Yannis Schumann
| Snapshot Date: 2026-03-18 13:45 -0400 (Wed, 18 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-19 11:57 -0400 (Thu, 19 Mar 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" | 4892 |
| 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: 2026-03-18 21:34:04 -0400 (Wed, 18 Mar 2026) |
| EndedAt: 2026-03-18 21:35:35 -0400 (Wed, 18 Mar 2026) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 26.281 1.201 18.655
* 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")
2026-03-18 21:34:58.349617 INFO::Formatting Data.
2026-03-18 21:34:58.350929 INFO::Replacing NaNs with NAs.
2026-03-18 21:34:58.36185 INFO::Removing potential empty rows and columns
2026-03-18 21:34:58.60408 INFO::Found 0 missing values.
2026-03-18 21:34:58.607441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:34:58.6081 INFO::Done
2026-03-18 21:34:58.608636 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:34:58.619749 INFO::Starting hierarchical adjustment
2026-03-18 21:34:58.620605 INFO::Found 3 batches.
2026-03-18 21:34:58.621165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:34:58.622259 INFO::Using default BPPARAM
2026-03-18 21:34:58.622809 INFO::Processing subtree level 1
2026-03-18 21:34:58.717864 INFO::Adjusting the last 1 batches sequentially
2026-03-18 21:34:58.719701 INFO::Done
2026-03-18 21:34:58.720396 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:34:58.722953 INFO::ASW Batch was -0.00672513247603823 prior to batch effect correction and is now -0.00672513247603823 .
2026-03-18 21:34:58.724011 INFO::Total function execution time is 0.375056505203247 s and adjustment time is 0.0992569923400879 s ( 26.46 )
2026-03-18 21:34:58.738155 INFO::Formatting Data.
2026-03-18 21:34:58.739349 INFO::Replacing NaNs with NAs.
2026-03-18 21:34:58.740469 INFO::Removing potential empty rows and columns
2026-03-18 21:34:58.74174 INFO::Found 0 missing values.
2026-03-18 21:34:58.742738 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.
2026-03-18 21:34:58.753816 INFO::Formatting Data.
2026-03-18 21:34:58.754611 INFO::Replacing NaNs with NAs.
2026-03-18 21:34:58.755517 INFO::Removing potential empty rows and columns
2026-03-18 21:34:58.756581 INFO::Found 0 missing values.
2026-03-18 21:34:58.757536 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.
2026-03-18 21:34:58.773344 INFO::Formatting Data.
2026-03-18 21:34:58.774153 INFO::Replacing NaNs with NAs.
2026-03-18 21:34:58.775205 INFO::Removing potential empty rows and columns
2026-03-18 21:34:58.776258 INFO::Found 0 missing values.
2026-03-18 21:34:58.77716 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.
2026-03-18 21:34:58.781581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:34:58.782141 INFO::Done
2026-03-18 21:34:58.782668 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:34:58.784649 INFO::Starting hierarchical adjustment
2026-03-18 21:34:58.785321 INFO::Found 2 batches.
2026-03-18 21:34:58.785849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:34:58.786458 INFO::Using default BPPARAM
2026-03-18 21:34:58.78698 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:34:58.787886 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-18 21:34:58.809048 INFO::Done
2026-03-18 21:34:58.809794 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:34:58.812071 INFO::ASW Batch was 0.056237585228395 prior to batch effect correction and is now -0.123609818605387 .
2026-03-18 21:34:58.812912 INFO::Total function execution time is 0.0396301746368408 s and adjustment time is 0.0238204002380371 s ( 60.11 )
2026-03-18 21:34:58.81581 INFO::Formatting Data.
2026-03-18 21:34:58.816465 INFO::Replacing NaNs with NAs.
2026-03-18 21:34:58.825454 INFO::Formatting Data.
2026-03-18 21:34:58.826235 INFO::Replacing NaNs with NAs.
2026-03-18 21:34:58.827159 INFO::Removing potential empty rows and columns
2026-03-18 21:34:58.828206 INFO::Found 0 missing values.
