Yannis Schumann
| Snapshot Date: 2025-11-10 13:45 -0500 (Mon, 10 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-11 12:03 -0500 (Tue, 11 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /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_1.6.0.tar.gz |
| StartedAt: 2025-11-10 18:54:20 -0500 (Mon, 10 Nov 2025) |
| EndedAt: 2025-11-10 18:54:51 -0500 (Mon, 10 Nov 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_1.6.0.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: 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 ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 9.921 0.479 7.168
* 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 ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "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")
2025-11-10 18:54:43.890853 INFO::Formatting Data.
2025-11-10 18:54:43.892268 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:43.896171 INFO::Removing potential empty rows and columns
2025-11-10 18:54:44.000901 INFO::Found 0 missing values.
2025-11-10 18:54:44.002174 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:44.002426 INFO::Done
2025-11-10 18:54:44.002624 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:44.008059 INFO::Starting hierarchical adjustment
2025-11-10 18:54:44.008382 INFO::Found 3 batches.
2025-11-10 18:54:44.008568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:44.008987 INFO::Using default BPPARAM
2025-11-10 18:54:44.009168 INFO::Processing subtree level 1
2025-11-10 18:54:44.061009 INFO::Adjusting the last 1 batches sequentially
2025-11-10 18:54:44.06222 INFO::Done
2025-11-10 18:54:44.062467 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:44.063909 INFO::ASW Batch was -0.112712057898561 prior to batch effect correction and is now -0.112712057898561 .
2025-11-10 18:54:44.064407 INFO::Total function execution time is 0.173840045928955 s and adjustment time is 0.0539009571075439 s ( 31.01 )
2025-11-10 18:54:44.071903 INFO::Formatting Data.
2025-11-10 18:54:44.072155 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:44.072464 INFO::Removing potential empty rows and columns
2025-11-10 18:54:44.072907 INFO::Found 0 missing values.
2025-11-10 18:54:44.073221 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-10 18:54:44.078169 INFO::Formatting Data.
2025-11-10 18:54:44.078445 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:44.078777 INFO::Removing potential empty rows and columns
2025-11-10 18:54:44.079159 INFO::Found 0 missing values.
2025-11-10 18:54:44.079479 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-10 18:54:44.085573 INFO::Formatting Data.
2025-11-10 18:54:44.085808 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:44.086086 INFO::Removing potential empty rows and columns
2025-11-10 18:54:44.086416 INFO::Found 0 missing values.
2025-11-10 18:54:44.086698 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-10 18:54:44.088072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:44.088275 INFO::Done
2025-11-10 18:54:44.088449 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:44.089159 INFO::Starting hierarchical adjustment
2025-11-10 18:54:44.089389 INFO::Found 2 batches.
2025-11-10 18:54:44.089554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:44.089809 INFO::Using default BPPARAM
2025-11-10 18:54:44.08998 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:44.090276 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 18:54:44.101674 INFO::Done
2025-11-10 18:54:44.10197 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:44.102772 INFO::ASW Batch was 0.0180471549285006 prior to batch effect correction and is now -0.10749149704242 .
2025-11-10 18:54:44.103517 INFO::Total function execution time is 0.0174851417541504 s and adjustment time is 0.0123121738433838 s ( 70.42 )
2025-11-10 18:54:44.104788 INFO::Formatting Data.
2025-11-10 18:54:44.105018 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:44.108085 INFO::Formatting Data.
2025-11-10 18:54:44.108308 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:44.108783 INFO::Removing potential empty rows and columns
2025-11-10 18:54:44.109277 INFO::Found 0 missing values.
2025-11-10 18:54:44.110516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:44.110779 INFO::Done
2025-11-10 18:54:44.110993 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:44.112007 INFO::Starting hierarchical adjustment
2025-11-10 18:54:44.112505 INFO::Found 2 batches.
2025-11-10 18:54:44.112762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:44.113014 INFO::Using default BPPARAM
2025-11-10 18:54:44.113262 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:44.113633 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:44.138677 INFO::Done
2025-11-10 18:54:44.13895 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:44.139606 INFO::ASW Batch was -0.032971075850662 prior to batch effect correction and is now -0.118688726523468 .
