchical adjustment
2026-02-18 21:43:40.06589 INFO::Found 3 batches.
2026-02-18 21:43:40.066396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:40.067443 INFO::Using default BPPARAM
2026-02-18 21:43:40.067989 INFO::Processing subtree level 1
2026-02-18 21:43:40.174044 INFO::Adjusting the last 1 batches sequentially
2026-02-18 21:43:40.176009 INFO::Done
2026-02-18 21:43:40.176686 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:40.179383 INFO::ASW Batch was -0.0821083344925321 prior to batch effect correction and is now -0.0821083344925321 .
2026-02-18 21:43:40.180521 INFO::Total function execution time is 0.374133586883545 s and adjustment time is 0.110267639160156 s ( 29.47 )
2026-02-18 21:43:40.195601 INFO::Formatting Data.
2026-02-18 21:43:40.196456 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:40.197497 INFO::Removing potential empty rows and columns
2026-02-18 21:43:40.198847 INFO::Found 0 missing values.
2026-02-18 21:43:40.199882 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.
2026-02-18 21:43:40.211919 INFO::Formatting Data.
2026-02-18 21:43:40.212775 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:40.213741 INFO::Removing potential empty rows and columns
2026-02-18 21:43:40.214833 INFO::Found 0 missing values.
2026-02-18 21:43:40.215816 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.
2026-02-18 21:43:40.233389 INFO::Formatting Data.
2026-02-18 21:43:40.23422 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:40.235141 INFO::Removing potential empty rows and columns
2026-02-18 21:43:40.236205 INFO::Found 0 missing values.
2026-02-18 21:43:40.237147 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.
2026-02-18 21:43:40.241464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:40.242 INFO::Done
2026-02-18 21:43:40.242491 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:40.244439 INFO::Starting hierarchical adjustment
2026-02-18 21:43:40.245125 INFO::Found 2 batches.
2026-02-18 21:43:40.245651 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:40.246249 INFO::Using default BPPARAM
2026-02-18 21:43:40.246762 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:40.247644 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-18 21:43:40.269086 INFO::Done
2026-02-18 21:43:40.269814 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:40.27204 INFO::ASW Batch was 0.000233689515601923 prior to batch effect correction and is now -0.0946801915950499 .
2026-02-18 21:43:40.272893 INFO::Total function execution time is 0.0396039485931396 s and adjustment time is 0.0240573883056641 s ( 60.74 )
2026-02-18 21:43:40.275763 INFO::Formatting Data.
2026-02-18 21:43:40.276392 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:40.285215 INFO::Formatting Data.
2026-02-18 21:43:40.285958 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:40.286837 INFO::Removing potential empty rows and columns
2026-02-18 21:43:40.287888 INFO::Found 0 missing values.
2026-02-18 21:43:40.290832 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:40.291383 INFO::Done
2026-02-18 21:43:40.291925 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:40.315374 INFO::Starting hierarchical adjustment
2026-02-18 21:43:40.317821 INFO::Found 2 batches.
2026-02-18 21:43:40.318371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:40.31892 INFO::Using default BPPARAM
2026-02-18 21:43:40.319404 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:40.32027 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-18 21:43:40.333794 INFO::Done
2026-02-18 21:43:40.334397 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:40.336281 INFO::ASW Batch was -0.0198862344275761 prior to batch effect correction and is now -0.113612499987563 .
2026-02-18 21:43:40.337007 INFO::Total function execution time is 0.0518534183502197 s and adjustment time is 0.0161519050598145 s ( 31.15 )
2026-02-18 21:43:40.337964 INFO::Formatting Data.
2026-02-18 21:43:40.338529 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:40.339302 INFO::Removing potential empty rows and columns
2026-02-18 21:43:40.340222 INFO::Found 0 missing values.
2026-02-18 21:43:40.342763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:40.343251 INFO::Done
2026-02-18 21:43:40.343726 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:40.345574 INFO::Starting hierarchical adjustment
2026-02-18 21:43:40.346226 INFO::Found 2 batches.
2026-02-18 21:43:40.346716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:40.347271 INFO::Using default BPPARAM
2026-02-18 21:43:40.347768 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:40.348584 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-18 21:43:40.362267 INFO::Done
2026-02-18 21:43:40.362898 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:40.364775 INFO::ASW Batch was -0.0198862344275761 prior to batch effect correction and is now -0.113612499987563 .
