Yannis Schumann
| Snapshot Date: 2026-02-17 13:40 -0500 (Tue, 17 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-18 11:32 -0500 (Wed, 18 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4867 |
| 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 169/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-17 21:33:43 -0500 (Tue, 17 Feb 2026) |
| EndedAt: 2026-02-17 21:35:12 -0500 (Tue, 17 Feb 2026) |
| EllapsedTime: 89.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.7.0’
* 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 23.762 1.78 17.948
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-17 21:34:35.355155 INFO::Formatting Data.
2026-02-17 21:34:35.356395 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:35.367706 INFO::Removing potential empty rows and columns
2026-02-17 21:34:35.600698 INFO::Found 0 missing values.
2026-02-17 21:34:35.603942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:35.604561 INFO::Done
2026-02-17 21:34:35.605099 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:35.61569 INFO::Starting hierarchical adjustment
2026-02-17 21:34:35.61647 INFO::Found 3 batches.
2026-02-17 21:34:35.616995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:35.61805 INFO::Using default BPPARAM
2026-02-17 21:34:35.618602 INFO::Processing subtree level 1
2026-02-17 21:34:35.713661 INFO::Adjusting the last 1 batches sequentially
2026-02-17 21:34:35.715464 INFO::Done
2026-02-17 21:34:35.716109 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:35.71859 INFO::ASW Batch was -0.0912898285795925 prior to batch effect correction and is now -0.0912898285795925 .
2026-02-17 21:34:35.71963 INFO::Total function execution time is 0.36505651473999 s and adjustment time is 0.0991401672363281 s ( 27.16 )
2026-02-17 21:34:35.732609 INFO::Formatting Data.
2026-02-17 21:34:35.733327 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:35.734242 INFO::Removing potential empty rows and columns
2026-02-17 21:34:35.735383 INFO::Found 0 missing values.
2026-02-17 21:34:35.736303 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.
2026-02-17 21:34:35.746696 INFO::Formatting Data.
2026-02-17 21:34:35.747381 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:35.748267 INFO::Removing potential empty rows and columns
2026-02-17 21:34:35.749328 INFO::Found 0 missing values.
2026-02-17 21:34:35.750214 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.
2026-02-17 21:34:35.765542 INFO::Formatting Data.
2026-02-17 21:34:35.766269 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:35.767124 INFO::Removing potential empty rows and columns
2026-02-17 21:34:35.768161 INFO::Found 0 missing values.
2026-02-17 21:34:35.769067 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.
2026-02-17 21:34:35.773413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:35.773967 INFO::Done
2026-02-17 21:34:35.774502 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:35.77649 INFO::Starting hierarchical adjustment
2026-02-17 21:34:35.777176 INFO::Found 2 batches.
2026-02-17 21:34:35.777729 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:35.778357 INFO::Using default BPPARAM
2026-02-17 21:34:35.778898 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:35.779793 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-17 21:34:35.799824 INFO::Done
2026-02-17 21:34:35.80056 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:35.802803 INFO::ASW Batch was 0.104944475429899 prior to batch effect correction and is now -0.129972496267427 .
2026-02-17 21:34:35.803633 INFO::Total function execution time is 0.0381338596343994 s and adjustment time is 0.0227580070495605 s ( 59.68 )
2026-02-17 21:34:35.806442 INFO::Formatting Data.
2026-02-17 21:34:35.807084 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:35.816144 INFO::Formatting Data.
2026-02-17 21:34:35.816858 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:35.817757 INFO::Removing potential empty rows and columns
2026-02-17 21:34:35.818811 INFO::Found 0 missing values.
2026-02-17 21:34:35.821795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:35.822345 INFO::Done
2026-02-17 21:34:35.822887 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:35.824923 INFO::Starting hierarchical adjustment
2026-02-17 21:34:35.825633 INFO::Found 2 batches.
2026-02-17 21:34:35.826174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:35.826817 INFO::Using default BPPARAM
2026-02-17 21:34:35.827358 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:35.828307 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-17 21:34:35.864509 INFO::Done
2026-02-17 21:34:35.865184 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:35.867111 INFO::ASW Batch was -0.0203406022742452 prior to batch effect correction and is now -0.117731164656464 .
