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This page was generated on 2024-06-19 12:10 -0400 (Wed, 19 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4687
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4402
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4351
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 154/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.1.0  (landing page)
Yannis Schumann
Snapshot Date: 2024-06-18 14:00 -0400 (Tue, 18 Jun 2024)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: devel
git_last_commit: 17da2e9
git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BERT on nebbiolo2

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: 1.1.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.0.tar.gz
StartedAt: 2024-06-18 20:55:32 -0400 (Tue, 18 Jun 2024)
EndedAt: 2024-06-18 20:56:59 -0400 (Tue, 18 Jun 2024)
EllapsedTime: 87.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.0’
* 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 loading without being on the library search path ... 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 24.394  1.134  17.743
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
2024-06-18 20:56:23.910581 INFO::Formatting Data.
2024-06-18 20:56:23.912059 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:23.923089 INFO::Removing potential empty rows and columns
2024-06-18 20:56:24.185315 INFO::Found  0  missing values.
2024-06-18 20:56:24.18905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:24.189707 INFO::Done
2024-06-18 20:56:24.190236 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:24.202607 INFO::Starting hierarchical adjustment
2024-06-18 20:56:24.203463 INFO::Found  3  batches.
2024-06-18 20:56:24.203995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:24.205112 INFO::Using default BPPARAM
2024-06-18 20:56:24.205643 INFO::Processing subtree level 1
2024-06-18 20:56:24.310801 INFO::Adjusting the last 1 batches sequentially
2024-06-18 20:56:24.312745 INFO::Done
2024-06-18 20:56:24.313396 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:24.316005 INFO::ASW Batch was -0.0471011690038482 prior to batch effect correction and is now -0.0471011690038482 .
2024-06-18 20:56:24.317084 INFO::Total function execution time is  0.407367944717407  s and adjustment time is  0.109436750411987 s ( 26.86 )
2024-06-18 20:56:24.331807 INFO::Formatting Data.
2024-06-18 20:56:24.33261 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:24.333536 INFO::Removing potential empty rows and columns
2024-06-18 20:56:24.33464 INFO::Found  0  missing values.
2024-06-18 20:56:24.33557 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.
2024-06-18 20:56:24.347 INFO::Formatting Data.
2024-06-18 20:56:24.347759 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:24.348721 INFO::Removing potential empty rows and columns
2024-06-18 20:56:24.34978 INFO::Found  0  missing values.
2024-06-18 20:56:24.350714 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.
2024-06-18 20:56:24.366775 INFO::Formatting Data.
2024-06-18 20:56:24.367532 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:24.368386 INFO::Removing potential empty rows and columns
2024-06-18 20:56:24.369393 INFO::Found  0  missing values.
2024-06-18 20:56:24.370274 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.
2024-06-18 20:56:24.374464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:24.374967 INFO::Done
2024-06-18 20:56:24.375456 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:24.377431 INFO::Starting hierarchical adjustment
2024-06-18 20:56:24.37809 INFO::Found  2  batches.
2024-06-18 20:56:24.37857 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:24.379159 INFO::Using default BPPARAM
2024-06-18 20:56:24.379637 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:24.380547 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:24.402515 INFO::Done
2024-06-18 20:56:24.403148 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:24.405071 INFO::ASW Batch was -0.088305681237318 prior to batch effect correction and is now -0.127626758764594 .
2024-06-18 20:56:24.405795 INFO::Total function execution time is  0.039109468460083  s and adjustment time is  0.0245366096496582 s ( 62.74 )
2024-06-18 20:56:24.40844 INFO::Formatting Data.
2024-06-18 20:56:24.409015 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:24.417282 INFO::Formatting Data.
2024-06-18 20:56:24.417897 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:24.418702 INFO::Removing potential empty rows and columns
2024-06-18 20:56:24.41965 INFO::Found  0  missing values.
2024-06-18 20:56:24.422288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:24.422773 INFO::Done
2024-06-18 20:56:24.423247 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:24.425148 INFO::Starting hierarchical adjustment
2024-06-18 20:56:24.425786 INFO::Found  2  batches.
2024-06-18 20:56:24.426275 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:24.426818 INFO::Using default BPPARAM
2024-06-18 20:56:24.427293 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:24.428113 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:24.442471 INFO::Done
2024-06-18 20:56:24.443097 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:24.445025 INFO::ASW Batch was 0.0145675714769909 prior to batch effect correction and is now -0.124658759043159 .
2024-06-18 20:56:24.445751 INFO::Total function execution time is  0.0284895896911621  s and adjustment time is  0.0168139934539795 s ( 59.02 )
2024-06-18 20:56:24.446742 INFO::Formatting Data.
2024-06-18 20:56:24.447284 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:24.448091 INFO::Removing potential empty rows and columns
2024-06-18 20:56:24.44908 INFO::Found  0  missing values.
2024-06-18 20:56:24.45173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:24.452214 INFO::Done
2024-06-18 20:56:24.4527 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:24.454586 INFO::Starting hierarchical adjustment
2024-06-18 20:56:24.455227 INFO::Found  2  batches.
2024-06-18 20:56:24.455714 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:24.456272 INFO::Using default BPPARAM
2024-06-18 20:56:24.456756 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:24.457589 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:24.472044 INFO::Done
2024-06-18 20:56:24.472702 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:24.474664 INFO::ASW Batch was 0.0145675714769909 prior to batch effect correction and is now -0.124658759043159 .
2024-06-18 20:56:24.475404 INFO::Total function execution time is  0.0286712646484375  s and adjustment time is  0.0169382095336914 s ( 59.08 )
2024-06-18 20:56:26.83446 INFO::Formatting Data.
2024-06-18 20:56:26.835208 INFO::Recognized SummarizedExperiment
2024-06-18 20:56:26.835671 INFO::Typecasting input to dataframe.
2024-06-18 20:56:26.86577 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:26.866923 INFO::Removing potential empty rows and columns
2024-06-18 20:56:26.870167 INFO::Found  0  missing values.
2024-06-18 20:56:26.876203 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:26.876764 INFO::Done
2024-06-18 20:56:26.877208 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:26.880364 INFO::Starting hierarchical adjustment
2024-06-18 20:56:26.880983 INFO::Found  2  batches.
2024-06-18 20:56:26.881425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:26.882364 INFO::Using default BPPARAM
2024-06-18 20:56:26.882831 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:26.883649 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:26.964166 INFO::Done
2024-06-18 20:56:26.964954 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:26.968176 INFO::ASW Batch was 0.000403728784377548 prior to batch effect correction and is now -0.0902431799766026 .
2024-06-18 20:56:26.96898 INFO::Total function execution time is  0.134841203689575  s and adjustment time is  0.0831732749938965 s ( 61.68 )
2024-06-18 20:56:26.985659 INFO::Formatting Data.
2024-06-18 20:56:26.986266 INFO::Recognized SummarizedExperiment
2024-06-18 20:56:26.98668 INFO::Typecasting input to dataframe.
2024-06-18 20:56:26.994776 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:26.995762 INFO::Removing potential empty rows and columns
2024-06-18 20:56:26.998595 INFO::Found  0  missing values.
2024-06-18 20:56:27.00404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:27.004534 INFO::Done
2024-06-18 20:56:27.004951 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:27.007703 INFO::Starting hierarchical adjustment
2024-06-18 20:56:27.008286 INFO::Found  2  batches.
2024-06-18 20:56:27.00872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:27.009218 INFO::Using default BPPARAM
2024-06-18 20:56:27.009658 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:27.010473 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:27.031149 INFO::Done
2024-06-18 20:56:27.031762 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:27.034689 INFO::ASW Batch was 0.00664568536935903 prior to batch effect correction and is now 0.00664568536935903 .
2024-06-18 20:56:27.035417 INFO::Total function execution time is  0.0497376918792725  s and adjustment time is  0.0229413509368896 s ( 46.12 )
2024-06-18 20:56:27.04994 INFO::Formatting Data.
2024-06-18 20:56:27.050588 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:27.051317 INFO::Removing potential empty rows and columns
2024-06-18 20:56:27.052139 INFO::Found  0  missing values.
2024-06-18 20:56:27.054462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:27.054886 INFO::Done
2024-06-18 20:56:27.055292 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:27.056913 INFO::Starting hierarchical adjustment
2024-06-18 20:56:27.057478 INFO::Found  3  batches.
2024-06-18 20:56:27.057918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:27.058419 INFO::Using default BPPARAM
2024-06-18 20:56:27.058837 INFO::Processing subtree level 1
2024-06-18 20:56:27.213918 INFO::Adjusting the last 1 batches sequentially
2024-06-18 20:56:27.215586 INFO::Done
2024-06-18 20:56:27.216167 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:27.218529 INFO::ASW Batch was -0.139559841301794 prior to batch effect correction and is now -0.184104766147893 .
2024-06-18 20:56:27.219412 INFO::Total function execution time is  0.169462919235229  s and adjustment time is  0.158199071884155 s ( 93.35 )
2024-06-18 20:56:27.233695 INFO::Skipping initial DF formatting
2024-06-18 20:56:27.234359 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:27.238271 INFO::Starting hierarchical adjustment
2024-06-18 20:56:27.239 INFO::Found  5  batches.
2024-06-18 20:56:27.239475 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:27.240044 INFO::Using default BPPARAM
2024-06-18 20:56:27.240557 INFO::Processing subtree level 1
2024-06-18 20:56:27.406936 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:27.408856 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:27.433105 INFO::Done
2024-06-18 20:56:27.433938 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:27.438599 INFO::ASW Batch was 0.495183794727009 prior to batch effect correction and is now 0.495183794727009 .
2024-06-18 20:56:27.439347 INFO::ASW Label was 0.367959648169366 prior to batch effect correction and is now 0.367959648169366 .
2024-06-18 20:56:27.440478 INFO::Total function execution time is  0.206788778305054  s and adjustment time is  0.194208860397339 s ( 93.92 )
2024-06-18 20:56:27.458539 INFO::Formatting Data.
2024-06-18 20:56:27.459312 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:27.460229 INFO::Removing potential empty rows and columns
2024-06-18 20:56:27.461254 INFO::Found  0  missing values.
2024-06-18 20:56:27.465402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:27.465972 INFO::Done
2024-06-18 20:56:27.466494 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:27.469523 INFO::Starting hierarchical adjustment
2024-06-18 20:56:27.470258 INFO::Found  5  batches.
2024-06-18 20:56:27.470786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:27.471398 INFO::Using default BPPARAM
2024-06-18 20:56:27.471956 INFO::Processing subtree level 1
2024-06-18 20:56:27.590632 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:27.59241 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:27.614735 INFO::Done
2024-06-18 20:56:27.61592 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:27.619673 INFO::ASW Batch was 0.54532148533048 prior to batch effect correction and is now -0.0259483899054848 .
2024-06-18 20:56:27.620293 INFO::ASW Label was 0.188641139590062 prior to batch effect correction and is now 0.809051439181315 .
2024-06-18 20:56:27.62121 INFO::Total function execution time is  0.16269063949585  s and adjustment time is  0.14448356628418 s ( 88.81 )
2024-06-18 20:56:27.622137 INFO::Formatting Data.
2024-06-18 20:56:27.622802 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:27.623776 INFO::Removing potential empty rows and columns
2024-06-18 20:56:27.624914 INFO::Found  0  missing values.
2024-06-18 20:56:27.629354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:27.629957 INFO::Done
2024-06-18 20:56:27.630507 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:27.633678 INFO::Starting hierarchical adjustment
2024-06-18 20:56:27.634438 INFO::Found  5  batches.
2024-06-18 20:56:27.634994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:27.635652 INFO::Using default BPPARAM
2024-06-18 20:56:27.63621 INFO::Processing subtree level 1
2024-06-18 20:56:27.766033 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:27.767764 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:27.785199 INFO::Done
2024-06-18 20:56:27.785946 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:27.789314 INFO::ASW Batch was 0.54532148533048 prior to batch effect correction and is now -0.0259483899054848 .
2024-06-18 20:56:27.789963 INFO::ASW Label was 0.188641139590062 prior to batch effect correction and is now 0.809051439181315 .
2024-06-18 20:56:27.790839 INFO::Total function execution time is  0.168695211410522  s and adjustment time is  0.150904417037964 s ( 89.45 )
2024-06-18 20:56:27.804506 INFO::Formatting Data.
2024-06-18 20:56:27.805268 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:27.806176 INFO::Removing potential empty rows and columns
2024-06-18 20:56:27.807179 INFO::Found  0  missing values.
2024-06-18 20:56:27.81133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:27.811889 INFO::Done
2024-06-18 20:56:27.812432 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:27.815469 INFO::Starting hierarchical adjustment
2024-06-18 20:56:27.816204 INFO::Found  5  batches.
2024-06-18 20:56:27.816771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:27.817375 INFO::Using default BPPARAM
2024-06-18 20:56:27.81791 INFO::Processing subtree level 1
2024-06-18 20:56:27.944271 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:27.946085 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:27.963804 INFO::Done
2024-06-18 20:56:27.964673 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:27.968078 INFO::ASW Batch was 0.641466526553231 prior to batch effect correction and is now -0.0941406327860551 .
2024-06-18 20:56:27.96877 INFO::ASW Label was 0.118616639053237 prior to batch effect correction and is now 0.822872427456449 .
2024-06-18 20:56:27.969687 INFO::Total function execution time is  0.165217399597168  s and adjustment time is  0.147700548171997 s ( 89.4 )
2024-06-18 20:56:27.970627 INFO::Formatting Data.
2024-06-18 20:56:27.971308 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:27.972237 INFO::Removing potential empty rows and columns
2024-06-18 20:56:27.973384 INFO::Found  0  missing values.
2024-06-18 20:56:27.977638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:27.978224 INFO::Done
2024-06-18 20:56:27.978756 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:27.981975 INFO::Starting hierarchical adjustment
2024-06-18 20:56:27.982735 INFO::Found  5  batches.
2024-06-18 20:56:27.983288 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:27.983918 INFO::Using default BPPARAM
2024-06-18 20:56:27.98447 INFO::Processing subtree level 1
2024-06-18 20:56:28.119009 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:28.120911 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:28.141061 INFO::Done
2024-06-18 20:56:28.142041 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:28.145911 INFO::ASW Batch was 0.641466526553231 prior to batch effect correction and is now -0.0941406327860551 .
2024-06-18 20:56:28.146599 INFO::ASW Label was 0.118616639053237 prior to batch effect correction and is now 0.822872427456449 .
2024-06-18 20:56:28.147583 INFO::Total function execution time is  0.176927089691162  s and adjustment time is  0.158378601074219 s ( 89.52 )
2024-06-18 20:56:28.163252 INFO::Formatting Data.
2024-06-18 20:56:28.164081 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:28.165084 INFO::Removing potential empty rows and columns
2024-06-18 20:56:28.166216 INFO::Found  0  missing values.
2024-06-18 20:56:28.169098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:28.169657 INFO::Done
2024-06-18 20:56:28.170191 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:28.173383 INFO::Starting hierarchical adjustment
2024-06-18 20:56:28.174185 INFO::Found  2  batches.
2024-06-18 20:56:28.174753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:28.175413 INFO::Using default BPPARAM
2024-06-18 20:56:28.175982 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:28.177008 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:28.193564 INFO::Done
2024-06-18 20:56:28.194324 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:28.201957 INFO::ASW Batch was 0.52646185174866 prior to batch effect correction and is now 0.0441131063889147 .
2024-06-18 20:56:28.202744 INFO::ASW Label was 0.604420581436608 prior to batch effect correction and is now 0.894868153639904 .
2024-06-18 20:56:28.203665 INFO::Total function execution time is  0.0404820442199707  s and adjustment time is  0.0195355415344238 s ( 48.26 )
2024-06-18 20:56:28.204539 INFO::Formatting Data.
2024-06-18 20:56:28.205148 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:28.206066 INFO::Removing potential empty rows and columns
2024-06-18 20:56:28.207089 INFO::Found  0  missing values.
2024-06-18 20:56:28.209852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:28.210388 INFO::Done
2024-06-18 20:56:28.210895 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:28.214051 INFO::Starting hierarchical adjustment
2024-06-18 20:56:28.214799 INFO::Found  2  batches.
2024-06-18 20:56:28.215315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:28.215929 INFO::Using default BPPARAM
2024-06-18 20:56:28.216522 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:28.217493 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:28.23286 INFO::Done
2024-06-18 20:56:28.233465 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:28.236278 INFO::ASW Batch was 0.52646185174866 prior to batch effect correction and is now 0.0441131063889147 .
2024-06-18 20:56:28.236859 INFO::ASW Label was 0.604420581436608 prior to batch effect correction and is now 0.894868153639904 .
2024-06-18 20:56:28.23759 INFO::Total function execution time is  0.0330982208251953  s and adjustment time is  0.0182254314422607 s ( 55.06 )
2024-06-18 20:56:28.248772 INFO::Formatting Data.
2024-06-18 20:56:28.24947 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:28.250332 INFO::Removing potential empty rows and columns
2024-06-18 20:56:28.251196 INFO::Found  0  missing values.
2024-06-18 20:56:28.25323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:28.253756 INFO::Done
2024-06-18 20:56:28.254279 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:28.256179 INFO::Starting hierarchical adjustment
2024-06-18 20:56:28.256906 INFO::Found  2  batches.
2024-06-18 20:56:28.257436 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:28.258049 INFO::Using default BPPARAM
2024-06-18 20:56:28.258556 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:28.259475 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:28.292454 INFO::Done
2024-06-18 20:56:28.293196 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:28.29522 INFO::ASW Batch was 0.161043686669658 prior to batch effect correction and is now -0.126239674939437 .
2024-06-18 20:56:28.296061 INFO::Total function execution time is  0.0473287105560303  s and adjustment time is  0.0356409549713135 s ( 75.31 )
2024-06-18 20:56:28.308077 INFO::Formatting Data.
2024-06-18 20:56:28.308866 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:28.309776 INFO::Removing potential empty rows and columns
2024-06-18 20:56:28.310764 INFO::Found  0  missing values.
2024-06-18 20:56:28.312049 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.
2024-06-18 20:56:28.349422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:28.350338 INFO::Done
2024-06-18 20:56:28.35091 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:28.354013 INFO::Starting hierarchical adjustment
2024-06-18 20:56:28.354767 INFO::Found  2  batches.
2024-06-18 20:56:28.355303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:28.35591 INFO::Using default BPPARAM
2024-06-18 20:56:28.356455 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:28.35747 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:28.376129 INFO::Done
2024-06-18 20:56:28.376868 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:28.380009 INFO::ASW Batch was 0.512657876599474 prior to batch effect correction and is now -0.0374439916674143 .
2024-06-18 20:56:28.380618 INFO::ASW Label was 0.606994978996011 prior to batch effect correction and is now 0.949825452917113 .
2024-06-18 20:56:28.381384 INFO::Total function execution time is  0.0733809471130371  s and adjustment time is  0.0214979648590088 s ( 29.3 )
2024-06-18 20:56:28.382147 INFO::Formatting Data.
2024-06-18 20:56:28.382777 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:28.383739 INFO::Removing potential empty rows and columns
2024-06-18 20:56:28.384792 INFO::Found  0  missing values.
2024-06-18 20:56:28.385747 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.
2024-06-18 20:56:28.39081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:28.391359 INFO::Done
2024-06-18 20:56:28.391884 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:28.395017 INFO::Starting hierarchical adjustment
2024-06-18 20:56:28.395738 INFO::Found  2  batches.
2024-06-18 20:56:28.396293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:28.396912 INFO::Using default BPPARAM
2024-06-18 20:56:28.397429 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:28.398426 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:28.417218 INFO::Done
2024-06-18 20:56:28.417899 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:28.421001 INFO::ASW Batch was 0.512657876599474 prior to batch effect correction and is now -0.0374439916674143 .
2024-06-18 20:56:28.421574 INFO::ASW Label was 0.606994978996011 prior to batch effect correction and is now 0.949825452917113 .
2024-06-18 20:56:28.422363 INFO::Total function execution time is  0.0402119159698486  s and adjustment time is  0.0216214656829834 s ( 53.77 )
2024-06-18 20:56:28.6476 INFO::Formatting Data.
2024-06-18 20:56:28.648992 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:28.650168 INFO::Removing potential empty rows and columns
2024-06-18 20:56:28.651389 INFO::Found  0  missing values.
2024-06-18 20:56:28.654611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:28.655174 INFO::Done
2024-06-18 20:56:28.655693 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:28.658114 INFO::Starting hierarchical adjustment
2024-06-18 20:56:28.658852 INFO::Found  3  batches.
2024-06-18 20:56:28.659387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:28.660024 INFO::Using default BPPARAM
2024-06-18 20:56:28.660563 INFO::Processing subtree level 1
2024-06-18 20:56:28.763495 INFO::Adjusting the last 1 batches sequentially
2024-06-18 20:56:28.765508 INFO::Done
2024-06-18 20:56:28.766275 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:28.769174 INFO::ASW Batch was 0.0310155755672019 prior to batch effect correction and is now 0.0310155755672019 .
2024-06-18 20:56:28.770354 INFO::Total function execution time is  0.123038768768311  s and adjustment time is  0.106784582138062 s ( 86.79 )
2024-06-18 20:56:28.77166 INFO::Formatting Data.
2024-06-18 20:56:28.772382 INFO::Typecasting input to dataframe.
2024-06-18 20:56:28.773281 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:28.774393 INFO::Removing potential empty rows and columns
2024-06-18 20:56:28.77565 INFO::Found  0  missing values.
2024-06-18 20:56:28.779026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:28.779656 INFO::Done
2024-06-18 20:56:28.780254 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:28.782713 INFO::Starting hierarchical adjustment
2024-06-18 20:56:28.783527 INFO::Found  3  batches.
2024-06-18 20:56:28.784114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:28.78481 INFO::Using default BPPARAM
2024-06-18 20:56:28.785411 INFO::Processing subtree level 1
2024-06-18 20:56:28.885549 INFO::Adjusting the last 1 batches sequentially
2024-06-18 20:56:28.887305 INFO::Done
2024-06-18 20:56:28.887961 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:28.890472 INFO::ASW Batch was 0.0310155755672019 prior to batch effect correction and is now 0.0310155755672019 .
2024-06-18 20:56:28.891431 INFO::Total function execution time is  0.119784355163574  s and adjustment time is  0.103960990905762 s ( 86.79 )
2024-06-18 20:56:28.905351 INFO::Formatting Data.
2024-06-18 20:56:28.906192 INFO::Typecasting input to dataframe.
2024-06-18 20:56:28.907094 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:28.908049 INFO::Removing potential empty rows and columns
2024-06-18 20:56:28.909227 INFO::Found  0  missing values.
2024-06-18 20:56:28.912575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:28.91313 INFO::Done
2024-06-18 20:56:28.913673 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:28.915737 INFO::Starting hierarchical adjustment
2024-06-18 20:56:28.916456 INFO::Found  3  batches.
2024-06-18 20:56:28.916988 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:28.917615 INFO::Using default BPPARAM
2024-06-18 20:56:28.918145 INFO::Processing subtree level 1
2024-06-18 20:56:29.01474 INFO::Adjusting the last 1 batches sequentially
2024-06-18 20:56:29.016503 INFO::Done
2024-06-18 20:56:29.01712 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:29.01957 INFO::ASW Batch was 0.0629085246569875 prior to batch effect correction and is now 0.0629085246569875 .
2024-06-18 20:56:29.020527 INFO::Total function execution time is  0.11522650718689  s and adjustment time is  0.100173234939575 s ( 86.94 )
2024-06-18 20:56:29.160701 INFO::Formatting Data.
2024-06-18 20:56:29.161635 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:29.162874 INFO::Removing potential empty rows and columns
2024-06-18 20:56:29.165723 INFO::Found  1000  missing values.
2024-06-18 20:56:29.185797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:29.186655 INFO::Done
2024-06-18 20:56:29.187275 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:29.193353 INFO::Starting hierarchical adjustment
2024-06-18 20:56:29.194185 INFO::Found  10  batches.
2024-06-18 20:56:29.194725 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:29.195333 INFO::Using default BPPARAM
2024-06-18 20:56:29.195853 INFO::Processing subtree level 1
2024-06-18 20:56:29.353683 INFO::Processing subtree level 2
2024-06-18 20:56:29.567472 INFO::Adjusting the last 1 batches sequentially
2024-06-18 20:56:29.569826 INFO::Done
2024-06-18 20:56:29.570639 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:29.57768 INFO::ASW Batch was 0.526033827912533 prior to batch effect correction and is now 0.526033827912533 .
2024-06-18 20:56:29.578497 INFO::ASW Label was 0.334799074693861 prior to batch effect correction and is now 0.334799074693861 .
2024-06-18 20:56:29.579614 INFO::Total function execution time is  0.419023275375366  s and adjustment time is  0.375763893127441 s ( 89.68 )
2024-06-18 20:56:29.58071 INFO::Formatting Data.
2024-06-18 20:56:29.581517 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:29.583009 INFO::Removing potential empty rows and columns
2024-06-18 20:56:29.586636 INFO::Found  1000  missing values.
2024-06-18 20:56:29.610479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:29.611393 INFO::Done
2024-06-18 20:56:29.612056 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:29.618812 INFO::Starting hierarchical adjustment
2024-06-18 20:56:29.619725 INFO::Found  10  batches.
2024-06-18 20:56:30.747641 INFO::Set up parallel execution backend with 2 workers
2024-06-18 20:56:30.749236 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-18 20:56:31.805426 INFO::Adjusting the last 2 batches sequentially
2024-06-18 20:56:31.806809 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-18 20:56:31.822412 INFO::Done
2024-06-18 20:56:31.823023 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:31.827615 INFO::ASW Batch was 0.526033827912533 prior to batch effect correction and is now 0.526033827912533 .
2024-06-18 20:56:31.828189 INFO::ASW Label was 0.334799074693861 prior to batch effect correction and is now 0.334799074693861 .
2024-06-18 20:56:31.828894 INFO::Total function execution time is  2.24827146530151  s and adjustment time is  2.20286822319031 s ( 97.98 )
2024-06-18 20:56:31.96094 INFO::Formatting Data.
2024-06-18 20:56:31.961684 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:31.962561 INFO::Removing potential empty rows and columns
2024-06-18 20:56:31.963567 INFO::Found  0  missing values.
2024-06-18 20:56:31.967067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:31.967585 INFO::Done
2024-06-18 20:56:31.96806 INFO::Acquiring quality metrics before batch effect correction.
2024-06-18 20:56:31.970726 INFO::Starting hierarchical adjustment
2024-06-18 20:56:31.971378 INFO::Found  3  batches.
2024-06-18 20:56:31.971849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-18 20:56:31.972422 INFO::Using default BPPARAM
2024-06-18 20:56:31.972909 INFO::Processing subtree level 1
2024-06-18 20:56:32.065275 INFO::Adjusting the last 1 batches sequentially
2024-06-18 20:56:32.066868 INFO::Done
2024-06-18 20:56:32.067455 INFO::Acquiring quality metrics after batch effect correction.
2024-06-18 20:56:32.070416 INFO::ASW Batch was 0.208214245024533 prior to batch effect correction and is now -0.135359931119681 .
2024-06-18 20:56:32.070997 INFO::ASW Label was -0.19476913244989 prior to batch effect correction and is now -0.0243005381401724 .
2024-06-18 20:56:32.071828 INFO::Total function execution time is  0.110926389694214  s and adjustment time is  0.0956039428710938 s ( 86.19 )
2024-06-18 20:56:32.178671 INFO::Formatting Data.
2024-06-18 20:56:32.179411 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.180233 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.181231 INFO::Found  2  missing values.
2024-06-18 20:56:32.183824 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.184307 INFO::Done
2024-06-18 20:56:32.207743 INFO::Found NA in Reference column
2024-06-18 20:56:32.216323 INFO::Require at least two references per batch.
2024-06-18 20:56:32.234411 INFO::Formatting Data.
2024-06-18 20:56:32.235128 INFO::Recognized SummarizedExperiment
2024-06-18 20:56:32.235618 INFO::Typecasting input to dataframe.
2024-06-18 20:56:32.244349 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.245446 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.24866 INFO::Found  0  missing values.
2024-06-18 20:56:32.25488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.255463 INFO::Done
2024-06-18 20:56:32.269377 INFO::Formatting Data.
2024-06-18 20:56:32.270069 INFO::Recognized SummarizedExperiment
2024-06-18 20:56:32.270556 INFO::Typecasting input to dataframe.
2024-06-18 20:56:32.286768 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.287944 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.29123 INFO::Found  0  missing values.
2024-06-18 20:56:32.301812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.302493 INFO::Done
2024-06-18 20:56:32.316631 INFO::Formatting Data.
2024-06-18 20:56:32.317361 INFO::Recognized SummarizedExperiment
2024-06-18 20:56:32.317858 INFO::Typecasting input to dataframe.
2024-06-18 20:56:32.333465 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.334437 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.335565 INFO::Found  0  missing values.
2024-06-18 20:56:32.336492 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.
2024-06-18 20:56:32.340746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.341332 INFO::Done
2024-06-18 20:56:32.351135 INFO::Formatting Data.
2024-06-18 20:56:32.35187 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.35272 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.353736 INFO::Found  0  missing values.
2024-06-18 20:56:32.360343 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.361027 INFO::Done
2024-06-18 20:56:32.372487 INFO::Formatting Data.
2024-06-18 20:56:32.373269 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.374138 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.375141 INFO::Found  0  missing values.
2024-06-18 20:56:32.377993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.378501 INFO::Done
2024-06-18 20:56:32.406666 INFO::Formatting Data.
2024-06-18 20:56:32.407464 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.408503 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.409609 INFO::Found  1  missing values.
2024-06-18 20:56:32.412134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.412703 INFO::Done
2024-06-18 20:56:32.430631 INFO::Formatting Data.
2024-06-18 20:56:32.431366 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.432163 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.433054 INFO::Found  2  missing values.
2024-06-18 20:56:32.433914 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.
2024-06-18 20:56:32.436048 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.436556 INFO::Done
2024-06-18 20:56:32.445576 INFO::Formatting Data.
2024-06-18 20:56:32.446258 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.447058 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.447937 INFO::Found  2  missing values.
2024-06-18 20:56:32.449442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.449926 INFO::Done
2024-06-18 20:56:32.459485 INFO::Formatting Data.
2024-06-18 20:56:32.460174 INFO::Typecasting input to dataframe.
2024-06-18 20:56:32.460917 INFO::Replacing NaNs with NAs.
2024-06-18 20:56:32.461712 INFO::Removing potential empty rows and columns
2024-06-18 20:56:32.462626 INFO::Found  0  missing values.
2024-06-18 20:56:32.465355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-18 20:56:32.465865 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 16.791   3.774  20.191 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT24.394 1.13417.743
compute_asw0.0240.0000.025
count_existing0.0140.0010.014
generate_data_covariables0.0130.0000.012
generate_dataset0.0120.0000.011