Yannis Schumann
| Snapshot Date: 2025-11-05 13:40 -0500 (Wed, 05 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-06 11:32 -0500 (Thu, 06 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 166/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-11-05 21:21:53 -0500 (Wed, 05 Nov 2025) |
| EndedAt: 2025-11-05 21:23:20 -0500 (Wed, 05 Nov 2025) |
| EllapsedTime: 87.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.538 1.308 17.048
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-11-05 21:22:44.216608 INFO::Formatting Data.
2025-11-05 21:22:44.217882 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:44.228596 INFO::Removing potential empty rows and columns
2025-11-05 21:22:44.460764 INFO::Found 0 missing values.
2025-11-05 21:22:44.46415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:44.464883 INFO::Done
2025-11-05 21:22:44.465428 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:44.476509 INFO::Starting hierarchical adjustment
2025-11-05 21:22:44.47735 INFO::Found 3 batches.
2025-11-05 21:22:44.477912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:44.478978 INFO::Using default BPPARAM
2025-11-05 21:22:44.47951 INFO::Processing subtree level 1
2025-11-05 21:22:44.574279 INFO::Adjusting the last 1 batches sequentially
2025-11-05 21:22:44.57612 INFO::Done
2025-11-05 21:22:44.576803 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:44.579457 INFO::ASW Batch was -0.0325837461376678 prior to batch effect correction and is now -0.0325837461376678 .
2025-11-05 21:22:44.580587 INFO::Total function execution time is 0.364523649215698 s and adjustment time is 0.0989081859588623 s ( 27.13 )
2025-11-05 21:22:44.593896 INFO::Formatting Data.
2025-11-05 21:22:44.594638 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:44.595562 INFO::Removing potential empty rows and columns
2025-11-05 21:22:44.596628 INFO::Found 0 missing values.
2025-11-05 21:22:44.597594 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.
2025-11-05 21:22:44.60804 INFO::Formatting Data.
2025-11-05 21:22:44.608744 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:44.609626 INFO::Removing potential empty rows and columns
2025-11-05 21:22:44.610638 INFO::Found 0 missing values.
2025-11-05 21:22:44.611553 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.
2025-11-05 21:22:44.627436 INFO::Formatting Data.
2025-11-05 21:22:44.62819 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:44.629043 INFO::Removing potential empty rows and columns
2025-11-05 21:22:44.630044 INFO::Found 0 missing values.
2025-11-05 21:22:44.630934 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.
2025-11-05 21:22:44.635169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:44.635863 INFO::Done
2025-11-05 21:22:44.636421 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:44.638414 INFO::Starting hierarchical adjustment
2025-11-05 21:22:44.639118 INFO::Found 2 batches.
2025-11-05 21:22:44.639631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:44.640266 INFO::Using default BPPARAM
2025-11-05 21:22:44.640922 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:44.641896 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-05 21:22:44.664299 INFO::Done
2025-11-05 21:22:44.665041 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:44.667104 INFO::ASW Batch was -0.027084475026488 prior to batch effect correction and is now -0.120180239042257 .
2025-11-05 21:22:44.667934 INFO::Total function execution time is 0.0405316352844238 s and adjustment time is 0.0252938270568848 s ( 62.41 )
2025-11-05 21:22:44.670617 INFO::Formatting Data.
2025-11-05 21:22:44.671251 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:44.679906 INFO::Formatting Data.
2025-11-05 21:22:44.680582 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:44.681469 INFO::Removing potential empty rows and columns
2025-11-05 21:22:44.682481 INFO::Found 0 missing values.
2025-11-05 21:22:44.685318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:44.685864 INFO::Done
2025-11-05 21:22:44.686397 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:44.688415 INFO::Starting hierarchical adjustment
2025-11-05 21:22:44.689132 INFO::Found 2 batches.
2025-11-05 21:22:44.689662 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:44.690291 INFO::Using default BPPARAM
2025-11-05 21:22:44.690834 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:44.691833 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-05 21:22:44.729214 INFO::Done
2025-11-05 21:22:44.729895 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:44.73175 INFO::ASW Batch was -0.037846127324874 prior to batch effect correction and is now -0.0988871334259963 .
2025-11-05 21:22:44.732514 INFO::Total function execution time is 0.0526540279388428 s and adjustment time is 0.0402076244354248 s ( 76.36 )
2025-11-05 21:22:44.733469 INFO::Formatting Data.
2025-11-05 21:22:44.734037 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:44.734828 INFO::Removing potential empty rows and columns
2025-11-05 21:22:44.735753 INFO::Found 0 missing values.
2025-11-05 21:22:44.738252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:44.738765 INFO::Done
2025-11-05 21:22:44.739254 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:44.74104 INFO::Starting hierarchical adjustment
2025-11-05 21:22:44.741686 INFO::Found 2 batches.
2025-11-05 21:22:44.742178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:44.742723 INFO::Using default BPPARAM
2025-11-05 21:22:44.743208 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:44.744051 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-05 21:22:44.757354 INFO::Done
2025-11-05 21:22:44.758 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:44.759837 INFO::ASW Batch was -0.037846127324874 prior to batch effect correction and is now -0.0988871334259963 .
2025-11-05 21:22:44.76056 INFO::Total function execution time is 0.027092456817627 s and adjustment time is 0.0157840251922607 s ( 58.26 )
2025-11-05 21:22:47.795806 INFO::Formatting Data.
2025-11-05 21:22:47.796552 INFO::Recognized SummarizedExperiment
2025-11-05 21:22:47.797075 INFO::Typecasting input to dataframe.
2025-11-05 21:22:47.826418 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:47.827579 INFO::Removing potential empty rows and columns
2025-11-05 21:22:47.830623 INFO::Found 0 missing values.
2025-11-05 21:22:47.836406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:47.836955 INFO::Done
2025-11-05 21:22:47.837434 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:47.840503 INFO::Starting hierarchical adjustment
2025-11-05 21:22:47.841159 INFO::Found 2 batches.
2025-11-05 21:22:47.841638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:47.842576 INFO::Using default BPPARAM
2025-11-05 21:22:47.843077 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:47.843979 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-05 21:22:47.890994 INFO::Done
2025-11-05 21:22:47.891627 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:47.894698 INFO::ASW Batch was 0.0133696019694981 prior to batch effect correction and is now -0.103757112656053 .
2025-11-05 21:22:47.895468 INFO::Total function execution time is 0.099942684173584 s and adjustment time is 0.0499393939971924 s ( 49.97 )
2025-11-05 21:22:47.913052 INFO::Formatting Data.
2025-11-05 21:22:47.913805 INFO::Recognized SummarizedExperiment
2025-11-05 21:22:47.91438 INFO::Typecasting input to dataframe.
2025-11-05 21:22:47.923795 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:47.924865 INFO::Removing potential empty rows and columns
2025-11-05 21:22:47.928216 INFO::Found 0 missing values.
2025-11-05 21:22:47.934687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:47.935256 INFO::Done
2025-11-05 21:22:47.935756 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:47.939046 INFO::Starting hierarchical adjustment
2025-11-05 21:22:47.939727 INFO::Found 2 batches.
2025-11-05 21:22:47.94024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:47.940815 INFO::Using default BPPARAM
2025-11-05 21:22:47.941329 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:47.942257 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-05 21:22:47.96527 INFO::Done
2025-11-05 21:22:47.965974 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:47.969435 INFO::ASW Batch was 0.014313045104685 prior to batch effect correction and is now 0.014313045104685 .
2025-11-05 21:22:47.970279 INFO::Total function execution time is 0.0572183132171631 s and adjustment time is 0.0256645679473877 s ( 44.85 )
2025-11-05 21:22:47.987981 INFO::Formatting Data.
2025-11-05 21:22:47.988753 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:47.989658 INFO::Removing potential empty rows and columns
2025-11-05 21:22:47.990675 INFO::Found 0 missing values.
2025-11-05 21:22:47.993568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:47.994113 INFO::Done
2025-11-05 21:22:47.994623 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:47.996589 INFO::Starting hierarchical adjustment
2025-11-05 21:22:47.997305 INFO::Found 3 batches.