2026-02-17 21:34:35.867899 INFO::Total function execution time is 0.0517761707305908 s and adjustment time is 0.0389974117279053 s ( 75.32 )
2026-02-17 21:34:35.868901 INFO::Formatting Data.
2026-02-17 21:34:35.869498 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:35.870313 INFO::Removing potential empty rows and columns
2026-02-17 21:34:35.871278 INFO::Found 0 missing values.
2026-02-17 21:34:35.873922 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:35.874458 INFO::Done
2026-02-17 21:34:35.874951 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:35.876785 INFO::Starting hierarchical adjustment
2026-02-17 21:34:35.877468 INFO::Found 2 batches.
2026-02-17 21:34:35.877965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:35.878551 INFO::Using default BPPARAM
2026-02-17 21:34:35.879041 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:35.879908 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-17 21:34:35.89364 INFO::Done
2026-02-17 21:34:35.894243 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:35.896118 INFO::ASW Batch was -0.0203406022742452 prior to batch effect correction and is now -0.117731164656464 .
2026-02-17 21:34:35.896884 INFO::Total function execution time is 0.0279736518859863 s and adjustment time is 0.0163156986236572 s ( 58.33 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-17 21:34:38.586905 INFO::Formatting Data.
2026-02-17 21:34:38.587609 INFO::Recognized SummarizedExperiment
2026-02-17 21:34:38.588108 INFO::Typecasting input to dataframe.
2026-02-17 21:34:38.617126 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:38.618298 INFO::Removing potential empty rows and columns
2026-02-17 21:34:38.622374 INFO::Found 0 missing values.
2026-02-17 21:34:38.629927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:38.630613 INFO::Done
2026-02-17 21:34:38.631163 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:38.634761 INFO::Starting hierarchical adjustment
2026-02-17 21:34:38.635528 INFO::Found 2 batches.
2026-02-17 21:34:38.636064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:38.637158 INFO::Using default BPPARAM
2026-02-17 21:34:38.637719 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:38.638705 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-17 21:34:38.694636 INFO::Done
2026-02-17 21:34:38.695343 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:38.69889 INFO::ASW Batch was -0.0135017611803695 prior to batch effect correction and is now -0.0931869523277174 .
2026-02-17 21:34:38.69974 INFO::Total function execution time is 0.113107204437256 s and adjustment time is 0.0592539310455322 s ( 52.39 )
Warning: stack imbalance in '{', 73 then 75
2026-02-17 21:34:38.717975 INFO::Formatting Data.
2026-02-17 21:34:38.718738 INFO::Recognized SummarizedExperiment
2026-02-17 21:34:38.719296 INFO::Typecasting input to dataframe.
2026-02-17 21:34:38.728557 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:38.729754 INFO::Removing potential empty rows and columns
2026-02-17 21:34:38.733636 INFO::Found 0 missing values.
2026-02-17 21:34:38.741115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:38.741767 INFO::Done
2026-02-17 21:34:38.742301 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:38.745928 INFO::Starting hierarchical adjustment
2026-02-17 21:34:38.746657 INFO::Found 2 batches.
2026-02-17 21:34:38.747185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:38.747822 INFO::Using default BPPARAM
2026-02-17 21:34:38.748356 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:38.749324 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-17 21:34:38.774894 INFO::Done
2026-02-17 21:34:38.775634 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:38.77917 INFO::ASW Batch was 0.011950171161205 prior to batch effect correction and is now 0.011950171161205 .
2026-02-17 21:34:38.780028 INFO::Total function execution time is 0.0620388984680176 s and adjustment time is 0.0283517837524414 s ( 45.7 )
2026-02-17 21:34:38.798321 INFO::Formatting Data.
2026-02-17 21:34:38.799157 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:38.800091 INFO::Removing potential empty rows and columns
2026-02-17 21:34:38.801135 INFO::Found 0 missing values.