2026-02-18 21:43:40.365494 INFO::Total function execution time is 0.0275242328643799 s and adjustment time is 0.0161604881286621 s ( 58.71 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-18 21:43:43.223866 INFO::Formatting Data.
2026-02-18 21:43:43.224686 INFO::Recognized SummarizedExperiment
2026-02-18 21:43:43.225207 INFO::Typecasting input to dataframe.
2026-02-18 21:43:43.256792 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:43.258063 INFO::Removing potential empty rows and columns
2026-02-18 21:43:43.261877 INFO::Found 0 missing values.
2026-02-18 21:43:43.268912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:43.269521 INFO::Done
2026-02-18 21:43:43.270049 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:43.273711 INFO::Starting hierarchical adjustment
2026-02-18 21:43:43.27441 INFO::Found 2 batches.
2026-02-18 21:43:43.274942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:43.275993 INFO::Using default BPPARAM
2026-02-18 21:43:43.276528 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:43.277485 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-18 21:43:43.332501 INFO::Done
2026-02-18 21:43:43.333189 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:43.336711 INFO::ASW Batch was -0.00415614405028373 prior to batch effect correction and is now -0.0908666523332914 .
2026-02-18 21:43:43.337533 INFO::Total function execution time is 0.114000797271729 s and adjustment time is 0.0581963062286377 s ( 51.05 )
Warning: stack imbalance in '{', 73 then 75
2026-02-18 21:43:43.355961 INFO::Formatting Data.
2026-02-18 21:43:43.35667 INFO::Recognized SummarizedExperiment
2026-02-18 21:43:43.357189 INFO::Typecasting input to dataframe.
2026-02-18 21:43:43.366181 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:43.367272 INFO::Removing potential empty rows and columns
2026-02-18 21:43:43.370898 INFO::Found 0 missing values.
2026-02-18 21:43:43.377912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:43.378495 INFO::Done
2026-02-18 21:43:43.379014 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:43.382532 INFO::Starting hierarchical adjustment
2026-02-18 21:43:43.383232 INFO::Found 2 batches.
2026-02-18 21:43:43.383758 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:43.384347 INFO::Using default BPPARAM
2026-02-18 21:43:43.384873 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:43.385821 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-18 21:43:43.410751 INFO::Done
2026-02-18 21:43:43.411476 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:43.415081 INFO::ASW Batch was -0.00953323332274358 prior to batch effect correction and is now -0.00953323332274358 .
2026-02-18 21:43:43.415911 INFO::Total function execution time is 0.0599355697631836 s and adjustment time is 0.0276114940643311 s ( 46.07 )
2026-02-18 21:43:43.434164 INFO::Formatting Data.
2026-02-18 21:43:43.434953 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:43.435842 INFO::Removing potential empty rows and columns
2026-02-18 21:43:43.436864 INFO::Found 0 missing values.
2026-02-18 21:43:43.439845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:43.440366 INFO::Done
2026-02-18 21:43:43.440882 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:43.442863 INFO::Starting hierarchical adjustment
2026-02-18 21:43:43.443562 INFO::Found 3 batches.
2026-02-18 21:43:43.444083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:43.44467 INFO::Using default BPPARAM
2026-02-18 21:43:43.445203 INFO::Processing subtree level 1
2026-02-18 21:43:43.579448 INFO::Adjusting the last 1 batches sequentially
2026-02-18 21:43:43.581234 INFO::Done
2026-02-18 21:43:43.581898 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:43.584358 INFO::ASW Batch was 0.00508885588271685 prior to batch effect correction and is now -0.190351454719578 .
2026-02-18 21:43:43.585302 INFO::Total function execution time is 0.151159763336182 s and adjustment time is 0.137801170349121 s ( 91.16 )
2026-02-18 21:43:43.599867 INFO::Skipping initial DF formatting
2026-02-18 21:43:43.600524 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:43.604591 INFO::Starting hierarchical adjustment
2026-02-18 21:43:43.605351 INFO::Found 5 batches.
2026-02-18 21:43:43.605898 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:43.60653 INFO::Using default BPPARAM
2026-02-18 21:43:43.607064 INFO::Processing subtree level 1
2026-02-18 21:43:43.904696 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:43.906633 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-18 21:43:43.927913 INFO::Done
2026-02-18 21:43:43.928778 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:43.933342 INFO::ASW Batch was 0.526650479518012 prior to batch effect correction and is now 0.526650479518012 .
