Yannis Schumann
| Snapshot Date: 2025-11-06 13:45 -0500 (Thu, 06 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-07 12:00 -0500 (Fri, 07 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2025-11-06 21:23:26 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 21:24:56 -0500 (Thu, 06 Nov 2025) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 23.314 1.243 17.004
* 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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")
2025-11-06 21:24:16.797653 INFO::Formatting Data.
2025-11-06 21:24:16.799176 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:16.811099 INFO::Removing potential empty rows and columns
2025-11-06 21:24:17.068857 INFO::Found 0 missing values.
2025-11-06 21:24:17.072211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:17.072813 INFO::Done
2025-11-06 21:24:17.073352 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:17.084463 INFO::Starting hierarchical adjustment
2025-11-06 21:24:17.085289 INFO::Found 3 batches.
2025-11-06 21:24:17.085819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:17.086958 INFO::Using default BPPARAM
2025-11-06 21:24:17.087504 INFO::Processing subtree level 1
2025-11-06 21:24:17.194636 INFO::Adjusting the last 1 batches sequentially
2025-11-06 21:24:17.19693 INFO::Done
2025-11-06 21:24:17.197768 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:17.201207 INFO::ASW Batch was -0.0387479415334421 prior to batch effect correction and is now -0.0387479415334421 .
2025-11-06 21:24:17.202474 INFO::Total function execution time is 0.40545392036438 s and adjustment time is 0.111774444580078 s ( 27.57 )
2025-11-06 21:24:17.217523 INFO::Formatting Data.
2025-11-06 21:24:17.218349 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:17.219718 INFO::Removing potential empty rows and columns
2025-11-06 21:24:17.220884 INFO::Found 0 missing values.
2025-11-06 21:24:17.221892 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.
2025-11-06 21:24:17.233028 INFO::Formatting Data.
2025-11-06 21:24:17.233735 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:17.234644 INFO::Removing potential empty rows and columns
2025-11-06 21:24:17.235692 INFO::Found 0 missing values.
2025-11-06 21:24:17.236639 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.
2025-11-06 21:24:17.252857 INFO::Formatting Data.
2025-11-06 21:24:17.253701 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:17.254625 INFO::Removing potential empty rows and columns
2025-11-06 21:24:17.255687 INFO::Found 0 missing values.
2025-11-06 21:24:17.256636 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.
2025-11-06 21:24:17.261219 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:17.261776 INFO::Done
2025-11-06 21:24:17.262323 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:17.264487 INFO::Starting hierarchical adjustment
2025-11-06 21:24:17.265207 INFO::Found 2 batches.
2025-11-06 21:24:17.265729 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:17.266392 INFO::Using default BPPARAM
2025-11-06 21:24:17.266928 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:17.2679 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 21:24:17.290972 INFO::Done
2025-11-06 21:24:17.2918 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:17.293997 INFO::ASW Batch was -0.0406366491197002 prior to batch effect correction and is now -0.122671209879558 .
2025-11-06 21:24:17.294821 INFO::Total function execution time is 0.0420479774475098 s and adjustment time is 0.0258815288543701 s ( 61.55 )
2025-11-06 21:24:17.297885 INFO::Formatting Data.
2025-11-06 21:24:17.298594 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:17.307935 INFO::Formatting Data.
2025-11-06 21:24:17.308668 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:17.309625 INFO::Removing potential empty rows and columns
2025-11-06 21:24:17.310735 INFO::Found 0 missing values.
2025-11-06 21:24:17.31383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:17.31441 INFO::Done
2025-11-06 21:24:17.314945 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:17.317292 INFO::Starting hierarchical adjustment
2025-11-06 21:24:17.318028 INFO::Found 2 batches.
2025-11-06 21:24:17.318648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:17.319387 INFO::Using default BPPARAM
2025-11-06 21:24:17.319998 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:17.320986 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 21:24:17.362782 INFO::Done
2025-11-06 21:24:17.363549 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:17.365695 INFO::ASW Batch was -0.0144774803562443 prior to batch effect correction and is now -0.110561915951313 .
