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This page was generated on 2024-05-04 11:38:53 -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 lconway


To the developers/maintainers of the BERT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BERT
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz
StartedAt: 2024-05-03 20:19:00 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 20:20:24 -0400 (Fri, 03 May 2024)
EllapsedTime: 83.4 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 27.551  1.633   19.82
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

BERT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BERT’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2024-05-03 20:20:03.100859 INFO::Formatting Data.
2024-05-03 20:20:03.10471 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:03.116437 INFO::Removing potential empty rows and columns
2024-05-03 20:20:03.402852 INFO::Found  0  missing values.
2024-05-03 20:20:03.406263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:03.40688 INFO::Done
2024-05-03 20:20:03.407399 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:03.421779 INFO::Starting hierarchical adjustment
2024-05-03 20:20:03.422903 INFO::Found  3  batches.
2024-05-03 20:20:03.423598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:03.425132 INFO::Using default BPPARAM
2024-05-03 20:20:03.425967 INFO::Processing subtree level 1
2024-05-03 20:20:03.583302 INFO::Adjusting the last 1 batches sequentially
2024-05-03 20:20:03.587814 INFO::Done
2024-05-03 20:20:03.588811 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:03.595477 INFO::ASW Batch was -0.120286556723252 prior to batch effect correction and is now -0.120286556723252 .
2024-05-03 20:20:03.597599 INFO::Total function execution time is  0.497148036956787  s and adjustment time is  0.165104866027832 s ( 33.21 )
2024-05-03 20:20:03.620309 INFO::Formatting Data.
2024-05-03 20:20:03.621653 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:03.623209 INFO::Removing potential empty rows and columns
2024-05-03 20:20:03.62475 INFO::Found  0  missing values.
2024-05-03 20:20:03.626199 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.
2024-05-03 20:20:03.643036 INFO::Formatting Data.
2024-05-03 20:20:03.644105 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:03.645385 INFO::Removing potential empty rows and columns
2024-05-03 20:20:03.646872 INFO::Found  0  missing values.
2024-05-03 20:20:03.648474 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.
2024-05-03 20:20:03.671719 INFO::Formatting Data.
2024-05-03 20:20:03.672531 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:03.673394 INFO::Removing potential empty rows and columns
2024-05-03 20:20:03.674328 INFO::Found  0  missing values.
2024-05-03 20:20:03.67519 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.
2024-05-03 20:20:03.679072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:03.679589 INFO::Done
2024-05-03 20:20:03.680052 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:03.681907 INFO::Starting hierarchical adjustment
2024-05-03 20:20:03.682541 INFO::Found  2  batches.
2024-05-03 20:20:03.683009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:03.683578 INFO::Using default BPPARAM
2024-05-03 20:20:03.684035 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:03.68485 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:03.708432 INFO::Done
2024-05-03 20:20:03.709081 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:03.710927 INFO::ASW Batch was -0.057844070779596 prior to batch effect correction and is now -0.103721863768822 .
2024-05-03 20:20:03.711655 INFO::Total function execution time is  0.0400331020355225  s and adjustment time is  0.0259909629821777 s ( 64.92 )
2024-05-03 20:20:03.714223 INFO::Formatting Data.
2024-05-03 20:20:03.714819 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:03.724083 INFO::Formatting Data.
2024-05-03 20:20:03.725125 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:03.726371 INFO::Removing potential empty rows and columns
2024-05-03 20:20:03.727807 INFO::Found  0  missing values.
2024-05-03 20:20:03.732075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:03.73286 INFO::Done
2024-05-03 20:20:03.733578 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:03.736239 INFO::Starting hierarchical adjustment
2024-05-03 20:20:03.737173 INFO::Found  2  batches.
2024-05-03 20:20:03.737876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:03.738663 INFO::Using default BPPARAM
2024-05-03 20:20:03.73936 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:03.740803 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:03.764995 INFO::Done
2024-05-03 20:20:03.765978 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:03.768843 INFO::ASW Batch was 0.0724735123027953 prior to batch effect correction and is now -0.0998347410357455 .
2024-05-03 20:20:03.769976 INFO::Total function execution time is  0.0459609031677246  s and adjustment time is  0.0279688835144043 s ( 60.85 )
2024-05-03 20:20:03.771037 INFO::Formatting Data.
2024-05-03 20:20:03.771629 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:03.773103 INFO::Removing potential empty rows and columns
2024-05-03 20:20:03.774365 INFO::Found  0  missing values.
2024-05-03 20:20:03.778365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:03.779264 INFO::Done
2024-05-03 20:20:03.780231 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:03.782194 INFO::Starting hierarchical adjustment
2024-05-03 20:20:03.782821 INFO::Found  2  batches.
2024-05-03 20:20:03.783294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:03.78382 INFO::Using default BPPARAM
2024-05-03 20:20:03.784276 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:03.7851 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:03.80535 INFO::Done
2024-05-03 20:20:03.806259 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:03.808224 INFO::ASW Batch was 0.0724735123027953 prior to batch effect correction and is now -0.0998347410357455 .
2024-05-03 20:20:03.809002 INFO::Total function execution time is  0.0379848480224609  s and adjustment time is  0.0225839614868164 s ( 59.46 )
2024-05-03 20:20:06.396464 INFO::Formatting Data.
2024-05-03 20:20:06.397465 INFO::Recognized SummarizedExperiment
2024-05-03 20:20:06.398229 INFO::Typecasting input to dataframe.
2024-05-03 20:20:07.255469 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:07.256739 INFO::Removing potential empty rows and columns
2024-05-03 20:20:07.259488 INFO::Found  0  missing values.
2024-05-03 20:20:07.266406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:07.267041 INFO::Done
2024-05-03 20:20:07.2677 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:07.270949 INFO::Starting hierarchical adjustment
2024-05-03 20:20:07.271535 INFO::Found  2  batches.
2024-05-03 20:20:07.271994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:07.273024 INFO::Using default BPPARAM
2024-05-03 20:20:07.273504 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:07.274431 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:07.32178 INFO::Done
2024-05-03 20:20:07.322666 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:07.327261 INFO::ASW Batch was -0.00653190866031194 prior to batch effect correction and is now -0.0886143803572082 .
2024-05-03 20:20:07.328353 INFO::Total function execution time is  0.932377815246582  s and adjustment time is  0.0502808094024658 s ( 5.39 )
2024-05-03 20:20:07.352122 INFO::Formatting Data.
2024-05-03 20:20:07.352869 INFO::Recognized SummarizedExperiment
2024-05-03 20:20:07.353455 INFO::Typecasting input to dataframe.
2024-05-03 20:20:07.360977 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:07.361977 INFO::Removing potential empty rows and columns
2024-05-03 20:20:07.364573 INFO::Found  0  missing values.
2024-05-03 20:20:07.370973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:07.371539 INFO::Done
2024-05-03 20:20:07.3725 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:07.376362 INFO::Starting hierarchical adjustment
2024-05-03 20:20:07.377382 INFO::Found  2  batches.
2024-05-03 20:20:07.378109 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:07.378898 INFO::Using default BPPARAM
2024-05-03 20:20:07.379557 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:07.380906 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:07.411179 INFO::Done
2024-05-03 20:20:07.412059 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:07.41679 INFO::ASW Batch was 0.00772545005685677 prior to batch effect correction and is now 0.00772545005685677 .
2024-05-03 20:20:07.417657 INFO::Total function execution time is  0.0654420852661133  s and adjustment time is  0.0339550971984863 s ( 51.89 )
2024-05-03 20:20:07.43997 INFO::Formatting Data.
2024-05-03 20:20:07.440865 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:07.441968 INFO::Removing potential empty rows and columns
2024-05-03 20:20:07.44283 INFO::Found  0  missing values.
2024-05-03 20:20:07.446827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:07.447628 INFO::Done
2024-05-03 20:20:07.44831 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:07.450667 INFO::Starting hierarchical adjustment
2024-05-03 20:20:07.451264 INFO::Found  3  batches.
2024-05-03 20:20:07.451686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:07.452303 INFO::Using default BPPARAM
2024-05-03 20:20:07.453254 INFO::Processing subtree level 1
2024-05-03 20:20:07.760561 INFO::Adjusting the last 1 batches sequentially
2024-05-03 20:20:07.768699 INFO::Done
2024-05-03 20:20:07.769808 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:07.776102 INFO::ASW Batch was -0.0166363160470837 prior to batch effect correction and is now -0.181465454160527 .
2024-05-03 20:20:07.779968 INFO::Total function execution time is  0.339025974273682  s and adjustment time is  0.31746506690979 s ( 93.64 )
2024-05-03 20:20:07.805826 INFO::Skipping initial DF formatting
2024-05-03 20:20:07.806565 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:07.811098 INFO::Starting hierarchical adjustment
2024-05-03 20:20:07.812298 INFO::Found  5  batches.
2024-05-03 20:20:07.812861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:07.81345 INFO::Using default BPPARAM
2024-05-03 20:20:07.813938 INFO::Processing subtree level 1
2024-05-03 20:20:08.046999 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:08.05923 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:08.10123 INFO::Done
2024-05-03 20:20:08.101942 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:08.107558 INFO::ASW Batch was 0.483339960802334 prior to batch effect correction and is now 0.483339960802334 .
2024-05-03 20:20:08.108376 INFO::ASW Label was 0.400253892629455 prior to batch effect correction and is now 0.400253892629455 .
2024-05-03 20:20:08.109426 INFO::Total function execution time is  0.303670883178711  s and adjustment time is  0.289189100265503 s ( 95.23 )
2024-05-03 20:20:08.137345 INFO::Formatting Data.
2024-05-03 20:20:08.138533 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:08.139793 INFO::Removing potential empty rows and columns
2024-05-03 20:20:08.140977 INFO::Found  0  missing values.
2024-05-03 20:20:08.145426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:08.146034 INFO::Done
2024-05-03 20:20:08.146532 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:08.150126 INFO::Starting hierarchical adjustment
2024-05-03 20:20:08.150942 INFO::Found  5  batches.
2024-05-03 20:20:08.151554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:08.152575 INFO::Using default BPPARAM
2024-05-03 20:20:08.153278 INFO::Processing subtree level 1
2024-05-03 20:20:08.297752 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:08.326493 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:08.360402 INFO::Done
2024-05-03 20:20:08.361208 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:08.365572 INFO::ASW Batch was 0.388321850507152 prior to batch effect correction and is now 0.0217418629085879 .
2024-05-03 20:20:08.366831 INFO::ASW Label was 0.402434912199033 prior to batch effect correction and is now 0.713127102926085 .
2024-05-03 20:20:08.368518 INFO::Total function execution time is  0.231243133544922  s and adjustment time is  0.209626913070679 s ( 90.65 )
2024-05-03 20:20:08.369838 INFO::Formatting Data.
2024-05-03 20:20:08.370696 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:08.371652 INFO::Removing potential empty rows and columns
2024-05-03 20:20:08.37265 INFO::Found  0  missing values.
2024-05-03 20:20:08.376615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:08.377118 INFO::Done
2024-05-03 20:20:08.377609 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:08.38117 INFO::Starting hierarchical adjustment
2024-05-03 20:20:08.382015 INFO::Found  5  batches.
2024-05-03 20:20:08.382501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:08.383735 INFO::Using default BPPARAM
2024-05-03 20:20:08.384365 INFO::Processing subtree level 1
2024-05-03 20:20:08.535353 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:08.552826 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:08.589299 INFO::Done
2024-05-03 20:20:08.590251 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:08.594211 INFO::ASW Batch was 0.388321850507152 prior to batch effect correction and is now 0.0217418629085879 .
2024-05-03 20:20:08.595938 INFO::ASW Label was 0.402434912199033 prior to batch effect correction and is now 0.713127102926085 .
2024-05-03 20:20:08.597285 INFO::Total function execution time is  0.227377891540527  s and adjustment time is  0.207360029220581 s ( 91.2 )
2024-05-03 20:20:08.61749 INFO::Formatting Data.
2024-05-03 20:20:08.618226 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:08.620313 INFO::Removing potential empty rows and columns
2024-05-03 20:20:08.621769 INFO::Found  0  missing values.
2024-05-03 20:20:08.628447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:08.629442 INFO::Done
2024-05-03 20:20:08.630427 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:08.635304 INFO::Starting hierarchical adjustment
2024-05-03 20:20:08.63607 INFO::Found  5  batches.
2024-05-03 20:20:08.636574 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:08.63713 INFO::Using default BPPARAM
2024-05-03 20:20:08.637621 INFO::Processing subtree level 1
2024-05-03 20:20:08.764074 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:08.785646 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:08.820887 INFO::Done
2024-05-03 20:20:08.82175 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:08.828126 INFO::ASW Batch was 0.321707222704228 prior to batch effect correction and is now -0.0975173017115611 .
2024-05-03 20:20:08.829381 INFO::ASW Label was 0.24791787527603 prior to batch effect correction and is now 0.826398321893765 .
2024-05-03 20:20:08.831802 INFO::Total function execution time is  0.214236974716187  s and adjustment time is  0.184905052185059 s ( 86.31 )
2024-05-03 20:20:08.832743 INFO::Formatting Data.
2024-05-03 20:20:08.833714 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:08.834923 INFO::Removing potential empty rows and columns
2024-05-03 20:20:08.835845 INFO::Found  0  missing values.
2024-05-03 20:20:08.84072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:08.841632 INFO::Done
2024-05-03 20:20:08.842388 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:08.846843 INFO::Starting hierarchical adjustment
2024-05-03 20:20:08.847778 INFO::Found  5  batches.
2024-05-03 20:20:08.848513 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:08.849491 INFO::Using default BPPARAM
2024-05-03 20:20:08.85026 INFO::Processing subtree level 1
2024-05-03 20:20:09.011677 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:09.021995 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:09.049463 INFO::Done
2024-05-03 20:20:09.050471 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:09.054854 INFO::ASW Batch was 0.321707222704228 prior to batch effect correction and is now -0.0975173017115611 .
2024-05-03 20:20:09.055509 INFO::ASW Label was 0.24791787527603 prior to batch effect correction and is now 0.826398321893765 .
2024-05-03 20:20:09.056443 INFO::Total function execution time is  0.223758935928345  s and adjustment time is  0.201925992965698 s ( 90.24 )
2024-05-03 20:20:09.080465 INFO::Formatting Data.
2024-05-03 20:20:09.081219 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:09.082964 INFO::Removing potential empty rows and columns
2024-05-03 20:20:09.08394 INFO::Found  0  missing values.
2024-05-03 20:20:09.086622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:09.087969 INFO::Done
2024-05-03 20:20:09.088722 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:09.091661 INFO::Starting hierarchical adjustment
2024-05-03 20:20:09.092306 INFO::Found  2  batches.
2024-05-03 20:20:09.092756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:09.09332 INFO::Using default BPPARAM
2024-05-03 20:20:09.094635 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:09.09548 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:09.112942 INFO::Done
2024-05-03 20:20:09.113768 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:09.116512 INFO::ASW Batch was 0.172295345794398 prior to batch effect correction and is now 0.00770917301012675 .
2024-05-03 20:20:09.117423 INFO::ASW Label was 0.817258247890259 prior to batch effect correction and is now 0.932371105680503 .
2024-05-03 20:20:09.118679 INFO::Total function execution time is  0.0382671356201172  s and adjustment time is  0.0206770896911621 s ( 54.03 )
2024-05-03 20:20:09.119424 INFO::Formatting Data.
2024-05-03 20:20:09.119964 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:09.120776 INFO::Removing potential empty rows and columns
2024-05-03 20:20:09.121904 INFO::Found  0  missing values.
2024-05-03 20:20:09.125887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:09.126397 INFO::Done
2024-05-03 20:20:09.12686 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:09.129357 INFO::Starting hierarchical adjustment
2024-05-03 20:20:09.1303 INFO::Found  2  batches.
2024-05-03 20:20:09.131211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:09.131878 INFO::Using default BPPARAM
2024-05-03 20:20:09.1326 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:09.133993 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:09.147594 INFO::Done
2024-05-03 20:20:09.148203 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:09.150675 INFO::ASW Batch was 0.172295345794398 prior to batch effect correction and is now 0.00770917301012675 .
2024-05-03 20:20:09.151204 INFO::ASW Label was 0.817258247890259 prior to batch effect correction and is now 0.932371105680503 .
2024-05-03 20:20:09.151884 INFO::Total function execution time is  0.0324921607971191  s and adjustment time is  0.017719030380249 s ( 54.53 )
2024-05-03 20:20:09.168789 INFO::Formatting Data.
2024-05-03 20:20:09.169835 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:09.1711 INFO::Removing potential empty rows and columns
2024-05-03 20:20:09.172336 INFO::Found  0  missing values.
2024-05-03 20:20:09.175968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:09.176707 INFO::Done
2024-05-03 20:20:09.177377 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:09.179848 INFO::Starting hierarchical adjustment
2024-05-03 20:20:09.18079 INFO::Found  2  batches.
2024-05-03 20:20:09.181471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:09.182263 INFO::Using default BPPARAM
2024-05-03 20:20:09.182941 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:09.184122 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:09.216079 INFO::Done
2024-05-03 20:20:09.21671 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:09.218714 INFO::ASW Batch was -0.0766885069280361 prior to batch effect correction and is now -0.147876115971728 .
2024-05-03 20:20:09.219857 INFO::Total function execution time is  0.0511898994445801  s and adjustment time is  0.0355069637298584 s ( 69.36 )
2024-05-03 20:20:09.237486 INFO::Formatting Data.
2024-05-03 20:20:09.238171 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:09.238948 INFO::Removing potential empty rows and columns
2024-05-03 20:20:09.239999 INFO::Found  0  missing values.
2024-05-03 20:20:09.241295 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.
2024-05-03 20:20:09.246329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:09.246859 INFO::Done
2024-05-03 20:20:09.247351 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:09.250169 INFO::Starting hierarchical adjustment
2024-05-03 20:20:09.250792 INFO::Found  2  batches.
2024-05-03 20:20:09.251277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:09.251798 INFO::Using default BPPARAM
2024-05-03 20:20:09.252237 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:09.253071 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:09.27287 INFO::Done
2024-05-03 20:20:09.273814 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:09.277847 INFO::ASW Batch was 0.636988876765494 prior to batch effect correction and is now 0.00533337824906933 .
2024-05-03 20:20:09.278452 INFO::ASW Label was 0.342694149461207 prior to batch effect correction and is now 0.896514689612021 .
2024-05-03 20:20:09.279311 INFO::Total function execution time is  0.0418450832366943  s and adjustment time is  0.0221209526062012 s ( 52.86 )
2024-05-03 20:20:09.280489 INFO::Formatting Data.
2024-05-03 20:20:09.281179 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:09.282185 INFO::Removing potential empty rows and columns
2024-05-03 20:20:09.283659 INFO::Found  0  missing values.
2024-05-03 20:20:09.284511 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.
2024-05-03 20:20:09.289993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:09.290736 INFO::Done
2024-05-03 20:20:09.291513 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:09.295005 INFO::Starting hierarchical adjustment
2024-05-03 20:20:09.296027 INFO::Found  2  batches.
2024-05-03 20:20:09.296813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:09.297741 INFO::Using default BPPARAM
2024-05-03 20:20:09.298505 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:09.300014 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:09.321904 INFO::Done
2024-05-03 20:20:09.322555 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:09.326849 INFO::ASW Batch was 0.636988876765494 prior to batch effect correction and is now 0.00533337824906933 .
2024-05-03 20:20:09.327607 INFO::ASW Label was 0.342694149461207 prior to batch effect correction and is now 0.896514689612021 .
2024-05-03 20:20:09.328877 INFO::Total function execution time is  0.0483479499816895  s and adjustment time is  0.0261011123657227 s ( 53.99 )
2024-05-03 20:20:09.590686 INFO::Formatting Data.
2024-05-03 20:20:09.59139 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:09.592178 INFO::Removing potential empty rows and columns
2024-05-03 20:20:09.593041 INFO::Found  0  missing values.
2024-05-03 20:20:09.596042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:09.596569 INFO::Done
2024-05-03 20:20:09.597016 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:09.599253 INFO::Starting hierarchical adjustment
2024-05-03 20:20:09.600343 INFO::Found  3  batches.
2024-05-03 20:20:09.601046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:09.601844 INFO::Using default BPPARAM
2024-05-03 20:20:09.60254 INFO::Processing subtree level 1
2024-05-03 20:20:09.745496 INFO::Adjusting the last 1 batches sequentially
2024-05-03 20:20:09.754013 INFO::Done
2024-05-03 20:20:09.75672 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:09.765346 INFO::ASW Batch was -0.0138208720575524 prior to batch effect correction and is now -0.0138208720575524 .
2024-05-03 20:20:09.767499 INFO::Total function execution time is  0.176122903823853  s and adjustment time is  0.153844118118286 s ( 87.35 )
2024-05-03 20:20:09.770051 INFO::Formatting Data.
2024-05-03 20:20:09.771106 INFO::Typecasting input to dataframe.
2024-05-03 20:20:09.772355 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:09.774284 INFO::Removing potential empty rows and columns
2024-05-03 20:20:09.775667 INFO::Found  0  missing values.
2024-05-03 20:20:09.78018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:09.78086 INFO::Done
2024-05-03 20:20:09.781772 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:09.784714 INFO::Starting hierarchical adjustment
2024-05-03 20:20:09.786076 INFO::Found  3  batches.
2024-05-03 20:20:09.786728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:09.787846 INFO::Using default BPPARAM
2024-05-03 20:20:09.788356 INFO::Processing subtree level 1
2024-05-03 20:20:09.916398 INFO::Adjusting the last 1 batches sequentially
2024-05-03 20:20:09.927813 INFO::Done
2024-05-03 20:20:09.930183 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:09.938864 INFO::ASW Batch was -0.0138208720575524 prior to batch effect correction and is now -0.0138208720575524 .
2024-05-03 20:20:09.940967 INFO::Total function execution time is  0.17094087600708  s and adjustment time is  0.141853094100952 s ( 82.98 )
2024-05-03 20:20:09.969501 INFO::Formatting Data.
2024-05-03 20:20:09.97106 INFO::Typecasting input to dataframe.
2024-05-03 20:20:09.971993 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:09.972916 INFO::Removing potential empty rows and columns
2024-05-03 20:20:09.975561 INFO::Found  0  missing values.
2024-05-03 20:20:09.978628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:09.979182 INFO::Done
2024-05-03 20:20:09.979653 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:09.981457 INFO::Starting hierarchical adjustment
2024-05-03 20:20:09.982067 INFO::Found  3  batches.
2024-05-03 20:20:09.982545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:09.983388 INFO::Using default BPPARAM
2024-05-03 20:20:09.983858 INFO::Processing subtree level 1
2024-05-03 20:20:10.105517 INFO::Adjusting the last 1 batches sequentially
2024-05-03 20:20:10.116881 INFO::Done
2024-05-03 20:20:10.119403 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:10.129952 INFO::ASW Batch was -0.10010154303703 prior to batch effect correction and is now -0.10010154303703 .
2024-05-03 20:20:10.134045 INFO::Total function execution time is  0.164990901947021  s and adjustment time is  0.134835004806519 s ( 81.72 )
2024-05-03 20:20:10.374772 INFO::Formatting Data.
2024-05-03 20:20:10.376157 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:10.378509 INFO::Removing potential empty rows and columns
2024-05-03 20:20:10.382711 INFO::Found  1000  missing values.
2024-05-03 20:20:10.406926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:10.407805 INFO::Done
2024-05-03 20:20:10.409119 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:10.417047 INFO::Starting hierarchical adjustment
2024-05-03 20:20:10.418004 INFO::Found  10  batches.
2024-05-03 20:20:10.418788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:10.419475 INFO::Using default BPPARAM
2024-05-03 20:20:10.420326 INFO::Processing subtree level 1
2024-05-03 20:20:10.592248 INFO::Processing subtree level 2
2024-05-03 20:20:10.828152 INFO::Adjusting the last 1 batches sequentially
2024-05-03 20:20:10.840077 INFO::Done
2024-05-03 20:20:10.841524 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:10.853453 INFO::ASW Batch was 0.481404630927758 prior to batch effect correction and is now 0.481404630927758 .
2024-05-03 20:20:10.854385 INFO::ASW Label was 0.340534340573678 prior to batch effect correction and is now 0.340534340573678 .
2024-05-03 20:20:10.856254 INFO::Total function execution time is  0.480991125106812  s and adjustment time is  0.422205924987793 s ( 87.78 )
2024-05-03 20:20:10.859099 INFO::Formatting Data.
2024-05-03 20:20:10.859847 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:10.861702 INFO::Removing potential empty rows and columns
2024-05-03 20:20:10.867071 INFO::Found  1000  missing values.
2024-05-03 20:20:10.892886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:10.893821 INFO::Done
2024-05-03 20:20:10.894816 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:10.902386 INFO::Starting hierarchical adjustment
2024-05-03 20:20:10.903779 INFO::Found  10  batches.
2024-05-03 20:20:11.931064 INFO::Set up parallel execution backend with 2 workers
2024-05-03 20:20:11.931975 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-03 20:20:13.231136 INFO::Adjusting the last 2 batches sequentially
2024-05-03 20:20:13.232339 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 20:20:13.247282 INFO::Done
2024-05-03 20:20:13.247942 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:13.252676 INFO::ASW Batch was 0.481404630927758 prior to batch effect correction and is now 0.481404630927758 .
2024-05-03 20:20:13.253228 INFO::ASW Label was 0.340534340573678 prior to batch effect correction and is now 0.340534340573678 .
2024-05-03 20:20:13.253873 INFO::Total function execution time is  2.39496397972107  s and adjustment time is  2.34379887580872 s ( 97.86 )
2024-05-03 20:20:13.500156 INFO::Formatting Data.
2024-05-03 20:20:13.501305 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:13.503225 INFO::Removing potential empty rows and columns
2024-05-03 20:20:13.505094 INFO::Found  0  missing values.
2024-05-03 20:20:13.509377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:13.510058 INFO::Done
2024-05-03 20:20:13.510783 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 20:20:13.513871 INFO::Starting hierarchical adjustment
2024-05-03 20:20:13.514722 INFO::Found  3  batches.
2024-05-03 20:20:13.515237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 20:20:13.516011 INFO::Using default BPPARAM
2024-05-03 20:20:13.516736 INFO::Processing subtree level 1
2024-05-03 20:20:13.677774 INFO::Adjusting the last 1 batches sequentially
2024-05-03 20:20:13.69461 INFO::Done
2024-05-03 20:20:13.695955 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 20:20:13.708478 INFO::ASW Batch was 0.211063784765991 prior to batch effect correction and is now -0.150788347352957 .
2024-05-03 20:20:13.710143 INFO::ASW Label was -0.176435083784057 prior to batch effect correction and is now 0.124291572773553 .
2024-05-03 20:20:13.712353 INFO::Total function execution time is  0.212270021438599  s and adjustment time is  0.18009090423584 s ( 84.84 )
2024-05-03 20:20:13.905364 INFO::Formatting Data.
2024-05-03 20:20:13.906147 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:13.907915 INFO::Removing potential empty rows and columns
2024-05-03 20:20:13.90904 INFO::Found  2  missing values.
2024-05-03 20:20:13.911881 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:13.912608 INFO::Done
2024-05-03 20:20:13.96252 INFO::Found NA in Reference column
2024-05-03 20:20:13.979168 INFO::Require at least two references per batch.
2024-05-03 20:20:14.009987 INFO::Formatting Data.
2024-05-03 20:20:14.011049 INFO::Recognized SummarizedExperiment
2024-05-03 20:20:14.012018 INFO::Typecasting input to dataframe.
2024-05-03 20:20:14.024076 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.02573 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.030801 INFO::Found  0  missing values.
2024-05-03 20:20:14.040129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.041052 INFO::Done
2024-05-03 20:20:14.057426 INFO::Formatting Data.
2024-05-03 20:20:14.05819 INFO::Recognized SummarizedExperiment
2024-05-03 20:20:14.059143 INFO::Typecasting input to dataframe.
2024-05-03 20:20:14.080209 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.081484 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.085302 INFO::Found  0  missing values.
2024-05-03 20:20:14.098588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.09956 INFO::Done
2024-05-03 20:20:14.117924 INFO::Formatting Data.
2024-05-03 20:20:14.118639 INFO::Recognized SummarizedExperiment
2024-05-03 20:20:14.119144 INFO::Typecasting input to dataframe.
2024-05-03 20:20:14.137241 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.138814 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.140469 INFO::Found  0  missing values.
2024-05-03 20:20:14.141866 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.
2024-05-03 20:20:14.147948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.148851 INFO::Done
2024-05-03 20:20:14.165897 INFO::Formatting Data.
2024-05-03 20:20:14.166753 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.168174 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.169559 INFO::Found  0  missing values.
2024-05-03 20:20:14.173531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.174313 INFO::Done
2024-05-03 20:20:14.190509 INFO::Formatting Data.
2024-05-03 20:20:14.191594 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.19282 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.194281 INFO::Found  0  missing values.
2024-05-03 20:20:14.198149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.19892 INFO::Done
2024-05-03 20:20:14.245999 INFO::Formatting Data.
2024-05-03 20:20:14.247103 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.248462 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.249934 INFO::Found  1  missing values.
2024-05-03 20:20:14.253213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.253713 INFO::Done
2024-05-03 20:20:14.281035 INFO::Formatting Data.
2024-05-03 20:20:14.2821 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.282993 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.284225 INFO::Found  2  missing values.
2024-05-03 20:20:14.285554 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.
2024-05-03 20:20:14.288849 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.289395 INFO::Done
2024-05-03 20:20:14.303816 INFO::Formatting Data.
2024-05-03 20:20:14.304837 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.305958 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.306908 INFO::Found  2  missing values.
2024-05-03 20:20:14.308404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.308915 INFO::Done
2024-05-03 20:20:14.326318 INFO::Formatting Data.
2024-05-03 20:20:14.327104 INFO::Typecasting input to dataframe.
2024-05-03 20:20:14.327894 INFO::Replacing NaNs with NAs.
2024-05-03 20:20:14.328738 INFO::Removing potential empty rows and columns
2024-05-03 20:20:14.329713 INFO::Found  0  missing values.
2024-05-03 20:20:14.333229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 20:20:14.333733 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 19.972   4.027  24.402 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT27.551 1.63319.820
compute_asw0.0250.0020.027
count_existing0.0140.0010.014
generate_data_covariables0.0170.0010.018
generate_dataset0.0130.0010.014