Yannis Schumann
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:28 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.2.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-03-31 20:06:24 -0400 (Mon, 31 Mar 2025) |
| EndedAt: 2025-03-31 20:07:51 -0400 (Mon, 31 Mar 2025) |
| EllapsedTime: 87.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* 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 25.023 1.14 17.852
* 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-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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")
2025-03-31 20:07:14.362116 INFO::Formatting Data.
2025-03-31 20:07:14.364007 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:14.376096 INFO::Removing potential empty rows and columns
2025-03-31 20:07:14.689018 INFO::Found 0 missing values.
2025-03-31 20:07:14.692923 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:14.693662 INFO::Done
2025-03-31 20:07:14.694191 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:14.70666 INFO::Starting hierarchical adjustment
2025-03-31 20:07:14.707615 INFO::Found 3 batches.
2025-03-31 20:07:14.70817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:14.709372 INFO::Using default BPPARAM
2025-03-31 20:07:14.709921 INFO::Processing subtree level 1
2025-03-31 20:07:14.809868 INFO::Adjusting the last 1 batches sequentially
2025-03-31 20:07:14.812024 INFO::Done
2025-03-31 20:07:14.812835 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:14.815557 INFO::ASW Batch was -0.0516493093073113 prior to batch effect correction and is now -0.0516493093073113 .
2025-03-31 20:07:14.816775 INFO::Total function execution time is 0.455627918243408 s and adjustment time is 0.104582786560059 s ( 22.95 )
2025-03-31 20:07:14.831256 INFO::Formatting Data.
2025-03-31 20:07:14.832142 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:14.833099 INFO::Removing potential empty rows and columns
2025-03-31 20:07:14.834226 INFO::Found 0 missing values.
2025-03-31 20:07:14.835165 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.
2025-03-31 20:07:14.846232 INFO::Formatting Data.
2025-03-31 20:07:14.847218 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:14.848185 INFO::Removing potential empty rows and columns
2025-03-31 20:07:14.84926 INFO::Found 0 missing values.
2025-03-31 20:07:14.850242 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.
2025-03-31 20:07:14.866878 INFO::Formatting Data.
2025-03-31 20:07:14.867722 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:14.868668 INFO::Removing potential empty rows and columns
2025-03-31 20:07:14.869736 INFO::Found 0 missing values.
2025-03-31 20:07:14.870709 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.
2025-03-31 20:07:14.875576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:14.876203 INFO::Done
2025-03-31 20:07:14.876708 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:14.878928 INFO::Starting hierarchical adjustment
2025-03-31 20:07:14.879678 INFO::Found 2 batches.
2025-03-31 20:07:14.880207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:14.88084 INFO::Using default BPPARAM
2025-03-31 20:07:14.881381 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:14.882388 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:14.913754 INFO::Done
2025-03-31 20:07:14.914748 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:14.917492 INFO::ASW Batch was -0.0494995626805578 prior to batch effect correction and is now -0.112859444184778 .
2025-03-31 20:07:14.918509 INFO::Total function execution time is 0.0517282485961914 s and adjustment time is 0.0341527462005615 s ( 66.02 )
2025-03-31 20:07:14.921898 INFO::Formatting Data.
2025-03-31 20:07:14.92259 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:14.933051 INFO::Formatting Data.
2025-03-31 20:07:14.934087 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:14.935169 INFO::Removing potential empty rows and columns
2025-03-31 20:07:14.936366 INFO::Found 0 missing values.
2025-03-31 20:07:14.939584 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:14.940161 INFO::Done
2025-03-31 20:07:14.940679 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:14.942925 INFO::Starting hierarchical adjustment
2025-03-31 20:07:14.943694 INFO::Found 2 batches.
2025-03-31 20:07:14.944283 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:14.944945 INFO::Using default BPPARAM
2025-03-31 20:07:14.945484 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:14.946518 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:14.963219 INFO::Done
2025-03-31 20:07:14.963978 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:14.966219 INFO::ASW Batch was -0.025120521044102 prior to batch effect correction and is now -0.109639614729839 .
2025-03-31 20:07:14.967151 INFO::Total function execution time is 0.0342502593994141 s and adjustment time is 0.0196688175201416 s ( 57.43 )
2025-03-31 20:07:14.968294 INFO::Formatting Data.
2025-03-31 20:07:14.968904 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:14.969802 INFO::Removing potential empty rows and columns
2025-03-31 20:07:14.970861 INFO::Found 0 missing values.
2025-03-31 20:07:14.973891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:14.974445 INFO::Done
2025-03-31 20:07:14.974957 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:14.977218 INFO::Starting hierarchical adjustment
2025-03-31 20:07:14.977934 INFO::Found 2 batches.
2025-03-31 20:07:14.978445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:14.979049 INFO::Using default BPPARAM
2025-03-31 20:07:14.979537 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:14.980476 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:14.998055 INFO::Done
2025-03-31 20:07:14.998946 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:15.00145 INFO::ASW Batch was -0.025120521044102 prior to batch effect correction and is now -0.109639614729839 .
2025-03-31 20:07:15.002379 INFO::Total function execution time is 0.0340659618377686 s and adjustment time is 0.0201916694641113 s ( 59.27 )
2025-03-31 20:07:17.903169 INFO::Formatting Data.
2025-03-31 20:07:17.903848 INFO::Recognized SummarizedExperiment
2025-03-31 20:07:17.904294 INFO::Typecasting input to dataframe.
2025-03-31 20:07:17.932744 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:17.933864 INFO::Removing potential empty rows and columns
2025-03-31 20:07:17.936938 INFO::Found 0 missing values.
2025-03-31 20:07:17.94275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:17.94327 INFO::Done
2025-03-31 20:07:17.943722 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:17.946719 INFO::Starting hierarchical adjustment
2025-03-31 20:07:17.947331 INFO::Found 2 batches.
2025-03-31 20:07:17.947783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:17.948729 INFO::Using default BPPARAM
2025-03-31 20:07:17.949183 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:17.950027 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:17.996182 INFO::Done
2025-03-31 20:07:17.996811 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:17.99982 INFO::ASW Batch was -0.0130570674237294 prior to batch effect correction and is now -0.0905283580577638 .
2025-03-31 20:07:18.000526 INFO::Total function execution time is 0.0976369380950928 s and adjustment time is 0.0489447116851807 s ( 50.13 )
2025-03-31 20:07:18.016055 INFO::Formatting Data.
2025-03-31 20:07:18.016706 INFO::Recognized SummarizedExperiment
2025-03-31 20:07:18.017163 INFO::Typecasting input to dataframe.
2025-03-31 20:07:18.025148 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:18.026278 INFO::Removing potential empty rows and columns
2025-03-31 20:07:18.029936 INFO::Found 0 missing values.
2025-03-31 20:07:18.03704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:18.037671 INFO::Done
2025-03-31 20:07:18.038184 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:18.041604 INFO::Starting hierarchical adjustment
2025-03-31 20:07:18.042302 INFO::Found 2 batches.
2025-03-31 20:07:18.042813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:18.043376 INFO::Using default BPPARAM
2025-03-31 20:07:18.043871 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:18.044804 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:18.070206 INFO::Done
2025-03-31 20:07:18.070985 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:18.074594 INFO::ASW Batch was -0.0248226944324886 prior to batch effect correction and is now -0.0248226944324886 .
2025-03-31 20:07:18.075475 INFO::Total function execution time is 0.0593752861022949 s and adjustment time is 0.0279889106750488 s ( 47.14 )
2025-03-31 20:07:18.093604 INFO::Formatting Data.
2025-03-31 20:07:18.094379 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:18.09524 INFO::Removing potential empty rows and columns
2025-03-31 20:07:18.096209 INFO::Found 0 missing values.
2025-03-31 20:07:18.099079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:18.099575 INFO::Done
2025-03-31 20:07:18.100058 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:18.102173 INFO::Starting hierarchical adjustment
2025-03-31 20:07:18.102832 INFO::Found 3 batches.
2025-03-31 20:07:18.103317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:18.103879 INFO::Using default BPPARAM
2025-03-31 20:07:18.104362 INFO::Processing subtree level 1
2025-03-31 20:07:18.228695 INFO::Adjusting the last 1 batches sequentially
2025-03-31 20:07:18.230457 INFO::Done
2025-03-31 20:07:18.231117 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:18.233554 INFO::ASW Batch was -0.070833210509915 prior to batch effect correction and is now -0.160774868071506 .
2025-03-31 20:07:18.23449 INFO::Total function execution time is 0.140916347503662 s and adjustment time is 0.12774658203125 s ( 90.65 )
2025-03-31 20:07:18.248512 INFO::Skipping initial DF formatting
2025-03-31 20:07:18.249203 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:18.25336 INFO::Starting hierarchical adjustment
2025-03-31 20:07:18.254149 INFO::Found 5 batches.
2025-03-31 20:07:18.25467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:18.255274 INFO::Using default BPPARAM
2025-03-31 20:07:18.255787 INFO::Processing subtree level 1
2025-03-31 20:07:18.372399 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:18.374011 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:18.393203 INFO::Done
2025-03-31 20:07:18.393904 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:18.398178 INFO::ASW Batch was 0.534216779163715 prior to batch effect correction and is now 0.534216779163715 .
2025-03-31 20:07:18.398798 INFO::ASW Label was 0.371852915529508 prior to batch effect correction and is now 0.371852915529508 .
2025-03-31 20:07:18.399597 INFO::Total function execution time is 0.15119457244873 s and adjustment time is 0.139203786849976 s ( 92.07 )
2025-03-31 20:07:18.416843 INFO::Formatting Data.
2025-03-31 20:07:18.417603 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:18.41852 INFO::Removing potential empty rows and columns
2025-03-31 20:07:18.419487 INFO::Found 0 missing values.
2025-03-31 20:07:18.423508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:18.424041 INFO::Done
2025-03-31 20:07:18.424542 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:18.4274 INFO::Starting hierarchical adjustment
2025-03-31 20:07:18.42809 INFO::Found 5 batches.
2025-03-31 20:07:18.4286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:18.429199 INFO::Using default BPPARAM
2025-03-31 20:07:18.429718 INFO::Processing subtree level 1
2025-03-31 20:07:18.531082 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:18.532717 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:18.548487 INFO::Done
2025-03-31 20:07:18.549191 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:18.552352 INFO::ASW Batch was 0.328370462293762 prior to batch effect correction and is now -0.0687707951441801 .
2025-03-31 20:07:18.552945 INFO::ASW Label was 0.399582920855494 prior to batch effect correction and is now 0.862288098082466 .
2025-03-31 20:07:18.553717 INFO::Total function execution time is 0.136959314346313 s and adjustment time is 0.120506286621094 s ( 87.99 )
2025-03-31 20:07:18.554519 INFO::Formatting Data.
2025-03-31 20:07:18.555218 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:18.556072 INFO::Removing potential empty rows and columns
2025-03-31 20:07:18.557037 INFO::Found 0 missing values.
2025-03-31 20:07:18.56104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:18.561558 INFO::Done
2025-03-31 20:07:18.562057 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:18.564923 INFO::Starting hierarchical adjustment
2025-03-31 20:07:18.5656 INFO::Found 5 batches.
2025-03-31 20:07:18.566104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:18.566694 INFO::Using default BPPARAM
2025-03-31 20:07:18.56719 INFO::Processing subtree level 1
2025-03-31 20:07:18.670783 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:18.672528 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:18.68936 INFO::Done
2025-03-31 20:07:18.690111 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:18.693313 INFO::ASW Batch was 0.328370462293762 prior to batch effect correction and is now -0.0687707951441801 .
2025-03-31 20:07:18.693897 INFO::ASW Label was 0.399582920855494 prior to batch effect correction and is now 0.862288098082466 .
2025-03-31 20:07:18.694685 INFO::Total function execution time is 0.140151500701904 s and adjustment time is 0.123854160308838 s ( 88.37 )
2025-03-31 20:07:18.708315 INFO::Formatting Data.
2025-03-31 20:07:18.709152 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:18.710067 INFO::Removing potential empty rows and columns
2025-03-31 20:07:18.711042 INFO::Found 0 missing values.
2025-03-31 20:07:18.715048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:18.71556 INFO::Done
2025-03-31 20:07:18.716083 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:18.719023 INFO::Starting hierarchical adjustment
2025-03-31 20:07:18.719712 INFO::Found 5 batches.
2025-03-31 20:07:18.72022 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:18.720812 INFO::Using default BPPARAM
2025-03-31 20:07:18.721317 INFO::Processing subtree level 1
2025-03-31 20:07:18.827331 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:18.829278 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:18.846519 INFO::Done
2025-03-31 20:07:18.847382 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:18.8509 INFO::ASW Batch was 0.341236144259511 prior to batch effect correction and is now -0.0232907158441129 .
2025-03-31 20:07:18.85152 INFO::ASW Label was 0.357890131474257 prior to batch effect correction and is now 0.811198444221742 .
2025-03-31 20:07:18.852373 INFO::Total function execution time is 0.144186019897461 s and adjustment time is 0.126904964447021 s ( 88.01 )
2025-03-31 20:07:18.853276 INFO::Formatting Data.
2025-03-31 20:07:18.853903 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:18.854812 INFO::Removing potential empty rows and columns
2025-03-31 20:07:18.856294 INFO::Found 0 missing values.
2025-03-31 20:07:18.861098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:18.861955 INFO::Done
2025-03-31 20:07:18.862459 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:18.865712 INFO::Starting hierarchical adjustment
2025-03-31 20:07:18.866442 INFO::Found 5 batches.
2025-03-31 20:07:18.866948 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:18.867545 INFO::Using default BPPARAM
2025-03-31 20:07:18.868047 INFO::Processing subtree level 1
2025-03-31 20:07:18.97611 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:18.977826 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:18.993984 INFO::Done
2025-03-31 20:07:18.994736 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:18.99804 INFO::ASW Batch was 0.341236144259511 prior to batch effect correction and is now -0.0232907158441129 .
2025-03-31 20:07:18.998617 INFO::ASW Label was 0.357890131474257 prior to batch effect correction and is now 0.811198444221742 .
2025-03-31 20:07:18.999425 INFO::Total function execution time is 0.146173000335693 s and adjustment time is 0.127662658691406 s ( 87.34 )
2025-03-31 20:07:19.013212 INFO::Formatting Data.
2025-03-31 20:07:19.014015 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:19.014961 INFO::Removing potential empty rows and columns
2025-03-31 20:07:19.015984 INFO::Found 0 missing values.
2025-03-31 20:07:19.018755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:19.01928 INFO::Done
2025-03-31 20:07:19.019789 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:19.022839 INFO::Starting hierarchical adjustment
2025-03-31 20:07:19.023521 INFO::Found 2 batches.
2025-03-31 20:07:19.024034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:19.024618 INFO::Using default BPPARAM
2025-03-31 20:07:19.025123 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:19.026017 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:19.041068 INFO::Done
2025-03-31 20:07:19.041754 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:19.044768 INFO::ASW Batch was 0.537898409182106 prior to batch effect correction and is now -0.02471728223513 .
2025-03-31 20:07:19.04533 INFO::ASW Label was 0.542095058478711 prior to batch effect correction and is now 0.912956430617744 .
2025-03-31 20:07:19.046109 INFO::Total function execution time is 0.0330173969268799 s and adjustment time is 0.0176801681518555 s ( 53.55 )
2025-03-31 20:07:19.04691 INFO::Formatting Data.
2025-03-31 20:07:19.047486 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:19.048338 INFO::Removing potential empty rows and columns
2025-03-31 20:07:19.049308 INFO::Found 0 missing values.
2025-03-31 20:07:19.051961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:19.052471 INFO::Done
2025-03-31 20:07:19.052969 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:19.055906 INFO::Starting hierarchical adjustment
2025-03-31 20:07:19.056574 INFO::Found 2 batches.
2025-03-31 20:07:19.057089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:19.057674 INFO::Using default BPPARAM
2025-03-31 20:07:19.058163 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:19.05903 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:19.074094 INFO::Done
2025-03-31 20:07:19.0748 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:19.077791 INFO::ASW Batch was 0.537898409182106 prior to batch effect correction and is now -0.02471728223513 .
2025-03-31 20:07:19.078365 INFO::ASW Label was 0.542095058478711 prior to batch effect correction and is now 0.912956430617744 .
2025-03-31 20:07:19.079142 INFO::Total function execution time is 0.0322577953338623 s and adjustment time is 0.0176327228546143 s ( 54.66 )
2025-03-31 20:07:19.090835 INFO::Formatting Data.
2025-03-31 20:07:19.091591 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:19.092494 INFO::Removing potential empty rows and columns
2025-03-31 20:07:19.093424 INFO::Found 0 missing values.
2025-03-31 20:07:19.095601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:19.096112 INFO::Done
2025-03-31 20:07:19.09659 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:19.098605 INFO::Starting hierarchical adjustment
2025-03-31 20:07:19.099281 INFO::Found 2 batches.
2025-03-31 20:07:19.099783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:19.100361 INFO::Using default BPPARAM
2025-03-31 20:07:19.100865 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:19.101741 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:19.133299 INFO::Done
2025-03-31 20:07:19.134027 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:19.136019 INFO::ASW Batch was 0.0196643715105505 prior to batch effect correction and is now -0.113006444583072 .
2025-03-31 20:07:19.136812 INFO::Total function execution time is 0.0461022853851318 s and adjustment time is 0.0341169834136963 s ( 74 )
2025-03-31 20:07:19.148605 INFO::Formatting Data.
2025-03-31 20:07:19.149343 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:19.150191 INFO::Removing potential empty rows and columns
2025-03-31 20:07:19.151137 INFO::Found 0 missing values.
2025-03-31 20:07:19.152222 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.
2025-03-31 20:07:19.156695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:19.157201 INFO::Done
2025-03-31 20:07:19.157683 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:19.160444 INFO::Starting hierarchical adjustment
2025-03-31 20:07:19.161107 INFO::Found 2 batches.
2025-03-31 20:07:19.161607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:19.162175 INFO::Using default BPPARAM
2025-03-31 20:07:19.162673 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:19.163554 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:19.179726 INFO::Done
2025-03-31 20:07:19.180366 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:19.183159 INFO::ASW Batch was 0.666039582787203 prior to batch effect correction and is now 0.0946934110580351 .
2025-03-31 20:07:19.183708 INFO::ASW Label was 0.433604496856687 prior to batch effect correction and is now 0.842114232511322 .
2025-03-31 20:07:19.184424 INFO::Total function execution time is 0.0358963012695312 s and adjustment time is 0.0187151432037354 s ( 52.14 )
2025-03-31 20:07:19.185165 INFO::Formatting Data.
2025-03-31 20:07:19.185743 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:19.18661 INFO::Removing potential empty rows and columns
2025-03-31 20:07:19.187563 INFO::Found 0 missing values.
2025-03-31 20:07:19.188412 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.
2025-03-31 20:07:19.192914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:19.193436 INFO::Done
2025-03-31 20:07:19.193917 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:19.196672 INFO::Starting hierarchical adjustment
2025-03-31 20:07:19.197329 INFO::Found 2 batches.
2025-03-31 20:07:19.19782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:19.198373 INFO::Using default BPPARAM
2025-03-31 20:07:19.198858 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:19.199715 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:19.224487 INFO::Done
2025-03-31 20:07:19.225505 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:19.229064 INFO::ASW Batch was 0.666039582787203 prior to batch effect correction and is now 0.0946934110580351 .
2025-03-31 20:07:19.229628 INFO::ASW Label was 0.433604496856687 prior to batch effect correction and is now 0.842114232511322 .
2025-03-31 20:07:19.230445 INFO::Total function execution time is 0.0452737808227539 s and adjustment time is 0.0270864963531494 s ( 59.83 )
2025-03-31 20:07:19.485057 INFO::Formatting Data.
2025-03-31 20:07:19.485809 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:19.486666 INFO::Removing potential empty rows and columns
2025-03-31 20:07:19.48763 INFO::Found 0 missing values.
2025-03-31 20:07:19.490463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:19.490967 INFO::Done
2025-03-31 20:07:19.491435 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:19.493346 INFO::Starting hierarchical adjustment
2025-03-31 20:07:19.494 INFO::Found 3 batches.
2025-03-31 20:07:19.494468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:19.49504 INFO::Using default BPPARAM
2025-03-31 20:07:19.495512 INFO::Processing subtree level 1
2025-03-31 20:07:19.607239 INFO::Adjusting the last 1 batches sequentially
2025-03-31 20:07:19.60949 INFO::Done
2025-03-31 20:07:19.610318 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:19.613181 INFO::ASW Batch was -0.0621590924859843 prior to batch effect correction and is now -0.0621590924859843 .
2025-03-31 20:07:19.61427 INFO::Total function execution time is 0.129197359085083 s and adjustment time is 0.115579843521118 s ( 89.46 )
2025-03-31 20:07:19.615513 INFO::Formatting Data.
2025-03-31 20:07:19.616246 INFO::Typecasting input to dataframe.
2025-03-31 20:07:19.617201 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:19.618357 INFO::Removing potential empty rows and columns
2025-03-31 20:07:19.619522 INFO::Found 0 missing values.
2025-03-31 20:07:19.622717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:19.623267 INFO::Done
2025-03-31 20:07:19.623798 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:19.626023 INFO::Starting hierarchical adjustment
2025-03-31 20:07:19.626781 INFO::Found 3 batches.
2025-03-31 20:07:19.627322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:19.62797 INFO::Using default BPPARAM
2025-03-31 20:07:19.628478 INFO::Processing subtree level 1
2025-03-31 20:07:19.742141 INFO::Adjusting the last 1 batches sequentially
2025-03-31 20:07:19.744285 INFO::Done
2025-03-31 20:07:19.745028 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:19.747732 INFO::ASW Batch was -0.0621590924859843 prior to batch effect correction and is now -0.0621590924859843 .
2025-03-31 20:07:19.748758 INFO::Total function execution time is 0.133236408233643 s and adjustment time is 0.117640256881714 s ( 88.29 )
2025-03-31 20:07:19.762432 INFO::Formatting Data.
2025-03-31 20:07:19.76335 INFO::Typecasting input to dataframe.
2025-03-31 20:07:19.764253 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:19.765213 INFO::Removing potential empty rows and columns
2025-03-31 20:07:19.766348 INFO::Found 0 missing values.
2025-03-31 20:07:19.76963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:19.770247 INFO::Done
2025-03-31 20:07:19.770776 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:19.772787 INFO::Starting hierarchical adjustment
2025-03-31 20:07:19.773512 INFO::Found 3 batches.
2025-03-31 20:07:19.774071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:19.774673 INFO::Using default BPPARAM
2025-03-31 20:07:19.775189 INFO::Processing subtree level 1
2025-03-31 20:07:19.877728 INFO::Adjusting the last 1 batches sequentially
2025-03-31 20:07:19.879959 INFO::Done
2025-03-31 20:07:19.880794 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:19.883607 INFO::ASW Batch was -0.147279547393247 prior to batch effect correction and is now -0.147279547393247 .
2025-03-31 20:07:19.884668 INFO::Total function execution time is 0.12233829498291 s and adjustment time is 0.106583595275879 s ( 87.12 )
2025-03-31 20:07:20.057249 INFO::Formatting Data.
2025-03-31 20:07:20.058146 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:20.059353 INFO::Removing potential empty rows and columns
2025-03-31 20:07:20.062371 INFO::Found 1000 missing values.
2025-03-31 20:07:20.082395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:20.08318 INFO::Done
2025-03-31 20:07:20.083755 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:20.08954 INFO::Starting hierarchical adjustment
2025-03-31 20:07:20.090359 INFO::Found 10 batches.
2025-03-31 20:07:20.090921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:20.091574 INFO::Using default BPPARAM
2025-03-31 20:07:20.092124 INFO::Processing subtree level 1
2025-03-31 20:07:20.254089 INFO::Processing subtree level 2
2025-03-31 20:07:20.417546 INFO::Adjusting the last 1 batches sequentially
2025-03-31 20:07:20.420061 INFO::Done
2025-03-31 20:07:20.420815 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:20.426941 INFO::ASW Batch was 0.514770363710125 prior to batch effect correction and is now 0.514770363710125 .
2025-03-31 20:07:20.427704 INFO::ASW Label was 0.30570611900172 prior to batch effect correction and is now 0.30570611900172 .
2025-03-31 20:07:20.428762 INFO::Total function execution time is 0.371589660644531 s and adjustment time is 0.329808712005615 s ( 88.76 )
2025-03-31 20:07:20.429682 INFO::Formatting Data.
2025-03-31 20:07:20.430338 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:20.431772 INFO::Removing potential empty rows and columns
2025-03-31 20:07:20.434731 INFO::Found 1000 missing values.
2025-03-31 20:07:20.454552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:20.455334 INFO::Done
2025-03-31 20:07:20.455922 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:20.461604 INFO::Starting hierarchical adjustment
2025-03-31 20:07:20.462463 INFO::Found 10 batches.
2025-03-31 20:07:21.766993 INFO::Set up parallel execution backend with 2 workers
2025-03-31 20:07:21.769194 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-31 20:07:22.861933 INFO::Adjusting the last 2 batches sequentially
2025-03-31 20:07:22.864084 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 20:07:22.879577 INFO::Done
2025-03-31 20:07:22.880219 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:22.884603 INFO::ASW Batch was 0.514770363710125 prior to batch effect correction and is now 0.514770363710125 .
2025-03-31 20:07:22.885188 INFO::ASW Label was 0.30570611900172 prior to batch effect correction and is now 0.30570611900172 .
2025-03-31 20:07:22.885876 INFO::Total function execution time is 2.45626592636108 s and adjustment time is 2.41727471351624 s ( 98.41 )
2025-03-31 20:07:23.026817 INFO::Formatting Data.
2025-03-31 20:07:23.027643 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.028548 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.029597 INFO::Found 0 missing values.
2025-03-31 20:07:23.033168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.033681 INFO::Done
2025-03-31 20:07:23.034152 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 20:07:23.036892 INFO::Starting hierarchical adjustment
2025-03-31 20:07:23.037564 INFO::Found 3 batches.
2025-03-31 20:07:23.038055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 20:07:23.03861 INFO::Using default BPPARAM
2025-03-31 20:07:23.039099 INFO::Processing subtree level 1
2025-03-31 20:07:23.151407 INFO::Adjusting the last 1 batches sequentially
2025-03-31 20:07:23.153416 INFO::Done
2025-03-31 20:07:23.154153 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 20:07:23.157558 INFO::ASW Batch was 0.143713440825991 prior to batch effect correction and is now -0.154857097161476 .
2025-03-31 20:07:23.158201 INFO::ASW Label was -0.213109501200115 prior to batch effect correction and is now -0.0123860685854982 .
2025-03-31 20:07:23.159196 INFO::Total function execution time is 0.132463932037354 s and adjustment time is 0.115973234176636 s ( 87.55 )
2025-03-31 20:07:23.281413 INFO::Formatting Data.
2025-03-31 20:07:23.282299 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.283219 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.284297 INFO::Found 2 missing values.
2025-03-31 20:07:23.287158 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.287683 INFO::Done
2025-03-31 20:07:23.313012 INFO::Found NA in Reference column
2025-03-31 20:07:23.321671 INFO::Require at least two references per batch.
2025-03-31 20:07:23.339913 INFO::Formatting Data.
2025-03-31 20:07:23.340569 INFO::Recognized SummarizedExperiment
2025-03-31 20:07:23.341048 INFO::Typecasting input to dataframe.
2025-03-31 20:07:23.349724 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.350796 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.354015 INFO::Found 0 missing values.
2025-03-31 20:07:23.360244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.360801 INFO::Done
2025-03-31 20:07:23.374635 INFO::Formatting Data.
2025-03-31 20:07:23.375336 INFO::Recognized SummarizedExperiment
2025-03-31 20:07:23.37581 INFO::Typecasting input to dataframe.
2025-03-31 20:07:23.392502 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.393661 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.396965 INFO::Found 0 missing values.
2025-03-31 20:07:23.407197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.407844 INFO::Done
2025-03-31 20:07:23.421998 INFO::Formatting Data.
2025-03-31 20:07:23.422702 INFO::Recognized SummarizedExperiment
2025-03-31 20:07:23.42318 INFO::Typecasting input to dataframe.
2025-03-31 20:07:23.438911 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.439887 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.440922 INFO::Found 0 missing values.
2025-03-31 20:07:23.441803 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.
2025-03-31 20:07:23.44598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.446473 INFO::Done
2025-03-31 20:07:23.455549 INFO::Formatting Data.
2025-03-31 20:07:23.456244 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.457042 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.457972 INFO::Found 0 missing values.
2025-03-31 20:07:23.460779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.461281 INFO::Done
2025-03-31 20:07:23.47191 INFO::Formatting Data.
2025-03-31 20:07:23.472685 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.473529 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.47453 INFO::Found 0 missing values.
2025-03-31 20:07:23.477353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.477847 INFO::Done
2025-03-31 20:07:23.504984 INFO::Formatting Data.
2025-03-31 20:07:23.505753 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.506773 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.507956 INFO::Found 1 missing values.
2025-03-31 20:07:23.510264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.510738 INFO::Done
2025-03-31 20:07:23.527159 INFO::Formatting Data.
2025-03-31 20:07:23.527895 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.528696 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.529554 INFO::Found 2 missing values.
2025-03-31 20:07:23.530359 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.
2025-03-31 20:07:23.532413 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.532891 INFO::Done
2025-03-31 20:07:23.541856 INFO::Formatting Data.
2025-03-31 20:07:23.542572 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.543363 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.544227 INFO::Found 2 missing values.
2025-03-31 20:07:23.54568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.546165 INFO::Done
2025-03-31 20:07:23.555408 INFO::Formatting Data.
2025-03-31 20:07:23.556084 INFO::Typecasting input to dataframe.
2025-03-31 20:07:23.556816 INFO::Replacing NaNs with NAs.
2025-03-31 20:07:23.557586 INFO::Removing potential empty rows and columns
2025-03-31 20:07:23.558477 INFO::Found 0 missing values.
2025-03-31 20:07:23.561089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 20:07:23.561553 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.042 3.460 20.306
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.023 | 1.140 | 17.852 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.014 | 0.000 | 0.013 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.010 | 0.001 | 0.011 | |