Yannis Schumann
| Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:03 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 165/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-10-22 21:27:12 -0400 (Wed, 22 Oct 2025) |
| EndedAt: 2025-10-22 21:28:44 -0400 (Wed, 22 Oct 2025) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 24.673 1.847 18.621
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-10-22 21:28:04.798581 INFO::Formatting Data.
2025-10-22 21:28:04.800815 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:04.820127 INFO::Removing potential empty rows and columns
2025-10-22 21:28:05.09501 INFO::Found 0 missing values.
2025-10-22 21:28:05.098525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:05.09927 INFO::Done
2025-10-22 21:28:05.099809 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:05.111473 INFO::Starting hierarchical adjustment
2025-10-22 21:28:05.112391 INFO::Found 3 batches.
2025-10-22 21:28:05.112944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:05.114068 INFO::Using default BPPARAM
2025-10-22 21:28:05.114628 INFO::Processing subtree level 1
2025-10-22 21:28:05.220466 INFO::Adjusting the last 1 batches sequentially
2025-10-22 21:28:05.222673 INFO::Done
2025-10-22 21:28:05.223523 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:05.226583 INFO::ASW Batch was -0.0224085553864004 prior to batch effect correction and is now -0.0224085553864004 .
2025-10-22 21:28:05.227899 INFO::Total function execution time is 0.430523872375488 s and adjustment time is 0.110429763793945 s ( 25.65 )
2025-10-22 21:28:05.244023 INFO::Formatting Data.
2025-10-22 21:28:05.244975 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:05.245977 INFO::Removing potential empty rows and columns
2025-10-22 21:28:05.247112 INFO::Found 0 missing values.
2025-10-22 21:28:05.248093 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-22 21:28:05.259112 INFO::Formatting Data.
2025-10-22 21:28:05.259953 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:05.260898 INFO::Removing potential empty rows and columns
2025-10-22 21:28:05.261995 INFO::Found 0 missing values.
2025-10-22 21:28:05.262982 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-22 21:28:05.279074 INFO::Formatting Data.
2025-10-22 21:28:05.279882 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:05.280813 INFO::Removing potential empty rows and columns
2025-10-22 21:28:05.281846 INFO::Found 0 missing values.
2025-10-22 21:28:05.282758 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-22 21:28:05.286973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:05.287532 INFO::Done
2025-10-22 21:28:05.288023 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:05.290088 INFO::Starting hierarchical adjustment
2025-10-22 21:28:05.290788 INFO::Found 2 batches.
2025-10-22 21:28:05.291316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:05.291916 INFO::Using default BPPARAM
2025-10-22 21:28:05.292441 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:05.293387 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-22 21:28:05.317142 INFO::Done
2025-10-22 21:28:05.317965 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:05.320458 INFO::ASW Batch was -0.0146876801043515 prior to batch effect correction and is now -0.109340201330919 .
2025-10-22 21:28:05.321421 INFO::Total function execution time is 0.0423824787139893 s and adjustment time is 0.0264143943786621 s ( 62.32 )
2025-10-22 21:28:05.324272 INFO::Formatting Data.
2025-10-22 21:28:05.324951 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:05.334006 INFO::Formatting Data.
2025-10-22 21:28:05.33484 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:05.335786 INFO::Removing potential empty rows and columns
2025-10-22 21:28:05.336843 INFO::Found 0 missing values.
2025-10-22 21:28:05.339751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:05.340302 INFO::Done
2025-10-22 21:28:05.340844 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:05.342972 INFO::Starting hierarchical adjustment
2025-10-22 21:28:05.343931 INFO::Found 2 batches.
2025-10-22 21:28:05.344493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:05.345098 INFO::Using default BPPARAM
2025-10-22 21:28:05.345683 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:05.346646 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:05.38439 INFO::Done
2025-10-22 21:28:05.385062 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:05.38704 INFO::ASW Batch was 0.00881741812751952 prior to batch effect correction and is now -0.120872839982166 .
2025-10-22 21:28:05.387845 INFO::Total function execution time is 0.0539250373840332 s and adjustment time is 0.04058837890625 s ( 75.27 )
2025-10-22 21:28:05.388921 INFO::Formatting Data.
2025-10-22 21:28:05.389503 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:05.390313 INFO::Removing potential empty rows and columns
2025-10-22 21:28:05.391285 INFO::Found 0 missing values.
2025-10-22 21:28:05.393833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:05.394341 INFO::Done
2025-10-22 21:28:05.394814 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:05.396717 INFO::Starting hierarchical adjustment
2025-10-22 21:28:05.397389 INFO::Found 2 batches.
2025-10-22 21:28:05.397867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:05.398426 INFO::Using default BPPARAM
2025-10-22 21:28:05.398895 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:05.399736 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:05.413535 INFO::Done
2025-10-22 21:28:05.41424 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:05.416148 INFO::ASW Batch was 0.00881741812751952 prior to batch effect correction and is now -0.120872839982166 .
2025-10-22 21:28:05.416894 INFO::Total function execution time is 0.0279860496520996 s and adjustment time is 0.0162522792816162 s ( 58.07 )
2025-10-22 21:28:08.600144 INFO::Formatting Data.
2025-10-22 21:28:08.600885 INFO::Recognized SummarizedExperiment
2025-10-22 21:28:08.601391 INFO::Typecasting input to dataframe.
2025-10-22 21:28:08.631694 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:08.632984 INFO::Removing potential empty rows and columns
2025-10-22 21:28:08.636892 INFO::Found 0 missing values.
2025-10-22 21:28:08.644022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:08.644727 INFO::Done
2025-10-22 21:28:08.645266 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:08.649032 INFO::Starting hierarchical adjustment
2025-10-22 21:28:08.649854 INFO::Found 2 batches.
2025-10-22 21:28:08.650426 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:08.651711 INFO::Using default BPPARAM
2025-10-22 21:28:08.652284 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:08.653367 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-22 21:28:08.713059 INFO::Done
2025-10-22 21:28:08.713881 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:08.717622 INFO::ASW Batch was 0.00586406006825402 prior to batch effect correction and is now -0.094733976748412 .
2025-10-22 21:28:08.718531 INFO::Total function execution time is 0.118672370910645 s and adjustment time is 0.0633268356323242 s ( 53.36 )
2025-10-22 21:28:08.73829 INFO::Formatting Data.
2025-10-22 21:28:08.739081 INFO::Recognized SummarizedExperiment
2025-10-22 21:28:08.739645 INFO::Typecasting input to dataframe.
2025-10-22 21:28:08.749452 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:08.750749 INFO::Removing potential empty rows and columns
2025-10-22 21:28:08.754714 INFO::Found 0 missing values.
2025-10-22 21:28:08.762108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:08.762866 INFO::Done
2025-10-22 21:28:08.771678 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:08.776521 INFO::Starting hierarchical adjustment
2025-10-22 21:28:08.777482 INFO::Found 2 batches.
2025-10-22 21:28:08.778047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:08.778719 INFO::Using default BPPARAM
2025-10-22 21:28:08.77926 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:08.780322 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-22 21:28:08.807044 INFO::Done
2025-10-22 21:28:08.807827 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:08.811442 INFO::ASW Batch was 0.00461190663591003 prior to batch effect correction and is now 0.00461190663591003 .
2025-10-22 21:28:08.812456 INFO::Total function execution time is 0.0741331577301025 s and adjustment time is 0.0297322273254395 s ( 40.11 )
2025-10-22 21:28:08.834446 INFO::Formatting Data.
2025-10-22 21:28:08.835332 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:08.836319 INFO::Removing potential empty rows and columns
2025-10-22 21:28:08.837432 INFO::Found 0 missing values.
2025-10-22 21:28:08.840498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:08.841036 INFO::Done
2025-10-22 21:28:08.841582 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:08.843704 INFO::Starting hierarchical adjustment
2025-10-22 21:28:08.844446 INFO::Found 3 batches.
2025-10-22 21:28:08.84497 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:08.845573 INFO::Using default BPPARAM
2025-10-22 21:28:08.846087 INFO::Processing subtree level 1
2025-10-22 21:28:08.986672 INFO::Adjusting the last 1 batches sequentially
2025-10-22 21:28:08.98844 INFO::Done
2025-10-22 21:28:08.98911 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:08.991723 INFO::ASW Batch was -0.00869479932848908 prior to batch effect correction and is now -0.179268830213344 .
2025-10-22 21:28:08.992747 INFO::Total function execution time is 0.158435583114624 s and adjustment time is 0.144137859344482 s ( 90.98 )
2025-10-22 21:28:09.0071 INFO::Skipping initial DF formatting
2025-10-22 21:28:09.007834 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:09.011969 INFO::Starting hierarchical adjustment
2025-10-22 21:28:09.012824 INFO::Found 5 batches.
2025-10-22 21:28:09.013403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:09.014024 INFO::Using default BPPARAM
2025-10-22 21:28:09.014591 INFO::Processing subtree level 1
2025-10-22 21:28:09.311405 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:09.313262 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-22 21:28:09.333941 INFO::Done
2025-10-22 21:28:09.334866 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:09.397395 INFO::ASW Batch was 0.559535605250383 prior to batch effect correction and is now 0.559535605250383 .
2025-10-22 21:28:09.399188 INFO::ASW Label was 0.299006638580554 prior to batch effect correction and is now 0.299006638580554 .
2025-10-22 21:28:09.400172 INFO::Total function execution time is 0.39311695098877 s and adjustment time is 0.321207046508789 s ( 81.71 )
2025-10-22 21:28:09.419397 INFO::Formatting Data.
2025-10-22 21:28:09.420461 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:09.421568 INFO::Removing potential empty rows and columns
2025-10-22 21:28:09.422668 INFO::Found 0 missing values.
2025-10-22 21:28:09.426953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:09.427593 INFO::Done
2025-10-22 21:28:09.428236 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:09.431807 INFO::Starting hierarchical adjustment
2025-10-22 21:28:09.432633 INFO::Found 5 batches.
2025-10-22 21:28:09.433208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:09.43383 INFO::Using default BPPARAM
2025-10-22 21:28:09.434389 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:09.581504 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:09.583369 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:09.601447 INFO::Done
2025-10-22 21:28:09.602268 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:09.605936 INFO::ASW Batch was 0.541738570119772 prior to batch effect correction and is now 0.0586572008738764 .
2025-10-22 21:28:09.606638 INFO::ASW Label was 0.323513036954821 prior to batch effect correction and is now 0.673132737366895 .
2025-10-22 21:28:09.607555 INFO::Total function execution time is 0.188310623168945 s and adjustment time is 0.168939590454102 s ( 89.71 )
2025-10-22 21:28:09.608526 INFO::Formatting Data.
2025-10-22 21:28:09.609229 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:09.610264 INFO::Removing potential empty rows and columns
2025-10-22 21:28:09.611415 INFO::Found 0 missing values.
2025-10-22 21:28:09.6158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:09.616396 INFO::Done
2025-10-22 21:28:09.616921 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:09.620165 INFO::Starting hierarchical adjustment
2025-10-22 21:28:09.620933 INFO::Found 5 batches.
2025-10-22 21:28:09.621479 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:09.62207 INFO::Using default BPPARAM
2025-10-22 21:28:09.622617 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:09.761224 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:09.763002 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:09.780604 INFO::Done
2025-10-22 21:28:09.781488 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:09.784847 INFO::ASW Batch was 0.541738570119772 prior to batch effect correction and is now 0.0586572008738764 .
2025-10-22 21:28:09.78551 INFO::ASW Label was 0.323513036954821 prior to batch effect correction and is now 0.673132737366895 .
2025-10-22 21:28:09.786362 INFO::Total function execution time is 0.177841663360596 s and adjustment time is 0.159756422042847 s ( 89.83 )
2025-10-22 21:28:09.8 INFO::Formatting Data.
2025-10-22 21:28:09.800796 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:09.8017 INFO::Removing potential empty rows and columns
2025-10-22 21:28:09.802679 INFO::Found 0 missing values.
2025-10-22 21:28:09.806685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:09.807298 INFO::Done
2025-10-22 21:28:09.807817 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:09.810867 INFO::Starting hierarchical adjustment
2025-10-22 21:28:09.811579 INFO::Found 5 batches.
2025-10-22 21:28:09.812107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:09.812732 INFO::Using default BPPARAM
2025-10-22 21:28:09.813269 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:09.954955 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:09.956886 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:09.975394 INFO::Done
2025-10-22 21:28:09.976238 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:09.97989 INFO::ASW Batch was 0.327212840338605 prior to batch effect correction and is now -0.101380148857053 .
2025-10-22 21:28:09.980636 INFO::ASW Label was 0.460638504704243 prior to batch effect correction and is now 0.891055180743516 .
2025-10-22 21:28:09.981576 INFO::Total function execution time is 0.181630611419678 s and adjustment time is 0.163911581039429 s ( 90.24 )
2025-10-22 21:28:09.982486 INFO::Formatting Data.
2025-10-22 21:28:09.983169 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:09.984163 INFO::Removing potential empty rows and columns
2025-10-22 21:28:09.98528 INFO::Found 0 missing values.
2025-10-22 21:28:09.989635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:09.990262 INFO::Done
2025-10-22 21:28:09.990823 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:09.994187 INFO::Starting hierarchical adjustment
2025-10-22 21:28:09.994992 INFO::Found 5 batches.
2025-10-22 21:28:09.995597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:09.996331 INFO::Using default BPPARAM
2025-10-22 21:28:09.996911 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:10.131434 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:10.133394 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:10.153149 INFO::Done
2025-10-22 21:28:10.154175 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.158271 INFO::ASW Batch was 0.327212840338605 prior to batch effect correction and is now -0.101380148857053 .
2025-10-22 21:28:10.158989 INFO::ASW Label was 0.460638504704243 prior to batch effect correction and is now 0.891055180743516 .
2025-10-22 21:28:10.159958 INFO::Total function execution time is 0.177461862564087 s and adjustment time is 0.158158540725708 s ( 89.12 )
2025-10-22 21:28:10.17583 INFO::Formatting Data.
2025-10-22 21:28:10.176863 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:10.17796 INFO::Removing potential empty rows and columns
2025-10-22 21:28:10.179135 INFO::Found 0 missing values.
2025-10-22 21:28:10.182131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:10.182728 INFO::Done
2025-10-22 21:28:10.183285 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:10.186649 INFO::Starting hierarchical adjustment
2025-10-22 21:28:10.187432 INFO::Found 2 batches.
2025-10-22 21:28:10.187991 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:10.188646 INFO::Using default BPPARAM
2025-10-22 21:28:10.189215 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:10.190196 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:10.206623 INFO::Done
2025-10-22 21:28:10.207374 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.210403 INFO::ASW Batch was 0.149331153958022 prior to batch effect correction and is now 0.0333326063927534 .
2025-10-22 21:28:10.211023 INFO::ASW Label was 0.845858105235847 prior to batch effect correction and is now 0.903476041538601 .
2025-10-22 21:28:10.21183 INFO::Total function execution time is 0.0362071990966797 s and adjustment time is 0.0193343162536621 s ( 53.4 )
2025-10-22 21:28:10.212658 INFO::Formatting Data.
2025-10-22 21:28:10.213287 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:10.21418 INFO::Removing potential empty rows and columns
2025-10-22 21:28:10.215169 INFO::Found 0 missing values.
2025-10-22 21:28:10.217906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:10.218462 INFO::Done
2025-10-22 21:28:10.218974 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:10.221982 INFO::Starting hierarchical adjustment
2025-10-22 21:28:10.222701 INFO::Found 2 batches.
2025-10-22 21:28:10.223245 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:10.223871 INFO::Using default BPPARAM
2025-10-22 21:28:10.224427 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:10.225364 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-22 21:28:10.240604 INFO::Done
2025-10-22 21:28:10.241351 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.244379 INFO::ASW Batch was 0.149331153958022 prior to batch effect correction and is now 0.0333326063927534 .
2025-10-22 21:28:10.245012 INFO::ASW Label was 0.845858105235847 prior to batch effect correction and is now 0.903476041538601 .
2025-10-22 21:28:10.245807 INFO::Total function execution time is 0.0331661701202393 s and adjustment time is 0.0180232524871826 s ( 54.34 )
2025-10-22 21:28:10.257378 INFO::Formatting Data.
2025-10-22 21:28:10.258185 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:10.259063 INFO::Removing potential empty rows and columns
2025-10-22 21:28:10.26 INFO::Found 0 missing values.
2025-10-22 21:28:10.262058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:10.2626 INFO::Done
2025-10-22 21:28:10.263102 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:10.265081 INFO::Starting hierarchical adjustment
2025-10-22 21:28:10.265801 INFO::Found 2 batches.
2025-10-22 21:28:10.266326 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:10.266895 INFO::Using default BPPARAM
2025-10-22 21:28:10.267406 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:10.268285 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-22 21:28:10.299741 INFO::Done
2025-10-22 21:28:10.300464 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.302412 INFO::ASW Batch was 0.158489603385719 prior to batch effect correction and is now -0.172694254967648 .
2025-10-22 21:28:10.303257 INFO::Total function execution time is 0.0460638999938965 s and adjustment time is 0.0340497493743896 s ( 73.92 )
2025-10-22 21:28:10.315264 INFO::Formatting Data.
2025-10-22 21:28:10.316058 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:10.316952 INFO::Removing potential empty rows and columns
2025-10-22 21:28:10.317983 INFO::Found 0 missing values.
2025-10-22 21:28:10.31916 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-22 21:28:10.323763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:10.32437 INFO::Done
2025-10-22 21:28:10.32489 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:10.327914 INFO::Starting hierarchical adjustment
2025-10-22 21:28:10.328645 INFO::Found 2 batches.
2025-10-22 21:28:10.329177 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:10.329773 INFO::Using default BPPARAM
2025-10-22 21:28:10.330305 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:10.331257 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-22 21:28:10.34781 INFO::Done
2025-10-22 21:28:10.348556 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.351586 INFO::ASW Batch was 0.470542485150853 prior to batch effect correction and is now -0.0145392894966083 .
2025-10-22 21:28:10.352257 INFO::ASW Label was 0.492990263995973 prior to batch effect correction and is now 0.89447587252716 .
2025-10-22 21:28:10.353034 INFO::Total function execution time is 0.0378811359405518 s and adjustment time is 0.0192744731903076 s ( 50.88 )
2025-10-22 21:28:10.353843 INFO::Formatting Data.
2025-10-22 21:28:10.354478 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:10.355402 INFO::Removing potential empty rows and columns
2025-10-22 21:28:10.356371 INFO::Found 0 missing values.
2025-10-22 21:28:10.357293 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-22 21:28:10.361732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:10.362277 INFO::Done
2025-10-22 21:28:10.362768 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:10.365718 INFO::Starting hierarchical adjustment
2025-10-22 21:28:10.366435 INFO::Found 2 batches.
2025-10-22 21:28:10.366947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:10.367545 INFO::Using default BPPARAM
2025-10-22 21:28:10.368048 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:10.368975 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-22 21:28:10.385435 INFO::Done
2025-10-22 21:28:10.386111 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.38913 INFO::ASW Batch was 0.470542485150853 prior to batch effect correction and is now -0.0145392894966083 .
2025-10-22 21:28:10.389742 INFO::ASW Label was 0.492990263995973 prior to batch effect correction and is now 0.89447587252716 .
2025-10-22 21:28:10.390551 INFO::Total function execution time is 0.0367214679718018 s and adjustment time is 0.0191140174865723 s ( 52.05 )
2025-10-22 21:28:10.620895 INFO::Formatting Data.
2025-10-22 21:28:10.621789 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:10.622729 INFO::Removing potential empty rows and columns
2025-10-22 21:28:10.62377 INFO::Found 0 missing values.
2025-10-22 21:28:10.626876 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:10.627492 INFO::Done
2025-10-22 21:28:10.628012 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:10.630138 INFO::Starting hierarchical adjustment
2025-10-22 21:28:10.630856 INFO::Found 3 batches.
2025-10-22 21:28:10.631407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:10.632001 INFO::Using default BPPARAM
2025-10-22 21:28:10.632558 INFO::Processing subtree level 1
2025-10-22 21:28:10.719351 INFO::Adjusting the last 1 batches sequentially
2025-10-22 21:28:10.721236 INFO::Done
2025-10-22 21:28:10.721894 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.724356 INFO::ASW Batch was -0.055925086077644 prior to batch effect correction and is now -0.055925086077644 .
2025-10-22 21:28:10.725282 INFO::Total function execution time is 0.10444164276123 s and adjustment time is 0.0904915332794189 s ( 86.64 )
2025-10-22 21:28:10.726412 INFO::Formatting Data.
2025-10-22 21:28:10.727072 INFO::Typecasting input to dataframe.
2025-10-22 21:28:10.727855 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:10.728817 INFO::Removing potential empty rows and columns
2025-10-22 21:28:10.729935 INFO::Found 0 missing values.
2025-10-22 21:28:10.733013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:10.733579 INFO::Done
2025-10-22 21:28:10.734097 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:10.736462 INFO::Starting hierarchical adjustment
2025-10-22 21:28:10.737216 INFO::Found 3 batches.
2025-10-22 21:28:10.737748 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:10.738385 INFO::Using default BPPARAM
2025-10-22 21:28:10.738913 INFO::Processing subtree level 1
2025-10-22 21:28:10.821634 INFO::Adjusting the last 1 batches sequentially
2025-10-22 21:28:10.823339 INFO::Done
2025-10-22 21:28:10.823962 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.826383 INFO::ASW Batch was -0.055925086077644 prior to batch effect correction and is now -0.055925086077644 .
2025-10-22 21:28:10.827318 INFO::Total function execution time is 0.100884199142456 s and adjustment time is 0.0862722396850586 s ( 85.52 )
2025-10-22 21:28:10.840461 INFO::Formatting Data.
2025-10-22 21:28:10.84131 INFO::Typecasting input to dataframe.
2025-10-22 21:28:10.842195 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:10.843093 INFO::Removing potential empty rows and columns
2025-10-22 21:28:10.844405 INFO::Found 0 missing values.
2025-10-22 21:28:10.847451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:10.848008 INFO::Done
2025-10-22 21:28:10.848545 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:10.850587 INFO::Starting hierarchical adjustment
2025-10-22 21:28:10.851331 INFO::Found 3 batches.
2025-10-22 21:28:10.851854 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:10.852493 INFO::Using default BPPARAM
2025-10-22 21:28:10.853009 INFO::Processing subtree level 1
2025-10-22 21:28:10.936983 INFO::Adjusting the last 1 batches sequentially
2025-10-22 21:28:10.938772 INFO::Done
2025-10-22 21:28:10.939468 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:10.941967 INFO::ASW Batch was -0.0770783592205966 prior to batch effect correction and is now -0.0770783592205966 .
2025-10-22 21:28:10.94292 INFO::Total function execution time is 0.102500677108765 s and adjustment time is 0.0875852108001709 s ( 85.45 )
2025-10-22 21:28:11.074803 INFO::Formatting Data.
2025-10-22 21:28:11.07565 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:11.07678 INFO::Removing potential empty rows and columns
2025-10-22 21:28:11.079515 INFO::Found 1000 missing values.
2025-10-22 21:28:11.098045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:11.098817 INFO::Done
2025-10-22 21:28:11.099395 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:11.104813 INFO::Starting hierarchical adjustment
2025-10-22 21:28:11.105677 INFO::Found 10 batches.
2025-10-22 21:28:11.106252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:11.10687 INFO::Using default BPPARAM
2025-10-22 21:28:11.107424 INFO::Processing subtree level 1
2025-10-22 21:28:11.237479 INFO::Processing subtree level 2
2025-10-22 21:28:11.384391 INFO::Adjusting the last 1 batches sequentially
2025-10-22 21:28:11.386567 INFO::Done
2025-10-22 21:28:11.387356 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:11.393221 INFO::ASW Batch was 0.517339919130327 prior to batch effect correction and is now 0.517339919130327 .
2025-10-22 21:28:11.393931 INFO::ASW Label was 0.298037969378762 prior to batch effect correction and is now 0.298037969378762 .
2025-10-22 21:28:11.394944 INFO::Total function execution time is 0.320189237594604 s and adjustment time is 0.281033277511597 s ( 87.77 )
2025-10-22 21:28:11.395843 INFO::Formatting Data.
2025-10-22 21:28:11.396509 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:11.397812 INFO::Removing potential empty rows and columns
2025-10-22 21:28:11.400675 INFO::Found 1000 missing values.
2025-10-22 21:28:11.419957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:11.420839 INFO::Done
2025-10-22 21:28:11.421446 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:11.427364 INFO::Starting hierarchical adjustment
2025-10-22 21:28:11.428244 INFO::Found 10 batches.
2025-10-22 21:28:12.677813 INFO::Set up parallel execution backend with 2 workers
2025-10-22 21:28:12.679963 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-22 21:28:14.135625 INFO::Adjusting the last 2 batches sequentially
2025-10-22 21:28:14.137612 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-22 21:28:14.154979 INFO::Done
2025-10-22 21:28:14.155683 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:14.160502 INFO::ASW Batch was 0.517339919130327 prior to batch effect correction and is now 0.517339919130327 .
2025-10-22 21:28:14.161126 INFO::ASW Label was 0.298037969378762 prior to batch effect correction and is now 0.298037969378762 .
2025-10-22 21:28:14.1619 INFO::Total function execution time is 2.76611661911011 s and adjustment time is 2.72689843177795 s ( 98.58 )
2025-10-22 21:28:14.328414 INFO::Formatting Data.
2025-10-22 21:28:14.329621 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.330853 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.332231 INFO::Found 0 missing values.
2025-10-22 21:28:14.336543 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.337189 INFO::Done
2025-10-22 21:28:14.337746 INFO::Acquiring quality metrics before batch effect correction.
2025-10-22 21:28:14.341331 INFO::Starting hierarchical adjustment
2025-10-22 21:28:14.342166 INFO::Found 3 batches.
2025-10-22 21:28:14.342749 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-22 21:28:14.34346 INFO::Using default BPPARAM
2025-10-22 21:28:14.344055 INFO::Processing subtree level 1
2025-10-22 21:28:14.466636 INFO::Adjusting the last 1 batches sequentially
2025-10-22 21:28:14.468883 INFO::Done
2025-10-22 21:28:14.469663 INFO::Acquiring quality metrics after batch effect correction.
2025-10-22 21:28:14.473253 INFO::ASW Batch was 0.164542460238137 prior to batch effect correction and is now -0.119623327209461 .
2025-10-22 21:28:14.473936 INFO::ASW Label was -0.205058471868002 prior to batch effect correction and is now -0.0964890915914659 .
2025-10-22 21:28:14.474891 INFO::Total function execution time is 0.146766901016235 s and adjustment time is 0.126863718032837 s ( 86.44 )
2025-10-22 21:28:14.60941 INFO::Formatting Data.
2025-10-22 21:28:14.610589 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.611564 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.612727 INFO::Found 2 missing values.
2025-10-22 21:28:14.615587 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.616167 INFO::Done
2025-10-22 21:28:14.642995 INFO::Found NA in Reference column
2025-10-22 21:28:14.652431 INFO::Require at least two references per batch.
2025-10-22 21:28:14.67336 INFO::Formatting Data.
2025-10-22 21:28:14.674251 INFO::Recognized SummarizedExperiment
2025-10-22 21:28:14.674783 INFO::Typecasting input to dataframe.
2025-10-22 21:28:14.685024 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.686248 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.689631 INFO::Found 0 missing values.
2025-10-22 21:28:14.69629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.697014 INFO::Done
2025-10-22 21:28:14.713247 INFO::Formatting Data.
2025-10-22 21:28:14.714109 INFO::Recognized SummarizedExperiment
2025-10-22 21:28:14.71467 INFO::Typecasting input to dataframe.
2025-10-22 21:28:14.732783 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.734167 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.737832 INFO::Found 0 missing values.
2025-10-22 21:28:14.748629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.749363 INFO::Done
2025-10-22 21:28:14.764553 INFO::Formatting Data.
2025-10-22 21:28:14.765362 INFO::Recognized SummarizedExperiment
2025-10-22 21:28:14.765926 INFO::Typecasting input to dataframe.
2025-10-22 21:28:14.782303 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.7834 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.784476 INFO::Found 0 missing values.
2025-10-22 21:28:14.785393 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-22 21:28:14.789741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.790338 INFO::Done
2025-10-22 21:28:14.799699 INFO::Formatting Data.
2025-10-22 21:28:14.800565 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.801507 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.802505 INFO::Found 0 missing values.
2025-10-22 21:28:14.80529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.805828 INFO::Done
2025-10-22 21:28:14.816994 INFO::Formatting Data.
2025-10-22 21:28:14.8179 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.818776 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.819789 INFO::Found 0 missing values.
2025-10-22 21:28:14.822625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.82324 INFO::Done
2025-10-22 21:28:14.855619 INFO::Formatting Data.
2025-10-22 21:28:14.856584 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.857711 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.858964 INFO::Found 1 missing values.
2025-10-22 21:28:14.861858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.862431 INFO::Done
2025-10-22 21:28:14.883382 INFO::Formatting Data.
2025-10-22 21:28:14.884283 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.88529 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.886376 INFO::Found 2 missing values.
2025-10-22 21:28:14.887368 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-22 21:28:14.889849 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.890445 INFO::Done
2025-10-22 21:28:14.901029 INFO::Formatting Data.
2025-10-22 21:28:14.901965 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.902885 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.903848 INFO::Found 2 missing values.
2025-10-22 21:28:14.905542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.906096 INFO::Done
2025-10-22 21:28:14.917972 INFO::Formatting Data.
2025-10-22 21:28:14.919022 INFO::Typecasting input to dataframe.
2025-10-22 21:28:14.91991 INFO::Replacing NaNs with NAs.
2025-10-22 21:28:14.920853 INFO::Removing potential empty rows and columns
2025-10-22 21:28:14.921955 INFO::Found 0 missing values.
2025-10-22 21:28:14.924973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-22 21:28:14.925542 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.410 3.845 21.866
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.673 | 1.847 | 18.621 | |
| compute_asw | 0.022 | 0.003 | 0.025 | |
| count_existing | 0.012 | 0.003 | 0.015 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.009 | 0.004 | 0.013 | |