Multiple platform build/check report for BioC 3.21 - CHECK results for BERT on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4502
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4467
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4422
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4406
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 kunpeng2

To the developers/maintainers of the BERT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: BERT

Version: 1.3.6

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.3.6.tar.gz

StartedAt: 2025-01-21 04:02:25 -0000 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 04:03:46 -0000 (Tue, 21 Jan 2025)

EllapsedTime: 81.1 seconds

RetCode: 1

Status: ERROR

CheckDir: BERT.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in parse(con): 8:3: unexpected symbol
  7:   url       = "https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202400100"
  8:   author
       ^
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 31.152  1.179  22.266
* 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:
  2025-01-21 04:03:41.889518 INFO::Typecasting input to dataframe.
  2025-01-21 04:03:41.890592 INFO::Replacing NaNs with NAs.
  2025-01-21 04:03:41.891798 INFO::Removing potential empty rows and columns
  2025-01-21 04:03:41.893282 INFO::Found  0  missing values.
  2025-01-21 04:03:41.897765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
  2025-01-21 04:03:41.89872 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, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log’
for details.

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘BERT’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-01-21 04:03:29.739134 INFO::Formatting Data.
2025-01-21 04:03:29.74091 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:29.757635 INFO::Removing potential empty rows and columns
2025-01-21 04:03:30.412613 INFO::Found  0  missing values.
2025-01-21 04:03:30.417741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:30.418685 INFO::Done
2025-01-21 04:03:30.419536 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:30.435899 INFO::Starting hierarchical adjustment
2025-01-21 04:03:30.437167 INFO::Found  3  batches.
2025-01-21 04:03:30.437992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:30.439626 INFO::Using default BPPARAM
2025-01-21 04:03:30.440461 INFO::Processing subtree level 1
2025-01-21 04:03:30.577482 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:03:30.580216 INFO::Done
2025-01-21 04:03:30.581312 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:30.58589 INFO::ASW Batch was -0.0787075354764118 prior to batch effect correction and is now -0.0787075354764118 .
2025-01-21 04:03:30.587821 INFO::Total function execution time is  0.849274396896362  s and adjustment time is  0.143275022506714 s ( 16.87 )
2025-01-21 04:03:30.610769 INFO::Formatting Data.
2025-01-21 04:03:30.611989 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:30.613572 INFO::Removing potential empty rows and columns
2025-01-21 04:03:30.615523 INFO::Found  0  missing values.
2025-01-21 04:03:30.617106 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.
2025-01-21 04:03:30.633321 INFO::Formatting Data.
2025-01-21 04:03:30.6344 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:30.635742 INFO::Removing potential empty rows and columns
2025-01-21 04:03:30.637377 INFO::Found  0  missing values.
2025-01-21 04:03:30.638812 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.
2025-01-21 04:03:30.662888 INFO::Formatting Data.
2025-01-21 04:03:30.664053 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:30.665594 INFO::Removing potential empty rows and columns
2025-01-21 04:03:30.667287 INFO::Found  0  missing values.
2025-01-21 04:03:30.668769 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.
2025-01-21 04:03:30.675878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:30.676899 INFO::Done
2025-01-21 04:03:30.677811 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:30.680891 INFO::Starting hierarchical adjustment
2025-01-21 04:03:30.682086 INFO::Found  2  batches.
2025-01-21 04:03:30.683008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:30.684007 INFO::Using default BPPARAM
2025-01-21 04:03:30.684912 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:30.6864 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:30.718089 INFO::Done
2025-01-21 04:03:30.71902 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:30.721823 INFO::ASW Batch was -0.0492257545003373 prior to batch effect correction and is now -0.109394671517316 .
2025-01-21 04:03:30.722982 INFO::Total function execution time is  0.0601627826690674  s and adjustment time is  0.036245584487915 s ( 60.25 )
2025-01-21 04:03:30.726613 INFO::Formatting Data.