2025-11-10 18:54:44.13986 INFO::Total function execution time is 0.0317690372467041 s and adjustment time is 0.0263161659240723 s ( 82.84 )
2025-11-10 18:54:44.140175 INFO::Formatting Data.
2025-11-10 18:54:44.140341 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:44.140604 INFO::Removing potential empty rows and columns
2025-11-10 18:54:44.140891 INFO::Found 0 missing values.
2025-11-10 18:54:44.141687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:44.141846 INFO::Done
2025-11-10 18:54:44.141998 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:44.142552 INFO::Starting hierarchical adjustment
2025-11-10 18:54:44.142758 INFO::Found 2 batches.
2025-11-10 18:54:44.142916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:44.143087 INFO::Using default BPPARAM
2025-11-10 18:54:44.143232 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:44.143472 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:44.148187 INFO::Done
2025-11-10 18:54:44.148396 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:44.148968 INFO::ASW Batch was -0.032971075850662 prior to batch effect correction and is now -0.118688726523468 .
2025-11-10 18:54:44.149183 INFO::Total function execution time is 0.00900506973266602 s and adjustment time is 0.00547003746032715 s ( 60.74 )
2025-11-10 18:54:45.268562 INFO::Formatting Data.
2025-11-10 18:54:45.268821 INFO::Recognized SummarizedExperiment
2025-11-10 18:54:45.268981 INFO::Typecasting input to dataframe.
2025-11-10 18:54:45.279198 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.279622 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.280784 INFO::Found 0 missing values.
2025-11-10 18:54:45.282962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.283155 INFO::Done
2025-11-10 18:54:45.283309 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.28452 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.284737 INFO::Found 2 batches.
2025-11-10 18:54:45.28489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.285214 INFO::Using default BPPARAM
2025-11-10 18:54:45.285366 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.285648 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 18:54:45.303149 INFO::Done
2025-11-10 18:54:45.303383 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.304569 INFO::ASW Batch was -0.00638107918773417 prior to batch effect correction and is now -0.0901025951182006 .
2025-11-10 18:54:45.304829 INFO::Total function execution time is 0.0363647937774658 s and adjustment time is 0.0184478759765625 s ( 50.73 )
2025-11-10 18:54:45.310824 INFO::Formatting Data.
2025-11-10 18:54:45.31103 INFO::Recognized SummarizedExperiment
2025-11-10 18:54:45.311186 INFO::Typecasting input to dataframe.
2025-11-10 18:54:45.314021 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.314368 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.315477 INFO::Found 0 missing values.
2025-11-10 18:54:45.317567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.31773 INFO::Done
2025-11-10 18:54:45.317884 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.319017 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.319228 INFO::Found 2 batches.
2025-11-10 18:54:45.319379 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.319552 INFO::Using default BPPARAM
2025-11-10 18:54:45.319694 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.319976 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 18:54:45.327702 INFO::Done
2025-11-10 18:54:45.327914 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.329063 INFO::ASW Batch was -0.00517162502140483 prior to batch effect correction and is now -0.00517162502140483 .
2025-11-10 18:54:45.329317 INFO::Total function execution time is 0.0184850692749023 s and adjustment time is 0.0085151195526123 s ( 46.06 )
2025-11-10 18:54:45.335547 INFO::Formatting Data.
2025-11-10 18:54:45.335759 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.336013 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.336306 INFO::Found 0 missing values.
2025-11-10 18:54:45.337124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.337284 INFO::Done
2025-11-10 18:54:45.337435 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.338014 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.338208 INFO::Found 3 batches.
2025-11-10 18:54:45.338349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.338516 INFO::Using default BPPARAM
2025-11-10 18:54:45.338687 INFO::Processing subtree level 1
2025-11-10 18:54:45.40792 INFO::Adjusting the last 1 batches sequentially
2025-11-10 18:54:45.409133 INFO::Done
2025-11-10 18:54:45.409344 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.411049 INFO::ASW Batch was -0.0506882766104499 prior to batch effect correction and is now -0.184882745013788 .
2025-11-10 18:54:45.41152 INFO::Total function execution time is 0.0759639739990234 s and adjustment time is 0.0709550380706787 s ( 93.41 )
2025-11-10 18:54:45.417428 INFO::Skipping initial DF formatting
2025-11-10 18:54:45.417781 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.41902 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.419249 INFO::Found 5 batches.