2026-03-18 21:34:58.83117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:34:58.831877 INFO::Done
2026-03-18 21:34:58.832398 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:34:58.857831 INFO::Starting hierarchical adjustment
2026-03-18 21:34:58.859223 INFO::Found 2 batches.
2026-03-18 21:34:58.859794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:34:58.860339 INFO::Using default BPPARAM
2026-03-18 21:34:58.860855 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:34:58.86175 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-18 21:34:58.875914 INFO::Done
2026-03-18 21:34:58.8766 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:34:58.878549 INFO::ASW Batch was -0.0186241936863269 prior to batch effect correction and is now -0.121803177256553 .
2026-03-18 21:34:58.879274 INFO::Total function execution time is 0.0538907051086426 s and adjustment time is 0.0168640613555908 s ( 31.29 )
2026-03-18 21:34:58.880301 INFO::Formatting Data.
2026-03-18 21:34:58.880887 INFO::Replacing NaNs with NAs.
2026-03-18 21:34:58.881693 INFO::Removing potential empty rows and columns
2026-03-18 21:34:58.882634 INFO::Found 0 missing values.
2026-03-18 21:34:58.885222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:34:58.885725 INFO::Done
2026-03-18 21:34:58.88619 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:34:58.88803 INFO::Starting hierarchical adjustment
2026-03-18 21:34:58.888691 INFO::Found 2 batches.
2026-03-18 21:34:58.889168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:34:58.889729 INFO::Using default BPPARAM
2026-03-18 21:34:58.89021 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:34:58.891062 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-18 21:34:58.905804 INFO::Done
2026-03-18 21:34:58.90646 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:34:58.908396 INFO::ASW Batch was -0.0186241936863269 prior to batch effect correction and is now -0.121803177256553 .
2026-03-18 21:34:58.909155 INFO::Total function execution time is 0.0288677215576172 s and adjustment time is 0.0172362327575684 s ( 59.71 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-18 21:35:01.598389 INFO::Formatting Data.
2026-03-18 21:35:01.599066 INFO::Recognized SummarizedExperiment
2026-03-18 21:35:01.599551 INFO::Typecasting input to dataframe.
2026-03-18 21:35:01.627745 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:01.628955 INFO::Removing potential empty rows and columns
2026-03-18 21:35:01.632658 INFO::Found 0 missing values.
2026-03-18 21:35:01.639697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:01.640283 INFO::Done
2026-03-18 21:35:01.640813 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:01.644338 INFO::Starting hierarchical adjustment
2026-03-18 21:35:01.645034 INFO::Found 2 batches.
2026-03-18 21:35:01.645556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:01.646612 INFO::Using default BPPARAM
2026-03-18 21:35:01.647148 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:01.648097 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-18 21:35:01.703425 INFO::Done
2026-03-18 21:35:01.704115 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:01.707624 INFO::ASW Batch was 0.013789936526733 prior to batch effect correction and is now -0.0926590630552513 .
2026-03-18 21:35:01.708422 INFO::Total function execution time is 0.110302925109863 s and adjustment time is 0.0585052967071533 s ( 53.04 )
Warning: stack imbalance in '{', 73 then 75
2026-03-18 21:35:01.726934 INFO::Formatting Data.
2026-03-18 21:35:01.727749 INFO::Recognized SummarizedExperiment
2026-03-18 21:35:01.728297 INFO::Typecasting input to dataframe.
2026-03-18 21:35:01.737301 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:01.738377 INFO::Removing potential empty rows and columns
2026-03-18 21:35:01.742021 INFO::Found 0 missing values.
2026-03-18 21:35:01.74897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:01.749549 INFO::Done
2026-03-18 21:35:01.750062 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:01.753527 INFO::Starting hierarchical adjustment
2026-03-18 21:35:01.754226 INFO::Found 2 batches.
