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This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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
palomino7Windows 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 merida1

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

raw results


Summary

Package: BERT
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz
StartedAt: 2024-10-17 01:34:20 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 01:37:11 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 170.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* 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 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 47.427  2.906    42.8
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

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


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

Tests output

BERT.Rcheck/tests/testthat.Rout


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

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2024-10-17 01:36:31.918433 INFO::Formatting Data.
2024-10-17 01:36:31.924499 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:31.963387 INFO::Removing potential empty rows and columns
2024-10-17 01:36:32.863276 INFO::Found  0  missing values.
2024-10-17 01:36:32.872453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:32.873867 INFO::Done
2024-10-17 01:36:32.875093 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:32.907087 INFO::Starting hierarchical adjustment
2024-10-17 01:36:32.909134 INFO::Found  3  batches.
2024-10-17 01:36:32.913467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:32.916381 INFO::Using default BPPARAM
2024-10-17 01:36:32.91805 INFO::Processing subtree level 1
2024-10-17 01:36:33.222585 INFO::Adjusting the last 1 batches sequentially
2024-10-17 01:36:33.22823 INFO::Done
2024-10-17 01:36:33.229765 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:33.235738 INFO::ASW Batch was -0.0721588642937645 prior to batch effect correction and is now -0.0721588642937645 .
2024-10-17 01:36:33.238187 INFO::Total function execution time is  1.32123398780823  s and adjustment time is  0.319500923156738 s ( 24.18 )
2024-10-17 01:36:33.275736 INFO::Formatting Data.
2024-10-17 01:36:33.278887 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:33.281331 INFO::Removing potential empty rows and columns
2024-10-17 01:36:33.284065 INFO::Found  0  missing values.
2024-10-17 01:36:33.286301 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.
2024-10-17 01:36:33.328391 INFO::Formatting Data.
2024-10-17 01:36:33.33004 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:33.332192 INFO::Removing potential empty rows and columns
2024-10-17 01:36:33.334865 INFO::Found  0  missing values.
2024-10-17 01:36:33.337272 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.
2024-10-17 01:36:33.38958 INFO::Formatting Data.
2024-10-17 01:36:33.391294 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:33.395232 INFO::Removing potential empty rows and columns
2024-10-17 01:36:33.398346 INFO::Found  0  missing values.
2024-10-17 01:36:33.400705 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.
2024-10-17 01:36:33.418897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:33.420351 INFO::Done
2024-10-17 01:36:33.421641 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:33.427549 INFO::Starting hierarchical adjustment
2024-10-17 01:36:33.431202 INFO::Found  2  batches.
2024-10-17 01:36:33.432718 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:33.434377 INFO::Using default BPPARAM
2024-10-17 01:36:33.435984 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:33.439753 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:33.506977 INFO::Done
2024-10-17 01:36:33.508511 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:33.513633 INFO::ASW Batch was 0.00676473197375659 prior to batch effect correction and is now -0.105912031490488 .
2024-10-17 01:36:33.517456 INFO::Total function execution time is  0.126353979110718  s and adjustment time is  0.0767338275909424 s ( 60.73 )
2024-10-17 01:36:33.52391 INFO::Formatting Data.
2024-10-17 01:36:33.525932 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:33.559601 INFO::Formatting Data.
2024-10-17 01:36:33.56135 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:33.563833 INFO::Removing potential empty rows and columns
2024-10-17 01:36:33.569993 INFO::Found  0  missing values.
2024-10-17 01:36:33.579644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:33.581263 INFO::Done
2024-10-17 01:36:33.582762 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:33.587943 INFO::Starting hierarchical adjustment
2024-10-17 01:36:33.591701 INFO::Found  2  batches.
2024-10-17 01:36:33.593553 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:33.595476 INFO::Using default BPPARAM
2024-10-17 01:36:33.597259 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:33.60014 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:33.652432 INFO::Done
2024-10-17 01:36:33.654031 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:33.659106 INFO::ASW Batch was -0.0328727343253622 prior to batch effect correction and is now -0.128487726470463 .
2024-10-17 01:36:33.662593 INFO::Total function execution time is  0.103044986724854  s and adjustment time is  0.0614728927612305 s ( 59.66 )
2024-10-17 01:36:33.665879 INFO::Formatting Data.
2024-10-17 01:36:33.667926 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:33.670675 INFO::Removing potential empty rows and columns
2024-10-17 01:36:33.675533 INFO::Found  0  missing values.
2024-10-17 01:36:33.684429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:33.68863 INFO::Done
2024-10-17 01:36:33.690364 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:33.695214 INFO::Starting hierarchical adjustment
2024-10-17 01:36:33.696975 INFO::Found  2  batches.
2024-10-17 01:36:33.700662 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:33.702306 INFO::Using default BPPARAM
2024-10-17 01:36:33.703557 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:33.705864 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:33.750489 INFO::Done
2024-10-17 01:36:33.751922 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:33.757992 INFO::ASW Batch was -0.0328727343253622 prior to batch effect correction and is now -0.128487726470463 .
2024-10-17 01:36:33.760002 INFO::Total function execution time is  0.0941698551177979  s and adjustment time is  0.0538599491119385 s ( 57.19 )
2024-10-17 01:36:40.093615 INFO::Formatting Data.
2024-10-17 01:36:40.09912 INFO::Recognized SummarizedExperiment
2024-10-17 01:36:40.100346 INFO::Typecasting input to dataframe.
2024-10-17 01:36:40.182593 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:40.185064 INFO::Removing potential empty rows and columns
2024-10-17 01:36:40.24249 INFO::Found  0  missing values.
2024-10-17 01:36:40.267186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:40.268481 INFO::Done
2024-10-17 01:36:40.269574 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:40.27874 INFO::Starting hierarchical adjustment
2024-10-17 01:36:40.280249 INFO::Found  2  batches.
2024-10-17 01:36:40.281299 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:40.284585 INFO::Using default BPPARAM
2024-10-17 01:36:40.285833 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:40.288193 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:40.447875 INFO::Done
2024-10-17 01:36:40.449993 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:40.458429 INFO::ASW Batch was 0.00520135683292958 prior to batch effect correction and is now -0.0915384644548691 .
2024-10-17 01:36:40.461435 INFO::Total function execution time is  0.368622064590454  s and adjustment time is  0.167854070663452 s ( 45.54 )
2024-10-17 01:36:40.512237 INFO::Formatting Data.
2024-10-17 01:36:40.513537 INFO::Recognized SummarizedExperiment
2024-10-17 01:36:40.514573 INFO::Typecasting input to dataframe.
2024-10-17 01:36:40.53684 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:40.539299 INFO::Removing potential empty rows and columns
2024-10-17 01:36:40.551467 INFO::Found  0  missing values.
2024-10-17 01:36:40.575044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:40.576206 INFO::Done
2024-10-17 01:36:40.577304 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:40.585753 INFO::Starting hierarchical adjustment
2024-10-17 01:36:40.587353 INFO::Found  2  batches.
2024-10-17 01:36:40.588448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:40.589663 INFO::Using default BPPARAM
2024-10-17 01:36:40.593602 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:40.596787 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:40.677144 INFO::Done
2024-10-17 01:36:40.678712 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:40.687296 INFO::ASW Batch was 0.00161008297574213 prior to batch effect correction and is now 0.00161008297574213 .
2024-10-17 01:36:40.690405 INFO::Total function execution time is  0.17815899848938  s and adjustment time is  0.0882959365844727 s ( 49.56 )
2024-10-17 01:36:40.737344 INFO::Formatting Data.
2024-10-17 01:36:40.738749 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:40.740484 INFO::Removing potential empty rows and columns
2024-10-17 01:36:40.742604 INFO::Found  0  missing values.
2024-10-17 01:36:40.749884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:40.751112 INFO::Done
2024-10-17 01:36:40.752616 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:40.758115 INFO::Starting hierarchical adjustment
2024-10-17 01:36:40.759806 INFO::Found  3  batches.
2024-10-17 01:36:40.760967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:40.762199 INFO::Using default BPPARAM
2024-10-17 01:36:40.763229 INFO::Processing subtree level 1
2024-10-17 01:36:41.261279 INFO::Adjusting the last 1 batches sequentially
2024-10-17 01:36:41.271913 INFO::Done
2024-10-17 01:36:41.275154 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:41.288457 INFO::ASW Batch was -0.0359544429028467 prior to batch effect correction and is now -0.152426564838622 .
2024-10-17 01:36:41.292821 INFO::Total function execution time is  0.554512977600098  s and adjustment time is  0.512365102767944 s ( 92.4 )
2024-10-17 01:36:41.337515 INFO::Skipping initial DF formatting
2024-10-17 01:36:41.339056 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:41.349116 INFO::Starting hierarchical adjustment
2024-10-17 01:36:41.351048 INFO::Found  5  batches.
2024-10-17 01:36:41.352363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:41.353976 INFO::Using default BPPARAM
2024-10-17 01:36:41.355388 INFO::Processing subtree level 1
2024-10-17 01:36:41.783623 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:41.796671 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:41.868151 INFO::Done
2024-10-17 01:36:41.870932 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:41.88516 INFO::ASW Batch was 0.509880633553985 prior to batch effect correction and is now 0.509880633553985 .
2024-10-17 01:36:41.886866 INFO::ASW Label was 0.380977466714864 prior to batch effect correction and is now 0.380977466714864 .
2024-10-17 01:36:41.890003 INFO::Total function execution time is  0.551902055740356  s and adjustment time is  0.51751184463501 s ( 93.77 )
2024-10-17 01:36:41.955367 INFO::Formatting Data.
2024-10-17 01:36:41.957722 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:41.96009 INFO::Removing potential empty rows and columns
2024-10-17 01:36:41.962781 INFO::Found  0  missing values.
2024-10-17 01:36:41.974491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:41.975982 INFO::Done
2024-10-17 01:36:41.977376 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:41.985097 INFO::Starting hierarchical adjustment
2024-10-17 01:36:41.988294 INFO::Found  5  batches.
2024-10-17 01:36:41.989721 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:41.991401 INFO::Using default BPPARAM
2024-10-17 01:36:41.992864 INFO::Processing subtree level 1
2024-10-17 01:36:42.341907 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:42.353179 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:42.40931 INFO::Done
2024-10-17 01:36:42.411559 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:42.421775 INFO::ASW Batch was 0.5065837968796 prior to batch effect correction and is now -0.013795157969534 .
2024-10-17 01:36:42.423347 INFO::ASW Label was 0.257258136842119 prior to batch effect correction and is now 0.764573670112439 .
2024-10-17 01:36:42.425332 INFO::Total function execution time is  0.471091985702515  s and adjustment time is  0.421457052230835 s ( 89.46 )
2024-10-17 01:36:42.431048 INFO::Formatting Data.
2024-10-17 01:36:42.432677 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:42.434912 INFO::Removing potential empty rows and columns
2024-10-17 01:36:42.437653 INFO::Found  0  missing values.
2024-10-17 01:36:42.455233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:42.456756 INFO::Done
2024-10-17 01:36:42.458069 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:42.465736 INFO::Starting hierarchical adjustment
2024-10-17 01:36:42.46767 INFO::Found  5  batches.
2024-10-17 01:36:42.469047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:42.470562 INFO::Using default BPPARAM
2024-10-17 01:36:42.471765 INFO::Processing subtree level 1
2024-10-17 01:36:42.800472 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:42.812051 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:42.867216 INFO::Done
2024-10-17 01:36:42.870106 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:42.880624 INFO::ASW Batch was 0.5065837968796 prior to batch effect correction and is now -0.013795157969534 .
2024-10-17 01:36:42.882181 INFO::ASW Label was 0.257258136842119 prior to batch effect correction and is now 0.764573670112439 .
2024-10-17 01:36:42.88427 INFO::Total function execution time is  0.453435897827148  s and adjustment time is  0.399926900863647 s ( 88.2 )
2024-10-17 01:36:42.929011 INFO::Formatting Data.
2024-10-17 01:36:42.931289 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:42.933652 INFO::Removing potential empty rows and columns
2024-10-17 01:36:42.936376 INFO::Found  0  missing values.
2024-10-17 01:36:42.952224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:42.953812 INFO::Done
2024-10-17 01:36:42.955204 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:42.962755 INFO::Starting hierarchical adjustment
2024-10-17 01:36:42.964712 INFO::Found  5  batches.
2024-10-17 01:36:42.966104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:42.967642 INFO::Using default BPPARAM
2024-10-17 01:36:42.968985 INFO::Processing subtree level 1
2024-10-17 01:36:43.299816 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:43.314048 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:43.370885 INFO::Done
2024-10-17 01:36:43.373482 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:43.384936 INFO::ASW Batch was 0.340936711553801 prior to batch effect correction and is now 0.0383058036767589 .
2024-10-17 01:36:43.386513 INFO::ASW Label was 0.431581159312848 prior to batch effect correction and is now 0.716255785117955 .
2024-10-17 01:36:43.38961 INFO::Total function execution time is  0.459685087203979  s and adjustment time is  0.406616926193237 s ( 88.46 )
2024-10-17 01:36:43.39227 INFO::Formatting Data.
2024-10-17 01:36:43.394492 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:43.396817 INFO::Removing potential empty rows and columns
2024-10-17 01:36:43.399481 INFO::Found  0  missing values.
2024-10-17 01:36:43.413655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:43.41562 INFO::Done
2024-10-17 01:36:43.417084 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:43.426554 INFO::Starting hierarchical adjustment
2024-10-17 01:36:43.42864 INFO::Found  5  batches.
2024-10-17 01:36:43.430273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:43.432479 INFO::Using default BPPARAM
2024-10-17 01:36:43.434575 INFO::Processing subtree level 1
2024-10-17 01:36:43.758765 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:43.779024 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:43.839957 INFO::Done
2024-10-17 01:36:43.842656 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:43.854991 INFO::ASW Batch was 0.340936711553801 prior to batch effect correction and is now 0.0383058036767589 .
2024-10-17 01:36:43.856588 INFO::ASW Label was 0.431581159312848 prior to batch effect correction and is now 0.716255785117955 .
2024-10-17 01:36:43.858704 INFO::Total function execution time is  0.466455936431885  s and adjustment time is  0.411742925643921 s ( 88.27 )
2024-10-17 01:36:43.896541 INFO::Formatting Data.
2024-10-17 01:36:43.898304 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:43.900595 INFO::Removing potential empty rows and columns
2024-10-17 01:36:43.905441 INFO::Found  0  missing values.
2024-10-17 01:36:43.912906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:43.914607 INFO::Done
2024-10-17 01:36:43.916208 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:43.927702 INFO::Starting hierarchical adjustment
2024-10-17 01:36:43.93017 INFO::Found  2  batches.
2024-10-17 01:36:43.931783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:43.933315 INFO::Using default BPPARAM
2024-10-17 01:36:43.934587 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:43.938206 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:43.985636 INFO::Done
2024-10-17 01:36:43.987101 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:43.994255 INFO::ASW Batch was 0.679734722263867 prior to batch effect correction and is now 0.0835480913165351 .
2024-10-17 01:36:43.997091 INFO::ASW Label was 0.431136705572764 prior to batch effect correction and is now 0.845201028550289 .
2024-10-17 01:36:44.000055 INFO::Total function execution time is  0.10359787940979  s and adjustment time is  0.0561800003051758 s ( 54.23 )
2024-10-17 01:36:44.002411 INFO::Formatting Data.
2024-10-17 01:36:44.004564 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:44.009013 INFO::Removing potential empty rows and columns
2024-10-17 01:36:44.011937 INFO::Found  0  missing values.
2024-10-17 01:36:44.023837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:44.025395 INFO::Done
2024-10-17 01:36:44.026885 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:44.036398 INFO::Starting hierarchical adjustment
2024-10-17 01:36:44.040444 INFO::Found  2  batches.
2024-10-17 01:36:44.042768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:44.046282 INFO::Using default BPPARAM
2024-10-17 01:36:44.047813 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:44.051781 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:44.099769 INFO::Done
2024-10-17 01:36:44.101345 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:44.14359 INFO::ASW Batch was 0.679734722263867 prior to batch effect correction and is now 0.0835480913165351 .
2024-10-17 01:36:44.14526 INFO::ASW Label was 0.431136705572764 prior to batch effect correction and is now 0.845201028550289 .
2024-10-17 01:36:44.147331 INFO::Total function execution time is  0.145116090774536  s and adjustment time is  0.0599169731140137 s ( 41.29 )
2024-10-17 01:36:44.185483 INFO::Formatting Data.
2024-10-17 01:36:44.187334 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:44.189704 INFO::Removing potential empty rows and columns
2024-10-17 01:36:44.194151 INFO::Found  0  missing values.
2024-10-17 01:36:44.20052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:44.201986 INFO::Done
2024-10-17 01:36:44.203328 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:44.210562 INFO::Starting hierarchical adjustment
2024-10-17 01:36:44.212596 INFO::Found  2  batches.
2024-10-17 01:36:44.214032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:44.217222 INFO::Using default BPPARAM
2024-10-17 01:36:44.219021 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:44.223049 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:44.342816 INFO::Done
2024-10-17 01:36:44.344567 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:44.349845 INFO::ASW Batch was 0.00400772950439554 prior to batch effect correction and is now -0.138771853885659 .
2024-10-17 01:36:44.351963 INFO::Total function execution time is  0.166573047637939  s and adjustment time is  0.130636930465698 s ( 78.43 )
2024-10-17 01:36:44.397159 INFO::Formatting Data.
2024-10-17 01:36:44.399019 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:44.401701 INFO::Removing potential empty rows and columns
2024-10-17 01:36:44.407861 INFO::Found  0  missing values.
2024-10-17 01:36:44.41136 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.
2024-10-17 01:36:44.433241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:44.434836 INFO::Done
2024-10-17 01:36:44.438248 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:44.447743 INFO::Starting hierarchical adjustment
2024-10-17 01:36:44.450898 INFO::Found  2  batches.
2024-10-17 01:36:44.452348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:44.455167 INFO::Using default BPPARAM
2024-10-17 01:36:44.457405 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:44.460698 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:44.520148 INFO::Done
2024-10-17 01:36:44.521643 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:44.532005 INFO::ASW Batch was 0.540595821284922 prior to batch effect correction and is now -0.0360230581640515 .
2024-10-17 01:36:44.533684 INFO::ASW Label was 0.542108446928681 prior to batch effect correction and is now 0.932574363850223 .
2024-10-17 01:36:44.538148 INFO::Total function execution time is  0.140978813171387  s and adjustment time is  0.0697159767150879 s ( 49.45 )
2024-10-17 01:36:44.542307 INFO::Formatting Data.
2024-10-17 01:36:44.544214 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:44.546617 INFO::Removing potential empty rows and columns
2024-10-17 01:36:44.551023 INFO::Found  0  missing values.
2024-10-17 01:36:44.554427 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.
2024-10-17 01:36:44.572374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:44.574056 INFO::Done
2024-10-17 01:36:44.576411 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:44.5841 INFO::Starting hierarchical adjustment
2024-10-17 01:36:44.586235 INFO::Found  2  batches.
2024-10-17 01:36:44.587632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:44.589127 INFO::Using default BPPARAM
2024-10-17 01:36:44.590391 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:44.592905 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:44.651114 INFO::Done
2024-10-17 01:36:44.65264 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:44.660616 INFO::ASW Batch was 0.540595821284922 prior to batch effect correction and is now -0.0360230581640515 .
2024-10-17 01:36:44.662169 INFO::ASW Label was 0.542108446928681 prior to batch effect correction and is now 0.932574363850223 .
2024-10-17 01:36:44.664159 INFO::Total function execution time is  0.122075080871582  s and adjustment time is  0.0653820037841797 s ( 53.56 )
2024-10-17 01:36:45.427028 INFO::Formatting Data.
2024-10-17 01:36:45.437568 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:45.441478 INFO::Removing potential empty rows and columns
2024-10-17 01:36:45.444472 INFO::Found  0  missing values.
2024-10-17 01:36:45.454978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:45.458051 INFO::Done
2024-10-17 01:36:45.459566 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:45.465253 INFO::Starting hierarchical adjustment
2024-10-17 01:36:45.467415 INFO::Found  3  batches.
2024-10-17 01:36:45.470203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:45.471945 INFO::Using default BPPARAM
2024-10-17 01:36:45.473381 INFO::Processing subtree level 1
2024-10-17 01:36:45.782546 INFO::Adjusting the last 1 batches sequentially
2024-10-17 01:36:45.79361 INFO::Done
2024-10-17 01:36:45.79631 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:45.811386 INFO::ASW Batch was 0.0801859461893326 prior to batch effect correction and is now 0.0801859461893326 .
2024-10-17 01:36:45.814629 INFO::Total function execution time is  0.387669086456299  s and adjustment time is  0.326684951782227 s ( 84.27 )
2024-10-17 01:36:45.81748 INFO::Formatting Data.
2024-10-17 01:36:45.819344 INFO::Typecasting input to dataframe.
2024-10-17 01:36:45.822776 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:45.825313 INFO::Removing potential empty rows and columns
2024-10-17 01:36:45.831602 INFO::Found  0  missing values.
2024-10-17 01:36:45.84198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:45.843421 INFO::Done
2024-10-17 01:36:45.846251 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:45.851553 INFO::Starting hierarchical adjustment
2024-10-17 01:36:45.855691 INFO::Found  3  batches.
2024-10-17 01:36:45.857295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:45.859217 INFO::Using default BPPARAM
2024-10-17 01:36:45.861975 INFO::Processing subtree level 1
2024-10-17 01:36:46.164566 INFO::Adjusting the last 1 batches sequentially
2024-10-17 01:36:46.175059 INFO::Done
2024-10-17 01:36:46.178883 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:46.19349 INFO::ASW Batch was 0.0801859461893326 prior to batch effect correction and is now 0.0801859461893326 .
2024-10-17 01:36:46.197937 INFO::Total function execution time is  0.379580974578857  s and adjustment time is  0.319830894470215 s ( 84.26 )
2024-10-17 01:36:46.238532 INFO::Formatting Data.
2024-10-17 01:36:46.240356 INFO::Typecasting input to dataframe.
2024-10-17 01:36:46.242627 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:46.244821 INFO::Removing potential empty rows and columns
2024-10-17 01:36:46.247496 INFO::Found  0  missing values.
2024-10-17 01:36:46.255915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:46.257411 INFO::Done
2024-10-17 01:36:46.259586 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:46.26501 INFO::Starting hierarchical adjustment
2024-10-17 01:36:46.267085 INFO::Found  3  batches.
2024-10-17 01:36:46.268612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:46.272092 INFO::Using default BPPARAM
2024-10-17 01:36:46.273735 INFO::Processing subtree level 1
2024-10-17 01:36:46.571529 INFO::Adjusting the last 1 batches sequentially
2024-10-17 01:36:46.58276 INFO::Done
2024-10-17 01:36:46.586816 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:46.601261 INFO::ASW Batch was -0.0878241249157908 prior to batch effect correction and is now -0.0878241249157908 .
2024-10-17 01:36:46.604759 INFO::Total function execution time is  0.366283178329468  s and adjustment time is  0.316076993942261 s ( 86.29 )
2024-10-17 01:36:47.096566 INFO::Formatting Data.
2024-10-17 01:36:47.098367 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:47.101443 INFO::Removing potential empty rows and columns
2024-10-17 01:36:47.110197 INFO::Found  1000  missing values.
2024-10-17 01:36:47.185152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:47.186564 INFO::Done
2024-10-17 01:36:47.187761 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:47.210984 INFO::Starting hierarchical adjustment
2024-10-17 01:36:47.213171 INFO::Found  10  batches.
2024-10-17 01:36:47.214669 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:47.216338 INFO::Using default BPPARAM
2024-10-17 01:36:47.21774 INFO::Processing subtree level 1
2024-10-17 01:36:47.757742 INFO::Processing subtree level 2
2024-10-17 01:36:48.424299 INFO::Adjusting the last 1 batches sequentially
2024-10-17 01:36:48.453182 INFO::Done
2024-10-17 01:36:48.456718 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:48.48484 INFO::ASW Batch was 0.517782499680678 prior to batch effect correction and is now 0.517782499680678 .
2024-10-17 01:36:48.486456 INFO::ASW Label was 0.304759689133907 prior to batch effect correction and is now 0.304759689133907 .
2024-10-17 01:36:48.489606 INFO::Total function execution time is  1.39266991615295  s and adjustment time is  1.24049091339111 s ( 89.07 )
2024-10-17 01:36:48.492153 INFO::Formatting Data.
2024-10-17 01:36:48.494284 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:48.497146 INFO::Removing potential empty rows and columns
2024-10-17 01:36:48.505996 INFO::Found  1000  missing values.
2024-10-17 01:36:48.58217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:48.583838 INFO::Done
2024-10-17 01:36:48.585272 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:48.599924 INFO::Starting hierarchical adjustment
2024-10-17 01:36:48.601943 INFO::Found  10  batches.
2024-10-17 01:36:50.121248 INFO::Set up parallel execution backend with 2 workers
2024-10-17 01:36:50.122443 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-17 01:36:52.101034 INFO::Adjusting the last 2 batches sequentially
2024-10-17 01:36:52.105303 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 01:36:52.161042 INFO::Done
2024-10-17 01:36:52.162325 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:52.174807 INFO::ASW Batch was 0.517782499680678 prior to batch effect correction and is now 0.517782499680678 .
2024-10-17 01:36:52.176227 INFO::ASW Label was 0.304759689133907 prior to batch effect correction and is now 0.304759689133907 .
2024-10-17 01:36:52.17801 INFO::Total function execution time is  3.6859929561615  s and adjustment time is  3.55955815315247 s ( 96.57 )
2024-10-17 01:36:52.670522 INFO::Formatting Data.
2024-10-17 01:36:52.672774 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:52.675026 INFO::Removing potential empty rows and columns
2024-10-17 01:36:52.680587 INFO::Found  0  missing values.
2024-10-17 01:36:52.698341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:52.700614 INFO::Done
2024-10-17 01:36:52.7021 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 01:36:52.710013 INFO::Starting hierarchical adjustment
2024-10-17 01:36:52.715972 INFO::Found  3  batches.
2024-10-17 01:36:52.717357 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 01:36:52.719043 INFO::Using default BPPARAM
2024-10-17 01:36:52.72044 INFO::Processing subtree level 1
2024-10-17 01:36:53.064095 INFO::Adjusting the last 1 batches sequentially
2024-10-17 01:36:53.072432 INFO::Done
2024-10-17 01:36:53.075049 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 01:36:53.095184 INFO::ASW Batch was 0.157197949995525 prior to batch effect correction and is now -0.16738832153891 .
2024-10-17 01:36:53.097138 INFO::ASW Label was -0.217059447504417 prior to batch effect correction and is now -0.0888802765427951 .
2024-10-17 01:36:53.101055 INFO::Total function execution time is  0.430008172988892  s and adjustment time is  0.356849908828735 s ( 82.99 )
2024-10-17 01:36:53.48993 INFO::Formatting Data.
2024-10-17 01:36:53.493735 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:53.496388 INFO::Removing potential empty rows and columns
2024-10-17 01:36:53.499426 INFO::Found  2  missing values.
2024-10-17 01:36:53.507949 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:53.509292 INFO::Done
2024-10-17 01:36:53.600364 INFO::Found NA in Reference column
2024-10-17 01:36:53.636378 INFO::Require at least two references per batch.
2024-10-17 01:36:53.70497 INFO::Formatting Data.
2024-10-17 01:36:53.706981 INFO::Recognized SummarizedExperiment
2024-10-17 01:36:53.708463 INFO::Typecasting input to dataframe.
2024-10-17 01:36:53.740776 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:53.743487 INFO::Removing potential empty rows and columns
2024-10-17 01:36:53.75739 INFO::Found  0  missing values.
2024-10-17 01:36:53.791501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:53.793041 INFO::Done
2024-10-17 01:36:53.850893 INFO::Formatting Data.
2024-10-17 01:36:53.852607 INFO::Recognized SummarizedExperiment
2024-10-17 01:36:53.853945 INFO::Typecasting input to dataframe.
2024-10-17 01:36:53.915643 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:53.918415 INFO::Removing potential empty rows and columns
2024-10-17 01:36:53.93285 INFO::Found  0  missing values.
2024-10-17 01:36:53.987532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:53.989111 INFO::Done
2024-10-17 01:36:54.042509 INFO::Formatting Data.
2024-10-17 01:36:54.044002 INFO::Recognized SummarizedExperiment
2024-10-17 01:36:54.046457 INFO::Typecasting input to dataframe.
2024-10-17 01:36:54.106521 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:54.110142 INFO::Removing potential empty rows and columns
2024-10-17 01:36:54.113173 INFO::Found  0  missing values.
2024-10-17 01:36:54.116861 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.
2024-10-17 01:36:54.134701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:54.136475 INFO::Done
2024-10-17 01:36:54.175548 INFO::Formatting Data.
2024-10-17 01:36:54.177383 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:54.180828 INFO::Removing potential empty rows and columns
2024-10-17 01:36:54.184104 INFO::Found  0  missing values.
2024-10-17 01:36:54.196164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:54.198041 INFO::Done
2024-10-17 01:36:54.23725 INFO::Formatting Data.
2024-10-17 01:36:54.239364 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:54.24439 INFO::Removing potential empty rows and columns
2024-10-17 01:36:54.247354 INFO::Found  0  missing values.
2024-10-17 01:36:54.262893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:54.264366 INFO::Done
2024-10-17 01:36:54.368223 INFO::Formatting Data.
2024-10-17 01:36:54.369982 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:54.372727 INFO::Removing potential empty rows and columns
2024-10-17 01:36:54.376827 INFO::Found  1  missing values.
2024-10-17 01:36:54.384857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:54.386541 INFO::Done
2024-10-17 01:36:54.44949 INFO::Formatting Data.
2024-10-17 01:36:54.451371 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:54.455398 INFO::Removing potential empty rows and columns
2024-10-17 01:36:54.458189 INFO::Found  2  missing values.
2024-10-17 01:36:54.460771 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.
2024-10-17 01:36:54.469414 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:54.4709 INFO::Done
2024-10-17 01:36:54.50535 INFO::Formatting Data.
2024-10-17 01:36:54.507213 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:54.509461 INFO::Removing potential empty rows and columns
2024-10-17 01:36:54.51353 INFO::Found  2  missing values.
2024-10-17 01:36:54.518072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:54.519633 INFO::Done
2024-10-17 01:36:54.558028 INFO::Formatting Data.
2024-10-17 01:36:54.560477 INFO::Typecasting input to dataframe.
2024-10-17 01:36:54.562728 INFO::Replacing NaNs with NAs.
2024-10-17 01:36:54.564963 INFO::Removing potential empty rows and columns
2024-10-17 01:36:54.567741 INFO::Found  0  missing values.
2024-10-17 01:36:54.578969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 01:36:54.58073 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 35.644   7.470  50.219

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT47.427 2.90642.800
compute_asw0.0580.0020.073
count_existing0.0290.0010.037
generate_data_covariables0.0260.0010.032
generate_dataset0.0250.0010.030