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This page was generated on 2024-07-12 17:40 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 156/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.0.0  (landing page)
Yannis Schumann
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_19
git_last_commit: 9a6bbaa
git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for BERT on merida1

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.

raw results


Summary

Package: BERT
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz
StartedAt: 2024-07-11 00:52:18 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 00:54:48 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 149.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* 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 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 46.064  2.677  37.733
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
2024-07-11 00:54:11.815806 INFO::Formatting Data.
2024-07-11 00:54:11.824565 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:11.862646 INFO::Removing potential empty rows and columns
2024-07-11 00:54:12.675835 INFO::Found  0  missing values.
2024-07-11 00:54:12.686128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:12.689657 INFO::Done
2024-07-11 00:54:12.691109 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:12.720571 INFO::Starting hierarchical adjustment
2024-07-11 00:54:12.724176 INFO::Found  3  batches.
2024-07-11 00:54:12.725463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:12.727791 INFO::Using default BPPARAM
2024-07-11 00:54:12.764466 INFO::Processing subtree level 1
2024-07-11 00:54:13.049642 INFO::Adjusting the last 1 batches sequentially
2024-07-11 00:54:13.056193 INFO::Done
2024-07-11 00:54:13.05781 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:13.06809 INFO::ASW Batch was -0.124431124294105 prior to batch effect correction and is now -0.124431124294105 .
2024-07-11 00:54:13.070375 INFO::Total function execution time is  1.25603604316711  s and adjustment time is  0.332847118377686 s ( 26.5 )
2024-07-11 00:54:13.10754 INFO::Formatting Data.
2024-07-11 00:54:13.109287 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:13.111782 INFO::Removing potential empty rows and columns
2024-07-11 00:54:13.114824 INFO::Found  0  missing values.
2024-07-11 00:54:13.11882 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.
2024-07-11 00:54:13.157031 INFO::Formatting Data.
2024-07-11 00:54:13.158862 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:13.161251 INFO::Removing potential empty rows and columns
2024-07-11 00:54:13.16415 INFO::Found  0  missing values.
2024-07-11 00:54:13.166733 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.
2024-07-11 00:54:13.216557 INFO::Formatting Data.
2024-07-11 00:54:13.218295 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:13.220556 INFO::Removing potential empty rows and columns
2024-07-11 00:54:13.223197 INFO::Found  0  missing values.
2024-07-11 00:54:13.225544 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.
2024-07-11 00:54:13.24253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:13.244017 INFO::Done
2024-07-11 00:54:13.24535 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:13.250938 INFO::Starting hierarchical adjustment
2024-07-11 00:54:13.254449 INFO::Found  2  batches.
2024-07-11 00:54:13.256559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:13.258377 INFO::Using default BPPARAM
2024-07-11 00:54:13.26009 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:13.264814 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:13.326932 INFO::Done
2024-07-11 00:54:13.328248 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:13.334231 INFO::ASW Batch was 0.0510073295241905 prior to batch effect correction and is now -0.107181916515805 .
2024-07-11 00:54:13.336544 INFO::Total function execution time is  0.121917009353638  s and adjustment time is  0.0729680061340332 s ( 59.85 )
2024-07-11 00:54:13.344054 INFO::Formatting Data.
2024-07-11 00:54:13.345719 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:13.369488 INFO::Formatting Data.
2024-07-11 00:54:13.372104 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:13.37427 INFO::Removing potential empty rows and columns
2024-07-11 00:54:13.377424 INFO::Found  0  missing values.
2024-07-11 00:54:13.386388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:13.387838 INFO::Done
2024-07-11 00:54:13.389128 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:13.396455 INFO::Starting hierarchical adjustment
2024-07-11 00:54:13.398375 INFO::Found  2  batches.
2024-07-11 00:54:13.399712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:13.401216 INFO::Using default BPPARAM
2024-07-11 00:54:13.403152 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:13.405461 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:13.456607 INFO::Done
2024-07-11 00:54:13.458223 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:13.462975 INFO::ASW Batch was 0.0535399092160965 prior to batch effect correction and is now -0.119713902208553 .
2024-07-11 00:54:13.464893 INFO::Total function execution time is  0.0954439640045166  s and adjustment time is  0.0585792064666748 s ( 61.38 )
2024-07-11 00:54:13.468781 INFO::Formatting Data.
2024-07-11 00:54:13.470254 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:13.472176 INFO::Removing potential empty rows and columns
2024-07-11 00:54:13.474701 INFO::Found  0  missing values.
2024-07-11 00:54:13.484477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:13.486088 INFO::Done
2024-07-11 00:54:13.487393 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:13.492955 INFO::Starting hierarchical adjustment
2024-07-11 00:54:13.494638 INFO::Found  2  batches.
2024-07-11 00:54:13.495741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:13.497837 INFO::Using default BPPARAM
2024-07-11 00:54:13.499934 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:13.502472 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:13.552617 INFO::Done
2024-07-11 00:54:13.554103 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:13.558833 INFO::ASW Batch was 0.0535399092160965 prior to batch effect correction and is now -0.119713902208553 .
2024-07-11 00:54:13.561743 INFO::Total function execution time is  0.092954158782959  s and adjustment time is  0.0581419467926025 s ( 62.55 )
2024-07-11 00:54:19.388595 INFO::Formatting Data.
2024-07-11 00:54:19.389953 INFO::Recognized SummarizedExperiment
2024-07-11 00:54:19.391084 INFO::Typecasting input to dataframe.
2024-07-11 00:54:20.447903 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:20.450625 INFO::Removing potential empty rows and columns
2024-07-11 00:54:20.460802 INFO::Found  0  missing values.
2024-07-11 00:54:20.479656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:20.480909 INFO::Done
2024-07-11 00:54:20.482053 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:20.491415 INFO::Starting hierarchical adjustment
2024-07-11 00:54:20.493009 INFO::Found  2  batches.
2024-07-11 00:54:20.494122 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:20.496294 INFO::Using default BPPARAM
2024-07-11 00:54:20.497538 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:20.500522 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:20.645068 INFO::Done
2024-07-11 00:54:20.6462 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:20.654257 INFO::ASW Batch was -0.0121775177983299 prior to batch effect correction and is now -0.0944224652725476 .
2024-07-11 00:54:20.65766 INFO::Total function execution time is  1.26986503601074  s and adjustment time is  0.152374029159546 s ( 12 )
2024-07-11 00:54:20.701278 INFO::Formatting Data.
2024-07-11 00:54:20.702596 INFO::Recognized SummarizedExperiment
2024-07-11 00:54:20.70368 INFO::Typecasting input to dataframe.
2024-07-11 00:54:20.726688 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:20.729002 INFO::Removing potential empty rows and columns
2024-07-11 00:54:20.739213 INFO::Found  0  missing values.
2024-07-11 00:54:20.761964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:20.763183 INFO::Done
2024-07-11 00:54:20.764827 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:20.774042 INFO::Starting hierarchical adjustment
2024-07-11 00:54:20.775753 INFO::Found  2  batches.
2024-07-11 00:54:20.777424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:20.779686 INFO::Using default BPPARAM
2024-07-11 00:54:20.780843 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:20.782946 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:20.856072 INFO::Done
2024-07-11 00:54:20.858317 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:20.867251 INFO::ASW Batch was -0.00315378834320045 prior to batch effect correction and is now -0.00315378834320045 .
2024-07-11 00:54:20.870152 INFO::Total function execution time is  0.168799877166748  s and adjustment time is  0.0807218551635742 s ( 47.82 )
2024-07-11 00:54:20.919858 INFO::Formatting Data.
2024-07-11 00:54:20.921669 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:20.923537 INFO::Removing potential empty rows and columns
2024-07-11 00:54:20.925749 INFO::Found  0  missing values.
2024-07-11 00:54:20.933891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:20.935171 INFO::Done
2024-07-11 00:54:20.936332 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:20.940443 INFO::Starting hierarchical adjustment
2024-07-11 00:54:20.943248 INFO::Found  3  batches.
2024-07-11 00:54:20.944424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:20.945704 INFO::Using default BPPARAM
2024-07-11 00:54:20.946757 INFO::Processing subtree level 1
2024-07-11 00:54:21.397573 INFO::Adjusting the last 1 batches sequentially
2024-07-11 00:54:21.407783 INFO::Done
2024-07-11 00:54:21.410327 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:21.422111 INFO::ASW Batch was -0.026526439822578 prior to batch effect correction and is now -0.153142057657869 .
2024-07-11 00:54:21.425393 INFO::Total function execution time is  0.50755500793457  s and adjustment time is  0.464833974838257 s ( 91.58 )
2024-07-11 00:54:21.466719 INFO::Skipping initial DF formatting
2024-07-11 00:54:21.468766 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:21.478696 INFO::Starting hierarchical adjustment
2024-07-11 00:54:21.480613 INFO::Found  5  batches.
2024-07-11 00:54:21.481985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:21.483624 INFO::Using default BPPARAM
2024-07-11 00:54:21.485062 INFO::Processing subtree level 1
2024-07-11 00:54:21.863646 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:21.87126 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:21.941376 INFO::Done
2024-07-11 00:54:21.94293 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:21.954278 INFO::ASW Batch was 0.535127230393458 prior to batch effect correction and is now 0.535127230393458 .
2024-07-11 00:54:21.955914 INFO::ASW Label was 0.336577680183336 prior to batch effect correction and is now 0.336577680183336 .
2024-07-11 00:54:21.958556 INFO::Total function execution time is  0.491815805435181  s and adjustment time is  0.461141109466553 s ( 93.76 )
2024-07-11 00:54:22.013214 INFO::Formatting Data.
2024-07-11 00:54:22.016117 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:22.018557 INFO::Removing potential empty rows and columns
2024-07-11 00:54:22.022513 INFO::Found  0  missing values.
2024-07-11 00:54:22.037305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:22.038812 INFO::Done
2024-07-11 00:54:22.040159 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:22.049332 INFO::Starting hierarchical adjustment
2024-07-11 00:54:22.051324 INFO::Found  5  batches.
2024-07-11 00:54:22.052737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:22.054458 INFO::Using default BPPARAM
2024-07-11 00:54:22.055854 INFO::Processing subtree level 1
2024-07-11 00:54:22.323983 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:22.336057 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:22.391712 INFO::Done
2024-07-11 00:54:22.393302 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:22.402484 INFO::ASW Batch was 0.584442360889467 prior to batch effect correction and is now -0.0350443272693764 .
2024-07-11 00:54:22.404531 INFO::ASW Label was 0.242975519124991 prior to batch effect correction and is now 0.816888977422521 .
2024-07-11 00:54:22.406738 INFO::Total function execution time is  0.393576145172119  s and adjustment time is  0.340795993804932 s ( 86.59 )
2024-07-11 00:54:22.409218 INFO::Formatting Data.
2024-07-11 00:54:22.41348 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:22.416572 INFO::Removing potential empty rows and columns
2024-07-11 00:54:22.419114 INFO::Found  0  missing values.
2024-07-11 00:54:22.432666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:22.434227 INFO::Done
2024-07-11 00:54:22.435572 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:22.442973 INFO::Starting hierarchical adjustment
2024-07-11 00:54:22.4449 INFO::Found  5  batches.
2024-07-11 00:54:22.446233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:22.447817 INFO::Using default BPPARAM
2024-07-11 00:54:22.449163 INFO::Processing subtree level 1
2024-07-11 00:54:22.708809 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:22.719841 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:22.778739 INFO::Done
2024-07-11 00:54:22.780825 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:22.790487 INFO::ASW Batch was 0.584442360889467 prior to batch effect correction and is now -0.0350443272693764 .
2024-07-11 00:54:22.79205 INFO::ASW Label was 0.242975519124991 prior to batch effect correction and is now 0.816888977422521 .
2024-07-11 00:54:22.79449 INFO::Total function execution time is  0.38530421257019  s and adjustment time is  0.334189891815186 s ( 86.73 )
2024-07-11 00:54:22.832573 INFO::Formatting Data.
2024-07-11 00:54:22.834279 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:22.836404 INFO::Removing potential empty rows and columns
2024-07-11 00:54:22.838927 INFO::Found  0  missing values.
2024-07-11 00:54:22.851599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:22.853154 INFO::Done
2024-07-11 00:54:22.854657 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:22.864024 INFO::Starting hierarchical adjustment
2024-07-11 00:54:22.867291 INFO::Found  5  batches.
2024-07-11 00:54:22.86866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:22.870464 INFO::Using default BPPARAM
2024-07-11 00:54:22.872208 INFO::Processing subtree level 1
2024-07-11 00:54:23.124283 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:23.142065 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:23.200163 INFO::Done
2024-07-11 00:54:23.203261 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:23.211695 INFO::ASW Batch was 0.333041783340594 prior to batch effect correction and is now -0.0195629048852473 .
2024-07-11 00:54:23.213354 INFO::ASW Label was 0.481987333267695 prior to batch effect correction and is now 0.818562903721811 .
2024-07-11 00:54:23.216747 INFO::Total function execution time is  0.383233070373535  s and adjustment time is  0.333271980285645 s ( 86.96 )
2024-07-11 00:54:23.218921 INFO::Formatting Data.
2024-07-11 00:54:23.220402 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:23.22262 INFO::Removing potential empty rows and columns
2024-07-11 00:54:23.225034 INFO::Found  0  missing values.
2024-07-11 00:54:23.23582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:23.23921 INFO::Done
2024-07-11 00:54:23.240638 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:23.247225 INFO::Starting hierarchical adjustment
2024-07-11 00:54:23.249591 INFO::Found  5  batches.
2024-07-11 00:54:23.25103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:23.252632 INFO::Using default BPPARAM
2024-07-11 00:54:23.253955 INFO::Processing subtree level 1
2024-07-11 00:54:23.508822 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:23.523539 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:23.582252 INFO::Done
2024-07-11 00:54:23.58387 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:23.591493 INFO::ASW Batch was 0.333041783340594 prior to batch effect correction and is now -0.0195629048852473 .
2024-07-11 00:54:23.592969 INFO::ASW Label was 0.481987333267695 prior to batch effect correction and is now 0.818562903721811 .
2024-07-11 00:54:23.596053 INFO::Total function execution time is  0.377088069915771  s and adjustment time is  0.333675861358643 s ( 88.49 )
2024-07-11 00:54:23.636685 INFO::Formatting Data.
2024-07-11 00:54:23.638507 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:23.642593 INFO::Removing potential empty rows and columns
2024-07-11 00:54:23.645064 INFO::Found  0  missing values.
2024-07-11 00:54:23.654287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:23.657629 INFO::Done
2024-07-11 00:54:23.659091 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:23.66706 INFO::Starting hierarchical adjustment
2024-07-11 00:54:23.66965 INFO::Found  2  batches.
2024-07-11 00:54:23.67099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:23.672505 INFO::Using default BPPARAM
2024-07-11 00:54:23.673735 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:23.676029 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:23.713426 INFO::Done
2024-07-11 00:54:23.714709 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:23.723507 INFO::ASW Batch was 0.371158200583978 prior to batch effect correction and is now 0.109587959919266 .
2024-07-11 00:54:23.725027 INFO::ASW Label was 0.661679735239454 prior to batch effect correction and is now 0.822388113776216 .
2024-07-11 00:54:23.727227 INFO::Total function execution time is  0.0907740592956543  s and adjustment time is  0.0441708564758301 s ( 48.66 )
2024-07-11 00:54:23.730652 INFO::Formatting Data.
2024-07-11 00:54:23.732296 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:23.734925 INFO::Removing potential empty rows and columns
2024-07-11 00:54:23.73778 INFO::Found  0  missing values.
2024-07-11 00:54:23.748116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:23.749605 INFO::Done
2024-07-11 00:54:23.750912 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:23.758874 INFO::Starting hierarchical adjustment
2024-07-11 00:54:23.76067 INFO::Found  2  batches.
2024-07-11 00:54:23.761903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:23.763506 INFO::Using default BPPARAM
2024-07-11 00:54:23.765209 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:23.76734 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:23.811439 INFO::Done
2024-07-11 00:54:23.8129 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:23.819937 INFO::ASW Batch was 0.371158200583978 prior to batch effect correction and is now 0.109587959919266 .
2024-07-11 00:54:23.82142 INFO::ASW Label was 0.661679735239454 prior to batch effect correction and is now 0.822388113776216 .
2024-07-11 00:54:23.823341 INFO::Total function execution time is  0.0937929153442383  s and adjustment time is  0.0511000156402588 s ( 54.48 )
2024-07-11 00:54:23.858895 INFO::Formatting Data.
2024-07-11 00:54:23.860579 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:23.862949 INFO::Removing potential empty rows and columns
2024-07-11 00:54:23.865393 INFO::Found  0  missing values.
2024-07-11 00:54:23.871975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:23.87338 INFO::Done
2024-07-11 00:54:23.874615 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:23.880427 INFO::Starting hierarchical adjustment
2024-07-11 00:54:23.882378 INFO::Found  2  batches.
2024-07-11 00:54:23.883761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:23.885269 INFO::Using default BPPARAM
2024-07-11 00:54:23.886603 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:23.888914 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:23.985328 INFO::Done
2024-07-11 00:54:23.986859 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:23.993147 INFO::ASW Batch was 0.195694097372827 prior to batch effect correction and is now -0.11632102764131 .
2024-07-11 00:54:23.995379 INFO::Total function execution time is  0.136625051498413  s and adjustment time is  0.10332202911377 s ( 75.62 )
2024-07-11 00:54:24.033605 INFO::Formatting Data.
2024-07-11 00:54:24.035709 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:24.040022 INFO::Removing potential empty rows and columns
2024-07-11 00:54:24.042592 INFO::Found  0  missing values.
2024-07-11 00:54:24.045781 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.
2024-07-11 00:54:24.059972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:24.06141 INFO::Done
2024-07-11 00:54:24.062609 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:24.070467 INFO::Starting hierarchical adjustment
2024-07-11 00:54:24.072299 INFO::Found  2  batches.
2024-07-11 00:54:24.073792 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:24.075255 INFO::Using default BPPARAM
2024-07-11 00:54:24.076531 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:24.078957 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:24.129153 INFO::Done
2024-07-11 00:54:24.130622 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:24.139939 INFO::ASW Batch was 0.418132127906053 prior to batch effect correction and is now -0.0245328796930432 .
2024-07-11 00:54:24.141537 INFO::ASW Label was 0.652948056357898 prior to batch effect correction and is now 0.925678554558516 .
2024-07-11 00:54:24.143513 INFO::Total function execution time is  0.109997987747192  s and adjustment time is  0.0572009086608887 s ( 52 )
2024-07-11 00:54:24.145832 INFO::Formatting Data.
2024-07-11 00:54:24.147554 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:24.150781 INFO::Removing potential empty rows and columns
2024-07-11 00:54:24.153606 INFO::Found  0  missing values.
2024-07-11 00:54:24.15576 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.
2024-07-11 00:54:24.170996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:24.173366 INFO::Done
2024-07-11 00:54:24.1748 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:24.181921 INFO::Starting hierarchical adjustment
2024-07-11 00:54:24.184836 INFO::Found  2  batches.
2024-07-11 00:54:24.186286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:24.187769 INFO::Using default BPPARAM
2024-07-11 00:54:24.189113 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:24.192466 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:24.242764 INFO::Done
2024-07-11 00:54:24.244246 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:24.250759 INFO::ASW Batch was 0.418132127906053 prior to batch effect correction and is now -0.0245328796930432 .
2024-07-11 00:54:24.252429 INFO::ASW Label was 0.652948056357898 prior to batch effect correction and is now 0.925678554558516 .
2024-07-11 00:54:24.254357 INFO::Total function execution time is  0.108580827713013  s and adjustment time is  0.0583438873291016 s ( 53.73 )
2024-07-11 00:54:24.912856 INFO::Formatting Data.
2024-07-11 00:54:24.914568 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:24.916691 INFO::Removing potential empty rows and columns
2024-07-11 00:54:24.920877 INFO::Found  0  missing values.
2024-07-11 00:54:24.929171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:24.931944 INFO::Done
2024-07-11 00:54:24.93338 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:24.938156 INFO::Starting hierarchical adjustment
2024-07-11 00:54:24.940122 INFO::Found  3  batches.
2024-07-11 00:54:24.942526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:24.944096 INFO::Using default BPPARAM
2024-07-11 00:54:24.945503 INFO::Processing subtree level 1
2024-07-11 00:54:25.192124 INFO::Adjusting the last 1 batches sequentially
2024-07-11 00:54:25.201794 INFO::Done
2024-07-11 00:54:25.205249 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:25.215009 INFO::ASW Batch was -0.0985195459488023 prior to batch effect correction and is now -0.0985195459488023 .
2024-07-11 00:54:25.221778 INFO::Total function execution time is  0.308583974838257  s and adjustment time is  0.262082099914551 s ( 84.93 )
2024-07-11 00:54:25.225766 INFO::Formatting Data.
2024-07-11 00:54:25.230229 INFO::Typecasting input to dataframe.
2024-07-11 00:54:25.232631 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:25.234812 INFO::Removing potential empty rows and columns
2024-07-11 00:54:25.237429 INFO::Found  0  missing values.
2024-07-11 00:54:25.245489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:25.246894 INFO::Done
2024-07-11 00:54:25.248579 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:25.253765 INFO::Starting hierarchical adjustment
2024-07-11 00:54:25.256515 INFO::Found  3  batches.
2024-07-11 00:54:25.259171 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:25.260965 INFO::Using default BPPARAM
2024-07-11 00:54:25.262414 INFO::Processing subtree level 1
2024-07-11 00:54:25.514621 INFO::Adjusting the last 1 batches sequentially
2024-07-11 00:54:25.525502 INFO::Done
2024-07-11 00:54:25.527909 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:25.536592 INFO::ASW Batch was -0.0985195459488023 prior to batch effect correction and is now -0.0985195459488023 .
2024-07-11 00:54:25.542507 INFO::Total function execution time is  0.316102981567383  s and adjustment time is  0.269413948059082 s ( 85.23 )
2024-07-11 00:54:25.583662 INFO::Formatting Data.
2024-07-11 00:54:25.585478 INFO::Typecasting input to dataframe.
2024-07-11 00:54:25.588325 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:25.590626 INFO::Removing potential empty rows and columns
2024-07-11 00:54:25.595328 INFO::Found  0  missing values.
2024-07-11 00:54:25.603577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:25.604925 INFO::Done
2024-07-11 00:54:25.606097 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:25.610368 INFO::Starting hierarchical adjustment
2024-07-11 00:54:25.612087 INFO::Found  3  batches.
2024-07-11 00:54:25.613389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:25.614907 INFO::Using default BPPARAM
2024-07-11 00:54:25.616309 INFO::Processing subtree level 1
2024-07-11 00:54:25.85443 INFO::Adjusting the last 1 batches sequentially
2024-07-11 00:54:25.866067 INFO::Done
2024-07-11 00:54:25.868494 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:25.877291 INFO::ASW Batch was -0.0853841597940645 prior to batch effect correction and is now -0.0853841597940645 .
2024-07-11 00:54:25.882469 INFO::Total function execution time is  0.298772811889648  s and adjustment time is  0.254283905029297 s ( 85.11 )
2024-07-11 00:54:26.290867 INFO::Formatting Data.
2024-07-11 00:54:26.295465 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:26.299582 INFO::Removing potential empty rows and columns
2024-07-11 00:54:26.310758 INFO::Found  1000  missing values.
2024-07-11 00:54:26.377857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:26.379307 INFO::Done
2024-07-11 00:54:26.382278 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:26.399012 INFO::Starting hierarchical adjustment
2024-07-11 00:54:26.400897 INFO::Found  10  batches.
2024-07-11 00:54:26.402287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:26.406481 INFO::Using default BPPARAM
2024-07-11 00:54:26.410675 INFO::Processing subtree level 1
2024-07-11 00:54:26.730533 INFO::Processing subtree level 2
2024-07-11 00:54:27.181345 INFO::Adjusting the last 1 batches sequentially
2024-07-11 00:54:27.194598 INFO::Done
2024-07-11 00:54:27.196816 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:27.212486 INFO::ASW Batch was 0.50470188283029 prior to batch effect correction and is now 0.50470188283029 .
2024-07-11 00:54:27.214022 INFO::ASW Label was 0.339935701836925 prior to batch effect correction and is now 0.339935701836925 .
2024-07-11 00:54:27.219679 INFO::Total function execution time is  0.928899049758911  s and adjustment time is  0.794046878814697 s ( 85.48 )
2024-07-11 00:54:27.222532 INFO::Formatting Data.
2024-07-11 00:54:27.224102 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:27.226926 INFO::Removing potential empty rows and columns
2024-07-11 00:54:27.235726 INFO::Found  1000  missing values.
2024-07-11 00:54:27.300815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:27.304395 INFO::Done
2024-07-11 00:54:27.307384 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:27.322189 INFO::Starting hierarchical adjustment
2024-07-11 00:54:27.324049 INFO::Found  10  batches.
2024-07-11 00:54:28.754074 INFO::Set up parallel execution backend with 2 workers
2024-07-11 00:54:28.755338 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-11 00:54:30.679842 INFO::Adjusting the last 2 batches sequentially
2024-07-11 00:54:30.682987 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 00:54:30.732483 INFO::Done
2024-07-11 00:54:30.733845 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:30.747048 INFO::ASW Batch was 0.50470188283029 prior to batch effect correction and is now 0.50470188283029 .
2024-07-11 00:54:30.74838 INFO::ASW Label was 0.339935701836925 prior to batch effect correction and is now 0.339935701836925 .
2024-07-11 00:54:30.749989 INFO::Total function execution time is  3.52760815620422  s and adjustment time is  3.40883278846741 s ( 96.63 )
2024-07-11 00:54:31.157616 INFO::Formatting Data.
2024-07-11 00:54:31.160343 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:31.164179 INFO::Removing potential empty rows and columns
2024-07-11 00:54:31.169486 INFO::Found  0  missing values.
2024-07-11 00:54:31.183625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:31.186508 INFO::Done
2024-07-11 00:54:31.187838 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 00:54:31.194535 INFO::Starting hierarchical adjustment
2024-07-11 00:54:31.198857 INFO::Found  3  batches.
2024-07-11 00:54:31.200328 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 00:54:31.20186 INFO::Using default BPPARAM
2024-07-11 00:54:31.203776 INFO::Processing subtree level 1
2024-07-11 00:54:31.515718 INFO::Adjusting the last 1 batches sequentially
2024-07-11 00:54:31.52788 INFO::Done
2024-07-11 00:54:31.529973 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 00:54:31.541918 INFO::ASW Batch was 0.249639474002554 prior to batch effect correction and is now -0.148246974518741 .
2024-07-11 00:54:31.54381 INFO::ASW Label was -0.176852572145166 prior to batch effect correction and is now 0.0533979819360249 .
2024-07-11 00:54:31.549052 INFO::Total function execution time is  0.390764951705933  s and adjustment time is  0.330394983291626 s ( 84.55 )
2024-07-11 00:54:31.902018 INFO::Formatting Data.
2024-07-11 00:54:31.903619 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:31.905992 INFO::Removing potential empty rows and columns
2024-07-11 00:54:31.909242 INFO::Found  2  missing values.
2024-07-11 00:54:31.917515 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:31.919012 INFO::Done
2024-07-11 00:54:32.015817 INFO::Found NA in Reference column
2024-07-11 00:54:32.050751 INFO::Require at least two references per batch.
2024-07-11 00:54:32.117141 INFO::Formatting Data.
2024-07-11 00:54:32.118798 INFO::Recognized SummarizedExperiment
2024-07-11 00:54:32.120212 INFO::Typecasting input to dataframe.
2024-07-11 00:54:32.15072 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.153409 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.16678 INFO::Found  0  missing values.
2024-07-11 00:54:32.194898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.19641 INFO::Done
2024-07-11 00:54:32.245371 INFO::Formatting Data.
2024-07-11 00:54:32.246984 INFO::Recognized SummarizedExperiment
2024-07-11 00:54:32.250038 INFO::Typecasting input to dataframe.
2024-07-11 00:54:32.303428 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.307126 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.320346 INFO::Found  0  missing values.
2024-07-11 00:54:32.364213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.365664 INFO::Done
2024-07-11 00:54:32.410913 INFO::Formatting Data.
2024-07-11 00:54:32.412931 INFO::Recognized SummarizedExperiment
2024-07-11 00:54:32.414335 INFO::Typecasting input to dataframe.
2024-07-11 00:54:32.468203 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.4703 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.472979 INFO::Found  0  missing values.
2024-07-11 00:54:32.47537 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.
2024-07-11 00:54:32.489602 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.491104 INFO::Done
2024-07-11 00:54:32.522272 INFO::Formatting Data.
2024-07-11 00:54:32.523975 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.526825 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.529543 INFO::Found  0  missing values.
2024-07-11 00:54:32.540445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.541923 INFO::Done
2024-07-11 00:54:32.575658 INFO::Formatting Data.
2024-07-11 00:54:32.577362 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.579481 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.582192 INFO::Found  0  missing values.
2024-07-11 00:54:32.591261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.592639 INFO::Done
2024-07-11 00:54:32.685933 INFO::Formatting Data.
2024-07-11 00:54:32.687726 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.690314 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.693933 INFO::Found  1  missing values.
2024-07-11 00:54:32.702056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.704676 INFO::Done
2024-07-11 00:54:32.762198 INFO::Formatting Data.
2024-07-11 00:54:32.763882 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.766032 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.768603 INFO::Found  2  missing values.
2024-07-11 00:54:32.772647 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.
2024-07-11 00:54:32.778529 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.780592 INFO::Done
2024-07-11 00:54:32.813253 INFO::Formatting Data.
2024-07-11 00:54:32.814996 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.817934 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.820759 INFO::Found  2  missing values.
2024-07-11 00:54:32.825055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.827504 INFO::Done
2024-07-11 00:54:32.859307 INFO::Formatting Data.
2024-07-11 00:54:32.861314 INFO::Typecasting input to dataframe.
2024-07-11 00:54:32.863376 INFO::Replacing NaNs with NAs.
2024-07-11 00:54:32.865591 INFO::Removing potential empty rows and columns
2024-07-11 00:54:32.868643 INFO::Found  0  missing values.
2024-07-11 00:54:32.878494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 00:54:32.879976 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 35.736   6.128  46.423

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT46.064 2.67737.733
compute_asw0.0580.0020.076
count_existing0.0290.0030.035
generate_data_covariables0.0260.0010.029
generate_dataset0.0240.0020.031