2025-11-06 21:24:17.366532 INFO::Total function execution time is 0.0586364269256592 s and adjustment time is 0.0448760986328125 s ( 76.53 )
2025-11-06 21:24:17.3676 INFO::Formatting Data.
2025-11-06 21:24:17.368218 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:17.369085 INFO::Removing potential empty rows and columns
2025-11-06 21:24:17.370131 INFO::Found 0 missing values.
2025-11-06 21:24:17.372899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:17.373451 INFO::Done
2025-11-06 21:24:17.373957 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:17.37601 INFO::Starting hierarchical adjustment
2025-11-06 21:24:17.376702 INFO::Found 2 batches.
2025-11-06 21:24:17.377212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:17.377796 INFO::Using default BPPARAM
2025-11-06 21:24:17.378301 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:17.379189 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 21:24:17.413727 INFO::Done
2025-11-06 21:24:17.414907 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:17.417775 INFO::ASW Batch was -0.0144774803562443 prior to batch effect correction and is now -0.110561915951313 .
2025-11-06 21:24:17.418714 INFO::Total function execution time is 0.0510919094085693 s and adjustment time is 0.0370371341705322 s ( 72.49 )
2025-11-06 21:24:20.522315 INFO::Formatting Data.
2025-11-06 21:24:20.523065 INFO::Recognized SummarizedExperiment
2025-11-06 21:24:20.523572 INFO::Typecasting input to dataframe.
2025-11-06 21:24:20.552547 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:20.553879 INFO::Removing potential empty rows and columns
2025-11-06 21:24:20.557684 INFO::Found 0 missing values.
2025-11-06 21:24:20.564708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:20.565307 INFO::Done
2025-11-06 21:24:20.565823 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:20.569435 INFO::Starting hierarchical adjustment
2025-11-06 21:24:20.57014 INFO::Found 2 batches.
2025-11-06 21:24:20.570665 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:20.571783 INFO::Using default BPPARAM
2025-11-06 21:24:20.572333 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:20.573318 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 21:24:20.629761 INFO::Done
2025-11-06 21:24:20.630558 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:20.63431 INFO::ASW Batch was -0.00059440755095304 prior to batch effect correction and is now -0.0886033582488072 .
2025-11-06 21:24:20.63516 INFO::Total function execution time is 0.113160848617554 s and adjustment time is 0.059725284576416 s ( 52.78 )
2025-11-06 21:24:20.654252 INFO::Formatting Data.
2025-11-06 21:24:20.65509 INFO::Recognized SummarizedExperiment
2025-11-06 21:24:20.655653 INFO::Typecasting input to dataframe.
2025-11-06 21:24:20.665504 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:20.666719 INFO::Removing potential empty rows and columns
2025-11-06 21:24:20.670425 INFO::Found 0 missing values.
2025-11-06 21:24:20.677525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:20.678137 INFO::Done
2025-11-06 21:24:20.678665 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:20.682268 INFO::Starting hierarchical adjustment
2025-11-06 21:24:20.682985 INFO::Found 2 batches.
2025-11-06 21:24:20.683512 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:20.684099 INFO::Using default BPPARAM
2025-11-06 21:24:20.684624 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:20.685592 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 21:24:20.710463 INFO::Done
2025-11-06 21:24:20.711181 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:20.714743 INFO::ASW Batch was -0.00140928646148152 prior to batch effect correction and is now -0.00140928646148152 .
2025-11-06 21:24:20.715579 INFO::Total function execution time is 0.0613694190979004 s and adjustment time is 0.0275881290435791 s ( 44.95 )
2025-11-06 21:24:20.733934 INFO::Formatting Data.
2025-11-06 21:24:20.734815 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:20.73573 INFO::Removing potential empty rows and columns
2025-11-06 21:24:20.736754 INFO::Found 0 missing values.
2025-11-06 21:24:20.739715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:20.740258 INFO::Done
2025-11-06 21:24:20.740769 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:20.74283 INFO::Starting hierarchical adjustment
2025-11-06 21:24:20.743558 INFO::Found 3 batches.
2025-11-06 21:24:20.744075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:20.744695 INFO::Using default BPPARAM
2025-11-06 21:24:20.745231 INFO::Processing subtree level 1
2025-11-06 21:24:20.906455 INFO::Adjusting the last 1 batches sequentially
2025-11-06 21:24:20.908967 INFO::Done
2025-11-06 21:24:20.909898 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:20.91329 INFO::ASW Batch was -0.0547198382535212 prior to batch effect correction and is now -0.194915964075429 .
2025-11-06 21:24:20.914544 INFO::Total function execution time is 0.180567741394043 s and adjustment time is 0.165469408035278 s ( 91.64 )
2025-11-06 21:24:20.931652 INFO::Skipping initial DF formatting
2025-11-06 21:24:20.932548 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:20.937097 INFO::Starting hierarchical adjustment
2025-11-06 21:24:20.938005 INFO::Found 5 batches.
2025-11-06 21:24:20.938597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:20.939261 INFO::Using default BPPARAM
2025-11-06 21:24:20.939802 INFO::Processing subtree level 1
2025-11-06 21:24:21.201442 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:21.203484 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 21:24:21.224428 INFO::Done
2025-11-06 21:24:21.225368 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:21.230073 INFO::ASW Batch was 0.567338088516019 prior to batch effect correction and is now 0.567338088516019 .
2025-11-06 21:24:21.230766 INFO::ASW Label was 0.303577282422845 prior to batch effect correction and is now 0.303577282422845 .
2025-11-06 21:24:21.231681 INFO::Total function execution time is 0.300211191177368 s and adjustment time is 0.286571502685547 s ( 95.46 )
2025-11-06 21:24:21.303801 INFO::Formatting Data.
2025-11-06 21:24:21.304612 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:21.305517 INFO::Removing potential empty rows and columns
2025-11-06 21:24:21.306551 INFO::Found 0 missing values.
2025-11-06 21:24:21.310465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:21.310973 INFO::Done
2025-11-06 21:24:21.311492 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:21.31441 INFO::Starting hierarchical adjustment
2025-11-06 21:24:21.315108 INFO::Found 5 batches.
2025-11-06 21:24:21.315655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:21.316288 INFO::Using default BPPARAM
2025-11-06 21:24:21.316812 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.
2025-11-06 21:24:21.457822 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:21.459395 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 21:24:21.475909 INFO::Done
2025-11-06 21:24:21.476615 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:21.48013 INFO::ASW Batch was 0.266948165338621 prior to batch effect correction and is now -0.0648156108964792 .
2025-11-06 21:24:21.480728 INFO::ASW Label was 0.474458292137436 prior to batch effect correction and is now 0.841448628139999 .
2025-11-06 21:24:21.481571 INFO::Total function execution time is 0.177839994430542 s and adjustment time is 0.160924673080444 s ( 90.49 )
2025-11-06 21:24:21.482453 INFO::Formatting Data.
2025-11-06 21:24:21.483079 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:21.483986 INFO::Removing potential empty rows and columns
2025-11-06 21:24:21.485042 INFO::Found 0 missing values.
2025-11-06 21:24:21.489379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:21.489909 INFO::Done
2025-11-06 21:24:21.490455 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:21.493513 INFO::Starting hierarchical adjustment
2025-11-06 21:24:21.494228 INFO::Found 5 batches.
2025-11-06 21:24:21.494794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:21.49541 INFO::Using default BPPARAM
2025-11-06 21:24:21.495913 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.
2025-11-06 21:24:21.628865 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:21.630675 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 21:24:21.648582 INFO::Done
2025-11-06 21:24:21.649433 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:21.653157 INFO::ASW Batch was 0.266948165338621 prior to batch effect correction and is now -0.0648156108964792 .
2025-11-06 21:24:21.653826 INFO::ASW Label was 0.474458292137436 prior to batch effect correction and is now 0.841448628139999 .
2025-11-06 21:24:21.654714 INFO::Total function execution time is 0.172239780426025 s and adjustment time is 0.154432773590088 s ( 89.66 )
2025-11-06 21:24:21.669484 INFO::Formatting Data.
2025-11-06 21:24:21.670393 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:21.67144 INFO::Removing potential empty rows and columns
2025-11-06 21:24:21.672563 INFO::Found 0 missing values.
2025-11-06 21:24:21.676856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:21.67746 INFO::Done
2025-11-06 21:24:21.678 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:21.681417 INFO::Starting hierarchical adjustment
2025-11-06 21:24:21.682257 INFO::Found 5 batches.
2025-11-06 21:24:21.682809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:21.683466 INFO::Using default BPPARAM
2025-11-06 21:24:21.684017 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.
2025-11-06 21:24:21.823367 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:21.825946 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 21:24:21.854043 INFO::Done
2025-11-06 21:24:21.855246 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:21.860695 INFO::ASW Batch was 0.571603751399334 prior to batch effect correction and is now 0.0051318678097706 .
2025-11-06 21:24:21.861733 INFO::ASW Label was 0.235111314436402 prior to batch effect correction and is now 0.711985448685092 .
2025-11-06 21:24:21.863055 INFO::Total function execution time is 0.193603992462158 s and adjustment time is 0.171882390975952 s ( 88.78 )
2025-11-06 21:24:21.864394 INFO::Formatting Data.
2025-11-06 21:24:21.865401 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:21.866812 INFO::Removing potential empty rows and columns
2025-11-06 21:24:21.868032 INFO::Found 0 missing values.
2025-11-06 21:24:21.872246 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:21.872806 INFO::Done
2025-11-06 21:24:21.873337 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:21.876566 INFO::Starting hierarchical adjustment
2025-11-06 21:24:21.877325 INFO::Found 5 batches.
2025-11-06 21:24:21.877871 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:21.878532 INFO::Using default BPPARAM
2025-11-06 21:24:21.879073 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.
2025-11-06 21:24:22.016629 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:22.018483 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 21:24:22.036536 INFO::Done
2025-11-06 21:24:22.037381 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.041144 INFO::ASW Batch was 0.571603751399334 prior to batch effect correction and is now 0.0051318678097706 .
2025-11-06 21:24:22.041886 INFO::ASW Label was 0.235111314436402 prior to batch effect correction and is now 0.711985448685092 .
2025-11-06 21:24:22.042782 INFO::Total function execution time is 0.178492546081543 s and adjustment time is 0.159305095672607 s ( 89.25 )
2025-11-06 21:24:22.058841 INFO::Formatting Data.
2025-11-06 21:24:22.059792 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.060861 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.062043 INFO::Found 0 missing values.
2025-11-06 21:24:22.065111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:22.065712 INFO::Done
2025-11-06 21:24:22.066287 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:22.069659 INFO::Starting hierarchical adjustment
2025-11-06 21:24:22.070463 INFO::Found 2 batches.
2025-11-06 21:24:22.071028 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:22.071709 INFO::Using default BPPARAM
2025-11-06 21:24:22.072304 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:22.073292 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 21:24:22.089823 INFO::Done
2025-11-06 21:24:22.09061 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.093935 INFO::ASW Batch was 0.530145190935395 prior to batch effect correction and is now -0.0251381868473254 .
2025-11-06 21:24:22.09461 INFO::ASW Label was 0.556911967114018 prior to batch effect correction and is now 0.929348469940276 .
2025-11-06 21:24:22.095455 INFO::Total function execution time is 0.0367815494537354 s and adjustment time is 0.0194871425628662 s ( 52.98 )
2025-11-06 21:24:22.096334 INFO::Formatting Data.
2025-11-06 21:24:22.096996 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.097942 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.099023 INFO::Found 0 missing values.
2025-11-06 21:24:22.101894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:22.10246 INFO::Done
2025-11-06 21:24:22.102976 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:22.106144 INFO::Starting hierarchical adjustment
2025-11-06 21:24:22.106902 INFO::Found 2 batches.
2025-11-06 21:24:22.107463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:22.108089 INFO::Using default BPPARAM
2025-11-06 21:24:22.108652 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:22.109627 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-06 21:24:22.125912 INFO::Done
2025-11-06 21:24:22.126725 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.13007 INFO::ASW Batch was 0.530145190935395 prior to batch effect correction and is now -0.0251381868473254 .
2025-11-06 21:24:22.130742 INFO::ASW Label was 0.556911967114018 prior to batch effect correction and is now 0.929348469940276 .
2025-11-06 21:24:22.131635 INFO::Total function execution time is 0.0353233814239502 s and adjustment time is 0.0191199779510498 s ( 54.13 )
2025-11-06 21:24:22.144274 INFO::Formatting Data.
2025-11-06 21:24:22.145315 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.146383 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.147457 INFO::Found 0 missing values.
2025-11-06 21:24:22.149837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:22.15043 INFO::Done
2025-11-06 21:24:22.150952 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:22.153101 INFO::Starting hierarchical adjustment
2025-11-06 21:24:22.153858 INFO::Found 2 batches.
2025-11-06 21:24:22.154437 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:22.155087 INFO::Using default BPPARAM
2025-11-06 21:24:22.15564 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:22.156619 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 21:24:22.191527 INFO::Done
2025-11-06 21:24:22.192344 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.194619 INFO::ASW Batch was -0.131338635369255 prior to batch effect correction and is now -0.161305181699479 .
2025-11-06 21:24:22.195562 INFO::Total function execution time is 0.0514492988586426 s and adjustment time is 0.0377726554870605 s ( 73.42 )
2025-11-06 21:24:22.210029 INFO::Formatting Data.
2025-11-06 21:24:22.211058 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.212146 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.213264 INFO::Found 0 missing values.
2025-11-06 21:24:22.214409 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.
2025-11-06 21:24:22.218934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:22.219808 INFO::Done
2025-11-06 21:24:22.220345 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:22.223411 INFO::Starting hierarchical adjustment
2025-11-06 21:24:22.224103 INFO::Found 2 batches.
2025-11-06 21:24:22.22464 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:22.225249 INFO::Using default BPPARAM
2025-11-06 21:24:22.225774 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:22.226691 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 21:24:22.244526 INFO::Done
2025-11-06 21:24:22.24524 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.248269 INFO::ASW Batch was 0.689146805311435 prior to batch effect correction and is now -0.0161030897977193 .
2025-11-06 21:24:22.248847 INFO::ASW Label was 0.377236821383306 prior to batch effect correction and is now 0.913834216172984 .
2025-11-06 21:24:22.249596 INFO::Total function execution time is 0.039808988571167 s and adjustment time is 0.0205278396606445 s ( 51.57 )
2025-11-06 21:24:22.250336 INFO::Formatting Data.
2025-11-06 21:24:22.250923 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.251784 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.252739 INFO::Found 0 missing values.
2025-11-06 21:24:22.253596 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.
2025-11-06 21:24:22.25782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:22.258361 INFO::Done
2025-11-06 21:24:22.258862 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:22.261668 INFO::Starting hierarchical adjustment
2025-11-06 21:24:22.262359 INFO::Found 2 batches.