2026-02-18 21:43:43.934036 INFO::ASW Label was 0.330822888093941 prior to batch effect correction and is now 0.330822888093941 .
2026-02-18 21:43:43.934913 INFO::Total function execution time is 0.335098028182983 s and adjustment time is 0.322643280029297 s ( 96.28 )
2026-02-18 21:43:44.004786 INFO::Formatting Data.
2026-02-18 21:43:44.005755 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.006908 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.008116 INFO::Found 0 missing values.
2026-02-18 21:43:44.013187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.013844 INFO::Done
2026-02-18 21:43:44.014387 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.017675 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.018406 INFO::Found 5 batches.
2026-02-18 21:43:44.018944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.019591 INFO::Using default BPPARAM
2026-02-18 21:43:44.020147 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.
2026-02-18 21:43:44.167474 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.169234 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-18 21:43:44.187405 INFO::Done
2026-02-18 21:43:44.188196 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:44.191922 INFO::ASW Batch was 0.391841403626267 prior to batch effect correction and is now -0.100903163400102 .
2026-02-18 21:43:44.192585 INFO::ASW Label was 0.335282753388267 prior to batch effect correction and is now 0.816752881066996 .
2026-02-18 21:43:44.193441 INFO::Total function execution time is 0.188829183578491 s and adjustment time is 0.16911244392395 s ( 89.56 )
2026-02-18 21:43:44.19439 INFO::Formatting Data.
2026-02-18 21:43:44.195066 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.196029 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.197169 INFO::Found 0 missing values.
2026-02-18 21:43:44.201883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.202574 INFO::Done
2026-02-18 21:43:44.203196 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.206415 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.207164 INFO::Found 5 batches.
2026-02-18 21:43:44.207704 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.208346 INFO::Using default BPPARAM
2026-02-18 21:43:44.208888 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.
2026-02-18 21:43:44.340251 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.342035 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-18 21:43:44.359722 INFO::Done
2026-02-18 21:43:44.360552 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:44.364372 INFO::ASW Batch was 0.391841403626267 prior to batch effect correction and is now -0.100903163400102 .
2026-02-18 21:43:44.36506 INFO::ASW Label was 0.335282753388267 prior to batch effect correction and is now 0.816752881066996 .
2026-02-18 21:43:44.365921 INFO::Total function execution time is 0.171544551849365 s and adjustment time is 0.152638912200928 s ( 88.98 )
2026-02-18 21:43:44.381368 INFO::Formatting Data.
2026-02-18 21:43:44.382262 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.383282 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.3844 INFO::Found 0 missing values.
2026-02-18 21:43:44.388911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.389559 INFO::Done
2026-02-18 21:43:44.390124 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.393703 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.394488 INFO::Found 5 batches.
2026-02-18 21:43:44.395056 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.395713 INFO::Using default BPPARAM
2026-02-18 21:43:44.39625 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.
2026-02-18 21:43:44.537548 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.539321 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-18 21:43:44.556748 INFO::Done
2026-02-18 21:43:44.557612 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:44.561578 INFO::ASW Batch was 0.363986335745779 prior to batch effect correction and is now -0.0934091636675756 .
2026-02-18 21:43:44.562292 INFO::ASW Label was 0.277552599020165 prior to batch effect correction and is now 0.886479079813877 .
2026-02-18 21:43:44.563246 INFO::Total function execution time is 0.181962251663208 s and adjustment time is 0.162356376647949 s ( 89.23 )
2026-02-18 21:43:44.564181 INFO::Formatting Data.
2026-02-18 21:43:44.56487 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.565883 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.566981 INFO::Found 0 missing values.
2026-02-18 21:43:44.585025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.587101 INFO::Done
2026-02-18 21:43:44.587789 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.593488 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.594541 INFO::Found 5 batches.
2026-02-18 21:43:44.595166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.596014 INFO::Using default BPPARAM
2026-02-18 21:43:44.596646 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.
2026-02-18 21:43:44.762431 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.76443 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-18 21:43:44.782923 INFO::Done
2026-02-18 21:43:44.783752 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:44.787543 INFO::ASW Batch was 0.363986335745779 prior to batch effect correction and is now -0.0934091636675756 .
2026-02-18 21:43:44.788282 INFO::ASW Label was 0.277552599020165 prior to batch effect correction and is now 0.886479079813877 .
2026-02-18 21:43:44.789443 INFO::Total function execution time is 0.225218057632446 s and adjustment time is 0.188615560531616 s ( 83.75 )
2026-02-18 21:43:44.806151 INFO::Formatting Data.
2026-02-18 21:43:44.807039 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.808087 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.809248 INFO::Found 0 missing values.
2026-02-18 21:43:44.812294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.812907 INFO::Done
2026-02-18 21:43:44.813467 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.816739 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.81753 INFO::Found 2 batches.
2026-02-18 21:43:44.818107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.818779 INFO::Using default BPPARAM
2026-02-18 21:43:44.819345 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.820357 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-18 21:43:44.836181 INFO::Done
2026-02-18 21:43:44.836902 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:44.84011 INFO::ASW Batch was 0.762890143255101 prior to batch effect correction and is now 0.0451501823913821 .
2026-02-18 21:43:44.840765 INFO::ASW Label was 0.288466532068337 prior to batch effect correction and is now 0.778457544451673 .
2026-02-18 21:43:44.841626 INFO::Total function execution time is 0.0355880260467529 s and adjustment time is 0.0188043117523193 s ( 52.84 )
2026-02-18 21:43:44.842489 INFO::Formatting Data.
2026-02-18 21:43:44.843163 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.844071 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.845119 INFO::Found 0 missing values.
2026-02-18 21:43:44.847936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.848487 INFO::Done
2026-02-18 21:43:44.849024 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.852171 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.852924 INFO::Found 2 batches.
2026-02-18 21:43:44.853449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.854081 INFO::Using default BPPARAM
2026-02-18 21:43:44.854594 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.855519 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-18 21:43:44.870649 INFO::Done
2026-02-18 21:43:44.871278 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:44.874273 INFO::ASW Batch was 0.762890143255101 prior to batch effect correction and is now 0.0451501823913821 .
2026-02-18 21:43:44.874863 INFO::ASW Label was 0.288466532068337 prior to batch effect correction and is now 0.778457544451673 .
2026-02-18 21:43:44.875665 INFO::Total function execution time is 0.0331907272338867 s and adjustment time is 0.0178561210632324 s ( 53.8 )
2026-02-18 21:43:44.88692 INFO::Formatting Data.
2026-02-18 21:43:44.887667 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.888574 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.889472 INFO::Found 0 missing values.
2026-02-18 21:43:44.891583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.892101 INFO::Done
2026-02-18 21:43:44.892617 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.89456 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.895258 INFO::Found 2 batches.
2026-02-18 21:43:44.895778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.896361 INFO::Using default BPPARAM
2026-02-18 21:43:44.896899 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.897781 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-18 21:43:44.929502 INFO::Done
2026-02-18 21:43:44.930265 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:44.932327 INFO::ASW Batch was -0.0153916055110327 prior to batch effect correction and is now -0.160744870848107 .
2026-02-18 21:43:44.933174 INFO::Total function execution time is 0.0463438034057617 s and adjustment time is 0.0343360900878906 s ( 74.09 )
2026-02-18 21:43:44.945279 INFO::Formatting Data.
2026-02-18 21:43:44.946093 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.946999 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.948018 INFO::Found 0 missing values.
2026-02-18 21:43:44.949232 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.
2026-02-18 21:43:44.95378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.954327 INFO::Done
2026-02-18 21:43:44.954856 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.957807 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.9585 INFO::Found 2 batches.
2026-02-18 21:43:44.959038 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.95963 INFO::Using default BPPARAM
2026-02-18 21:43:44.960134 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.961035 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-18 21:43:44.977526 INFO::Done
2026-02-18 21:43:44.978195 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:44.981153 INFO::ASW Batch was 0.269366838736239 prior to batch effect correction and is now 0.0919777745365252 .
2026-02-18 21:43:44.98174 INFO::ASW Label was 0.818810331914382 prior to batch effect correction and is now 0.891969426195438 .
2026-02-18 21:43:44.982491 INFO::Total function execution time is 0.0373373031616211 s and adjustment time is 0.0191292762756348 s ( 51.23 )
2026-02-18 21:43:44.983277 INFO::Formatting Data.
2026-02-18 21:43:44.983896 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:44.984795 INFO::Removing potential empty rows and columns
2026-02-18 21:43:44.985759 INFO::Found 0 missing values.
2026-02-18 21:43:44.98667 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.
2026-02-18 21:43:44.991089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:44.99163 INFO::Done
2026-02-18 21:43:44.992131 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:44.995058 INFO::Starting hierarchical adjustment
2026-02-18 21:43:44.995751 INFO::Found 2 batches.
2026-02-18 21:43:44.996261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:44.996863 INFO::Using default BPPARAM
2026-02-18 21:43:44.997349 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:44.99824 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-18 21:43:45.014792 INFO::Done
2026-02-18 21:43:45.015464 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:45.018441 INFO::ASW Batch was 0.269366838736239 prior to batch effect correction and is now 0.0919777745365252 .
2026-02-18 21:43:45.019023 INFO::ASW Label was 0.818810331914382 prior to batch effect correction and is now 0.891969426195438 .
2026-02-18 21:43:45.019813 INFO::Total function execution time is 0.0365545749664307 s and adjustment time is 0.0191555023193359 s ( 52.4 )
2026-02-18 21:43:45.229322 INFO::Formatting Data.
2026-02-18 21:43:45.230219 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:45.231174 INFO::Removing potential empty rows and columns
2026-02-18 21:43:45.232247 INFO::Found 0 missing values.
2026-02-18 21:43:45.235404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:45.23596 INFO::Done
2026-02-18 21:43:45.236469 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:45.238606 INFO::Starting hierarchical adjustment
2026-02-18 21:43:45.239311 INFO::Found 3 batches.
2026-02-18 21:43:45.239856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:45.240458 INFO::Using default BPPARAM
2026-02-18 21:43:45.241004 INFO::Processing subtree level 1
2026-02-18 21:43:45.330632 INFO::Adjusting the last 1 batches sequentially
2026-02-18 21:43:45.332603 INFO::Done
2026-02-18 21:43:45.333277 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:45.335873 INFO::ASW Batch was -0.0313869575532458 prior to batch effect correction and is now -0.0313869575532458 .
2026-02-18 21:43:45.336862 INFO::Total function execution time is 0.107637405395508 s and adjustment time is 0.0933980941772461 s ( 86.77 )
2026-02-18 21:43:45.337915 INFO::Formatting Data.
2026-02-18 21:43:45.338573 INFO::Typecasting input to dataframe.
2026-02-18 21:43:45.339329 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:45.340286 INFO::Removing potential empty rows and columns
2026-02-18 21:43:45.341396 INFO::Found 0 missing values.
2026-02-18 21:43:45.344622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:45.345174 INFO::Done
2026-02-18 21:43:45.345711 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:45.355051 INFO::Starting hierarchical adjustment
2026-02-18 21:43:45.35596 INFO::Found 3 batches.
2026-02-18 21:43:45.356498 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:45.357167 INFO::Using default BPPARAM
2026-02-18 21:43:45.357707 INFO::Processing subtree level 1
2026-02-18 21:43:45.451045 INFO::Adjusting the last 1 batches sequentially
2026-02-18 21:43:45.452985 INFO::Done
2026-02-18 21:43:45.453707 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:45.456407 INFO::ASW Batch was -0.0313869575532458 prior to batch effect correction and is now -0.0313869575532458 .
2026-02-18 21:43:45.457519 INFO::Total function execution time is 0.119534492492676 s and adjustment time is 0.0971915721893311 s ( 81.31 )
2026-02-18 21:43:45.472844 INFO::Formatting Data.
2026-02-18 21:43:45.473742 INFO::Typecasting input to dataframe.
2026-02-18 21:43:45.474667 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:45.475656 INFO::Removing potential empty rows and columns
2026-02-18 21:43:45.476849 INFO::Found 0 missing values.
2026-02-18 21:43:45.480002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:45.480551 INFO::Done
2026-02-18 21:43:45.481076 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:45.483339 INFO::Starting hierarchical adjustment
2026-02-18 21:43:45.484087 INFO::Found 3 batches.
2026-02-18 21:43:45.484633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:45.485275 INFO::Using default BPPARAM
2026-02-18 21:43:45.485823 INFO::Processing subtree level 1
2026-02-18 21:43:45.575545 INFO::Adjusting the last 1 batches sequentially
2026-02-18 21:43:45.577539 INFO::Done
2026-02-18 21:43:45.578201 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:45.580895 INFO::ASW Batch was -0.00180320046508651 prior to batch effect correction and is now -0.00180320046508651 .