2025-11-10 18:54:45.419408 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.419602 INFO::Using default BPPARAM
2025-11-10 18:54:45.419752 INFO::Processing subtree level 1
2025-11-10 18:54:45.532639 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.53597 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 18:54:45.544377 INFO::Done
2025-11-10 18:54:45.544723 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.547484 INFO::ASW Batch was 0.46676292755375 prior to batch effect correction and is now 0.46676292755375 .
2025-11-10 18:54:45.547698 INFO::ASW Label was 0.409498245816548 prior to batch effect correction and is now 0.409498245816548 .
2025-11-10 18:54:45.548357 INFO::Total function execution time is 0.130902051925659 s and adjustment time is 0.125172853469849 s ( 95.62 )
2025-11-10 18:54:45.59331 INFO::Formatting Data.
2025-11-10 18:54:45.593628 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.593953 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.594325 INFO::Found 0 missing values.
2025-11-10 18:54:45.59577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.595943 INFO::Done
2025-11-10 18:54:45.596103 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.59715 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.597364 INFO::Found 5 batches.
2025-11-10 18:54:45.59753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.597759 INFO::Using default BPPARAM
2025-11-10 18:54:45.597927 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.666341 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.669124 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.683171 INFO::Done
2025-11-10 18:54:45.683538 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.685728 INFO::ASW Batch was 0.529312817616163 prior to batch effect correction and is now -0.0462081375888569 .
2025-11-10 18:54:45.686071 INFO::ASW Label was 0.317464855854941 prior to batch effect correction and is now 0.732720066138759 .
2025-11-10 18:54:45.686501 INFO::Total function execution time is 0.0931789875030518 s and adjustment time is 0.0858421325683594 s ( 92.13 )
2025-11-10 18:54:45.687148 INFO::Formatting Data.
2025-11-10 18:54:45.687428 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.687837 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.688325 INFO::Found 0 missing values.
2025-11-10 18:54:45.690404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.690737 INFO::Done
2025-11-10 18:54:45.691011 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.692396 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.692722 INFO::Found 5 batches.
2025-11-10 18:54:45.692947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.693327 INFO::Using default BPPARAM
2025-11-10 18:54:45.693887 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.748888 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.751154 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.760318 INFO::Done
2025-11-10 18:54:45.760705 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.762391 INFO::ASW Batch was 0.529312817616163 prior to batch effect correction and is now -0.0462081375888569 .
2025-11-10 18:54:45.76263 INFO::ASW Label was 0.317464855854941 prior to batch effect correction and is now 0.732720066138759 .
2025-11-10 18:54:45.763103 INFO::Total function execution time is 0.0757977962493896 s and adjustment time is 0.0676579475402832 s ( 89.26 )
2025-11-10 18:54:45.770555 INFO::Formatting Data.
2025-11-10 18:54:45.770886 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.771281 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.771749 INFO::Found 0 missing values.
2025-11-10 18:54:45.773108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.773274 INFO::Done
2025-11-10 18:54:45.773438 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.774461 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.774717 INFO::Found 5 batches.
2025-11-10 18:54:45.774893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.775098 INFO::Using default BPPARAM
2025-11-10 18:54:45.775277 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.829638 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.831407 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.839956 INFO::Done
2025-11-10 18:54:45.840385 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.842197 INFO::ASW Batch was 0.499406006361366 prior to batch effect correction and is now -0.0903594518298697 .
2025-11-10 18:54:45.842423 INFO::ASW Label was 0.19761953513298 prior to batch effect correction and is now 0.80526932603244 .
2025-11-10 18:54:45.842732 INFO::Total function execution time is 0.0721819400787354 s and adjustment time is 0.0652890205383301 s ( 90.45 )
2025-11-10 18:54:45.843012 INFO::Formatting Data.
2025-11-10 18:54:45.843214 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.843511 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.843857 INFO::Found 0 missing values.
2025-11-10 18:54:45.845164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.84536 INFO::Done
2025-11-10 18:54:45.84567 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.846785 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.847044 INFO::Found 5 batches.