2026-03-18 21:35:01.754746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:01.755328 INFO::Using default BPPARAM
2026-03-18 21:35:01.755849 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:01.756798 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-18 21:35:01.781434 INFO::Done
2026-03-18 21:35:01.782151 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:01.785693 INFO::ASW Batch was 0.00148186294669788 prior to batch effect correction and is now 0.00148186294669788 .
2026-03-18 21:35:01.78658 INFO::Total function execution time is 0.0595996379852295 s and adjustment time is 0.0273144245147705 s ( 45.83 )
2026-03-18 21:35:01.804292 INFO::Formatting Data.
2026-03-18 21:35:01.805136 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:01.806031 INFO::Removing potential empty rows and columns
2026-03-18 21:35:01.807033 INFO::Found 0 missing values.
2026-03-18 21:35:01.809925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:01.810453 INFO::Done
2026-03-18 21:35:01.810961 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:01.812911 INFO::Starting hierarchical adjustment
2026-03-18 21:35:01.813598 INFO::Found 3 batches.
2026-03-18 21:35:01.814111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:01.814709 INFO::Using default BPPARAM
2026-03-18 21:35:01.81521 INFO::Processing subtree level 1
2026-03-18 21:35:01.941249 INFO::Adjusting the last 1 batches sequentially
2026-03-18 21:35:01.942944 INFO::Done
2026-03-18 21:35:01.94356 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:01.945923 INFO::ASW Batch was -0.0411884883216906 prior to batch effect correction and is now -0.170404359000634 .
2026-03-18 21:35:01.946797 INFO::Total function execution time is 0.142558813095093 s and adjustment time is 0.129483699798584 s ( 90.83 )
2026-03-18 21:35:01.960377 INFO::Skipping initial DF formatting
2026-03-18 21:35:01.961015 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:01.964882 INFO::Starting hierarchical adjustment
2026-03-18 21:35:01.965606 INFO::Found 5 batches.
2026-03-18 21:35:01.966126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:01.966736 INFO::Using default BPPARAM
2026-03-18 21:35:01.967259 INFO::Processing subtree level 1
2026-03-18 21:35:02.207679 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:02.20954 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-18 21:35:02.229999 INFO::Done
2026-03-18 21:35:02.230822 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:02.235312 INFO::ASW Batch was 0.541053487739004 prior to batch effect correction and is now 0.541053487739004 .
2026-03-18 21:35:02.236012 INFO::ASW Label was 0.354554665565722 prior to batch effect correction and is now 0.354554665565722 .
2026-03-18 21:35:02.236911 INFO::Total function execution time is 0.276549816131592 s and adjustment time is 0.264479398727417 s ( 95.64 )
2026-03-18 21:35:02.309996 INFO::Formatting Data.
2026-03-18 21:35:02.310886 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:02.311876 INFO::Removing potential empty rows and columns
2026-03-18 21:35:02.312917 INFO::Found 0 missing values.
2026-03-18 21:35:02.317038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:02.3176 INFO::Done
2026-03-18 21:35:02.318107 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:02.321272 INFO::Starting hierarchical adjustment
2026-03-18 21:35:02.321995 INFO::Found 5 batches.
2026-03-18 21:35:02.322532 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:02.32315 INFO::Using default BPPARAM
2026-03-18 21:35:02.323709 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.
2026-03-18 21:35:02.457198 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:02.458996 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-18 21:35:02.477638 INFO::Done
2026-03-18 21:35:02.47847 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:02.482396 INFO::ASW Batch was 0.289775054692932 prior to batch effect correction and is now -0.0521233084066326 .
2026-03-18 21:35:02.483128 INFO::ASW Label was 0.42311757851621 prior to batch effect correction and is now 0.862038654481215 .
2026-03-18 21:35:02.484041 INFO::Total function execution time is 0.174155712127686 s and adjustment time is 0.155736446380615 s ( 89.42 )
2026-03-18 21:35:02.485022 INFO::Formatting Data.
2026-03-18 21:35:02.485698 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:02.4867 INFO::Removing potential empty rows and columns
2026-03-18 21:35:02.487888 INFO::Found 0 missing values.