2026-02-17 21:34:38.80416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:38.804714 INFO::Done
2026-02-17 21:34:38.805237 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:38.807294 INFO::Starting hierarchical adjustment
2026-02-17 21:34:38.808007 INFO::Found 3 batches.
2026-02-17 21:34:38.808552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:38.80915 INFO::Using default BPPARAM
2026-02-17 21:34:38.809699 INFO::Processing subtree level 1
2026-02-17 21:34:38.942247 INFO::Adjusting the last 1 batches sequentially
2026-02-17 21:34:38.944031 INFO::Done
2026-02-17 21:34:38.944683 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:38.947195 INFO::ASW Batch was -0.00902141346693466 prior to batch effect correction and is now -0.164746928914477 .
2026-02-17 21:34:38.948121 INFO::Total function execution time is 0.149849414825439 s and adjustment time is 0.136142730712891 s ( 90.85 )
2026-02-17 21:34:38.962147 INFO::Skipping initial DF formatting
2026-02-17 21:34:38.962847 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:38.966865 INFO::Starting hierarchical adjustment
2026-02-17 21:34:38.967658 INFO::Found 5 batches.
2026-02-17 21:34:38.968212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:38.968858 INFO::Using default BPPARAM
2026-02-17 21:34:38.969419 INFO::Processing subtree level 1
2026-02-17 21:34:39.181186 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:39.182754 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-17 21:34:39.202854 INFO::Done
2026-02-17 21:34:39.203622 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:39.249572 INFO::ASW Batch was 0.533632852104237 prior to batch effect correction and is now 0.533632852104237 .
2026-02-17 21:34:39.250297 INFO::ASW Label was 0.327366934931863 prior to batch effect correction and is now 0.327366934931863 .
2026-02-17 21:34:39.251126 INFO::Total function execution time is 0.289053440093994 s and adjustment time is 0.235332250595093 s ( 81.41 )
2026-02-17 21:34:39.267713 INFO::Formatting Data.
2026-02-17 21:34:39.268425 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:39.26932 INFO::Removing potential empty rows and columns
2026-02-17 21:34:39.270305 INFO::Found 0 missing values.
2026-02-17 21:34:39.274482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:39.27502 INFO::Done
2026-02-17 21:34:39.275544 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:39.278551 INFO::Starting hierarchical adjustment
2026-02-17 21:34:39.279242 INFO::Found 5 batches.
2026-02-17 21:34:39.279771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:39.280384 INFO::Using default BPPARAM
2026-02-17 21:34:39.280956 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.
2026-02-17 21:34:39.409159 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:39.410799 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-17 21:34:39.427758 INFO::Done
2026-02-17 21:34:39.428497 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:39.431804 INFO::ASW Batch was 0.325501002307348 prior to batch effect correction and is now -0.100955324585738 .
2026-02-17 21:34:39.432451 INFO::ASW Label was 0.482472647427332 prior to batch effect correction and is now 0.840224402650431 .
2026-02-17 21:34:39.433279 INFO::Total function execution time is 0.165607929229736 s and adjustment time is 0.148637294769287 s ( 89.75 )
2026-02-17 21:34:39.434121 INFO::Formatting Data.
2026-02-17 21:34:39.43482 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:39.435725 INFO::Removing potential empty rows and columns
2026-02-17 21:34:39.436814 INFO::Found 0 missing values.
2026-02-17 21:34:39.441023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:39.441605 INFO::Done
2026-02-17 21:34:39.442159 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:39.445215 INFO::Starting hierarchical adjustment
2026-02-17 21:34:39.445937 INFO::Found 5 batches.
2026-02-17 21:34:39.446478 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:39.447123 INFO::Using default BPPARAM
2026-02-17 21:34:39.447657 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.
2026-02-17 21:34:39.57128 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:39.572926 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-17 21:34:39.589013 INFO::Done
2026-02-17 21:34:39.589806 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:39.593137 INFO::ASW Batch was 0.325501002307348 prior to batch effect correction and is now -0.100955324585738 .
2026-02-17 21:34:39.593774 INFO::ASW Label was 0.482472647427332 prior to batch effect correction and is now 0.840224402650431 .
