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This page was generated on 2024-06-28 17:44 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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: 2024-06-26 14:00 -0400 (Wed, 26 Jun 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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

CHECK results for BERT on kjohnson1

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

raw results


Summary

Package: BERT
Version: 1.0.0
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: 2024-06-27 12:19:12 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 12:20:32 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 79.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* 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 28.97  1.086  20.491
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘BERT’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2024-06-27 12:20:11.848841 INFO::Formatting Data.
2024-06-27 12:20:11.853247 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:11.865381 INFO::Removing potential empty rows and columns
2024-06-27 12:20:12.153532 INFO::Found  0  missing values.
2024-06-27 12:20:12.157497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:12.158174 INFO::Done
2024-06-27 12:20:12.15871 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:12.175469 INFO::Starting hierarchical adjustment
2024-06-27 12:20:12.176416 INFO::Found  3  batches.
2024-06-27 12:20:12.17697 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:12.178304 INFO::Using default BPPARAM
2024-06-27 12:20:12.178812 INFO::Processing subtree level 1
2024-06-27 12:20:12.29865 INFO::Adjusting the last 1 batches sequentially
2024-06-27 12:20:12.302423 INFO::Done
2024-06-27 12:20:12.303129 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:12.308474 INFO::ASW Batch was -0.104522078395771 prior to batch effect correction and is now -0.104522078395771 .
2024-06-27 12:20:12.309822 INFO::Total function execution time is  0.462235927581787  s and adjustment time is  0.126152992248535 s ( 27.29 )
2024-06-27 12:20:12.329847 INFO::Formatting Data.
2024-06-27 12:20:12.330949 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:12.332106 INFO::Removing potential empty rows and columns
2024-06-27 12:20:12.333435 INFO::Found  0  missing values.
2024-06-27 12:20:12.334524 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.
2024-06-27 12:20:12.347324 INFO::Formatting Data.
2024-06-27 12:20:12.348275 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:12.349184 INFO::Removing potential empty rows and columns
2024-06-27 12:20:12.350234 INFO::Found  0  missing values.
2024-06-27 12:20:12.351143 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.
2024-06-27 12:20:12.370261 INFO::Formatting Data.
2024-06-27 12:20:12.371096 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:12.371972 INFO::Removing potential empty rows and columns
2024-06-27 12:20:12.372965 INFO::Found  0  missing values.
2024-06-27 12:20:12.373848 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.
2024-06-27 12:20:12.377979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:12.378624 INFO::Done
2024-06-27 12:20:12.379113 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:12.381363 INFO::Starting hierarchical adjustment
2024-06-27 12:20:12.382142 INFO::Found  2  batches.
2024-06-27 12:20:12.382641 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:12.383324 INFO::Using default BPPARAM
2024-06-27 12:20:12.383791 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:12.384713 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:12.410939 INFO::Done
2024-06-27 12:20:12.411696 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:12.413882 INFO::ASW Batch was 0.141271960872646 prior to batch effect correction and is now -0.122054117275502 .
2024-06-27 12:20:12.414778 INFO::Total function execution time is  0.0446629524230957  s and adjustment time is  0.0288870334625244 s ( 64.68 )
2024-06-27 12:20:12.418188 INFO::Formatting Data.
2024-06-27 12:20:12.418801 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:12.427893 INFO::Formatting Data.
2024-06-27 12:20:12.428716 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:12.429725 INFO::Removing potential empty rows and columns
2024-06-27 12:20:12.430886 INFO::Found  0  missing values.
2024-06-27 12:20:12.433591 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:12.434185 INFO::Done
2024-06-27 12:20:12.434645 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:12.436808 INFO::Starting hierarchical adjustment
2024-06-27 12:20:12.437576 INFO::Found  2  batches.
2024-06-27 12:20:12.438057 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:12.438598 INFO::Using default BPPARAM
2024-06-27 12:20:12.439045 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:12.439871 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:12.45525 INFO::Done
2024-06-27 12:20:12.455957 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:12.457945 INFO::ASW Batch was -0.00647190336781507 prior to batch effect correction and is now -0.125004863381294 .
2024-06-27 12:20:12.458694 INFO::Total function execution time is  0.0308840274810791  s and adjustment time is  0.0177829265594482 s ( 57.58 )
2024-06-27 12:20:12.459711 INFO::Formatting Data.
2024-06-27 12:20:12.460289 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:12.461143 INFO::Removing potential empty rows and columns
2024-06-27 12:20:12.462246 INFO::Found  0  missing values.
2024-06-27 12:20:12.464914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:12.465436 INFO::Done
2024-06-27 12:20:12.465884 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:12.46793 INFO::Starting hierarchical adjustment
2024-06-27 12:20:12.468581 INFO::Found  2  batches.
2024-06-27 12:20:12.469059 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:12.469611 INFO::Using default BPPARAM
2024-06-27 12:20:12.470047 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:12.470884 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:12.487142 INFO::Done
2024-06-27 12:20:12.48791 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:12.489939 INFO::ASW Batch was -0.00647190336781507 prior to batch effect correction and is now -0.125004863381294 .
2024-06-27 12:20:12.49076 INFO::Total function execution time is  0.0310359001159668  s and adjustment time is  0.018639087677002 s ( 60.06 )
2024-06-27 12:20:15.24664 INFO::Formatting Data.
2024-06-27 12:20:15.247469 INFO::Recognized SummarizedExperiment
2024-06-27 12:20:15.247924 INFO::Typecasting input to dataframe.
2024-06-27 12:20:16.177141 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:16.178402 INFO::Removing potential empty rows and columns
2024-06-27 12:20:16.181418 INFO::Found  0  missing values.
2024-06-27 12:20:16.187048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:16.187602 INFO::Done
2024-06-27 12:20:16.188009 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:16.191392 INFO::Starting hierarchical adjustment
2024-06-27 12:20:16.191993 INFO::Found  2  batches.
2024-06-27 12:20:16.192387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:16.193445 INFO::Using default BPPARAM
2024-06-27 12:20:16.193843 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:16.194623 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:16.24322 INFO::Done
2024-06-27 12:20:16.243883 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:16.247309 INFO::ASW Batch was 0.0104524422642709 prior to batch effect correction and is now -0.111296463887397 .
2024-06-27 12:20:16.248069 INFO::Total function execution time is  1.00191402435303  s and adjustment time is  0.051285982131958 s ( 5.12 )
2024-06-27 12:20:16.264571 INFO::Formatting Data.
2024-06-27 12:20:16.265297 INFO::Recognized SummarizedExperiment
2024-06-27 12:20:16.26571 INFO::Typecasting input to dataframe.
2024-06-27 12:20:16.274004 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:16.275097 INFO::Removing potential empty rows and columns
2024-06-27 12:20:16.278202 INFO::Found  0  missing values.
2024-06-27 12:20:16.284068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:16.284613 INFO::Done
2024-06-27 12:20:16.285031 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:16.288485 INFO::Starting hierarchical adjustment
2024-06-27 12:20:16.289112 INFO::Found  2  batches.
2024-06-27 12:20:16.289526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:16.290012 INFO::Using default BPPARAM
2024-06-27 12:20:16.290387 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:16.291174 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:16.313201 INFO::Done
2024-06-27 12:20:16.313875 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:16.317184 INFO::ASW Batch was 0.00878734550235978 prior to batch effect correction and is now 0.00878734550235978 .
2024-06-27 12:20:16.31794 INFO::Total function execution time is  0.053408145904541  s and adjustment time is  0.0241448879241943 s ( 45.21 )
2024-06-27 12:20:16.335137 INFO::Formatting Data.
2024-06-27 12:20:16.335854 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:16.33663 INFO::Removing potential empty rows and columns
2024-06-27 12:20:16.337501 INFO::Found  0  missing values.
2024-06-27 12:20:16.339889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:16.340413 INFO::Done
2024-06-27 12:20:16.340825 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:16.342716 INFO::Starting hierarchical adjustment
2024-06-27 12:20:16.343301 INFO::Found  3  batches.
2024-06-27 12:20:16.343706 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:16.344179 INFO::Using default BPPARAM
2024-06-27 12:20:16.344571 INFO::Processing subtree level 1
2024-06-27 12:20:16.552206 INFO::Adjusting the last 1 batches sequentially
2024-06-27 12:20:16.557495 INFO::Done
2024-06-27 12:20:16.558126 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:16.563487 INFO::ASW Batch was 0.0268597999280766 prior to batch effect correction and is now -0.158057965267454 .
2024-06-27 12:20:16.565484 INFO::Total function execution time is  0.230349063873291  s and adjustment time is  0.214276075363159 s ( 93.02 )
2024-06-27 12:20:16.585885 INFO::Skipping initial DF formatting
2024-06-27 12:20:16.586765 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:16.591524 INFO::Starting hierarchical adjustment
2024-06-27 12:20:16.592498 INFO::Found  5  batches.
2024-06-27 12:20:16.59307 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:16.593805 INFO::Using default BPPARAM
2024-06-27 12:20:16.594383 INFO::Processing subtree level 1
2024-06-27 12:20:16.756992 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:16.763523 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:16.799818 INFO::Done
2024-06-27 12:20:16.800835 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:16.806569 INFO::ASW Batch was 0.46771631706766 prior to batch effect correction and is now 0.46771631706766 .
2024-06-27 12:20:16.807401 INFO::ASW Label was 0.396536708724152 prior to batch effect correction and is now 0.396536708724152 .
2024-06-27 12:20:16.808504 INFO::Total function execution time is  0.222661972045898  s and adjustment time is  0.207443952560425 s ( 93.17 )
2024-06-27 12:20:16.831461 INFO::Formatting Data.
2024-06-27 12:20:16.832536 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:16.833751 INFO::Removing potential empty rows and columns
2024-06-27 12:20:16.834876 INFO::Found  0  missing values.
2024-06-27 12:20:16.838599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:16.839274 INFO::Done
2024-06-27 12:20:16.839779 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:16.84282 INFO::Starting hierarchical adjustment
2024-06-27 12:20:16.843622 INFO::Found  5  batches.
2024-06-27 12:20:16.844129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:16.844789 INFO::Using default BPPARAM
2024-06-27 12:20:16.845266 INFO::Processing subtree level 1
2024-06-27 12:20:16.998003 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.007015 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.037474 INFO::Done
2024-06-27 12:20:17.038523 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.043474 INFO::ASW Batch was 0.357829854433918 prior to batch effect correction and is now -0.0783224035851205 .
2024-06-27 12:20:17.044204 INFO::ASW Label was 0.324597613433974 prior to batch effect correction and is now 0.852129830604101 .
2024-06-27 12:20:17.046679 INFO::Total function execution time is  0.214515209197998  s and adjustment time is  0.193931102752686 s ( 90.4 )
2024-06-27 12:20:17.047885 INFO::Formatting Data.
2024-06-27 12:20:17.048707 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:17.049637 INFO::Removing potential empty rows and columns
2024-06-27 12:20:17.050713 INFO::Found  0  missing values.
2024-06-27 12:20:17.054364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:17.055101 INFO::Done
2024-06-27 12:20:17.056042 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:17.058964 INFO::Starting hierarchical adjustment
2024-06-27 12:20:17.059723 INFO::Found  5  batches.
2024-06-27 12:20:17.060229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:17.060851 INFO::Using default BPPARAM
2024-06-27 12:20:17.061316 INFO::Processing subtree level 1
2024-06-27 12:20:17.209259 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.215208 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.241331 INFO::Done
2024-06-27 12:20:17.242218 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.247045 INFO::ASW Batch was 0.357829854433918 prior to batch effect correction and is now -0.0783224035851205 .
2024-06-27 12:20:17.247721 INFO::ASW Label was 0.324597613433974 prior to batch effect correction and is now 0.852129830604101 .
2024-06-27 12:20:17.249797 INFO::Total function execution time is  0.201761960983276  s and adjustment time is  0.181700944900513 s ( 90.06 )
2024-06-27 12:20:17.270247 INFO::Formatting Data.
2024-06-27 12:20:17.271124 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:17.272036 INFO::Removing potential empty rows and columns
2024-06-27 12:20:17.273594 INFO::Found  0  missing values.
2024-06-27 12:20:17.27783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:17.278396 INFO::Done
2024-06-27 12:20:17.278858 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:17.281675 INFO::Starting hierarchical adjustment
2024-06-27 12:20:17.28239 INFO::Found  5  batches.
2024-06-27 12:20:17.282849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:17.283456 INFO::Using default BPPARAM
2024-06-27 12:20:17.283904 INFO::Processing subtree level 1
2024-06-27 12:20:17.403663 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.407999 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.432323 INFO::Done
2024-06-27 12:20:17.433139 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.437224 INFO::ASW Batch was 0.431478693346222 prior to batch effect correction and is now 0.0298365643134532 .
2024-06-27 12:20:17.437914 INFO::ASW Label was 0.493032558321654 prior to batch effect correction and is now 0.624514479030887 .
2024-06-27 12:20:17.438961 INFO::Total function execution time is  0.168742895126343  s and adjustment time is  0.150041103363037 s ( 88.92 )
2024-06-27 12:20:17.439885 INFO::Formatting Data.
2024-06-27 12:20:17.440526 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:17.441511 INFO::Removing potential empty rows and columns
2024-06-27 12:20:17.442651 INFO::Found  0  missing values.
2024-06-27 12:20:17.446193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:17.446796 INFO::Done
2024-06-27 12:20:17.447337 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:17.450106 INFO::Starting hierarchical adjustment
2024-06-27 12:20:17.450888 INFO::Found  5  batches.
2024-06-27 12:20:17.451397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:17.452217 INFO::Using default BPPARAM
2024-06-27 12:20:17.452714 INFO::Processing subtree level 1
2024-06-27 12:20:17.588415 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.591005 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.608586 INFO::Done
2024-06-27 12:20:17.609408 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.612785 INFO::ASW Batch was 0.431478693346222 prior to batch effect correction and is now 0.0298365643134532 .
2024-06-27 12:20:17.613414 INFO::ASW Label was 0.493032558321654 prior to batch effect correction and is now 0.624514479030887 .
2024-06-27 12:20:17.614247 INFO::Total function execution time is  0.174293041229248  s and adjustment time is  0.157819986343384 s ( 90.55 )
2024-06-27 12:20:17.631798 INFO::Formatting Data.
2024-06-27 12:20:17.632629 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:17.633516 INFO::Removing potential empty rows and columns
2024-06-27 12:20:17.634594 INFO::Found  0  missing values.
2024-06-27 12:20:17.637053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:17.637542 INFO::Done
2024-06-27 12:20:17.638051 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:17.640829 INFO::Starting hierarchical adjustment
2024-06-27 12:20:17.641584 INFO::Found  2  batches.
2024-06-27 12:20:17.642066 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:17.642717 INFO::Using default BPPARAM
2024-06-27 12:20:17.643164 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.643966 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.657856 INFO::Done
2024-06-27 12:20:17.658592 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.661336 INFO::ASW Batch was 0.482894692689347 prior to batch effect correction and is now -0.0038646005160568 .
2024-06-27 12:20:17.661949 INFO::ASW Label was 0.591198522593892 prior to batch effect correction and is now 0.901911851011605 .
2024-06-27 12:20:17.662761 INFO::Total function execution time is  0.0310831069946289  s and adjustment time is  0.0163819789886475 s ( 52.7 )
2024-06-27 12:20:17.663402 INFO::Formatting Data.
2024-06-27 12:20:17.663919 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:17.664684 INFO::Removing potential empty rows and columns
2024-06-27 12:20:17.66555 INFO::Found  0  missing values.
2024-06-27 12:20:17.667959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:17.668466 INFO::Done
2024-06-27 12:20:17.668884 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:17.671543 INFO::Starting hierarchical adjustment
2024-06-27 12:20:17.672262 INFO::Found  2  batches.
2024-06-27 12:20:17.672757 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:17.673294 INFO::Using default BPPARAM
2024-06-27 12:20:17.673726 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.674512 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.688431 INFO::Done
2024-06-27 12:20:17.68917 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.692005 INFO::ASW Batch was 0.482894692689347 prior to batch effect correction and is now -0.0038646005160568 .
2024-06-27 12:20:17.692617 INFO::ASW Label was 0.591198522593892 prior to batch effect correction and is now 0.901911851011605 .
2024-06-27 12:20:17.693408 INFO::Total function execution time is  0.0299439430236816  s and adjustment time is  0.0162849426269531 s ( 54.38 )
2024-06-27 12:20:17.705219 INFO::Formatting Data.
2024-06-27 12:20:17.70596 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:17.706745 INFO::Removing potential empty rows and columns
2024-06-27 12:20:17.707569 INFO::Found  0  missing values.
2024-06-27 12:20:17.709508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:17.710023 INFO::Done
2024-06-27 12:20:17.710503 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:17.712364 INFO::Starting hierarchical adjustment
2024-06-27 12:20:17.712973 INFO::Found  2  batches.
2024-06-27 12:20:17.713455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:17.713988 INFO::Using default BPPARAM
2024-06-27 12:20:17.714424 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.715167 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.748089 INFO::Done
2024-06-27 12:20:17.748827 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.750782 INFO::ASW Batch was -0.0524786519579094 prior to batch effect correction and is now -0.168848519397533 .
2024-06-27 12:20:17.751603 INFO::Total function execution time is  0.0464789867401123  s and adjustment time is  0.0351991653442383 s ( 75.73 )
2024-06-27 12:20:17.763801 INFO::Formatting Data.
2024-06-27 12:20:17.764584 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:17.765386 INFO::Removing potential empty rows and columns
2024-06-27 12:20:17.766329 INFO::Found  0  missing values.
2024-06-27 12:20:17.767721 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.
2024-06-27 12:20:17.771906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:17.772499 INFO::Done
2024-06-27 12:20:17.772954 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:17.775722 INFO::Starting hierarchical adjustment
2024-06-27 12:20:17.77644 INFO::Found  2  batches.
2024-06-27 12:20:17.776884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:17.777397 INFO::Using default BPPARAM
2024-06-27 12:20:17.777817 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.778676 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.794436 INFO::Done
2024-06-27 12:20:17.79518 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.798016 INFO::ASW Batch was 0.51080141969522 prior to batch effect correction and is now -0.0314937113620933 .
2024-06-27 12:20:17.798608 INFO::ASW Label was 0.472329451167537 prior to batch effect correction and is now 0.832321273146657 .
2024-06-27 12:20:17.799301 INFO::Total function execution time is  0.0356218814849854  s and adjustment time is  0.0180759429931641 s ( 50.74 )
2024-06-27 12:20:17.79993 INFO::Formatting Data.
2024-06-27 12:20:17.800424 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:17.801254 INFO::Removing potential empty rows and columns
2024-06-27 12:20:17.80214 INFO::Found  0  missing values.
2024-06-27 12:20:17.802951 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.
2024-06-27 12:20:17.806837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:17.80743 INFO::Done
2024-06-27 12:20:17.807887 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:17.81059 INFO::Starting hierarchical adjustment
2024-06-27 12:20:17.811295 INFO::Found  2  batches.
2024-06-27 12:20:17.811752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:17.812289 INFO::Using default BPPARAM
2024-06-27 12:20:17.812713 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:17.813535 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:17.829396 INFO::Done
2024-06-27 12:20:17.830154 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:17.832943 INFO::ASW Batch was 0.51080141969522 prior to batch effect correction and is now -0.0314937113620933 .
2024-06-27 12:20:17.833523 INFO::ASW Label was 0.472329451167537 prior to batch effect correction and is now 0.832321273146657 .
2024-06-27 12:20:17.834275 INFO::Total function execution time is  0.0342910289764404  s and adjustment time is  0.0181760787963867 s ( 53.01 )
2024-06-27 12:20:18.038391 INFO::Formatting Data.
2024-06-27 12:20:18.039259 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:18.040112 INFO::Removing potential empty rows and columns
2024-06-27 12:20:18.041132 INFO::Found  0  missing values.
2024-06-27 12:20:18.043731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:18.044274 INFO::Done
2024-06-27 12:20:18.044788 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:18.046744 INFO::Starting hierarchical adjustment
2024-06-27 12:20:18.047389 INFO::Found  3  batches.
2024-06-27 12:20:18.047845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:18.048425 INFO::Using default BPPARAM
2024-06-27 12:20:18.048912 INFO::Processing subtree level 1
2024-06-27 12:20:18.215063 INFO::Adjusting the last 1 batches sequentially
2024-06-27 12:20:18.222579 INFO::Done
2024-06-27 12:20:18.224013 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:18.231639 INFO::ASW Batch was -0.0914417883138821 prior to batch effect correction and is now -0.0914417883138821 .
2024-06-27 12:20:18.234227 INFO::Total function execution time is  0.195536851882935  s and adjustment time is  0.175249099731445 s ( 89.62 )
2024-06-27 12:20:18.236674 INFO::Formatting Data.
2024-06-27 12:20:18.237814 INFO::Typecasting input to dataframe.
2024-06-27 12:20:18.238928 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:18.240598 INFO::Removing potential empty rows and columns
2024-06-27 12:20:18.242973 INFO::Found  0  missing values.
2024-06-27 12:20:18.248472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:18.249444 INFO::Done
2024-06-27 12:20:18.250254 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:18.253287 INFO::Starting hierarchical adjustment
2024-06-27 12:20:18.254397 INFO::Found  3  batches.
2024-06-27 12:20:18.255286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:18.256456 INFO::Using default BPPARAM
2024-06-27 12:20:18.257207 INFO::Processing subtree level 1
2024-06-27 12:20:18.43041 INFO::Adjusting the last 1 batches sequentially
2024-06-27 12:20:18.433057 INFO::Done
2024-06-27 12:20:18.433678 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:18.436738 INFO::ASW Batch was -0.0914417883138821 prior to batch effect correction and is now -0.0914417883138821 .
2024-06-27 12:20:18.437935 INFO::Total function execution time is  0.201417922973633  s and adjustment time is  0.178904056549072 s ( 88.82 )
2024-06-27 12:20:18.453925 INFO::Formatting Data.
2024-06-27 12:20:18.454793 INFO::Typecasting input to dataframe.
2024-06-27 12:20:18.455586 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:18.456511 INFO::Removing potential empty rows and columns
2024-06-27 12:20:18.457731 INFO::Found  0  missing values.
2024-06-27 12:20:18.460473 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:18.4611 INFO::Done
2024-06-27 12:20:18.461588 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:18.463598 INFO::Starting hierarchical adjustment
2024-06-27 12:20:18.464303 INFO::Found  3  batches.
2024-06-27 12:20:18.464856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:18.465464 INFO::Using default BPPARAM
2024-06-27 12:20:18.465939 INFO::Processing subtree level 1
2024-06-27 12:20:18.593667 INFO::Adjusting the last 1 batches sequentially
2024-06-27 12:20:18.598293 INFO::Done
2024-06-27 12:20:18.598941 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:18.603745 INFO::ASW Batch was -0.110575577475175 prior to batch effect correction and is now -0.110575577475175 .
2024-06-27 12:20:18.60587 INFO::Total function execution time is  0.151794910430908  s and adjustment time is  0.134109020233154 s ( 88.35 )
2024-06-27 12:20:18.778998 INFO::Formatting Data.
2024-06-27 12:20:18.779936 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:18.781191 INFO::Removing potential empty rows and columns
2024-06-27 12:20:18.784402 INFO::Found  1000  missing values.
2024-06-27 12:20:18.802661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:18.803535 INFO::Done
2024-06-27 12:20:18.804178 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:18.810723 INFO::Starting hierarchical adjustment
2024-06-27 12:20:18.811592 INFO::Found  10  batches.
2024-06-27 12:20:18.812127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:18.81283 INFO::Using default BPPARAM
2024-06-27 12:20:18.813295 INFO::Processing subtree level 1
2024-06-27 12:20:18.963675 INFO::Processing subtree level 2
2024-06-27 12:20:19.131073 INFO::Adjusting the last 1 batches sequentially
2024-06-27 12:20:19.137428 INFO::Done
2024-06-27 12:20:19.138194 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:19.147121 INFO::ASW Batch was 0.477611796050946 prior to batch effect correction and is now 0.477611796050946 .
2024-06-27 12:20:19.147957 INFO::ASW Label was 0.332181459180181 prior to batch effect correction and is now 0.332181459180181 .
2024-06-27 12:20:19.150093 INFO::Total function execution time is  0.371128082275391  s and adjustment time is  0.325966119766235 s ( 87.83 )
2024-06-27 12:20:19.151116 INFO::Formatting Data.
2024-06-27 12:20:19.15173 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:19.153251 INFO::Removing potential empty rows and columns
2024-06-27 12:20:19.156367 INFO::Found  1000  missing values.
2024-06-27 12:20:19.174199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:19.17504 INFO::Done
2024-06-27 12:20:19.175593 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:19.18162 INFO::Starting hierarchical adjustment
2024-06-27 12:20:19.182543 INFO::Found  10  batches.
2024-06-27 12:20:20.431779 INFO::Set up parallel execution backend with 2 workers
2024-06-27 12:20:20.432837 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-27 12:20:21.812107 INFO::Adjusting the last 2 batches sequentially
2024-06-27 12:20:21.814043 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 12:20:21.831983 INFO::Done
2024-06-27 12:20:21.832801 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:21.838663 INFO::ASW Batch was 0.477611796050946 prior to batch effect correction and is now 0.477611796050946 .
2024-06-27 12:20:21.83947 INFO::ASW Label was 0.332181459180181 prior to batch effect correction and is now 0.332181459180181 .
2024-06-27 12:20:21.840276 INFO::Total function execution time is  2.68918514251709  s and adjustment time is  2.64956402778625 s ( 98.53 )
2024-06-27 12:20:22.033923 INFO::Formatting Data.
2024-06-27 12:20:22.035028 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.036105 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.037283 INFO::Found  0  missing values.
2024-06-27 12:20:22.041172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.041975 INFO::Done
2024-06-27 12:20:22.042524 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 12:20:22.046263 INFO::Starting hierarchical adjustment
2024-06-27 12:20:22.047271 INFO::Found  3  batches.
2024-06-27 12:20:22.047919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 12:20:22.048595 INFO::Using default BPPARAM
2024-06-27 12:20:22.049108 INFO::Processing subtree level 1
2024-06-27 12:20:22.184883 INFO::Adjusting the last 1 batches sequentially
2024-06-27 12:20:22.189404 INFO::Done
2024-06-27 12:20:22.19006 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 12:20:22.19733 INFO::ASW Batch was 0.197271165437677 prior to batch effect correction and is now -0.181108977511688 .
2024-06-27 12:20:22.198426 INFO::ASW Label was -0.168174886061019 prior to batch effect correction and is now 0.168498614031334 .
2024-06-27 12:20:22.200561 INFO::Total function execution time is  0.166746854782104  s and adjustment time is  0.142340183258057 s ( 85.36 )
2024-06-27 12:20:22.348136 INFO::Formatting Data.
2024-06-27 12:20:22.34921 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.350217 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.351429 INFO::Found  2  missing values.
2024-06-27 12:20:22.354502 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.355075 INFO::Done
2024-06-27 12:20:22.387896 INFO::Found NA in Reference column
2024-06-27 12:20:22.399189 INFO::Require at least two references per batch.
2024-06-27 12:20:22.42215 INFO::Formatting Data.
2024-06-27 12:20:22.42309 INFO::Recognized SummarizedExperiment
2024-06-27 12:20:22.423606 INFO::Typecasting input to dataframe.
2024-06-27 12:20:22.43579 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.43729 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.441836 INFO::Found  0  missing values.
2024-06-27 12:20:22.449814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.450471 INFO::Done
2024-06-27 12:20:22.468271 INFO::Formatting Data.
2024-06-27 12:20:22.469254 INFO::Recognized SummarizedExperiment
2024-06-27 12:20:22.469819 INFO::Typecasting input to dataframe.
2024-06-27 12:20:22.490632 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.492376 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.496382 INFO::Found  0  missing values.
2024-06-27 12:20:22.508737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.509546 INFO::Done
2024-06-27 12:20:22.526669 INFO::Formatting Data.
2024-06-27 12:20:22.527602 INFO::Recognized SummarizedExperiment
2024-06-27 12:20:22.528169 INFO::Typecasting input to dataframe.
2024-06-27 12:20:22.546524 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.547686 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.548722 INFO::Found  0  missing values.
2024-06-27 12:20:22.549634 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.
2024-06-27 12:20:22.554099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.554791 INFO::Done
2024-06-27 12:20:22.56703 INFO::Formatting Data.
2024-06-27 12:20:22.567895 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.568771 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.569747 INFO::Found  0  missing values.
2024-06-27 12:20:22.572444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.573002 INFO::Done
2024-06-27 12:20:22.585884 INFO::Formatting Data.
2024-06-27 12:20:22.586811 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.587676 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.588641 INFO::Found  0  missing values.
2024-06-27 12:20:22.591583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.592204 INFO::Done
2024-06-27 12:20:22.626312 INFO::Formatting Data.
2024-06-27 12:20:22.627266 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.628305 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.629454 INFO::Found  1  missing values.
2024-06-27 12:20:22.632759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.633413 INFO::Done
2024-06-27 12:20:22.655221 INFO::Formatting Data.
2024-06-27 12:20:22.656136 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.657094 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.658083 INFO::Found  2  missing values.
2024-06-27 12:20:22.658992 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.
2024-06-27 12:20:22.661197 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.661787 INFO::Done
2024-06-27 12:20:22.673708 INFO::Formatting Data.
2024-06-27 12:20:22.674647 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.675668 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.676687 INFO::Found  2  missing values.
2024-06-27 12:20:22.678296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.678819 INFO::Done
2024-06-27 12:20:22.691664 INFO::Formatting Data.
2024-06-27 12:20:22.692493 INFO::Typecasting input to dataframe.
2024-06-27 12:20:22.693301 INFO::Replacing NaNs with NAs.
2024-06-27 12:20:22.694401 INFO::Removing potential empty rows and columns
2024-06-27 12:20:22.695464 INFO::Found  0  missing values.
2024-06-27 12:20:22.698831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 12:20:22.699365 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 20.523   3.976  24.951

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT28.970 1.08620.491
compute_asw0.0300.0010.032
count_existing0.0170.0010.018
generate_data_covariables0.0150.0010.016
generate_dataset0.0140.0000.015