2026-03-18 21:35:02.492584 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:02.493208 INFO::Done
2026-03-18 21:35:02.493834 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:02.497269 INFO::Starting hierarchical adjustment
2026-03-18 21:35:02.498047 INFO::Found 5 batches.
2026-03-18 21:35:02.498607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:02.499269 INFO::Using default BPPARAM
2026-03-18 21:35:02.499848 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.
2026-03-18 21:35:02.629471 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:02.631762 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-18 21:35:02.656056 INFO::Done
2026-03-18 21:35:02.657032 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:02.661933 INFO::ASW Batch was 0.289775054692932 prior to batch effect correction and is now -0.0521233084066326 .
2026-03-18 21:35:02.662837 INFO::ASW Label was 0.42311757851621 prior to batch effect correction and is now 0.862038654481215 .
2026-03-18 21:35:02.664066 INFO::Total function execution time is 0.178973913192749 s and adjustment time is 0.158133268356323 s ( 88.36 )
2026-03-18 21:35:02.677993 INFO::Formatting Data.
2026-03-18 21:35:02.684503 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:02.686153 INFO::Removing potential empty rows and columns
2026-03-18 21:35:02.687284 INFO::Found 0 missing values.
2026-03-18 21:35:02.691547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:02.692075 INFO::Done
2026-03-18 21:35:02.692601 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:02.695932 INFO::Starting hierarchical adjustment
2026-03-18 21:35:02.696692 INFO::Found 5 batches.
2026-03-18 21:35:02.697237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:02.697922 INFO::Using default BPPARAM
2026-03-18 21:35:02.698446 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.
2026-03-18 21:35:02.817123 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:02.818827 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-18 21:35:02.835824 INFO::Done
2026-03-18 21:35:02.836593 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:02.840147 INFO::ASW Batch was 0.338312275424735 prior to batch effect correction and is now 0.0414589096050941 .
2026-03-18 21:35:02.840791 INFO::ASW Label was 0.461991128539131 prior to batch effect correction and is now 0.730699173583123 .
2026-03-18 21:35:02.841638 INFO::Total function execution time is 0.163659334182739 s and adjustment time is 0.139290332794189 s ( 85.11 )
2026-03-18 21:35:02.842534 INFO::Formatting Data.
2026-03-18 21:35:02.843191 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:02.844106 INFO::Removing potential empty rows and columns
2026-03-18 21:35:02.84514 INFO::Found 0 missing values.
2026-03-18 21:35:02.849301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:02.849875 INFO::Done
2026-03-18 21:35:02.850403 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:02.853407 INFO::Starting hierarchical adjustment
2026-03-18 21:35:02.854207 INFO::Found 5 batches.
2026-03-18 21:35:02.85477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:02.855388 INFO::Using default BPPARAM
2026-03-18 21:35:02.855949 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.
2026-03-18 21:35:02.987154 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:02.989159 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-18 21:35:03.012573 INFO::Done
2026-03-18 21:35:03.013604 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.018653 INFO::ASW Batch was 0.338312275424735 prior to batch effect correction and is now 0.0414589096050941 .
2026-03-18 21:35:03.019879 INFO::ASW Label was 0.461991128539131 prior to batch effect correction and is now 0.730699173583123 .
2026-03-18 21:35:03.021936 INFO::Total function execution time is 0.179189205169678 s and adjustment time is 0.158427476882935 s ( 88.41 )
2026-03-18 21:35:03.044211 INFO::Formatting Data.
2026-03-18 21:35:03.045151 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.046196 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.047318 INFO::Found 0 missing values.
2026-03-18 21:35:03.050244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:03.050826 INFO::Done
2026-03-18 21:35:03.051355 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:03.054679 INFO::Starting hierarchical adjustment
2026-03-18 21:35:03.055473 INFO::Found 2 batches.
2026-03-18 21:35:03.056051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:03.056705 INFO::Using default BPPARAM
2026-03-18 21:35:03.057262 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:03.0583 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-18 21:35:03.074533 INFO::Done
2026-03-18 21:35:03.07533 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.078645 INFO::ASW Batch was 0.360657678318028 prior to batch effect correction and is now -0.0253159567873514 .