2025-11-05 21:22:47.997833 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:47.998436 INFO::Using default BPPARAM
2025-11-05 21:22:47.99897 INFO::Processing subtree level 1
2025-11-05 21:22:48.136191 INFO::Adjusting the last 1 batches sequentially
2025-11-05 21:22:48.138228 INFO::Done
2025-11-05 21:22:48.138959 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:48.141729 INFO::ASW Batch was -0.0246917577369455 prior to batch effect correction and is now -0.154897129224253 .
2025-11-05 21:22:48.142764 INFO::Total function execution time is 0.154806613922119 s and adjustment time is 0.141011953353882 s ( 91.09 )
2025-11-05 21:22:48.159798 INFO::Skipping initial DF formatting
2025-11-05 21:22:48.160622 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:48.164776 INFO::Starting hierarchical adjustment
2025-11-05 21:22:48.165569 INFO::Found 5 batches.
2025-11-05 21:22:48.16616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:48.166799 INFO::Using default BPPARAM
2025-11-05 21:22:48.167369 INFO::Processing subtree level 1
2025-11-05 21:22:48.282619 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:48.284276 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-05 21:22:48.303378 INFO::Done
2025-11-05 21:22:48.304083 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:48.308276 INFO::ASW Batch was 0.452323770417659 prior to batch effect correction and is now 0.452323770417659 .
2025-11-05 21:22:48.308889 INFO::ASW Label was 0.414356830312112 prior to batch effect correction and is now 0.414356830312112 .
2025-11-05 21:22:48.309743 INFO::Total function execution time is 0.15008807182312 s and adjustment time is 0.137964248657227 s ( 91.92 )
2025-11-05 21:22:48.326977 INFO::Formatting Data.
2025-11-05 21:22:48.327748 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:48.328678 INFO::Removing potential empty rows and columns
2025-11-05 21:22:48.329678 INFO::Found 0 missing values.
2025-11-05 21:22:48.333715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:48.334275 INFO::Done
2025-11-05 21:22:48.334808 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:48.337793 INFO::Starting hierarchical adjustment
2025-11-05 21:22:48.338524 INFO::Found 5 batches.
2025-11-05 21:22:48.339089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:48.339721 INFO::Using default BPPARAM
2025-11-05 21:22:48.340276 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.
2025-11-05 21:22:48.443265 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:48.444793 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-05 21:22:48.460306 INFO::Done
2025-11-05 21:22:48.460986 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:48.46412 INFO::ASW Batch was 0.429091684660014 prior to batch effect correction and is now -0.0626078664053687 .
2025-11-05 21:22:48.464719 INFO::ASW Label was 0.348091285114101 prior to batch effect correction and is now 0.802849721232358 .
2025-11-05 21:22:48.465549 INFO::Total function execution time is 0.138643741607666 s and adjustment time is 0.121915102005005 s ( 87.93 )
2025-11-05 21:22:48.466411 INFO::Formatting Data.
2025-11-05 21:22:48.467052 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:48.467943 INFO::Removing potential empty rows and columns
2025-11-05 21:22:48.468926 INFO::Found 0 missing values.
2025-11-05 21:22:48.472903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:48.473462 INFO::Done
2025-11-05 21:22:48.473996 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:48.476952 INFO::Starting hierarchical adjustment
2025-11-05 21:22:48.477651 INFO::Found 5 batches.
2025-11-05 21:22:48.478194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:48.478823 INFO::Using default BPPARAM
2025-11-05 21:22:48.479388 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.
2025-11-05 21:22:48.587329 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:48.589228 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-05 21:22:48.607243 INFO::Done
2025-11-05 21:22:48.608102 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:48.611682 INFO::ASW Batch was 0.429091684660014 prior to batch effect correction and is now -0.0626078664053687 .
2025-11-05 21:22:48.612386 INFO::ASW Label was 0.348091285114101 prior to batch effect correction and is now 0.802849721232358 .