2025-11-10 18:54:45.84723 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.847449 INFO::Using default BPPARAM
2025-11-10 18:54:45.847773 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.902022 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.904599 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.915274 INFO::Done
2025-11-10 18:54:45.915726 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.917741 INFO::ASW Batch was 0.499406006361366 prior to batch effect correction and is now -0.0903594518298697 .
2025-11-10 18:54:45.918134 INFO::ASW Label was 0.19761953513298 prior to batch effect correction and is now 0.80526932603244 .
2025-11-10 18:54:45.918731 INFO::Total function execution time is 0.0756480693817139 s and adjustment time is 0.0682601928710938 s ( 90.23 )
2025-11-10 18:54:45.926917 INFO::Formatting Data.
2025-11-10 18:54:45.927199 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.927546 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.927952 INFO::Found 0 missing values.
2025-11-10 18:54:45.928964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.929157 INFO::Done
2025-11-10 18:54:45.929345 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.9304 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.930665 INFO::Found 2 batches.
2025-11-10 18:54:45.930843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.931088 INFO::Using default BPPARAM
2025-11-10 18:54:45.931259 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.931545 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.936923 INFO::Done
2025-11-10 18:54:45.937146 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.938133 INFO::ASW Batch was 0.740125405885485 prior to batch effect correction and is now -0.000798943494046283 .
2025-11-10 18:54:45.938333 INFO::ASW Label was 0.299601781813296 prior to batch effect correction and is now 0.826626978622875 .
2025-11-10 18:54:45.938597 INFO::Total function execution time is 0.0117349624633789 s and adjustment time is 0.006317138671875 s ( 53.83 )
2025-11-10 18:54:45.938842 INFO::Formatting Data.
2025-11-10 18:54:45.939044 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.939346 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.939705 INFO::Found 0 missing values.
2025-11-10 18:54:45.940709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.940908 INFO::Done
2025-11-10 18:54:45.941105 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.942049 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.944305 INFO::Found 2 batches.
2025-11-10 18:54:45.946985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.947216 INFO::Using default BPPARAM
2025-11-10 18:54:45.947406 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.947696 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-10 18:54:45.952684 INFO::Done
2025-11-10 18:54:45.9529 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.95386 INFO::ASW Batch was 0.740125405885485 prior to batch effect correction and is now -0.000798943494046283 .
2025-11-10 18:54:45.954071 INFO::ASW Label was 0.299601781813296 prior to batch effect correction and is now 0.826626978622875 .
2025-11-10 18:54:45.954364 INFO::Total function execution time is 0.0155110359191895 s and adjustment time is 0.00841498374938965 s ( 54.25 )
2025-11-10 18:54:45.959108 INFO::Formatting Data.
2025-11-10 18:54:45.959345 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.95966 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.959989 INFO::Found 0 missing values.
2025-11-10 18:54:45.960778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.960986 INFO::Done
2025-11-10 18:54:45.961174 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.961808 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.96202 INFO::Found 2 batches.
2025-11-10 18:54:45.962196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.962431 INFO::Using default BPPARAM
2025-11-10 18:54:45.962612 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.962934 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 18:54:45.97482 INFO::Done
2025-11-10 18:54:45.975057 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.975763 INFO::ASW Batch was 0.0860806797616253 prior to batch effect correction and is now -0.115277394369282 .
2025-11-10 18:54:45.976052 INFO::Total function execution time is 0.0169551372528076 s and adjustment time is 0.0128250122070312 s ( 75.64 )
2025-11-10 18:54:45.981771 INFO::Formatting Data.
2025-11-10 18:54:45.982097 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:45.982474 INFO::Removing potential empty rows and columns
2025-11-10 18:54:45.982915 INFO::Found 0 missing values.
2025-11-10 18:54:45.983439 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-10 18:54:45.985242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:45.985463 INFO::Done
2025-11-10 18:54:45.985671 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:45.986965 INFO::Starting hierarchical adjustment
2025-11-10 18:54:45.987321 INFO::Found 2 batches.
2025-11-10 18:54:45.987579 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:45.987853 INFO::Using default BPPARAM
2025-11-10 18:54:45.988121 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:45.988535 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 18:54:45.997253 INFO::Done
2025-11-10 18:54:45.997831 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:45.999954 INFO::ASW Batch was 0.702610261111858 prior to batch effect correction and is now 0.0256912713958272 .
2025-11-10 18:54:46.000246 INFO::ASW Label was 0.385449432187786 prior to batch effect correction and is now 0.886130601210393 .
2025-11-10 18:54:46.000555 INFO::Total function execution time is 0.0188190937042236 s and adjustment time is 0.00997686386108398 s ( 53.01 )
2025-11-10 18:54:46.00084 INFO::Formatting Data.
2025-11-10 18:54:46.001051 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:46.001369 INFO::Removing potential empty rows and columns
2025-11-10 18:54:46.001742 INFO::Found 0 missing values.
2025-11-10 18:54:46.002079 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-10 18:54:46.003942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:46.004234 INFO::Done
2025-11-10 18:54:46.004442 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:46.005942 INFO::Starting hierarchical adjustment
2025-11-10 18:54:46.006234 INFO::Found 2 batches.
2025-11-10 18:54:46.006419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:46.006642 INFO::Using default BPPARAM
2025-11-10 18:54:46.006819 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:46.007175 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 18:54:46.014197 INFO::Done
2025-11-10 18:54:46.014447 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:46.015481 INFO::ASW Batch was 0.702610261111858 prior to batch effect correction and is now 0.0256912713958272 .
2025-11-10 18:54:46.015743 INFO::ASW Label was 0.385449432187786 prior to batch effect correction and is now 0.886130601210393 .
2025-11-10 18:54:46.016045 INFO::Total function execution time is 0.0152180194854736 s and adjustment time is 0.00801205635070801 s ( 52.65 )
2025-11-10 18:54:46.091544 INFO::Formatting Data.
2025-11-10 18:54:46.091859 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:46.092154 INFO::Removing potential empty rows and columns
2025-11-10 18:54:46.092478 INFO::Found 0 missing values.
2025-11-10 18:54:46.093369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:46.093545 INFO::Done
2025-11-10 18:54:46.093733 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:46.094393 INFO::Starting hierarchical adjustment
2025-11-10 18:54:46.094611 INFO::Found 3 batches.
2025-11-10 18:54:46.094773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:46.094954 INFO::Using default BPPARAM
2025-11-10 18:54:46.095106 INFO::Processing subtree level 1
2025-11-10 18:54:46.137112 INFO::Adjusting the last 1 batches sequentially
2025-11-10 18:54:46.138552 INFO::Done
2025-11-10 18:54:46.1388 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:46.140824 INFO::ASW Batch was -0.0953646908628973 prior to batch effect correction and is now -0.0953646908628973 .
2025-11-10 18:54:46.141497 INFO::Total function execution time is 0.049962043762207 s and adjustment time is 0.0439760684967041 s ( 88.02 )
2025-11-10 18:54:46.141949 INFO::Formatting Data.
2025-11-10 18:54:46.142327 INFO::Typecasting input to dataframe.
2025-11-10 18:54:46.1426 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:46.142972 INFO::Removing potential empty rows and columns
2025-11-10 18:54:46.143412 INFO::Found 0 missing values.
2025-11-10 18:54:46.14437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:46.144567 INFO::Done
2025-11-10 18:54:46.144724 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:46.145357 INFO::Starting hierarchical adjustment
2025-11-10 18:54:46.1456 INFO::Found 3 batches.
2025-11-10 18:54:46.14576 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:46.145996 INFO::Using default BPPARAM
2025-11-10 18:54:46.146186 INFO::Processing subtree level 1
2025-11-10 18:54:46.191259 INFO::Adjusting the last 1 batches sequentially
2025-11-10 18:54:46.192683 INFO::Done
2025-11-10 18:54:46.192912 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:46.194812 INFO::ASW Batch was -0.0953646908628973 prior to batch effect correction and is now -0.0953646908628973 .
2025-11-10 18:54:46.19545 INFO::Total function execution time is 0.0534849166870117 s and adjustment time is 0.0471241474151611 s ( 88.11 )
2025-11-10 18:54:46.201622 INFO::Formatting Data.
2025-11-10 18:54:46.201877 INFO::Typecasting input to dataframe.
2025-11-10 18:54:46.20215 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:46.202446 INFO::Removing potential empty rows and columns
2025-11-10 18:54:46.202825 INFO::Found 0 missing values.
