Yannis Schumann
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 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 2025-10-24 12:04 -0400 (Fri, 24 Oct 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" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 166/2359 | 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 12.7.6 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: 2025-10-23 19:34:42 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 19:36:09 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 87.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 26.27 1.459 18.867
* 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-x86_64/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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")
2025-10-23 19:35:47.119758 INFO::Formatting Data.
2025-10-23 19:35:47.122951 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:47.133126 INFO::Removing potential empty rows and columns
2025-10-23 19:35:47.438728 INFO::Found 0 missing values.
2025-10-23 19:35:47.443348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:47.444369 INFO::Done
2025-10-23 19:35:47.44528 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:47.463229 INFO::Starting hierarchical adjustment
2025-10-23 19:35:47.464529 INFO::Found 3 batches.
2025-10-23 19:35:47.465124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:47.466233 INFO::Using default BPPARAM
2025-10-23 19:35:47.466817 INFO::Processing subtree level 1
2025-10-23 19:35:47.633227 INFO::Adjusting the last 1 batches sequentially
2025-10-23 19:35:47.638605 INFO::Done
2025-10-23 19:35:47.639774 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:47.647666 INFO::ASW Batch was -0.0477834432158319 prior to batch effect correction and is now -0.0477834432158319 .
2025-10-23 19:35:47.650154 INFO::Total function execution time is 0.530505180358887 s and adjustment time is 0.174215078353882 s ( 32.84 )
2025-10-23 19:35:47.673731 INFO::Formatting Data.
2025-10-23 19:35:47.674548 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:47.675456 INFO::Removing potential empty rows and columns
2025-10-23 19:35:47.676483 INFO::Found 0 missing values.
2025-10-23 19:35:47.67746 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.
2025-10-23 19:35:47.69009 INFO::Formatting Data.
2025-10-23 19:35:47.690982 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:47.69191 INFO::Removing potential empty rows and columns
2025-10-23 19:35:47.6929 INFO::Found 0 missing values.
2025-10-23 19:35:47.693808 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.
2025-10-23 19:35:47.716196 INFO::Formatting Data.
2025-10-23 19:35:47.71745 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:47.7189 INFO::Removing potential empty rows and columns
2025-10-23 19:35:47.720468 INFO::Found 0 missing values.
2025-10-23 19:35:47.721441 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.
2025-10-23 19:35:47.727213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:47.728124 INFO::Done
2025-10-23 19:35:47.728906 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:47.731151 INFO::Starting hierarchical adjustment
2025-10-23 19:35:47.731839 INFO::Found 2 batches.
2025-10-23 19:35:47.732351 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:47.73315 INFO::Using default BPPARAM
2025-10-23 19:35:47.733773 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:47.734657 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 19:35:47.762976 INFO::Done
2025-10-23 19:35:47.763689 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:47.766385 INFO::ASW Batch was -0.0151925155506989 prior to batch effect correction and is now -0.114783045337055 .
2025-10-23 19:35:47.767416 INFO::Total function execution time is 0.0513780117034912 s and adjustment time is 0.0312321186065674 s ( 60.79 )
2025-10-23 19:35:47.770279 INFO::Formatting Data.
2025-10-23 19:35:47.770953 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:47.784857 INFO::Formatting Data.
2025-10-23 19:35:47.786002 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:47.787713 INFO::Removing potential empty rows and columns
2025-10-23 19:35:47.788844 INFO::Found 0 missing values.
2025-10-23 19:35:47.791719 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:47.792686 INFO::Done
2025-10-23 19:35:47.79353 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:47.796811 INFO::Starting hierarchical adjustment
2025-10-23 19:35:47.797986 INFO::Found 2 batches.
2025-10-23 19:35:47.798881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:47.799824 INFO::Using default BPPARAM
2025-10-23 19:35:47.801238 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:47.802541 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 19:35:47.861122 INFO::Done
2025-10-23 19:35:47.86187 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:47.863786 INFO::ASW Batch was -0.0210493135680368 prior to batch effect correction and is now -0.121132715754831 .
