Multiple platform build/check report for BioC 3.21 - CHECK results for BERT on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4464
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4418
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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*

CHECK results for BERT on kjohnson3

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: 1.3.6

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_1.3.6.tar.gz

StartedAt: 2025-01-26 20:23:39 -0500 (Sun, 26 Jan 2025)

EndedAt: 2025-01-26 20:24:09 -0500 (Sun, 26 Jan 2025)

EllapsedTime: 30.4 seconds

RetCode: 1

Status: ERROR

CheckDir: BERT.Rcheck

Warnings: NA

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_1.3.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.6’
* 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 9.419  0.388   6.713
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2025-01-26 20:24:05.525571 INFO::Typecasting input to dataframe.
  2025-01-26 20:24:05.525819 INFO::Replacing NaNs with NAs.
  2025-01-26 20:24:05.526069 INFO::Removing potential empty rows and columns
  2025-01-26 20:24:05.526364 INFO::Found  0  missing values.
  2025-01-26 20:24:05.527339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
  2025-01-26 20:24:05.52751 INFO::Done
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 134 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_generate_Dataset.R:154:5'): generate_truncated_dataset works ───
  Error in `generate_truncated_dataset(100, 3, 10, 0.1, 0.1, 2)`: could not find function "generate_truncated_dataset"
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 134 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log’
for details.

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/4.5-arm64/Resources/library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.3.6’
** 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.fail


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
2025-01-26 20:24:01.74993 INFO::Formatting Data.
2025-01-26 20:24:01.751751 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:01.761879 INFO::Removing potential empty rows and columns
2025-01-26 20:24:01.871162 INFO::Found  0  missing values.
2025-01-26 20:24:01.8725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:01.872735 INFO::Done
2025-01-26 20:24:01.872924 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:01.878965 INFO::Starting hierarchical adjustment
2025-01-26 20:24:01.879261 INFO::Found  3  batches.
2025-01-26 20:24:01.879442 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:01.87988 INFO::Using default BPPARAM
2025-01-26 20:24:01.880055 INFO::Processing subtree level 1
2025-01-26 20:24:01.930812 INFO::Adjusting the last 1 batches sequentially
2025-01-26 20:24:01.932046 INFO::Done
2025-01-26 20:24:01.932301 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:01.934121 INFO::ASW Batch was -0.0625000583722504 prior to batch effect correction and is now -0.0625000583722504 .
2025-01-26 20:24:01.934863 INFO::Total function execution time is  0.185266971588135  s and adjustment time is  0.0528450012207031 s ( 28.52 )
2025-01-26 20:24:01.943116 INFO::Formatting Data.
2025-01-26 20:24:01.943388 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:01.943717 INFO::Removing potential empty rows and columns
2025-01-26 20:24:01.9443 INFO::Found  0  missing values.
2025-01-26 20:24:01.944657 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.
2025-01-26 20:24:01.949089 INFO::Formatting Data.
2025-01-26 20:24:01.949359 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:01.94966 INFO::Removing potential empty rows and columns
2025-01-26 20:24:01.950023 INFO::Found  0  missing values.
2025-01-26 20:24:01.95032 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.
2025-01-26 20:24:01.95635 INFO::Formatting Data.
2025-01-26 20:24:01.956629 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:01.956934 INFO::Removing potential empty rows and columns
2025-01-26 20:24:01.957279 INFO::Found  0  missing values.
2025-01-26 20:24:01.95761 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.
2025-01-26 20:24:01.959132 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:01.959324 INFO::Done
2025-01-26 20:24:01.959506 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:01.960305 INFO::Starting hierarchical adjustment
2025-01-26 20:24:01.960538 INFO::Found  2  batches.
2025-01-26 20:24:01.960713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:01.961023 INFO::Using default BPPARAM
2025-01-26 20:24:01.96119 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:01.9615 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:01.972784 INFO::Done
2025-01-26 20:24:01.97307 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:01.973856 INFO::ASW Batch was -0.0300258619545238 prior to batch effect correction and is now -0.110296390542387 .
2025-01-26 20:24:01.97412 INFO::Total function execution time is  0.0177969932556152  s and adjustment time is  0.0122690200805664 s ( 68.94 )
2025-01-26 20:24:01.975211 INFO::Formatting Data.
2025-01-26 20:24:01.975427 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:01.978671 INFO::Formatting Data.
2025-01-26 20:24:01.978977 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:01.979266 INFO::Removing potential empty rows and columns
2025-01-26 20:24:01.979728 INFO::Found  0  missing values.
2025-01-26 20:24:02.004807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:02.005061 INFO::Done
2025-01-26 20:24:02.00526 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:02.00608 INFO::Starting hierarchical adjustment
2025-01-26 20:24:02.006342 INFO::Found  2  batches.
2025-01-26 20:24:02.006519 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:02.006736 INFO::Using default BPPARAM
2025-01-26 20:24:02.006914 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:02.007228 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:02.012275 INFO::Done
2025-01-26 20:24:02.012498 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:02.013126 INFO::ASW Batch was 0.0526355646409493 prior to batch effect correction and is now -0.103543759195089 .
2025-01-26 20:24:02.013384 INFO::Total function execution time is  0.0347640514373779  s and adjustment time is  0.00598406791687012 s ( 17.21 )
2025-01-26 20:24:02.013709 INFO::Formatting Data.
2025-01-26 20:24:02.013889 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:02.014139 INFO::Removing potential empty rows and columns
2025-01-26 20:24:02.014454 INFO::Found  0  missing values.
2025-01-26 20:24:02.015304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:02.015479 INFO::Done
2025-01-26 20:24:02.015649 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:02.016281 INFO::Starting hierarchical adjustment
2025-01-26 20:24:02.016494 INFO::Found  2  batches.
2025-01-26 20:24:02.016681 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:02.016893 INFO::Using default BPPARAM
2025-01-26 20:24:02.017058 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:02.017355 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:02.022222 INFO::Done
2025-01-26 20:24:02.022425 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:02.023079 INFO::ASW Batch was 0.0526355646409493 prior to batch effect correction and is now -0.103543759195089 .
2025-01-26 20:24:02.023362 INFO::Total function execution time is  0.0096430778503418  s and adjustment time is  0.00577211380004883 s ( 59.86 )
2025-01-26 20:24:03.116404 INFO::Formatting Data.
2025-01-26 20:24:03.116659 INFO::Recognized SummarizedExperiment
2025-01-26 20:24:03.116819 INFO::Typecasting input to dataframe.
2025-01-26 20:24:03.126422 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.126783 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.127821 INFO::Found  0  missing values.
2025-01-26 20:24:03.129839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.130013 INFO::Done
2025-01-26 20:24:03.130163 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.131362 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.13157 INFO::Found  2  batches.
2025-01-26 20:24:03.131716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.132018 INFO::Using default BPPARAM
2025-01-26 20:24:03.132163 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.132437 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.149199 INFO::Done
2025-01-26 20:24:03.149433 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.150614 INFO::ASW Batch was 0.0106776178665858 prior to batch effect correction and is now -0.089947407348025 .
2025-01-26 20:24:03.150866 INFO::Total function execution time is  0.0345580577850342  s and adjustment time is  0.017657995223999 s ( 51.1 )
2025-01-26 20:24:03.156698 INFO::Formatting Data.
2025-01-26 20:24:03.156903 INFO::Recognized SummarizedExperiment
2025-01-26 20:24:03.157056 INFO::Typecasting input to dataframe.
2025-01-26 20:24:03.159917 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.160265 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.161354 INFO::Found  0  missing values.
2025-01-26 20:24:03.163388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.163551 INFO::Done
2025-01-26 20:24:03.163702 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.164837 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.165045 INFO::Found  2  batches.
2025-01-26 20:24:03.165193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.165373 INFO::Using default BPPARAM
2025-01-26 20:24:03.165769 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.166134 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.17393 INFO::Done
2025-01-26 20:24:03.174139 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.175266 INFO::ASW Batch was -0.00777109767755977 prior to batch effect correction and is now -0.00777109767755977 .
2025-01-26 20:24:03.175521 INFO::Total function execution time is  0.0188131332397461  s and adjustment time is  0.00892210006713867 s ( 47.42 )
2025-01-26 20:24:03.181534 INFO::Formatting Data.
2025-01-26 20:24:03.181738 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.18199 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.18228 INFO::Found  0  missing values.
2025-01-26 20:24:03.183082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.183232 INFO::Done
2025-01-26 20:24:03.183378 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.183923 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.184109 INFO::Found  3  batches.
2025-01-26 20:24:03.184249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.184415 INFO::Using default BPPARAM
2025-01-26 20:24:03.184551 INFO::Processing subtree level 1
2025-01-26 20:24:03.239034 INFO::Adjusting the last 1 batches sequentially
2025-01-26 20:24:03.240412 INFO::Done
2025-01-26 20:24:03.240778 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.242562 INFO::ASW Batch was -0.0922096766398983 prior to batch effect correction and is now -0.160769246753351 .
2025-01-26 20:24:03.243198 INFO::Total function execution time is  0.0616099834442139  s and adjustment time is  0.0563340187072754 s ( 91.44 )
2025-01-26 20:24:03.250292 INFO::Skipping initial DF formatting
2025-01-26 20:24:03.250611 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.252314 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.25265 INFO::Found  5  batches.
2025-01-26 20:24:03.252848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.253119 INFO::Using default BPPARAM
2025-01-26 20:24:03.253302 INFO::Processing subtree level 1
2025-01-26 20:24:03.297276 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.298817 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.307624 INFO::Done
2025-01-26 20:24:03.308149 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.311101 INFO::ASW Batch was 0.537441595403499 prior to batch effect correction and is now 0.537441595403499 .
2025-01-26 20:24:03.311421 INFO::ASW Label was 0.332761383779754 prior to batch effect correction and is now 0.332761383779754 .
2025-01-26 20:24:03.312013 INFO::Total function execution time is  0.0617268085479736  s and adjustment time is  0.0550210475921631 s ( 89.14 )
2025-01-26 20:24:03.320413 INFO::Formatting Data.
2025-01-26 20:24:03.320653 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.320993 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.321393 INFO::Found  0  missing values.
2025-01-26 20:24:03.32258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.322756 INFO::Done
2025-01-26 20:24:03.32291 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.323851 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.3241 INFO::Found  5  batches.
2025-01-26 20:24:03.324277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.324525 INFO::Using default BPPARAM
2025-01-26 20:24:03.324712 INFO::Processing subtree level 1
2025-01-26 20:24:03.368711 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.369806 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.378249 INFO::Done
2025-01-26 20:24:03.378501 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.379751 INFO::ASW Batch was 0.550300297478416 prior to batch effect correction and is now -0.103657949276645 .
2025-01-26 20:24:03.379981 INFO::ASW Label was 0.187425730913125 prior to batch effect correction and is now 0.851506760643624 .
2025-01-26 20:24:03.380295 INFO::Total function execution time is  0.0598790645599365  s and adjustment time is  0.0541939735412598 s ( 90.51 )
2025-01-26 20:24:03.380597 INFO::Formatting Data.
2025-01-26 20:24:03.380769 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.381029 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.381378 INFO::Found  0  missing values.
2025-01-26 20:24:03.382669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.382896 INFO::Done
2025-01-26 20:24:03.383078 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.384083 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.384343 INFO::Found  5  batches.
2025-01-26 20:24:03.384518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.384758 INFO::Using default BPPARAM
2025-01-26 20:24:03.384948 INFO::Processing subtree level 1
2025-01-26 20:24:03.43157 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.433188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.441893 INFO::Done
2025-01-26 20:24:03.442179 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.443612 INFO::ASW Batch was 0.550300297478416 prior to batch effect correction and is now -0.103657949276645 .
2025-01-26 20:24:03.443846 INFO::ASW Label was 0.187425730913125 prior to batch effect correction and is now 0.851506760643624 .
2025-01-26 20:24:03.4442 INFO::Total function execution time is  0.0635349750518799  s and adjustment time is  0.0576059818267822 s ( 90.67 )
2025-01-26 20:24:03.450395 INFO::Formatting Data.
2025-01-26 20:24:03.45063 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.450936 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.451295 INFO::Found  0  missing values.
2025-01-26 20:24:03.452485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.452679 INFO::Done
2025-01-26 20:24:03.452837 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.45375 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.453998 INFO::Found  5  batches.
2025-01-26 20:24:03.45416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.454401 INFO::Using default BPPARAM
2025-01-26 20:24:03.454579 INFO::Processing subtree level 1
2025-01-26 20:24:03.505678 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.506773 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.514835 INFO::Done
2025-01-26 20:24:03.515198 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.5167 INFO::ASW Batch was 0.391253127087973 prior to batch effect correction and is now -0.0600728778479194 .
2025-01-26 20:24:03.516966 INFO::ASW Label was 0.317911435394026 prior to batch effect correction and is now 0.85672936618935 .
2025-01-26 20:24:03.517364 INFO::Total function execution time is  0.0669481754302979  s and adjustment time is  0.060870885848999 s ( 90.92 )
2025-01-26 20:24:03.517727 INFO::Formatting Data.
2025-01-26 20:24:03.517976 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.518321 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.518755 INFO::Found  0  missing values.
2025-01-26 20:24:03.519987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.520157 INFO::Done
2025-01-26 20:24:03.520325 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.521177 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.521437 INFO::Found  5  batches.
2025-01-26 20:24:03.5216 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.521836 INFO::Using default BPPARAM
2025-01-26 20:24:03.521999 INFO::Processing subtree level 1
2025-01-26 20:24:03.568677 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.570065 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.578884 INFO::Done
2025-01-26 20:24:03.579167 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.580633 INFO::ASW Batch was 0.391253127087973 prior to batch effect correction and is now -0.0600728778479194 .
2025-01-26 20:24:03.580858 INFO::ASW Label was 0.317911435394026 prior to batch effect correction and is now 0.85672936618935 .
2025-01-26 20:24:03.581195 INFO::Total function execution time is  0.0634369850158691  s and adjustment time is  0.0575070381164551 s ( 90.65 )
2025-01-26 20:24:03.587971 INFO::Formatting Data.
2025-01-26 20:24:03.588236 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.588571 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.588995 INFO::Found  0  missing values.
2025-01-26 20:24:03.589872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.590057 INFO::Done
2025-01-26 20:24:03.590235 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.591177 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.591421 INFO::Found  2  batches.
2025-01-26 20:24:03.591593 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.59189 INFO::Using default BPPARAM
2025-01-26 20:24:03.592082 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.592354 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.597282 INFO::Done
2025-01-26 20:24:03.597513 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.644114 INFO::ASW Batch was 0.314061718837754 prior to batch effect correction and is now 0.0100157865261047 .
2025-01-26 20:24:03.644392 INFO::ASW Label was 0.690334212948497 prior to batch effect correction and is now 0.931850856800258 .
2025-01-26 20:24:03.644694 INFO::Total function execution time is  0.0567572116851807  s and adjustment time is  0.00590395927429199 s ( 10.4 )
2025-01-26 20:24:03.644952 INFO::Formatting Data.
2025-01-26 20:24:03.645174 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.645501 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.64588 INFO::Found  0  missing values.
2025-01-26 20:24:03.646955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.647167 INFO::Done
2025-01-26 20:24:03.647381 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.648605 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.64892 INFO::Found  2  batches.
2025-01-26 20:24:03.649154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.649465 INFO::Using default BPPARAM
2025-01-26 20:24:03.649794 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.650338 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.658512 INFO::Done
2025-01-26 20:24:03.658786 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.659961 INFO::ASW Batch was 0.314061718837754 prior to batch effect correction and is now 0.0100157865261047 .
2025-01-26 20:24:03.660142 INFO::ASW Label was 0.690334212948497 prior to batch effect correction and is now 0.931850856800258 .
2025-01-26 20:24:03.660434 INFO::Total function execution time is  0.0154740810394287  s and adjustment time is  0.00964689254760742 s ( 62.34 )
2025-01-26 20:24:03.664927 INFO::Formatting Data.
2025-01-26 20:24:03.665152 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.665483 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.665758 INFO::Found  0  missing values.
2025-01-26 20:24:03.666459 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.666648 INFO::Done
2025-01-26 20:24:03.666834 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.667475 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.667687 INFO::Found  2  batches.
2025-01-26 20:24:03.667877 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.668082 INFO::Using default BPPARAM
2025-01-26 20:24:03.668242 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.66849 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.68196 INFO::Done
2025-01-26 20:24:03.68226 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.683038 INFO::ASW Batch was -0.0779763899931202 prior to batch effect correction and is now -0.15604597626078 .
2025-01-26 20:24:03.68334 INFO::Total function execution time is  0.0184540748596191  s and adjustment time is  0.0142850875854492 s ( 77.41 )
2025-01-26 20:24:03.688397 INFO::Formatting Data.
2025-01-26 20:24:03.688646 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.688962 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.68933 INFO::Found  0  missing values.
2025-01-26 20:24:03.689816 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.
2025-01-26 20:24:03.691685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.692012 INFO::Done
2025-01-26 20:24:03.692219 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.693279 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.693522 INFO::Found  2  batches.
2025-01-26 20:24:03.693702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.6939 INFO::Using default BPPARAM
2025-01-26 20:24:03.694066 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.69442 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.701142 INFO::Done
2025-01-26 20:24:03.701397 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.702666 INFO::ASW Batch was 0.31883857050608 prior to batch effect correction and is now 0.012095329243046 .
2025-01-26 20:24:03.702921 INFO::ASW Label was 0.723029288512108 prior to batch effect correction and is now 0.905159141789897 .
2025-01-26 20:24:03.703232 INFO::Total function execution time is  0.0148711204528809  s and adjustment time is  0.00764298439025879 s ( 51.39 )
2025-01-26 20:24:03.703514 INFO::Formatting Data.
2025-01-26 20:24:03.703732 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.704032 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.704355 INFO::Found  0  missing values.
2025-01-26 20:24:03.704652 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.
2025-01-26 20:24:03.706191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.706383 INFO::Done
2025-01-26 20:24:03.706562 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.707505 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.70778 INFO::Found  2  batches.
2025-01-26 20:24:03.707955 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.708171 INFO::Using default BPPARAM
2025-01-26 20:24:03.708352 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:03.708731 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:03.715636 INFO::Done
2025-01-26 20:24:03.715919 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.717286 INFO::ASW Batch was 0.31883857050608 prior to batch effect correction and is now 0.012095329243046 .
2025-01-26 20:24:03.717701 INFO::ASW Label was 0.723029288512108 prior to batch effect correction and is now 0.905159141789897 .
2025-01-26 20:24:03.718121 INFO::Total function execution time is  0.0145699977874756  s and adjustment time is  0.00789093971252441 s ( 54.16 )
2025-01-26 20:24:03.799518 INFO::Formatting Data.
2025-01-26 20:24:03.799828 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.800162 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.80056 INFO::Found  0  missing values.
2025-01-26 20:24:03.801677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.801867 INFO::Done
2025-01-26 20:24:03.80204 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.802734 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.802968 INFO::Found  3  batches.
2025-01-26 20:24:03.803118 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.803309 INFO::Using default BPPARAM
2025-01-26 20:24:03.803467 INFO::Processing subtree level 1
2025-01-26 20:24:03.855162 INFO::Adjusting the last 1 batches sequentially
2025-01-26 20:24:03.856845 INFO::Done
2025-01-26 20:24:03.857156 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.858826 INFO::ASW Batch was -0.085865615120498 prior to batch effect correction and is now -0.085865615120498 .
2025-01-26 20:24:03.85928 INFO::Total function execution time is  0.0597889423370361  s and adjustment time is  0.0539121627807617 s ( 90.17 )
2025-01-26 20:24:03.859732 INFO::Formatting Data.
2025-01-26 20:24:03.859951 INFO::Typecasting input to dataframe.
2025-01-26 20:24:03.860247 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.860697 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.861125 INFO::Found  0  missing values.
2025-01-26 20:24:03.862204 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.862422 INFO::Done
2025-01-26 20:24:03.862607 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.863304 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.863631 INFO::Found  3  batches.
2025-01-26 20:24:03.863799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.864059 INFO::Using default BPPARAM
2025-01-26 20:24:03.864256 INFO::Processing subtree level 1
2025-01-26 20:24:03.920119 INFO::Adjusting the last 1 batches sequentially
2025-01-26 20:24:03.921288 INFO::Done
2025-01-26 20:24:03.92154 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.922929 INFO::ASW Batch was -0.085865615120498 prior to batch effect correction and is now -0.085865615120498 .
2025-01-26 20:24:03.923336 INFO::Total function execution time is  0.0635828971862793  s and adjustment time is  0.0576989650726318 s ( 90.75 )
2025-01-26 20:24:03.929277 INFO::Formatting Data.
2025-01-26 20:24:03.929554 INFO::Typecasting input to dataframe.
2025-01-26 20:24:03.929846 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:03.930166 INFO::Removing potential empty rows and columns
2025-01-26 20:24:03.930574 INFO::Found  0  missing values.
2025-01-26 20:24:03.931578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:03.931802 INFO::Done
2025-01-26 20:24:03.932005 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:03.932958 INFO::Starting hierarchical adjustment
2025-01-26 20:24:03.933197 INFO::Found  3  batches.
2025-01-26 20:24:03.933372 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:03.933617 INFO::Using default BPPARAM
2025-01-26 20:24:03.933804 INFO::Processing subtree level 1
2025-01-26 20:24:03.987308 INFO::Adjusting the last 1 batches sequentially
2025-01-26 20:24:03.989044 INFO::Done
2025-01-26 20:24:03.989446 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:03.991232 INFO::ASW Batch was -0.0609265351794059 prior to batch effect correction and is now -0.0609265351794059 .
2025-01-26 20:24:03.991742 INFO::Total function execution time is  0.0624568462371826  s and adjustment time is  0.0558938980102539 s ( 89.49 )
2025-01-26 20:24:04.072481 INFO::Formatting Data.
2025-01-26 20:24:04.072776 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:04.073223 INFO::Removing potential empty rows and columns
2025-01-26 20:24:04.074439 INFO::Found  1000  missing values.
2025-01-26 20:24:04.081988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:04.082243 INFO::Done
2025-01-26 20:24:04.082446 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:04.084696 INFO::Starting hierarchical adjustment
2025-01-26 20:24:04.084997 INFO::Found  10  batches.
2025-01-26 20:24:04.085204 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:04.085502 INFO::Using default BPPARAM
2025-01-26 20:24:04.0857 INFO::Processing subtree level 1
2025-01-26 20:24:04.172707 INFO::Processing subtree level 2
2025-01-26 20:24:04.242581 INFO::Adjusting the last 1 batches sequentially
2025-01-26 20:24:04.24405 INFO::Done
2025-01-26 20:24:04.24429 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:04.247513 INFO::ASW Batch was 0.534431598332299 prior to batch effect correction and is now 0.534431598332299 .
2025-01-26 20:24:04.24781 INFO::ASW Label was 0.297786711302711 prior to batch effect correction and is now 0.297786711302711 .
2025-01-26 20:24:04.24833 INFO::Total function execution time is  0.175837993621826  s and adjustment time is  0.159111976623535 s ( 90.49 )
2025-01-26 20:24:04.248717 INFO::Formatting Data.
2025-01-26 20:24:04.249097 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:04.249715 INFO::Removing potential empty rows and columns
2025-01-26 20:24:04.250808 INFO::Found  1000  missing values.
2025-01-26 20:24:04.257282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:04.257508 INFO::Done
2025-01-26 20:24:04.257697 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:04.259834 INFO::Starting hierarchical adjustment
2025-01-26 20:24:04.260121 INFO::Found  10  batches.
2025-01-26 20:24:04.728482 INFO::Set up parallel execution backend with 2 workers
2025-01-26 20:24:04.728764 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-26 20:24:05.231284 INFO::Adjusting the last 2 batches sequentially
2025-01-26 20:24:05.231867 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-26 20:24:05.237461 INFO::Done
2025-01-26 20:24:05.237677 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:05.239491 INFO::ASW Batch was 0.534431598332299 prior to batch effect correction and is now 0.534431598332299 .
2025-01-26 20:24:05.239682 INFO::ASW Label was 0.297786711302711 prior to batch effect correction and is now 0.297786711302711 .
2025-01-26 20:24:05.239916 INFO::Total function execution time is  0.991228818893433  s and adjustment time is  0.977390050888062 s ( 98.6 )
2025-01-26 20:24:05.305368 INFO::Formatting Data.
2025-01-26 20:24:05.305666 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.306006 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.306441 INFO::Found  0  missing values.
2025-01-26 20:24:05.30776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.30796 INFO::Done
2025-01-26 20:24:05.308147 INFO::Acquiring quality metrics before batch effect correction.
2025-01-26 20:24:05.309142 INFO::Starting hierarchical adjustment
2025-01-26 20:24:05.309378 INFO::Found  3  batches.
2025-01-26 20:24:05.309556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-26 20:24:05.309834 INFO::Using default BPPARAM
2025-01-26 20:24:05.310009 INFO::Processing subtree level 1
2025-01-26 20:24:05.368573 INFO::Adjusting the last 1 batches sequentially
2025-01-26 20:24:05.370795 INFO::Done
2025-01-26 20:24:05.371061 INFO::Acquiring quality metrics after batch effect correction.
2025-01-26 20:24:05.373648 INFO::ASW Batch was 0.133882487935274 prior to batch effect correction and is now -0.145791622250014 .
2025-01-26 20:24:05.373931 INFO::ASW Label was -0.214270711021226 prior to batch effect correction and is now -0.139971185055296 .
2025-01-26 20:24:05.374426 INFO::Total function execution time is  0.0690431594848633  s and adjustment time is  0.0614709854125977 s ( 89.03 )
2025-01-26 20:24:05.423394 INFO::Formatting Data.
2025-01-26 20:24:05.423735 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.42409 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.424521 INFO::Found  2  missing values.
2025-01-26 20:24:05.425445 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.425613 INFO::Done
2025-01-26 20:24:05.434422 INFO::Found NA in Reference column
2025-01-26 20:24:05.437505 INFO::Require at least two references per batch.
2025-01-26 20:24:05.444952 INFO::Formatting Data.
2025-01-26 20:24:05.445165 INFO::Recognized SummarizedExperiment
2025-01-26 20:24:05.44533 INFO::Typecasting input to dataframe.
2025-01-26 20:24:05.44904 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.449405 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.450701 INFO::Found  0  missing values.
2025-01-26 20:24:05.453009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.453179 INFO::Done
2025-01-26 20:24:05.458117 INFO::Formatting Data.
2025-01-26 20:24:05.458342 INFO::Recognized SummarizedExperiment
2025-01-26 20:24:05.458513 INFO::Typecasting input to dataframe.
2025-01-26 20:24:05.463955 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.46435 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.465597 INFO::Found  0  missing values.
2025-01-26 20:24:05.469293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.469472 INFO::Done
2025-01-26 20:24:05.474392 INFO::Formatting Data.
2025-01-26 20:24:05.474596 INFO::Recognized SummarizedExperiment
2025-01-26 20:24:05.474759 INFO::Typecasting input to dataframe.
2025-01-26 20:24:05.479723 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.480015 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.480353 INFO::Found  0  missing values.
2025-01-26 20:24:05.480621 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.
2025-01-26 20:24:05.481921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.482098 INFO::Done
2025-01-26 20:24:05.485646 INFO::Formatting Data.
2025-01-26 20:24:05.485868 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.486134 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.486425 INFO::Found  0  missing values.
2025-01-26 20:24:05.487258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.487423 INFO::Done
2025-01-26 20:24:05.491614 INFO::Formatting Data.
2025-01-26 20:24:05.491829 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.492091 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.492403 INFO::Found  0  missing values.
2025-01-26 20:24:05.493241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.49341 INFO::Done
2025-01-26 20:24:05.504359 INFO::Formatting Data.
2025-01-26 20:24:05.504681 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.505011 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.505408 INFO::Found  1  missing values.
2025-01-26 20:24:05.506223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.506399 INFO::Done
2025-01-26 20:24:05.513723 INFO::Formatting Data.
2025-01-26 20:24:05.514031 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.514342 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.514728 INFO::Found  2  missing values.
2025-01-26 20:24:05.515029 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.
2025-01-26 20:24:05.515857 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.516049 INFO::Done
2025-01-26 20:24:05.520113 INFO::Formatting Data.
2025-01-26 20:24:05.52036 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.520692 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.520969 INFO::Found  2  missing values.
2025-01-26 20:24:05.52146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.521644 INFO::Done
2025-01-26 20:24:05.525315 INFO::Formatting Data.
2025-01-26 20:24:05.525571 INFO::Typecasting input to dataframe.
2025-01-26 20:24:05.525819 INFO::Replacing NaNs with NAs.
2025-01-26 20:24:05.526069 INFO::Removing potential empty rows and columns
2025-01-26 20:24:05.526364 INFO::Found  0  missing values.
2025-01-26 20:24:05.527339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-26 20:24:05.52751 INFO::Done
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 134 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_generate_Dataset.R:154:5'): generate_truncated_dataset works ───
Error in `generate_truncated_dataset(100, 3, 10, 0.1, 0.1, 2)`: could not find function "generate_truncated_dataset"

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 134 ]
Error: Test failures
Execution halted

Example timings

BERT.Rcheck/BERT-Ex.timings

name	user	system	elapsed
BERT	9.419	0.388	6.713
compute_asw	0.009	0.001	0.011
count_existing	0.005	0.001	0.005
generate_data_covariables	0.005	0.000	0.005
generate_dataset	0.005	0.001	0.005