2026-02-17 21:34:39.594642 INFO::Total function execution time is 0.160516977310181 s and adjustment time is 0.143171548843384 s ( 89.19 )
2026-02-17 21:34:39.608206 INFO::Formatting Data.
2026-02-17 21:34:39.608963 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:39.609871 INFO::Removing potential empty rows and columns
2026-02-17 21:34:39.610893 INFO::Found 0 missing values.
2026-02-17 21:34:39.615093 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:39.615692 INFO::Done
2026-02-17 21:34:39.616219 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:39.61935 INFO::Starting hierarchical adjustment
2026-02-17 21:34:39.620096 INFO::Found 5 batches.
2026-02-17 21:34:39.620644 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:39.621286 INFO::Using default BPPARAM
2026-02-17 21:34:39.621865 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.
2026-02-17 21:34:39.754585 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:39.756179 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-17 21:34:39.771641 INFO::Done
2026-02-17 21:34:39.772399 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:39.775566 INFO::ASW Batch was 0.451649977238173 prior to batch effect correction and is now 0.022692930153321 .
2026-02-17 21:34:39.776189 INFO::ASW Label was 0.36480770900236 prior to batch effect correction and is now 0.754692950528808 .
2026-02-17 21:34:39.776983 INFO::Total function execution time is 0.168830633163452 s and adjustment time is 0.151667594909668 s ( 89.83 )
2026-02-17 21:34:39.777824 INFO::Formatting Data.
2026-02-17 21:34:39.778498 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:39.779356 INFO::Removing potential empty rows and columns
2026-02-17 21:34:39.780389 INFO::Found 0 missing values.
2026-02-17 21:34:39.784532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:39.785124 INFO::Done
2026-02-17 21:34:39.785766 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:39.788706 INFO::Starting hierarchical adjustment
2026-02-17 21:34:39.789436 INFO::Found 5 batches.
2026-02-17 21:34:39.789993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:39.790622 INFO::Using default BPPARAM
2026-02-17 21:34:39.791145 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.
2026-02-17 21:34:39.912479 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:39.914049 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-17 21:34:39.930094 INFO::Done
2026-02-17 21:34:39.930841 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:39.934434 INFO::ASW Batch was 0.451649977238173 prior to batch effect correction and is now 0.022692930153321 .
2026-02-17 21:34:39.935035 INFO::ASW Label was 0.36480770900236 prior to batch effect correction and is now 0.754692950528808 .
2026-02-17 21:34:39.935881 INFO::Total function execution time is 0.158054351806641 s and adjustment time is 0.140788555145264 s ( 89.08 )
2026-02-17 21:34:39.949163 INFO::Formatting Data.
2026-02-17 21:34:39.949922 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:39.950826 INFO::Removing potential empty rows and columns
2026-02-17 21:34:39.951836 INFO::Found 0 missing values.
2026-02-17 21:34:39.95451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:39.955072 INFO::Done
2026-02-17 21:34:39.955611 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:39.958532 INFO::Starting hierarchical adjustment
2026-02-17 21:34:39.959223 INFO::Found 2 batches.
2026-02-17 21:34:39.959768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:39.9604 INFO::Using default BPPARAM
2026-02-17 21:34:39.960949 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:39.96185 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-17 21:34:39.98766 INFO::Done
2026-02-17 21:34:39.988548 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:39.99169 INFO::ASW Batch was 0.624041729208889 prior to batch effect correction and is now 0.0279374563543859 .
2026-02-17 21:34:39.992283 INFO::ASW Label was 0.417075189943765 prior to batch effect correction and is now 0.895811785689729 .
2026-02-17 21:34:39.993118 INFO::Total function execution time is 0.0440199375152588 s and adjustment time is 0.0285196304321289 s ( 64.79 )
2026-02-17 21:34:39.993922 INFO::Formatting Data.
2026-02-17 21:34:39.994539 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:39.995412 INFO::Removing potential empty rows and columns
2026-02-17 21:34:39.996397 INFO::Found 0 missing values.
2026-02-17 21:34:39.998991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:39.999567 INFO::Done
2026-02-17 21:34:40.000084 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:40.002884 INFO::Starting hierarchical adjustment
2026-02-17 21:34:40.003586 INFO::Found 2 batches.
2026-02-17 21:34:40.004102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:40.004749 INFO::Using default BPPARAM
2026-02-17 21:34:40.005289 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:40.006175 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-17 21:34:40.020733 INFO::Done
2026-02-17 21:34:40.021389 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:40.024249 INFO::ASW Batch was 0.624041729208889 prior to batch effect correction and is now 0.0279374563543859 .
2026-02-17 21:34:40.024863 INFO::ASW Label was 0.417075189943765 prior to batch effect correction and is now 0.895811785689729 .
2026-02-17 21:34:40.025646 INFO::Total function execution time is 0.031733512878418 s and adjustment time is 0.0172851085662842 s ( 54.47 )
2026-02-17 21:34:40.038108 INFO::Formatting Data.
2026-02-17 21:34:40.038982 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:40.03992 INFO::Removing potential empty rows and columns
2026-02-17 21:34:40.040858 INFO::Found 0 missing values.
2026-02-17 21:34:40.043013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:40.043558 INFO::Done
2026-02-17 21:34:40.044079 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:40.046021 INFO::Starting hierarchical adjustment
2026-02-17 21:34:40.046748 INFO::Found 2 batches.
2026-02-17 21:34:40.04727 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:40.047886 INFO::Using default BPPARAM
2026-02-17 21:34:40.048442 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:40.049341 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-17 21:34:40.080229 INFO::Done
2026-02-17 21:34:40.080959 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:40.082883 INFO::ASW Batch was -0.174561985235406 prior to batch effect correction and is now -0.164450308163905 .
2026-02-17 21:34:40.083691 INFO::Total function execution time is 0.0456976890563965 s and adjustment time is 0.0336081981658936 s ( 73.54 )
2026-02-17 21:34:40.095128 INFO::Formatting Data.
2026-02-17 21:34:40.095854 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:40.096713 INFO::Removing potential empty rows and columns
2026-02-17 21:34:40.097683 INFO::Found 0 missing values.
2026-02-17 21:34:40.098818 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.
2026-02-17 21:34:40.103186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:40.103731 INFO::Done
2026-02-17 21:34:40.104232 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:40.10703 INFO::Starting hierarchical adjustment
2026-02-17 21:34:40.107718 INFO::Found 2 batches.
2026-02-17 21:34:40.108236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:40.108858 INFO::Using default BPPARAM
2026-02-17 21:34:40.109365 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:40.110257 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-17 21:34:40.12572 INFO::Done
2026-02-17 21:34:40.126398 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:40.129187 INFO::ASW Batch was 0.492687010599223 prior to batch effect correction and is now 0.101850846899221 .
2026-02-17 21:34:40.129764 INFO::ASW Label was 0.421235775213839 prior to batch effect correction and is now 0.865118635312302 .
2026-02-17 21:34:40.130547 INFO::Total function execution time is 0.0354797840118408 s and adjustment time is 0.018115758895874 s ( 51.06 )
2026-02-17 21:34:40.131317 INFO::Formatting Data.
2026-02-17 21:34:40.13194 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:40.132827 INFO::Removing potential empty rows and columns
2026-02-17 21:34:40.133754 INFO::Found 0 missing values.
2026-02-17 21:34:40.134614 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.
2026-02-17 21:34:40.138916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:40.139465 INFO::Done
2026-02-17 21:34:40.139971 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:40.142769 INFO::Starting hierarchical adjustment
2026-02-17 21:34:40.143456 INFO::Found 2 batches.
2026-02-17 21:34:40.144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:40.144603 INFO::Using default BPPARAM
2026-02-17 21:34:40.145109 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:40.146007 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-17 21:34:40.161731 INFO::Done
2026-02-17 21:34:40.162424 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:40.165219 INFO::ASW Batch was 0.492687010599223 prior to batch effect correction and is now 0.101850846899221 .
2026-02-17 21:34:40.165826 INFO::ASW Label was 0.421235775213839 prior to batch effect correction and is now 0.865118635312302 .
2026-02-17 21:34:40.166621 INFO::Total function execution time is 0.0353209972381592 s and adjustment time is 0.0184009075164795 s ( 52.1 )
2026-02-17 21:34:40.371547 INFO::Formatting Data.
2026-02-17 21:34:40.372345 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:40.373293 INFO::Removing potential empty rows and columns
2026-02-17 21:34:40.374406 INFO::Found 0 missing values.
2026-02-17 21:34:40.377566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:40.378168 INFO::Done
2026-02-17 21:34:40.378747 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:40.380871 INFO::Starting hierarchical adjustment
2026-02-17 21:34:40.381617 INFO::Found 3 batches.
2026-02-17 21:34:40.382168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:40.382837 INFO::Using default BPPARAM
2026-02-17 21:34:40.383397 INFO::Processing subtree level 1
2026-02-17 21:34:40.473208 INFO::Adjusting the last 1 batches sequentially
2026-02-17 21:34:40.475011 INFO::Done
2026-02-17 21:34:40.475687 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:40.478201 INFO::ASW Batch was 0.0284850107788945 prior to batch effect correction and is now 0.0284850107788945 .
2026-02-17 21:34:40.479402 INFO::Total function execution time is 0.107847929000854 s and adjustment time is 0.0935492515563965 s ( 86.74 )
2026-02-17 21:34:40.480675 INFO::Formatting Data.
2026-02-17 21:34:40.481421 INFO::Typecasting input to dataframe.
2026-02-17 21:34:40.482213 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:40.483209 INFO::Removing potential empty rows and columns
2026-02-17 21:34:40.484335 INFO::Found 0 missing values.
2026-02-17 21:34:40.487936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:40.488656 INFO::Done
2026-02-17 21:34:40.489234 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:40.491507 INFO::Starting hierarchical adjustment
2026-02-17 21:34:40.492272 INFO::Found 3 batches.
2026-02-17 21:34:40.492876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:40.49353 INFO::Using default BPPARAM
2026-02-17 21:34:40.494097 INFO::Processing subtree level 1
2026-02-17 21:34:40.580737 INFO::Adjusting the last 1 batches sequentially
2026-02-17 21:34:40.582587 INFO::Done
2026-02-17 21:34:40.583271 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:40.585759 INFO::ASW Batch was 0.0284850107788945 prior to batch effect correction and is now 0.0284850107788945 .
2026-02-17 21:34:40.58672 INFO::Total function execution time is 0.106041193008423 s and adjustment time is 0.090461254119873 s ( 85.31 )
2026-02-17 21:34:40.600092 INFO::Formatting Data.
2026-02-17 21:34:40.600908 INFO::Typecasting input to dataframe.
2026-02-17 21:34:40.601782 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:40.6027 INFO::Removing potential empty rows and columns
2026-02-17 21:34:40.603792 INFO::Found 0 missing values.
2026-02-17 21:34:40.606834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:40.607398 INFO::Done
2026-02-17 21:34:40.607933 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:40.60998 INFO::Starting hierarchical adjustment
2026-02-17 21:34:40.610711 INFO::Found 3 batches.
2026-02-17 21:34:40.611257 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:40.611902 INFO::Using default BPPARAM
2026-02-17 21:34:40.612473 INFO::Processing subtree level 1
2026-02-17 21:34:40.697955 INFO::Adjusting the last 1 batches sequentially
2026-02-17 21:34:40.699761 INFO::Done
2026-02-17 21:34:40.700464 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:40.702998 INFO::ASW Batch was 0.00373853732458396 prior to batch effect correction and is now 0.00373853732458396 .
2026-02-17 21:34:40.704073 INFO::Total function execution time is 0.104031801223755 s and adjustment time is 0.0891814231872559 s ( 85.73 )
2026-02-17 21:34:40.840173 INFO::Formatting Data.
2026-02-17 21:34:40.841004 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:40.842132 INFO::Removing potential empty rows and columns
2026-02-17 21:34:40.845172 INFO::Found 1000 missing values.
2026-02-17 21:34:40.865138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:40.865898 INFO::Done
2026-02-17 21:34:40.866487 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:40.872008 INFO::Starting hierarchical adjustment
2026-02-17 21:34:40.872803 INFO::Found 10 batches.
2026-02-17 21:34:40.873358 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:40.874038 INFO::Using default BPPARAM
2026-02-17 21:34:40.874602 INFO::Processing subtree level 1
2026-02-17 21:34:41.01571 INFO::Processing subtree level 2
2026-02-17 21:34:41.167222 INFO::Adjusting the last 1 batches sequentially
2026-02-17 21:34:41.169443 INFO::Done
2026-02-17 21:34:41.170193 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:41.176457 INFO::ASW Batch was 0.510163043300024 prior to batch effect correction and is now 0.510163043300024 .
2026-02-17 21:34:41.177282 INFO::ASW Label was 0.353766583721226 prior to batch effect correction and is now 0.353766583721226 .
2026-02-17 21:34:41.178355 INFO::Total function execution time is 0.338197708129883 s and adjustment time is 0.296769857406616 s ( 87.75 )
2026-02-17 21:34:41.179379 INFO::Formatting Data.
2026-02-17 21:34:41.180135 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:41.181576 INFO::Removing potential empty rows and columns
2026-02-17 21:34:41.184925 INFO::Found 1000 missing values.
2026-02-17 21:34:41.207914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:41.208764 INFO::Done
2026-02-17 21:34:41.20942 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:41.215364 INFO::Starting hierarchical adjustment
2026-02-17 21:34:41.216229 INFO::Found 10 batches.
2026-02-17 21:34:42.178421 INFO::Set up parallel execution backend with 2 workers
2026-02-17 21:34:42.180296 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-17 21:34:43.398935 INFO::Adjusting the last 2 batches sequentially
2026-02-17 21:34:43.401006 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-17 21:34:43.417063 INFO::Done
2026-02-17 21:34:43.417729 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:43.422326 INFO::ASW Batch was 0.510163043300024 prior to batch effect correction and is now 0.510163043300024 .
2026-02-17 21:34:43.422923 INFO::ASW Label was 0.353766583721226 prior to batch effect correction and is now 0.353766583721226 .
2026-02-17 21:34:43.423654 INFO::Total function execution time is 2.24434924125671 s and adjustment time is 2.20099711418152 s ( 98.07 )
2026-02-17 21:34:43.578834 INFO::Formatting Data.
2026-02-17 21:34:43.57976 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:43.580725 INFO::Removing potential empty rows and columns
2026-02-17 21:34:43.581836 INFO::Found 0 missing values.
2026-02-17 21:34:43.585601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:43.586153 INFO::Done
2026-02-17 21:34:43.586695 INFO::Acquiring quality metrics before batch effect correction.
2026-02-17 21:34:43.589671 INFO::Starting hierarchical adjustment
2026-02-17 21:34:43.590417 INFO::Found 3 batches.
2026-02-17 21:34:43.590966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-17 21:34:43.591624 INFO::Using default BPPARAM
2026-02-17 21:34:43.592171 INFO::Processing subtree level 1
2026-02-17 21:34:43.696216 INFO::Adjusting the last 1 batches sequentially
2026-02-17 21:34:43.697984 INFO::Done
2026-02-17 21:34:43.698643 INFO::Acquiring quality metrics after batch effect correction.
2026-02-17 21:34:43.701856 INFO::ASW Batch was 0.294767785731948 prior to batch effect correction and is now -0.126372101138579 .
2026-02-17 21:34:43.702494 INFO::ASW Label was -0.238148624995025 prior to batch effect correction and is now -0.0662037084970852 .
2026-02-17 21:34:43.703445 INFO::Total function execution time is 0.124724149703979 s and adjustment time is 0.107718944549561 s ( 86.37 )
2026-02-17 21:34:43.817443 INFO::Formatting Data.
2026-02-17 21:34:43.818254 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:43.819152 INFO::Removing potential empty rows and columns
2026-02-17 21:34:43.82019 INFO::Found 2 missing values.
