Yannis Schumann
| Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 Sep 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 2025-09-23 12:03 -0400 (Tue, 23 Sep 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" | 4816 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
| 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 163/2334 | 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 12.7.1 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: 2025-09-22 21:16:26 -0400 (Mon, 22 Sep 2025) |
| EndedAt: 2025-09-22 21:18:34 -0400 (Mon, 22 Sep 2025) |
| EllapsedTime: 128.1 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 28.256 1.747 23.789
* 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")
2025-09-22 21:17:39.878274 INFO::Formatting Data.
2025-09-22 21:17:39.87978 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:39.892707 INFO::Removing potential empty rows and columns
2025-09-22 21:17:40.313941 INFO::Found 0 missing values.
2025-09-22 21:17:40.317796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:40.318547 INFO::Done
2025-09-22 21:17:40.319167 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:40.332254 INFO::Starting hierarchical adjustment
2025-09-22 21:17:40.333249 INFO::Found 3 batches.
2025-09-22 21:17:40.3339 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:40.3352 INFO::Using default BPPARAM
2025-09-22 21:17:40.335847 INFO::Processing subtree level 1
2025-09-22 21:17:40.464367 INFO::Adjusting the last 1 batches sequentially
2025-09-22 21:17:40.46659 INFO::Done
2025-09-22 21:17:40.467418 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:40.47053 INFO::ASW Batch was -0.0307284649388164 prior to batch effect correction and is now -0.0307284649388164 .
2025-09-22 21:17:40.471874 INFO::Total function execution time is 0.594269037246704 s and adjustment time is 0.133514881134033 s ( 22.47 )
2025-09-22 21:17:40.487872 INFO::Formatting Data.
2025-09-22 21:17:40.488683 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:40.489797 INFO::Removing potential empty rows and columns
2025-09-22 21:17:40.491086 INFO::Found 0 missing values.
2025-09-22 21:17:40.492201 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.
2025-09-22 21:17:40.504865 INFO::Formatting Data.
2025-09-22 21:17:40.505814 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:40.506895 INFO::Removing potential empty rows and columns
2025-09-22 21:17:40.508152 INFO::Found 0 missing values.
2025-09-22 21:17:40.509168 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.
2025-09-22 21:17:40.527763 INFO::Formatting Data.
2025-09-22 21:17:40.528712 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:40.529805 INFO::Removing potential empty rows and columns
2025-09-22 21:17:40.53106 INFO::Found 0 missing values.
2025-09-22 21:17:40.532176 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.
2025-09-22 21:17:40.537507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:40.538172 INFO::Done
2025-09-22 21:17:40.538789 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:40.54121 INFO::Starting hierarchical adjustment
2025-09-22 21:17:40.542067 INFO::Found 2 batches.
2025-09-22 21:17:40.542681 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:40.543438 INFO::Using default BPPARAM
2025-09-22 21:17:40.544069 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:40.545235 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 21:17:40.571865 INFO::Done
2025-09-22 21:17:40.5727 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:40.575175 INFO::ASW Batch was -0.0659809185639914 prior to batch effect correction and is now -0.126409339844563 .
2025-09-22 21:17:40.576123 INFO::Total function execution time is 0.0484886169433594 s and adjustment time is 0.0299358367919922 s ( 61.74 )
2025-09-22 21:17:40.579381 INFO::Formatting Data.
2025-09-22 21:17:40.58014 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:40.590734 INFO::Formatting Data.
2025-09-22 21:17:40.591629 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:40.592703 INFO::Removing potential empty rows and columns
2025-09-22 21:17:40.593945 INFO::Found 0 missing values.
2025-09-22 21:17:40.597365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:40.598013 INFO::Done
2025-09-22 21:17:40.598607 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:40.601095 INFO::Starting hierarchical adjustment
2025-09-22 21:17:40.601933 INFO::Found 2 batches.
2025-09-22 21:17:40.602548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:40.603287 INFO::Using default BPPARAM
2025-09-22 21:17:40.603917 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:40.605046 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 21:17:40.651503 INFO::Done
2025-09-22 21:17:40.652341 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:40.65462 INFO::ASW Batch was 0.0103822118486135 prior to batch effect correction and is now -0.134469402784044 .
2025-09-22 21:17:40.655516 INFO::Total function execution time is 0.0648772716522217 s and adjustment time is 0.0496993064880371 s ( 76.61 )
2025-09-22 21:17:40.656739 INFO::Formatting Data.
2025-09-22 21:17:40.657429 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:40.658391 INFO::Removing potential empty rows and columns
2025-09-22 21:17:40.659562 INFO::Found 0 missing values.
2025-09-22 21:17:40.662655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:40.663235 INFO::Done
2025-09-22 21:17:40.663786 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:40.665911 INFO::Starting hierarchical adjustment
2025-09-22 21:17:40.666662 INFO::Found 2 batches.
2025-09-22 21:17:40.667239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:40.667884 INFO::Using default BPPARAM
2025-09-22 21:17:40.668441 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:40.669404 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 21:17:40.68551 INFO::Done
2025-09-22 21:17:40.686217 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:40.688358 INFO::ASW Batch was 0.0103822118486135 prior to batch effect correction and is now -0.134469402784044 .
2025-09-22 21:17:40.689218 INFO::Total function execution time is 0.0325064659118652 s and adjustment time is 0.0189862251281738 s ( 58.41 )
2025-09-22 21:17:44.834528 INFO::Formatting Data.
2025-09-22 21:17:44.835433 INFO::Recognized SummarizedExperiment
2025-09-22 21:17:44.836024 INFO::Typecasting input to dataframe.
2025-09-22 21:17:44.886007 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:44.887498 INFO::Removing potential empty rows and columns
2025-09-22 21:17:44.894938 INFO::Found 0 missing values.
2025-09-22 21:17:44.903806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:44.904638 INFO::Done
2025-09-22 21:17:44.905279 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:44.909732 INFO::Starting hierarchical adjustment
2025-09-22 21:17:44.910619 INFO::Found 2 batches.
2025-09-22 21:17:44.911234 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:44.912488 INFO::Using default BPPARAM
2025-09-22 21:17:44.913111 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:44.914246 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 21:17:44.983674 INFO::Done
2025-09-22 21:17:44.984529 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:44.988988 INFO::ASW Batch was -0.00377320040241365 prior to batch effect correction and is now -0.0939625474287569 .
2025-09-22 21:17:44.990046 INFO::Total function execution time is 0.155876398086548 s and adjustment time is 0.0732047557830811 s ( 46.96 )
2025-09-22 21:17:45.012027 INFO::Formatting Data.
2025-09-22 21:17:45.012962 INFO::Recognized SummarizedExperiment
2025-09-22 21:17:45.013595 INFO::Typecasting input to dataframe.
2025-09-22 21:17:45.025349 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:45.02686 INFO::Removing potential empty rows and columns
2025-09-22 21:17:45.0315 INFO::Found 0 missing values.
2025-09-22 21:17:45.040604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:45.04143 INFO::Done
2025-09-22 21:17:45.042089 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:45.046613 INFO::Starting hierarchical adjustment
2025-09-22 21:17:45.047555 INFO::Found 2 batches.
2025-09-22 21:17:45.048182 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:45.048899 INFO::Using default BPPARAM
2025-09-22 21:17:45.049502 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:45.052814 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 21:17:45.10113 INFO::Done
2025-09-22 21:17:45.102182 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:45.107523 INFO::ASW Batch was -0.0107634433249323 prior to batch effect correction and is now -0.0107634433249323 .
2025-09-22 21:17:45.108824 INFO::Total function execution time is 0.0967390537261963 s and adjustment time is 0.0536880493164062 s ( 55.5 )
2025-09-22 21:17:45.135759 INFO::Formatting Data.
2025-09-22 21:17:45.136875 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:45.138162 INFO::Removing potential empty rows and columns
2025-09-22 21:17:45.139623 INFO::Found 0 missing values.
2025-09-22 21:17:45.144469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:45.14531 INFO::Done
2025-09-22 21:17:45.146104 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:45.148943 INFO::Starting hierarchical adjustment
2025-09-22 21:17:45.149925 INFO::Found 3 batches.
2025-09-22 21:17:45.150688 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:45.151555 INFO::Using default BPPARAM
2025-09-22 21:17:45.15232 INFO::Processing subtree level 1
2025-09-22 21:17:45.314905 INFO::Adjusting the last 1 batches sequentially
2025-09-22 21:17:45.316948 INFO::Done
2025-09-22 21:17:45.317694 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:45.320549 INFO::ASW Batch was 0.0435996944940068 prior to batch effect correction and is now -0.161899933463543 .
2025-09-22 21:17:45.321649 INFO::Total function execution time is 0.18602180480957 s and adjustment time is 0.167223930358887 s ( 89.89 )
2025-09-22 21:17:45.352178 INFO::Skipping initial DF formatting
2025-09-22 21:17:45.353097 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:45.362057 INFO::Starting hierarchical adjustment
2025-09-22 21:17:45.363086 INFO::Found 5 batches.
2025-09-22 21:17:45.363775 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:45.364519 INFO::Using default BPPARAM
2025-09-22 21:17:45.365169 INFO::Processing subtree level 1
2025-09-22 21:17:45.720337 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:45.728725 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 21:17:45.777684 INFO::Done
2025-09-22 21:17:45.7787 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:45.784198 INFO::ASW Batch was 0.490939883761892 prior to batch effect correction and is now 0.490939883761892 .
2025-09-22 21:17:45.785164 INFO::ASW Label was 0.396906879049493 prior to batch effect correction and is now 0.396906879049493 .
2025-09-22 21:17:45.786515 INFO::Total function execution time is 0.434374570846558 s and adjustment time is 0.414730072021484 s ( 95.48 )
2025-09-22 21:17:45.9502 INFO::Formatting Data.
2025-09-22 21:17:45.951107 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:45.952173 INFO::Removing potential empty rows and columns
2025-09-22 21:17:45.953491 INFO::Found 0 missing values.
2025-09-22 21:17:45.958918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:45.959545 INFO::Done
2025-09-22 21:17:45.960343 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:45.964605 INFO::Starting hierarchical adjustment
2025-09-22 21:17:45.965441 INFO::Found 5 batches.
2025-09-22 21:17:45.966064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:45.966888 INFO::Using default BPPARAM
2025-09-22 21:17:45.967726 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.
2025-09-22 21:17:46.186195 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:46.188539 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 21:17:46.223867 INFO::Done
2025-09-22 21:17:46.224979 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:46.230178 INFO::ASW Batch was 0.469446999274861 prior to batch effect correction and is now -0.039641748517078 .
2025-09-22 21:17:46.23114 INFO::ASW Label was 0.279903866020218 prior to batch effect correction and is now 0.676786756025664 .
2025-09-22 21:17:46.232444 INFO::Total function execution time is 0.282217979431152 s and adjustment time is 0.258503198623657 s ( 91.6 )
2025-09-22 21:17:46.237227 INFO::Formatting Data.
2025-09-22 21:17:46.238263 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:46.24373 INFO::Removing potential empty rows and columns
2025-09-22 21:17:46.24534 INFO::Found 0 missing values.
2025-09-22 21:17:46.259355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:46.260298 INFO::Done
2025-09-22 21:17:46.261149 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:46.274083 INFO::Starting hierarchical adjustment
2025-09-22 21:17:46.275282 INFO::Found 5 batches.
2025-09-22 21:17:46.276129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:46.281126 INFO::Using default BPPARAM
2025-09-22 21:17:46.282037 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.
2025-09-22 21:17:46.465402 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:46.467562 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 21:17:46.517361 INFO::Done
2025-09-22 21:17:46.518367 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:46.524764 INFO::ASW Batch was 0.469446999274861 prior to batch effect correction and is now -0.039641748517078 .
2025-09-22 21:17:46.525568 INFO::ASW Label was 0.279903866020218 prior to batch effect correction and is now 0.676786756025664 .
2025-09-22 21:17:46.526627 INFO::Total function execution time is 0.289449691772461 s and adjustment time is 0.24224591255188 s ( 83.69 )
2025-09-22 21:17:46.570773 INFO::Formatting Data.
2025-09-22 21:17:46.571986 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:46.573263 INFO::Removing potential empty rows and columns
2025-09-22 21:17:46.574663 INFO::Found 0 missing values.
2025-09-22 21:17:46.580168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:46.580944 INFO::Done
2025-09-22 21:17:46.581728 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:46.585927 INFO::Starting hierarchical adjustment
2025-09-22 21:17:46.586926 INFO::Found 5 batches.
2025-09-22 21:17:46.587619 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:46.588419 INFO::Using default BPPARAM
2025-09-22 21:17:46.589146 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.
2025-09-22 21:17:46.764188 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:46.766149 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 21:17:46.804542 INFO::Done
2025-09-22 21:17:46.805465 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:46.816422 INFO::ASW Batch was 0.368809000690839 prior to batch effect correction and is now -0.024121840748175 .
2025-09-22 21:17:46.817286 INFO::ASW Label was 0.471546400370552 prior to batch effect correction and is now 0.802552746995381 .
2025-09-22 21:17:46.818314 INFO::Total function execution time is 0.247769594192505 s and adjustment time is 0.217814683914185 s ( 87.91 )
2025-09-22 21:17:46.819362 INFO::Formatting Data.
2025-09-22 21:17:46.82014 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:46.82127 INFO::Removing potential empty rows and columns
2025-09-22 21:17:46.822561 INFO::Found 0 missing values.
2025-09-22 21:17:46.827762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:46.828515 INFO::Done
2025-09-22 21:17:46.82917 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:46.832868 INFO::Starting hierarchical adjustment
2025-09-22 21:17:46.833834 INFO::Found 5 batches.
2025-09-22 21:17:46.834489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:46.835256 INFO::Using default BPPARAM
2025-09-22 21:17:46.835937 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.
2025-09-22 21:17:47.02902 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:47.031169 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 21:17:47.069799 INFO::Done
2025-09-22 21:17:47.070773 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:47.075253 INFO::ASW Batch was 0.368809000690839 prior to batch effect correction and is now -0.024121840748175 .
2025-09-22 21:17:47.076203 INFO::ASW Label was 0.471546400370552 prior to batch effect correction and is now 0.802552746995381 .
2025-09-22 21:17:47.077292 INFO::Total function execution time is 0.257915258407593 s and adjustment time is 0.236120939254761 s ( 91.55 )
2025-09-22 21:17:47.092366 INFO::Formatting Data.
2025-09-22 21:17:47.093278 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:47.094324 INFO::Removing potential empty rows and columns
2025-09-22 21:17:47.095508 INFO::Found 0 missing values.
2025-09-22 21:17:47.098609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:47.099252 INFO::Done
2025-09-22 21:17:47.099845 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:47.103203 INFO::Starting hierarchical adjustment
2025-09-22 21:17:47.104033 INFO::Found 2 batches.
2025-09-22 21:17:47.104638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:47.105346 INFO::Using default BPPARAM
2025-09-22 21:17:47.105951 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:47.106988 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 21:17:47.123884 INFO::Done
2025-09-22 21:17:47.12468 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:47.128091 INFO::ASW Batch was 0.360788899482314 prior to batch effect correction and is now 0.111926553708371 .
2025-09-22 21:17:47.128795 INFO::ASW Label was 0.654577627724257 prior to batch effect correction and is now 0.826525505565348 .
2025-09-22 21:17:47.129671 INFO::Total function execution time is 0.0374040603637695 s and adjustment time is 0.0199847221374512 s ( 53.43 )
2025-09-22 21:17:47.130546 INFO::Formatting Data.
2025-09-22 21:17:47.131254 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:47.132247 INFO::Removing potential empty rows and columns
2025-09-22 21:17:47.133375 INFO::Found 0 missing values.
2025-09-22 21:17:47.136404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:47.13703 INFO::Done
2025-09-22 21:17:47.1376 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:47.140962 INFO::Starting hierarchical adjustment
2025-09-22 21:17:47.141795 INFO::Found 2 batches.
2025-09-22 21:17:47.142396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:47.143085 INFO::Using default BPPARAM
2025-09-22 21:17:47.143675 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:47.14473 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 21:17:47.173795 INFO::Done
2025-09-22 21:17:47.174603 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:47.185177 INFO::ASW Batch was 0.360788899482314 prior to batch effect correction and is now 0.111926553708371 .
2025-09-22 21:17:47.185954 INFO::ASW Label was 0.654577627724257 prior to batch effect correction and is now 0.826525505565348 .
2025-09-22 21:17:47.186857 INFO::Total function execution time is 0.0563042163848877 s and adjustment time is 0.0321300029754639 s ( 57.07 )
2025-09-22 21:17:47.213517 INFO::Formatting Data.
2025-09-22 21:17:47.214434 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:47.215446 INFO::Removing potential empty rows and columns
2025-09-22 21:17:47.220567 INFO::Found 0 missing values.
2025-09-22 21:17:47.227062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:47.22776 INFO::Done
2025-09-22 21:17:47.228351 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:47.234621 INFO::Starting hierarchical adjustment
2025-09-22 21:17:47.235475 INFO::Found 2 batches.
2025-09-22 21:17:47.236084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:47.236769 INFO::Using default BPPARAM
2025-09-22 21:17:47.23735 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:47.238402 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 21:17:47.304664 INFO::Done
2025-09-22 21:17:47.305475 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:47.307698 INFO::ASW Batch was -0.0503331059407119 prior to batch effect correction and is now -0.1157760171541 .
2025-09-22 21:17:47.308643 INFO::Total function execution time is 0.0952315330505371 s and adjustment time is 0.0693123340606689 s ( 72.78 )
2025-09-22 21:17:47.321731 INFO::Formatting Data.
2025-09-22 21:17:47.322588 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:47.323573 INFO::Removing potential empty rows and columns
2025-09-22 21:17:47.324689 INFO::Found 0 missing values.
2025-09-22 21:17:47.325983 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.
2025-09-22 21:17:47.334596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:47.335324 INFO::Done
2025-09-22 21:17:47.335942 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:47.343152 INFO::Starting hierarchical adjustment
2025-09-22 21:17:47.344053 INFO::Found 2 batches.
2025-09-22 21:17:47.344666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:47.349395 INFO::Using default BPPARAM
2025-09-22 21:17:47.350027 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:47.351147 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 21:17:47.389288 INFO::Done
2025-09-22 21:17:47.390104 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:47.39749 INFO::ASW Batch was 0.770215685928551 prior to batch effect correction and is now 0.224476621408218 .
2025-09-22 21:17:47.402243 INFO::ASW Label was 0.390852850290158 prior to batch effect correction and is now 0.776034786944382 .
2025-09-22 21:17:47.403124 INFO::Total function execution time is 0.0815045833587646 s and adjustment time is 0.0453729629516602 s ( 55.67 )
2025-09-22 21:17:47.403995 INFO::Formatting Data.
2025-09-22 21:17:47.404697 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:47.405778 INFO::Removing potential empty rows and columns
2025-09-22 21:17:47.406918 INFO::Found 0 missing values.
2025-09-22 21:17:47.40796 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.
2025-09-22 21:17:47.421211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:47.421948 INFO::Done
2025-09-22 21:17:47.422555 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:47.425962 INFO::Starting hierarchical adjustment
2025-09-22 21:17:47.426787 INFO::Found 2 batches.
2025-09-22 21:17:47.427393 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:47.42808 INFO::Using default BPPARAM
2025-09-22 21:17:47.428661 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:47.429748 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 21:17:47.448795 INFO::Done
2025-09-22 21:17:47.449564 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:47.452819 INFO::ASW Batch was 0.770215685928551 prior to batch effect correction and is now 0.224476621408218 .
2025-09-22 21:17:47.45347 INFO::ASW Label was 0.390852850290158 prior to batch effect correction and is now 0.776034786944382 .
2025-09-22 21:17:47.454341 INFO::Total function execution time is 0.0503616333007812 s and adjustment time is 0.0221521854400635 s ( 43.99 )
2025-09-22 21:17:47.786878 INFO::Formatting Data.
2025-09-22 21:17:47.787859 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:47.79294 INFO::Removing potential empty rows and columns
2025-09-22 21:17:47.794186 INFO::Found 0 missing values.
2025-09-22 21:17:47.801786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:47.802492 INFO::Done
2025-09-22 21:17:47.803148 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:47.809512 INFO::Starting hierarchical adjustment
2025-09-22 21:17:47.810365 INFO::Found 3 batches.
2025-09-22 21:17:47.810976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:47.811659 INFO::Using default BPPARAM
2025-09-22 21:17:47.812277 INFO::Processing subtree level 1
2025-09-22 21:17:47.971486 INFO::Adjusting the last 1 batches sequentially
2025-09-22 21:17:47.973468 INFO::Done
2025-09-22 21:17:47.974194 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:47.97695 INFO::ASW Batch was -0.0461113853664006 prior to batch effect correction and is now -0.0461113853664006 .
2025-09-22 21:17:47.978022 INFO::Total function execution time is 0.191236734390259 s and adjustment time is 0.163273572921753 s ( 85.38 )
2025-09-22 21:17:47.979255 INFO::Formatting Data.
2025-09-22 21:17:47.980015 INFO::Typecasting input to dataframe.
2025-09-22 21:17:47.980874 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:47.981956 INFO::Removing potential empty rows and columns
2025-09-22 21:17:47.983224 INFO::Found 0 missing values.
2025-09-22 21:17:47.986796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:47.987421 INFO::Done
2025-09-22 21:17:47.988059 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:47.990394 INFO::Starting hierarchical adjustment
2025-09-22 21:17:47.991225 INFO::Found 3 batches.
2025-09-22 21:17:47.991852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:47.992569 INFO::Using default BPPARAM
2025-09-22 21:17:47.993196 INFO::Processing subtree level 1
2025-09-22 21:17:48.105101 INFO::Adjusting the last 1 batches sequentially
2025-09-22 21:17:48.10734 INFO::Done
2025-09-22 21:17:48.108124 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:48.110984 INFO::ASW Batch was -0.0461113853664006 prior to batch effect correction and is now -0.0461113853664006 .
2025-09-22 21:17:48.112103 INFO::Total function execution time is 0.132811307907104 s and adjustment time is 0.116253137588501 s ( 87.53 )
2025-09-22 21:17:48.136937 INFO::Formatting Data.
2025-09-22 21:17:48.137988 INFO::Typecasting input to dataframe.
2025-09-22 21:17:48.138995 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:48.140093 INFO::Removing potential empty rows and columns
2025-09-22 21:17:48.141374 INFO::Found 0 missing values.
2025-09-22 21:17:48.144909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:48.145524 INFO::Done
2025-09-22 21:17:48.146147 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:48.148629 INFO::Starting hierarchical adjustment
2025-09-22 21:17:48.149477 INFO::Found 3 batches.
2025-09-22 21:17:48.15009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:48.150818 INFO::Using default BPPARAM
2025-09-22 21:17:48.151454 INFO::Processing subtree level 1
2025-09-22 21:17:48.277604 INFO::Adjusting the last 1 batches sequentially
2025-09-22 21:17:48.279835 INFO::Done
2025-09-22 21:17:48.280577 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:48.287767 INFO::ASW Batch was -0.0201928893776223 prior to batch effect correction and is now -0.0201928893776223 .
2025-09-22 21:17:48.289044 INFO::Total function execution time is 0.152233839035034 s and adjustment time is 0.130493402481079 s ( 85.72 )
2025-09-22 21:17:48.60449 INFO::Formatting Data.
2025-09-22 21:17:48.605541 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:48.606916 INFO::Removing potential empty rows and columns
2025-09-22 21:17:48.610237 INFO::Found 1000 missing values.
2025-09-22 21:17:48.641359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:48.642265 INFO::Done
2025-09-22 21:17:48.642934 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:48.649601 INFO::Starting hierarchical adjustment
2025-09-22 21:17:48.650524 INFO::Found 10 batches.
2025-09-22 21:17:48.651164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:48.651922 INFO::Using default BPPARAM
2025-09-22 21:17:48.652533 INFO::Processing subtree level 1
2025-09-22 21:17:48.97073 INFO::Processing subtree level 2
2025-09-22 21:17:49.252786 INFO::Adjusting the last 1 batches sequentially
2025-09-22 21:17:49.255437 INFO::Done
2025-09-22 21:17:49.256292 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:49.26336 INFO::ASW Batch was 0.513221963744618 prior to batch effect correction and is now 0.513221963744618 .
2025-09-22 21:17:49.264142 INFO::ASW Label was 0.322246954712377 prior to batch effect correction and is now 0.322246954712377 .
2025-09-22 21:17:49.265287 INFO::Total function execution time is 0.66093111038208 s and adjustment time is 0.605064630508423 s ( 91.55 )
2025-09-22 21:17:49.266461 INFO::Formatting Data.
2025-09-22 21:17:49.267316 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:49.268983 INFO::Removing potential empty rows and columns
2025-09-22 21:17:49.272434 INFO::Found 1000 missing values.
2025-09-22 21:17:49.29903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:49.300077 INFO::Done
2025-09-22 21:17:49.301558 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:49.309266 INFO::Starting hierarchical adjustment
2025-09-22 21:17:49.310347 INFO::Found 10 batches.
2025-09-22 21:17:50.366816 INFO::Set up parallel execution backend with 2 workers
2025-09-22 21:17:50.369055 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-22 21:17:51.793258 INFO::Adjusting the last 2 batches sequentially
2025-09-22 21:17:51.796624 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 21:17:51.819346 INFO::Done
2025-09-22 21:17:51.820163 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:51.830195 INFO::ASW Batch was 0.513221963744618 prior to batch effect correction and is now 0.513221963744618 .
2025-09-22 21:17:51.830933 INFO::ASW Label was 0.322246954712377 prior to batch effect correction and is now 0.322246954712377 .
2025-09-22 21:17:51.835843 INFO::Total function execution time is 2.56542921066284 s and adjustment time is 2.50918745994568 s ( 97.81 )
2025-09-22 21:17:52.089508 INFO::Formatting Data.
2025-09-22 21:17:52.090442 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.091517 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.093026 INFO::Found 0 missing values.
2025-09-22 21:17:52.097919 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.098543 INFO::Done
2025-09-22 21:17:52.09921 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 21:17:52.102961 INFO::Starting hierarchical adjustment
2025-09-22 21:17:52.103803 INFO::Found 3 batches.
2025-09-22 21:17:52.104426 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 21:17:52.105149 INFO::Using default BPPARAM
2025-09-22 21:17:52.105783 INFO::Processing subtree level 1
2025-09-22 21:17:52.282604 INFO::Adjusting the last 1 batches sequentially
2025-09-22 21:17:52.284963 INFO::Done
2025-09-22 21:17:52.289937 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 21:17:52.298577 INFO::ASW Batch was 0.287904914197866 prior to batch effect correction and is now -0.20518546977917 .
2025-09-22 21:17:52.299522 INFO::ASW Label was -0.205677232353144 prior to batch effect correction and is now 0.128328560178928 .
2025-09-22 21:17:52.303824 INFO::Total function execution time is 0.21130108833313 s and adjustment time is 0.181294202804565 s ( 85.8 )
2025-09-22 21:17:52.48699 INFO::Formatting Data.
2025-09-22 21:17:52.488247 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.489611 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.491216 INFO::Found 2 missing values.
2025-09-22 21:17:52.495836 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.496641 INFO::Done
2025-09-22 21:17:52.538453 INFO::Found NA in Reference column
2025-09-22 21:17:52.552814 INFO::Require at least two references per batch.
2025-09-22 21:17:52.584984 INFO::Formatting Data.
2025-09-22 21:17:52.586053 INFO::Recognized SummarizedExperiment
2025-09-22 21:17:52.586907 INFO::Typecasting input to dataframe.
2025-09-22 21:17:52.601817 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.603546 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.609755 INFO::Found 0 missing values.
2025-09-22 21:17:52.62128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.622288 INFO::Done
2025-09-22 21:17:52.647747 INFO::Formatting Data.
2025-09-22 21:17:52.648804 INFO::Recognized SummarizedExperiment
2025-09-22 21:17:52.649629 INFO::Typecasting input to dataframe.
2025-09-22 21:17:52.677212 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.679013 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.685004 INFO::Found 0 missing values.
2025-09-22 21:17:52.703556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.704551 INFO::Done
2025-09-22 21:17:52.729273 INFO::Formatting Data.
2025-09-22 21:17:52.730357 INFO::Recognized SummarizedExperiment
2025-09-22 21:17:52.731211 INFO::Typecasting input to dataframe.
2025-09-22 21:17:52.758286 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.759818 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.761486 INFO::Found 0 missing values.
2025-09-22 21:17:52.762854 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.
2025-09-22 21:17:52.769867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.77069 INFO::Done
2025-09-22 21:17:52.78545 INFO::Formatting Data.
2025-09-22 21:17:52.786581 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.787912 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.789433 INFO::Found 0 missing values.
2025-09-22 21:17:52.79403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.794836 INFO::Done
2025-09-22 21:17:52.811556 INFO::Formatting Data.
2025-09-22 21:17:52.812659 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.814042 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.815577 INFO::Found 0 missing values.
2025-09-22 21:17:52.819968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.820698 INFO::Done
2025-09-22 21:17:52.863068 INFO::Formatting Data.
2025-09-22 21:17:52.864183 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.865699 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.867427 INFO::Found 1 missing values.
2025-09-22 21:17:52.871404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.872194 INFO::Done
2025-09-22 21:17:52.899888 INFO::Formatting Data.
2025-09-22 21:17:52.901006 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.902216 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.903566 INFO::Found 2 missing values.
2025-09-22 21:17:52.90486 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.
2025-09-22 21:17:52.908238 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.909042 INFO::Done
2025-09-22 21:17:52.923538 INFO::Formatting Data.
2025-09-22 21:17:52.924667 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.925946 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.927289 INFO::Found 2 missing values.
2025-09-22 21:17:52.929629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.930399 INFO::Done
2025-09-22 21:17:52.945542 INFO::Formatting Data.
2025-09-22 21:17:52.946629 INFO::Typecasting input to dataframe.
2025-09-22 21:17:52.947831 INFO::Replacing NaNs with NAs.
2025-09-22 21:17:52.949087 INFO::Removing potential empty rows and columns
2025-09-22 21:17:52.950554 INFO::Found 0 missing values.
2025-09-22 21:17:52.954961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 21:17:52.955712 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.772 4.744 29.533
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.256 | 1.747 | 23.789 | |
| compute_asw | 0.029 | 0.001 | 0.030 | |
| count_existing | 0.016 | 0.002 | 0.025 | |
| generate_data_covariables | 0.016 | 0.000 | 0.015 | |
| generate_dataset | 0.013 | 0.002 | 0.014 | |