2026-03-18 21:35:03.079272 INFO::ASW Label was 0.691033010521837 prior to batch effect correction and is now 0.932611264514564 .
2026-03-18 21:35:03.08012 INFO::Total function execution time is 0.0360527038574219 s and adjustment time is 0.0191817283630371 s ( 53.2 )
2026-03-18 21:35:03.080981 INFO::Formatting Data.
2026-03-18 21:35:03.08163 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.082561 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.083615 INFO::Found 0 missing values.
2026-03-18 21:35:03.086498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:03.087066 INFO::Done
2026-03-18 21:35:03.08762 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:03.090863 INFO::Starting hierarchical adjustment
2026-03-18 21:35:03.091614 INFO::Found 2 batches.
2026-03-18 21:35:03.092161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:03.092817 INFO::Using default BPPARAM
2026-03-18 21:35:03.093364 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:03.094354 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-18 21:35:03.110437 INFO::Done
2026-03-18 21:35:03.111271 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.114724 INFO::ASW Batch was 0.360657678318028 prior to batch effect correction and is now -0.0253159567873514 .
2026-03-18 21:35:03.11548 INFO::ASW Label was 0.691033010521837 prior to batch effect correction and is now 0.932611264514564 .
2026-03-18 21:35:03.116437 INFO::Total function execution time is 0.0354361534118652 s and adjustment time is 0.0189306735992432 s ( 53.42 )
2026-03-18 21:35:03.12917 INFO::Formatting Data.
2026-03-18 21:35:03.130005 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.130939 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.131896 INFO::Found 0 missing values.
2026-03-18 21:35:03.134076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:03.134648 INFO::Done
2026-03-18 21:35:03.135169 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:03.137251 INFO::Starting hierarchical adjustment
2026-03-18 21:35:03.137994 INFO::Found 2 batches.
2026-03-18 21:35:03.138547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:03.13917 INFO::Using default BPPARAM
2026-03-18 21:35:03.139729 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:03.140682 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-18 21:35:03.174397 INFO::Done
2026-03-18 21:35:03.175208 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.177423 INFO::ASW Batch was -0.0676492954204492 prior to batch effect correction and is now -0.108728056280241 .
2026-03-18 21:35:03.178325 INFO::Total function execution time is 0.0492589473724365 s and adjustment time is 0.0365111827850342 s ( 74.12 )
2026-03-18 21:35:03.191225 INFO::Formatting Data.
2026-03-18 21:35:03.192072 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.193033 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.19409 INFO::Found 0 missing values.
2026-03-18 21:35:03.195339 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.
2026-03-18 21:35:03.200171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:03.200773 INFO::Done
2026-03-18 21:35:03.201311 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:03.204502 INFO::Starting hierarchical adjustment
2026-03-18 21:35:03.20524 INFO::Found 2 batches.
2026-03-18 21:35:03.205789 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:03.206412 INFO::Using default BPPARAM
2026-03-18 21:35:03.206958 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:03.207921 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-18 21:35:03.225603 INFO::Done
2026-03-18 21:35:03.226405 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.229801 INFO::ASW Batch was 0.727766593252241 prior to batch effect correction and is now -0.0271062913858267 .
2026-03-18 21:35:03.230479 INFO::ASW Label was 0.325796706800493 prior to batch effect correction and is now 0.887191571576515 .
2026-03-18 21:35:03.231364 INFO::Total function execution time is 0.0402417182922363 s and adjustment time is 0.0204553604125977 s ( 50.83 )
2026-03-18 21:35:03.232283 INFO::Formatting Data.
2026-03-18 21:35:03.232962 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.234027 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.235139 INFO::Found 0 missing values.
2026-03-18 21:35:03.236187 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.
2026-03-18 21:35:03.241199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:03.241861 INFO::Done
2026-03-18 21:35:03.242407 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:03.245662 INFO::Starting hierarchical adjustment
2026-03-18 21:35:03.246428 INFO::Found 2 batches.