2026-02-17 21:34:43.822934 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:43.823506 INFO::Done
2026-02-17 21:34:43.850417 INFO::Found NA in Reference column
2026-02-17 21:34:43.859536 INFO::Require at least two references per batch.
2026-02-17 21:34:43.87897 INFO::Formatting Data.
2026-02-17 21:34:43.87973 INFO::Recognized SummarizedExperiment
2026-02-17 21:34:43.880265 INFO::Typecasting input to dataframe.
2026-02-17 21:34:43.88931 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:43.89039 INFO::Removing potential empty rows and columns
2026-02-17 21:34:43.893826 INFO::Found 0 missing values.
2026-02-17 21:34:43.90039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:43.900964 INFO::Done
2026-02-17 21:34:43.915587 INFO::Formatting Data.
2026-02-17 21:34:43.916303 INFO::Recognized SummarizedExperiment
2026-02-17 21:34:43.916837 INFO::Typecasting input to dataframe.
2026-02-17 21:34:43.933273 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:43.934479 INFO::Removing potential empty rows and columns
2026-02-17 21:34:43.937965 INFO::Found 0 missing values.
2026-02-17 21:34:43.948784 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:43.949448 INFO::Done
2026-02-17 21:34:43.963927 INFO::Formatting Data.
2026-02-17 21:34:43.964634 INFO::Recognized SummarizedExperiment
2026-02-17 21:34:43.965137 INFO::Typecasting input to dataframe.
2026-02-17 21:34:43.98059 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:43.981592 INFO::Removing potential empty rows and columns
2026-02-17 21:34:43.982672 INFO::Found 0 missing values.
2026-02-17 21:34:43.983551 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.
2026-02-17 21:34:43.987757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:43.988349 INFO::Done
2026-02-17 21:34:43.998305 INFO::Formatting Data.
2026-02-17 21:34:43.999184 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:44.000104 INFO::Removing potential empty rows and columns
2026-02-17 21:34:44.001104 INFO::Found 0 missing values.
2026-02-17 21:34:44.003947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:44.004503 INFO::Done
2026-02-17 21:34:44.016183 INFO::Formatting Data.
2026-02-17 21:34:44.01696 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:44.017828 INFO::Removing potential empty rows and columns
2026-02-17 21:34:44.018845 INFO::Found 0 missing values.
2026-02-17 21:34:44.021708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:44.022232 INFO::Done
2026-02-17 21:34:44.051573 INFO::Formatting Data.
2026-02-17 21:34:44.052401 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:44.053419 INFO::Removing potential empty rows and columns
2026-02-17 21:34:44.054545 INFO::Found 1 missing values.
2026-02-17 21:34:44.057043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:44.05761 INFO::Done
2026-02-17 21:34:44.076251 INFO::Formatting Data.
2026-02-17 21:34:44.077081 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:44.077976 INFO::Removing potential empty rows and columns
2026-02-17 21:34:44.078906 INFO::Found 2 missing values.
2026-02-17 21:34:44.079791 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.
2026-02-17 21:34:44.082107 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:44.082628 INFO::Done
2026-02-17 21:34:44.092264 INFO::Formatting Data.
2026-02-17 21:34:44.093011 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:44.093888 INFO::Removing potential empty rows and columns
2026-02-17 21:34:44.094783 INFO::Found 2 missing values.
2026-02-17 21:34:44.096276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:44.096918 INFO::Done
2026-02-17 21:34:44.10673 INFO::Formatting Data.
2026-02-17 21:34:44.107462 INFO::Typecasting input to dataframe.
2026-02-17 21:34:44.108224 INFO::Replacing NaNs with NAs.
2026-02-17 21:34:44.109052 INFO::Removing potential empty rows and columns
2026-02-17 21:34:44.110025 INFO::Found 0 missing values.
2026-02-17 21:34:44.112796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-17 21:34:44.113314 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.659 3.224 19.625
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.762 | 1.780 | 17.948 | |
| compute_asw | 0.023 | 0.002 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.015 | |
| generate_data_covariables | 0.011 | 0.002 | 0.013 | |
| generate_dataset | 0.010 | 0.001 | 0.012 | |