2025-11-10 18:54:46.203751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:46.203929 INFO::Done
2025-11-10 18:54:46.204098 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:46.204754 INFO::Starting hierarchical adjustment
2025-11-10 18:54:46.204976 INFO::Found 3 batches.
2025-11-10 18:54:46.205131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:46.20535 INFO::Using default BPPARAM
2025-11-10 18:54:46.205512 INFO::Processing subtree level 1
2025-11-10 18:54:46.245454 INFO::Adjusting the last 1 batches sequentially
2025-11-10 18:54:46.24709 INFO::Done
2025-11-10 18:54:46.247328 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:46.249107 INFO::ASW Batch was -0.0507205417920694 prior to batch effect correction and is now -0.0507205417920694 .
2025-11-10 18:54:46.249788 INFO::Total function execution time is 0.0481441020965576 s and adjustment time is 0.0421481132507324 s ( 87.55 )
2025-11-10 18:54:46.314296 INFO::Formatting Data.
2025-11-10 18:54:46.314557 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:46.314919 INFO::Removing potential empty rows and columns
2025-11-10 18:54:46.315816 INFO::Found 1000 missing values.
2025-11-10 18:54:46.321755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:46.321998 INFO::Done
2025-11-10 18:54:46.322177 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:46.324345 INFO::Starting hierarchical adjustment
2025-11-10 18:54:46.324698 INFO::Found 10 batches.
2025-11-10 18:54:46.324893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:46.325253 INFO::Using default BPPARAM
2025-11-10 18:54:46.325419 INFO::Processing subtree level 1
2025-11-10 18:54:46.388848 INFO::Processing subtree level 2
2025-11-10 18:54:46.446432 INFO::Adjusting the last 1 batches sequentially
2025-11-10 18:54:46.448021 INFO::Done
2025-11-10 18:54:46.448393 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:46.451021 INFO::ASW Batch was 0.574273208950831 prior to batch effect correction and is now 0.574273208950831 .
2025-11-10 18:54:46.451338 INFO::ASW Label was 0.26181208591739 prior to batch effect correction and is now 0.26181208591739 .
2025-11-10 18:54:46.451742 INFO::Total function execution time is 0.137432098388672 s and adjustment time is 0.123385906219482 s ( 89.78 )
2025-11-10 18:54:46.452055 INFO::Formatting Data.
2025-11-10 18:54:46.452259 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:46.452643 INFO::Removing potential empty rows and columns
2025-11-10 18:54:46.453553 INFO::Found 1000 missing values.
2025-11-10 18:54:46.459111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:46.459359 INFO::Done
2025-11-10 18:54:46.459539 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:46.461417 INFO::Starting hierarchical adjustment
2025-11-10 18:54:46.461679 INFO::Found 10 batches.
2025-11-10 18:54:46.94652 INFO::Set up parallel execution backend with 2 workers
2025-11-10 18:54:46.946821 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-10 18:54:47.426728 INFO::Adjusting the last 2 batches sequentially
2025-11-10 18:54:47.427327 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-10 18:54:47.432872 INFO::Done
2025-11-10 18:54:47.433077 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:47.434816 INFO::ASW Batch was 0.574273208950831 prior to batch effect correction and is now 0.574273208950831 .
2025-11-10 18:54:47.434979 INFO::ASW Label was 0.26181208591739 prior to batch effect correction and is now 0.26181208591739 .
2025-11-10 18:54:47.435204 INFO::Total function execution time is 0.983155012130737 s and adjustment time is 0.971251964569092 s ( 98.79 )
2025-11-10 18:54:47.504097 INFO::Formatting Data.
2025-11-10 18:54:47.504371 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.504688 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.505064 INFO::Found 0 missing values.
2025-11-10 18:54:47.506249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.506421 INFO::Done
2025-11-10 18:54:47.506587 INFO::Acquiring quality metrics before batch effect correction.
2025-11-10 18:54:47.50754 INFO::Starting hierarchical adjustment
2025-11-10 18:54:47.507774 INFO::Found 3 batches.
