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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 159/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.2.0  (landing page)
Yannis Schumann
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_20
git_last_commit: 9764e3f
git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

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: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2024-12-19 20:23:38 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 20:28:38 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 300.2 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 20.242   1.12  14.596
* 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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")
2024-12-19 20:28:05.027732 INFO::Formatting Data.
2024-12-19 20:28:05.028875 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:05.039011 INFO::Removing potential empty rows and columns
2024-12-19 20:28:05.2872 INFO::Found  0  missing values.
2024-12-19 20:28:05.290552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:05.291129 INFO::Done
2024-12-19 20:28:05.291656 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:05.302414 INFO::Starting hierarchical adjustment
2024-12-19 20:28:05.303144 INFO::Found  3  batches.
2024-12-19 20:28:05.303658 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:05.30474 INFO::Using default BPPARAM
2024-12-19 20:28:05.305303 INFO::Processing subtree level 1
2024-12-19 20:28:05.400835 INFO::Adjusting the last 1 batches sequentially
2024-12-19 20:28:05.402529 INFO::Done
2024-12-19 20:28:05.403183 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:05.405659 INFO::ASW Batch was -0.0312090884590066 prior to batch effect correction and is now -0.0312090884590066 .
2024-12-19 20:28:05.406662 INFO::Total function execution time is  0.379496812820435  s and adjustment time is  0.099536657333374 s ( 26.23 )
2024-12-19 20:28:05.41967 INFO::Formatting Data.
2024-12-19 20:28:05.420341 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:05.421211 INFO::Removing potential empty rows and columns
2024-12-19 20:28:05.422255 INFO::Found  0  missing values.
2024-12-19 20:28:05.42316 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.
2024-12-19 20:28:05.433654 INFO::Formatting Data.
2024-12-19 20:28:05.434267 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:05.435108 INFO::Removing potential empty rows and columns
2024-12-19 20:28:05.436077 INFO::Found  0  missing values.
2024-12-19 20:28:05.436943 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.
2024-12-19 20:28:05.452045 INFO::Formatting Data.
2024-12-19 20:28:05.452697 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:05.453516 INFO::Removing potential empty rows and columns
2024-12-19 20:28:05.454511 INFO::Found  0  missing values.
2024-12-19 20:28:05.455375 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.
2024-12-19 20:28:05.459705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:05.460219 INFO::Done
2024-12-19 20:28:05.460797 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:05.462741 INFO::Starting hierarchical adjustment
2024-12-19 20:28:05.463402 INFO::Found  2  batches.
2024-12-19 20:28:05.463909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:05.464565 INFO::Using default BPPARAM
2024-12-19 20:28:05.465053 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:05.465916 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:05.486887 INFO::Done
2024-12-19 20:28:05.487472 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:05.489345 INFO::ASW Batch was 0.060399482473919 prior to batch effect correction and is now -0.131583801891591 .
2024-12-19 20:28:05.49006 INFO::Total function execution time is  0.038057804107666  s and adjustment time is  0.0236251354217529 s ( 62.08 )
2024-12-19 20:28:05.492814 INFO::Formatting Data.
2024-12-19 20:28:05.493396 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:05.501736 INFO::Formatting Data.
2024-12-19 20:28:05.502358 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:05.503261 INFO::Removing potential empty rows and columns
2024-12-19 20:28:05.504249 INFO::Found  0  missing values.
2024-12-19 20:28:05.507057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:05.507605 INFO::Done
2024-12-19 20:28:05.508093 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:05.510184 INFO::Starting hierarchical adjustment
2024-12-19 20:28:05.51088 INFO::Found  2  batches.
2024-12-19 20:28:05.511405 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:05.511984 INFO::Using default BPPARAM
2024-12-19 20:28:05.512525 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:05.513539 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:05.527749 INFO::Done
2024-12-19 20:28:05.528273 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:05.530072 INFO::ASW Batch was 0.00930596919309599 prior to batch effect correction and is now -0.106605523066065 .
2024-12-19 20:28:05.530779 INFO::Total function execution time is  0.0290424823760986  s and adjustment time is  0.0170083045959473 s ( 58.56 )
2024-12-19 20:28:05.531737 INFO::Formatting Data.
2024-12-19 20:28:05.532292 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:05.533066 INFO::Removing potential empty rows and columns
2024-12-19 20:28:05.533997 INFO::Found  0  missing values.
2024-12-19 20:28:05.536668 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:05.537165 INFO::Done
2024-12-19 20:28:05.537643 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:05.539483 INFO::Starting hierarchical adjustment
2024-12-19 20:28:05.540137 INFO::Found  2  batches.
2024-12-19 20:28:05.540628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:05.541182 INFO::Using default BPPARAM
2024-12-19 20:28:05.541674 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:05.542513 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:05.556614 INFO::Done
2024-12-19 20:28:05.557143 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:05.558936 INFO::ASW Batch was 0.00930596919309599 prior to batch effect correction and is now -0.106605523066065 .
2024-12-19 20:28:05.559647 INFO::Total function execution time is  0.0279104709625244  s and adjustment time is  0.0166199207305908 s ( 59.55 )
2024-12-19 20:28:07.517062 INFO::Formatting Data.
2024-12-19 20:28:07.517843 INFO::Recognized SummarizedExperiment
2024-12-19 20:28:07.518335 INFO::Typecasting input to dataframe.
2024-12-19 20:28:07.549826 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:07.550971 INFO::Removing potential empty rows and columns
2024-12-19 20:28:07.55453 INFO::Found  0  missing values.
2024-12-19 20:28:07.561005 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:07.561497 INFO::Done
2024-12-19 20:28:07.561956 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:07.565555 INFO::Starting hierarchical adjustment
2024-12-19 20:28:07.566219 INFO::Found  2  batches.
2024-12-19 20:28:07.566753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:07.567804 INFO::Using default BPPARAM
2024-12-19 20:28:07.56828 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:07.569159 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:07.620007 INFO::Done
2024-12-19 20:28:07.620585 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:07.623426 INFO::ASW Batch was 0.0235204642896388 prior to batch effect correction and is now -0.0859722015743775 .
2024-12-19 20:28:07.624134 INFO::Total function execution time is  0.107441902160645  s and adjustment time is  0.0539393424987793 s ( 50.2 )
2024-12-19 20:28:07.639627 INFO::Formatting Data.
2024-12-19 20:28:07.640195 INFO::Recognized SummarizedExperiment
2024-12-19 20:28:07.640668 INFO::Typecasting input to dataframe.
2024-12-19 20:28:07.648814 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:07.64977 INFO::Removing potential empty rows and columns
2024-12-19 20:28:07.652915 INFO::Found  0  missing values.
2024-12-19 20:28:07.65917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:07.65966 INFO::Done
2024-12-19 20:28:07.660109 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:07.663235 INFO::Starting hierarchical adjustment
2024-12-19 20:28:07.663871 INFO::Found  2  batches.
2024-12-19 20:28:07.664336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:07.664879 INFO::Using default BPPARAM
2024-12-19 20:28:07.665349 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:07.666203 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:07.688494 INFO::Done
2024-12-19 20:28:07.689089 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:07.692243 INFO::ASW Batch was -0.0170059429209791 prior to batch effect correction and is now -0.0170059429209791 .
2024-12-19 20:28:07.693002 INFO::Total function execution time is  0.0533359050750732  s and adjustment time is  0.0247414112091064 s ( 46.39 )
2024-12-19 20:28:07.709239 INFO::Formatting Data.
2024-12-19 20:28:07.709921 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:07.710695 INFO::Removing potential empty rows and columns
2024-12-19 20:28:07.711608 INFO::Found  0  missing values.
2024-12-19 20:28:07.714075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:07.714528 INFO::Done
2024-12-19 20:28:07.714931 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:07.716582 INFO::Starting hierarchical adjustment
2024-12-19 20:28:07.717173 INFO::Found  3  batches.
2024-12-19 20:28:07.717621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:07.718095 INFO::Using default BPPARAM
2024-12-19 20:28:07.718525 INFO::Processing subtree level 1
2024-12-19 20:28:07.860327 INFO::Adjusting the last 1 batches sequentially
2024-12-19 20:28:07.86195 INFO::Done
2024-12-19 20:28:07.862538 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:07.864739 INFO::ASW Batch was -0.0967498019638465 prior to batch effect correction and is now -0.158208657638122 .
2024-12-19 20:28:07.865592 INFO::Total function execution time is  0.156335115432739  s and adjustment time is  0.144887685775757 s ( 92.68 )
2024-12-19 20:28:07.87909 INFO::Skipping initial DF formatting
2024-12-19 20:28:07.879647 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:07.883201 INFO::Starting hierarchical adjustment
2024-12-19 20:28:07.883884 INFO::Found  5  batches.
2024-12-19 20:28:07.884388 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:07.884962 INFO::Using default BPPARAM
2024-12-19 20:28:07.885458 INFO::Processing subtree level 1
2024-12-19 20:28:08.009549 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:08.011012 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:08.029347 INFO::Done
2024-12-19 20:28:08.029956 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:08.033754 INFO::ASW Batch was 0.521343090035324 prior to batch effect correction and is now 0.521343090035324 .
2024-12-19 20:28:08.03429 INFO::ASW Label was 0.396119401097219 prior to batch effect correction and is now 0.396119401097219 .
2024-12-19 20:28:08.035059 INFO::Total function execution time is  0.155982732772827  s and adjustment time is  0.145568609237671 s ( 93.32 )
2024-12-19 20:28:08.050658 INFO::Formatting Data.
2024-12-19 20:28:08.051314 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:08.052125 INFO::Removing potential empty rows and columns
2024-12-19 20:28:08.053028 INFO::Found  0  missing values.
2024-12-19 20:28:08.056648 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:08.057124 INFO::Done
2024-12-19 20:28:08.057596 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:08.060227 INFO::Starting hierarchical adjustment
2024-12-19 20:28:08.060875 INFO::Found  5  batches.
2024-12-19 20:28:08.06136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:08.061924 INFO::Using default BPPARAM
2024-12-19 20:28:08.062401 INFO::Processing subtree level 1
2024-12-19 20:28:08.1878 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:08.189577 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:08.206386 INFO::Done
2024-12-19 20:28:08.207138 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:08.210239 INFO::ASW Batch was 0.378998790417028 prior to batch effect correction and is now -0.0398308691596533 .
2024-12-19 20:28:08.210837 INFO::ASW Label was 0.358324011528598 prior to batch effect correction and is now 0.817710975666792 .
2024-12-19 20:28:08.211627 INFO::Total function execution time is  0.160999059677124  s and adjustment time is  0.145595073699951 s ( 90.43 )
2024-12-19 20:28:08.212441 INFO::Formatting Data.
2024-12-19 20:28:08.213029 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:08.21387 INFO::Removing potential empty rows and columns
2024-12-19 20:28:08.214788 INFO::Found  0  missing values.
2024-12-19 20:28:08.218563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:08.219068 INFO::Done
2024-12-19 20:28:08.219556 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:08.222382 INFO::Starting hierarchical adjustment
2024-12-19 20:28:08.223066 INFO::Found  5  batches.
2024-12-19 20:28:08.2236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:08.224173 INFO::Using default BPPARAM
2024-12-19 20:28:08.224673 INFO::Processing subtree level 1
2024-12-19 20:28:08.343543 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:08.345207 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:08.364963 INFO::Done
2024-12-19 20:28:08.365671 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:08.368947 INFO::ASW Batch was 0.378998790417028 prior to batch effect correction and is now -0.0398308691596533 .
2024-12-19 20:28:08.369554 INFO::ASW Label was 0.358324011528598 prior to batch effect correction and is now 0.817710975666792 .
2024-12-19 20:28:08.370427 INFO::Total function execution time is  0.157972812652588  s and adjustment time is  0.142033100128174 s ( 89.91 )
2024-12-19 20:28:08.384671 INFO::Formatting Data.
2024-12-19 20:28:08.385394 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:08.386326 INFO::Removing potential empty rows and columns
2024-12-19 20:28:08.387396 INFO::Found  0  missing values.
2024-12-19 20:28:08.391686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:08.392255 INFO::Done
2024-12-19 20:28:08.392778 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:08.395739 INFO::Starting hierarchical adjustment
2024-12-19 20:28:08.39649 INFO::Found  5  batches.
2024-12-19 20:28:08.39702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:08.397677 INFO::Using default BPPARAM
2024-12-19 20:28:08.398201 INFO::Processing subtree level 1
2024-12-19 20:28:08.615412 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:08.617091 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:08.635162 INFO::Done
2024-12-19 20:28:08.636006 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:08.639389 INFO::ASW Batch was 0.325487563480758 prior to batch effect correction and is now -0.0463895567990692 .
2024-12-19 20:28:08.640048 INFO::ASW Label was 0.449941960841126 prior to batch effect correction and is now 0.806976811719498 .
2024-12-19 20:28:08.640901 INFO::Total function execution time is  0.256234169006348  s and adjustment time is  0.238794565200806 s ( 93.19 )
2024-12-19 20:28:08.641831 INFO::Formatting Data.
2024-12-19 20:28:08.642485 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:08.643414 INFO::Removing potential empty rows and columns
2024-12-19 20:28:08.644477 INFO::Found  0  missing values.
2024-12-19 20:28:08.669974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:08.670867 INFO::Done
2024-12-19 20:28:08.671391 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:08.674221 INFO::Starting hierarchical adjustment
2024-12-19 20:28:08.674894 INFO::Found  5  batches.
2024-12-19 20:28:08.675404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:08.67596 INFO::Using default BPPARAM
2024-12-19 20:28:08.676464 INFO::Processing subtree level 1
2024-12-19 20:28:08.816633 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:08.818464 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:08.83601 INFO::Done
2024-12-19 20:28:08.836804 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:08.840507 INFO::ASW Batch was 0.325487563480758 prior to batch effect correction and is now -0.0463895567990692 .
2024-12-19 20:28:08.841129 INFO::ASW Label was 0.449941960841126 prior to batch effect correction and is now 0.806976811719498 .
2024-12-19 20:28:08.842001 INFO::Total function execution time is  0.200185537338257  s and adjustment time is  0.161208629608154 s ( 80.53 )
2024-12-19 20:28:08.858653 INFO::Formatting Data.
2024-12-19 20:28:08.859547 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:08.860606 INFO::Removing potential empty rows and columns
2024-12-19 20:28:08.861856 INFO::Found  0  missing values.
2024-12-19 20:28:08.864708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:08.865238 INFO::Done
2024-12-19 20:28:08.865763 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:08.868975 INFO::Starting hierarchical adjustment
2024-12-19 20:28:08.869688 INFO::Found  2  batches.
2024-12-19 20:28:08.870204 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:08.870812 INFO::Using default BPPARAM
2024-12-19 20:28:08.871333 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:08.872212 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:08.887196 INFO::Done
2024-12-19 20:28:08.887781 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:08.89065 INFO::ASW Batch was 0.281290548277478 prior to batch effect correction and is now 0.0380998138947216 .
2024-12-19 20:28:08.891183 INFO::ASW Label was 0.683068658042136 prior to batch effect correction and is now 0.907785135780783 .
2024-12-19 20:28:08.891936 INFO::Total function execution time is  0.0334055423736572  s and adjustment time is  0.017672061920166 s ( 52.9 )
2024-12-19 20:28:08.892667 INFO::Formatting Data.
2024-12-19 20:28:08.893238 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:08.894067 INFO::Removing potential empty rows and columns
2024-12-19 20:28:08.895031 INFO::Found  0  missing values.
2024-12-19 20:28:08.897686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:08.898171 INFO::Done
2024-12-19 20:28:08.898657 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:08.901392 INFO::Starting hierarchical adjustment
2024-12-19 20:28:08.90207 INFO::Found  2  batches.
2024-12-19 20:28:08.902588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:08.903144 INFO::Using default BPPARAM
2024-12-19 20:28:08.903637 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:08.904474 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:08.91803 INFO::Done
2024-12-19 20:28:08.918569 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:08.92121 INFO::ASW Batch was 0.281290548277478 prior to batch effect correction and is now 0.0380998138947216 .
2024-12-19 20:28:08.921717 INFO::ASW Label was 0.683068658042136 prior to batch effect correction and is now 0.907785135780783 .
2024-12-19 20:28:08.922398 INFO::Total function execution time is  0.0297336578369141  s and adjustment time is  0.0161178112030029 s ( 54.21 )
2024-12-19 20:28:08.933107 INFO::Formatting Data.
2024-12-19 20:28:08.933716 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:08.934539 INFO::Removing potential empty rows and columns
2024-12-19 20:28:08.935378 INFO::Found  0  missing values.
2024-12-19 20:28:08.937379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:08.937873 INFO::Done
2024-12-19 20:28:08.938355 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:08.940039 INFO::Starting hierarchical adjustment
2024-12-19 20:28:08.940672 INFO::Found  2  batches.
2024-12-19 20:28:08.941147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:08.941695 INFO::Using default BPPARAM
2024-12-19 20:28:08.942172 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:08.943005 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:08.972597 INFO::Done
2024-12-19 20:28:08.97323 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:08.975166 INFO::ASW Batch was 0.0395680225963744 prior to batch effect correction and is now -0.0839949703277646 .
2024-12-19 20:28:08.97598 INFO::Total function execution time is  0.042853832244873  s and adjustment time is  0.0320422649383545 s ( 74.77 )
2024-12-19 20:28:08.986919 INFO::Formatting Data.
2024-12-19 20:28:08.98755 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:08.988362 INFO::Removing potential empty rows and columns
2024-12-19 20:28:08.989262 INFO::Found  0  missing values.
2024-12-19 20:28:08.99032 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.
2024-12-19 20:28:08.994536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:08.995006 INFO::Done
2024-12-19 20:28:08.995502 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:08.998197 INFO::Starting hierarchical adjustment
2024-12-19 20:28:08.998876 INFO::Found  2  batches.
2024-12-19 20:28:08.99946 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:09.000005 INFO::Using default BPPARAM
2024-12-19 20:28:09.000547 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:09.001424 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:09.017545 INFO::Done
2024-12-19 20:28:09.018186 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:09.020941 INFO::ASW Batch was 0.592098061526084 prior to batch effect correction and is now 0.0648070484148646 .
2024-12-19 20:28:09.021545 INFO::ASW Label was 0.504021037736221 prior to batch effect correction and is now 0.858533741969089 .
2024-12-19 20:28:09.022354 INFO::Total function execution time is  0.0354211330413818  s and adjustment time is  0.0188014507293701 s ( 53.08 )
2024-12-19 20:28:09.02324 INFO::Formatting Data.
2024-12-19 20:28:09.023888 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:09.024715 INFO::Removing potential empty rows and columns
2024-12-19 20:28:09.025623 INFO::Found  0  missing values.
2024-12-19 20:28:09.026438 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.
2024-12-19 20:28:09.030552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:09.031034 INFO::Done
2024-12-19 20:28:09.031495 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:09.034039 INFO::Starting hierarchical adjustment
2024-12-19 20:28:09.034682 INFO::Found  2  batches.
2024-12-19 20:28:09.035146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:09.03569 INFO::Using default BPPARAM
2024-12-19 20:28:09.036147 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:09.036967 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:09.051905 INFO::Done
2024-12-19 20:28:09.052448 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:09.055034 INFO::ASW Batch was 0.592098061526084 prior to batch effect correction and is now 0.0648070484148646 .
2024-12-19 20:28:09.055549 INFO::ASW Label was 0.504021037736221 prior to batch effect correction and is now 0.858533741969089 .
2024-12-19 20:28:09.056247 INFO::Total function execution time is  0.0330438613891602  s and adjustment time is  0.01735520362854 s ( 52.52 )
2024-12-19 20:28:09.240761 INFO::Formatting Data.
2024-12-19 20:28:09.241483 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:09.242318 INFO::Removing potential empty rows and columns
2024-12-19 20:28:09.243273 INFO::Found  0  missing values.
2024-12-19 20:28:09.246083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:09.2466 INFO::Done
2024-12-19 20:28:09.247092 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:09.24898 INFO::Starting hierarchical adjustment
2024-12-19 20:28:09.249638 INFO::Found  3  batches.
2024-12-19 20:28:09.250113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:09.250671 INFO::Using default BPPARAM
2024-12-19 20:28:09.251155 INFO::Processing subtree level 1
2024-12-19 20:28:09.378403 INFO::Adjusting the last 1 batches sequentially
2024-12-19 20:28:09.380042 INFO::Done
2024-12-19 20:28:09.380641 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:09.382863 INFO::ASW Batch was 0.0250986560534673 prior to batch effect correction and is now 0.0250986560534673 .
2024-12-19 20:28:09.383736 INFO::Total function execution time is  0.143014907836914  s and adjustment time is  0.130524396896362 s ( 91.27 )
2024-12-19 20:28:09.38473 INFO::Formatting Data.
2024-12-19 20:28:09.385354 INFO::Typecasting input to dataframe.
2024-12-19 20:28:09.386076 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:09.386968 INFO::Removing potential empty rows and columns
2024-12-19 20:28:09.388039 INFO::Found  0  missing values.
2024-12-19 20:28:09.390933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:09.391453 INFO::Done
2024-12-19 20:28:09.391951 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:09.393773 INFO::Starting hierarchical adjustment
2024-12-19 20:28:09.394437 INFO::Found  3  batches.
2024-12-19 20:28:09.39492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:09.395509 INFO::Using default BPPARAM
2024-12-19 20:28:09.395993 INFO::Processing subtree level 1
2024-12-19 20:28:09.524241 INFO::Adjusting the last 1 batches sequentially
2024-12-19 20:28:09.525811 INFO::Done
2024-12-19 20:28:09.526384 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:09.528548 INFO::ASW Batch was 0.0250986560534673 prior to batch effect correction and is now 0.0250986560534673 .
2024-12-19 20:28:09.529382 INFO::Total function execution time is  0.144636869430542  s and adjustment time is  0.131504535675049 s ( 90.92 )
2024-12-19 20:28:09.5408 INFO::Formatting Data.
2024-12-19 20:28:09.541432 INFO::Typecasting input to dataframe.
2024-12-19 20:28:09.542171 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:09.543015 INFO::Removing potential empty rows and columns
2024-12-19 20:28:09.543968 INFO::Found  0  missing values.
2024-12-19 20:28:09.55108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:09.55187 INFO::Done
2024-12-19 20:28:09.552343 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:09.55455 INFO::Starting hierarchical adjustment
2024-12-19 20:28:09.581169 INFO::Found  3  batches.
2024-12-19 20:28:09.581726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:09.58236 INFO::Using default BPPARAM
2024-12-19 20:28:09.582899 INFO::Processing subtree level 1
2024-12-19 20:28:09.685475 INFO::Adjusting the last 1 batches sequentially
2024-12-19 20:28:09.687156 INFO::Done
2024-12-19 20:28:09.687759 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:09.690114 INFO::ASW Batch was -0.13502353739894 prior to batch effect correction and is now -0.13502353739894 .
2024-12-19 20:28:09.691043 INFO::Total function execution time is  0.150235891342163  s and adjustment time is  0.106159925460815 s ( 70.66 )
2024-12-19 20:28:09.838486 INFO::Formatting Data.
2024-12-19 20:28:09.839114 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:09.840161 INFO::Removing potential empty rows and columns
2024-12-19 20:28:09.84275 INFO::Found  1000  missing values.
2024-12-19 20:28:09.860265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:09.860805 INFO::Done
2024-12-19 20:28:09.861278 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:09.866441 INFO::Starting hierarchical adjustment
2024-12-19 20:28:09.86709 INFO::Found  10  batches.
2024-12-19 20:28:09.867583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:09.868135 INFO::Using default BPPARAM
2024-12-19 20:28:09.868615 INFO::Processing subtree level 1
2024-12-19 20:28:10.025541 INFO::Processing subtree level 2
2024-12-19 20:28:10.213232 INFO::Adjusting the last 1 batches sequentially
2024-12-19 20:28:10.215372 INFO::Done
2024-12-19 20:28:10.216021 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:10.221835 INFO::ASW Batch was 0.512930112183896 prior to batch effect correction and is now 0.512930112183896 .
2024-12-19 20:28:10.222628 INFO::ASW Label was 0.317764271126608 prior to batch effect correction and is now 0.317764271126608 .
2024-12-19 20:28:10.223769 INFO::Total function execution time is  0.385211706161499  s and adjustment time is  0.348339319229126 s ( 90.43 )
2024-12-19 20:28:10.224698 INFO::Formatting Data.
2024-12-19 20:28:10.225393 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:10.226957 INFO::Removing potential empty rows and columns
2024-12-19 20:28:10.229813 INFO::Found  1000  missing values.
2024-12-19 20:28:10.24914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:10.249963 INFO::Done
2024-12-19 20:28:10.250562 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:10.256323 INFO::Starting hierarchical adjustment
2024-12-19 20:28:10.257224 INFO::Found  10  batches.
2024-12-19 20:28:11.408414 INFO::Set up parallel execution backend with 2 workers
2024-12-19 20:28:11.409767 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-12-19 20:28:12.481983 INFO::Adjusting the last 2 batches sequentially
2024-12-19 20:28:12.48331 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 20:28:12.49814 INFO::Done
2024-12-19 20:28:12.498652 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:12.502873 INFO::ASW Batch was 0.512930112183896 prior to batch effect correction and is now 0.512930112183896 .
2024-12-19 20:28:12.503349 INFO::ASW Label was 0.317764271126608 prior to batch effect correction and is now 0.317764271126608 .
2024-12-19 20:28:12.504016 INFO::Total function execution time is  2.27937006950378  s and adjustment time is  2.24116325378418 s ( 98.32 )
2024-12-19 20:28:12.638239 INFO::Formatting Data.
2024-12-19 20:28:12.638903 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:12.639733 INFO::Removing potential empty rows and columns
2024-12-19 20:28:12.640723 INFO::Found  0  missing values.
2024-12-19 20:28:12.644079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:12.644574 INFO::Done
2024-12-19 20:28:12.645027 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 20:28:12.647522 INFO::Starting hierarchical adjustment
2024-12-19 20:28:12.648142 INFO::Found  3  batches.
2024-12-19 20:28:12.648607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 20:28:12.649148 INFO::Using default BPPARAM
2024-12-19 20:28:12.649636 INFO::Processing subtree level 1
2024-12-19 20:28:12.746727 INFO::Adjusting the last 1 batches sequentially
2024-12-19 20:28:12.748329 INFO::Done
2024-12-19 20:28:12.748901 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 20:28:12.751757 INFO::ASW Batch was 0.139449088296783 prior to batch effect correction and is now -0.143773293727807 .
2024-12-19 20:28:12.752309 INFO::ASW Label was -0.155792652950543 prior to batch effect correction and is now -0.00166635637754286 .
2024-12-19 20:28:12.753103 INFO::Total function execution time is  0.114877700805664  s and adjustment time is  0.100294351577759 s ( 87.31 )
2024-12-19 20:28:12.853961 INFO::Formatting Data.
2024-12-19 20:28:12.854652 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:12.855451 INFO::Removing potential empty rows and columns
2024-12-19 20:28:12.856386 INFO::Found  2  missing values.
2024-12-19 20:28:12.858864 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:12.859338 INFO::Done
2024-12-19 20:28:12.882293 INFO::Found NA in Reference column
2024-12-19 20:28:12.890486 INFO::Require at least two references per batch.
2024-12-19 20:28:12.908248 INFO::Formatting Data.
2024-12-19 20:28:12.908859 INFO::Recognized SummarizedExperiment
2024-12-19 20:28:12.909334 INFO::Typecasting input to dataframe.
2024-12-19 20:28:12.917886 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:12.918859 INFO::Removing potential empty rows and columns
2024-12-19 20:28:12.922002 INFO::Found  0  missing values.
2024-12-19 20:28:12.927997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:12.928484 INFO::Done
2024-12-19 20:28:12.94194 INFO::Formatting Data.
2024-12-19 20:28:12.942504 INFO::Recognized SummarizedExperiment
2024-12-19 20:28:12.942948 INFO::Typecasting input to dataframe.
2024-12-19 20:28:12.97061 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:12.972148 INFO::Removing potential empty rows and columns
2024-12-19 20:28:12.97639 INFO::Found  0  missing values.
2024-12-19 20:28:12.988644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:12.989211 INFO::Done
2024-12-19 20:28:13.007345 INFO::Formatting Data.
2024-12-19 20:28:13.008102 INFO::Recognized SummarizedExperiment
2024-12-19 20:28:13.008726 INFO::Typecasting input to dataframe.
2024-12-19 20:28:13.027968 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:13.028918 INFO::Removing potential empty rows and columns
2024-12-19 20:28:13.029994 INFO::Found  0  missing values.
2024-12-19 20:28:13.030904 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.
2024-12-19 20:28:13.035542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:13.036084 INFO::Done
2024-12-19 20:28:13.046391 INFO::Formatting Data.
2024-12-19 20:28:13.047092 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:13.047954 INFO::Removing potential empty rows and columns
2024-12-19 20:28:13.048974 INFO::Found  0  missing values.
2024-12-19 20:28:13.053921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:13.05467 INFO::Done
2024-12-19 20:28:13.067718 INFO::Formatting Data.
2024-12-19 20:28:13.068638 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:13.06956 INFO::Removing potential empty rows and columns
2024-12-19 20:28:13.07065 INFO::Found  0  missing values.
2024-12-19 20:28:13.073921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:13.074448 INFO::Done
2024-12-19 20:28:13.105772 INFO::Formatting Data.
2024-12-19 20:28:13.107115 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:13.108374 INFO::Removing potential empty rows and columns
2024-12-19 20:28:13.109756 INFO::Found  1  missing values.
2024-12-19 20:28:13.113485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:13.114006 INFO::Done
2024-12-19 20:28:13.132757 INFO::Formatting Data.
2024-12-19 20:28:13.133515 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:13.134444 INFO::Removing potential empty rows and columns
2024-12-19 20:28:13.135725 INFO::Found  2  missing values.
2024-12-19 20:28:13.13675 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.
2024-12-19 20:28:13.139076 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:13.139659 INFO::Done
2024-12-19 20:28:13.151545 INFO::Formatting Data.
2024-12-19 20:28:13.152364 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:13.153346 INFO::Removing potential empty rows and columns
2024-12-19 20:28:13.154369 INFO::Found  2  missing values.
2024-12-19 20:28:13.156279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:13.15692 INFO::Done
2024-12-19 20:28:13.169156 INFO::Formatting Data.
2024-12-19 20:28:13.170089 INFO::Typecasting input to dataframe.
2024-12-19 20:28:13.17121 INFO::Replacing NaNs with NAs.
2024-12-19 20:28:13.17219 INFO::Removing potential empty rows and columns
2024-12-19 20:28:13.173279 INFO::Found  0  missing values.
2024-12-19 20:28:13.176687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 20:28:13.17727 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 14.590   3.712  17.913

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT20.242 1.12014.596
compute_asw0.0230.0000.023
count_existing0.0120.0010.013
generate_data_covariables0.0110.0010.011
generate_dataset0.0110.0000.011