2025-11-05 21:22:48.613344 INFO::Total function execution time is 0.146915912628174 s and adjustment time is 0.129664182662964 s ( 88.26 )
2025-11-05 21:22:48.629358 INFO::Formatting Data.
2025-11-05 21:22:48.630339 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:48.631377 INFO::Removing potential empty rows and columns
2025-11-05 21:22:48.632537 INFO::Found 0 missing values.
2025-11-05 21:22:48.637197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:48.637814 INFO::Done
2025-11-05 21:22:48.638982 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:48.642532 INFO::Starting hierarchical adjustment
2025-11-05 21:22:48.643343 INFO::Found 5 batches.
2025-11-05 21:22:48.643976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:48.644606 INFO::Using default BPPARAM
2025-11-05 21:22:48.645164 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.
2025-11-05 21:22:48.752518 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:48.754386 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-05 21:22:48.772242 INFO::Done
2025-11-05 21:22:48.773094 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:48.776679 INFO::ASW Batch was 0.481013328183526 prior to batch effect correction and is now -0.0816580013799789 .
2025-11-05 21:22:48.777407 INFO::ASW Label was 0.24250523724456 prior to batch effect correction and is now 0.880838880045425 .
2025-11-05 21:22:48.778334 INFO::Total function execution time is 0.149107217788696 s and adjustment time is 0.129018545150757 s ( 86.53 )
2025-11-05 21:22:48.779293 INFO::Formatting Data.
2025-11-05 21:22:48.779995 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:48.780974 INFO::Removing potential empty rows and columns
2025-11-05 21:22:48.782096 INFO::Found 0 missing values.
2025-11-05 21:22:48.786598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:48.787208 INFO::Done
2025-11-05 21:22:48.787777 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:48.79111 INFO::Starting hierarchical adjustment
2025-11-05 21:22:48.791893 INFO::Found 5 batches.
2025-11-05 21:22:48.792457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:48.793165 INFO::Using default BPPARAM
2025-11-05 21:22:48.793787 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.
2025-11-05 21:22:48.905736 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:48.907373 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-05 21:22:48.92379 INFO::Done
2025-11-05 21:22:48.924536 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:48.927884 INFO::ASW Batch was 0.481013328183526 prior to batch effect correction and is now -0.0816580013799789 .
2025-11-05 21:22:48.928496 INFO::ASW Label was 0.24250523724456 prior to batch effect correction and is now 0.880838880045425 .
2025-11-05 21:22:48.929343 INFO::Total function execution time is 0.150058031082153 s and adjustment time is 0.132053375244141 s ( 88 )
2025-11-05 21:22:48.943067 INFO::Formatting Data.
2025-11-05 21:22:48.943821 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:48.944775 INFO::Removing potential empty rows and columns
2025-11-05 21:22:48.945817 INFO::Found 0 missing values.
2025-11-05 21:22:48.948587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:48.949148 INFO::Done
2025-11-05 21:22:48.949709 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:48.952703 INFO::Starting hierarchical adjustment
2025-11-05 21:22:48.953419 INFO::Found 2 batches.
2025-11-05 21:22:48.953967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:48.954609 INFO::Using default BPPARAM
2025-11-05 21:22:48.955154 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:48.956052 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-05 21:22:48.970524 INFO::Done
2025-11-05 21:22:48.971174 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:48.974079 INFO::ASW Batch was 0.655159375881963 prior to batch effect correction and is now 0.00950466682640357 .
2025-11-05 21:22:48.97467 INFO::ASW Label was 0.4543207383475 prior to batch effect correction and is now 0.932481400950578 .
2025-11-05 21:22:48.975466 INFO::Total function execution time is 0.032477855682373 s and adjustment time is 0.0172407627105713 s ( 53.08 )
2025-11-05 21:22:48.976284 INFO::Formatting Data.
2025-11-05 21:22:48.976931 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:48.977778 INFO::Removing potential empty rows and columns
2025-11-05 21:22:48.978759 INFO::Found 0 missing values.