2026-03-18 21:35:03.24699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:03.247638 INFO::Using default BPPARAM
2026-03-18 21:35:03.24818 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:03.249158 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-18 21:35:03.26859 INFO::Done
2026-03-18 21:35:03.269405 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.27271 INFO::ASW Batch was 0.727766593252241 prior to batch effect correction and is now -0.0271062913858267 .
2026-03-18 21:35:03.273351 INFO::ASW Label was 0.325796706800493 prior to batch effect correction and is now 0.887191571576515 .
2026-03-18 21:35:03.274235 INFO::Total function execution time is 0.0419631004333496 s and adjustment time is 0.0222630500793457 s ( 53.05 )
2026-03-18 21:35:03.508434 INFO::Formatting Data.
2026-03-18 21:35:03.509572 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.510669 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.511983 INFO::Found 0 missing values.
2026-03-18 21:35:03.515195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:03.515765 INFO::Done
2026-03-18 21:35:03.516291 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:03.519324 INFO::Starting hierarchical adjustment
2026-03-18 21:35:03.520119 INFO::Found 3 batches.
2026-03-18 21:35:03.520682 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:03.521383 INFO::Using default BPPARAM
2026-03-18 21:35:03.521911 INFO::Processing subtree level 1
2026-03-18 21:35:03.613818 INFO::Adjusting the last 1 batches sequentially
2026-03-18 21:35:03.616302 INFO::Done
2026-03-18 21:35:03.617235 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.620943 INFO::ASW Batch was -0.0329854816932449 prior to batch effect correction and is now -0.0329854816932449 .
2026-03-18 21:35:03.622342 INFO::Total function execution time is 0.114120006561279 s and adjustment time is 0.0963509082794189 s ( 84.43 )
2026-03-18 21:35:03.623842 INFO::Formatting Data.
2026-03-18 21:35:03.624731 INFO::Typecasting input to dataframe.
2026-03-18 21:35:03.625745 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.627004 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.628535 INFO::Found 0 missing values.
2026-03-18 21:35:03.632771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:03.633591 INFO::Done
2026-03-18 21:35:03.634373 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:03.637165 INFO::Starting hierarchical adjustment
2026-03-18 21:35:03.637934 INFO::Found 3 batches.
2026-03-18 21:35:03.638467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:03.639168 INFO::Using default BPPARAM
2026-03-18 21:35:03.639719 INFO::Processing subtree level 1
2026-03-18 21:35:03.723337 INFO::Adjusting the last 1 batches sequentially
2026-03-18 21:35:03.72521 INFO::Done
2026-03-18 21:35:03.725884 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.728402 INFO::ASW Batch was -0.0329854816932449 prior to batch effect correction and is now -0.0329854816932449 .
2026-03-18 21:35:03.729346 INFO::Total function execution time is 0.105550289154053 s and adjustment time is 0.0874052047729492 s ( 82.81 )
2026-03-18 21:35:03.743125 INFO::Formatting Data.
2026-03-18 21:35:03.743942 INFO::Typecasting input to dataframe.
2026-03-18 21:35:03.744817 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.745738 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.746819 INFO::Found 0 missing values.
2026-03-18 21:35:03.749887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:03.750444 INFO::Done
2026-03-18 21:35:03.750991 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:03.75323 INFO::Starting hierarchical adjustment
2026-03-18 21:35:03.753984 INFO::Found 3 batches.
2026-03-18 21:35:03.754534 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:03.75516 INFO::Using default BPPARAM
2026-03-18 21:35:03.755721 INFO::Processing subtree level 1
2026-03-18 21:35:03.844094 INFO::Adjusting the last 1 batches sequentially
2026-03-18 21:35:03.846051 INFO::Done
2026-03-18 21:35:03.846743 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:03.849418 INFO::ASW Batch was -0.0340413425851733 prior to batch effect correction and is now -0.0340413425851733 .