2025-01-21 04:03:30.727602 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:30.739863 INFO::Formatting Data.
2025-01-21 04:03:30.740897 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:30.742114 INFO::Removing potential empty rows and columns
2025-01-21 04:03:30.743595 INFO::Found  0  missing values.
2025-01-21 04:03:30.747921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:30.749816 INFO::Done
2025-01-21 04:03:30.750785 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:30.75393 INFO::Starting hierarchical adjustment
2025-01-21 04:03:30.75509 INFO::Found  2  batches.
2025-01-21 04:03:30.7559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:30.800089 INFO::Using default BPPARAM
2025-01-21 04:03:30.800908 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:30.802214 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:30.823351 INFO::Done
2025-01-21 04:03:30.824236 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:30.827088 INFO::ASW Batch was 0.0392642054962666 prior to batch effect correction and is now -0.112179303611796 .
2025-01-21 04:03:30.828215 INFO::Total function execution time is  0.0884041786193848  s and adjustment time is  0.0684924125671387 s ( 77.48 )
2025-01-21 04:03:30.829764 INFO::Formatting Data.
2025-01-21 04:03:30.830575 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:30.831766 INFO::Removing potential empty rows and columns
2025-01-21 04:03:30.833253 INFO::Found  0  missing values.
2025-01-21 04:03:30.837525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:30.838365 INFO::Done
2025-01-21 04:03:30.839153 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:30.841956 INFO::Starting hierarchical adjustment
2025-01-21 04:03:30.843019 INFO::Found  2  batches.
2025-01-21 04:03:30.843787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:30.844682 INFO::Using default BPPARAM
2025-01-21 04:03:30.845452 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:30.846738 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:30.867925 INFO::Done
2025-01-21 04:03:30.868861 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:30.871584 INFO::ASW Batch was 0.0392642054962666 prior to batch effect correction and is now -0.112179303611796 .
2025-01-21 04:03:30.872749 INFO::Total function execution time is  0.0429480075836182  s and adjustment time is  0.0251109600067139 s ( 58.47 )
2025-01-21 04:03:34.777687 INFO::Formatting Data.
2025-01-21 04:03:34.778679 INFO::Recognized SummarizedExperiment
2025-01-21 04:03:34.77954 INFO::Typecasting input to dataframe.
2025-01-21 04:03:34.824967 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:34.826548 INFO::Removing potential empty rows and columns
2025-01-21 04:03:34.831578 INFO::Found  0  missing values.
2025-01-21 04:03:34.8414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:34.842269 INFO::Done
2025-01-21 04:03:34.842994 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:34.847724 INFO::Starting hierarchical adjustment
2025-01-21 04:03:34.848787 INFO::Found  2  batches.
2025-01-21 04:03:34.849486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:34.850789 INFO::Using default BPPARAM
2025-01-21 04:03:34.851542 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:34.852805 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:34.932362 INFO::Done
2025-01-21 04:03:34.933347 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:34.938478 INFO::ASW Batch was 0.0215134122803609 prior to batch effect correction and is now -0.0889481328185482 .
2025-01-21 04:03:34.939841 INFO::Total function execution time is  0.162577867507935  s and adjustment time is  0.0837640762329102 s ( 51.52 )
2025-01-21 04:03:34.96655 INFO::Formatting Data.
2025-01-21 04:03:34.96762 INFO::Recognized SummarizedExperiment
2025-01-21 04:03:34.968529 INFO::Typecasting input to dataframe.
2025-01-21 04:03:34.982342 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:34.983898 INFO::Removing potential empty rows and columns
2025-01-21 04:03:34.988957 INFO::Found  0  missing values.
2025-01-21 04:03:34.998712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:34.999575 INFO::Done
2025-01-21 04:03:35.000299 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:35.005008 INFO::Starting hierarchical adjustment
2025-01-21 04:03:35.006022 INFO::Found  2  batches.
2025-01-21 04:03:35.006741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:35.007573 INFO::Using default BPPARAM
2025-01-21 04:03:35.008288 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:35.00962 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:35.043421 INFO::Done
2025-01-21 04:03:35.044272 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:35.048943 INFO::ASW Batch was 0.015251894049772 prior to batch effect correction and is now 0.015251894049772 .
2025-01-21 04:03:35.050098 INFO::Total function execution time is  0.0835254192352295  s and adjustment time is  0.0375702381134033 s ( 44.98 )
2025-01-21 04:03:35.074437 INFO::Formatting Data.
2025-01-21 04:03:35.075467 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:35.076721 INFO::Removing potential empty rows and columns
2025-01-21 04:03:35.078201 INFO::Found  0  missing values.
2025-01-21 04:03:35.082681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:35.083601 INFO::Done
2025-01-21 04:03:35.084405 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:35.087261 INFO::Starting hierarchical adjustment
2025-01-21 04:03:35.088312 INFO::Found  3  batches.
2025-01-21 04:03:35.089126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:35.089977 INFO::Using default BPPARAM
2025-01-21 04:03:35.09074 INFO::Processing subtree level 1
2025-01-21 04:03:35.255276 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:03:35.257611 INFO::Done
2025-01-21 04:03:35.258441 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:35.261709 INFO::ASW Batch was -0.103085093070996 prior to batch effect correction and is now -0.139520151268125 .
2025-01-21 04:03:35.263077 INFO::Total function execution time is  0.188625335693359  s and adjustment time is  0.169515371322632 s ( 89.87 )
2025-01-21 04:03:35.28292 INFO::Skipping initial DF formatting
2025-01-21 04:03:35.283878 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:35.289341 INFO::Starting hierarchical adjustment
2025-01-21 04:03:35.290467 INFO::Found  5  batches.
2025-01-21 04:03:35.291258 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:35.292125 INFO::Using default BPPARAM
2025-01-21 04:03:35.292905 INFO::Processing subtree level 1
2025-01-21 04:03:35.438457 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:35.440635 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:35.467721 INFO::Done
2025-01-21 04:03:35.468669 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:35.474383 INFO::ASW Batch was 0.535824086851253 prior to batch effect correction and is now 0.535824086851253 .
2025-01-21 04:03:35.475311 INFO::ASW Label was 0.350097633156592 prior to batch effect correction and is now 0.350097633156592 .
2025-01-21 04:03:35.47648 INFO::Total function execution time is  0.193604946136475  s and adjustment time is  0.17745304107666 s ( 91.66 )
2025-01-21 04:03:35.501108 INFO::Formatting Data.
2025-01-21 04:03:35.502166 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:35.503501 INFO::Removing potential empty rows and columns
2025-01-21 04:03:35.504952 INFO::Found  0  missing values.
2025-01-21 04:03:35.510775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:35.511699 INFO::Done
2025-01-21 04:03:35.512464 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:35.516638 INFO::Starting hierarchical adjustment
2025-01-21 04:03:35.517774 INFO::Found  5  batches.
2025-01-21 04:03:35.51853 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:35.519416 INFO::Using default BPPARAM
2025-01-21 04:03:35.520131 INFO::Processing subtree level 1
2025-01-21 04:03:35.648313 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:35.650443 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:35.672302 INFO::Done
2025-01-21 04:03:35.673263 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:35.687358 INFO::ASW Batch was 0.388270970267383 prior to batch effect correction and is now 0.0457271231907048 .
2025-01-21 04:03:35.688607 INFO::ASW Label was 0.452581148864195 prior to batch effect correction and is now 0.660995046460309 .
2025-01-21 04:03:35.689916 INFO::Total function execution time is  0.18889045715332  s and adjustment time is  0.154729604721069 s ( 81.91 )
2025-01-21 04:03:35.69112 INFO::Formatting Data.
2025-01-21 04:03:35.691921 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:35.693225 INFO::Removing potential empty rows and columns
2025-01-21 04:03:35.694692 INFO::Found  0  missing values.
2025-01-21 04:03:35.700455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:35.701336 INFO::Done
2025-01-21 04:03:35.70206 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:35.706071 INFO::Starting hierarchical adjustment
2025-01-21 04:03:35.707137 INFO::Found  5  batches.
2025-01-21 04:03:35.707866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:35.708816 INFO::Using default BPPARAM
2025-01-21 04:03:35.709555 INFO::Processing subtree level 1
2025-01-21 04:03:35.838614 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:35.840885 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:35.863626 INFO::Done
2025-01-21 04:03:35.86459 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:35.869079 INFO::ASW Batch was 0.388270970267383 prior to batch effect correction and is now 0.0457271231907048 .
2025-01-21 04:03:35.870012 INFO::ASW Label was 0.452581148864195 prior to batch effect correction and is now 0.660995046460309 .
2025-01-21 04:03:35.871193 INFO::Total function execution time is  0.180030345916748  s and adjustment time is  0.156705856323242 s ( 87.04 )
2025-01-21 04:03:35.890943 INFO::Formatting Data.
2025-01-21 04:03:35.891991 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:35.893339 INFO::Removing potential empty rows and columns
2025-01-21 04:03:35.894681 INFO::Found  0  missing values.
2025-01-21 04:03:35.900557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:35.901456 INFO::Done
2025-01-21 04:03:35.902198 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:35.906111 INFO::Starting hierarchical adjustment
2025-01-21 04:03:35.907266 INFO::Found  5  batches.
2025-01-21 04:03:35.908021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:35.908923 INFO::Using default BPPARAM
2025-01-21 04:03:35.909662 INFO::Processing subtree level 1
2025-01-21 04:03:36.043223 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:36.045635 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:36.067861 INFO::Done
2025-01-21 04:03:36.068877 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:36.073601 INFO::ASW Batch was 0.587488838964559 prior to batch effect correction and is now -0.0341962991341338 .
2025-01-21 04:03:36.074605 INFO::ASW Label was 0.150392033389201 prior to batch effect correction and is now 0.737511599710934 .
2025-01-21 04:03:36.075836 INFO::Total function execution time is  0.184903860092163  s and adjustment time is  0.160815954208374 s ( 86.97 )
2025-01-21 04:03:36.077104 INFO::Formatting Data.
2025-01-21 04:03:36.078091 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:36.079467 INFO::Removing potential empty rows and columns
2025-01-21 04:03:36.081014 INFO::Found  0  missing values.
2025-01-21 04:03:36.087468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:36.088419 INFO::Done
2025-01-21 04:03:36.089271 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:36.093535 INFO::Starting hierarchical adjustment
2025-01-21 04:03:36.094757 INFO::Found  5  batches.
2025-01-21 04:03:36.095617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:36.096533 INFO::Using default BPPARAM
2025-01-21 04:03:36.097366 INFO::Processing subtree level 1
2025-01-21 04:03:36.230964 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:36.233138 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:36.255146 INFO::Done
2025-01-21 04:03:36.2561 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:36.260682 INFO::ASW Batch was 0.587488838964559 prior to batch effect correction and is now -0.0341962991341338 .
2025-01-21 04:03:36.261612 INFO::ASW Label was 0.150392033389201 prior to batch effect correction and is now 0.737511599710934 .
2025-01-21 04:03:36.262786 INFO::Total function execution time is  0.185682535171509  s and adjustment time is  0.160588026046753 s ( 86.49 )
2025-01-21 04:03:36.28226 INFO::Formatting Data.
2025-01-21 04:03:36.283358 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:36.284689 INFO::Removing potential empty rows and columns
2025-01-21 04:03:36.286151 INFO::Found  0  missing values.
2025-01-21 04:03:36.290195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:36.291132 INFO::Done
2025-01-21 04:03:36.291898 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:36.295945 INFO::Starting hierarchical adjustment
2025-01-21 04:03:36.29711 INFO::Found  2  batches.
2025-01-21 04:03:36.297866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:36.298706 INFO::Using default BPPARAM
2025-01-21 04:03:36.299457 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:36.300752 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:36.320799 INFO::Done
2025-01-21 04:03:36.321684 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:36.325608 INFO::ASW Batch was 0.55965849801911 prior to batch effect correction and is now 0.0348387605680048 .
2025-01-21 04:03:36.326507 INFO::ASW Label was 0.535907775880818 prior to batch effect correction and is now 0.903175466660382 .
2025-01-21 04:03:36.327615 INFO::Total function execution time is  0.0454492568969727  s and adjustment time is  0.0238945484161377 s ( 52.57 )
2025-01-21 04:03:36.328696 INFO::Formatting Data.
2025-01-21 04:03:36.329552 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:36.330745 INFO::Removing potential empty rows and columns
2025-01-21 04:03:36.332112 INFO::Found  0  missing values.
2025-01-21 04:03:36.335972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:36.336838 INFO::Done
2025-01-21 04:03:36.337594 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:36.416536 INFO::Starting hierarchical adjustment
2025-01-21 04:03:36.417695 INFO::Found  2  batches.
2025-01-21 04:03:36.418538 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:36.419462 INFO::Using default BPPARAM
2025-01-21 04:03:36.420241 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:36.421631 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:36.444282 INFO::Done
2025-01-21 04:03:36.445316 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:36.449787 INFO::ASW Batch was 0.55965849801911 prior to batch effect correction and is now 0.0348387605680048 .
2025-01-21 04:03:36.450787 INFO::ASW Label was 0.535907775880818 prior to batch effect correction and is now 0.903175466660382 .
2025-01-21 04:03:36.452091 INFO::Total function execution time is  0.123334884643555  s and adjustment time is  0.0268001556396484 s ( 21.73 )
2025-01-21 04:03:36.469742 INFO::Formatting Data.
2025-01-21 04:03:36.470847 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:36.472185 INFO::Removing potential empty rows and columns
2025-01-21 04:03:36.473589 INFO::Found  0  missing values.
2025-01-21 04:03:36.476805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:36.47772 INFO::Done
2025-01-21 04:03:36.47849 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:36.481165 INFO::Starting hierarchical adjustment
2025-01-21 04:03:36.482307 INFO::Found  2  batches.
2025-01-21 04:03:36.483095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:36.483974 INFO::Using default BPPARAM
2025-01-21 04:03:36.484742 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:36.486078 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:36.542321 INFO::Done
2025-01-21 04:03:36.543415 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:36.546425 INFO::ASW Batch was -0.094940974242749 prior to batch effect correction and is now -0.140085549848794 .
2025-01-21 04:03:36.547713 INFO::Total function execution time is  0.0780210494995117  s and adjustment time is  0.0602142810821533 s ( 77.18 )
2025-01-21 04:03:36.565866 INFO::Formatting Data.
2025-01-21 04:03:36.566981 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:36.568347 INFO::Removing potential empty rows and columns
2025-01-21 04:03:36.569993 INFO::Found  0  missing values.
2025-01-21 04:03:36.571707 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.
2025-01-21 04:03:36.579047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:36.580015 INFO::Done
2025-01-21 04:03:36.580852 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:36.585143 INFO::Starting hierarchical adjustment
2025-01-21 04:03:36.58632 INFO::Found  2  batches.
2025-01-21 04:03:36.587167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:36.588086 INFO::Using default BPPARAM
2025-01-21 04:03:36.588917 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:36.590386 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:36.616489 INFO::Done
2025-01-21 04:03:36.617531 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:36.622135 INFO::ASW Batch was 0.573279220245373 prior to batch effect correction and is now 0.132948851990276 .
2025-01-21 04:03:36.623223 INFO::ASW Label was 0.569945883813594 prior to batch effect correction and is now 0.847728235363226 .
2025-01-21 04:03:36.624677 INFO::Total function execution time is  0.0588500499725342  s and adjustment time is  0.0303802490234375 s ( 51.62 )
2025-01-21 04:03:36.625988 INFO::Formatting Data.
2025-01-21 04:03:36.627087 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:36.628665 INFO::Removing potential empty rows and columns
2025-01-21 04:03:36.630466 INFO::Found  0  missing values.
2025-01-21 04:03:36.632086 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.
2025-01-21 04:03:36.640212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:36.641304 INFO::Done
2025-01-21 04:03:36.642236 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:36.646782 INFO::Starting hierarchical adjustment
2025-01-21 04:03:36.64806 INFO::Found  2  batches.
2025-01-21 04:03:36.649029 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:36.650038 INFO::Using default BPPARAM
2025-01-21 04:03:36.650907 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:36.65246 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:36.677573 INFO::Done
2025-01-21 04:03:36.678477 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:36.682661 INFO::ASW Batch was 0.573279220245373 prior to batch effect correction and is now 0.132948851990276 .
2025-01-21 04:03:36.683592 INFO::ASW Label was 0.569945883813594 prior to batch effect correction and is now 0.847728235363226 .
2025-01-21 04:03:36.684782 INFO::Total function execution time is  0.0588617324829102  s and adjustment time is  0.0297830104827881 s ( 50.6 )
2025-01-21 04:03:36.993533 INFO::Formatting Data.
2025-01-21 04:03:36.994523 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:36.995748 INFO::Removing potential empty rows and columns
2025-01-21 04:03:36.997141 INFO::Found  0  missing values.
2025-01-21 04:03:37.00142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:37.002295 INFO::Done
2025-01-21 04:03:37.003042 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:37.00578 INFO::Starting hierarchical adjustment
2025-01-21 04:03:37.006854 INFO::Found  3  batches.
2025-01-21 04:03:37.007639 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:37.008488 INFO::Using default BPPARAM
2025-01-21 04:03:37.009243 INFO::Processing subtree level 1
2025-01-21 04:03:37.135995 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:03:37.13858 INFO::Done
2025-01-21 04:03:37.139446 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:37.142899 INFO::ASW Batch was 0.0135216202797152 prior to batch effect correction and is now 0.0135216202797152 .
2025-01-21 04:03:37.144314 INFO::Total function execution time is  0.150784015655518  s and adjustment time is  0.13188099861145 s ( 87.46 )
2025-01-21 04:03:37.14585 INFO::Formatting Data.
2025-01-21 04:03:37.146813 INFO::Typecasting input to dataframe.
2025-01-21 04:03:37.147945 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:37.149323 INFO::Removing potential empty rows and columns
2025-01-21 04:03:37.150984 INFO::Found  0  missing values.
2025-01-21 04:03:37.155698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:37.156729 INFO::Done
2025-01-21 04:03:37.157498 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:37.160488 INFO::Starting hierarchical adjustment
2025-01-21 04:03:37.161569 INFO::Found  3  batches.
2025-01-21 04:03:37.162403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:37.16333 INFO::Using default BPPARAM
2025-01-21 04:03:37.164133 INFO::Processing subtree level 1
2025-01-21 04:03:37.286768 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:03:37.289309 INFO::Done
2025-01-21 04:03:37.290205 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:37.293679 INFO::ASW Batch was 0.0135216202797152 prior to batch effect correction and is now 0.0135216202797152 .
2025-01-21 04:03:37.295151 INFO::Total function execution time is  0.149235963821411  s and adjustment time is  0.127954244613647 s ( 85.74 )
2025-01-21 04:03:37.314382 INFO::Formatting Data.
2025-01-21 04:03:37.315494 INFO::Typecasting input to dataframe.
2025-01-21 04:03:37.316761 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:37.318079 INFO::Removing potential empty rows and columns
2025-01-21 04:03:37.31972 INFO::Found  0  missing values.
2025-01-21 04:03:37.324178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:37.325032 INFO::Done
2025-01-21 04:03:37.325824 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:37.328583 INFO::Starting hierarchical adjustment
2025-01-21 04:03:37.329701 INFO::Found  3  batches.
2025-01-21 04:03:37.330452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:37.331316 INFO::Using default BPPARAM
2025-01-21 04:03:37.332127 INFO::Processing subtree level 1
2025-01-21 04:03:37.456469 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:03:37.459073 INFO::Done
2025-01-21 04:03:37.459981 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:37.463528 INFO::ASW Batch was -0.0620637231711457 prior to batch effect correction and is now -0.0620637231711457 .
2025-01-21 04:03:37.464931 INFO::Total function execution time is  0.150624752044678  s and adjustment time is  0.129639625549316 s ( 86.07 )
2025-01-21 04:03:37.663785 INFO::Formatting Data.
2025-01-21 04:03:37.664874 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:37.666506 INFO::Removing potential empty rows and columns
2025-01-21 04:03:37.671164 INFO::Found  1000  missing values.
2025-01-21 04:03:37.702912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:37.703904 INFO::Done
2025-01-21 04:03:37.704692 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:37.712934 INFO::Starting hierarchical adjustment
2025-01-21 04:03:37.714189 INFO::Found  10  batches.
2025-01-21 04:03:37.714975 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:37.715895 INFO::Using default BPPARAM
2025-01-21 04:03:37.716756 INFO::Processing subtree level 1
2025-01-21 04:03:37.912607 INFO::Processing subtree level 2
2025-01-21 04:03:38.129208 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:03:38.132029 INFO::Done
2025-01-21 04:03:38.132918 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:38.14124 INFO::ASW Batch was 0.565937684092646 prior to batch effect correction and is now 0.565937684092646 .
2025-01-21 04:03:38.142286 INFO::ASW Label was 0.26482590647378 prior to batch effect correction and is now 0.26482590647378 .
2025-01-21 04:03:38.143595 INFO::Total function execution time is  0.479882478713989  s and adjustment time is  0.418140649795532 s ( 87.13 )
2025-01-21 04:03:38.14486 INFO::Formatting Data.
2025-01-21 04:03:38.14578 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:38.147655 INFO::Removing potential empty rows and columns
2025-01-21 04:03:38.152328 INFO::Found  1000  missing values.
2025-01-21 04:03:38.183843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:38.184935 INFO::Done
2025-01-21 04:03:38.185811 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:38.194045 INFO::Starting hierarchical adjustment
2025-01-21 04:03:38.195346 INFO::Found  10  batches.
2025-01-21 04:03:39.408628 INFO::Set up parallel execution backend with 2 workers
2025-01-21 04:03:39.410681 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-21 04:03:40.877525 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:03:40.879634 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:03:40.904833 INFO::Done
2025-01-21 04:03:40.905737 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:40.912538 INFO::ASW Batch was 0.565937684092646 prior to batch effect correction and is now 0.565937684092646 .
2025-01-21 04:03:40.913378 INFO::ASW Label was 0.26482590647378 prior to batch effect correction and is now 0.26482590647378 .
2025-01-21 04:03:40.914391 INFO::Total function execution time is  2.76956129074097  s and adjustment time is  2.70973253250122 s ( 97.84 )
2025-01-21 04:03:41.102769 INFO::Formatting Data.
2025-01-21 04:03:41.103896 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.105234 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.106817 INFO::Found  0  missing values.
2025-01-21 04:03:41.112542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.113414 INFO::Done
2025-01-21 04:03:41.114174 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:03:41.118083 INFO::Starting hierarchical adjustment
2025-01-21 04:03:41.119162 INFO::Found  3  batches.
2025-01-21 04:03:41.119936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:03:41.120856 INFO::Using default BPPARAM
2025-01-21 04:03:41.121623 INFO::Processing subtree level 1
2025-01-21 04:03:41.255072 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:03:41.257601 INFO::Done
2025-01-21 04:03:41.258494 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:03:41.263187 INFO::ASW Batch was 0.196181643131085 prior to batch effect correction and is now -0.162144629058529 .
2025-01-21 04:03:41.264176 INFO::ASW Label was -0.147847635188121 prior to batch effect correction and is now -0.0724329880057475 .
2025-01-21 04:03:41.265483 INFO::Total function execution time is  0.16278338432312  s and adjustment time is  0.138648509979248 s ( 85.17 )
2025-01-21 04:03:41.441962 INFO::Formatting Data.
2025-01-21 04:03:41.443022 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.44428 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.445866 INFO::Found  2  missing values.
2025-01-21 04:03:41.450182 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.451015 INFO::Done
2025-01-21 04:03:41.491533 INFO::Found NA in Reference column
2025-01-21 04:03:41.506682 INFO::Require at least two references per batch.
2025-01-21 04:03:41.537911 INFO::Formatting Data.
2025-01-21 04:03:41.53891 INFO::Recognized SummarizedExperiment
2025-01-21 04:03:41.539667 INFO::Typecasting input to dataframe.
2025-01-21 04:03:41.554097 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.555773 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.561608 INFO::Found  0  missing values.
2025-01-21 04:03:41.572893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.573843 INFO::Done
2025-01-21 04:03:41.596032 INFO::Formatting Data.
2025-01-21 04:03:41.597049 INFO::Recognized SummarizedExperiment
2025-01-21 04:03:41.597775 INFO::Typecasting input to dataframe.
2025-01-21 04:03:41.623526 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.62523 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.631091 INFO::Found  0  missing values.
2025-01-21 04:03:41.649776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.650725 INFO::Done
2025-01-21 04:03:41.672632 INFO::Formatting Data.
2025-01-21 04:03:41.673621 INFO::Recognized SummarizedExperiment
2025-01-21 04:03:41.674355 INFO::Typecasting input to dataframe.
2025-01-21 04:03:41.699453 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.700867 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.702418 INFO::Found  0  missing values.
2025-01-21 04:03:41.7037 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.
2025-01-21 04:03:41.710298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.711224 INFO::Done
2025-01-21 04:03:41.725649 INFO::Formatting Data.
2025-01-21 04:03:41.726701 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.727925 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.72938 INFO::Found  0  missing values.
2025-01-21 04:03:41.733638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.734453 INFO::Done
2025-01-21 04:03:41.751106 INFO::Formatting Data.
2025-01-21 04:03:41.752169 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.753377 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.754813 INFO::Found  0  missing values.
2025-01-21 04:03:41.759204 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.760037 INFO::Done
2025-01-21 04:03:41.804869 INFO::Formatting Data.
2025-01-21 04:03:41.805948 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.8074 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.809154 INFO::Found  1  missing values.
2025-01-21 04:03:41.81297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.813825 INFO::Done
2025-01-21 04:03:41.842307 INFO::Formatting Data.
2025-01-21 04:03:41.843386 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.844678 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.84604 INFO::Found  2  missing values.
2025-01-21 04:03:41.847318 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.
2025-01-21 04:03:41.850614 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.851466 INFO::Done
2025-01-21 04:03:41.866619 INFO::Formatting Data.
2025-01-21 04:03:41.867684 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.868899 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.870229 INFO::Found  2  missing values.
2025-01-21 04:03:41.872546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.873296 INFO::Done
2025-01-21 04:03:41.888452 INFO::Formatting Data.
2025-01-21 04:03:41.889518 INFO::Typecasting input to dataframe.
2025-01-21 04:03:41.890592 INFO::Replacing NaNs with NAs.
2025-01-21 04:03:41.891798 INFO::Removing potential empty rows and columns
2025-01-21 04:03:41.893282 INFO::Found  0  missing values.
2025-01-21 04:03:41.897765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:03:41.89872 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	31.152	1.179	22.266
compute_asw	0.036	0.000	0.036
count_existing	0.019	0.000	0.021
generate_data_covariables	0.017	0.000	0.017
generate_dataset	0.011	0.004	0.015