2025-11-05 21:22:48.981406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:48.981964 INFO::Done
2025-11-05 21:22:48.982504 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:48.985369 INFO::Starting hierarchical adjustment
2025-11-05 21:22:48.986067 INFO::Found 2 batches.
2025-11-05 21:22:48.986611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:48.987225 INFO::Using default BPPARAM
2025-11-05 21:22:48.987767 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:48.988672 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-05 21:22:49.003037 INFO::Done
2025-11-05 21:22:49.003676 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:49.006576 INFO::ASW Batch was 0.655159375881963 prior to batch effect correction and is now 0.00950466682640357 .
2025-11-05 21:22:49.00717 INFO::ASW Label was 0.4543207383475 prior to batch effect correction and is now 0.932481400950578 .
2025-11-05 21:22:49.007967 INFO::Total function execution time is 0.0316824913024902 s and adjustment time is 0.0171079635620117 s ( 54 )
2025-11-05 21:22:49.018796 INFO::Formatting Data.
2025-11-05 21:22:49.019528 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:49.020409 INFO::Removing potential empty rows and columns
2025-11-05 21:22:49.021318 INFO::Found 0 missing values.
2025-11-05 21:22:49.023391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:49.023934 INFO::Done
2025-11-05 21:22:49.024485 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:49.026395 INFO::Starting hierarchical adjustment
2025-11-05 21:22:49.027102 INFO::Found 2 batches.
2025-11-05 21:22:49.027633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:49.028255 INFO::Using default BPPARAM
2025-11-05 21:22:49.028779 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:49.029672 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-05 21:22:49.060637 INFO::Done
2025-11-05 21:22:49.061354 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:49.063346 INFO::ASW Batch was 0.0605936577580555 prior to batch effect correction and is now -0.0927037044467377 .
2025-11-05 21:22:49.06417 INFO::Total function execution time is 0.0454370975494385 s and adjustment time is 0.0336439609527588 s ( 74.05 )
2025-11-05 21:22:49.075713 INFO::Formatting Data.
2025-11-05 21:22:49.076498 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:49.077376 INFO::Removing potential empty rows and columns
2025-11-05 21:22:49.078378 INFO::Found 0 missing values.
2025-11-05 21:22:49.079499 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.
2025-11-05 21:22:49.083989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:49.084552 INFO::Done
2025-11-05 21:22:49.085088 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:49.087987 INFO::Starting hierarchical adjustment
2025-11-05 21:22:49.088675 INFO::Found 2 batches.
2025-11-05 21:22:49.089231 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:49.08983 INFO::Using default BPPARAM
2025-11-05 21:22:49.090371 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:49.09131 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-05 21:22:49.107253 INFO::Done
2025-11-05 21:22:49.107918 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:49.110799 INFO::ASW Batch was 0.705576630546449 prior to batch effect correction and is now 0.180787316314599 .
2025-11-05 21:22:49.111401 INFO::ASW Label was 0.392377421781327 prior to batch effect correction and is now 0.802902361533686 .
2025-11-05 21:22:49.112169 INFO::Total function execution time is 0.0365326404571533 s and adjustment time is 0.0187065601348877 s ( 51.21 )
2025-11-05 21:22:49.113002 INFO::Formatting Data.
2025-11-05 21:22:49.113619 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:49.114531 INFO::Removing potential empty rows and columns
2025-11-05 21:22:49.115512 INFO::Found 0 missing values.
2025-11-05 21:22:49.116398 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.
2025-11-05 21:22:49.120836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:49.121385 INFO::Done
2025-11-05 21:22:49.121924 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:49.124732 INFO::Starting hierarchical adjustment
2025-11-05 21:22:49.125444 INFO::Found 2 batches.
2025-11-05 21:22:49.125976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:49.12661 INFO::Using default BPPARAM
2025-11-05 21:22:49.127144 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:49.128059 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-05 21:22:49.14402 INFO::Done
2025-11-05 21:22:49.144671 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:49.147496 INFO::ASW Batch was 0.705576630546449 prior to batch effect correction and is now 0.180787316314599 .
2025-11-05 21:22:49.148077 INFO::ASW Label was 0.392377421781327 prior to batch effect correction and is now 0.802902361533686 .
2025-11-05 21:22:49.148883 INFO::Total function execution time is 0.0358929634094238 s and adjustment time is 0.0187060832977295 s ( 52.12 )
2025-11-05 21:22:49.35968 INFO::Formatting Data.
2025-11-05 21:22:49.360658 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:49.361635 INFO::Removing potential empty rows and columns
2025-11-05 21:22:49.362719 INFO::Found 0 missing values.
2025-11-05 21:22:49.365767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:49.366362 INFO::Done
2025-11-05 21:22:49.366898 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:49.369187 INFO::Starting hierarchical adjustment
2025-11-05 21:22:49.369914 INFO::Found 3 batches.
2025-11-05 21:22:49.370449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:49.371135 INFO::Using default BPPARAM
2025-11-05 21:22:49.371681 INFO::Processing subtree level 1
2025-11-05 21:22:49.468531 INFO::Adjusting the last 1 batches sequentially
2025-11-05 21:22:49.470582 INFO::Done
2025-11-05 21:22:49.471318 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:49.47405 INFO::ASW Batch was -0.0887550842606128 prior to batch effect correction and is now -0.0887550842606128 .
2025-11-05 21:22:49.475078 INFO::Total function execution time is 0.115669250488281 s and adjustment time is 0.100803852081299 s ( 87.15 )
2025-11-05 21:22:49.476245 INFO::Formatting Data.
2025-11-05 21:22:49.476942 INFO::Typecasting input to dataframe.
2025-11-05 21:22:49.477732 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:49.478708 INFO::Removing potential empty rows and columns
2025-11-05 21:22:49.47986 INFO::Found 0 missing values.
2025-11-05 21:22:49.483018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:49.483575 INFO::Done
2025-11-05 21:22:49.484137 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:49.486183 INFO::Starting hierarchical adjustment
2025-11-05 21:22:49.48691 INFO::Found 3 batches.
2025-11-05 21:22:49.487445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:49.488108 INFO::Using default BPPARAM
2025-11-05 21:22:49.488659 INFO::Processing subtree level 1
2025-11-05 21:22:49.577245 INFO::Adjusting the last 1 batches sequentially
2025-11-05 21:22:49.579629 INFO::Done
2025-11-05 21:22:49.580364 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:49.583155 INFO::ASW Batch was -0.0887550842606128 prior to batch effect correction and is now -0.0887550842606128 .
2025-11-05 21:22:49.584162 INFO::Total function execution time is 0.107872724533081 s and adjustment time is 0.0927896499633789 s ( 86.02 )
2025-11-05 21:22:49.596884 INFO::Formatting Data.
2025-11-05 21:22:49.597663 INFO::Typecasting input to dataframe.
2025-11-05 21:22:49.598547 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:49.5995 INFO::Removing potential empty rows and columns
2025-11-05 21:22:49.600564 INFO::Found 0 missing values.
2025-11-05 21:22:49.603526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:49.604083 INFO::Done
2025-11-05 21:22:49.604617 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:49.606601 INFO::Starting hierarchical adjustment
2025-11-05 21:22:49.607371 INFO::Found 3 batches.
2025-11-05 21:22:49.607926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:49.60856 INFO::Using default BPPARAM
2025-11-05 21:22:49.609114 INFO::Processing subtree level 1
2025-11-05 21:22:49.694666 INFO::Adjusting the last 1 batches sequentially
2025-11-05 21:22:49.696429 INFO::Done
2025-11-05 21:22:49.697076 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:49.699504 INFO::ASW Batch was -0.0424690473314252 prior to batch effect correction and is now -0.0424690473314252 .
2025-11-05 21:22:49.70047 INFO::Total function execution time is 0.103657007217407 s and adjustment time is 0.089195728302002 s ( 86.05 )
2025-11-05 21:22:49.836725 INFO::Formatting Data.
2025-11-05 21:22:49.837527 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:49.838624 INFO::Removing potential empty rows and columns
2025-11-05 21:22:49.841347 INFO::Found 1000 missing values.
2025-11-05 21:22:49.859849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:49.860556 INFO::Done
2025-11-05 21:22:49.861141 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:49.866523 INFO::Starting hierarchical adjustment
2025-11-05 21:22:49.867311 INFO::Found 10 batches.
2025-11-05 21:22:49.867867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:49.868488 INFO::Using default BPPARAM
2025-11-05 21:22:49.869072 INFO::Processing subtree level 1
2025-11-05 21:22:49.998499 INFO::Processing subtree level 2
2025-11-05 21:22:50.136588 INFO::Adjusting the last 1 batches sequentially
2025-11-05 21:22:50.13853 INFO::Done
2025-11-05 21:22:50.139217 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:50.144732 INFO::ASW Batch was 0.512525416632592 prior to batch effect correction and is now 0.512525416632592 .
2025-11-05 21:22:50.145432 INFO::ASW Label was 0.320080563103064 prior to batch effect correction and is now 0.320080563103064 .
2025-11-05 21:22:50.146377 INFO::Total function execution time is 0.309700489044189 s and adjustment time is 0.271363973617554 s ( 87.62 )
2025-11-05 21:22:50.147242 INFO::Formatting Data.
2025-11-05 21:22:50.147913 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:50.149166 INFO::Removing potential empty rows and columns
2025-11-05 21:22:50.15196 INFO::Found 1000 missing values.
2025-11-05 21:22:50.171124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:50.171908 INFO::Done
2025-11-05 21:22:50.172513 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:50.178097 INFO::Starting hierarchical adjustment
2025-11-05 21:22:50.178906 INFO::Found 10 batches.
2025-11-05 21:22:51.309929 INFO::Set up parallel execution backend with 2 workers
2025-11-05 21:22:51.316189 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-05 21:22:52.459073 INFO::Adjusting the last 2 batches sequentially
2025-11-05 21:22:52.46178 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-05 21:22:52.477495 INFO::Done
2025-11-05 21:22:52.478124 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:52.482557 INFO::ASW Batch was 0.512525416632592 prior to batch effect correction and is now 0.512525416632592 .
2025-11-05 21:22:52.4831 INFO::ASW Label was 0.320080563103064 prior to batch effect correction and is now 0.320080563103064 .
2025-11-05 21:22:52.483818 INFO::Total function execution time is 2.33661985397339 s and adjustment time is 2.2987813949585 s ( 98.38 )
2025-11-05 21:22:52.627374 INFO::Formatting Data.
2025-11-05 21:22:52.628162 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:52.629128 INFO::Removing potential empty rows and columns
2025-11-05 21:22:52.630181 INFO::Found 0 missing values.
2025-11-05 21:22:52.63373 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:52.634305 INFO::Done
2025-11-05 21:22:52.63482 INFO::Acquiring quality metrics before batch effect correction.
2025-11-05 21:22:52.637706 INFO::Starting hierarchical adjustment
2025-11-05 21:22:52.638429 INFO::Found 3 batches.
2025-11-05 21:22:52.638963 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-05 21:22:52.63955 INFO::Using default BPPARAM
2025-11-05 21:22:52.640094 INFO::Processing subtree level 1
2025-11-05 21:22:52.742592 INFO::Adjusting the last 1 batches sequentially
2025-11-05 21:22:52.744421 INFO::Done
2025-11-05 21:22:52.745105 INFO::Acquiring quality metrics after batch effect correction.
2025-11-05 21:22:52.748277 INFO::ASW Batch was 0.156124520549065 prior to batch effect correction and is now -0.159412338139005 .
2025-11-05 21:22:52.7489 INFO::ASW Label was -0.223750878731287 prior to batch effect correction and is now -0.144963786456426 .
2025-11-05 21:22:52.749769 INFO::Total function execution time is 0.122436761856079 s and adjustment time is 0.106106042861938 s ( 86.66 )
2025-11-05 21:22:52.868637 INFO::Formatting Data.
2025-11-05 21:22:52.869601 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:52.870517 INFO::Removing potential empty rows and columns
2025-11-05 21:22:52.871597 INFO::Found 2 missing values.
2025-11-05 21:22:52.874368 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:52.874933 INFO::Done
2025-11-05 21:22:52.901204 INFO::Found NA in Reference column
2025-11-05 21:22:52.910474 INFO::Require at least two references per batch.
2025-11-05 21:22:52.930493 INFO::Formatting Data.
2025-11-05 21:22:52.931223 INFO::Recognized SummarizedExperiment
2025-11-05 21:22:52.931756 INFO::Typecasting input to dataframe.
2025-11-05 21:22:52.94106 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:52.942103 INFO::Removing potential empty rows and columns
2025-11-05 21:22:52.945402 INFO::Found 0 missing values.
2025-11-05 21:22:52.951649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:52.952237 INFO::Done
2025-11-05 21:22:52.966746 INFO::Formatting Data.
2025-11-05 21:22:52.967382 INFO::Recognized SummarizedExperiment
2025-11-05 21:22:52.967907 INFO::Typecasting input to dataframe.
2025-11-05 21:22:52.984155 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:52.985292 INFO::Removing potential empty rows and columns
2025-11-05 21:22:52.988605 INFO::Found 0 missing values.
2025-11-05 21:22:52.998764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:52.999383 INFO::Done
2025-11-05 21:22:53.014109 INFO::Formatting Data.
2025-11-05 21:22:53.014759 INFO::Recognized SummarizedExperiment
2025-11-05 21:22:53.015279 INFO::Typecasting input to dataframe.
2025-11-05 21:22:53.030816 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:53.031741 INFO::Removing potential empty rows and columns
2025-11-05 21:22:53.032761 INFO::Found 0 missing values.
2025-11-05 21:22:53.033652 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.
2025-11-05 21:22:53.037884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:53.038406 INFO::Done
2025-11-05 21:22:53.048014 INFO::Formatting Data.
2025-11-05 21:22:53.048698 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:53.04955 INFO::Removing potential empty rows and columns
2025-11-05 21:22:53.050551 INFO::Found 0 missing values.
2025-11-05 21:22:53.05335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:53.053911 INFO::Done
2025-11-05 21:22:53.06433 INFO::Formatting Data.
2025-11-05 21:22:53.065031 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:53.065852 INFO::Removing potential empty rows and columns
2025-11-05 21:22:53.066773 INFO::Found 0 missing values.
2025-11-05 21:22:53.069502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:53.070079 INFO::Done
2025-11-05 21:22:53.098356 INFO::Formatting Data.
2025-11-05 21:22:53.099185 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:53.100248 INFO::Removing potential empty rows and columns
2025-11-05 21:22:53.101435 INFO::Found 1 missing values.
2025-11-05 21:22:53.104072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:53.104713 INFO::Done
2025-11-05 21:22:53.123417 INFO::Formatting Data.
2025-11-05 21:22:53.124305 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:53.125217 INFO::Removing potential empty rows and columns
2025-11-05 21:22:53.12621 INFO::Found 2 missing values.
2025-11-05 21:22:53.127151 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.
2025-11-05 21:22:53.129431 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:53.13003 INFO::Done
2025-11-05 21:22:53.140151 INFO::Formatting Data.
2025-11-05 21:22:53.140874 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:53.141725 INFO::Removing potential empty rows and columns
2025-11-05 21:22:53.14267 INFO::Found 2 missing values.
2025-11-05 21:22:53.144233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:53.144758 INFO::Done
2025-11-05 21:22:53.154789 INFO::Formatting Data.
2025-11-05 21:22:53.155533 INFO::Typecasting input to dataframe.
2025-11-05 21:22:53.156417 INFO::Replacing NaNs with NAs.
2025-11-05 21:22:53.157323 INFO::Removing potential empty rows and columns
2025-11-05 21:22:53.158499 INFO::Found 0 missing values.
2025-11-05 21:22:53.161678 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-05 21:22:53.162284 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.824 3.450 20.022
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.538 | 1.308 | 17.048 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.010 | 0.002 | 0.012 | |
| generate_dataset | 0.010 | 0.002 | 0.012 | |