2026-02-18 21:43:45.581869 INFO::Total function execution time is 0.109152793884277 s and adjustment time is 0.0935766696929932 s ( 85.73 )
2026-02-18 21:43:45.720487 INFO::Formatting Data.
2026-02-18 21:43:45.721253 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:45.722362 INFO::Removing potential empty rows and columns
2026-02-18 21:43:45.725118 INFO::Found 1000 missing values.
2026-02-18 21:43:45.743912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:45.744716 INFO::Done
2026-02-18 21:43:45.745267 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:45.750921 INFO::Starting hierarchical adjustment
2026-02-18 21:43:45.751726 INFO::Found 10 batches.
2026-02-18 21:43:45.752273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:45.752898 INFO::Using default BPPARAM
2026-02-18 21:43:45.753432 INFO::Processing subtree level 1
2026-02-18 21:43:45.887492 INFO::Processing subtree level 2
2026-02-18 21:43:46.029971 INFO::Adjusting the last 1 batches sequentially
2026-02-18 21:43:46.032995 INFO::Done
2026-02-18 21:43:46.034046 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:46.042743 INFO::ASW Batch was 0.474974054678561 prior to batch effect correction and is now 0.474974054678561 .
2026-02-18 21:43:46.043623 INFO::ASW Label was 0.36383757788929 prior to batch effect correction and is now 0.36383757788929 .
2026-02-18 21:43:46.044613 INFO::Total function execution time is 0.324166297912598 s and adjustment time is 0.281368255615234 s ( 86.8 )
2026-02-18 21:43:46.045456 INFO::Formatting Data.
2026-02-18 21:43:46.046209 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:46.047471 INFO::Removing potential empty rows and columns
2026-02-18 21:43:46.051673 INFO::Found 1000 missing values.
2026-02-18 21:43:46.082975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:46.084234 INFO::Done
2026-02-18 21:43:46.085173 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:46.094095 INFO::Starting hierarchical adjustment
2026-02-18 21:43:46.095299 INFO::Found 10 batches.
2026-02-18 21:43:47.332277 INFO::Set up parallel execution backend with 2 workers
2026-02-18 21:43:47.334467 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-18 21:43:48.415106 INFO::Adjusting the last 2 batches sequentially
2026-02-18 21:43:48.416845 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-18 21:43:48.432394 INFO::Done
2026-02-18 21:43:48.432997 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:48.437287 INFO::ASW Batch was 0.474974054678561 prior to batch effect correction and is now 0.474974054678561 .
2026-02-18 21:43:48.437808 INFO::ASW Label was 0.36383757788929 prior to batch effect correction and is now 0.36383757788929 .
2026-02-18 21:43:48.438495 INFO::Total function execution time is 2.39309406280518 s and adjustment time is 2.33737850189209 s ( 97.67 )
2026-02-18 21:43:48.580962 INFO::Formatting Data.
2026-02-18 21:43:48.581746 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:48.582655 INFO::Removing potential empty rows and columns
2026-02-18 21:43:48.583719 INFO::Found 0 missing values.
2026-02-18 21:43:48.587242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:48.587774 INFO::Done
2026-02-18 21:43:48.588263 INFO::Acquiring quality metrics before batch effect correction.
2026-02-18 21:43:48.590983 INFO::Starting hierarchical adjustment
2026-02-18 21:43:48.591668 INFO::Found 3 batches.
2026-02-18 21:43:48.592177 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-18 21:43:48.592772 INFO::Using default BPPARAM
2026-02-18 21:43:48.593279 INFO::Processing subtree level 1
2026-02-18 21:43:48.700286 INFO::Adjusting the last 1 batches sequentially
2026-02-18 21:43:48.701968 INFO::Done
2026-02-18 21:43:48.702582 INFO::Acquiring quality metrics after batch effect correction.
2026-02-18 21:43:48.705683 INFO::ASW Batch was 0.212535966369119 prior to batch effect correction and is now -0.155407393395724 .
2026-02-18 21:43:48.706261 INFO::ASW Label was -0.174582914973042 prior to batch effect correction and is now 0.0453418075936578 .
2026-02-18 21:43:48.707138 INFO::Total function execution time is 0.126233339309692 s and adjustment time is 0.11042857170105 s ( 87.48 )
2026-02-18 21:43:48.819907 INFO::Formatting Data.