2026-03-18 21:35:03.850478 INFO::Total function execution time is 0.107376575469971 s and adjustment time is 0.0922019481658936 s ( 85.87 )
2026-03-18 21:35:03.992287 INFO::Formatting Data.
2026-03-18 21:35:03.993188 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:03.994395 INFO::Removing potential empty rows and columns
2026-03-18 21:35:03.997253 INFO::Found 1000 missing values.
2026-03-18 21:35:04.016486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:04.017276 INFO::Done
2026-03-18 21:35:04.017861 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:04.023554 INFO::Starting hierarchical adjustment
2026-03-18 21:35:04.024426 INFO::Found 10 batches.
2026-03-18 21:35:04.025005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:04.025647 INFO::Using default BPPARAM
2026-03-18 21:35:04.026191 INFO::Processing subtree level 1
2026-03-18 21:35:04.156959 INFO::Processing subtree level 2
2026-03-18 21:35:04.297983 INFO::Adjusting the last 1 batches sequentially
2026-03-18 21:35:04.300214 INFO::Done
2026-03-18 21:35:04.300989 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:04.306872 INFO::ASW Batch was 0.459877382446464 prior to batch effect correction and is now 0.459877382446464 .
2026-03-18 21:35:04.307654 INFO::ASW Label was 0.422281014065501 prior to batch effect correction and is now 0.422281014065501 .
2026-03-18 21:35:04.308649 INFO::Total function execution time is 0.316430568695068 s and adjustment time is 0.275928974151611 s ( 87.2 )
2026-03-18 21:35:04.309541 INFO::Formatting Data.
2026-03-18 21:35:04.310214 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:04.311546 INFO::Removing potential empty rows and columns
2026-03-18 21:35:04.314394 INFO::Found 1000 missing values.
2026-03-18 21:35:04.33428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:04.335117 INFO::Done
2026-03-18 21:35:04.335698 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:04.341386 INFO::Starting hierarchical adjustment
2026-03-18 21:35:04.342249 INFO::Found 10 batches.
2026-03-18 21:35:05.442122 INFO::Set up parallel execution backend with 2 workers
2026-03-18 21:35:05.444114 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-18 21:35:06.642222 INFO::Adjusting the last 2 batches sequentially
2026-03-18 21:35:06.64541 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-18 21:35:06.663054 INFO::Done
2026-03-18 21:35:06.663845 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:06.668936 INFO::ASW Batch was 0.459877382446464 prior to batch effect correction and is now 0.459877382446464 .
2026-03-18 21:35:06.669557 INFO::ASW Label was 0.422281014065501 prior to batch effect correction and is now 0.422281014065501 .
2026-03-18 21:35:06.67033 INFO::Total function execution time is 2.36082792282104 s and adjustment time is 2.32093930244446 s ( 98.31 )
2026-03-18 21:35:06.809429 INFO::Formatting Data.
2026-03-18 21:35:06.810224 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:06.811126 INFO::Removing potential empty rows and columns
2026-03-18 21:35:06.812168 INFO::Found 0 missing values.
2026-03-18 21:35:06.815774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:06.816319 INFO::Done
2026-03-18 21:35:06.816836 INFO::Acquiring quality metrics before batch effect correction.
2026-03-18 21:35:06.81971 INFO::Starting hierarchical adjustment
2026-03-18 21:35:06.820415 INFO::Found 3 batches.
2026-03-18 21:35:06.820953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-18 21:35:06.821573 INFO::Using default BPPARAM
2026-03-18 21:35:06.822075 INFO::Processing subtree level 1
2026-03-18 21:35:06.921099 INFO::Adjusting the last 1 batches sequentially
2026-03-18 21:35:06.92287 INFO::Done
2026-03-18 21:35:06.923538 INFO::Acquiring quality metrics after batch effect correction.
2026-03-18 21:35:06.926708 INFO::ASW Batch was 0.240476581965387 prior to batch effect correction and is now -0.147117530895078 .
