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This page was generated on 2024-11-20 12:05 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 159/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.2.0  (landing page)
Yannis Schumann
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_20
git_last_commit: 9764e3f
git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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  

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: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz
StartedAt: 2024-11-19 19:46:19 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 19:51:02 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 283.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 18.913  1.015   13.62
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

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


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

Tests output

BERT.Rcheck/tests/testthat.Rout


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

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2024-11-19 19:50:47.51007 INFO::Formatting Data.
2024-11-19 19:50:47.513652 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:47.525336 INFO::Removing potential empty rows and columns
2024-11-19 19:50:47.74723 INFO::Found  0  missing values.
2024-11-19 19:50:47.752777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:47.753374 INFO::Done
2024-11-19 19:50:47.753848 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:47.766123 INFO::Starting hierarchical adjustment
2024-11-19 19:50:47.766909 INFO::Found  3  batches.
2024-11-19 19:50:47.767436 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:47.768436 INFO::Using default BPPARAM
2024-11-19 19:50:47.768925 INFO::Processing subtree level 1
2024-11-19 19:50:47.884367 INFO::Adjusting the last 1 batches sequentially
2024-11-19 19:50:47.889809 INFO::Done
2024-11-19 19:50:47.891402 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:47.895439 INFO::ASW Batch was -0.103429430827051 prior to batch effect correction and is now -0.103429430827051 .
2024-11-19 19:50:47.897728 INFO::Total function execution time is  0.388397932052612  s and adjustment time is  0.12303614616394 s ( 31.68 )
2024-11-19 19:50:47.916793 INFO::Formatting Data.
2024-11-19 19:50:47.917501 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:47.918355 INFO::Removing potential empty rows and columns
2024-11-19 19:50:47.919431 INFO::Found  0  missing values.
2024-11-19 19:50:47.920859 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.
2024-11-19 19:50:47.931971 INFO::Formatting Data.
2024-11-19 19:50:47.932669 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:47.93345 INFO::Removing potential empty rows and columns
2024-11-19 19:50:47.934734 INFO::Found  0  missing values.
2024-11-19 19:50:47.935865 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.
2024-11-19 19:50:47.954303 INFO::Formatting Data.
2024-11-19 19:50:47.955285 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:47.956189 INFO::Removing potential empty rows and columns
2024-11-19 19:50:47.957208 INFO::Found  0  missing values.
2024-11-19 19:50:47.958166 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.
2024-11-19 19:50:47.963439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:47.963981 INFO::Done
2024-11-19 19:50:47.964452 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:47.966786 INFO::Starting hierarchical adjustment
2024-11-19 19:50:47.967399 INFO::Found  2  batches.
2024-11-19 19:50:47.967872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:47.968424 INFO::Using default BPPARAM
2024-11-19 19:50:47.968884 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:47.969695 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:47.989529 INFO::Done
2024-11-19 19:50:47.990177 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:47.992031 INFO::ASW Batch was -0.0541305739948224 prior to batch effect correction and is now -0.097811248984215 .
2024-11-19 19:50:47.992758 INFO::Total function execution time is  0.038538932800293  s and adjustment time is  0.0222339630126953 s ( 57.69 )
2024-11-19 19:50:47.995416 INFO::Formatting Data.
2024-11-19 19:50:47.996095 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:48.004226 INFO::Formatting Data.
2024-11-19 19:50:48.004849 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:48.005641 INFO::Removing potential empty rows and columns
2024-11-19 19:50:48.006519 INFO::Found  0  missing values.
2024-11-19 19:50:48.008932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:48.009485 INFO::Done
2024-11-19 19:50:48.00997 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:48.011794 INFO::Starting hierarchical adjustment
2024-11-19 19:50:48.012385 INFO::Found  2  batches.
2024-11-19 19:50:48.012824 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:48.013325 INFO::Using default BPPARAM
2024-11-19 19:50:48.013772 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:48.01463 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:48.029099 INFO::Done
2024-11-19 19:50:48.029719 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:48.03145 INFO::ASW Batch was -0.00944061599440379 prior to batch effect correction and is now -0.12493092454038 .
2024-11-19 19:50:48.032427 INFO::Total function execution time is  0.0282478332519531  s and adjustment time is  0.0168111324310303 s ( 59.51 )
2024-11-19 19:50:48.033497 INFO::Formatting Data.
2024-11-19 19:50:48.034018 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:48.03507 INFO::Removing potential empty rows and columns
2024-11-19 19:50:48.035979 INFO::Found  0  missing values.
2024-11-19 19:50:48.038698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:48.039169 INFO::Done
2024-11-19 19:50:48.039596 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:48.041362 INFO::Starting hierarchical adjustment
2024-11-19 19:50:48.04195 INFO::Found  2  batches.
2024-11-19 19:50:48.042573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:48.043103 INFO::Using default BPPARAM
2024-11-19 19:50:48.043548 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:48.044353 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:48.059802 INFO::Done
2024-11-19 19:50:48.060407 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:48.062263 INFO::ASW Batch was -0.00944061599440379 prior to batch effect correction and is now -0.12493092454038 .
2024-11-19 19:50:48.062967 INFO::Total function execution time is  0.0294809341430664  s and adjustment time is  0.0179450511932373 s ( 60.87 )
2024-11-19 19:50:50.549456 INFO::Formatting Data.
2024-11-19 19:50:50.550025 INFO::Recognized SummarizedExperiment
2024-11-19 19:50:50.550428 INFO::Typecasting input to dataframe.
2024-11-19 19:50:50.575563 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:50.576497 INFO::Removing potential empty rows and columns
2024-11-19 19:50:50.578943 INFO::Found  0  missing values.
2024-11-19 19:50:50.583805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:50.584286 INFO::Done
2024-11-19 19:50:50.584716 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:50.58793 INFO::Starting hierarchical adjustment
2024-11-19 19:50:50.588516 INFO::Found  2  batches.
2024-11-19 19:50:50.588932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:50.589782 INFO::Using default BPPARAM
2024-11-19 19:50:50.590198 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:50.59101 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:50.630247 INFO::Done
2024-11-19 19:50:50.630809 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:50.633529 INFO::ASW Batch was 0.0115161962520812 prior to batch effect correction and is now -0.090947776758668 .
2024-11-19 19:50:50.634194 INFO::Total function execution time is  0.0849599838256836  s and adjustment time is  0.041827917098999 s ( 49.23 )
2024-11-19 19:50:50.653247 INFO::Formatting Data.
2024-11-19 19:50:50.653886 INFO::Recognized SummarizedExperiment
2024-11-19 19:50:50.654355 INFO::Typecasting input to dataframe.
2024-11-19 19:50:50.661967 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:50.662985 INFO::Removing potential empty rows and columns
2024-11-19 19:50:50.666072 INFO::Found  0  missing values.
2024-11-19 19:50:50.672066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:50.672637 INFO::Done
2024-11-19 19:50:50.673119 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:50.676207 INFO::Starting hierarchical adjustment
2024-11-19 19:50:50.676819 INFO::Found  2  batches.
2024-11-19 19:50:50.677271 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:50.677814 INFO::Using default BPPARAM
2024-11-19 19:50:50.67826 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:50.679126 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:50.699746 INFO::Done
2024-11-19 19:50:50.700359 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:50.703489 INFO::ASW Batch was 0.0258347703496519 prior to batch effect correction and is now 0.0258347703496519 .
2024-11-19 19:50:50.704221 INFO::Total function execution time is  0.0509679317474365  s and adjustment time is  0.0230171680450439 s ( 45.16 )
2024-11-19 19:50:50.722097 INFO::Formatting Data.
2024-11-19 19:50:50.722827 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:50.723921 INFO::Removing potential empty rows and columns
2024-11-19 19:50:50.724851 INFO::Found  0  missing values.
2024-11-19 19:50:50.727279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:50.727708 INFO::Done
2024-11-19 19:50:50.728118 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:50.729901 INFO::Starting hierarchical adjustment
2024-11-19 19:50:50.730433 INFO::Found  3  batches.
2024-11-19 19:50:50.730823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:50.731311 INFO::Using default BPPARAM
2024-11-19 19:50:50.731726 INFO::Processing subtree level 1
2024-11-19 19:50:50.867226 INFO::Adjusting the last 1 batches sequentially
2024-11-19 19:50:50.874457 INFO::Done
2024-11-19 19:50:50.875344 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:50.882327 INFO::ASW Batch was -0.0447063887108222 prior to batch effect correction and is now -0.172175075335561 .
2024-11-19 19:50:50.884921 INFO::Total function execution time is  0.162229061126709  s and adjustment time is  0.144083023071289 s ( 88.81 )
2024-11-19 19:50:50.903653 INFO::Skipping initial DF formatting
2024-11-19 19:50:50.904661 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:50.907941 INFO::Starting hierarchical adjustment
2024-11-19 19:50:50.908616 INFO::Found  5  batches.
2024-11-19 19:50:50.90908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:50.910051 INFO::Using default BPPARAM
2024-11-19 19:50:50.910878 INFO::Processing subtree level 1
2024-11-19 19:50:51.023816 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.031758 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.053267 INFO::Done
2024-11-19 19:50:51.054182 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.060697 INFO::ASW Batch was 0.507603977478603 prior to batch effect correction and is now 0.507603977478603 .
2024-11-19 19:50:51.061291 INFO::ASW Label was 0.377987728178966 prior to batch effect correction and is now 0.377987728178966 .
2024-11-19 19:50:51.063959 INFO::Total function execution time is  0.159914970397949  s and adjustment time is  0.144770860671997 s ( 90.53 )
2024-11-19 19:50:51.084558 INFO::Formatting Data.
2024-11-19 19:50:51.085237 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.086001 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.087405 INFO::Found  0  missing values.
2024-11-19 19:50:51.090659 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.091129 INFO::Done
2024-11-19 19:50:51.091569 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.093977 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.094566 INFO::Found  5  batches.
2024-11-19 19:50:51.094999 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.095815 INFO::Using default BPPARAM
2024-11-19 19:50:51.096266 INFO::Processing subtree level 1
2024-11-19 19:50:51.195738 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.202611 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.225304 INFO::Done
2024-11-19 19:50:51.225937 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.230498 INFO::ASW Batch was 0.360589155044161 prior to batch effect correction and is now -0.0809596345653075 .
2024-11-19 19:50:51.231525 INFO::ASW Label was 0.466099586959771 prior to batch effect correction and is now 0.726341543415703 .
2024-11-19 19:50:51.23265 INFO::Total function execution time is  0.148133039474487  s and adjustment time is  0.130825042724609 s ( 88.32 )
2024-11-19 19:50:51.233797 INFO::Formatting Data.
2024-11-19 19:50:51.234379 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.235661 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.237062 INFO::Found  0  missing values.
2024-11-19 19:50:51.240528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.240942 INFO::Done
2024-11-19 19:50:51.241332 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.244508 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.245553 INFO::Found  5  batches.
2024-11-19 19:50:51.246016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.24654 INFO::Using default BPPARAM
2024-11-19 19:50:51.246972 INFO::Processing subtree level 1
2024-11-19 19:50:51.336256 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.349307 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.373417 INFO::Done
2024-11-19 19:50:51.37404 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.378012 INFO::ASW Batch was 0.360589155044161 prior to batch effect correction and is now -0.0809596345653075 .
2024-11-19 19:50:51.378542 INFO::ASW Label was 0.466099586959771 prior to batch effect correction and is now 0.726341543415703 .
2024-11-19 19:50:51.380048 INFO::Total function execution time is  0.146255016326904  s and adjustment time is  0.128371000289917 s ( 87.77 )
2024-11-19 19:50:51.396733 INFO::Formatting Data.
2024-11-19 19:50:51.397357 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.39897 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.400071 INFO::Found  0  missing values.
2024-11-19 19:50:51.404038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.404553 INFO::Done
2024-11-19 19:50:51.405046 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.40795 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.408901 INFO::Found  5  batches.
2024-11-19 19:50:51.409325 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.40981 INFO::Using default BPPARAM
2024-11-19 19:50:51.410225 INFO::Processing subtree level 1
2024-11-19 19:50:51.503232 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.50935 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.531253 INFO::Done
2024-11-19 19:50:51.531869 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.536428 INFO::ASW Batch was 0.307693649627469 prior to batch effect correction and is now -0.0568850553439126 .
2024-11-19 19:50:51.536959 INFO::ASW Label was 0.486012538926672 prior to batch effect correction and is now 0.863976141503791 .
2024-11-19 19:50:51.537882 INFO::Total function execution time is  0.141200065612793  s and adjustment time is  0.122781991958618 s ( 86.96 )
2024-11-19 19:50:51.538613 INFO::Formatting Data.
2024-11-19 19:50:51.539124 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.540626 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.541607 INFO::Found  0  missing values.
2024-11-19 19:50:51.545121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.545526 INFO::Done
2024-11-19 19:50:51.545927 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.548143 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.548978 INFO::Found  5  batches.
2024-11-19 19:50:51.549368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.550223 INFO::Using default BPPARAM
2024-11-19 19:50:51.550649 INFO::Processing subtree level 1
2024-11-19 19:50:51.638425 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.653115 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.676964 INFO::Done
2024-11-19 19:50:51.677592 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.683199 INFO::ASW Batch was 0.307693649627469 prior to batch effect correction and is now -0.0568850553439126 .
2024-11-19 19:50:51.683754 INFO::ASW Label was 0.486012538926672 prior to batch effect correction and is now 0.863976141503791 .
2024-11-19 19:50:51.684967 INFO::Total function execution time is  0.146336078643799  s and adjustment time is  0.128062009811401 s ( 87.51 )
2024-11-19 19:50:51.703061 INFO::Formatting Data.
2024-11-19 19:50:51.703762 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.704844 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.705755 INFO::Found  0  missing values.
2024-11-19 19:50:51.708326 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.708741 INFO::Done
2024-11-19 19:50:51.709137 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.711367 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.71196 INFO::Found  2  batches.
2024-11-19 19:50:51.712717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.713251 INFO::Using default BPPARAM
2024-11-19 19:50:51.713704 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.714481 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.726171 INFO::Done
2024-11-19 19:50:51.726701 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.729333 INFO::ASW Batch was 0.38988637780227 prior to batch effect correction and is now 0.0803095996956802 .
2024-11-19 19:50:51.729803 INFO::ASW Label was 0.696632835695487 prior to batch effect correction and is now 0.886737414289698 .
2024-11-19 19:50:51.73041 INFO::Total function execution time is  0.027479887008667  s and adjustment time is  0.0143449306488037 s ( 52.2 )
2024-11-19 19:50:51.731047 INFO::Formatting Data.
2024-11-19 19:50:51.73154 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.732229 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.733066 INFO::Found  0  missing values.
2024-11-19 19:50:51.735193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.735603 INFO::Done
2024-11-19 19:50:51.735996 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.738262 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.738873 INFO::Found  2  batches.
2024-11-19 19:50:51.739316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.739839 INFO::Using default BPPARAM
2024-11-19 19:50:51.740278 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.741363 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.753895 INFO::Done
2024-11-19 19:50:51.754515 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.75703 INFO::ASW Batch was 0.38988637780227 prior to batch effect correction and is now 0.0803095996956802 .
2024-11-19 19:50:51.757514 INFO::ASW Label was 0.696632835695487 prior to batch effect correction and is now 0.886737414289698 .
2024-11-19 19:50:51.758178 INFO::Total function execution time is  0.0271179676055908  s and adjustment time is  0.0151240825653076 s ( 55.77 )
2024-11-19 19:50:51.771161 INFO::Formatting Data.
2024-11-19 19:50:51.771876 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.772704 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.773478 INFO::Found  0  missing values.
2024-11-19 19:50:51.77521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.775837 INFO::Done
2024-11-19 19:50:51.776332 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.777888 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.778439 INFO::Found  2  batches.
2024-11-19 19:50:51.778882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.779372 INFO::Using default BPPARAM
2024-11-19 19:50:51.779794 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.780479 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.805954 INFO::Done
2024-11-19 19:50:51.806547 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.808157 INFO::ASW Batch was 0.0722047798550737 prior to batch effect correction and is now -0.139789640370017 .
2024-11-19 19:50:51.808827 INFO::Total function execution time is  0.0378389358520508  s and adjustment time is  0.0276000499725342 s ( 72.94 )
2024-11-19 19:50:51.821638 INFO::Formatting Data.
2024-11-19 19:50:51.822268 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.823044 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.824409 INFO::Found  0  missing values.
2024-11-19 19:50:51.825451 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.
2024-11-19 19:50:51.828909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.829336 INFO::Done
2024-11-19 19:50:51.829761 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.832109 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.832699 INFO::Found  2  batches.
2024-11-19 19:50:51.833144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.833662 INFO::Using default BPPARAM
2024-11-19 19:50:51.834109 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.834872 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.849018 INFO::Done
2024-11-19 19:50:51.849607 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.852005 INFO::ASW Batch was 0.692122975801133 prior to batch effect correction and is now 0.0218829035761456 .
2024-11-19 19:50:51.852475 INFO::ASW Label was 0.401769910590119 prior to batch effect correction and is now 0.902315669711984 .
2024-11-19 19:50:51.853124 INFO::Total function execution time is  0.0315549373626709  s and adjustment time is  0.0164110660552979 s ( 52.01 )
2024-11-19 19:50:51.853776 INFO::Formatting Data.
2024-11-19 19:50:51.854314 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:51.855567 INFO::Removing potential empty rows and columns
2024-11-19 19:50:51.856347 INFO::Found  0  missing values.
2024-11-19 19:50:51.857089 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.
2024-11-19 19:50:51.860795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:51.861244 INFO::Done
2024-11-19 19:50:51.861659 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:51.863998 INFO::Starting hierarchical adjustment
2024-11-19 19:50:51.864564 INFO::Found  2  batches.
2024-11-19 19:50:51.864981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:51.865482 INFO::Using default BPPARAM
2024-11-19 19:50:51.865915 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:51.866674 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:51.879874 INFO::Done
2024-11-19 19:50:51.880453 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:51.882765 INFO::ASW Batch was 0.692122975801133 prior to batch effect correction and is now 0.0218829035761456 .
2024-11-19 19:50:51.883254 INFO::ASW Label was 0.401769910590119 prior to batch effect correction and is now 0.902315669711984 .
2024-11-19 19:50:51.883901 INFO::Total function execution time is  0.0301430225372314  s and adjustment time is  0.0153830051422119 s ( 51.03 )
2024-11-19 19:50:52.056794 INFO::Formatting Data.
2024-11-19 19:50:52.057745 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:52.058603 INFO::Removing potential empty rows and columns
2024-11-19 19:50:52.059451 INFO::Found  0  missing values.
2024-11-19 19:50:52.061913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:52.062382 INFO::Done
2024-11-19 19:50:52.062798 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:52.064505 INFO::Starting hierarchical adjustment
2024-11-19 19:50:52.065093 INFO::Found  3  batches.
2024-11-19 19:50:52.06554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:52.066049 INFO::Using default BPPARAM
2024-11-19 19:50:52.066442 INFO::Processing subtree level 1
2024-11-19 19:50:52.151926 INFO::Adjusting the last 1 batches sequentially
2024-11-19 19:50:52.158064 INFO::Done
2024-11-19 19:50:52.159254 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:52.164778 INFO::ASW Batch was -0.115957595488708 prior to batch effect correction and is now -0.115957595488708 .
2024-11-19 19:50:52.167996 INFO::Total function execution time is  0.110524892807007  s and adjustment time is  0.0930690765380859 s ( 84.21 )
2024-11-19 19:50:52.169721 INFO::Formatting Data.
2024-11-19 19:50:52.170245 INFO::Typecasting input to dataframe.
2024-11-19 19:50:52.171195 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:52.172409 INFO::Removing potential empty rows and columns
2024-11-19 19:50:52.173356 INFO::Found  0  missing values.
2024-11-19 19:50:52.176721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:52.177913 INFO::Done
2024-11-19 19:50:52.17837 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:52.180344 INFO::Starting hierarchical adjustment
2024-11-19 19:50:52.180872 INFO::Found  3  batches.
2024-11-19 19:50:52.181283 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:52.182114 INFO::Using default BPPARAM
2024-11-19 19:50:52.182523 INFO::Processing subtree level 1
2024-11-19 19:50:52.388114 INFO::Adjusting the last 1 batches sequentially
2024-11-19 19:50:52.390853 INFO::Done
2024-11-19 19:50:52.391506 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:52.394903 INFO::ASW Batch was -0.115957595488708 prior to batch effect correction and is now -0.115957595488708 .
2024-11-19 19:50:52.407065 INFO::Total function execution time is  0.234923124313354  s and adjustment time is  0.210057020187378 s ( 89.42 )
2024-11-19 19:50:52.433989 INFO::Formatting Data.
2024-11-19 19:50:52.435027 INFO::Typecasting input to dataframe.
2024-11-19 19:50:52.43576 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:52.437098 INFO::Removing potential empty rows and columns
2024-11-19 19:50:52.439356 INFO::Found  0  missing values.
2024-11-19 19:50:52.442161 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:52.443039 INFO::Done
2024-11-19 19:50:52.443824 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:52.445482 INFO::Starting hierarchical adjustment
2024-11-19 19:50:52.446027 INFO::Found  3  batches.
2024-11-19 19:50:52.446914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:52.447727 INFO::Using default BPPARAM
2024-11-19 19:50:52.448144 INFO::Processing subtree level 1
2024-11-19 19:50:52.664587 INFO::Adjusting the last 1 batches sequentially
2024-11-19 19:50:52.666939 INFO::Done
2024-11-19 19:50:52.667528 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:52.670362 INFO::ASW Batch was -0.0946305087837037 prior to batch effect correction and is now -0.0946305087837037 .
2024-11-19 19:50:52.671458 INFO::Total function execution time is  0.237734079360962  s and adjustment time is  0.220998048782349 s ( 92.96 )
2024-11-19 19:50:52.963892 INFO::Formatting Data.
2024-11-19 19:50:52.964671 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:52.965769 INFO::Removing potential empty rows and columns
2024-11-19 19:50:52.969216 INFO::Found  1000  missing values.
2024-11-19 19:50:52.986939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:52.987557 INFO::Done
2024-11-19 19:50:52.988063 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:52.992513 INFO::Starting hierarchical adjustment
2024-11-19 19:50:52.993194 INFO::Found  10  batches.
2024-11-19 19:50:52.993632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:52.994143 INFO::Using default BPPARAM
2024-11-19 19:50:52.994578 INFO::Processing subtree level 1
2024-11-19 19:50:53.145268 INFO::Processing subtree level 2
2024-11-19 19:50:53.337984 INFO::Adjusting the last 1 batches sequentially
2024-11-19 19:50:53.345205 INFO::Done
2024-11-19 19:50:53.347291 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:53.355436 INFO::ASW Batch was 0.473726305261237 prior to batch effect correction and is now 0.473726305261237 .
2024-11-19 19:50:53.356962 INFO::ASW Label was 0.349040565708307 prior to batch effect correction and is now 0.349040565708307 .
2024-11-19 19:50:53.358948 INFO::Total function execution time is  0.394670009613037  s and adjustment time is  0.352100849151611 s ( 89.21 )
2024-11-19 19:50:53.360047 INFO::Formatting Data.
2024-11-19 19:50:53.360561 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:53.361902 INFO::Removing potential empty rows and columns
2024-11-19 19:50:53.365152 INFO::Found  1000  missing values.
2024-11-19 19:50:53.381468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:53.382075 INFO::Done
2024-11-19 19:50:53.38254 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:53.386929 INFO::Starting hierarchical adjustment
2024-11-19 19:50:53.38791 INFO::Found  10  batches.
2024-11-19 19:50:54.209877 INFO::Set up parallel execution backend with 2 workers
2024-11-19 19:50:54.21051 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-19 19:50:55.23012 INFO::Adjusting the last 2 batches sequentially
2024-11-19 19:50:55.231248 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 19:50:55.243744 INFO::Done
2024-11-19 19:50:55.244274 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:55.24866 INFO::ASW Batch was 0.473726305261237 prior to batch effect correction and is now 0.473726305261237 .
2024-11-19 19:50:55.249187 INFO::ASW Label was 0.349040565708307 prior to batch effect correction and is now 0.349040565708307 .
2024-11-19 19:50:55.249764 INFO::Total function execution time is  1.88975787162781  s and adjustment time is  1.85593891143799 s ( 98.21 )
2024-11-19 19:50:55.411071 INFO::Formatting Data.
2024-11-19 19:50:55.411739 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.412895 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.414132 INFO::Found  0  missing values.
2024-11-19 19:50:55.416861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.417265 INFO::Done
2024-11-19 19:50:55.417667 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 19:50:55.419894 INFO::Starting hierarchical adjustment
2024-11-19 19:50:55.420481 INFO::Found  3  batches.
2024-11-19 19:50:55.420971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 19:50:55.421814 INFO::Using default BPPARAM
2024-11-19 19:50:55.422301 INFO::Processing subtree level 1
2024-11-19 19:50:55.529622 INFO::Adjusting the last 1 batches sequentially
2024-11-19 19:50:55.539837 INFO::Done
2024-11-19 19:50:55.541376 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 19:50:55.549893 INFO::ASW Batch was 0.154135485964991 prior to batch effect correction and is now -0.166514069475374 .
2024-11-19 19:50:55.550912 INFO::ASW Label was -0.1765719379588 prior to batch effect correction and is now -0.0780603295623283 .
2024-11-19 19:50:55.55304 INFO::Total function execution time is  0.142015933990479  s and adjustment time is  0.119432926177979 s ( 84.1 )
2024-11-19 19:50:55.697977 INFO::Formatting Data.
2024-11-19 19:50:55.698716 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.699836 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.700723 INFO::Found  2  missing values.
2024-11-19 19:50:55.703113 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.703547 INFO::Done
2024-11-19 19:50:55.735113 INFO::Found NA in Reference column
2024-11-19 19:50:55.746435 INFO::Require at least two references per batch.
2024-11-19 19:50:55.767421 INFO::Formatting Data.
2024-11-19 19:50:55.768084 INFO::Recognized SummarizedExperiment
2024-11-19 19:50:55.768546 INFO::Typecasting input to dataframe.
2024-11-19 19:50:55.776825 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.777783 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.780714 INFO::Found  0  missing values.
2024-11-19 19:50:55.786605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.787154 INFO::Done
2024-11-19 19:50:55.800812 INFO::Formatting Data.
2024-11-19 19:50:55.801484 INFO::Recognized SummarizedExperiment
2024-11-19 19:50:55.80193 INFO::Typecasting input to dataframe.
2024-11-19 19:50:55.816502 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.817553 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.8203 INFO::Found  0  missing values.
2024-11-19 19:50:55.828587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.829312 INFO::Done
2024-11-19 19:50:55.843245 INFO::Formatting Data.
2024-11-19 19:50:55.843828 INFO::Recognized SummarizedExperiment
2024-11-19 19:50:55.844263 INFO::Typecasting input to dataframe.
2024-11-19 19:50:55.858882 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.859758 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.860687 INFO::Found  0  missing values.
2024-11-19 19:50:55.86147 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.
2024-11-19 19:50:55.865382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.865833 INFO::Done
2024-11-19 19:50:55.877953 INFO::Formatting Data.
2024-11-19 19:50:55.87862 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.879386 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.880235 INFO::Found  0  missing values.
2024-11-19 19:50:55.882731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.883184 INFO::Done
2024-11-19 19:50:55.895354 INFO::Formatting Data.
2024-11-19 19:50:55.896011 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.896774 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.897615 INFO::Found  0  missing values.
2024-11-19 19:50:55.900499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.90095 INFO::Done
2024-11-19 19:50:55.93481 INFO::Formatting Data.
2024-11-19 19:50:55.935504 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.936583 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.93754 INFO::Found  1  missing values.
2024-11-19 19:50:55.939542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.939956 INFO::Done
2024-11-19 19:50:55.961134 INFO::Formatting Data.
2024-11-19 19:50:55.961847 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.962575 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.963344 INFO::Found  2  missing values.
2024-11-19 19:50:55.964102 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.
2024-11-19 19:50:55.965942 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.966374 INFO::Done
2024-11-19 19:50:55.979056 INFO::Formatting Data.
2024-11-19 19:50:55.979844 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.980634 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.981389 INFO::Found  2  missing values.
2024-11-19 19:50:55.982656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:55.983277 INFO::Done
2024-11-19 19:50:55.995189 INFO::Formatting Data.
2024-11-19 19:50:55.99587 INFO::Typecasting input to dataframe.
2024-11-19 19:50:55.996554 INFO::Replacing NaNs with NAs.
2024-11-19 19:50:55.997305 INFO::Removing potential empty rows and columns
2024-11-19 19:50:55.998489 INFO::Found  0  missing values.
2024-11-19 19:50:56.00085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 19:50:56.001277 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 15.232   3.025  18.556

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT18.913 1.01513.620
compute_asw0.0210.0010.023
count_existing0.0120.0010.014
generate_data_covariables0.0110.0010.011
generate_dataset0.0100.0010.011