2026-02-18 21:43:48.820684 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:48.821547 INFO::Removing potential empty rows and columns
2026-02-18 21:43:48.822532 INFO::Found 2 missing values.
2026-02-18 21:43:48.825185 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:48.825694 INFO::Done
2026-02-18 21:43:48.850826 INFO::Found NA in Reference column
2026-02-18 21:43:48.859686 INFO::Require at least two references per batch.
2026-02-18 21:43:48.878653 INFO::Formatting Data.
2026-02-18 21:43:48.879328 INFO::Recognized SummarizedExperiment
2026-02-18 21:43:48.879832 INFO::Typecasting input to dataframe.
2026-02-18 21:43:48.888819 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:48.889874 INFO::Removing potential empty rows and columns
2026-02-18 21:43:48.89307 INFO::Found 0 missing values.
2026-02-18 21:43:48.899328 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:48.899867 INFO::Done
2026-02-18 21:43:48.923679 INFO::Formatting Data.
2026-02-18 21:43:48.924409 INFO::Recognized SummarizedExperiment
2026-02-18 21:43:48.924945 INFO::Typecasting input to dataframe.
2026-02-18 21:43:48.942693 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:48.943946 INFO::Removing potential empty rows and columns
2026-02-18 21:43:48.947666 INFO::Found 0 missing values.
2026-02-18 21:43:48.958955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:48.959588 INFO::Done
2026-02-18 21:43:48.975672 INFO::Formatting Data.
2026-02-18 21:43:48.976418 INFO::Recognized SummarizedExperiment
2026-02-18 21:43:48.976966 INFO::Typecasting input to dataframe.
2026-02-18 21:43:48.994131 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:48.995169 INFO::Removing potential empty rows and columns
2026-02-18 21:43:48.996261 INFO::Found 0 missing values.
2026-02-18 21:43:48.997182 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.
2026-02-18 21:43:49.001608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:49.002144 INFO::Done
2026-02-18 21:43:49.01235 INFO::Formatting Data.
2026-02-18 21:43:49.013146 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:49.013991 INFO::Removing potential empty rows and columns
2026-02-18 21:43:49.014962 INFO::Found 0 missing values.
2026-02-18 21:43:49.017804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:49.018336 INFO::Done
2026-02-18 21:43:49.029594 INFO::Formatting Data.
2026-02-18 21:43:49.030368 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:49.031441 INFO::Removing potential empty rows and columns
2026-02-18 21:43:49.032405 INFO::Found 0 missing values.
2026-02-18 21:43:49.035189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:49.035719 INFO::Done
2026-02-18 21:43:49.064358 INFO::Formatting Data.
2026-02-18 21:43:49.065252 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:49.066278 INFO::Removing potential empty rows and columns
2026-02-18 21:43:49.067426 INFO::Found 1 missing values.
2026-02-18 21:43:49.07 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:49.070548 INFO::Done
2026-02-18 21:43:49.089358 INFO::Formatting Data.
2026-02-18 21:43:49.090148 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:49.091082 INFO::Removing potential empty rows and columns
2026-02-18 21:43:49.092001 INFO::Found 2 missing values.
2026-02-18 21:43:49.092903 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.
2026-02-18 21:43:49.095131 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:49.095658 INFO::Done
2026-02-18 21:43:49.105444 INFO::Formatting Data.
2026-02-18 21:43:49.106217 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:49.107061 INFO::Removing potential empty rows and columns
2026-02-18 21:43:49.107978 INFO::Found 2 missing values.
2026-02-18 21:43:49.109571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:49.11007 INFO::Done
2026-02-18 21:43:49.120086 INFO::Formatting Data.
2026-02-18 21:43:49.120786 INFO::Typecasting input to dataframe.
2026-02-18 21:43:49.121547 INFO::Replacing NaNs with NAs.
2026-02-18 21:43:49.122355 INFO::Removing potential empty rows and columns
2026-02-18 21:43:49.12332 INFO::Found 0 missing values.
2026-02-18 21:43:49.1261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-18 21:43:49.126626 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.536 3.833 21.006
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.758 | 1.319 | 18.312 | |
| compute_asw | 0.025 | 0.001 | 0.026 | |
| count_existing | 0.013 | 0.002 | 0.015 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.008 | 0.003 | 0.012 | |