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This page was generated on 2024-05-04 11:40:17 -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 kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: BERT
Version: 1.0.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings BERT_1.0.0.tar.gz
StartedAt: 2024-05-04 05:11:41 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 05:13:08 -0000 (Sat, 04 May 2024)
EllapsedTime: 87.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 31.247  1.486  22.636
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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: aarch64-unknown-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")
2024-05-04 05:12:53.415115 INFO::Formatting Data.
2024-05-04 05:12:53.417056 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:53.435614 INFO::Removing potential empty rows and columns
2024-05-04 05:12:53.905412 INFO::Found  0  missing values.
2024-05-04 05:12:53.910886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:53.911826 INFO::Done
2024-05-04 05:12:53.912642 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:53.930497 INFO::Starting hierarchical adjustment
2024-05-04 05:12:53.93177 INFO::Found  3  batches.
2024-05-04 05:12:53.932596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:53.934422 INFO::Using default BPPARAM
2024-05-04 05:12:53.935489 INFO::Processing subtree level 1
2024-05-04 05:12:54.059693 INFO::Adjusting the last 1 batches sequentially
2024-05-04 05:12:54.062273 INFO::Done
2024-05-04 05:12:54.063314 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:54.067278 INFO::ASW Batch was -0.0770424822355978 prior to batch effect correction and is now -0.0770424822355978 .
2024-05-04 05:12:54.069067 INFO::Total function execution time is  0.654872894287109  s and adjustment time is  0.130740642547607 s ( 19.96 )
2024-05-04 05:12:54.091375 INFO::Formatting Data.
2024-05-04 05:12:54.092484 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:54.093908 INFO::Removing potential empty rows and columns
2024-05-04 05:12:54.095771 INFO::Found  0  missing values.
2024-05-04 05:12:54.097245 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.
2024-05-04 05:12:54.114753 INFO::Formatting Data.
2024-05-04 05:12:54.115945 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:54.117437 INFO::Removing potential empty rows and columns
2024-05-04 05:12:54.119215 INFO::Found  0  missing values.
2024-05-04 05:12:54.120779 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.
2024-05-04 05:12:54.145141 INFO::Formatting Data.
2024-05-04 05:12:54.14627 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:54.1476 INFO::Removing potential empty rows and columns
2024-05-04 05:12:54.149174 INFO::Found  0  missing values.
2024-05-04 05:12:54.150598 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.
2024-05-04 05:12:54.157369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:54.158302 INFO::Done
2024-05-04 05:12:54.159122 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:54.162075 INFO::Starting hierarchical adjustment
2024-05-04 05:12:54.163251 INFO::Found  2  batches.
2024-05-04 05:12:54.164085 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:54.165006 INFO::Using default BPPARAM
2024-05-04 05:12:54.165808 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:54.167256 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:54.199254 INFO::Done
2024-05-04 05:12:54.200135 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:54.202981 INFO::ASW Batch was 0.0239595839749778 prior to batch effect correction and is now -0.110680651855233 .
2024-05-04 05:12:54.204175 INFO::Total function execution time is  0.0591142177581787  s and adjustment time is  0.0362298488616943 s ( 61.29 )
2024-05-04 05:12:54.20813 INFO::Formatting Data.
2024-05-04 05:12:54.209154 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:54.221919 INFO::Formatting Data.
2024-05-04 05:12:54.223137 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:54.224578 INFO::Removing potential empty rows and columns
2024-05-04 05:12:54.226168 INFO::Found  0  missing values.
2024-05-04 05:12:54.230708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:54.231618 INFO::Done
2024-05-04 05:12:54.23242 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:54.235428 INFO::Starting hierarchical adjustment
2024-05-04 05:12:54.236599 INFO::Found  2  batches.
2024-05-04 05:12:54.237438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:54.238382 INFO::Using default BPPARAM
2024-05-04 05:12:54.239237 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:54.240666 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:54.262696 INFO::Done
2024-05-04 05:12:54.263708 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:54.26689 INFO::ASW Batch was 0.0123287332922742 prior to batch effect correction and is now -0.12284013172079 .
2024-05-04 05:12:54.268202 INFO::Total function execution time is  0.0462956428527832  s and adjustment time is  0.0263168811798096 s ( 56.85 )
2024-05-04 05:12:54.26995 INFO::Formatting Data.
2024-05-04 05:12:54.27098 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:54.272422 INFO::Removing potential empty rows and columns
2024-05-04 05:12:54.274113 INFO::Found  0  missing values.
2024-05-04 05:12:54.27915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:54.280171 INFO::Done
2024-05-04 05:12:54.281116 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:54.284432 INFO::Starting hierarchical adjustment
2024-05-04 05:12:54.285654 INFO::Found  2  batches.
2024-05-04 05:12:54.2866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:54.287662 INFO::Using default BPPARAM
2024-05-04 05:12:54.288548 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:54.29007 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:54.313543 INFO::Done
2024-05-04 05:12:54.31462 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:54.317843 INFO::ASW Batch was 0.0123287332922742 prior to batch effect correction and is now -0.12284013172079 .
2024-05-04 05:12:54.319187 INFO::Total function execution time is  0.0492165088653564  s and adjustment time is  0.0281438827514648 s ( 57.18 )
2024-05-04 05:12:57.275349 INFO::Formatting Data.
2024-05-04 05:12:57.276311 INFO::Recognized SummarizedExperiment
2024-05-04 05:12:57.277087 INFO::Typecasting input to dataframe.
2024-05-04 05:12:57.322002 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:57.323675 INFO::Removing potential empty rows and columns
2024-05-04 05:12:57.329142 INFO::Found  0  missing values.
2024-05-04 05:12:57.339762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:57.340664 INFO::Done
2024-05-04 05:12:57.341383 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:57.346519 INFO::Starting hierarchical adjustment
2024-05-04 05:12:57.347619 INFO::Found  2  batches.
2024-05-04 05:12:57.348348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:57.349806 INFO::Using default BPPARAM
2024-05-04 05:12:57.350589 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:57.352 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:57.462175 INFO::Done
2024-05-04 05:12:57.463034 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:57.467748 INFO::ASW Batch was -0.0142878927682951 prior to batch effect correction and is now -0.094028997248016 .
2024-05-04 05:12:57.468939 INFO::Total function execution time is  0.19408392906189  s and adjustment time is  0.114755392074585 s ( 59.13 )
2024-05-04 05:12:57.492069 INFO::Formatting Data.
2024-05-04 05:12:57.49297 INFO::Recognized SummarizedExperiment
2024-05-04 05:12:57.493654 INFO::Typecasting input to dataframe.
2024-05-04 05:12:57.505708 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:57.507322 INFO::Removing potential empty rows and columns
2024-05-04 05:12:57.512399 INFO::Found  0  missing values.
2024-05-04 05:12:57.522464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:57.523355 INFO::Done
2024-05-04 05:12:57.524091 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:57.528905 INFO::Starting hierarchical adjustment
2024-05-04 05:12:57.530024 INFO::Found  2  batches.
2024-05-04 05:12:57.530786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:57.53161 INFO::Using default BPPARAM
2024-05-04 05:12:57.532283 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:57.533612 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:57.567829 INFO::Done
2024-05-04 05:12:57.568695 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:57.573588 INFO::ASW Batch was 0.00816754347981801 prior to batch effect correction and is now 0.00816754347981801 .
2024-05-04 05:12:57.574844 INFO::Total function execution time is  0.0827162265777588  s and adjustment time is  0.0380120277404785 s ( 45.95 )
2024-05-04 05:12:57.599612 INFO::Formatting Data.
2024-05-04 05:12:57.600709 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:57.601916 INFO::Removing potential empty rows and columns
2024-05-04 05:12:57.603377 INFO::Found  0  missing values.
2024-05-04 05:12:57.607562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:57.608408 INFO::Done
2024-05-04 05:12:57.609111 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:57.611825 INFO::Starting hierarchical adjustment
2024-05-04 05:12:57.612883 INFO::Found  3  batches.
2024-05-04 05:12:57.613628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:57.614468 INFO::Using default BPPARAM
2024-05-04 05:12:57.618845 INFO::Processing subtree level 1
2024-05-04 05:12:57.8416 INFO::Adjusting the last 1 batches sequentially
2024-05-04 05:12:57.844198 INFO::Done
2024-05-04 05:12:57.84519 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:57.849035 INFO::ASW Batch was -0.0564128491395442 prior to batch effect correction and is now -0.164038405772297 .
2024-05-04 05:12:57.850552 INFO::Total function execution time is  0.250905275344849  s and adjustment time is  0.231489896774292 s ( 92.26 )
2024-05-04 05:12:57.875162 INFO::Skipping initial DF formatting
2024-05-04 05:12:57.876179 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:57.882633 INFO::Starting hierarchical adjustment
2024-05-04 05:12:57.883905 INFO::Found  5  batches.
2024-05-04 05:12:57.884722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:57.885651 INFO::Using default BPPARAM
2024-05-04 05:12:57.886507 INFO::Processing subtree level 1
2024-05-04 05:12:58.085974 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:58.088527 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:58.125856 INFO::Done
2024-05-04 05:12:58.126986 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:58.134675 INFO::ASW Batch was 0.507196280284333 prior to batch effect correction and is now 0.507196280284333 .
2024-05-04 05:12:58.13592 INFO::ASW Label was 0.393221113664488 prior to batch effect correction and is now 0.393221113664488 .
2024-05-04 05:12:58.13745 INFO::Total function execution time is  0.262293815612793  s and adjustment time is  0.242175579071045 s ( 92.33 )
2024-05-04 05:12:58.168458 INFO::Formatting Data.
2024-05-04 05:12:58.169575 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:58.170985 INFO::Removing potential empty rows and columns
2024-05-04 05:12:58.172539 INFO::Found  0  missing values.
2024-05-04 05:12:58.179137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:58.180075 INFO::Done
2024-05-04 05:12:58.180976 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:58.185617 INFO::Starting hierarchical adjustment
2024-05-04 05:12:58.186862 INFO::Found  5  batches.
2024-05-04 05:12:58.187762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:58.188708 INFO::Using default BPPARAM
2024-05-04 05:12:58.189576 INFO::Processing subtree level 1
2024-05-04 05:12:58.353618 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:58.355923 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:58.380419 INFO::Done
2024-05-04 05:12:58.381462 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:58.386827 INFO::ASW Batch was 0.41340251495171 prior to batch effect correction and is now -0.0843180894092762 .
2024-05-04 05:12:58.387971 INFO::ASW Label was 0.216396402698137 prior to batch effect correction and is now 0.834950043140367 .
2024-05-04 05:12:58.389412 INFO::Total function execution time is  0.220961809158325  s and adjustment time is  0.193795919418335 s ( 87.71 )
2024-05-04 05:12:58.390854 INFO::Formatting Data.
2024-05-04 05:12:58.391967 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:58.393473 INFO::Removing potential empty rows and columns
2024-05-04 05:12:58.395167 INFO::Found  0  missing values.
2024-05-04 05:12:58.402308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:58.403383 INFO::Done
2024-05-04 05:12:58.404348 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:58.409255 INFO::Starting hierarchical adjustment
2024-05-04 05:12:58.4106 INFO::Found  5  batches.
2024-05-04 05:12:58.411604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:58.412659 INFO::Using default BPPARAM
2024-05-04 05:12:58.413561 INFO::Processing subtree level 1
2024-05-04 05:12:58.568027 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:58.570169 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:58.593336 INFO::Done
2024-05-04 05:12:58.594405 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:58.599378 INFO::ASW Batch was 0.41340251495171 prior to batch effect correction and is now -0.0843180894092762 .
2024-05-04 05:12:58.600358 INFO::ASW Label was 0.216396402698137 prior to batch effect correction and is now 0.834950043140367 .
2024-05-04 05:12:58.601609 INFO::Total function execution time is  0.210769653320312  s and adjustment time is  0.183045625686646 s ( 86.85 )
2024-05-04 05:12:58.621784 INFO::Formatting Data.
2024-05-04 05:12:58.622898 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:58.624271 INFO::Removing potential empty rows and columns
2024-05-04 05:12:58.625729 INFO::Found  0  missing values.
2024-05-04 05:12:58.632238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:58.633143 INFO::Done
2024-05-04 05:12:58.633956 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:58.638474 INFO::Starting hierarchical adjustment
2024-05-04 05:12:58.639675 INFO::Found  5  batches.
2024-05-04 05:12:58.640508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:58.641434 INFO::Using default BPPARAM
2024-05-04 05:12:58.642242 INFO::Processing subtree level 1
2024-05-04 05:12:58.794637 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:58.796862 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:58.820373 INFO::Done
2024-05-04 05:12:58.821356 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:58.826132 INFO::ASW Batch was 0.251620051934903 prior to batch effect correction and is now -0.0531749847388741 .
2024-05-04 05:12:58.827168 INFO::ASW Label was 0.543833440322417 prior to batch effect correction and is now 0.807811874181266 .
2024-05-04 05:12:58.828527 INFO::Total function execution time is  0.206766128540039  s and adjustment time is  0.180930137634277 s ( 87.5 )
2024-05-04 05:12:58.829971 INFO::Formatting Data.
2024-05-04 05:12:58.830971 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:58.832324 INFO::Removing potential empty rows and columns
2024-05-04 05:12:58.83393 INFO::Found  0  missing values.
2024-05-04 05:12:58.840418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:58.841329 INFO::Done
2024-05-04 05:12:58.842118 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:58.84644 INFO::Starting hierarchical adjustment
2024-05-04 05:12:58.847625 INFO::Found  5  batches.
2024-05-04 05:12:58.848445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:58.849379 INFO::Using default BPPARAM
2024-05-04 05:12:58.850192 INFO::Processing subtree level 1
2024-05-04 05:12:59.005088 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:59.007324 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:59.030329 INFO::Done
2024-05-04 05:12:59.031375 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:59.036132 INFO::ASW Batch was 0.251620051934903 prior to batch effect correction and is now -0.0531749847388741 .
2024-05-04 05:12:59.037096 INFO::ASW Label was 0.543833440322417 prior to batch effect correction and is now 0.807811874181266 .
2024-05-04 05:12:59.038371 INFO::Total function execution time is  0.208351373672485  s and adjustment time is  0.182890653610229 s ( 87.78 )
2024-05-04 05:12:59.059263 INFO::Formatting Data.
2024-05-04 05:12:59.060384 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:59.06173 INFO::Removing potential empty rows and columns
2024-05-04 05:12:59.063278 INFO::Found  0  missing values.
2024-05-04 05:12:59.067581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:59.068459 INFO::Done
2024-05-04 05:12:59.069227 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:59.073519 INFO::Starting hierarchical adjustment
2024-05-04 05:12:59.074657 INFO::Found  2  batches.
2024-05-04 05:12:59.075506 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:59.076412 INFO::Using default BPPARAM
2024-05-04 05:12:59.077219 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:59.078674 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:59.100566 INFO::Done
2024-05-04 05:12:59.101506 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:59.105961 INFO::ASW Batch was 0.691449198067638 prior to batch effect correction and is now -0.0101979024475233 .
2024-05-04 05:12:59.106972 INFO::ASW Label was 0.342722649113005 prior to batch effect correction and is now 0.877245307695085 .
2024-05-04 05:12:59.10834 INFO::Total function execution time is  0.0491306781768799  s and adjustment time is  0.0261259078979492 s ( 53.18 )
2024-05-04 05:12:59.109624 INFO::Formatting Data.
2024-05-04 05:12:59.110604 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:59.111961 INFO::Removing potential empty rows and columns
2024-05-04 05:12:59.113457 INFO::Found  0  missing values.
2024-05-04 05:12:59.117684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:59.118587 INFO::Done
2024-05-04 05:12:59.119411 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:59.123681 INFO::Starting hierarchical adjustment
2024-05-04 05:12:59.124843 INFO::Found  2  batches.
2024-05-04 05:12:59.125743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:59.126688 INFO::Using default BPPARAM
2024-05-04 05:12:59.127521 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:59.128892 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:59.151088 INFO::Done
2024-05-04 05:12:59.152009 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:59.156262 INFO::ASW Batch was 0.691449198067638 prior to batch effect correction and is now -0.0101979024475233 .
2024-05-04 05:12:59.157196 INFO::ASW Label was 0.342722649113005 prior to batch effect correction and is now 0.877245307695085 .
2024-05-04 05:12:59.158355 INFO::Total function execution time is  0.0487484931945801  s and adjustment time is  0.0264718532562256 s ( 54.3 )
2024-05-04 05:12:59.17522 INFO::Formatting Data.
2024-05-04 05:12:59.176311 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:59.177594 INFO::Removing potential empty rows and columns
2024-05-04 05:12:59.17894 INFO::Found  0  missing values.
2024-05-04 05:12:59.182261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:59.183197 INFO::Done
2024-05-04 05:12:59.183995 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:59.186892 INFO::Starting hierarchical adjustment
2024-05-04 05:12:59.188105 INFO::Found  2  batches.
2024-05-04 05:12:59.188972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:59.189877 INFO::Using default BPPARAM
2024-05-04 05:12:59.190718 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:59.192177 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:59.239649 INFO::Done
2024-05-04 05:12:59.240578 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:59.243356 INFO::ASW Batch was -0.0706372606424751 prior to batch effect correction and is now -0.150861279410714 .
2024-05-04 05:12:59.244558 INFO::Total function execution time is  0.0694408416748047  s and adjustment time is  0.0517697334289551 s ( 74.55 )
2024-05-04 05:12:59.261743 INFO::Formatting Data.
2024-05-04 05:12:59.262826 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:59.26418 INFO::Removing potential empty rows and columns
2024-05-04 05:12:59.265626 INFO::Found  0  missing values.
2024-05-04 05:12:59.267311 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.
2024-05-04 05:12:59.2951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:59.296807 INFO::Done
2024-05-04 05:12:59.297689 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:59.302269 INFO::Starting hierarchical adjustment
2024-05-04 05:12:59.303436 INFO::Found  2  batches.
2024-05-04 05:12:59.304296 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:59.305164 INFO::Using default BPPARAM
2024-05-04 05:12:59.305945 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:59.30744 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:59.333452 INFO::Done
2024-05-04 05:12:59.334446 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:59.339026 INFO::ASW Batch was 0.894440958520749 prior to batch effect correction and is now 0.0342341966856379 .
2024-05-04 05:12:59.340007 INFO::ASW Label was 0.0961398242945182 prior to batch effect correction and is now 0.743465278307553 .
2024-05-04 05:12:59.341256 INFO::Total function execution time is  0.0795645713806152  s and adjustment time is  0.0302548408508301 s ( 38.03 )
2024-05-04 05:12:59.342463 INFO::Formatting Data.
2024-05-04 05:12:59.343469 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:59.344887 INFO::Removing potential empty rows and columns
2024-05-04 05:12:59.346444 INFO::Found  0  missing values.
2024-05-04 05:12:59.34785 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.
2024-05-04 05:12:59.355608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:59.356577 INFO::Done
2024-05-04 05:12:59.35744 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:59.362114 INFO::Starting hierarchical adjustment
2024-05-04 05:12:59.363383 INFO::Found  2  batches.
2024-05-04 05:12:59.364311 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:59.365269 INFO::Using default BPPARAM
2024-05-04 05:12:59.366097 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:12:59.367659 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:12:59.3944 INFO::Done
2024-05-04 05:12:59.395378 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:59.400034 INFO::ASW Batch was 0.894440958520749 prior to batch effect correction and is now 0.0342341966856379 .
2024-05-04 05:12:59.401033 INFO::ASW Label was 0.0961398242945182 prior to batch effect correction and is now 0.743465278307553 .
2024-05-04 05:12:59.402317 INFO::Total function execution time is  0.0598633289337158  s and adjustment time is  0.0312628746032715 s ( 52.22 )
2024-05-04 05:12:59.746006 INFO::Formatting Data.
2024-05-04 05:12:59.747317 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:59.748851 INFO::Removing potential empty rows and columns
2024-05-04 05:12:59.750661 INFO::Found  0  missing values.
2024-05-04 05:12:59.755875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:59.756862 INFO::Done
2024-05-04 05:12:59.757773 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:59.761269 INFO::Starting hierarchical adjustment
2024-05-04 05:12:59.762544 INFO::Found  3  batches.
2024-05-04 05:12:59.763505 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:59.764537 INFO::Using default BPPARAM
2024-05-04 05:12:59.76544 INFO::Processing subtree level 1
2024-05-04 05:12:59.894 INFO::Adjusting the last 1 batches sequentially
2024-05-04 05:12:59.896359 INFO::Done
2024-05-04 05:12:59.89719 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:12:59.90062 INFO::ASW Batch was -0.0627176489702436 prior to batch effect correction and is now -0.0627176489702436 .
2024-05-04 05:12:59.90212 INFO::Total function execution time is  0.156293392181396  s and adjustment time is  0.134150505065918 s ( 85.83 )
2024-05-04 05:12:59.903723 INFO::Formatting Data.
2024-05-04 05:12:59.904739 INFO::Typecasting input to dataframe.
2024-05-04 05:12:59.905897 INFO::Replacing NaNs with NAs.
2024-05-04 05:12:59.907287 INFO::Removing potential empty rows and columns
2024-05-04 05:12:59.90887 INFO::Found  0  missing values.
2024-05-04 05:12:59.913424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:12:59.914368 INFO::Done
2024-05-04 05:12:59.9152 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:12:59.918018 INFO::Starting hierarchical adjustment
2024-05-04 05:12:59.919094 INFO::Found  3  batches.
2024-05-04 05:12:59.919872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:12:59.92077 INFO::Using default BPPARAM
2024-05-04 05:12:59.921569 INFO::Processing subtree level 1
2024-05-04 05:13:00.04297 INFO::Adjusting the last 1 batches sequentially
2024-05-04 05:13:00.045432 INFO::Done
2024-05-04 05:13:00.046451 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:13:00.05013 INFO::ASW Batch was -0.0627176489702436 prior to batch effect correction and is now -0.0627176489702436 .
2024-05-04 05:13:00.05167 INFO::Total function execution time is  0.14788556098938  s and adjustment time is  0.126538991928101 s ( 85.57 )
2024-05-04 05:13:00.071177 INFO::Formatting Data.
2024-05-04 05:13:00.072327 INFO::Typecasting input to dataframe.
2024-05-04 05:13:00.073548 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:00.074857 INFO::Removing potential empty rows and columns
2024-05-04 05:13:00.076434 INFO::Found  0  missing values.
2024-05-04 05:13:00.080972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:00.081869 INFO::Done
2024-05-04 05:13:00.082665 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:13:00.085536 INFO::Starting hierarchical adjustment
2024-05-04 05:13:00.086656 INFO::Found  3  batches.
2024-05-04 05:13:00.087476 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:13:00.088368 INFO::Using default BPPARAM
2024-05-04 05:13:00.089147 INFO::Processing subtree level 1
2024-05-04 05:13:00.208205 INFO::Adjusting the last 1 batches sequentially
2024-05-04 05:13:00.210949 INFO::Done
2024-05-04 05:13:00.211924 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:13:00.215451 INFO::ASW Batch was -0.0517686924366849 prior to batch effect correction and is now -0.0517686924366849 .
2024-05-04 05:13:00.216849 INFO::Total function execution time is  0.145750999450684  s and adjustment time is  0.124498605728149 s ( 85.42 )
2024-05-04 05:13:00.421903 INFO::Formatting Data.
2024-05-04 05:13:00.423069 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:00.424787 INFO::Removing potential empty rows and columns
2024-05-04 05:13:00.42945 INFO::Found  1000  missing values.
2024-05-04 05:13:00.460171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:00.461112 INFO::Done
2024-05-04 05:13:00.461983 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:13:00.469968 INFO::Starting hierarchical adjustment
2024-05-04 05:13:00.47135 INFO::Found  10  batches.
2024-05-04 05:13:00.472189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:13:00.473079 INFO::Using default BPPARAM
2024-05-04 05:13:00.473837 INFO::Processing subtree level 1
2024-05-04 05:13:00.656823 INFO::Processing subtree level 2
2024-05-04 05:13:00.94594 INFO::Adjusting the last 1 batches sequentially
2024-05-04 05:13:00.948828 INFO::Done
2024-05-04 05:13:00.949863 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:13:00.958358 INFO::ASW Batch was 0.482962191843931 prior to batch effect correction and is now 0.482962191843931 .
2024-05-04 05:13:00.95946 INFO::ASW Label was 0.336342564894138 prior to batch effect correction and is now 0.336342564894138 .
2024-05-04 05:13:00.96089 INFO::Total function execution time is  0.539000272750854  s and adjustment time is  0.477774858474731 s ( 88.64 )
2024-05-04 05:13:00.962284 INFO::Formatting Data.
2024-05-04 05:13:00.963409 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:00.965263 INFO::Removing potential empty rows and columns
2024-05-04 05:13:00.97024 INFO::Found  1000  missing values.
2024-05-04 05:13:01.002079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:01.003079 INFO::Done
2024-05-04 05:13:01.003967 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:13:01.011868 INFO::Starting hierarchical adjustment
2024-05-04 05:13:01.013083 INFO::Found  10  batches.
2024-05-04 05:13:02.34219 INFO::Set up parallel execution backend with 2 workers
2024-05-04 05:13:02.34382 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-04 05:13:03.73131 INFO::Adjusting the last 2 batches sequentially
2024-05-04 05:13:03.732985 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-04 05:13:03.757329 INFO::Done
2024-05-04 05:13:03.758119 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:13:03.764661 INFO::ASW Batch was 0.482962191843931 prior to batch effect correction and is now 0.482962191843931 .
2024-05-04 05:13:03.765511 INFO::ASW Label was 0.336342564894138 prior to batch effect correction and is now 0.336342564894138 .
2024-05-04 05:13:03.766563 INFO::Total function execution time is  2.80440211296082  s and adjustment time is  2.74450421333313 s ( 97.86 )
2024-05-04 05:13:03.945196 INFO::Formatting Data.
2024-05-04 05:13:03.946346 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:03.947694 INFO::Removing potential empty rows and columns
2024-05-04 05:13:03.949295 INFO::Found  0  missing values.
2024-05-04 05:13:03.954911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:03.955801 INFO::Done
2024-05-04 05:13:03.956531 INFO::Acquiring quality metrics before batch effect correction.
2024-05-04 05:13:03.960326 INFO::Starting hierarchical adjustment
2024-05-04 05:13:03.961422 INFO::Found  3  batches.
2024-05-04 05:13:03.962168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-04 05:13:03.963069 INFO::Using default BPPARAM
2024-05-04 05:13:03.963832 INFO::Processing subtree level 1
2024-05-04 05:13:04.093537 INFO::Adjusting the last 1 batches sequentially
2024-05-04 05:13:04.095894 INFO::Done
2024-05-04 05:13:04.096739 INFO::Acquiring quality metrics after batch effect correction.
2024-05-04 05:13:04.101168 INFO::ASW Batch was 0.125494317507777 prior to batch effect correction and is now -0.143688913627906 .
2024-05-04 05:13:04.102129 INFO::ASW Label was -0.185627256900691 prior to batch effect correction and is now -0.0582047108292829 .
2024-05-04 05:13:04.103429 INFO::Total function execution time is  0.158252000808716  s and adjustment time is  0.134691953659058 s ( 85.11 )
2024-05-04 05:13:04.268397 INFO::Formatting Data.
2024-05-04 05:13:04.269382 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.270571 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.272026 INFO::Found  2  missing values.
2024-05-04 05:13:04.276114 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.276926 INFO::Done
2024-05-04 05:13:04.315504 INFO::Found NA in Reference column
2024-05-04 05:13:04.329248 INFO::Require at least two references per batch.
2024-05-04 05:13:04.358673 INFO::Formatting Data.
2024-05-04 05:13:04.359609 INFO::Recognized SummarizedExperiment
2024-05-04 05:13:04.360326 INFO::Typecasting input to dataframe.
2024-05-04 05:13:04.37419 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.375874 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.381655 INFO::Found  0  missing values.
2024-05-04 05:13:04.392631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.393503 INFO::Done
2024-05-04 05:13:04.415227 INFO::Formatting Data.
2024-05-04 05:13:04.416158 INFO::Recognized SummarizedExperiment
2024-05-04 05:13:04.416858 INFO::Typecasting input to dataframe.
2024-05-04 05:13:04.441835 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.443456 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.449002 INFO::Found  0  missing values.
2024-05-04 05:13:04.467055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.46794 INFO::Done
2024-05-04 05:13:04.489991 INFO::Formatting Data.
2024-05-04 05:13:04.49097 INFO::Recognized SummarizedExperiment
2024-05-04 05:13:04.491702 INFO::Typecasting input to dataframe.
2024-05-04 05:13:04.516034 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.517387 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.519073 INFO::Found  0  missing values.
2024-05-04 05:13:04.520386 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.
2024-05-04 05:13:04.527062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.527986 INFO::Done
2024-05-04 05:13:04.542508 INFO::Formatting Data.
2024-05-04 05:13:04.543609 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.544768 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.546157 INFO::Found  0  missing values.
2024-05-04 05:13:04.550744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.551589 INFO::Done
2024-05-04 05:13:04.567523 INFO::Formatting Data.
2024-05-04 05:13:04.568496 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.569613 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.571001 INFO::Found  0  missing values.
2024-05-04 05:13:04.575275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.576088 INFO::Done
2024-05-04 05:13:04.618441 INFO::Formatting Data.
2024-05-04 05:13:04.619467 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.620858 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.62245 INFO::Found  1  missing values.
2024-05-04 05:13:04.6261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.626933 INFO::Done
2024-05-04 05:13:04.654373 INFO::Formatting Data.
2024-05-04 05:13:04.655372 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.656498 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.657779 INFO::Found  2  missing values.
2024-05-04 05:13:04.65903 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.
2024-05-04 05:13:04.662265 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.663107 INFO::Done
2024-05-04 05:13:04.677663 INFO::Formatting Data.
2024-05-04 05:13:04.678704 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.67991 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.681188 INFO::Found  2  missing values.
2024-05-04 05:13:04.683477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.684235 INFO::Done
2024-05-04 05:13:04.699524 INFO::Formatting Data.
2024-05-04 05:13:04.700513 INFO::Typecasting input to dataframe.
2024-05-04 05:13:04.701625 INFO::Replacing NaNs with NAs.
2024-05-04 05:13:04.702844 INFO::Removing potential empty rows and columns
2024-05-04 05:13:04.704275 INFO::Found  0  missing values.
2024-05-04 05:13:04.708569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-04 05:13:04.709455 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 21.863   5.247  26.670 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT31.247 1.48622.636
compute_asw0.0320.0040.036
count_existing0.0190.0000.019
generate_data_covariables0.0140.0040.017
generate_dataset0.0120.0040.016