2025-11-06 21:24:22.262867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:22.263458 INFO::Using default BPPARAM
2025-11-06 21:24:22.263967 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:22.26485 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 21:24:22.280526 INFO::Done
2025-11-06 21:24:22.281183 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.283959 INFO::ASW Batch was 0.689146805311435 prior to batch effect correction and is now -0.0161030897977193 .
2025-11-06 21:24:22.284525 INFO::ASW Label was 0.377236821383306 prior to batch effect correction and is now 0.913834216172984 .
2025-11-06 21:24:22.285276 INFO::Total function execution time is 0.0349583625793457 s and adjustment time is 0.0182855129241943 s ( 52.31 )
2025-11-06 21:24:22.48521 INFO::Formatting Data.
2025-11-06 21:24:22.48624 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.487244 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.488376 INFO::Found 0 missing values.
2025-11-06 21:24:22.491511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:22.49206 INFO::Done
2025-11-06 21:24:22.492684 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:22.495086 INFO::Starting hierarchical adjustment
2025-11-06 21:24:22.495798 INFO::Found 3 batches.
2025-11-06 21:24:22.496334 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:22.497 INFO::Using default BPPARAM
2025-11-06 21:24:22.497539 INFO::Processing subtree level 1
2025-11-06 21:24:22.593987 INFO::Adjusting the last 1 batches sequentially
2025-11-06 21:24:22.595859 INFO::Done
2025-11-06 21:24:22.596506 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.599012 INFO::ASW Batch was -0.100238125962564 prior to batch effect correction and is now -0.100238125962564 .
2025-11-06 21:24:22.599975 INFO::Total function execution time is 0.115200757980347 s and adjustment time is 0.100194931030273 s ( 86.97 )
2025-11-06 21:24:22.601128 INFO::Formatting Data.
2025-11-06 21:24:22.601784 INFO::Typecasting input to dataframe.
2025-11-06 21:24:22.602589 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.603553 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.604679 INFO::Found 0 missing values.
2025-11-06 21:24:22.607743 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:22.608298 INFO::Done
2025-11-06 21:24:22.608832 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:22.610831 INFO::Starting hierarchical adjustment
2025-11-06 21:24:22.611557 INFO::Found 3 batches.
2025-11-06 21:24:22.612081 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:22.612705 INFO::Using default BPPARAM
2025-11-06 21:24:22.613259 INFO::Processing subtree level 1
2025-11-06 21:24:22.700973 INFO::Adjusting the last 1 batches sequentially
2025-11-06 21:24:22.702995 INFO::Done
2025-11-06 21:24:22.703706 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.706424 INFO::ASW Batch was -0.100238125962564 prior to batch effect correction and is now -0.100238125962564 .
2025-11-06 21:24:22.707444 INFO::Total function execution time is 0.106310844421387 s and adjustment time is 0.0915451049804688 s ( 86.11 )
2025-11-06 21:24:22.723363 INFO::Formatting Data.
2025-11-06 21:24:22.724378 INFO::Typecasting input to dataframe.
2025-11-06 21:24:22.725479 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.726586 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.727812 INFO::Found 0 missing values.
2025-11-06 21:24:22.73097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:22.73155 INFO::Done
2025-11-06 21:24:22.732085 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:22.734331 INFO::Starting hierarchical adjustment
2025-11-06 21:24:22.73506 INFO::Found 3 batches.
2025-11-06 21:24:22.735638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:22.736277 INFO::Using default BPPARAM
2025-11-06 21:24:22.736832 INFO::Processing subtree level 1
2025-11-06 21:24:22.829665 INFO::Adjusting the last 1 batches sequentially
2025-11-06 21:24:22.831671 INFO::Done
2025-11-06 21:24:22.832439 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:22.835251 INFO::ASW Batch was -0.0565855038960866 prior to batch effect correction and is now -0.0565855038960866 .
2025-11-06 21:24:22.836299 INFO::Total function execution time is 0.113024950027466 s and adjustment time is 0.0967485904693604 s ( 85.6 )
2025-11-06 21:24:22.987384 INFO::Formatting Data.
2025-11-06 21:24:22.988276 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:22.98946 INFO::Removing potential empty rows and columns
2025-11-06 21:24:22.992474 INFO::Found 1000 missing values.
2025-11-06 21:24:23.011527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:23.012461 INFO::Done
2025-11-06 21:24:23.013063 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:23.018787 INFO::Starting hierarchical adjustment
2025-11-06 21:24:23.019651 INFO::Found 10 batches.
2025-11-06 21:24:23.020211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:23.020857 INFO::Using default BPPARAM
2025-11-06 21:24:23.021421 INFO::Processing subtree level 1
2025-11-06 21:24:23.170428 INFO::Processing subtree level 2
2025-11-06 21:24:23.313542 INFO::Adjusting the last 1 batches sequentially
2025-11-06 21:24:23.315617 INFO::Done
2025-11-06 21:24:23.316344 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:23.322038 INFO::ASW Batch was 0.518445965094799 prior to batch effect correction and is now 0.518445965094799 .
2025-11-06 21:24:23.322744 INFO::ASW Label was 0.308854505841285 prior to batch effect correction and is now 0.308854505841285 .
2025-11-06 21:24:23.323735 INFO::Total function execution time is 0.336460113525391 s and adjustment time is 0.296122074127197 s ( 88.01 )
2025-11-06 21:24:23.324645 INFO::Formatting Data.
2025-11-06 21:24:23.325341 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:23.326628 INFO::Removing potential empty rows and columns
2025-11-06 21:24:23.329424 INFO::Found 1000 missing values.
2025-11-06 21:24:23.34811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:23.348934 INFO::Done
2025-11-06 21:24:23.349575 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:23.355252 INFO::Starting hierarchical adjustment
2025-11-06 21:24:23.356073 INFO::Found 10 batches.
2025-11-06 21:24:24.536325 INFO::Set up parallel execution backend with 2 workers
2025-11-06 21:24:24.541818 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-06 21:24:25.679606 INFO::Adjusting the last 2 batches sequentially
2025-11-06 21:24:25.681333 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-06 21:24:25.696711 INFO::Done
2025-11-06 21:24:25.697291 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:25.701549 INFO::ASW Batch was 0.518445965094799 prior to batch effect correction and is now 0.518445965094799 .
2025-11-06 21:24:25.70205 INFO::ASW Label was 0.308854505841285 prior to batch effect correction and is now 0.308854505841285 .
2025-11-06 21:24:25.70274 INFO::Total function execution time is 2.37815594673157 s and adjustment time is 2.34081077575684 s ( 98.43 )
2025-11-06 21:24:25.841839 INFO::Formatting Data.
2025-11-06 21:24:25.842548 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:25.84338 INFO::Removing potential empty rows and columns
2025-11-06 21:24:25.844392 INFO::Found 0 missing values.
2025-11-06 21:24:25.847794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:25.848316 INFO::Done
2025-11-06 21:24:25.848804 INFO::Acquiring quality metrics before batch effect correction.
2025-11-06 21:24:25.851455 INFO::Starting hierarchical adjustment
2025-11-06 21:24:25.852125 INFO::Found 3 batches.
2025-11-06 21:24:25.852624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-06 21:24:25.853206 INFO::Using default BPPARAM
2025-11-06 21:24:25.853703 INFO::Processing subtree level 1
2025-11-06 21:24:25.954395 INFO::Adjusting the last 1 batches sequentially
2025-11-06 21:24:25.956061 INFO::Done
2025-11-06 21:24:25.956661 INFO::Acquiring quality metrics after batch effect correction.
2025-11-06 21:24:25.959792 INFO::ASW Batch was 0.250559810772103 prior to batch effect correction and is now -0.125787196067693 .
2025-11-06 21:24:25.960394 INFO::ASW Label was -0.206514396517518 prior to batch effect correction and is now -0.0665351390022784 .
2025-11-06 21:24:25.961282 INFO::Total function execution time is 0.119436025619507 s and adjustment time is 0.104067325592041 s ( 87.13 )
2025-11-06 21:24:26.068079 INFO::Formatting Data.
2025-11-06 21:24:26.068889 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.069743 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.070725 INFO::Found 2 missing values.
2025-11-06 21:24:26.073384 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.073889 INFO::Done
2025-11-06 21:24:26.098211 INFO::Found NA in Reference column
2025-11-06 21:24:26.106784 INFO::Require at least two references per batch.
2025-11-06 21:24:26.125414 INFO::Formatting Data.
2025-11-06 21:24:26.126099 INFO::Recognized SummarizedExperiment
2025-11-06 21:24:26.126624 INFO::Typecasting input to dataframe.
2025-11-06 21:24:26.135519 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.136564 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.139748 INFO::Found 0 missing values.
2025-11-06 21:24:26.145885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.146416 INFO::Done
2025-11-06 21:24:26.160818 INFO::Formatting Data.
2025-11-06 21:24:26.161511 INFO::Recognized SummarizedExperiment
2025-11-06 21:24:26.162014 INFO::Typecasting input to dataframe.
2025-11-06 21:24:26.178031 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.179167 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.182469 INFO::Found 0 missing values.
2025-11-06 21:24:26.192248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.192808 INFO::Done
2025-11-06 21:24:26.207165 INFO::Formatting Data.
2025-11-06 21:24:26.207792 INFO::Recognized SummarizedExperiment
2025-11-06 21:24:26.208284 INFO::Typecasting input to dataframe.
2025-11-06 21:24:26.223682 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.224633 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.225659 INFO::Found 0 missing values.
2025-11-06 21:24:26.226535 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.
2025-11-06 21:24:26.230593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.23109 INFO::Done
2025-11-06 21:24:26.240014 INFO::Formatting Data.
2025-11-06 21:24:26.240747 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.241703 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.242683 INFO::Found 0 missing values.
2025-11-06 21:24:26.245423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.245928 INFO::Done
2025-11-06 21:24:26.256107 INFO::Formatting Data.
2025-11-06 21:24:26.256933 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.257808 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.258848 INFO::Found 0 missing values.
2025-11-06 21:24:26.261791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.262332 INFO::Done
2025-11-06 21:24:26.290785 INFO::Formatting Data.
2025-11-06 21:24:26.291591 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.292674 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.293882 INFO::Found 1 missing values.
2025-11-06 21:24:26.296617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.29726 INFO::Done
2025-11-06 21:24:26.315981 INFO::Formatting Data.
2025-11-06 21:24:26.316834 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.317696 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.318597 INFO::Found 2 missing values.
2025-11-06 21:24:26.319489 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.
2025-11-06 21:24:26.321684 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.322229 INFO::Done
2025-11-06 21:24:26.331697 INFO::Formatting Data.
2025-11-06 21:24:26.332508 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.333364 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.334311 INFO::Found 2 missing values.
2025-11-06 21:24:26.335902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.336468 INFO::Done
2025-11-06 21:24:26.346272 INFO::Formatting Data.
2025-11-06 21:24:26.347036 INFO::Typecasting input to dataframe.
2025-11-06 21:24:26.347831 INFO::Replacing NaNs with NAs.
2025-11-06 21:24:26.348659 INFO::Removing potential empty rows and columns
2025-11-06 21:24:26.349648 INFO::Found 0 missing values.
2025-11-06 21:24:26.35238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-06 21:24:26.352867 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.808 3.795 21.336
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.314 | 1.243 | 17.004 | |
| compute_asw | 0.026 | 0.000 | 0.025 | |
| count_existing | 0.012 | 0.002 | 0.015 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.012 | 0.001 | 0.012 | |