2026-03-18 21:35:06.927298 INFO::ASW Label was -0.21341875956884 prior to batch effect correction and is now -0.112820220471231 .
2026-03-18 21:35:06.928157 INFO::Total function execution time is 0.118800401687622 s and adjustment time is 0.102580308914185 s ( 86.35 )
2026-03-18 21:35:07.04284 INFO::Formatting Data.
2026-03-18 21:35:07.043612 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.044466 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.04546 INFO::Found 2 missing values.
2026-03-18 21:35:07.048091 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.048605 INFO::Done
2026-03-18 21:35:07.074023 INFO::Found NA in Reference column
2026-03-18 21:35:07.082901 INFO::Require at least two references per batch.
2026-03-18 21:35:07.101747 INFO::Formatting Data.
2026-03-18 21:35:07.102444 INFO::Recognized SummarizedExperiment
2026-03-18 21:35:07.102957 INFO::Typecasting input to dataframe.
2026-03-18 21:35:07.111732 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.112826 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.11606 INFO::Found 0 missing values.
2026-03-18 21:35:07.122275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.122838 INFO::Done
2026-03-18 21:35:07.137366 INFO::Formatting Data.
2026-03-18 21:35:07.138049 INFO::Recognized SummarizedExperiment
2026-03-18 21:35:07.138545 INFO::Typecasting input to dataframe.
2026-03-18 21:35:07.154632 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.15586 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.159137 INFO::Found 0 missing values.
2026-03-18 21:35:07.168948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.169524 INFO::Done
2026-03-18 21:35:07.183882 INFO::Formatting Data.
2026-03-18 21:35:07.184547 INFO::Recognized SummarizedExperiment
2026-03-18 21:35:07.185038 INFO::Typecasting input to dataframe.
2026-03-18 21:35:07.200337 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.201346 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.202362 INFO::Found 0 missing values.
2026-03-18 21:35:07.203222 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.
2026-03-18 21:35:07.207258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.207761 INFO::Done
2026-03-18 21:35:07.216954 INFO::Formatting Data.
2026-03-18 21:35:07.217624 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.218406 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.219326 INFO::Found 0 missing values.
2026-03-18 21:35:07.22196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.222456 INFO::Done
2026-03-18 21:35:07.232883 INFO::Formatting Data.
2026-03-18 21:35:07.233665 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.234618 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.235588 INFO::Found 0 missing values.
2026-03-18 21:35:07.23825 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.238776 INFO::Done
2026-03-18 21:35:07.26658 INFO::Formatting Data.
2026-03-18 21:35:07.267384 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.268422 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.269557 INFO::Found 1 missing values.
2026-03-18 21:35:07.272053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.272579 INFO::Done
2026-03-18 21:35:07.301004 INFO::Formatting Data.
2026-03-18 21:35:07.30204 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.30295 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.303965 INFO::Found 2 missing values.
2026-03-18 21:35:07.304868 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.
2026-03-18 21:35:07.307108 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.30764 INFO::Done
2026-03-18 21:35:07.317353 INFO::Formatting Data.
2026-03-18 21:35:07.318135 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.319005 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.319899 INFO::Found 2 missing values.
2026-03-18 21:35:07.321444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.321975 INFO::Done
2026-03-18 21:35:07.331684 INFO::Formatting Data.
2026-03-18 21:35:07.332362 INFO::Typecasting input to dataframe.
2026-03-18 21:35:07.333107 INFO::Replacing NaNs with NAs.
2026-03-18 21:35:07.333904 INFO::Removing potential empty rows and columns
2026-03-18 21:35:07.334915 INFO::Found 0 missing values.
2026-03-18 21:35:07.337613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-18 21:35:07.338119 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.196 3.270 21.208
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.281 | 1.201 | 18.655 | |
| compute_asw | 0.023 | 0.001 | 0.024 | |
| count_existing | 0.013 | 0.000 | 0.014 | |
| generate_data_covariables | 0.011 | 0.000 | 0.012 | |
| generate_dataset | 0.010 | 0.000 | 0.011 | |