Yannis Schumann
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:03 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /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: 2025-10-23 21:25:45 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 21:27:13 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 87.1 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 24.386 1.101 17.279
* 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")
2025-10-23 21:26:36.134831 INFO::Formatting Data.
2025-10-23 21:26:36.1362 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:36.147668 INFO::Removing potential empty rows and columns
2025-10-23 21:26:36.398731 INFO::Found 0 missing values.
2025-10-23 21:26:36.402251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:36.402946 INFO::Done
2025-10-23 21:26:36.40353 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:36.414931 INFO::Starting hierarchical adjustment
2025-10-23 21:26:36.415771 INFO::Found 3 batches.
2025-10-23 21:26:36.416336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:36.417439 INFO::Using default BPPARAM
2025-10-23 21:26:36.417984 INFO::Processing subtree level 1
2025-10-23 21:26:36.515327 INFO::Adjusting the last 1 batches sequentially
2025-10-23 21:26:36.517234 INFO::Done
2025-10-23 21:26:36.517921 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:36.520625 INFO::ASW Batch was -0.0928568267000692 prior to batch effect correction and is now -0.0928568267000692 .
2025-10-23 21:26:36.521729 INFO::Total function execution time is 0.387647151947021 s and adjustment time is 0.10159969329834 s ( 26.21 )
2025-10-23 21:26:36.535207 INFO::Formatting Data.
2025-10-23 21:26:36.535959 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:36.536913 INFO::Removing potential empty rows and columns
2025-10-23 21:26:36.538064 INFO::Found 0 missing values.
2025-10-23 21:26:36.538996 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-23 21:26:36.549547 INFO::Formatting Data.
2025-10-23 21:26:36.550332 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:36.551218 INFO::Removing potential empty rows and columns
2025-10-23 21:26:36.552232 INFO::Found 0 missing values.
2025-10-23 21:26:36.553139 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-23 21:26:36.568516 INFO::Formatting Data.
2025-10-23 21:26:36.569255 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:36.570107 INFO::Removing potential empty rows and columns
2025-10-23 21:26:36.571168 INFO::Found 0 missing values.
2025-10-23 21:26:36.57207 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-23 21:26:36.5763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:36.576834 INFO::Done
2025-10-23 21:26:36.577357 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:36.579371 INFO::Starting hierarchical adjustment
2025-10-23 21:26:36.580061 INFO::Found 2 batches.
2025-10-23 21:26:36.580595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:36.581214 INFO::Using default BPPARAM
2025-10-23 21:26:36.58172 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:36.582645 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 21:26:36.60488 INFO::Done
2025-10-23 21:26:36.605611 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:36.607694 INFO::ASW Batch was 0.0659212367064253 prior to batch effect correction and is now -0.0879829771115699 .
2025-10-23 21:26:36.608521 INFO::Total function execution time is 0.0400609970092773 s and adjustment time is 0.0249302387237549 s ( 62.23 )
2025-10-23 21:26:36.61129 INFO::Formatting Data.
2025-10-23 21:26:36.611932 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:36.620689 INFO::Formatting Data.
2025-10-23 21:26:36.621457 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:36.622366 INFO::Removing potential empty rows and columns
2025-10-23 21:26:36.623425 INFO::Found 0 missing values.
2025-10-23 21:26:36.626302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:36.626839 INFO::Done
2025-10-23 21:26:36.627381 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:36.629478 INFO::Starting hierarchical adjustment
2025-10-23 21:26:36.630206 INFO::Found 2 batches.
2025-10-23 21:26:36.630744 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:36.631367 INFO::Using default BPPARAM
2025-10-23 21:26:36.631936 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:36.632879 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:36.673343 INFO::Done
2025-10-23 21:26:36.674035 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:36.676033 INFO::ASW Batch was 0.00507797122610624 prior to batch effect correction and is now -0.11831598155392 .
2025-10-23 21:26:36.676839 INFO::Total function execution time is 0.0562012195587158 s and adjustment time is 0.0432608127593994 s ( 76.97 )
2025-10-23 21:26:36.677872 INFO::Formatting Data.
2025-10-23 21:26:36.678464 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:36.679292 INFO::Removing potential empty rows and columns
2025-10-23 21:26:36.680278 INFO::Found 0 missing values.
2025-10-23 21:26:36.682879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:36.683402 INFO::Done
2025-10-23 21:26:36.683876 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:36.685761 INFO::Starting hierarchical adjustment
2025-10-23 21:26:36.68643 INFO::Found 2 batches.
2025-10-23 21:26:36.686914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:36.687477 INFO::Using default BPPARAM
2025-10-23 21:26:36.687952 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:36.688773 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:36.702582 INFO::Done
2025-10-23 21:26:36.703222 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:36.705222 INFO::ASW Batch was 0.00507797122610624 prior to batch effect correction and is now -0.11831598155392 .
2025-10-23 21:26:36.70596 INFO::Total function execution time is 0.0280900001525879 s and adjustment time is 0.0162694454193115 s ( 57.92 )
2025-10-23 21:26:39.637024 INFO::Formatting Data.
2025-10-23 21:26:39.637929 INFO::Recognized SummarizedExperiment
2025-10-23 21:26:39.63848 INFO::Typecasting input to dataframe.
2025-10-23 21:26:39.669724 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:39.671176 INFO::Removing potential empty rows and columns
2025-10-23 21:26:39.675205 INFO::Found 0 missing values.
2025-10-23 21:26:39.682554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:39.68335 INFO::Done
2025-10-23 21:26:39.683974 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:39.687921 INFO::Starting hierarchical adjustment
2025-10-23 21:26:39.688693 INFO::Found 2 batches.
2025-10-23 21:26:39.689228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:39.690419 INFO::Using default BPPARAM
2025-10-23 21:26:39.690963 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:39.69199 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 21:26:39.751813 INFO::Done
2025-10-23 21:26:39.75266 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:39.756467 INFO::ASW Batch was -0.0199319503319046 prior to batch effect correction and is now -0.0943684548375258 .
2025-10-23 21:26:39.757348 INFO::Total function execution time is 0.120662927627563 s and adjustment time is 0.0632271766662598 s ( 52.4 )
2025-10-23 21:26:39.776649 INFO::Formatting Data.
2025-10-23 21:26:39.777402 INFO::Recognized SummarizedExperiment
2025-10-23 21:26:39.777946 INFO::Typecasting input to dataframe.
2025-10-23 21:26:39.787585 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:39.7888 INFO::Removing potential empty rows and columns
2025-10-23 21:26:39.792595 INFO::Found 0 missing values.
2025-10-23 21:26:39.799827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:39.800501 INFO::Done
2025-10-23 21:26:39.80104 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:39.804698 INFO::Starting hierarchical adjustment
2025-10-23 21:26:39.80547 INFO::Found 2 batches.
2025-10-23 21:26:39.805996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:39.806626 INFO::Using default BPPARAM
2025-10-23 21:26:39.807163 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:39.808159 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 21:26:39.833317 INFO::Done
2025-10-23 21:26:39.834015 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:39.837636 INFO::ASW Batch was 0.0167340959773349 prior to batch effect correction and is now 0.0167340959773349 .
2025-10-23 21:26:39.838515 INFO::Total function execution time is 0.0618462562561035 s and adjustment time is 0.0279662609100342 s ( 45.22 )
2025-10-23 21:26:39.856493 INFO::Formatting Data.
2025-10-23 21:26:39.857295 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:39.858194 INFO::Removing potential empty rows and columns
2025-10-23 21:26:39.859224 INFO::Found 0 missing values.
2025-10-23 21:26:39.862176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:39.862695 INFO::Done
2025-10-23 21:26:39.863206 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:39.865221 INFO::Starting hierarchical adjustment
2025-10-23 21:26:39.865893 INFO::Found 3 batches.
2025-10-23 21:26:39.866439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:39.867014 INFO::Using default BPPARAM
2025-10-23 21:26:39.867536 INFO::Processing subtree level 1
2025-10-23 21:26:40.001852 INFO::Adjusting the last 1 batches sequentially
2025-10-23 21:26:40.003587 INFO::Done
2025-10-23 21:26:40.004247 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:40.006637 INFO::ASW Batch was -0.015057347567778 prior to batch effect correction and is now -0.152310979930636 .
2025-10-23 21:26:40.007531 INFO::Total function execution time is 0.151073694229126 s and adjustment time is 0.137811422348022 s ( 91.22 )
2025-10-23 21:26:40.021466 INFO::Skipping initial DF formatting
2025-10-23 21:26:40.022171 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:40.031456 INFO::Starting hierarchical adjustment
2025-10-23 21:26:40.03244 INFO::Found 5 batches.
2025-10-23 21:26:40.033024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:40.033671 INFO::Using default BPPARAM
2025-10-23 21:26:40.034229 INFO::Processing subtree level 1
2025-10-23 21:26:40.261853 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:40.263554 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 21:26:40.283627 INFO::Done
2025-10-23 21:26:40.284392 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:40.288746 INFO::ASW Batch was 0.4569835021854 prior to batch effect correction and is now 0.4569835021854 .
2025-10-23 21:26:40.289403 INFO::ASW Label was 0.403887186307072 prior to batch effect correction and is now 0.403887186307072 .
2025-10-23 21:26:40.290281 INFO::Total function execution time is 0.268866777420044 s and adjustment time is 0.251382350921631 s ( 93.5 )
2025-10-23 21:26:40.36274 INFO::Formatting Data.
2025-10-23 21:26:40.3635 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:40.364404 INFO::Removing potential empty rows and columns
2025-10-23 21:26:40.36536 INFO::Found 0 missing values.
2025-10-23 21:26:40.369268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:40.36981 INFO::Done
2025-10-23 21:26:40.37036 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:40.373318 INFO::Starting hierarchical adjustment
2025-10-23 21:26:40.374093 INFO::Found 5 batches.
2025-10-23 21:26:40.374712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:40.375315 INFO::Using default BPPARAM
2025-10-23 21:26:40.375812 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:40.506878 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:40.508624 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:40.526274 INFO::Done
2025-10-23 21:26:40.526996 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:40.530519 INFO::ASW Batch was 0.569215556943772 prior to batch effect correction and is now -0.110361931127843 .
2025-10-23 21:26:40.531157 INFO::ASW Label was 0.318178637500162 prior to batch effect correction and is now 0.740444553791294 .
2025-10-23 21:26:40.53202 INFO::Total function execution time is 0.169342994689941 s and adjustment time is 0.152302265167236 s ( 89.94 )
2025-10-23 21:26:40.532907 INFO::Formatting Data.
2025-10-23 21:26:40.533585 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:40.534538 INFO::Removing potential empty rows and columns
2025-10-23 21:26:40.535684 INFO::Found 0 missing values.
2025-10-23 21:26:40.539989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:40.540559 INFO::Done
2025-10-23 21:26:40.541092 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:40.544198 INFO::Starting hierarchical adjustment
2025-10-23 21:26:40.544916 INFO::Found 5 batches.
2025-10-23 21:26:40.545477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:40.54607 INFO::Using default BPPARAM
2025-10-23 21:26:40.546629 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:40.670327 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:40.671876 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:40.68805 INFO::Done
2025-10-23 21:26:40.688832 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:40.692243 INFO::ASW Batch was 0.569215556943772 prior to batch effect correction and is now -0.110361931127843 .
2025-10-23 21:26:40.692851 INFO::ASW Label was 0.318178637500162 prior to batch effect correction and is now 0.740444553791294 .
2025-10-23 21:26:40.693678 INFO::Total function execution time is 0.160757780075073 s and adjustment time is 0.143253326416016 s ( 89.11 )
2025-10-23 21:26:40.707129 INFO::Formatting Data.
2025-10-23 21:26:40.707922 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:40.708855 INFO::Removing potential empty rows and columns
2025-10-23 21:26:40.709865 INFO::Found 0 missing values.
2025-10-23 21:26:40.71385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:40.714431 INFO::Done
2025-10-23 21:26:40.714947 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:40.71795 INFO::Starting hierarchical adjustment
2025-10-23 21:26:40.718655 INFO::Found 5 batches.
2025-10-23 21:26:40.719189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:40.719796 INFO::Using default BPPARAM
2025-10-23 21:26:40.720323 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:40.854406 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:40.856331 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:40.874752 INFO::Done
2025-10-23 21:26:40.875615 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:40.879814 INFO::ASW Batch was 0.432544711861502 prior to batch effect correction and is now -0.0758057446990331 .
2025-10-23 21:26:40.880677 INFO::ASW Label was 0.229868807556827 prior to batch effect correction and is now 0.725626670877373 .
2025-10-23 21:26:40.881606 INFO::Total function execution time is 0.174538612365723 s and adjustment time is 0.156184911727905 s ( 89.48 )
2025-10-23 21:26:40.882507 INFO::Formatting Data.
