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This page was generated on 2024-05-04 11:37:27 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for BERT on palomino3


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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
StartedAt: 2024-05-04 00:50:05 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:52:17 -0400 (Sat, 04 May 2024)
EllapsedTime: 132.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 8.38   0.52   17.59
* 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:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
2024-05-04 00:51:06.513913 INFO::Formatting Data.
2024-05-04 00:51:06.516228 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:06.52556 INFO::Removing potential empty rows and columns
2024-05-04 00:51:06.726753 INFO::Found  0  missing values.
2024-05-04 00:51:06.729885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:06.730711 INFO::Done
2024-05-04 00:51:06.731444 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:06.74549 INFO::Starting hierarchical adjustment
2024-05-04 00:51:06.746567 INFO::Found  3  batches.
2024-05-04 00:51:06.74745 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:06.748797 INFO::Using default BPPARAM
2024-05-04 00:51:06.749532 INFO::Processing subtree level 1
2024-05-04 00:51:09.475924 INFO::Adjusting the last 1 batches sequentially
2024-05-04 00:51:09.478268 INFO::Done
2024-05-04 00:51:09.479501 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:09.482543 INFO::ASW Batch was -0.145405191544979 prior to batch effect correction and is now -0.145405191544979 .
2024-05-04 00:51:09.484198 INFO::Total function execution time is  2.97081589698792  s and adjustment time is  2.73182702064514 s ( 91.96 )
2024-05-04 00:51:09.504764 INFO::Formatting Data.
2024-05-04 00:51:09.505753 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:09.506823 INFO::Removing potential empty rows and columns
2024-05-04 00:51:09.508068 INFO::Found  0  missing values.
2024-05-04 00:51:09.509139 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.
2024-05-04 00:51:09.518115 INFO::Formatting Data.
2024-05-04 00:51:09.519071 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:09.52013 INFO::Removing potential empty rows and columns
2024-05-04 00:51:09.521237 INFO::Found  0  missing values.
2024-05-04 00:51:09.522283 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.
2024-05-04 00:51:09.53959 INFO::Formatting Data.
2024-05-04 00:51:09.540546 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:09.541593 INFO::Removing potential empty rows and columns
2024-05-04 00:51:09.542702 INFO::Found  0  missing values.
2024-05-04 00:51:09.543759 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.
2024-05-04 00:51:09.547489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:09.548217 INFO::Done
2024-05-04 00:51:09.548992 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:09.551074 INFO::Starting hierarchical adjustment
2024-05-04 00:51:09.551933 INFO::Found  2  batches.
2024-05-04 00:51:09.552717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:09.553558 INFO::Using default BPPARAM
2024-05-04 00:51:09.5543 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:09.555379 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:09.571545 INFO::Done
2024-05-04 00:51:09.57238 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:09.574396 INFO::ASW Batch was -0.08681077539528 prior to batch effect correction and is now -0.12437245459808 .
2024-05-04 00:51:09.575332 INFO::Total function execution time is  0.0358490943908691  s and adjustment time is  0.0197250843048096 s ( 55.02 )
2024-05-04 00:51:09.578098 INFO::Formatting Data.
2024-05-04 00:51:09.579537 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:09.588182 INFO::Formatting Data.
2024-05-04 00:51:09.589133 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:09.59018 INFO::Removing potential empty rows and columns
2024-05-04 00:51:09.591286 INFO::Found  0  missing values.
2024-05-04 00:51:09.593705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:09.594481 INFO::Done
2024-05-04 00:51:09.595302 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:09.60036 INFO::Starting hierarchical adjustment
2024-05-04 00:51:09.601334 INFO::Found  2  batches.
2024-05-04 00:51:09.602143 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:09.602949 INFO::Using default BPPARAM
2024-05-04 00:51:09.603656 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:09.604722 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:09.617088 INFO::Done
2024-05-04 00:51:09.617924 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:09.620111 INFO::ASW Batch was 0.10516449427697 prior to batch effect correction and is now -0.111603517151132 .
2024-05-04 00:51:09.6211 INFO::Total function execution time is  0.03298020362854  s and adjustment time is  0.0159420967102051 s ( 48.34 )
2024-05-04 00:51:09.622275 INFO::Formatting Data.
2024-05-04 00:51:09.62305 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:09.624067 INFO::Removing potential empty rows and columns
2024-05-04 00:51:09.625158 INFO::Found  0  missing values.
2024-05-04 00:51:09.627681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:09.628413 INFO::Done
2024-05-04 00:51:09.629131 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:09.631335 INFO::Starting hierarchical adjustment
2024-05-04 00:51:09.632214 INFO::Found  2  batches.
2024-05-04 00:51:09.632972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:09.633762 INFO::Using default BPPARAM
2024-05-04 00:51:09.634467 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:09.635526 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:09.647907 INFO::Done
2024-05-04 00:51:09.64878 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:09.651007 INFO::ASW Batch was 0.10516449427697 prior to batch effect correction and is now -0.111603517151132 .
2024-05-04 00:51:09.651978 INFO::Total function execution time is  0.0296919345855713  s and adjustment time is  0.0158100128173828 s ( 53.25 )
2024-05-04 00:51:12.443779 INFO::Formatting Data.
2024-05-04 00:51:12.445268 INFO::Recognized SummarizedExperiment
2024-05-04 00:51:12.446485 INFO::Typecasting input to dataframe.
2024-05-04 00:51:12.492474 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:12.494189 INFO::Removing potential empty rows and columns
2024-05-04 00:51:12.497601 INFO::Found  0  missing values.
2024-05-04 00:51:12.503697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:12.504611 INFO::Done
2024-05-04 00:51:12.505441 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:12.50935 INFO::Starting hierarchical adjustment
2024-05-04 00:51:12.510286 INFO::Found  2  batches.
2024-05-04 00:51:12.511019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:12.512327 INFO::Using default BPPARAM
2024-05-04 00:51:12.513116 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:12.514408 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:12.560597 INFO::Done
2024-05-04 00:51:12.561548 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:12.56552 INFO::ASW Batch was 0.0171922285075062 prior to batch effect correction and is now -0.0958361262414035 .
2024-05-04 00:51:12.566613 INFO::Total function execution time is  0.123349189758301  s and adjustment time is  0.0504150390625 s ( 40.87 )
2024-05-04 00:51:12.586133 INFO::Formatting Data.
2024-05-04 00:51:12.587103 INFO::Recognized SummarizedExperiment
2024-05-04 00:51:12.587885 INFO::Typecasting input to dataframe.
2024-05-04 00:51:12.596169 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:12.597542 INFO::Removing potential empty rows and columns
2024-05-04 00:51:12.600489 INFO::Found  0  missing values.
2024-05-04 00:51:12.606184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:12.606944 INFO::Done
2024-05-04 00:51:12.607695 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:12.611588 INFO::Starting hierarchical adjustment
2024-05-04 00:51:12.612501 INFO::Found  2  batches.
2024-05-04 00:51:12.613234 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:12.614039 INFO::Using default BPPARAM
2024-05-04 00:51:12.614783 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:12.61599 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:12.645555 INFO::Done
2024-05-04 00:51:12.647078 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:12.653378 INFO::ASW Batch was -0.0187702673788175 prior to batch effect correction and is now -0.0187702673788175 .
2024-05-04 00:51:12.655107 INFO::Total function execution time is  0.0688748359680176  s and adjustment time is  0.0330619812011719 s ( 48 )
2024-05-04 00:51:12.682833 INFO::Formatting Data.
2024-05-04 00:51:12.683874 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:12.68496 INFO::Removing potential empty rows and columns
2024-05-04 00:51:12.686175 INFO::Found  0  missing values.
2024-05-04 00:51:12.689036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:12.689837 INFO::Done
2024-05-04 00:51:12.69057 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:12.692833 INFO::Starting hierarchical adjustment
2024-05-04 00:51:12.69379 INFO::Found  3  batches.
2024-05-04 00:51:12.69457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:12.695467 INFO::Using default BPPARAM
2024-05-04 00:51:12.696351 INFO::Processing subtree level 1
2024-05-04 00:51:22.311647 INFO::Adjusting the last 1 batches sequentially
2024-05-04 00:51:22.313952 INFO::Done
2024-05-04 00:51:22.315239 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:22.318305 INFO::ASW Batch was -0.0312072636465257 prior to batch effect correction and is now -0.133940104048834 .
2024-05-04 00:51:22.319788 INFO::Total function execution time is  9.63713312149048  s and adjustment time is  9.62027406692505 s ( 99.83 )
2024-05-04 00:51:22.342416 INFO::Skipping initial DF formatting
2024-05-04 00:51:22.343693 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:22.34973 INFO::Starting hierarchical adjustment
2024-05-04 00:51:22.351102 INFO::Found  5  batches.
2024-05-04 00:51:22.352189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:22.353357 INFO::Using default BPPARAM
2024-05-04 00:51:22.354422 INFO::Processing subtree level 1
2024-05-04 00:51:25.394236 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:25.396098 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:25.419388 INFO::Done
2024-05-04 00:51:25.420837 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:25.427595 INFO::ASW Batch was 0.485235053851732 prior to batch effect correction and is now 0.485235053851732 .
2024-05-04 00:51:25.428958 INFO::ASW Label was 0.390220554666484 prior to batch effect correction and is now 0.390220554666484 .
2024-05-04 00:51:25.430549 INFO::Total function execution time is  3.08823704719543  s and adjustment time is  3.06843614578247 s ( 99.36 )
2024-05-04 00:51:25.458527 INFO::Formatting Data.
2024-05-04 00:51:25.46022 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:25.462066 INFO::Removing potential empty rows and columns
2024-05-04 00:51:25.463774 INFO::Found  0  missing values.
2024-05-04 00:51:25.469475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:25.470786 INFO::Done
2024-05-04 00:51:25.472046 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:25.476996 INFO::Starting hierarchical adjustment
2024-05-04 00:51:25.478527 INFO::Found  5  batches.
2024-05-04 00:51:25.479795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:25.481109 INFO::Using default BPPARAM
2024-05-04 00:51:25.482284 INFO::Processing subtree level 1
2024-05-04 00:51:28.553336 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:28.555575 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:28.575642 INFO::Done
2024-05-04 00:51:28.577172 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:28.582275 INFO::ASW Batch was 0.476405078306989 prior to batch effect correction and is now -0.0902934145310345 .
2024-05-04 00:51:28.583712 INFO::ASW Label was 0.298925161686522 prior to batch effect correction and is now 0.813979186250672 .
2024-05-04 00:51:28.585378 INFO::Total function execution time is  3.12694692611694  s and adjustment time is  3.09727692604065 s ( 99.05 )
2024-05-04 00:51:28.587024 INFO::Formatting Data.
2024-05-04 00:51:28.588408 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:28.590181 INFO::Removing potential empty rows and columns
2024-05-04 00:51:28.592062 INFO::Found  0  missing values.
2024-05-04 00:51:28.598059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:28.599414 INFO::Done
2024-05-04 00:51:28.600661 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:28.605593 INFO::Starting hierarchical adjustment
2024-05-04 00:51:28.607172 INFO::Found  5  batches.
2024-05-04 00:51:28.608447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:28.60981 INFO::Using default BPPARAM
2024-05-04 00:51:28.611051 INFO::Processing subtree level 1
2024-05-04 00:51:31.525636 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:31.52766 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:31.544783 INFO::Done
2024-05-04 00:51:31.546106 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:31.550417 INFO::ASW Batch was 0.476405078306989 prior to batch effect correction and is now -0.0902934145310345 .
2024-05-04 00:51:31.551571 INFO::ASW Label was 0.298925161686522 prior to batch effect correction and is now 0.813979186250672 .
2024-05-04 00:51:31.552942 INFO::Total function execution time is  2.96596789360046  s and adjustment time is  2.9378068447113 s ( 99.05 )
2024-05-04 00:51:31.572508 INFO::Formatting Data.
2024-05-04 00:51:31.574002 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:31.575571 INFO::Removing potential empty rows and columns
2024-05-04 00:51:31.577165 INFO::Found  0  missing values.
2024-05-04 00:51:31.582304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:31.58342 INFO::Done
2024-05-04 00:51:31.584247 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:31.587314 INFO::Starting hierarchical adjustment
2024-05-04 00:51:31.588207 INFO::Found  5  batches.
2024-05-04 00:51:31.588921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:31.589859 INFO::Using default BPPARAM
2024-05-04 00:51:31.59112 INFO::Processing subtree level 1
2024-05-04 00:51:34.910039 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:34.911559 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:34.924883 INFO::Done
2024-05-04 00:51:34.926137 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:34.929604 INFO::ASW Batch was 0.323010006898288 prior to batch effect correction and is now -0.0288285753784685 .
2024-05-04 00:51:34.930415 INFO::ASW Label was 0.383871206642166 prior to batch effect correction and is now 0.832425380018448 .
2024-05-04 00:51:34.931387 INFO::Total function execution time is  3.35906195640564  s and adjustment time is  3.33673310279846 s ( 99.34 )
2024-05-04 00:51:34.932332 INFO::Formatting Data.
2024-05-04 00:51:34.933248 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:34.934804 INFO::Removing potential empty rows and columns
2024-05-04 00:51:34.935891 INFO::Found  0  missing values.
2024-05-04 00:51:34.939395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:34.940125 INFO::Done
2024-05-04 00:51:34.940915 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:34.944169 INFO::Starting hierarchical adjustment
2024-05-04 00:51:34.945122 INFO::Found  5  batches.
2024-05-04 00:51:34.945859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:34.946638 INFO::Using default BPPARAM
2024-05-04 00:51:34.947501 INFO::Processing subtree level 1
2024-05-04 00:51:38.114377 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:38.116478 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:38.136101 INFO::Done
2024-05-04 00:51:38.137512 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:38.142284 INFO::ASW Batch was 0.323010006898288 prior to batch effect correction and is now -0.0288285753784685 .
2024-05-04 00:51:38.143568 INFO::ASW Label was 0.383871206642166 prior to batch effect correction and is now 0.832425380018448 .
2024-05-04 00:51:38.145115 INFO::Total function execution time is  3.21270895004272  s and adjustment time is  3.19103479385376 s ( 99.33 )
2024-05-04 00:51:38.16969 INFO::Formatting Data.
2024-05-04 00:51:38.171217 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:38.172947 INFO::Removing potential empty rows and columns
2024-05-04 00:51:38.174777 INFO::Found  0  missing values.
2024-05-04 00:51:38.178972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:38.180197 INFO::Done
2024-05-04 00:51:38.181382 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:38.186082 INFO::Starting hierarchical adjustment
2024-05-04 00:51:38.18752 INFO::Found  2  batches.
2024-05-04 00:51:38.188718 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:38.189977 INFO::Using default BPPARAM
2024-05-04 00:51:38.191076 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:38.192715 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:38.211306 INFO::Done
2024-05-04 00:51:38.21259 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:38.216959 INFO::ASW Batch was 0.476013618771348 prior to batch effect correction and is now -0.00585563331501546 .
2024-05-04 00:51:38.218133 INFO::ASW Label was 0.560975678613396 prior to batch effect correction and is now 0.898049339025324 .
2024-05-04 00:51:38.21958 INFO::Total function execution time is  0.0500259399414062  s and adjustment time is  0.023975133895874 s ( 47.93 )
2024-05-04 00:51:38.221008 INFO::Formatting Data.
2024-05-04 00:51:38.222227 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:38.223755 INFO::Removing potential empty rows and columns
2024-05-04 00:51:38.225413 INFO::Found  0  missing values.
2024-05-04 00:51:38.229179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:38.230267 INFO::Done
2024-05-04 00:51:38.231362 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:38.235747 INFO::Starting hierarchical adjustment
2024-05-04 00:51:38.237053 INFO::Found  2  batches.
2024-05-04 00:51:38.238136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:38.239343 INFO::Using default BPPARAM
2024-05-04 00:51:38.240403 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:38.242064 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:38.261161 INFO::Done
2024-05-04 00:51:38.262537 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:38.267233 INFO::ASW Batch was 0.476013618771348 prior to batch effect correction and is now -0.00585563331501546 .
2024-05-04 00:51:38.268484 INFO::ASW Label was 0.560975678613396 prior to batch effect correction and is now 0.898049339025324 .
2024-05-04 00:51:38.269965 INFO::Total function execution time is  0.0489609241485596  s and adjustment time is  0.0242509841918945 s ( 49.53 )
2024-05-04 00:51:38.291591 INFO::Formatting Data.
2024-05-04 00:51:38.293091 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:38.294759 INFO::Removing potential empty rows and columns
2024-05-04 00:51:38.296412 INFO::Found  0  missing values.
2024-05-04 00:51:38.29968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:38.300842 INFO::Done
2024-05-04 00:51:38.302014 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:38.305087 INFO::Starting hierarchical adjustment
2024-05-04 00:51:38.306438 INFO::Found  2  batches.
2024-05-04 00:51:38.307581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:38.308833 INFO::Using default BPPARAM
2024-05-04 00:51:38.309998 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:38.311661 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:38.352536 INFO::Done
2024-05-04 00:51:38.353917 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:38.357156 INFO::ASW Batch was 0.0107090837591648 prior to batch effect correction and is now -0.0847022934874481 .
2024-05-04 00:51:38.35881 INFO::Total function execution time is  0.0673089027404785  s and adjustment time is  0.0462319850921631 s ( 68.69 )
2024-05-04 00:51:38.381886 INFO::Formatting Data.
2024-05-04 00:51:38.383431 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:38.385126 INFO::Removing potential empty rows and columns
2024-05-04 00:51:38.386902 INFO::Found  0  missing values.
2024-05-04 00:51:38.388767 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.
2024-05-04 00:51:38.395053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:38.396284 INFO::Done
2024-05-04 00:51:38.397523 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:38.402105 INFO::Starting hierarchical adjustment
2024-05-04 00:51:38.403546 INFO::Found  2  batches.
2024-05-04 00:51:38.404704 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:38.405956 INFO::Using default BPPARAM
2024-05-04 00:51:38.407117 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:38.408857 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:38.431757 INFO::Done
2024-05-04 00:51:38.433169 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:38.437959 INFO::ASW Batch was 0.622071545697545 prior to batch effect correction and is now -0.0170107369091014 .
2024-05-04 00:51:38.439275 INFO::ASW Label was 0.469572516824201 prior to batch effect correction and is now 0.928517955530619 .
2024-05-04 00:51:38.440828 INFO::Total function execution time is  0.0591239929199219  s and adjustment time is  0.0283548831939697 s ( 47.96 )
2024-05-04 00:51:38.442347 INFO::Formatting Data.
2024-05-04 00:51:38.443635 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:38.445403 INFO::Removing potential empty rows and columns
2024-05-04 00:51:38.447152 INFO::Found  0  missing values.
2024-05-04 00:51:38.448845 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.
2024-05-04 00:51:38.455082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:38.456257 INFO::Done
2024-05-04 00:51:38.457395 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:38.461787 INFO::Starting hierarchical adjustment
2024-05-04 00:51:38.463032 INFO::Found  2  batches.
2024-05-04 00:51:38.464116 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:38.465377 INFO::Using default BPPARAM
2024-05-04 00:51:38.466519 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:51:38.468245 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:51:38.491296 INFO::Done
2024-05-04 00:51:38.492669 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:38.497289 INFO::ASW Batch was 0.622071545697545 prior to batch effect correction and is now -0.0170107369091014 .
2024-05-04 00:51:38.498553 INFO::ASW Label was 0.469572516824201 prior to batch effect correction and is now 0.928517955530619 .
2024-05-04 00:51:38.500107 INFO::Total function execution time is  0.0577528476715088  s and adjustment time is  0.0283529758453369 s ( 49.09 )
2024-05-04 00:51:38.790118 INFO::Formatting Data.
2024-05-04 00:51:38.791852 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:38.793916 INFO::Removing potential empty rows and columns
2024-05-04 00:51:38.795428 INFO::Found  0  missing values.
2024-05-04 00:51:38.798828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:38.799685 INFO::Done
2024-05-04 00:51:38.800495 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:38.802982 INFO::Starting hierarchical adjustment
2024-05-04 00:51:38.803989 INFO::Found  3  batches.
2024-05-04 00:51:38.804848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:38.805744 INFO::Using default BPPARAM
2024-05-04 00:51:38.80659 INFO::Processing subtree level 1
2024-05-04 00:51:41.688433 INFO::Adjusting the last 1 batches sequentially
2024-05-04 00:51:41.690645 INFO::Done
2024-05-04 00:51:41.691874 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:41.694895 INFO::ASW Batch was -0.000808513950351455 prior to batch effect correction and is now -0.000808513950351455 .
2024-05-04 00:51:41.696394 INFO::Total function execution time is  2.90643501281738  s and adjustment time is  2.88678908348083 s ( 99.32 )
2024-05-04 00:51:41.698033 INFO::Formatting Data.
2024-05-04 00:51:41.69926 INFO::Typecasting input to dataframe.
2024-05-04 00:51:41.700634 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:41.702171 INFO::Removing potential empty rows and columns
2024-05-04 00:51:41.703825 INFO::Found  0  missing values.
2024-05-04 00:51:41.707796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:41.708895 INFO::Done
2024-05-04 00:51:41.710004 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:41.712899 INFO::Starting hierarchical adjustment
2024-05-04 00:51:41.713835 INFO::Found  3  batches.
2024-05-04 00:51:41.714544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:41.71532 INFO::Using default BPPARAM
2024-05-04 00:51:41.716011 INFO::Processing subtree level 1
2024-05-04 00:51:44.564204 INFO::Adjusting the last 1 batches sequentially
2024-05-04 00:51:44.56677 INFO::Done
2024-05-04 00:51:44.568293 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:44.572159 INFO::ASW Batch was -0.000808513950351455 prior to batch effect correction and is now -0.000808513950351455 .
2024-05-04 00:51:44.573687 INFO::Total function execution time is  2.87566208839417  s and adjustment time is  2.85299301147461 s ( 99.21 )
2024-05-04 00:51:44.593733 INFO::Formatting Data.
2024-05-04 00:51:44.594672 INFO::Typecasting input to dataframe.
2024-05-04 00:51:44.595751 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:44.596966 INFO::Removing potential empty rows and columns
2024-05-04 00:51:44.598112 INFO::Found  0  missing values.
2024-05-04 00:51:44.601181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:44.602019 INFO::Done
2024-05-04 00:51:44.602725 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:44.604869 INFO::Starting hierarchical adjustment
2024-05-04 00:51:44.606076 INFO::Found  3  batches.
2024-05-04 00:51:44.607261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:44.608433 INFO::Using default BPPARAM
2024-05-04 00:51:44.609539 INFO::Processing subtree level 1
2024-05-04 00:51:47.202731 INFO::Adjusting the last 1 batches sequentially
2024-05-04 00:51:47.20522 INFO::Done
2024-05-04 00:51:47.206692 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:47.210242 INFO::ASW Batch was -0.0998359029723796 prior to batch effect correction and is now -0.0998359029723796 .
2024-05-04 00:51:47.21195 INFO::Total function execution time is  2.61821508407593  s and adjustment time is  2.59930419921875 s ( 99.28 )
2024-05-04 00:51:50.426879 INFO::Formatting Data.
2024-05-04 00:51:50.428451 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:50.430493 INFO::Removing potential empty rows and columns
2024-05-04 00:51:50.434188 INFO::Found  1000  missing values.
2024-05-04 00:51:50.451664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:50.452632 INFO::Done
2024-05-04 00:51:50.45338 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:50.460126 INFO::Starting hierarchical adjustment
2024-05-04 00:51:50.461178 INFO::Found  10  batches.
2024-05-04 00:51:50.461911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:51:50.462687 INFO::Using default BPPARAM
2024-05-04 00:51:50.463391 INFO::Processing subtree level 1
2024-05-04 00:51:53.378977 INFO::Processing subtree level 2
2024-05-04 00:51:56.228496 INFO::Adjusting the last 1 batches sequentially
2024-05-04 00:51:56.231064 INFO::Done
2024-05-04 00:51:56.232348 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:51:56.241439 INFO::ASW Batch was 0.447758000398614 prior to batch effect correction and is now 0.447758000398614 .
2024-05-04 00:51:56.242857 INFO::ASW Label was 0.370551464761479 prior to batch effect correction and is now 0.370551464761479 .
2024-05-04 00:51:56.244534 INFO::Total function execution time is  5.81779003143311  s and adjustment time is  5.76997900009155 s ( 99.18 )
2024-05-04 00:51:56.246101 INFO::Formatting Data.
2024-05-04 00:51:56.24745 INFO::Replacing NaNs with NAs.
2024-05-04 00:51:56.249431 INFO::Removing potential empty rows and columns
2024-05-04 00:51:56.253143 INFO::Found  1000  missing values.
2024-05-04 00:51:56.269969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:51:56.271142 INFO::Done
2024-05-04 00:51:56.271942 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:51:56.278221 INFO::Starting hierarchical adjustment
2024-05-04 00:51:56.279281 INFO::Found  10  batches.
2024-05-04 00:51:56.963081 INFO::Set up parallel execution backend with 2 workers
2024-05-04 00:51:56.964095 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-04 00:52:00.086788 INFO::Adjusting the last 2 batches sequentially
2024-05-04 00:52:00.088284 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 00:52:00.10292 INFO::Done
2024-05-04 00:52:00.103816 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:52:00.10964 INFO::ASW Batch was 0.447758000398614 prior to batch effect correction and is now 0.447758000398614 .
2024-05-04 00:52:00.110554 INFO::ASW Label was 0.370551464761479 prior to batch effect correction and is now 0.370551464761479 .
2024-05-04 00:52:00.111526 INFO::Total function execution time is  3.8655309677124  s and adjustment time is  3.82377696037292 s ( 98.92 )
2024-05-04 00:52:03.169854 INFO::Formatting Data.
2024-05-04 00:52:03.171081 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:03.172236 INFO::Removing potential empty rows and columns
2024-05-04 00:52:03.173371 INFO::Found  0  missing values.
2024-05-04 00:52:03.176961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:03.177783 INFO::Done
2024-05-04 00:52:03.178513 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 00:52:03.181549 INFO::Starting hierarchical adjustment
2024-05-04 00:52:03.182552 INFO::Found  3  batches.
2024-05-04 00:52:03.183285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 00:52:03.184199 INFO::Using default BPPARAM
2024-05-04 00:52:03.184921 INFO::Processing subtree level 1
2024-05-04 00:52:06.122851 INFO::Adjusting the last 1 batches sequentially
2024-05-04 00:52:06.125229 INFO::Done
2024-05-04 00:52:06.126753 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 00:52:06.13122 INFO::ASW Batch was 0.178413346828993 prior to batch effect correction and is now -0.126787031745286 .
2024-05-04 00:52:06.132512 INFO::ASW Label was -0.171557812150079 prior to batch effect correction and is now 0.0766585624315616 .
2024-05-04 00:52:06.134028 INFO::Total function execution time is  2.96425986289978  s and adjustment time is  2.94280004501343 s ( 99.28 )
2024-05-04 00:52:06.331304 INFO::Formatting Data.
2024-05-04 00:52:06.332368 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.333458 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.334619 INFO::Found  2  missing values.
2024-05-04 00:52:06.337172 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.337908 INFO::Done
2024-05-04 00:52:06.382806 INFO::Found NA in Reference column
2024-05-04 00:52:06.403698 INFO::Require at least two references per batch.
2024-05-04 00:52:06.435446 INFO::Formatting Data.
2024-05-04 00:52:06.436909 INFO::Recognized SummarizedExperiment
2024-05-04 00:52:06.438105 INFO::Typecasting input to dataframe.
2024-05-04 00:52:06.449682 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.451678 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.456059 INFO::Found  0  missing values.
2024-05-04 00:52:06.464088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.465467 INFO::Done
2024-05-04 00:52:06.486169 INFO::Formatting Data.
2024-05-04 00:52:06.487602 INFO::Recognized SummarizedExperiment
2024-05-04 00:52:06.488829 INFO::Typecasting input to dataframe.
2024-05-04 00:52:06.510894 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.512968 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.517424 INFO::Found  0  missing values.
2024-05-04 00:52:06.529589 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.530984 INFO::Done
2024-05-04 00:52:06.552019 INFO::Formatting Data.
2024-05-04 00:52:06.553513 INFO::Recognized SummarizedExperiment
2024-05-04 00:52:06.554714 INFO::Typecasting input to dataframe.
2024-05-04 00:52:06.576019 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.577885 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.57982 INFO::Found  0  missing values.
2024-05-04 00:52:06.58156 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.
2024-05-04 00:52:06.587414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.588679 INFO::Done
2024-05-04 00:52:06.607731 INFO::Formatting Data.
2024-05-04 00:52:06.609255 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.610927 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.612689 INFO::Found  0  missing values.
2024-05-04 00:52:06.616713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.617912 INFO::Done
2024-05-04 00:52:06.638368 INFO::Formatting Data.
2024-05-04 00:52:06.639925 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.641619 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.64344 INFO::Found  0  missing values.
2024-05-04 00:52:06.647523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.648719 INFO::Done
2024-05-04 00:52:06.702694 INFO::Formatting Data.
2024-05-04 00:52:06.704301 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.706207 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.708156 INFO::Found  1  missing values.
2024-05-04 00:52:06.711818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.713034 INFO::Done
2024-05-04 00:52:06.747742 INFO::Formatting Data.
2024-05-04 00:52:06.749284 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.750879 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.752558 INFO::Found  2  missing values.
2024-05-04 00:52:06.754216 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.
2024-05-04 00:52:06.757358 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.758493 INFO::Done
2024-05-04 00:52:06.777776 INFO::Formatting Data.
2024-05-04 00:52:06.779342 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.780993 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.782693 INFO::Found  2  missing values.
2024-05-04 00:52:06.785241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.786433 INFO::Done
2024-05-04 00:52:06.807629 INFO::Formatting Data.
2024-05-04 00:52:06.809162 INFO::Typecasting input to dataframe.
2024-05-04 00:52:06.810867 INFO::Replacing NaNs with NAs.
2024-05-04 00:52:06.812596 INFO::Removing potential empty rows and columns
2024-05-04 00:52:06.814506 INFO::Found  0  missing values.
2024-05-04 00:52:06.818681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 00:52:06.820055 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
  28.82    1.53   74.76 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT 8.38 0.5217.59
compute_asw0.030.000.03
count_existing0.020.000.02
generate_data_covariables0.010.000.01
generate_dataset0.020.000.02