2025-10-23 19:35:47.864544 INFO::Total function execution time is 0.0798468589782715 s and adjustment time is 0.0633950233459473 s ( 79.4 )
2025-10-23 19:35:47.865522 INFO::Formatting Data.
2025-10-23 19:35:47.866419 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:47.867548 INFO::Removing potential empty rows and columns
2025-10-23 19:35:47.86888 INFO::Found 0 missing values.
2025-10-23 19:35:47.871566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:47.872102 INFO::Done
2025-10-23 19:35:47.872609 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:47.874899 INFO::Starting hierarchical adjustment
2025-10-23 19:35:47.875678 INFO::Found 2 batches.
2025-10-23 19:35:47.876245 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:47.87698 INFO::Using default BPPARAM
2025-10-23 19:35:47.877699 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:47.878965 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 19:35:47.897638 INFO::Done
2025-10-23 19:35:47.898406 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:47.901063 INFO::ASW Batch was -0.0210493135680368 prior to batch effect correction and is now -0.121132715754831 .
2025-10-23 19:35:47.901949 INFO::Total function execution time is 0.0363428592681885 s and adjustment time is 0.0220949649810791 s ( 60.8 )
2025-10-23 19:35:51.289699 INFO::Formatting Data.
2025-10-23 19:35:51.290594 INFO::Recognized SummarizedExperiment
2025-10-23 19:35:51.291301 INFO::Typecasting input to dataframe.
2025-10-23 19:35:51.326038 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:51.327181 INFO::Removing potential empty rows and columns
2025-10-23 19:35:51.330724 INFO::Found 0 missing values.
2025-10-23 19:35:51.340022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:51.341152 INFO::Done
2025-10-23 19:35:51.342008 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:51.345633 INFO::Starting hierarchical adjustment
2025-10-23 19:35:51.34637 INFO::Found 2 batches.
2025-10-23 19:35:51.346925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:51.348298 INFO::Using default BPPARAM
2025-10-23 19:35:51.348997 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:51.350408 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 19:35:51.411444 INFO::Done
2025-10-23 19:35:51.412162 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:51.416969 INFO::ASW Batch was -0.00620081057947684 prior to batch effect correction and is now -0.0947250124063809 .
2025-10-23 19:35:51.418407 INFO::Total function execution time is 0.129035949707031 s and adjustment time is 0.0651860237121582 s ( 50.52 )
2025-10-23 19:35:51.441256 INFO::Formatting Data.
2025-10-23 19:35:51.442327 INFO::Recognized SummarizedExperiment
2025-10-23 19:35:51.443062 INFO::Typecasting input to dataframe.
2025-10-23 19:35:51.455401 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:51.45659 INFO::Removing potential empty rows and columns
2025-10-23 19:35:51.459929 INFO::Found 0 missing values.
2025-10-23 19:35:51.469528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:51.470269 INFO::Done
2025-10-23 19:35:51.47077 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:51.474086 INFO::Starting hierarchical adjustment
2025-10-23 19:35:51.474812 INFO::Found 2 batches.
2025-10-23 19:35:51.475422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:51.476227 INFO::Using default BPPARAM
2025-10-23 19:35:51.476948 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:51.478381 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 19:35:51.508502 INFO::Done
2025-10-23 19:35:51.509581 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:51.514185 INFO::ASW Batch was -0.0242405814298914 prior to batch effect correction and is now -0.0242405814298914 .
2025-10-23 19:35:51.515058 INFO::Total function execution time is 0.0738601684570312 s and adjustment time is 0.0337390899658203 s ( 45.68 )
2025-10-23 19:35:51.539136 INFO::Formatting Data.
2025-10-23 19:35:51.539935 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:51.540776 INFO::Removing potential empty rows and columns
2025-10-23 19:35:51.541674 INFO::Found 0 missing values.
2025-10-23 19:35:51.544513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:51.545273 INFO::Done
2025-10-23 19:35:51.545983 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:51.54876 INFO::Starting hierarchical adjustment
2025-10-23 19:35:51.549614 INFO::Found 3 batches.
2025-10-23 19:35:51.550098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:51.550637 INFO::Using default BPPARAM
2025-10-23 19:35:51.551105 INFO::Processing subtree level 1
2025-10-23 19:35:51.724267 INFO::Adjusting the last 1 batches sequentially
2025-10-23 19:35:51.736221 INFO::Done
2025-10-23 19:35:51.738479 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:51.7478 INFO::ASW Batch was -0.0395636028815812 prior to batch effect correction and is now -0.152291263845776 .
2025-10-23 19:35:51.750152 INFO::Total function execution time is 0.211001873016357 s and adjustment time is 0.186720132827759 s ( 88.49 )
2025-10-23 19:35:51.774374 INFO::Skipping initial DF formatting
2025-10-23 19:35:51.775502 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:51.781503 INFO::Starting hierarchical adjustment
2025-10-23 19:35:51.782745 INFO::Found 5 batches.
2025-10-23 19:35:51.783545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:51.784802 INFO::Using default BPPARAM
2025-10-23 19:35:51.785501 INFO::Processing subtree level 1
2025-10-23 19:35:52.139776 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:52.142286 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 19:35:52.206509 INFO::Done
2025-10-23 19:35:52.208505 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:52.222115 INFO::ASW Batch was 0.473360983012521 prior to batch effect correction and is now 0.473360983012521 .
2025-10-23 19:35:52.222961 INFO::ASW Label was 0.411131248907021 prior to batch effect correction and is now 0.411131248907021 .
2025-10-23 19:35:52.226704 INFO::Total function execution time is 0.451174020767212 s and adjustment time is 0.424091100692749 s ( 94 )
2025-10-23 19:35:52.330715 INFO::Formatting Data.
2025-10-23 19:35:52.331991 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:52.332964 INFO::Removing potential empty rows and columns
2025-10-23 19:35:52.333865 INFO::Found 0 missing values.
2025-10-23 19:35:52.338948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:52.339905 INFO::Done
2025-10-23 19:35:52.340537 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:52.343471 INFO::Starting hierarchical adjustment
2025-10-23 19:35:52.344194 INFO::Found 5 batches.
2025-10-23 19:35:52.344806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:52.345491 INFO::Using default BPPARAM
2025-10-23 19:35:52.346012 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.
2025-10-23 19:35:52.526329 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:52.529352 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 19:35:52.566591 INFO::Done
2025-10-23 19:35:52.568423 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:52.576358 INFO::ASW Batch was 0.317233454162591 prior to batch effect correction and is now -0.0863116533335111 .
2025-10-23 19:35:52.577806 INFO::ASW Label was 0.512246766884903 prior to batch effect correction and is now 0.796122080078673 .
2025-10-23 19:35:52.579792 INFO::Total function execution time is 0.248898983001709 s and adjustment time is 0.222350120544434 s ( 89.33 )
2025-10-23 19:35:52.581649 INFO::Formatting Data.
2025-10-23 19:35:52.58272 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:52.586509 INFO::Removing potential empty rows and columns
2025-10-23 19:35:52.58997 INFO::Found 0 missing values.
2025-10-23 19:35:52.598338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:52.599769 INFO::Done
2025-10-23 19:35:52.600963 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:52.607348 INFO::Starting hierarchical adjustment
2025-10-23 19:35:52.608749 INFO::Found 5 batches.
2025-10-23 19:35:52.609931 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:52.611067 INFO::Using default BPPARAM
2025-10-23 19:35:52.612048 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.
2025-10-23 19:35:52.777962 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:52.782628 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 19:35:52.81872 INFO::Done
2025-10-23 19:35:52.820168 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:52.826916 INFO::ASW Batch was 0.317233454162591 prior to batch effect correction and is now -0.0863116533335111 .
2025-10-23 19:35:52.828323 INFO::ASW Label was 0.512246766884903 prior to batch effect correction and is now 0.796122080078673 .
2025-10-23 19:35:52.830137 INFO::Total function execution time is 0.248437881469727 s and adjustment time is 0.210144996643066 s ( 84.59 )
2025-10-23 19:35:52.862994 INFO::Formatting Data.
2025-10-23 19:35:52.864425 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:52.866035 INFO::Removing potential empty rows and columns
2025-10-23 19:35:52.867584 INFO::Found 0 missing values.
2025-10-23 19:35:52.874942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:52.876336 INFO::Done
2025-10-23 19:35:52.877494 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:52.883218 INFO::Starting hierarchical adjustment
2025-10-23 19:35:52.884581 INFO::Found 5 batches.
2025-10-23 19:35:52.885707 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:52.886861 INFO::Using default BPPARAM
2025-10-23 19:35:52.887649 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.
2025-10-23 19:35:53.066427 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:53.072782 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 19:35:53.103702 INFO::Done
2025-10-23 19:35:53.105268 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:53.111377 INFO::ASW Batch was 0.443221599159767 prior to batch effect correction and is now -0.0853189296147152 .
2025-10-23 19:35:53.112632 INFO::ASW Label was 0.313957472334853 prior to batch effect correction and is now 0.825816301940098 .
2025-10-23 19:35:53.114067 INFO::Total function execution time is 0.251209020614624 s and adjustment time is 0.21937084197998 s ( 87.33 )
2025-10-23 19:35:53.115292 INFO::Formatting Data.
2025-10-23 19:35:53.116559 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:53.118028 INFO::Removing potential empty rows and columns
2025-10-23 19:35:53.120248 INFO::Found 0 missing values.
2025-10-23 19:35:53.128471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:53.129467 INFO::Done
2025-10-23 19:35:53.130232 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:53.135059 INFO::Starting hierarchical adjustment
2025-10-23 19:35:53.136192 INFO::Found 5 batches.
2025-10-23 19:35:53.136936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:53.137833 INFO::Using default BPPARAM
2025-10-23 19:35:53.138922 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.
2025-10-23 19:35:53.327933 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:53.332254 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 19:35:53.372768 INFO::Done
2025-10-23 19:35:53.374491 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:53.38258 INFO::ASW Batch was 0.443221599159767 prior to batch effect correction and is now -0.0853189296147152 .
2025-10-23 19:35:53.383639 INFO::ASW Label was 0.313957472334853 prior to batch effect correction and is now 0.825816301940098 .
2025-10-23 19:35:53.385026 INFO::Total function execution time is 0.269766807556152 s and adjustment time is 0.236772060394287 s ( 87.77 )
2025-10-23 19:35:53.409603 INFO::Formatting Data.
2025-10-23 19:35:53.411097 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:53.412352 INFO::Removing potential empty rows and columns
2025-10-23 19:35:53.414132 INFO::Found 0 missing values.
2025-10-23 19:35:53.419236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:53.420207 INFO::Done
2025-10-23 19:35:53.421044 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:53.425505 INFO::Starting hierarchical adjustment
2025-10-23 19:35:53.426796 INFO::Found 2 batches.
2025-10-23 19:35:53.427817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:53.428896 INFO::Using default BPPARAM
2025-10-23 19:35:53.429802 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:53.431489 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 19:35:53.457795 INFO::Done
2025-10-23 19:35:53.459271 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:53.464332 INFO::ASW Batch was 0.448452118928346 prior to batch effect correction and is now 0.0147372048688054 .
2025-10-23 19:35:53.465254 INFO::ASW Label was 0.66980505188781 prior to batch effect correction and is now 0.928440743357152 .
2025-10-23 19:35:53.466267 INFO::Total function execution time is 0.0568230152130127 s and adjustment time is 0.0312199592590332 s ( 54.94 )
2025-10-23 19:35:53.467299 INFO::Formatting Data.
2025-10-23 19:35:53.468667 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:53.471329 INFO::Removing potential empty rows and columns
2025-10-23 19:35:53.473469 INFO::Found 0 missing values.
2025-10-23 19:35:53.477384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:53.478148 INFO::Done
2025-10-23 19:35:53.478806 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:53.483846 INFO::Starting hierarchical adjustment
2025-10-23 19:35:53.484967 INFO::Found 2 batches.
2025-10-23 19:35:53.485958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:53.486951 INFO::Using default BPPARAM
2025-10-23 19:35:53.487596 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:53.4887 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 19:35:53.510885 INFO::Done
2025-10-23 19:35:53.512148 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:53.51566 INFO::ASW Batch was 0.448452118928346 prior to batch effect correction and is now 0.0147372048688054 .
2025-10-23 19:35:53.51682 INFO::ASW Label was 0.66980505188781 prior to batch effect correction and is now 0.928440743357152 .
2025-10-23 19:35:53.517987 INFO::Total function execution time is 0.050753116607666 s and adjustment time is 0.0260751247406006 s ( 51.38 )
2025-10-23 19:35:53.539125 INFO::Formatting Data.
2025-10-23 19:35:53.540627 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:53.542213 INFO::Removing potential empty rows and columns
2025-10-23 19:35:53.543564 INFO::Found 0 missing values.
2025-10-23 19:35:53.54632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:53.546995 INFO::Done
2025-10-23 19:35:53.547624 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:53.550218 INFO::Starting hierarchical adjustment
2025-10-23 19:35:53.551068 INFO::Found 2 batches.
2025-10-23 19:35:53.551714 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:53.552778 INFO::Using default BPPARAM
2025-10-23 19:35:53.553411 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:53.554554 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 19:35:53.599796 INFO::Done
2025-10-23 19:35:53.601012 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:53.604793 INFO::ASW Batch was 0.0904467386441767 prior to batch effect correction and is now -0.102995221890019 .
2025-10-23 19:35:53.606318 INFO::Total function execution time is 0.0673031806945801 s and adjustment time is 0.0488700866699219 s ( 72.61 )
2025-10-23 19:35:53.628184 INFO::Formatting Data.
2025-10-23 19:35:53.629584 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:53.631199 INFO::Removing potential empty rows and columns
2025-10-23 19:35:53.633019 INFO::Found 0 missing values.
2025-10-23 19:35:53.63514 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.
2025-10-23 19:35:53.643813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:53.644698 INFO::Done
2025-10-23 19:35:53.645692 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:53.651079 INFO::Starting hierarchical adjustment
2025-10-23 19:35:53.652145 INFO::Found 2 batches.
2025-10-23 19:35:53.652879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:53.653648 INFO::Using default BPPARAM
2025-10-23 19:35:53.654443 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:53.655675 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 19:35:53.688598 INFO::Done
2025-10-23 19:35:53.689651 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:53.69819 INFO::ASW Batch was 0.856782796681298 prior to batch effect correction and is now -0.0264670128920892 .
2025-10-23 19:35:53.700901 INFO::ASW Label was 0.124483754154289 prior to batch effect correction and is now 0.768074375869224 .
2025-10-23 19:35:53.704296 INFO::Total function execution time is 0.0762181282043457 s and adjustment time is 0.0366420745849609 s ( 48.08 )
2025-10-23 19:35:53.706431 INFO::Formatting Data.
2025-10-23 19:35:53.708623 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:53.712113 INFO::Removing potential empty rows and columns
2025-10-23 19:35:53.715244 INFO::Found 0 missing values.
2025-10-23 19:35:53.717341 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.
2025-10-23 19:35:53.72767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:53.729446 INFO::Done
2025-10-23 19:35:53.730621 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:53.738344 INFO::Starting hierarchical adjustment
2025-10-23 19:35:53.739923 INFO::Found 2 batches.
2025-10-23 19:35:53.743492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:53.744973 INFO::Using default BPPARAM
2025-10-23 19:35:53.746566 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:53.748689 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 19:35:53.776565 INFO::Done
2025-10-23 19:35:53.778108 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:53.783155 INFO::ASW Batch was 0.856782796681298 prior to batch effect correction and is now -0.0264670128920892 .
2025-10-23 19:35:53.78428 INFO::ASW Label was 0.124483754154289 prior to batch effect correction and is now 0.768074375869224 .
2025-10-23 19:35:53.785384 INFO::Total function execution time is 0.079028844833374 s and adjustment time is 0.0370121002197266 s ( 46.83 )
2025-10-23 19:35:54.111019 INFO::Formatting Data.
2025-10-23 19:35:54.113061 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:54.115414 INFO::Removing potential empty rows and columns
2025-10-23 19:35:54.118279 INFO::Found 0 missing values.
2025-10-23 19:35:54.122483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:54.123842 INFO::Done
2025-10-23 19:35:54.124659 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:54.127921 INFO::Starting hierarchical adjustment
2025-10-23 19:35:54.128844 INFO::Found 3 batches.
2025-10-23 19:35:54.12958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:54.130229 INFO::Using default BPPARAM
2025-10-23 19:35:54.130712 INFO::Processing subtree level 1
2025-10-23 19:35:54.265313 INFO::Adjusting the last 1 batches sequentially
2025-10-23 19:35:54.278987 INFO::Done
2025-10-23 19:35:54.283047 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:54.295802 INFO::ASW Batch was -0.0604970433830267 prior to batch effect correction and is now -0.0604970433830267 .
2025-10-23 19:35:54.298835 INFO::Total function execution time is 0.187743902206421 s and adjustment time is 0.150321960449219 s ( 80.07 )
2025-10-23 19:35:54.301509 INFO::Formatting Data.
2025-10-23 19:35:54.30226 INFO::Typecasting input to dataframe.
2025-10-23 19:35:54.303261 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:54.304357 INFO::Removing potential empty rows and columns
2025-10-23 19:35:54.306001 INFO::Found 0 missing values.
2025-10-23 19:35:54.308985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:54.310283 INFO::Done
2025-10-23 19:35:54.311076 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:54.312944 INFO::Starting hierarchical adjustment
2025-10-23 19:35:54.314313 INFO::Found 3 batches.
2025-10-23 19:35:54.314786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:54.315335 INFO::Using default BPPARAM
2025-10-23 19:35:54.316499 INFO::Processing subtree level 1
2025-10-23 19:35:54.427679 INFO::Adjusting the last 1 batches sequentially
2025-10-23 19:35:54.44249 INFO::Done
2025-10-23 19:35:54.444549 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:54.456731 INFO::ASW Batch was -0.0604970433830267 prior to batch effect correction and is now -0.0604970433830267 .
2025-10-23 19:35:54.459116 INFO::Total function execution time is 0.157271862030029 s and adjustment time is 0.128201961517334 s ( 81.52 )
2025-10-23 19:35:54.48349 INFO::Formatting Data.
2025-10-23 19:35:54.48437 INFO::Typecasting input to dataframe.
2025-10-23 19:35:54.485309 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:54.486633 INFO::Removing potential empty rows and columns
2025-10-23 19:35:54.487883 INFO::Found 0 missing values.
2025-10-23 19:35:54.492283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:54.493188 INFO::Done
2025-10-23 19:35:54.494065 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:54.496336 INFO::Starting hierarchical adjustment
2025-10-23 19:35:54.497835 INFO::Found 3 batches.
2025-10-23 19:35:54.498669 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:54.499521 INFO::Using default BPPARAM
2025-10-23 19:35:54.500229 INFO::Processing subtree level 1
2025-10-23 19:35:54.634865 INFO::Adjusting the last 1 batches sequentially
2025-10-23 19:35:54.649381 INFO::Done
2025-10-23 19:35:54.650885 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:54.666067 INFO::ASW Batch was -0.162411986976861 prior to batch effect correction and is now -0.162411986976861 .
2025-10-23 19:35:54.67068 INFO::Total function execution time is 0.186705827713013 s and adjustment time is 0.151751041412354 s ( 81.28 )
2025-10-23 19:35:54.915911 INFO::Formatting Data.
2025-10-23 19:35:54.917338 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:54.918466 INFO::Removing potential empty rows and columns
2025-10-23 19:35:54.922292 INFO::Found 1000 missing values.
2025-10-23 19:35:54.94814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:54.948926 INFO::Done
2025-10-23 19:35:54.949478 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:54.956407 INFO::Starting hierarchical adjustment
2025-10-23 19:35:54.958166 INFO::Found 10 batches.
2025-10-23 19:35:54.95899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:54.959788 INFO::Using default BPPARAM
2025-10-23 19:35:54.960467 INFO::Processing subtree level 1
2025-10-23 19:35:55.130381 INFO::Processing subtree level 2
2025-10-23 19:35:55.343686 INFO::Adjusting the last 1 batches sequentially
2025-10-23 19:35:55.363235 INFO::Done
2025-10-23 19:35:55.365565 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:55.380918 INFO::ASW Batch was 0.521575230633939 prior to batch effect correction and is now 0.521575230633939 .
2025-10-23 19:35:55.382188 INFO::ASW Label was 0.307937922292781 prior to batch effect correction and is now 0.307937922292781 .
2025-10-23 19:35:55.386382 INFO::Total function execution time is 0.469238996505737 s and adjustment time is 0.405241012573242 s ( 86.36 )
2025-10-23 19:35:55.388005 INFO::Formatting Data.
2025-10-23 19:35:55.389081 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:55.390951 INFO::Removing potential empty rows and columns
2025-10-23 19:35:55.395346 INFO::Found 1000 missing values.
2025-10-23 19:35:55.419651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:55.420689 INFO::Done
2025-10-23 19:35:55.421998 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:55.429503 INFO::Starting hierarchical adjustment
2025-10-23 19:35:55.431178 INFO::Found 10 batches.
2025-10-23 19:35:56.628209 INFO::Set up parallel execution backend with 2 workers
2025-10-23 19:35:56.629122 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-23 19:35:57.960949 INFO::Adjusting the last 2 batches sequentially
2025-10-23 19:35:57.962766 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 19:35:57.979887 INFO::Done
2025-10-23 19:35:57.980797 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:57.987684 INFO::ASW Batch was 0.521575230633939 prior to batch effect correction and is now 0.521575230633939 .
2025-10-23 19:35:57.988313 INFO::ASW Label was 0.307937922292781 prior to batch effect correction and is now 0.307937922292781 .
2025-10-23 19:35:57.988995 INFO::Total function execution time is 2.6011791229248 s and adjustment time is 2.54894590377808 s ( 97.99 )
2025-10-23 19:35:58.233018 INFO::Formatting Data.
2025-10-23 19:35:58.23488 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:58.236371 INFO::Removing potential empty rows and columns
2025-10-23 19:35:58.238228 INFO::Found 0 missing values.
2025-10-23 19:35:58.243215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:58.244129 INFO::Done
2025-10-23 19:35:58.245763 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 19:35:58.250074 INFO::Starting hierarchical adjustment
2025-10-23 19:35:58.251233 INFO::Found 3 batches.
2025-10-23 19:35:58.252043 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 19:35:58.252885 INFO::Using default BPPARAM
2025-10-23 19:35:58.253599 INFO::Processing subtree level 1
2025-10-23 19:35:58.434061 INFO::Adjusting the last 1 batches sequentially
2025-10-23 19:35:58.442874 INFO::Done
2025-10-23 19:35:58.446212 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 19:35:58.458257 INFO::ASW Batch was 0.24086991921622 prior to batch effect correction and is now -0.131486147983014 .
2025-10-23 19:35:58.459837 INFO::ASW Label was -0.192804554758222 prior to batch effect correction and is now 0.0206688053864495 .
2025-10-23 19:35:58.464464 INFO::Total function execution time is 0.229835987091064 s and adjustment time is 0.191819906234741 s ( 83.46 )
2025-10-23 19:35:58.67679 INFO::Formatting Data.
2025-10-23 19:35:58.678037 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:58.679402 INFO::Removing potential empty rows and columns
2025-10-23 19:35:58.680989 INFO::Found 2 missing values.
2025-10-23 19:35:58.685225 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:58.685908 INFO::Done
2025-10-23 19:35:58.73299 INFO::Found NA in Reference column
2025-10-23 19:35:58.750189 INFO::Require at least two references per batch.
2025-10-23 19:35:58.784163 INFO::Formatting Data.
2025-10-23 19:35:58.785398 INFO::Recognized SummarizedExperiment
2025-10-23 19:35:58.786229 INFO::Typecasting input to dataframe.
2025-10-23 19:35:58.797398 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:58.798782 INFO::Removing potential empty rows and columns
2025-10-23 19:35:58.803612 INFO::Found 0 missing values.
2025-10-23 19:35:58.810412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:58.811571 INFO::Done
2025-10-23 19:35:58.833941 INFO::Formatting Data.
2025-10-23 19:35:58.834727 INFO::Recognized SummarizedExperiment
2025-10-23 19:35:58.835346 INFO::Typecasting input to dataframe.
2025-10-23 19:35:58.8579 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:58.859747 INFO::Removing potential empty rows and columns
2025-10-23 19:35:58.86458 INFO::Found 0 missing values.
2025-10-23 19:35:58.879726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:58.880665 INFO::Done
2025-10-23 19:35:58.905585 INFO::Formatting Data.
2025-10-23 19:35:58.906475 INFO::Recognized SummarizedExperiment
2025-10-23 19:35:58.907278 INFO::Typecasting input to dataframe.
2025-10-23 19:35:58.929299 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:58.930732 INFO::Removing potential empty rows and columns
2025-10-23 19:35:58.932245 INFO::Found 0 missing values.
2025-10-23 19:35:58.933532 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.
2025-10-23 19:35:58.93929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:58.940229 INFO::Done
2025-10-23 19:35:58.955269 INFO::Formatting Data.
2025-10-23 19:35:58.956011 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:58.956809 INFO::Removing potential empty rows and columns
2025-10-23 19:35:58.957704 INFO::Found 0 missing values.
2025-10-23 19:35:58.960121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:58.960659 INFO::Done
2025-10-23 19:35:58.975697 INFO::Formatting Data.
2025-10-23 19:35:58.976813 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:58.977858 INFO::Removing potential empty rows and columns
2025-10-23 19:35:58.978877 INFO::Found 0 missing values.
2025-10-23 19:35:58.981662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:58.982582 INFO::Done
2025-10-23 19:35:59.026698 INFO::Formatting Data.
2025-10-23 19:35:59.027466 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:59.02843 INFO::Removing potential empty rows and columns
2025-10-23 19:35:59.029542 INFO::Found 1 missing values.
2025-10-23 19:35:59.032343 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:59.032928 INFO::Done
2025-10-23 19:35:59.061183 INFO::Formatting Data.
2025-10-23 19:35:59.06213 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:59.063378 INFO::Removing potential empty rows and columns
2025-10-23 19:35:59.064864 INFO::Found 2 missing values.
2025-10-23 19:35:59.066216 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.
2025-10-23 19:35:59.068774 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:59.069662 INFO::Done
2025-10-23 19:35:59.087156 INFO::Formatting Data.
2025-10-23 19:35:59.088254 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:59.089397 INFO::Removing potential empty rows and columns
2025-10-23 19:35:59.090722 INFO::Found 2 missing values.
2025-10-23 19:35:59.092986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:59.093815 INFO::Done
2025-10-23 19:35:59.109927 INFO::Formatting Data.
2025-10-23 19:35:59.111032 INFO::Typecasting input to dataframe.
2025-10-23 19:35:59.112215 INFO::Replacing NaNs with NAs.
2025-10-23 19:35:59.113443 INFO::Removing potential empty rows and columns
2025-10-23 19:35:59.114861 INFO::Found 0 missing values.
2025-10-23 19:35:59.119129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 19:35:59.120032 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.415 4.336 25.077
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.270 | 1.459 | 18.867 | |
| compute_asw | 0.026 | 0.001 | 0.028 | |
| count_existing | 0.015 | 0.001 | 0.016 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |