Yannis Schumann
| Snapshot Date: 2025-08-19 13:45 -0400 (Tue, 19 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-20 12:05 -0400 (Wed, 20 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
| 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 162/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.5.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-08-19 18:19:12 -0400 (Tue, 19 Aug 2025) |
| EndedAt: 2025-08-19 18:19:43 -0400 (Tue, 19 Aug 2025) |
| EllapsedTime: 31.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* 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 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 9.718 0.402 6.98
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** 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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")
2025-08-19 18:19:35.57362 INFO::Formatting Data.
2025-08-19 18:19:35.575392 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:35.580309 INFO::Removing potential empty rows and columns
2025-08-19 18:19:35.688034 INFO::Found 0 missing values.
2025-08-19 18:19:35.689292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:35.689521 INFO::Done
2025-08-19 18:19:35.689729 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:35.695683 INFO::Starting hierarchical adjustment
2025-08-19 18:19:35.696035 INFO::Found 3 batches.
2025-08-19 18:19:35.696227 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:35.696667 INFO::Using default BPPARAM
2025-08-19 18:19:35.696882 INFO::Processing subtree level 1
2025-08-19 18:19:35.751981 INFO::Adjusting the last 1 batches sequentially
2025-08-19 18:19:35.753332 INFO::Done
2025-08-19 18:19:35.753593 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:35.754934 INFO::ASW Batch was 0.012633129572048 prior to batch effect correction and is now 0.012633129572048 .
2025-08-19 18:19:35.755466 INFO::Total function execution time is 0.182443141937256 s and adjustment time is 0.0573561191558838 s ( 31.44 )
2025-08-19 18:19:35.763026 INFO::Formatting Data.
2025-08-19 18:19:35.763319 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:35.763683 INFO::Removing potential empty rows and columns
2025-08-19 18:19:35.764153 INFO::Found 0 missing values.
2025-08-19 18:19:35.764502 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.
2025-08-19 18:19:35.769768 INFO::Formatting Data.
2025-08-19 18:19:35.770015 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:35.770302 INFO::Removing potential empty rows and columns
2025-08-19 18:19:35.770651 INFO::Found 0 missing values.
2025-08-19 18:19:35.770955 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.
2025-08-19 18:19:35.777735 INFO::Formatting Data.
2025-08-19 18:19:35.778021 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:35.778368 INFO::Removing potential empty rows and columns
2025-08-19 18:19:35.778737 INFO::Found 0 missing values.
2025-08-19 18:19:35.779042 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.
2025-08-19 18:19:35.78043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:35.780617 INFO::Done
2025-08-19 18:19:35.780788 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:35.781481 INFO::Starting hierarchical adjustment
2025-08-19 18:19:35.781697 INFO::Found 2 batches.
2025-08-19 18:19:35.781861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:35.782093 INFO::Using default BPPARAM
2025-08-19 18:19:35.782249 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:35.782532 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 18:19:35.79356 INFO::Done
2025-08-19 18:19:35.793869 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:35.794628 INFO::ASW Batch was -0.0177784879659895 prior to batch effect correction and is now -0.116808346203681 .
2025-08-19 18:19:35.794896 INFO::Total function execution time is 0.0172038078308105 s and adjustment time is 0.0118849277496338 s ( 69.08 )
2025-08-19 18:19:35.795948 INFO::Formatting Data.
2025-08-19 18:19:35.796153 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:35.799109 INFO::Formatting Data.
2025-08-19 18:19:35.799335 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:35.799615 INFO::Removing potential empty rows and columns
2025-08-19 18:19:35.799953 INFO::Found 0 missing values.
2025-08-19 18:19:35.800859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:35.801034 INFO::Done
2025-08-19 18:19:35.801197 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:35.801879 INFO::Starting hierarchical adjustment
2025-08-19 18:19:35.802083 INFO::Found 2 batches.
2025-08-19 18:19:35.80232 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:35.802598 INFO::Using default BPPARAM
2025-08-19 18:19:35.802786 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:35.803069 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 18:19:35.82237 INFO::Done
2025-08-19 18:19:35.822595 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:35.823206 INFO::ASW Batch was 0.162240217920796 prior to batch effect correction and is now -0.115364286303074 .
2025-08-19 18:19:35.823449 INFO::Total function execution time is 0.0243408679962158 s and adjustment time is 0.0203220844268799 s ( 83.49 )
2025-08-19 18:19:35.823745 INFO::Formatting Data.
2025-08-19 18:19:35.823911 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:35.824154 INFO::Removing potential empty rows and columns
2025-08-19 18:19:35.82443 INFO::Found 0 missing values.
2025-08-19 18:19:35.825193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:35.825345 INFO::Done
2025-08-19 18:19:35.825556 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:35.826171 INFO::Starting hierarchical adjustment
2025-08-19 18:19:35.82638 INFO::Found 2 batches.
2025-08-19 18:19:35.826537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:35.826709 INFO::Using default BPPARAM
2025-08-19 18:19:35.826848 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:35.827089 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 18:19:35.831808 INFO::Done
2025-08-19 18:19:35.832021 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:35.832617 INFO::ASW Batch was 0.162240217920796 prior to batch effect correction and is now -0.115364286303074 .
2025-08-19 18:19:35.832849 INFO::Total function execution time is 0.0090939998626709 s and adjustment time is 0.00546979904174805 s ( 60.15 )
2025-08-19 18:19:36.996123 INFO::Formatting Data.
2025-08-19 18:19:36.996398 INFO::Recognized SummarizedExperiment
2025-08-19 18:19:36.996565 INFO::Typecasting input to dataframe.
2025-08-19 18:19:37.007142 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.00757 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.008746 INFO::Found 0 missing values.
2025-08-19 18:19:37.010861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.011068 INFO::Done
2025-08-19 18:19:37.011225 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.01241 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.012632 INFO::Found 2 batches.
2025-08-19 18:19:37.012783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.013114 INFO::Using default BPPARAM
2025-08-19 18:19:37.013266 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.013555 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 18:19:37.031151 INFO::Done
2025-08-19 18:19:37.031401 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.032624 INFO::ASW Batch was -0.00131810539464567 prior to batch effect correction and is now -0.0882886867161906 .
2025-08-19 18:19:37.032885 INFO::Total function execution time is 0.0368649959564209 s and adjustment time is 0.0185470581054688 s ( 50.31 )
2025-08-19 18:19:37.038978 INFO::Formatting Data.
2025-08-19 18:19:37.039193 INFO::Recognized SummarizedExperiment
2025-08-19 18:19:37.039348 INFO::Typecasting input to dataframe.
2025-08-19 18:19:37.042159 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.042523 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.043635 INFO::Found 0 missing values.
2025-08-19 18:19:37.045686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.045846 INFO::Done
2025-08-19 18:19:37.046003 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.047144 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.04735 INFO::Found 2 batches.
2025-08-19 18:19:37.047499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.047674 INFO::Using default BPPARAM
2025-08-19 18:19:37.047813 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.048086 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 18:19:37.055868 INFO::Done
2025-08-19 18:19:37.056078 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.057207 INFO::ASW Batch was 0.00883413762747225 prior to batch effect correction and is now 0.00883413762747225 .
2025-08-19 18:19:37.057453 INFO::Total function execution time is 0.0184760093688965 s and adjustment time is 0.00855016708374023 s ( 46.28 )
2025-08-19 18:19:37.065574 INFO::Formatting Data.
2025-08-19 18:19:37.065817 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.066095 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.066411 INFO::Found 0 missing values.
2025-08-19 18:19:37.067253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.067411 INFO::Done
2025-08-19 18:19:37.067562 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.068161 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.068363 INFO::Found 3 batches.
2025-08-19 18:19:37.068511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.068687 INFO::Using default BPPARAM
2025-08-19 18:19:37.06883 INFO::Processing subtree level 1
2025-08-19 18:19:37.127589 INFO::Adjusting the last 1 batches sequentially
2025-08-19 18:19:37.129833 INFO::Done
2025-08-19 18:19:37.130024 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.132424 INFO::ASW Batch was -0.105896680082098 prior to batch effect correction and is now -0.152897081441277 .
2025-08-19 18:19:37.132939 INFO::Total function execution time is 0.0673627853393555 s and adjustment time is 0.0615041255950928 s ( 91.3 )
2025-08-19 18:19:37.138897 INFO::Skipping initial DF formatting
2025-08-19 18:19:37.139115 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.140536 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.140786 INFO::Found 5 batches.
2025-08-19 18:19:37.140967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.141307 INFO::Using default BPPARAM
2025-08-19 18:19:37.141463 INFO::Processing subtree level 1
2025-08-19 18:19:37.239791 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.241043 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 18:19:37.257889 INFO::Done
2025-08-19 18:19:37.258485 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.261481 INFO::ASW Batch was 0.489034643344948 prior to batch effect correction and is now 0.489034643344948 .
2025-08-19 18:19:37.261859 INFO::ASW Label was 0.430893924380369 prior to batch effect correction and is now 0.430893924380369 .
2025-08-19 18:19:37.262572 INFO::Total function execution time is 0.12366509437561 s and adjustment time is 0.117131948471069 s ( 94.72 )
2025-08-19 18:19:37.308273 INFO::Formatting Data.
2025-08-19 18:19:37.308615 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.308968 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.309344 INFO::Found 0 missing values.
2025-08-19 18:19:37.310878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.31106 INFO::Done
2025-08-19 18:19:37.311228 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.312347 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.312618 INFO::Found 5 batches.
2025-08-19 18:19:37.312823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.31311 INFO::Using default BPPARAM
2025-08-19 18:19:37.313342 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.
2025-08-19 18:19:37.377851 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.380369 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 18:19:37.390679 INFO::Done
2025-08-19 18:19:37.391065 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.39298 INFO::ASW Batch was 0.332106166385673 prior to batch effect correction and is now -0.0229122673218538 .
2025-08-19 18:19:37.393431 INFO::ASW Label was 0.531107349577623 prior to batch effect correction and is now 0.746269618572215 .
2025-08-19 18:19:37.393907 INFO::Total function execution time is 0.0856428146362305 s and adjustment time is 0.0780980587005615 s ( 91.19 )
2025-08-19 18:19:37.394349 INFO::Formatting Data.
2025-08-19 18:19:37.3946 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.395132 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.395729 INFO::Found 0 missing values.
2025-08-19 18:19:37.397895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.398176 INFO::Done
2025-08-19 18:19:37.398452 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.399793 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.400061 INFO::Found 5 batches.
2025-08-19 18:19:37.400269 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.400557 INFO::Using default BPPARAM
2025-08-19 18:19:37.400795 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.
2025-08-19 18:19:37.456785 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.463192 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 18:19:37.474777 INFO::Done
2025-08-19 18:19:37.475061 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.477225 INFO::ASW Batch was 0.332106166385673 prior to batch effect correction and is now -0.0229122673218538 .
2025-08-19 18:19:37.477505 INFO::ASW Label was 0.531107349577623 prior to batch effect correction and is now 0.746269618572215 .
2025-08-19 18:19:37.478032 INFO::Total function execution time is 0.0836591720581055 s and adjustment time is 0.0747530460357666 s ( 89.35 )
2025-08-19 18:19:37.484761 INFO::Formatting Data.
2025-08-19 18:19:37.485031 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.485397 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.485824 INFO::Found 0 missing values.
2025-08-19 18:19:37.487305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.48754 INFO::Done
2025-08-19 18:19:37.487722 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.48924 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.489516 INFO::Found 5 batches.
2025-08-19 18:19:37.489735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.490017 INFO::Using default BPPARAM
2025-08-19 18:19:37.490208 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.
2025-08-19 18:19:37.550987 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.552944 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 18:19:37.563234 INFO::Done
2025-08-19 18:19:37.563537 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.565543 INFO::ASW Batch was 0.445801376551084 prior to batch effect correction and is now -0.0690439120657251 .
2025-08-19 18:19:37.56578 INFO::ASW Label was 0.326443070198223 prior to batch effect correction and is now 0.78864290119178 .
2025-08-19 18:19:37.566148 INFO::Total function execution time is 0.0813989639282227 s and adjustment time is 0.073775053024292 s ( 90.63 )
2025-08-19 18:19:37.566509 INFO::Formatting Data.
2025-08-19 18:19:37.566874 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.567197 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.567589 INFO::Found 0 missing values.
2025-08-19 18:19:37.569067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.569251 INFO::Done
2025-08-19 18:19:37.569439 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.570462 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.570729 INFO::Found 5 batches.
2025-08-19 18:19:37.570941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.571215 INFO::Using default BPPARAM
2025-08-19 18:19:37.571388 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.
2025-08-19 18:19:37.62972 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.632108 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 18:19:37.646118 INFO::Done
2025-08-19 18:19:37.646497 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.64888 INFO::ASW Batch was 0.445801376551084 prior to batch effect correction and is now -0.0690439120657251 .
2025-08-19 18:19:37.64923 INFO::ASW Label was 0.326443070198223 prior to batch effect correction and is now 0.78864290119178 .
2025-08-19 18:19:37.649701 INFO::Total function execution time is 0.08315110206604 s and adjustment time is 0.0754029750823975 s ( 90.68 )
2025-08-19 18:19:37.657879 INFO::Formatting Data.
2025-08-19 18:19:37.658164 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.658493 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.658921 INFO::Found 0 missing values.
2025-08-19 18:19:37.659922 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.66011 INFO::Done
2025-08-19 18:19:37.660331 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.661337 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.661698 INFO::Found 2 batches.
2025-08-19 18:19:37.661883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.66212 INFO::Using default BPPARAM
2025-08-19 18:19:37.6623 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.662568 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 18:19:37.66784 INFO::Done
2025-08-19 18:19:37.668046 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.669072 INFO::ASW Batch was 0.751355564087004 prior to batch effect correction and is now -0.00842905178530761 .
2025-08-19 18:19:37.669369 INFO::ASW Label was 0.305920524293731 prior to batch effect correction and is now 0.881467339490268 .
2025-08-19 18:19:37.66966 INFO::Total function execution time is 0.0118222236633301 s and adjustment time is 0.00619006156921387 s ( 52.36 )
2025-08-19 18:19:37.669941 INFO::Formatting Data.
2025-08-19 18:19:37.670272 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.670635 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.671015 INFO::Found 0 missing values.
2025-08-19 18:19:37.671978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.67217 INFO::Done
2025-08-19 18:19:37.672372 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.673423 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.67368 INFO::Found 2 batches.
2025-08-19 18:19:37.673842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.674028 INFO::Using default BPPARAM
2025-08-19 18:19:37.674194 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.674496 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 18:19:37.67983 INFO::Done
2025-08-19 18:19:37.680036 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.681014 INFO::ASW Batch was 0.751355564087004 prior to batch effect correction and is now -0.00842905178530761 .
2025-08-19 18:19:37.681224 INFO::ASW Label was 0.305920524293731 prior to batch effect correction and is now 0.881467339490268 .
2025-08-19 18:19:37.681484 INFO::Total function execution time is 0.0115358829498291 s and adjustment time is 0.00619697570800781 s ( 53.72 )
2025-08-19 18:19:37.686846 INFO::Formatting Data.
2025-08-19 18:19:37.687114 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.687406 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.687726 INFO::Found 0 missing values.
2025-08-19 18:19:37.688428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.688617 INFO::Done
2025-08-19 18:19:37.68892 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.68973 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.690021 INFO::Found 2 batches.
2025-08-19 18:19:37.690206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.690484 INFO::Using default BPPARAM
2025-08-19 18:19:37.69067 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.691043 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 18:19:37.70607 INFO::Done
2025-08-19 18:19:37.706342 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.707369 INFO::ASW Batch was 0.0913252503794593 prior to batch effect correction and is now -0.103166680525985 .
2025-08-19 18:19:37.707713 INFO::Total function execution time is 0.0208778381347656 s and adjustment time is 0.016106128692627 s ( 77.14 )
2025-08-19 18:19:37.712674 INFO::Formatting Data.
2025-08-19 18:19:37.712906 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.713191 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.713526 INFO::Found 0 missing values.
2025-08-19 18:19:37.714031 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.
2025-08-19 18:19:37.715629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.715822 INFO::Done
2025-08-19 18:19:37.716071 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.717187 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.717416 INFO::Found 2 batches.
2025-08-19 18:19:37.717602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.717839 INFO::Using default BPPARAM
2025-08-19 18:19:37.718005 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.718293 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 18:19:37.7241 INFO::Done
2025-08-19 18:19:37.72433 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.72531 INFO::ASW Batch was 0.691628021268431 prior to batch effect correction and is now 0.112559572721655 .
2025-08-19 18:19:37.725496 INFO::ASW Label was 0.39787770943375 prior to batch effect correction and is now 0.823795796693824 .
2025-08-19 18:19:37.725735 INFO::Total function execution time is 0.0130860805511475 s and adjustment time is 0.00671911239624023 s ( 51.35 )
2025-08-19 18:19:37.725962 INFO::Formatting Data.
2025-08-19 18:19:37.726132 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.726408 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.726705 INFO::Found 0 missing values.
2025-08-19 18:19:37.72698 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.
2025-08-19 18:19:37.728655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.72886 INFO::Done
2025-08-19 18:19:37.72903 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.730004 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.730241 INFO::Found 2 batches.
2025-08-19 18:19:37.730417 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.730615 INFO::Using default BPPARAM
2025-08-19 18:19:37.730774 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:37.731058 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 18:19:37.736502 INFO::Done
2025-08-19 18:19:37.736727 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.737756 INFO::ASW Batch was 0.691628021268431 prior to batch effect correction and is now 0.112559572721655 .
2025-08-19 18:19:37.737973 INFO::ASW Label was 0.39787770943375 prior to batch effect correction and is now 0.823795796693824 .
2025-08-19 18:19:37.738231 INFO::Total function execution time is 0.0122580528259277 s and adjustment time is 0.00629997253417969 s ( 51.39 )
2025-08-19 18:19:37.807455 INFO::Formatting Data.
2025-08-19 18:19:37.807774 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.808083 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.808422 INFO::Found 0 missing values.
2025-08-19 18:19:37.809303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.809483 INFO::Done
2025-08-19 18:19:37.809635 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.810277 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.810474 INFO::Found 3 batches.
2025-08-19 18:19:37.810622 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.8108 INFO::Using default BPPARAM
2025-08-19 18:19:37.810942 INFO::Processing subtree level 1
2025-08-19 18:19:37.850996 INFO::Adjusting the last 1 batches sequentially
2025-08-19 18:19:37.852544 INFO::Done
2025-08-19 18:19:37.85275 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.85446 INFO::ASW Batch was -0.0465054021834032 prior to batch effect correction and is now -0.0465054021834032 .
2025-08-19 18:19:37.854871 INFO::Total function execution time is 0.0474550724029541 s and adjustment time is 0.0421090126037598 s ( 88.73 )
2025-08-19 18:19:37.855235 INFO::Formatting Data.
2025-08-19 18:19:37.855432 INFO::Typecasting input to dataframe.
2025-08-19 18:19:37.855661 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.855959 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.856362 INFO::Found 0 missing values.
2025-08-19 18:19:37.857313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.857484 INFO::Done
2025-08-19 18:19:37.85765 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.858362 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.858625 INFO::Found 3 batches.
2025-08-19 18:19:37.858811 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.859056 INFO::Using default BPPARAM
2025-08-19 18:19:37.859229 INFO::Processing subtree level 1
2025-08-19 18:19:37.900937 INFO::Adjusting the last 1 batches sequentially
2025-08-19 18:19:37.902042 INFO::Done
2025-08-19 18:19:37.902417 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.903984 INFO::ASW Batch was -0.0465054021834032 prior to batch effect correction and is now -0.0465054021834032 .
2025-08-19 18:19:37.904334 INFO::Total function execution time is 0.0490829944610596 s and adjustment time is 0.0434601306915283 s ( 88.54 )
2025-08-19 18:19:37.9105 INFO::Formatting Data.
2025-08-19 18:19:37.910751 INFO::Typecasting input to dataframe.
2025-08-19 18:19:37.911021 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:37.911337 INFO::Removing potential empty rows and columns
2025-08-19 18:19:37.911746 INFO::Found 0 missing values.
2025-08-19 18:19:37.91273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:37.912915 INFO::Done
2025-08-19 18:19:37.913078 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:37.913673 INFO::Starting hierarchical adjustment
2025-08-19 18:19:37.913888 INFO::Found 3 batches.
2025-08-19 18:19:37.91404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:37.914247 INFO::Using default BPPARAM
2025-08-19 18:19:37.914409 INFO::Processing subtree level 1
2025-08-19 18:19:37.9527 INFO::Adjusting the last 1 batches sequentially
2025-08-19 18:19:37.954595 INFO::Done
2025-08-19 18:19:37.954799 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:37.956926 INFO::ASW Batch was -0.0694835971673435 prior to batch effect correction and is now -0.0694835971673435 .
2025-08-19 18:19:37.957397 INFO::Total function execution time is 0.0470421314239502 s and adjustment time is 0.0407440662384033 s ( 86.61 )
2025-08-19 18:19:38.02697 INFO::Formatting Data.
2025-08-19 18:19:38.027374 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:38.027871 INFO::Removing potential empty rows and columns
2025-08-19 18:19:38.028934 INFO::Found 1000 missing values.
2025-08-19 18:19:38.034669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:38.034882 INFO::Done
2025-08-19 18:19:38.035066 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:38.037249 INFO::Starting hierarchical adjustment
2025-08-19 18:19:38.037498 INFO::Found 10 batches.
2025-08-19 18:19:38.037679 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:38.037923 INFO::Using default BPPARAM
2025-08-19 18:19:38.038506 INFO::Processing subtree level 1
2025-08-19 18:19:38.091736 INFO::Processing subtree level 2
2025-08-19 18:19:38.156716 INFO::Adjusting the last 1 batches sequentially
2025-08-19 18:19:38.158993 INFO::Done
2025-08-19 18:19:38.159328 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:38.163888 INFO::ASW Batch was 0.505084664509634 prior to batch effect correction and is now 0.505084664509634 .
2025-08-19 18:19:38.164152 INFO::ASW Label was 0.323458390936859 prior to batch effect correction and is now 0.323458390936859 .
2025-08-19 18:19:38.164861 INFO::Total function execution time is 0.137764930725098 s and adjustment time is 0.121531963348389 s ( 88.22 )
2025-08-19 18:19:38.165337 INFO::Formatting Data.
2025-08-19 18:19:38.16567 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:38.166274 INFO::Removing potential empty rows and columns
2025-08-19 18:19:38.168373 INFO::Found 1000 missing values.
2025-08-19 18:19:38.174043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:38.174254 INFO::Done
2025-08-19 18:19:38.174439 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:38.176293 INFO::Starting hierarchical adjustment
2025-08-19 18:19:38.176542 INFO::Found 10 batches.
2025-08-19 18:19:38.635197 INFO::Set up parallel execution backend with 2 workers
2025-08-19 18:19:38.635486 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-19 18:19:39.137601 INFO::Adjusting the last 2 batches sequentially
2025-08-19 18:19:39.138161 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 18:19:39.143481 INFO::Done
2025-08-19 18:19:39.14368 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:39.145426 INFO::ASW Batch was 0.505084664509634 prior to batch effect correction and is now 0.505084664509634 .
2025-08-19 18:19:39.145593 INFO::ASW Label was 0.323458390936859 prior to batch effect correction and is now 0.323458390936859 .
2025-08-19 18:19:39.14582 INFO::Total function execution time is 0.980534076690674 s and adjustment time is 0.966991901397705 s ( 98.62 )
2025-08-19 18:19:39.210566 INFO::Formatting Data.
2025-08-19 18:19:39.210862 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.211214 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.21165 INFO::Found 0 missing values.
2025-08-19 18:19:39.212928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.213116 INFO::Done
2025-08-19 18:19:39.213283 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 18:19:39.214234 INFO::Starting hierarchical adjustment
2025-08-19 18:19:39.214474 INFO::Found 3 batches.
2025-08-19 18:19:39.21463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 18:19:39.214867 INFO::Using default BPPARAM
2025-08-19 18:19:39.215036 INFO::Processing subtree level 1
2025-08-19 18:19:39.273817 INFO::Adjusting the last 1 batches sequentially
2025-08-19 18:19:39.276071 INFO::Done
2025-08-19 18:19:39.27635 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 18:19:39.27896 INFO::ASW Batch was 0.171369485767228 prior to batch effect correction and is now -0.143827961978331 .
2025-08-19 18:19:39.279223 INFO::ASW Label was -0.167436693998489 prior to batch effect correction and is now -0.00187422682588275 .
2025-08-19 18:19:39.27984 INFO::Total function execution time is 0.0692861080169678 s and adjustment time is 0.0616278648376465 s ( 88.95 )
2025-08-19 18:19:39.33126 INFO::Formatting Data.
2025-08-19 18:19:39.331617 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.331969 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.332418 INFO::Found 2 missing values.
2025-08-19 18:19:39.333457 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.333839 INFO::Done
2025-08-19 18:19:39.344771 INFO::Found NA in Reference column
2025-08-19 18:19:39.348513 INFO::Require at least two references per batch.
2025-08-19 18:19:39.357106 INFO::Formatting Data.
2025-08-19 18:19:39.357359 INFO::Recognized SummarizedExperiment
2025-08-19 18:19:39.357535 INFO::Typecasting input to dataframe.
2025-08-19 18:19:39.361567 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.361942 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.363261 INFO::Found 0 missing values.
2025-08-19 18:19:39.365778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.365971 INFO::Done
2025-08-19 18:19:39.37146 INFO::Formatting Data.
2025-08-19 18:19:39.371688 INFO::Recognized SummarizedExperiment
2025-08-19 18:19:39.371872 INFO::Typecasting input to dataframe.
2025-08-19 18:19:39.377669 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.378085 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.379421 INFO::Found 0 missing values.
2025-08-19 18:19:39.383364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.383566 INFO::Done
2025-08-19 18:19:39.389402 INFO::Formatting Data.
2025-08-19 18:19:39.389693 INFO::Recognized SummarizedExperiment
2025-08-19 18:19:39.389878 INFO::Typecasting input to dataframe.
2025-08-19 18:19:39.395429 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.39577 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.396167 INFO::Found 0 missing values.
2025-08-19 18:19:39.396472 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.
2025-08-19 18:19:39.397963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.398147 INFO::Done
2025-08-19 18:19:39.402514 INFO::Formatting Data.
2025-08-19 18:19:39.402748 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.40303 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.403362 INFO::Found 0 missing values.
2025-08-19 18:19:39.404319 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.404493 INFO::Done
2025-08-19 18:19:39.409004 INFO::Formatting Data.
2025-08-19 18:19:39.409234 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.409512 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.409857 INFO::Found 0 missing values.
2025-08-19 18:19:39.410851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.411041 INFO::Done
2025-08-19 18:19:39.422754 INFO::Formatting Data.
2025-08-19 18:19:39.423032 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.423369 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.423804 INFO::Found 1 missing values.
2025-08-19 18:19:39.424716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.42491 INFO::Done
2025-08-19 18:19:39.432399 INFO::Formatting Data.
2025-08-19 18:19:39.432633 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.432901 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.433202 INFO::Found 2 missing values.
2025-08-19 18:19:39.433477 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.
2025-08-19 18:19:39.435178 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.435426 INFO::Done
2025-08-19 18:19:39.43951 INFO::Formatting Data.
2025-08-19 18:19:39.439772 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.440066 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.440378 INFO::Found 2 missing values.
2025-08-19 18:19:39.440897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.441076 INFO::Done
2025-08-19 18:19:39.4452 INFO::Formatting Data.
2025-08-19 18:19:39.44544 INFO::Typecasting input to dataframe.
2025-08-19 18:19:39.445711 INFO::Replacing NaNs with NAs.
2025-08-19 18:19:39.446002 INFO::Removing potential empty rows and columns
2025-08-19 18:19:39.446354 INFO::Found 0 missing values.
2025-08-19 18:19:39.447275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 18:19:39.447452 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.637 1.565 8.385
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.718 | 0.402 | 6.980 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.005 | 0.001 | 0.004 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |