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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 159/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.2.0  (landing page)
Yannis Schumann
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
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 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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 kjohnson1

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: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2024-12-20 12:10:10 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 12:11:19 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 68.5 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 25.755  1.072  17.423
* 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-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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")
2024-12-20 12:11:01.985912 INFO::Formatting Data.
2024-12-20 12:11:01.987688 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:01.992285 INFO::Removing potential empty rows and columns
2024-12-20 12:11:02.241233 INFO::Found  0  missing values.
2024-12-20 12:11:02.244559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:02.245248 INFO::Done
2024-12-20 12:11:02.245811 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:02.260775 INFO::Starting hierarchical adjustment
2024-12-20 12:11:02.261712 INFO::Found  3  batches.
2024-12-20 12:11:02.262328 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:02.263494 INFO::Using default BPPARAM
2024-12-20 12:11:02.2641 INFO::Processing subtree level 1
2024-12-20 12:11:02.360971 INFO::Adjusting the last 1 batches sequentially
2024-12-20 12:11:02.362208 INFO::Done
2024-12-20 12:11:02.362588 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:02.364276 INFO::ASW Batch was -0.0221318219387726 prior to batch effect correction and is now -0.0221318219387726 .
2024-12-20 12:11:02.365409 INFO::Total function execution time is  0.380264043807983  s and adjustment time is  0.100754022598267 s ( 26.5 )
2024-12-20 12:11:02.372634 INFO::Formatting Data.
2024-12-20 12:11:02.372964 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:02.37333 INFO::Removing potential empty rows and columns
2024-12-20 12:11:02.373801 INFO::Found  0  missing values.
2024-12-20 12:11:02.374151 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.
2024-12-20 12:11:02.378587 INFO::Formatting Data.
2024-12-20 12:11:02.378999 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:02.379315 INFO::Removing potential empty rows and columns
2024-12-20 12:11:02.379682 INFO::Found  0  missing values.
2024-12-20 12:11:02.380015 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.
2024-12-20 12:11:02.387113 INFO::Formatting Data.
2024-12-20 12:11:02.387443 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:02.38777 INFO::Removing potential empty rows and columns
2024-12-20 12:11:02.388309 INFO::Found  0  missing values.
2024-12-20 12:11:02.388736 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.
2024-12-20 12:11:02.391051 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:02.391299 INFO::Done
2024-12-20 12:11:02.391474 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:02.392188 INFO::Starting hierarchical adjustment
2024-12-20 12:11:02.392424 INFO::Found  2  batches.
2024-12-20 12:11:02.392599 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:02.392837 INFO::Using default BPPARAM
2024-12-20 12:11:02.393002 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:02.39329 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:02.402517 INFO::Done
2024-12-20 12:11:02.402801 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:02.404382 INFO::ASW Batch was 0.00644414674901464 prior to batch effect correction and is now -0.123575987623341 .
2024-12-20 12:11:02.405321 INFO::Total function execution time is  0.0181140899658203  s and adjustment time is  0.0101180076599121 s ( 55.86 )
2024-12-20 12:11:02.408696 INFO::Formatting Data.
2024-12-20 12:11:02.409487 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:02.418301 INFO::Formatting Data.
2024-12-20 12:11:02.418974 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:02.419752 INFO::Removing potential empty rows and columns
2024-12-20 12:11:02.420637 INFO::Found  0  missing values.
2024-12-20 12:11:02.423123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:02.423607 INFO::Done
2024-12-20 12:11:02.424052 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:02.425832 INFO::Starting hierarchical adjustment
2024-12-20 12:11:02.426461 INFO::Found  2  batches.
2024-12-20 12:11:02.426937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:02.427537 INFO::Using default BPPARAM
2024-12-20 12:11:02.428052 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:02.428874 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:02.442429 INFO::Done
2024-12-20 12:11:02.44304 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:02.44484 INFO::ASW Batch was 0.0247090868130389 prior to batch effect correction and is now -0.130529762348995 .
2024-12-20 12:11:02.445582 INFO::Total function execution time is  0.027324914932251  s and adjustment time is  0.0160717964172363 s ( 58.82 )
2024-12-20 12:11:02.446522 INFO::Formatting Data.
2024-12-20 12:11:02.447067 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:02.447833 INFO::Removing potential empty rows and columns
2024-12-20 12:11:02.448701 INFO::Found  0  missing values.
2024-12-20 12:11:02.451055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:02.451559 INFO::Done
2024-12-20 12:11:02.451976 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:02.453627 INFO::Starting hierarchical adjustment
2024-12-20 12:11:02.454236 INFO::Found  2  batches.
2024-12-20 12:11:02.454656 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:02.45515 INFO::Using default BPPARAM
2024-12-20 12:11:02.455585 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:02.456359 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:02.469502 INFO::Done
2024-12-20 12:11:02.470087 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:02.471828 INFO::ASW Batch was 0.0247090868130389 prior to batch effect correction and is now -0.130529762348995 .
2024-12-20 12:11:02.472515 INFO::Total function execution time is  0.0260019302368164  s and adjustment time is  0.0153591632843018 s ( 59.07 )
2024-12-20 12:11:04.484474 INFO::Formatting Data.
2024-12-20 12:11:04.485134 INFO::Recognized SummarizedExperiment
2024-12-20 12:11:04.485574 INFO::Typecasting input to dataframe.
2024-12-20 12:11:04.515122 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:04.516176 INFO::Removing potential empty rows and columns
2024-12-20 12:11:04.519149 INFO::Found  0  missing values.
2024-12-20 12:11:04.524927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:04.525195 INFO::Done
2024-12-20 12:11:04.525354 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:04.526575 INFO::Starting hierarchical adjustment
2024-12-20 12:11:04.526798 INFO::Found  2  batches.
2024-12-20 12:11:04.526944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:04.527317 INFO::Using default BPPARAM
2024-12-20 12:11:04.527466 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:04.52776 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:04.550499 INFO::Done
2024-12-20 12:11:04.550747 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:04.551971 INFO::ASW Batch was -0.0134472232099193 prior to batch effect correction and is now -0.100733903644094 .
2024-12-20 12:11:04.552266 INFO::Total function execution time is  0.0681600570678711  s and adjustment time is  0.0237231254577637 s ( 34.81 )
2024-12-20 12:11:04.558812 INFO::Formatting Data.
2024-12-20 12:11:04.559129 INFO::Recognized SummarizedExperiment
2024-12-20 12:11:04.559308 INFO::Typecasting input to dataframe.
2024-12-20 12:11:04.56293 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:04.563395 INFO::Removing potential empty rows and columns
2024-12-20 12:11:04.564635 INFO::Found  0  missing values.
2024-12-20 12:11:04.567135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:04.567377 INFO::Done
2024-12-20 12:11:04.567545 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:04.568932 INFO::Starting hierarchical adjustment
2024-12-20 12:11:04.569214 INFO::Found  2  batches.
2024-12-20 12:11:04.569382 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:04.569573 INFO::Using default BPPARAM
2024-12-20 12:11:04.56972 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:04.570043 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:04.579411 INFO::Done
2024-12-20 12:11:04.579746 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:04.581401 INFO::ASW Batch was -0.0054705488999672 prior to batch effect correction and is now -0.0054705488999672 .
2024-12-20 12:11:04.58184 INFO::Total function execution time is  0.0230038166046143  s and adjustment time is  0.0102159976959229 s ( 44.41 )
2024-12-20 12:11:04.595217 INFO::Formatting Data.
2024-12-20 12:11:04.596012 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:04.596778 INFO::Removing potential empty rows and columns
2024-12-20 12:11:04.597618 INFO::Found  0  missing values.
2024-12-20 12:11:04.600084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:04.600546 INFO::Done
2024-12-20 12:11:04.600967 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:04.602619 INFO::Starting hierarchical adjustment
2024-12-20 12:11:04.603181 INFO::Found  3  batches.
2024-12-20 12:11:04.603597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:04.604089 INFO::Using default BPPARAM
2024-12-20 12:11:04.604498 INFO::Processing subtree level 1
2024-12-20 12:11:04.722526 INFO::Adjusting the last 1 batches sequentially
2024-12-20 12:11:04.724683 INFO::Done
2024-12-20 12:11:04.724899 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:04.726228 INFO::ASW Batch was -0.0498053262316416 prior to batch effect correction and is now -0.147287184281028 .
2024-12-20 12:11:04.726768 INFO::Total function execution time is  0.131673097610474  s and adjustment time is  0.121654987335205 s ( 92.39 )
2024-12-20 12:11:04.732978 INFO::Skipping initial DF formatting
2024-12-20 12:11:04.733235 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:04.734593 INFO::Starting hierarchical adjustment
2024-12-20 12:11:04.73484 INFO::Found  5  batches.
2024-12-20 12:11:04.735039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:04.735263 INFO::Using default BPPARAM
2024-12-20 12:11:04.735546 INFO::Processing subtree level 1
2024-12-20 12:11:04.823775 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:04.825465 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:04.83468 INFO::Done
2024-12-20 12:11:04.8351 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:04.83702 INFO::ASW Batch was 0.536945944903161 prior to batch effect correction and is now 0.536945944903161 .
2024-12-20 12:11:04.837261 INFO::ASW Label was 0.366886698564887 prior to batch effect correction and is now 0.366886698564887 .
2024-12-20 12:11:04.837813 INFO::Total function execution time is  0.104819059371948  s and adjustment time is  0.0998740196228027 s ( 95.28 )
2024-12-20 12:11:04.845843 INFO::Formatting Data.
2024-12-20 12:11:04.846123 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:04.84646 INFO::Removing potential empty rows and columns
2024-12-20 12:11:04.846866 INFO::Found  0  missing values.
2024-12-20 12:11:04.848092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:04.848289 INFO::Done
2024-12-20 12:11:04.848462 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:04.849436 INFO::Starting hierarchical adjustment
2024-12-20 12:11:04.849683 INFO::Found  5  batches.
2024-12-20 12:11:04.849855 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:04.850083 INFO::Using default BPPARAM
2024-12-20 12:11:04.850358 INFO::Processing subtree level 1
2024-12-20 12:11:04.900332 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:04.901948 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:04.910734 INFO::Done
2024-12-20 12:11:04.911035 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:04.912283 INFO::ASW Batch was 0.489062725118497 prior to batch effect correction and is now -0.106228933880548 .
2024-12-20 12:11:04.9125 INFO::ASW Label was 0.265930016565179 prior to batch effect correction and is now 0.806646377729261 .
2024-12-20 12:11:04.912913 INFO::Total function execution time is  0.0670959949493408  s and adjustment time is  0.0610880851745605 s ( 91.05 )
2024-12-20 12:11:04.913301 INFO::Formatting Data.
2024-12-20 12:11:04.913493 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:04.913784 INFO::Removing potential empty rows and columns
2024-12-20 12:11:04.914363 INFO::Found  0  missing values.
2024-12-20 12:11:04.915588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:04.915782 INFO::Done
2024-12-20 12:11:04.915963 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:04.91692 INFO::Starting hierarchical adjustment
2024-12-20 12:11:04.917158 INFO::Found  5  batches.
2024-12-20 12:11:04.917311 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:04.91752 INFO::Using default BPPARAM
2024-12-20 12:11:04.917784 INFO::Processing subtree level 1
2024-12-20 12:11:04.982378 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:04.986206 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:04.99638 INFO::Done
2024-12-20 12:11:04.996689 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:04.998138 INFO::ASW Batch was 0.489062725118497 prior to batch effect correction and is now -0.106228933880548 .
2024-12-20 12:11:04.99836 INFO::ASW Label was 0.265930016565179 prior to batch effect correction and is now 0.806646377729261 .
2024-12-20 12:11:04.998767 INFO::Total function execution time is  0.085446834564209  s and adjustment time is  0.0792350769042969 s ( 92.73 )
2024-12-20 12:11:05.004497 INFO::Formatting Data.
2024-12-20 12:11:05.004747 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.005054 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.005397 INFO::Found  0  missing values.
2024-12-20 12:11:05.006622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.006849 INFO::Done
2024-12-20 12:11:05.007015 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.007982 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.008315 INFO::Found  5  batches.
2024-12-20 12:11:05.008489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.008701 INFO::Using default BPPARAM
2024-12-20 12:11:05.008952 INFO::Processing subtree level 1
2024-12-20 12:11:05.064825 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:05.066142 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:05.07751 INFO::Done
2024-12-20 12:11:05.077922 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.079766 INFO::ASW Batch was 0.226519091498063 prior to batch effect correction and is now -0.0904643907262888 .
2024-12-20 12:11:05.080035 INFO::ASW Label was 0.554226310200305 prior to batch effect correction and is now 0.882115217703745 .
2024-12-20 12:11:05.080678 INFO::Total function execution time is  0.0761809349060059  s and adjustment time is  0.069195032119751 s ( 90.83 )
2024-12-20 12:11:05.081226 INFO::Formatting Data.
2024-12-20 12:11:05.081432 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.081742 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.082224 INFO::Found  0  missing values.
2024-12-20 12:11:05.083557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.083775 INFO::Done
2024-12-20 12:11:05.083937 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.084928 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.085184 INFO::Found  5  batches.
2024-12-20 12:11:05.085357 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.085596 INFO::Using default BPPARAM
2024-12-20 12:11:05.085857 INFO::Processing subtree level 1
2024-12-20 12:11:05.142439 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:05.144383 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:05.151976 INFO::Done
2024-12-20 12:11:05.152332 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.153558 INFO::ASW Batch was 0.226519091498063 prior to batch effect correction and is now -0.0904643907262888 .
2024-12-20 12:11:05.15384 INFO::ASW Label was 0.554226310200305 prior to batch effect correction and is now 0.882115217703745 .
2024-12-20 12:11:05.154252 INFO::Total function execution time is  0.0731110572814941  s and adjustment time is  0.066831111907959 s ( 91.41 )
2024-12-20 12:11:05.159901 INFO::Formatting Data.
2024-12-20 12:11:05.16016 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.160468 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.160811 INFO::Found  0  missing values.
2024-12-20 12:11:05.161642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.161808 INFO::Done
2024-12-20 12:11:05.161965 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.162971 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.163279 INFO::Found  2  batches.
2024-12-20 12:11:05.163451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.163665 INFO::Using default BPPARAM
2024-12-20 12:11:05.163826 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:05.164107 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:05.174229 INFO::Done
2024-12-20 12:11:05.175258 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.178302 INFO::ASW Batch was 0.354331187475997 prior to batch effect correction and is now -0.0367611761941123 .
2024-12-20 12:11:05.178881 INFO::ASW Label was 0.699854902802537 prior to batch effect correction and is now 0.9431768334255 .
2024-12-20 12:11:05.179615 INFO::Total function execution time is  0.0196290016174316  s and adjustment time is  0.0109272003173828 s ( 55.67 )
2024-12-20 12:11:05.180253 INFO::Formatting Data.
2024-12-20 12:11:05.180796 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.181517 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.182344 INFO::Found  0  missing values.
2024-12-20 12:11:05.18461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.185074 INFO::Done
2024-12-20 12:11:05.185501 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.188006 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.188631 INFO::Found  2  batches.
2024-12-20 12:11:05.189063 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.189556 INFO::Using default BPPARAM
2024-12-20 12:11:05.189958 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:05.19068 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:05.20325 INFO::Done
2024-12-20 12:11:05.203838 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.206308 INFO::ASW Batch was 0.354331187475997 prior to batch effect correction and is now -0.0367611761941123 .
2024-12-20 12:11:05.206848 INFO::ASW Label was 0.699854902802537 prior to batch effect correction and is now 0.9431768334255 .
2024-12-20 12:11:05.20758 INFO::Total function execution time is  0.0273160934448242  s and adjustment time is  0.0147240161895752 s ( 53.9 )
2024-12-20 12:11:05.218009 INFO::Formatting Data.
2024-12-20 12:11:05.218659 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.219378 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.220122 INFO::Found  0  missing values.
2024-12-20 12:11:05.221915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.222369 INFO::Done
2024-12-20 12:11:05.222803 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.224348 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.224915 INFO::Found  2  batches.
2024-12-20 12:11:05.225319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.225786 INFO::Using default BPPARAM
2024-12-20 12:11:05.226189 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:05.22687 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:05.254249 INFO::Done
2024-12-20 12:11:05.254848 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.256439 INFO::ASW Batch was 0.132915238573211 prior to batch effect correction and is now -0.149087283094351 .
2024-12-20 12:11:05.257103 INFO::Total function execution time is  0.0391561985015869  s and adjustment time is  0.0294380187988281 s ( 75.18 )
2024-12-20 12:11:05.268717 INFO::Formatting Data.
2024-12-20 12:11:05.269401 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.27018 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.271073 INFO::Found  0  missing values.
2024-12-20 12:11:05.272225 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.
2024-12-20 12:11:05.276381 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.276967 INFO::Done
2024-12-20 12:11:05.277452 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.280197 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.28088 INFO::Found  2  batches.
2024-12-20 12:11:05.281322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.281812 INFO::Using default BPPARAM
2024-12-20 12:11:05.282228 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:05.283063 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:05.298091 INFO::Done
2024-12-20 12:11:05.298713 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.301267 INFO::ASW Batch was 0.55615673047819 prior to batch effect correction and is now 0.0770221107626591 .
2024-12-20 12:11:05.301827 INFO::ASW Label was 0.537627429399798 prior to batch effect correction and is now 0.851264972475286 .
2024-12-20 12:11:05.302516 INFO::Total function execution time is  0.0338518619537354  s and adjustment time is  0.0173180103302002 s ( 51.16 )
2024-12-20 12:11:05.303291 INFO::Formatting Data.
2024-12-20 12:11:05.303808 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.304581 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.305398 INFO::Found  0  missing values.
2024-12-20 12:11:05.306164 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.
2024-12-20 12:11:05.309955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.310494 INFO::Done
2024-12-20 12:11:05.31095 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.313492 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.314096 INFO::Found  2  batches.
2024-12-20 12:11:05.314524 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.315014 INFO::Using default BPPARAM
2024-12-20 12:11:05.315414 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:05.316247 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:05.330642 INFO::Done
2024-12-20 12:11:05.331229 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.333788 INFO::ASW Batch was 0.55615673047819 prior to batch effect correction and is now 0.0770221107626591 .
2024-12-20 12:11:05.334332 INFO::ASW Label was 0.537627429399798 prior to batch effect correction and is now 0.851264972475286 .
2024-12-20 12:11:05.335029 INFO::Total function execution time is  0.0317280292510986  s and adjustment time is  0.0166420936584473 s ( 52.45 )
2024-12-20 12:11:05.52181 INFO::Formatting Data.
2024-12-20 12:11:05.522176 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.522564 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.523008 INFO::Found  0  missing values.
2024-12-20 12:11:05.524213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.524468 INFO::Done
2024-12-20 12:11:05.524654 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.525409 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.525647 INFO::Found  3  batches.
2024-12-20 12:11:05.525801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.525984 INFO::Using default BPPARAM
2024-12-20 12:11:05.52613 INFO::Processing subtree level 1
2024-12-20 12:11:05.575183 INFO::Adjusting the last 1 batches sequentially
2024-12-20 12:11:05.579153 INFO::Done
2024-12-20 12:11:05.579605 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.581843 INFO::ASW Batch was -0.125210983202525 prior to batch effect correction and is now -0.125210983202525 .
2024-12-20 12:11:05.582493 INFO::Total function execution time is  0.0607020854949951  s and adjustment time is  0.0535209178924561 s ( 88.17 )
2024-12-20 12:11:05.583016 INFO::Formatting Data.
2024-12-20 12:11:05.583221 INFO::Typecasting input to dataframe.
2024-12-20 12:11:05.583618 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.584099 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.584812 INFO::Found  0  missing values.
2024-12-20 12:11:05.585864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.586077 INFO::Done
2024-12-20 12:11:05.586263 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.587035 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.587435 INFO::Found  3  batches.
2024-12-20 12:11:05.587616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.587961 INFO::Using default BPPARAM
2024-12-20 12:11:05.588128 INFO::Processing subtree level 1
2024-12-20 12:11:05.684529 INFO::Adjusting the last 1 batches sequentially
2024-12-20 12:11:05.686845 INFO::Done
2024-12-20 12:11:05.688387 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.694003 INFO::ASW Batch was -0.125210983202525 prior to batch effect correction and is now -0.125210983202525 .
2024-12-20 12:11:05.694751 INFO::Total function execution time is  0.111722946166992  s and adjustment time is  0.0995340347290039 s ( 89.09 )
2024-12-20 12:11:05.700974 INFO::Formatting Data.
2024-12-20 12:11:05.701269 INFO::Typecasting input to dataframe.
2024-12-20 12:11:05.701554 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.701996 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.702587 INFO::Found  0  missing values.
2024-12-20 12:11:05.703503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.70369 INFO::Done
2024-12-20 12:11:05.703865 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.704683 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.705027 INFO::Found  3  batches.
2024-12-20 12:11:05.705188 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.705514 INFO::Using default BPPARAM
2024-12-20 12:11:05.705672 INFO::Processing subtree level 1
2024-12-20 12:11:05.865543 INFO::Adjusting the last 1 batches sequentially
2024-12-20 12:11:05.868186 INFO::Done
2024-12-20 12:11:05.868933 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:05.878439 INFO::ASW Batch was -0.129182662454067 prior to batch effect correction and is now -0.129182662454067 .
2024-12-20 12:11:05.879593 INFO::Total function execution time is  0.17861795425415  s and adjustment time is  0.163229942321777 s ( 91.38 )
2024-12-20 12:11:05.979883 INFO::Formatting Data.
2024-12-20 12:11:05.980236 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:05.980641 INFO::Removing potential empty rows and columns
2024-12-20 12:11:05.981674 INFO::Found  1000  missing values.
2024-12-20 12:11:05.989287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:05.989526 INFO::Done
2024-12-20 12:11:05.989704 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:05.991827 INFO::Starting hierarchical adjustment
2024-12-20 12:11:05.992231 INFO::Found  10  batches.
2024-12-20 12:11:05.9924 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:05.992689 INFO::Using default BPPARAM
2024-12-20 12:11:05.992868 INFO::Processing subtree level 1
2024-12-20 12:11:06.080911 INFO::Processing subtree level 2
2024-12-20 12:11:06.280756 INFO::Adjusting the last 1 batches sequentially
2024-12-20 12:11:06.28605 INFO::Done
2024-12-20 12:11:06.28669 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:06.293642 INFO::ASW Batch was 0.526566287064506 prior to batch effect correction and is now 0.526566287064506 .
2024-12-20 12:11:06.29438 INFO::ASW Label was 0.30056944913587 prior to batch effect correction and is now 0.30056944913587 .
2024-12-20 12:11:06.295375 INFO::Total function execution time is  0.315367937088013  s and adjustment time is  0.29380202293396 s ( 93.16 )
2024-12-20 12:11:06.296246 INFO::Formatting Data.
2024-12-20 12:11:06.296768 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:06.297949 INFO::Removing potential empty rows and columns
2024-12-20 12:11:06.301195 INFO::Found  1000  missing values.
2024-12-20 12:11:06.319643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:06.320508 INFO::Done
2024-12-20 12:11:06.321072 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:06.327335 INFO::Starting hierarchical adjustment
2024-12-20 12:11:06.328266 INFO::Found  10  batches.
2024-12-20 12:11:07.481819 INFO::Set up parallel execution backend with 2 workers
2024-12-20 12:11:07.482402 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-12-20 12:11:08.776483 INFO::Adjusting the last 2 batches sequentially
2024-12-20 12:11:08.77815 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 12:11:08.794544 INFO::Done
2024-12-20 12:11:08.795283 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:08.800748 INFO::ASW Batch was 0.526566287064506 prior to batch effect correction and is now 0.526566287064506 .
2024-12-20 12:11:08.801319 INFO::ASW Label was 0.30056944913587 prior to batch effect correction and is now 0.30056944913587 .
2024-12-20 12:11:08.802013 INFO::Total function execution time is  2.50577092170715  s and adjustment time is  2.46643686294556 s ( 98.43 )
2024-12-20 12:11:08.969357 INFO::Formatting Data.
2024-12-20 12:11:08.970227 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:08.971541 INFO::Removing potential empty rows and columns
2024-12-20 12:11:08.972689 INFO::Found  0  missing values.
2024-12-20 12:11:08.976837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:08.977484 INFO::Done
2024-12-20 12:11:08.978012 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 12:11:08.980934 INFO::Starting hierarchical adjustment
2024-12-20 12:11:08.981696 INFO::Found  3  batches.
2024-12-20 12:11:08.982193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 12:11:08.982849 INFO::Using default BPPARAM
2024-12-20 12:11:08.983306 INFO::Processing subtree level 1
2024-12-20 12:11:09.119228 INFO::Adjusting the last 1 batches sequentially
2024-12-20 12:11:09.124752 INFO::Done
2024-12-20 12:11:09.125394 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 12:11:09.131291 INFO::ASW Batch was 0.203375530564875 prior to batch effect correction and is now -0.172416148565244 .
2024-12-20 12:11:09.131948 INFO::ASW Label was -0.193706649901848 prior to batch effect correction and is now 0.0548355039331515 .
2024-12-20 12:11:09.133569 INFO::Total function execution time is  0.163974046707153  s and adjustment time is  0.14317798614502 s ( 87.32 )
2024-12-20 12:11:09.264878 INFO::Formatting Data.
2024-12-20 12:11:09.265816 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.267114 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.26824 INFO::Found  2  missing values.
2024-12-20 12:11:09.270902 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.271419 INFO::Done
2024-12-20 12:11:09.302306 INFO::Found NA in Reference column
2024-12-20 12:11:09.312258 INFO::Require at least two references per batch.
2024-12-20 12:11:09.333875 INFO::Formatting Data.
2024-12-20 12:11:09.334742 INFO::Recognized SummarizedExperiment
2024-12-20 12:11:09.335256 INFO::Typecasting input to dataframe.
2024-12-20 12:11:09.346894 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.348136 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.351913 INFO::Found  0  missing values.
2024-12-20 12:11:09.358872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.359534 INFO::Done
2024-12-20 12:11:09.375139 INFO::Formatting Data.
2024-12-20 12:11:09.375937 INFO::Recognized SummarizedExperiment
2024-12-20 12:11:09.376425 INFO::Typecasting input to dataframe.
2024-12-20 12:11:09.393388 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.394779 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.398406 INFO::Found  0  missing values.
2024-12-20 12:11:09.409364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.410079 INFO::Done
2024-12-20 12:11:09.42569 INFO::Formatting Data.
2024-12-20 12:11:09.426543 INFO::Recognized SummarizedExperiment
2024-12-20 12:11:09.427048 INFO::Typecasting input to dataframe.
2024-12-20 12:11:09.44441 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.445622 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.44671 INFO::Found  0  missing values.
2024-12-20 12:11:09.44765 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.
2024-12-20 12:11:09.451928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.452495 INFO::Done
2024-12-20 12:11:09.463884 INFO::Formatting Data.
2024-12-20 12:11:09.464665 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.465492 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.466446 INFO::Found  0  missing values.
2024-12-20 12:11:09.469201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.469774 INFO::Done
2024-12-20 12:11:09.481833 INFO::Formatting Data.
2024-12-20 12:11:09.482639 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.483472 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.484381 INFO::Found  0  missing values.
2024-12-20 12:11:09.486953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.487446 INFO::Done
2024-12-20 12:11:09.518744 INFO::Formatting Data.
2024-12-20 12:11:09.519659 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.520778 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.52218 INFO::Found  1  missing values.
2024-12-20 12:11:09.524904 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.525478 INFO::Done
2024-12-20 12:11:09.546246 INFO::Formatting Data.
2024-12-20 12:11:09.547171 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.548045 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.548997 INFO::Found  2  missing values.
2024-12-20 12:11:09.5499 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.
2024-12-20 12:11:09.552358 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.552894 INFO::Done
2024-12-20 12:11:09.564642 INFO::Formatting Data.
2024-12-20 12:11:09.565483 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.566317 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.567232 INFO::Found  2  missing values.
2024-12-20 12:11:09.568994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.569554 INFO::Done
2024-12-20 12:11:09.581439 INFO::Formatting Data.
2024-12-20 12:11:09.582324 INFO::Typecasting input to dataframe.
2024-12-20 12:11:09.583144 INFO::Replacing NaNs with NAs.
2024-12-20 12:11:09.583994 INFO::Removing potential empty rows and columns
2024-12-20 12:11:09.585033 INFO::Found  0  missing values.
2024-12-20 12:11:09.587881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 12:11:09.588477 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 13.243   2.404  16.364

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT25.755 1.07217.423
compute_asw0.0230.0010.024
count_existing0.0050.0000.006
generate_data_covariables0.0040.0010.005
generate_dataset0.0040.0000.004