2025-10-23 21:26:40.883196 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:40.884215 INFO::Removing potential empty rows and columns
2025-10-23 21:26:40.885364 INFO::Found 0 missing values.
2025-10-23 21:26:40.889768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:40.890365 INFO::Done
2025-10-23 21:26:40.89093 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:40.894183 INFO::Starting hierarchical adjustment
2025-10-23 21:26:40.894979 INFO::Found 5 batches.
2025-10-23 21:26:40.895576 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:40.896246 INFO::Using default BPPARAM
2025-10-23 21:26:40.896814 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:41.029183 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:41.030985 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:41.048083 INFO::Done
2025-10-23 21:26:41.048895 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.052752 INFO::ASW Batch was 0.432544711861502 prior to batch effect correction and is now -0.0758057446990331 .
2025-10-23 21:26:41.053562 INFO::ASW Label was 0.229868807556827 prior to batch effect correction and is now 0.725626670877373 .
2025-10-23 21:26:41.054526 INFO::Total function execution time is 0.172012805938721 s and adjustment time is 0.153249502182007 s ( 89.09 )
2025-10-23 21:26:41.069783 INFO::Formatting Data.
2025-10-23 21:26:41.070643 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.0717 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.072846 INFO::Found 0 missing values.
2025-10-23 21:26:41.075814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:41.076443 INFO::Done
2025-10-23 21:26:41.077013 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:41.080292 INFO::Starting hierarchical adjustment
2025-10-23 21:26:41.081033 INFO::Found 2 batches.
2025-10-23 21:26:41.081604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:41.082258 INFO::Using default BPPARAM
2025-10-23 21:26:41.082824 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:41.083768 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:41.099002 INFO::Done
2025-10-23 21:26:41.099677 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.102757 INFO::ASW Batch was 0.621989991890922 prior to batch effect correction and is now 0.0243703435332262 .
2025-10-23 21:26:41.103401 INFO::ASW Label was 0.446096699333773 prior to batch effect correction and is now 0.888481633032817 .
2025-10-23 21:26:41.104217 INFO::Total function execution time is 0.0345268249511719 s and adjustment time is 0.0181052684783936 s ( 52.44 )
2025-10-23 21:26:41.105034 INFO::Formatting Data.
2025-10-23 21:26:41.105693 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.106602 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.107639 INFO::Found 0 missing values.
2025-10-23 21:26:41.110444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:41.110998 INFO::Done
2025-10-23 21:26:41.111547 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:41.114527 INFO::Starting hierarchical adjustment
2025-10-23 21:26:41.11527 INFO::Found 2 batches.
2025-10-23 21:26:41.115809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:41.116443 INFO::Using default BPPARAM
2025-10-23 21:26:41.116973 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:41.117906 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 21:26:41.133153 INFO::Done
2025-10-23 21:26:41.133819 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.136777 INFO::ASW Batch was 0.621989991890922 prior to batch effect correction and is now 0.0243703435332262 .
2025-10-23 21:26:41.137412 INFO::ASW Label was 0.446096699333773 prior to batch effect correction and is now 0.888481633032817 .
2025-10-23 21:26:41.13823 INFO::Total function execution time is 0.0331928730010986 s and adjustment time is 0.0180211067199707 s ( 54.29 )
2025-10-23 21:26:41.149495 INFO::Formatting Data.
2025-10-23 21:26:41.150349 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.151287 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.152219 INFO::Found 0 missing values.
2025-10-23 21:26:41.154382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:41.154931 INFO::Done
2025-10-23 21:26:41.155458 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:41.157424 INFO::Starting hierarchical adjustment
2025-10-23 21:26:41.15811 INFO::Found 2 batches.
2025-10-23 21:26:41.158647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:41.159262 INFO::Using default BPPARAM
2025-10-23 21:26:41.159794 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:41.160713 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 21:26:41.192578 INFO::Done
2025-10-23 21:26:41.193315 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.195337 INFO::ASW Batch was 0.0153048029724404 prior to batch effect correction and is now -0.0790334395577725 .
2025-10-23 21:26:41.1962 INFO::Total function execution time is 0.0467517375946045 s and adjustment time is 0.0345799922943115 s ( 73.97 )
2025-10-23 21:26:41.208291 INFO::Formatting Data.
2025-10-23 21:26:41.209087 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.210008 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.211043 INFO::Found 0 missing values.
2025-10-23 21:26:41.212217 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-23 21:26:41.217081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:41.217671 INFO::Done
2025-10-23 21:26:41.218211 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:41.221248 INFO::Starting hierarchical adjustment
2025-10-23 21:26:41.221962 INFO::Found 2 batches.
2025-10-23 21:26:41.222518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:41.223138 INFO::Using default BPPARAM
2025-10-23 21:26:41.223675 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:41.224615 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 21:26:41.241555 INFO::Done
2025-10-23 21:26:41.24227 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.24525 INFO::ASW Batch was 0.55931283595227 prior to batch effect correction and is now -0.00177754142213299 .
2025-10-23 21:26:41.245851 INFO::ASW Label was 0.397393424196784 prior to batch effect correction and is now 0.887569756059235 .
2025-10-23 21:26:41.246651 INFO::Total function execution time is 0.0384676456451416 s and adjustment time is 0.0197055339813232 s ( 51.23 )
2025-10-23 21:26:41.247463 INFO::Formatting Data.
2025-10-23 21:26:41.248082 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.249001 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.249989 INFO::Found 0 missing values.
2025-10-23 21:26:41.25091 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-23 21:26:41.255445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:41.255998 INFO::Done
2025-10-23 21:26:41.256535 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:41.259451 INFO::Starting hierarchical adjustment
2025-10-23 21:26:41.260153 INFO::Found 2 batches.
2025-10-23 21:26:41.260686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:41.261298 INFO::Using default BPPARAM
2025-10-23 21:26:41.261824 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:41.262733 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 21:26:41.279231 INFO::Done
2025-10-23 21:26:41.279902 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.282839 INFO::ASW Batch was 0.55931283595227 prior to batch effect correction and is now -0.00177754142213299 .
2025-10-23 21:26:41.283453 INFO::ASW Label was 0.397393424196784 prior to batch effect correction and is now 0.887569756059235 .
2025-10-23 21:26:41.284252 INFO::Total function execution time is 0.0367980003356934 s and adjustment time is 0.0191898345947266 s ( 52.15 )
2025-10-23 21:26:41.49835 INFO::Formatting Data.
2025-10-23 21:26:41.499312 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.500282 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.501388 INFO::Found 0 missing values.
2025-10-23 21:26:41.504464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:41.505013 INFO::Done
2025-10-23 21:26:41.505547 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:41.507823 INFO::Starting hierarchical adjustment
2025-10-23 21:26:41.508548 INFO::Found 3 batches.
2025-10-23 21:26:41.509067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:41.509743 INFO::Using default BPPARAM
2025-10-23 21:26:41.510278 INFO::Processing subtree level 1
2025-10-23 21:26:41.608414 INFO::Adjusting the last 1 batches sequentially
2025-10-23 21:26:41.610298 INFO::Done
2025-10-23 21:26:41.610928 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.613453 INFO::ASW Batch was 0.0180109937156211 prior to batch effect correction and is now 0.0180109937156211 .
2025-10-23 21:26:41.614439 INFO::Total function execution time is 0.11652684211731 s and adjustment time is 0.101888656616211 s ( 87.44 )
2025-10-23 21:26:41.615562 INFO::Formatting Data.
2025-10-23 21:26:41.616263 INFO::Typecasting input to dataframe.
2025-10-23 21:26:41.617007 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.617961 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.619069 INFO::Found 0 missing values.
2025-10-23 21:26:41.622207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:41.622759 INFO::Done
2025-10-23 21:26:41.62331 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:41.625327 INFO::Starting hierarchical adjustment
2025-10-23 21:26:41.62605 INFO::Found 3 batches.
2025-10-23 21:26:41.626601 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:41.627246 INFO::Using default BPPARAM
2025-10-23 21:26:41.627773 INFO::Processing subtree level 1
2025-10-23 21:26:41.716857 INFO::Adjusting the last 1 batches sequentially
2025-10-23 21:26:41.718742 INFO::Done
2025-10-23 21:26:41.719429 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.721963 INFO::ASW Batch was 0.0180109937156211 prior to batch effect correction and is now 0.0180109937156211 .
2025-10-23 21:26:41.722953 INFO::Total function execution time is 0.107368946075439 s and adjustment time is 0.0928173065185547 s ( 86.45 )
2025-10-23 21:26:41.736063 INFO::Formatting Data.
2025-10-23 21:26:41.737004 INFO::Typecasting input to dataframe.
2025-10-23 21:26:41.737885 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.738838 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.739938 INFO::Found 0 missing values.
2025-10-23 21:26:41.742982 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:41.743544 INFO::Done
2025-10-23 21:26:41.744062 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:41.746088 INFO::Starting hierarchical adjustment
2025-10-23 21:26:41.746819 INFO::Found 3 batches.
2025-10-23 21:26:41.747386 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:41.748016 INFO::Using default BPPARAM
2025-10-23 21:26:41.748588 INFO::Processing subtree level 1
2025-10-23 21:26:41.83675 INFO::Adjusting the last 1 batches sequentially
2025-10-23 21:26:41.838625 INFO::Done
2025-10-23 21:26:41.839306 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:41.841998 INFO::ASW Batch was -0.11398902775356 prior to batch effect correction and is now -0.11398902775356 .
2025-10-23 21:26:41.842978 INFO::Total function execution time is 0.106967449188232 s and adjustment time is 0.0919387340545654 s ( 85.95 )
2025-10-23 21:26:41.985285 INFO::Formatting Data.
2025-10-23 21:26:41.986308 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:41.987568 INFO::Removing potential empty rows and columns
2025-10-23 21:26:41.990453 INFO::Found 1000 missing values.
2025-10-23 21:26:42.009728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:42.010519 INFO::Done
2025-10-23 21:26:42.011082 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:42.016639 INFO::Starting hierarchical adjustment
2025-10-23 21:26:42.017466 INFO::Found 10 batches.
2025-10-23 21:26:42.018016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:42.01867 INFO::Using default BPPARAM
2025-10-23 21:26:42.019225 INFO::Processing subtree level 1
2025-10-23 21:26:42.15864 INFO::Processing subtree level 2
2025-10-23 21:26:42.302614 INFO::Adjusting the last 1 batches sequentially
2025-10-23 21:26:42.304994 INFO::Done
2025-10-23 21:26:42.30574 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:42.311368 INFO::ASW Batch was 0.538625215481196 prior to batch effect correction and is now 0.538625215481196 .
2025-10-23 21:26:42.312075 INFO::ASW Label was 0.314770972291396 prior to batch effect correction and is now 0.314770972291396 .
2025-10-23 21:26:42.313054 INFO::Total function execution time is 0.327896118164062 s and adjustment time is 0.287631273269653 s ( 87.72 )
2025-10-23 21:26:42.313974 INFO::Formatting Data.
2025-10-23 21:26:42.314644 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:42.315918 INFO::Removing potential empty rows and columns
2025-10-23 21:26:42.318712 INFO::Found 1000 missing values.
2025-10-23 21:26:42.337663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:42.338434 INFO::Done
2025-10-23 21:26:42.339002 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:42.344546 INFO::Starting hierarchical adjustment
2025-10-23 21:26:42.345376 INFO::Found 10 batches.
2025-10-23 21:26:43.43391 INFO::Set up parallel execution backend with 2 workers
2025-10-23 21:26:43.436356 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-23 21:26:44.64811 INFO::Adjusting the last 2 batches sequentially
2025-10-23 21:26:44.650061 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 21:26:44.666581 INFO::Done
2025-10-23 21:26:44.66725 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:44.671762 INFO::ASW Batch was 0.538625215481196 prior to batch effect correction and is now 0.538625215481196 .
2025-10-23 21:26:44.672304 INFO::ASW Label was 0.314770972291396 prior to batch effect correction and is now 0.314770972291396 .
2025-10-23 21:26:44.673014 INFO::Total function execution time is 2.35908007621765 s and adjustment time is 2.32137250900269 s ( 98.4 )
2025-10-23 21:26:44.824028 INFO::Formatting Data.
2025-10-23 21:26:44.824873 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:44.82581 INFO::Removing potential empty rows and columns
2025-10-23 21:26:44.826872 INFO::Found 0 missing values.
2025-10-23 21:26:44.830468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:44.830998 INFO::Done
2025-10-23 21:26:44.831501 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 21:26:44.834294 INFO::Starting hierarchical adjustment
2025-10-23 21:26:44.834963 INFO::Found 3 batches.
2025-10-23 21:26:44.835472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 21:26:44.836047 INFO::Using default BPPARAM
2025-10-23 21:26:44.836561 INFO::Processing subtree level 1
2025-10-23 21:26:44.938885 INFO::Adjusting the last 1 batches sequentially
2025-10-23 21:26:44.940649 INFO::Done
2025-10-23 21:26:44.941273 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 21:26:44.944422 INFO::ASW Batch was 0.16508863201037 prior to batch effect correction and is now -0.134627467111163 .
2025-10-23 21:26:44.945023 INFO::ASW Label was -0.167839133945045 prior to batch effect correction and is now 0.0145038540227819 .
2025-10-23 21:26:44.945904 INFO::Total function execution time is 0.121938705444336 s and adjustment time is 0.105806827545166 s ( 86.77 )
2025-10-23 21:26:45.057329 INFO::Formatting Data.
2025-10-23 21:26:45.058183 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.059064 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.060086 INFO::Found 2 missing values.
2025-10-23 21:26:45.062837 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.063365 INFO::Done
2025-10-23 21:26:45.089902 INFO::Found NA in Reference column
2025-10-23 21:26:45.098935 INFO::Require at least two references per batch.
2025-10-23 21:26:45.118676 INFO::Formatting Data.
2025-10-23 21:26:45.119447 INFO::Recognized SummarizedExperiment
2025-10-23 21:26:45.119971 INFO::Typecasting input to dataframe.
2025-10-23 21:26:45.129328 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.130497 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.133873 INFO::Found 0 missing values.
2025-10-23 21:26:45.140356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.14093 INFO::Done
2025-10-23 21:26:45.156168 INFO::Formatting Data.
2025-10-23 21:26:45.156901 INFO::Recognized SummarizedExperiment
2025-10-23 21:26:45.157439 INFO::Typecasting input to dataframe.
2025-10-23 21:26:45.174331 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.175535 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.178891 INFO::Found 0 missing values.
2025-10-23 21:26:45.189594 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.190285 INFO::Done
2025-10-23 21:26:45.205676 INFO::Formatting Data.
2025-10-23 21:26:45.206428 INFO::Recognized SummarizedExperiment
2025-10-23 21:26:45.206936 INFO::Typecasting input to dataframe.
2025-10-23 21:26:45.222884 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.223959 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.225108 INFO::Found 0 missing values.
2025-10-23 21:26:45.22605 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-23 21:26:45.230311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.230836 INFO::Done
2025-10-23 21:26:45.240557 INFO::Formatting Data.
2025-10-23 21:26:45.241317 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.242167 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.243124 INFO::Found 0 missing values.
2025-10-23 21:26:45.245806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.246314 INFO::Done
2025-10-23 21:26:45.256439 INFO::Formatting Data.
2025-10-23 21:26:45.257268 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.258148 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.259096 INFO::Found 0 missing values.
2025-10-23 21:26:45.261867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.262426 INFO::Done
2025-10-23 21:26:45.290598 INFO::Formatting Data.
2025-10-23 21:26:45.291428 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.29245 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.293596 INFO::Found 1 missing values.
2025-10-23 21:26:45.296143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.29667 INFO::Done
2025-10-23 21:26:45.324521 INFO::Formatting Data.
2025-10-23 21:26:45.325359 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.326258 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.327217 INFO::Found 2 missing values.
2025-10-23 21:26:45.328136 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-23 21:26:45.33042 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.330985 INFO::Done
2025-10-23 21:26:45.340931 INFO::Formatting Data.
2025-10-23 21:26:45.341718 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.342575 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.343488 INFO::Found 2 missing values.
2025-10-23 21:26:45.345037 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.34557 INFO::Done
2025-10-23 21:26:45.355848 INFO::Formatting Data.
2025-10-23 21:26:45.356662 INFO::Typecasting input to dataframe.
2025-10-23 21:26:45.357471 INFO::Replacing NaNs with NAs.
2025-10-23 21:26:45.358328 INFO::Removing potential empty rows and columns
2025-10-23 21:26:45.359334 INFO::Found 0 missing values.
2025-10-23 21:26:45.362165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 21:26:45.362685 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.031 3.556 20.306
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.386 | 1.101 | 17.279 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.012 | 0.001 | 0.014 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.009 | 0.003 | 0.012 | |