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This page was generated on 2024-05-04 11:36:18 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 156/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.0.0  (landing page)
Yannis Schumann
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_19
git_last_commit: 9a6bbaa
git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for BERT on nebbiolo1


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

raw results


Summary

Package: BERT
Version: 1.0.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz
StartedAt: 2024-05-03 21:00:43 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:02:13 -0400 (Fri, 03 May 2024)
EllapsedTime: 89.4 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 24.675  1.169  17.739
* 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-3.19-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 beta (2024-04-15 r86425) -- "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")
2024-05-03 21:01:36.51177 INFO::Formatting Data.
2024-05-03 21:01:36.51345 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:36.524218 INFO::Removing potential empty rows and columns
2024-05-03 21:01:36.774114 INFO::Found  0  missing values.
2024-05-03 21:01:36.777612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:36.778317 INFO::Done
2024-05-03 21:01:36.778893 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:36.791134 INFO::Starting hierarchical adjustment
2024-05-03 21:01:36.792047 INFO::Found  3  batches.
2024-05-03 21:01:36.792586 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:36.793711 INFO::Using default BPPARAM
2024-05-03 21:01:36.794281 INFO::Processing subtree level 1
2024-05-03 21:01:36.883623 INFO::Adjusting the last 1 batches sequentially
2024-05-03 21:01:36.885414 INFO::Done
2024-05-03 21:01:36.886075 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:36.888566 INFO::ASW Batch was 0.0416507221885453 prior to batch effect correction and is now 0.0416507221885453 .
2024-05-03 21:01:36.889635 INFO::Total function execution time is  0.37879467010498  s and adjustment time is  0.0935544967651367 s ( 24.7 )
2024-05-03 21:01:36.903276 INFO::Formatting Data.
2024-05-03 21:01:36.904074 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:36.905051 INFO::Removing potential empty rows and columns
2024-05-03 21:01:36.90617 INFO::Found  0  missing values.
2024-05-03 21:01:36.907216 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-03 21:01:36.918507 INFO::Formatting Data.
2024-05-03 21:01:36.919277 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:36.920195 INFO::Removing potential empty rows and columns
2024-05-03 21:01:36.921332 INFO::Found  0  missing values.
2024-05-03 21:01:36.922283 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-03 21:01:36.938421 INFO::Formatting Data.
2024-05-03 21:01:36.939193 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:36.940074 INFO::Removing potential empty rows and columns
2024-05-03 21:01:36.941079 INFO::Found  0  missing values.
2024-05-03 21:01:36.941961 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-03 21:01:36.946182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:36.946699 INFO::Done
2024-05-03 21:01:36.94719 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:36.949119 INFO::Starting hierarchical adjustment
2024-05-03 21:01:36.949791 INFO::Found  2  batches.
2024-05-03 21:01:36.950288 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:36.950896 INFO::Using default BPPARAM
2024-05-03 21:01:36.95139 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:36.952265 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:36.974039 INFO::Done
2024-05-03 21:01:36.974736 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:36.976762 INFO::ASW Batch was 0.0126994706326246 prior to batch effect correction and is now -0.102476377073645 .
2024-05-03 21:01:36.977576 INFO::Total function execution time is  0.0392165184020996  s and adjustment time is  0.0243501663208008 s ( 62.09 )
2024-05-03 21:01:36.980292 INFO::Formatting Data.
2024-05-03 21:01:36.980927 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:36.989209 INFO::Formatting Data.
2024-05-03 21:01:36.989863 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:36.990694 INFO::Removing potential empty rows and columns
2024-05-03 21:01:36.991647 INFO::Found  0  missing values.
2024-05-03 21:01:36.994329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:36.994829 INFO::Done
2024-05-03 21:01:36.995307 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:36.997185 INFO::Starting hierarchical adjustment
2024-05-03 21:01:36.99784 INFO::Found  2  batches.
2024-05-03 21:01:36.998327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:36.998918 INFO::Using default BPPARAM
2024-05-03 21:01:36.99941 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:37.000253 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:37.014472 INFO::Done
2024-05-03 21:01:37.015116 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:37.017006 INFO::ASW Batch was -0.0152346396355173 prior to batch effect correction and is now -0.11699521440991 .
2024-05-03 21:01:37.017745 INFO::Total function execution time is  0.0285739898681641  s and adjustment time is  0.0167446136474609 s ( 58.6 )
2024-05-03 21:01:37.0188 INFO::Formatting Data.
2024-05-03 21:01:37.019367 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:37.020182 INFO::Removing potential empty rows and columns
2024-05-03 21:01:37.021189 INFO::Found  0  missing values.
2024-05-03 21:01:37.023872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:37.024373 INFO::Done
2024-05-03 21:01:37.02487 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:37.026755 INFO::Starting hierarchical adjustment
2024-05-03 21:01:37.027408 INFO::Found  2  batches.
2024-05-03 21:01:37.02791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:37.028472 INFO::Using default BPPARAM
2024-05-03 21:01:37.028979 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:37.029833 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:37.044367 INFO::Done
2024-05-03 21:01:37.045069 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:37.047034 INFO::ASW Batch was -0.0152346396355173 prior to batch effect correction and is now -0.11699521440991 .
2024-05-03 21:01:37.047788 INFO::Total function execution time is  0.0289950370788574  s and adjustment time is  0.0170600414276123 s ( 58.84 )
2024-05-03 21:01:39.242175 INFO::Formatting Data.
2024-05-03 21:01:39.243253 INFO::Recognized SummarizedExperiment
2024-05-03 21:01:39.243869 INFO::Typecasting input to dataframe.
2024-05-03 21:01:39.278306 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:39.279734 INFO::Removing potential empty rows and columns
2024-05-03 21:01:39.283863 INFO::Found  0  missing values.
2024-05-03 21:01:39.291424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:39.292042 INFO::Done
2024-05-03 21:01:39.292564 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:39.296309 INFO::Starting hierarchical adjustment
2024-05-03 21:01:39.297048 INFO::Found  2  batches.
2024-05-03 21:01:39.297553 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:39.298656 INFO::Using default BPPARAM
2024-05-03 21:01:39.299175 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:39.300191 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:39.395106 INFO::Done
2024-05-03 21:01:39.395924 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:39.399353 INFO::ASW Batch was -0.0236126661945875 prior to batch effect correction and is now -0.0894659594454457 .
2024-05-03 21:01:39.40016 INFO::Total function execution time is  0.158441781997681  s and adjustment time is  0.0981988906860352 s ( 61.98 )
2024-05-03 21:01:39.422696 INFO::Formatting Data.
2024-05-03 21:01:39.423418 INFO::Recognized SummarizedExperiment
2024-05-03 21:01:39.423914 INFO::Typecasting input to dataframe.
2024-05-03 21:01:39.433831 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:39.435 INFO::Removing potential empty rows and columns
2024-05-03 21:01:39.438416 INFO::Found  0  missing values.
2024-05-03 21:01:39.444986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:39.445491 INFO::Done
2024-05-03 21:01:39.445951 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:39.449005 INFO::Starting hierarchical adjustment
2024-05-03 21:01:39.449681 INFO::Found  2  batches.
2024-05-03 21:01:39.450165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:39.450709 INFO::Using default BPPARAM
2024-05-03 21:01:39.451176 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:39.452113 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:39.474076 INFO::Done
2024-05-03 21:01:39.474716 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:39.478004 INFO::ASW Batch was -0.0100878085470991 prior to batch effect correction and is now -0.0100878085470991 .
2024-05-03 21:01:39.478781 INFO::Total function execution time is  0.0560698509216309  s and adjustment time is  0.0245182514190674 s ( 43.73 )
2024-05-03 21:01:39.494973 INFO::Formatting Data.
2024-05-03 21:01:39.495665 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:39.496479 INFO::Removing potential empty rows and columns
2024-05-03 21:01:39.497411 INFO::Found  0  missing values.
2024-05-03 21:01:39.50006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:39.500549 INFO::Done
2024-05-03 21:01:39.501038 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:39.502848 INFO::Starting hierarchical adjustment
2024-05-03 21:01:39.503454 INFO::Found  3  batches.
2024-05-03 21:01:39.503919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:39.504451 INFO::Using default BPPARAM
2024-05-03 21:01:39.504963 INFO::Processing subtree level 1
2024-05-03 21:01:39.675635 INFO::Adjusting the last 1 batches sequentially
2024-05-03 21:01:39.67837 INFO::Done
2024-05-03 21:01:39.679372 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:39.682679 INFO::ASW Batch was -0.100858085789061 prior to batch effect correction and is now -0.152736693156514 .
2024-05-03 21:01:39.683901 INFO::Total function execution time is  0.188865661621094  s and adjustment time is  0.174886226654053 s ( 92.6 )
2024-05-03 21:01:39.703156 INFO::Skipping initial DF formatting
2024-05-03 21:01:39.70407 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:39.709129 INFO::Starting hierarchical adjustment
2024-05-03 21:01:39.709965 INFO::Found  5  batches.
2024-05-03 21:01:39.710527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:39.711195 INFO::Using default BPPARAM
2024-05-03 21:01:39.711747 INFO::Processing subtree level 1
2024-05-03 21:01:39.880181 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:39.882939 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:39.921344 INFO::Done
2024-05-03 21:01:39.922718 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:39.927641 INFO::ASW Batch was 0.557136344295379 prior to batch effect correction and is now 0.557136344295379 .
2024-05-03 21:01:39.928406 INFO::ASW Label was 0.365340081783398 prior to batch effect correction and is now 0.365340081783398 .
2024-05-03 21:01:39.929447 INFO::Total function execution time is  0.226390600204468  s and adjustment time is  0.211401224136353 s ( 93.38 )
2024-05-03 21:01:39.948698 INFO::Formatting Data.
2024-05-03 21:01:39.949606 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:39.950619 INFO::Removing potential empty rows and columns
2024-05-03 21:01:39.951745 INFO::Found  0  missing values.
2024-05-03 21:01:39.956006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:39.956566 INFO::Done
2024-05-03 21:01:39.957117 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:39.960212 INFO::Starting hierarchical adjustment
2024-05-03 21:01:39.96097 INFO::Found  5  batches.
2024-05-03 21:01:39.961539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:39.962185 INFO::Using default BPPARAM
2024-05-03 21:01:39.962753 INFO::Processing subtree level 1
2024-05-03 21:01:40.086984 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.088871 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.106656 INFO::Done
2024-05-03 21:01:40.107555 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.111756 INFO::ASW Batch was 0.188153524950227 prior to batch effect correction and is now -0.0302228903670908 .
2024-05-03 21:01:40.112679 INFO::ASW Label was 0.574517119884809 prior to batch effect correction and is now 0.829708010922304 .
2024-05-03 21:01:40.113698 INFO::Total function execution time is  0.165111303329468  s and adjustment time is  0.145810127258301 s ( 88.31 )
2024-05-03 21:01:40.114653 INFO::Formatting Data.
2024-05-03 21:01:40.11533 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:40.116355 INFO::Removing potential empty rows and columns
2024-05-03 21:01:40.117523 INFO::Found  0  missing values.
2024-05-03 21:01:40.12186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:40.122478 INFO::Done
2024-05-03 21:01:40.123034 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:40.126115 INFO::Starting hierarchical adjustment
2024-05-03 21:01:40.126842 INFO::Found  5  batches.
2024-05-03 21:01:40.127392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:40.128079 INFO::Using default BPPARAM
2024-05-03 21:01:40.128645 INFO::Processing subtree level 1
2024-05-03 21:01:40.241558 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.24333 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.259803 INFO::Done
2024-05-03 21:01:40.260551 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.26398 INFO::ASW Batch was 0.188153524950227 prior to batch effect correction and is now -0.0302228903670908 .
2024-05-03 21:01:40.264623 INFO::ASW Label was 0.574517119884809 prior to batch effect correction and is now 0.829708010922304 .
2024-05-03 21:01:40.265472 INFO::Total function execution time is  0.150847434997559  s and adjustment time is  0.133078575134277 s ( 88.22 )
2024-05-03 21:01:40.281847 INFO::Formatting Data.
2024-05-03 21:01:40.282862 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:40.283903 INFO::Removing potential empty rows and columns
2024-05-03 21:01:40.284983 INFO::Found  0  missing values.
2024-05-03 21:01:40.289286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:40.289845 INFO::Done
2024-05-03 21:01:40.290385 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:40.293858 INFO::Starting hierarchical adjustment
2024-05-03 21:01:40.294585 INFO::Found  5  batches.
2024-05-03 21:01:40.29511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:40.295797 INFO::Using default BPPARAM
2024-05-03 21:01:40.296337 INFO::Processing subtree level 1
2024-05-03 21:01:40.410139 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.411746 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.428697 INFO::Done
2024-05-03 21:01:40.429488 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.433058 INFO::ASW Batch was 0.409732203847541 prior to batch effect correction and is now -0.0905681208609874 .
2024-05-03 21:01:40.433758 INFO::ASW Label was 0.211514479372491 prior to batch effect correction and is now 0.877159952635034 .
2024-05-03 21:01:40.434653 INFO::Total function execution time is  0.153115510940552  s and adjustment time is  0.134225368499756 s ( 87.66 )
2024-05-03 21:01:40.435534 INFO::Formatting Data.
2024-05-03 21:01:40.43619 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:40.437195 INFO::Removing potential empty rows and columns
2024-05-03 21:01:40.438181 INFO::Found  0  missing values.
2024-05-03 21:01:40.442198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:40.44275 INFO::Done
2024-05-03 21:01:40.443288 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:40.44629 INFO::Starting hierarchical adjustment
2024-05-03 21:01:40.447001 INFO::Found  5  batches.
2024-05-03 21:01:40.447515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:40.448123 INFO::Using default BPPARAM
2024-05-03 21:01:40.448661 INFO::Processing subtree level 1
2024-05-03 21:01:40.568606 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.570375 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.586914 INFO::Done
2024-05-03 21:01:40.587742 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.591025 INFO::ASW Batch was 0.409732203847541 prior to batch effect correction and is now -0.0905681208609874 .
2024-05-03 21:01:40.591732 INFO::ASW Label was 0.211514479372491 prior to batch effect correction and is now 0.877159952635034 .
2024-05-03 21:01:40.592648 INFO::Total function execution time is  0.157106161117554  s and adjustment time is  0.140029668807983 s ( 89.13 )
2024-05-03 21:01:40.608149 INFO::Formatting Data.
2024-05-03 21:01:40.609036 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:40.610034 INFO::Removing potential empty rows and columns
2024-05-03 21:01:40.611128 INFO::Found  0  missing values.
2024-05-03 21:01:40.614111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:40.614667 INFO::Done
2024-05-03 21:01:40.6152 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:40.618437 INFO::Starting hierarchical adjustment
2024-05-03 21:01:40.619165 INFO::Found  2  batches.
2024-05-03 21:01:40.619731 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:40.620379 INFO::Using default BPPARAM
2024-05-03 21:01:40.620979 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.621949 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.636595 INFO::Done
2024-05-03 21:01:40.637255 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.640379 INFO::ASW Batch was 0.591465938343518 prior to batch effect correction and is now -0.0276049858063221 .
2024-05-03 21:01:40.641046 INFO::ASW Label was 0.437678817906159 prior to batch effect correction and is now 0.898871718956448 .
2024-05-03 21:01:40.641958 INFO::Total function execution time is  0.0339019298553467  s and adjustment time is  0.0175983905792236 s ( 51.91 )
2024-05-03 21:01:40.642904 INFO::Formatting Data.
2024-05-03 21:01:40.643583 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:40.644488 INFO::Removing potential empty rows and columns
2024-05-03 21:01:40.645522 INFO::Found  0  missing values.
2024-05-03 21:01:40.648356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:40.648943 INFO::Done
2024-05-03 21:01:40.649486 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:40.652494 INFO::Starting hierarchical adjustment
2024-05-03 21:01:40.653374 INFO::Found  2  batches.
2024-05-03 21:01:40.653934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:40.654591 INFO::Using default BPPARAM
2024-05-03 21:01:40.655125 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.656107 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.672151 INFO::Done
2024-05-03 21:01:40.672836 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.675829 INFO::ASW Batch was 0.591465938343518 prior to batch effect correction and is now -0.0276049858063221 .
2024-05-03 21:01:40.676399 INFO::ASW Label was 0.437678817906159 prior to batch effect correction and is now 0.898871718956448 .
2024-05-03 21:01:40.677229 INFO::Total function execution time is  0.0343723297119141  s and adjustment time is  0.01896071434021 s ( 55.16 )
2024-05-03 21:01:40.688688 INFO::Formatting Data.
2024-05-03 21:01:40.689418 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:40.690262 INFO::Removing potential empty rows and columns
2024-05-03 21:01:40.691155 INFO::Found  0  missing values.
2024-05-03 21:01:40.693222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:40.693785 INFO::Done
2024-05-03 21:01:40.694298 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:40.696243 INFO::Starting hierarchical adjustment
2024-05-03 21:01:40.696962 INFO::Found  2  batches.
2024-05-03 21:01:40.69749 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:40.698113 INFO::Using default BPPARAM
2024-05-03 21:01:40.698648 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.699556 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.730963 INFO::Done
2024-05-03 21:01:40.731667 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.733611 INFO::ASW Batch was 0.0515172193272295 prior to batch effect correction and is now -0.130863339301644 .
2024-05-03 21:01:40.734393 INFO::Total function execution time is  0.0457620620727539  s and adjustment time is  0.0341596603393555 s ( 74.65 )
2024-05-03 21:01:40.745792 INFO::Formatting Data.
2024-05-03 21:01:40.746578 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:40.747444 INFO::Removing potential empty rows and columns
2024-05-03 21:01:40.748436 INFO::Found  0  missing values.
2024-05-03 21:01:40.74966 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-03 21:01:40.754202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:40.754764 INFO::Done
2024-05-03 21:01:40.789719 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:40.793049 INFO::Starting hierarchical adjustment
2024-05-03 21:01:40.793801 INFO::Found  2  batches.
2024-05-03 21:01:40.794344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:40.794972 INFO::Using default BPPARAM
2024-05-03 21:01:40.795515 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.796532 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.815356 INFO::Done
2024-05-03 21:01:40.816093 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.819215 INFO::ASW Batch was 0.459377002937553 prior to batch effect correction and is now 0.080290987688744 .
2024-05-03 21:01:40.819807 INFO::ASW Label was 0.554945586692493 prior to batch effect correction and is now 0.869938268507952 .
2024-05-03 21:01:40.820648 INFO::Total function execution time is  0.074864387512207  s and adjustment time is  0.0217103958129883 s ( 29 )
2024-05-03 21:01:40.821506 INFO::Formatting Data.
2024-05-03 21:01:40.822111 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:40.823049 INFO::Removing potential empty rows and columns
2024-05-03 21:01:40.824077 INFO::Found  0  missing values.
2024-05-03 21:01:40.825028 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-03 21:01:40.829983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:40.830665 INFO::Done
2024-05-03 21:01:40.831182 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:40.834291 INFO::Starting hierarchical adjustment
2024-05-03 21:01:40.835031 INFO::Found  2  batches.
2024-05-03 21:01:40.835574 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:40.836211 INFO::Using default BPPARAM
2024-05-03 21:01:40.836762 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:40.837823 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:40.856668 INFO::Done
2024-05-03 21:01:40.85737 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:40.860418 INFO::ASW Batch was 0.459377002937553 prior to batch effect correction and is now 0.080290987688744 .
2024-05-03 21:01:40.861059 INFO::ASW Label was 0.554945586692493 prior to batch effect correction and is now 0.869938268507952 .
2024-05-03 21:01:40.861906 INFO::Total function execution time is  0.0404114723205566  s and adjustment time is  0.0217993259429932 s ( 53.94 )
2024-05-03 21:01:41.073564 INFO::Formatting Data.
2024-05-03 21:01:41.074408 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:41.075328 INFO::Removing potential empty rows and columns
2024-05-03 21:01:41.076346 INFO::Found  0  missing values.
2024-05-03 21:01:41.079364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:41.079891 INFO::Done
2024-05-03 21:01:41.080396 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:41.082427 INFO::Starting hierarchical adjustment
2024-05-03 21:01:41.083107 INFO::Found  3  batches.
2024-05-03 21:01:41.083618 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:41.084194 INFO::Using default BPPARAM
2024-05-03 21:01:41.084726 INFO::Processing subtree level 1
2024-05-03 21:01:41.18254 INFO::Adjusting the last 1 batches sequentially
2024-05-03 21:01:41.184222 INFO::Done
2024-05-03 21:01:41.184832 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:41.187191 INFO::ASW Batch was -0.141783480813346 prior to batch effect correction and is now -0.141783480813346 .
2024-05-03 21:01:41.188114 INFO::Total function execution time is  0.114622116088867  s and adjustment time is  0.101240396499634 s ( 88.33 )
2024-05-03 21:01:41.189232 INFO::Formatting Data.
2024-05-03 21:01:41.189878 INFO::Typecasting input to dataframe.
2024-05-03 21:01:41.190625 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:41.19151 INFO::Removing potential empty rows and columns
2024-05-03 21:01:41.192559 INFO::Found  0  missing values.
2024-05-03 21:01:41.195498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:41.196027 INFO::Done
2024-05-03 21:01:41.196581 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:41.198689 INFO::Starting hierarchical adjustment
2024-05-03 21:01:41.199407 INFO::Found  3  batches.
2024-05-03 21:01:41.199953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:41.200604 INFO::Using default BPPARAM
2024-05-03 21:01:41.201156 INFO::Processing subtree level 1
2024-05-03 21:01:41.292065 INFO::Adjusting the last 1 batches sequentially
2024-05-03 21:01:41.293777 INFO::Done
2024-05-03 21:01:41.294394 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:41.296671 INFO::ASW Batch was -0.141783480813346 prior to batch effect correction and is now -0.141783480813346 .
2024-05-03 21:01:41.297617 INFO::Total function execution time is  0.108356237411499  s and adjustment time is  0.094496488571167 s ( 87.21 )
2024-05-03 21:01:41.310361 INFO::Formatting Data.
2024-05-03 21:01:41.311242 INFO::Typecasting input to dataframe.
2024-05-03 21:01:41.312121 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:41.313049 INFO::Removing potential empty rows and columns
2024-05-03 21:01:41.314081 INFO::Found  0  missing values.
2024-05-03 21:01:41.316915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:41.317426 INFO::Done
2024-05-03 21:01:41.317922 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:41.319845 INFO::Starting hierarchical adjustment
2024-05-03 21:01:41.320559 INFO::Found  3  batches.
2024-05-03 21:01:41.321093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:41.32169 INFO::Using default BPPARAM
2024-05-03 21:01:41.3222 INFO::Processing subtree level 1
2024-05-03 21:01:41.412299 INFO::Adjusting the last 1 batches sequentially
2024-05-03 21:01:41.414147 INFO::Done
2024-05-03 21:01:41.414807 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:41.417367 INFO::ASW Batch was -0.143055910296877 prior to batch effect correction and is now -0.143055910296877 .
2024-05-03 21:01:41.418312 INFO::Total function execution time is  0.108072519302368  s and adjustment time is  0.0936951637268066 s ( 86.7 )
2024-05-03 21:01:41.563628 INFO::Formatting Data.
2024-05-03 21:01:41.564448 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:41.565506 INFO::Removing potential empty rows and columns
2024-05-03 21:01:41.568031 INFO::Found  1000  missing values.
2024-05-03 21:01:41.586338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:41.587069 INFO::Done
2024-05-03 21:01:41.587631 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:41.593255 INFO::Starting hierarchical adjustment
2024-05-03 21:01:41.594104 INFO::Found  10  batches.
2024-05-03 21:01:41.594696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:41.595355 INFO::Using default BPPARAM
2024-05-03 21:01:41.595881 INFO::Processing subtree level 1
2024-05-03 21:01:41.726197 INFO::Processing subtree level 2
2024-05-03 21:01:41.92109 INFO::Adjusting the last 1 batches sequentially
2024-05-03 21:01:41.923272 INFO::Done
2024-05-03 21:01:41.924047 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:41.930713 INFO::ASW Batch was 0.519440250726608 prior to batch effect correction and is now 0.519440250726608 .
2024-05-03 21:01:41.931462 INFO::ASW Label was 0.355118787529197 prior to batch effect correction and is now 0.355118787529197 .
2024-05-03 21:01:41.932544 INFO::Total function execution time is  0.368951082229614  s and adjustment time is  0.329316377639771 s ( 89.26 )
2024-05-03 21:01:41.933555 INFO::Formatting Data.
2024-05-03 21:01:41.934341 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:41.935754 INFO::Removing potential empty rows and columns
2024-05-03 21:01:41.939189 INFO::Found  1000  missing values.
2024-05-03 21:01:41.961642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:41.962492 INFO::Done
2024-05-03 21:01:41.963153 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:41.969815 INFO::Starting hierarchical adjustment
2024-05-03 21:01:41.970651 INFO::Found  10  batches.
2024-05-03 21:01:43.060709 INFO::Set up parallel execution backend with 2 workers
2024-05-03 21:01:43.065778 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-03 21:01:44.218302 INFO::Adjusting the last 2 batches sequentially
2024-05-03 21:01:44.219757 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-03 21:01:44.235395 INFO::Done
2024-05-03 21:01:44.236035 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:44.240664 INFO::ASW Batch was 0.519440250726608 prior to batch effect correction and is now 0.519440250726608 .
2024-05-03 21:01:44.24123 INFO::ASW Label was 0.355118787529197 prior to batch effect correction and is now 0.355118787529197 .
2024-05-03 21:01:44.241954 INFO::Total function execution time is  2.30846619606018  s and adjustment time is  2.26490163803101 s ( 98.11 )
2024-05-03 21:01:44.382231 INFO::Formatting Data.
2024-05-03 21:01:44.38308 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.38405 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.385186 INFO::Found  0  missing values.
2024-05-03 21:01:44.388957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.389534 INFO::Done
2024-05-03 21:01:44.39007 INFO::Acquiring quality metrics before batch effect correction.
2024-05-03 21:01:44.392924 INFO::Starting hierarchical adjustment
2024-05-03 21:01:44.393644 INFO::Found  3  batches.
2024-05-03 21:01:44.394183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-03 21:01:44.394829 INFO::Using default BPPARAM
2024-05-03 21:01:44.395368 INFO::Processing subtree level 1
2024-05-03 21:01:44.495676 INFO::Adjusting the last 1 batches sequentially
2024-05-03 21:01:44.497362 INFO::Done
2024-05-03 21:01:44.497991 INFO::Acquiring quality metrics after batch effect correction.
2024-05-03 21:01:44.501004 INFO::ASW Batch was 0.192275704686832 prior to batch effect correction and is now -0.146735573231181 .
2024-05-03 21:01:44.501592 INFO::ASW Label was -0.175314653509889 prior to batch effect correction and is now -0.0110504755138043 .
2024-05-03 21:01:44.502458 INFO::Total function execution time is  0.120273590087891  s and adjustment time is  0.103844165802002 s ( 86.34 )
2024-05-03 21:01:44.612465 INFO::Formatting Data.
2024-05-03 21:01:44.61346 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.614541 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.615584 INFO::Found  2  missing values.
2024-05-03 21:01:44.618361 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.61888 INFO::Done
2024-05-03 21:01:44.645293 INFO::Found NA in Reference column
2024-05-03 21:01:44.654026 INFO::Require at least two references per batch.
2024-05-03 21:01:44.672597 INFO::Formatting Data.
2024-05-03 21:01:44.67353 INFO::Recognized SummarizedExperiment
2024-05-03 21:01:44.674273 INFO::Typecasting input to dataframe.
2024-05-03 21:01:44.688919 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.690831 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.69658 INFO::Found  0  missing values.
2024-05-03 21:01:44.70757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.708605 INFO::Done
2024-05-03 21:01:44.733194 INFO::Formatting Data.
2024-05-03 21:01:44.734307 INFO::Recognized SummarizedExperiment
2024-05-03 21:01:44.735128 INFO::Typecasting input to dataframe.
2024-05-03 21:01:44.763047 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.764923 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.770654 INFO::Found  0  missing values.
2024-05-03 21:01:44.788531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.789676 INFO::Done
2024-05-03 21:01:44.806869 INFO::Formatting Data.
2024-05-03 21:01:44.807746 INFO::Recognized SummarizedExperiment
2024-05-03 21:01:44.808284 INFO::Typecasting input to dataframe.
2024-05-03 21:01:44.824677 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.825778 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.826939 INFO::Found  0  missing values.
2024-05-03 21:01:44.827903 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-03 21:01:44.832321 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.83296 INFO::Done
2024-05-03 21:01:44.842951 INFO::Formatting Data.
2024-05-03 21:01:44.843739 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.844648 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.845708 INFO::Found  0  missing values.
2024-05-03 21:01:44.848485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.849018 INFO::Done
2024-05-03 21:01:44.859527 INFO::Formatting Data.
2024-05-03 21:01:44.86031 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.861183 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.862122 INFO::Found  0  missing values.
2024-05-03 21:01:44.864903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.865441 INFO::Done
2024-05-03 21:01:44.893426 INFO::Formatting Data.
2024-05-03 21:01:44.894248 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.895263 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.896338 INFO::Found  1  missing values.
2024-05-03 21:01:44.898804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.899304 INFO::Done
2024-05-03 21:01:44.91783 INFO::Formatting Data.
2024-05-03 21:01:44.918712 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.919661 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.920684 INFO::Found  2  missing values.
2024-05-03 21:01:44.921609 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-03 21:01:44.923803 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.924334 INFO::Done
2024-05-03 21:01:44.933863 INFO::Formatting Data.
2024-05-03 21:01:44.934633 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.935486 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.936372 INFO::Found  2  missing values.
2024-05-03 21:01:44.93791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.938408 INFO::Done
2024-05-03 21:01:44.948623 INFO::Formatting Data.
2024-05-03 21:01:44.949523 INFO::Typecasting input to dataframe.
2024-05-03 21:01:44.950317 INFO::Replacing NaNs with NAs.
2024-05-03 21:01:44.95118 INFO::Removing potential empty rows and columns
2024-05-03 21:01:44.952125 INFO::Found  0  missing values.
2024-05-03 21:01:44.954938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-03 21:01:44.955481 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.506   3.385  20.613 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT24.675 1.16917.739
compute_asw0.0200.0080.028
count_existing0.0060.0120.018
generate_data_covariables0.0110.0040.015
generate_dataset0.0110.0040.015