2025-11-10 18:54:47.507933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-10 18:54:47.50815 INFO::Using default BPPARAM
2025-11-10 18:54:47.508313 INFO::Processing subtree level 1
2025-11-10 18:54:47.55727 INFO::Adjusting the last 1 batches sequentially
2025-11-10 18:54:47.558839 INFO::Done
2025-11-10 18:54:47.559087 INFO::Acquiring quality metrics after batch effect correction.
2025-11-10 18:54:47.561524 INFO::ASW Batch was 0.267707125638066 prior to batch effect correction and is now -0.135550621357382 .
2025-11-10 18:54:47.561889 INFO::ASW Label was -0.219116529870739 prior to batch effect correction and is now -0.0548988114933708 .
2025-11-10 18:54:47.562632 INFO::Total function execution time is 0.0584218502044678 s and adjustment time is 0.051102876663208 s ( 87.47 )
2025-11-10 18:54:47.612147 INFO::Formatting Data.
2025-11-10 18:54:47.612478 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.612805 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.613214 INFO::Found 2 missing values.
2025-11-10 18:54:47.614195 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.614374 INFO::Done
2025-11-10 18:54:47.624543 INFO::Found NA in Reference column
2025-11-10 18:54:47.628066 INFO::Require at least two references per batch.
2025-11-10 18:54:47.637076 INFO::Formatting Data.
2025-11-10 18:54:47.637363 INFO::Recognized SummarizedExperiment
2025-11-10 18:54:47.637575 INFO::Typecasting input to dataframe.
2025-11-10 18:54:47.642379 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.642807 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.644279 INFO::Found 0 missing values.
2025-11-10 18:54:47.646987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.647207 INFO::Done
2025-11-10 18:54:47.653511 INFO::Formatting Data.
2025-11-10 18:54:47.653747 INFO::Recognized SummarizedExperiment
2025-11-10 18:54:47.653938 INFO::Typecasting input to dataframe.
2025-11-10 18:54:47.66177 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.662268 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.663721 INFO::Found 0 missing values.
2025-11-10 18:54:47.667982 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.668195 INFO::Done
2025-11-10 18:54:47.67435 INFO::Formatting Data.
2025-11-10 18:54:47.674574 INFO::Recognized SummarizedExperiment
2025-11-10 18:54:47.674745 INFO::Typecasting input to dataframe.
2025-11-10 18:54:47.679917 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.680234 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.680589 INFO::Found 0 missing values.
2025-11-10 18:54:47.680877 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-10 18:54:47.682197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.682368 INFO::Done
2025-11-10 18:54:47.686489 INFO::Formatting Data.
2025-11-10 18:54:47.686722 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.68699 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.68729 INFO::Found 0 missing values.
2025-11-10 18:54:47.688158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.688328 INFO::Done
2025-11-10 18:54:47.692392 INFO::Formatting Data.
2025-11-10 18:54:47.692616 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.692866 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.693207 INFO::Found 0 missing values.
2025-11-10 18:54:47.694214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.69439 INFO::Done
2025-11-10 18:54:47.706154 INFO::Formatting Data.
2025-11-10 18:54:47.70647 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.706815 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.707243 INFO::Found 1 missing values.
2025-11-10 18:54:47.708123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.708383 INFO::Done
2025-11-10 18:54:47.71601 INFO::Formatting Data.
2025-11-10 18:54:47.71625 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.716531 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.716825 INFO::Found 2 missing values.
2025-11-10 18:54:47.717112 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-10 18:54:47.717848 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.718029 INFO::Done
2025-11-10 18:54:47.722296 INFO::Formatting Data.
2025-11-10 18:54:47.722519 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.722785 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.723081 INFO::Found 2 missing values.
2025-11-10 18:54:47.723608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.7239 INFO::Done
2025-11-10 18:54:47.728191 INFO::Formatting Data.
2025-11-10 18:54:47.728438 INFO::Typecasting input to dataframe.
2025-11-10 18:54:47.728704 INFO::Replacing NaNs with NAs.
2025-11-10 18:54:47.728967 INFO::Removing potential empty rows and columns
2025-11-10 18:54:47.729325 INFO::Found 0 missing values.
2025-11-10 18:54:47.730199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-10 18:54:47.730403 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.647 1.621 8.437
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.921 | 0.479 | 7.168 | |
| compute_asw | 0.009 | 0.000 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.006 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |