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) (2025-01-20 r87609) -- "Unsuffered Consequences"	4659
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4454
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4465
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4419
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4409
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: 2025-01-28 03:47:18 -0000 (Tue, 28 Jan 2025)

EndedAt: 2025-01-28 03:48:40 -0000 (Tue, 28 Jan 2025)

EllapsedTime: 82.1 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 ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 32.215  1.268  22.675
* 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:
  2025-01-28 03:48:36.130882 INFO::Typecasting input to dataframe.
  2025-01-28 03:48:36.132183 INFO::Replacing NaNs with NAs.
  2025-01-28 03:48:36.133617 INFO::Removing potential empty rows and columns
  2025-01-28 03:48:36.135298 INFO::Found  0  missing values.
  2025-01-28 03:48:36.140137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
  2025-01-28 03:48:36.141093 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
  ‘/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")
2025-01-28 03:48:23.520061 INFO::Formatting Data.
2025-01-28 03:48:23.521741 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:23.538576 INFO::Removing potential empty rows and columns
2025-01-28 03:48:23.923502 INFO::Found  0  missing values.
2025-01-28 03:48:23.928587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:23.929526 INFO::Done
2025-01-28 03:48:23.930351 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:23.946035 INFO::Starting hierarchical adjustment
2025-01-28 03:48:23.94743 INFO::Found  3  batches.
2025-01-28 03:48:23.948255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:23.949846 INFO::Using default BPPARAM
2025-01-28 03:48:23.950681 INFO::Processing subtree level 1
2025-01-28 03:48:24.107153 INFO::Adjusting the last 1 batches sequentially
2025-01-28 03:48:24.109881 INFO::Done
2025-01-28 03:48:24.110877 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:24.114947 INFO::ASW Batch was -0.053563475583936 prior to batch effect correction and is now -0.053563475583936 .
2025-01-28 03:48:24.116737 INFO::Total function execution time is  0.597297191619873  s and adjustment time is  0.162790775299072 s ( 27.25 )
2025-01-28 03:48:24.138 INFO::Formatting Data.
2025-01-28 03:48:24.1391 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:24.140479 INFO::Removing potential empty rows and columns
2025-01-28 03:48:24.142214 INFO::Found  0  missing values.
2025-01-28 03:48:24.143718 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.
2025-01-28 03:48:24.160812 INFO::Formatting Data.
2025-01-28 03:48:24.161819 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:24.163036 INFO::Removing potential empty rows and columns
2025-01-28 03:48:24.164452 INFO::Found  0  missing values.
2025-01-28 03:48:24.165739 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.
2025-01-28 03:48:24.187868 INFO::Formatting Data.
2025-01-28 03:48:24.18886 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:24.190001 INFO::Removing potential empty rows and columns
2025-01-28 03:48:24.191554 INFO::Found  0  missing values.
2025-01-28 03:48:24.193046 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.
2025-01-28 03:48:24.201408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:24.202545 INFO::Done
2025-01-28 03:48:24.203372 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:24.206975 INFO::Starting hierarchical adjustment
2025-01-28 03:48:24.208347 INFO::Found  2  batches.
2025-01-28 03:48:24.209336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:24.210414 INFO::Using default BPPARAM
2025-01-28 03:48:24.211219 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:24.212739 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:24.247704 INFO::Done
2025-01-28 03:48:24.248702 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:24.251714 INFO::ASW Batch was -0.0351268277711662 prior to batch effect correction and is now -0.127039914650912 .
2025-01-28 03:48:24.25291 INFO::Total function execution time is  0.0651097297668457  s and adjustment time is  0.0395932197570801 s ( 60.81 )
2025-01-28 03:48:24.256856 INFO::Formatting Data.
2025-01-28 03:48:24.257925 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:24.270885 INFO::Formatting Data.
2025-01-28 03:48:24.271907 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:24.273246 INFO::Removing potential empty rows and columns
2025-01-28 03:48:24.274773 INFO::Found  0  missing values.
2025-01-28 03:48:24.279355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:24.280302 INFO::Done
2025-01-28 03:48:24.281144 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:24.284277 INFO::Starting hierarchical adjustment
2025-01-28 03:48:24.285497 INFO::Found  2  batches.
2025-01-28 03:48:24.286348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:24.349833 INFO::Using default BPPARAM
2025-01-28 03:48:24.350703 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:24.352232 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:24.378223 INFO::Done
2025-01-28 03:48:24.379352 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:24.382947 INFO::ASW Batch was -0.0108752496488959 prior to batch effect correction and is now -0.115954733428056 .
2025-01-28 03:48:24.384367 INFO::Total function execution time is  0.113508462905884  s and adjustment time is  0.0929079055786133 s ( 81.85 )
2025-01-28 03:48:24.386254 INFO::Formatting Data.
2025-01-28 03:48:24.38726 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:24.388717 INFO::Removing potential empty rows and columns
2025-01-28 03:48:24.390633 INFO::Found  0  missing values.
2025-01-28 03:48:24.39601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:24.397035 INFO::Done
2025-01-28 03:48:24.397985 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:24.401294 INFO::Starting hierarchical adjustment
2025-01-28 03:48:24.402519 INFO::Found  2  batches.
2025-01-28 03:48:24.403367 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:24.404359 INFO::Using default BPPARAM
2025-01-28 03:48:24.406787 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:24.40854 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:24.435001 INFO::Done
2025-01-28 03:48:24.436058 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:24.439317 INFO::ASW Batch was -0.0108752496488959 prior to batch effect correction and is now -0.115954733428056 .
2025-01-28 03:48:24.44062 INFO::Total function execution time is  0.0543866157531738  s and adjustment time is  0.0327091217041016 s ( 60.14 )
2025-01-28 03:48:28.52249 INFO::Formatting Data.
2025-01-28 03:48:28.523414 INFO::Recognized SummarizedExperiment
2025-01-28 03:48:28.524271 INFO::Typecasting input to dataframe.
2025-01-28 03:48:28.566614 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:28.568084 INFO::Removing potential empty rows and columns
2025-01-28 03:48:28.573284 INFO::Found  0  missing values.
2025-01-28 03:48:28.582961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:28.58379 INFO::Done
2025-01-28 03:48:28.5845 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:28.589405 INFO::Starting hierarchical adjustment
2025-01-28 03:48:28.590717 INFO::Found  2  batches.
2025-01-28 03:48:28.591454 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:28.592834 INFO::Using default BPPARAM
2025-01-28 03:48:28.593587 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:28.594884 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:28.671864 INFO::Done
2025-01-28 03:48:28.672782 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:28.6776 INFO::ASW Batch was 0.0137773898990521 prior to batch effect correction and is now -0.0924319423845993 .
2025-01-28 03:48:28.678831 INFO::Total function execution time is  0.15674901008606  s and adjustment time is  0.0814082622528076 s ( 51.94 )
2025-01-28 03:48:28.703906 INFO::Formatting Data.
2025-01-28 03:48:28.704874 INFO::Recognized SummarizedExperiment
2025-01-28 03:48:28.705614 INFO::Typecasting input to dataframe.
2025-01-28 03:48:28.718898 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:28.720536 INFO::Removing potential empty rows and columns
2025-01-28 03:48:28.725926 INFO::Found  0  missing values.
2025-01-28 03:48:28.73635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:28.73727 INFO::Done
2025-01-28 03:48:28.738019 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:28.743063 INFO::Starting hierarchical adjustment
2025-01-28 03:48:28.744196 INFO::Found  2  batches.
2025-01-28 03:48:28.745008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:28.745842 INFO::Using default BPPARAM
2025-01-28 03:48:28.746625 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:28.748025 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:28.782749 INFO::Done
2025-01-28 03:48:28.783625 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:28.788702 INFO::ASW Batch was 0.00375544420282801 prior to batch effect correction and is now 0.00375544420282801 .
2025-01-28 03:48:28.789925 INFO::Total function execution time is  0.0859799385070801  s and adjustment time is  0.0387592315673828 s ( 45.08 )
2025-01-28 03:48:28.815896 INFO::Formatting Data.
2025-01-28 03:48:28.816996 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:28.818451 INFO::Removing potential empty rows and columns
2025-01-28 03:48:28.819995 INFO::Found  0  missing values.
2025-01-28 03:48:28.824582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:28.825449 INFO::Done
2025-01-28 03:48:28.826257 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:28.82905 INFO::Starting hierarchical adjustment
2025-01-28 03:48:28.830106 INFO::Found  3  batches.
2025-01-28 03:48:28.830928 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:28.831818 INFO::Using default BPPARAM
2025-01-28 03:48:28.832619 INFO::Processing subtree level 1
2025-01-28 03:48:29.008856 INFO::Adjusting the last 1 batches sequentially
2025-01-28 03:48:29.011383 INFO::Done
2025-01-28 03:48:29.01217 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:29.01548 INFO::ASW Batch was -0.0728196149263748 prior to batch effect correction and is now -0.161337292405731 .
2025-01-28 03:48:29.016762 INFO::Total function execution time is  0.20087194442749  s and adjustment time is  0.181497573852539 s ( 90.35 )
2025-01-28 03:48:29.036461 INFO::Skipping initial DF formatting
2025-01-28 03:48:29.037346 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:29.042683 INFO::Starting hierarchical adjustment
2025-01-28 03:48:29.043768 INFO::Found  5  batches.
2025-01-28 03:48:29.044556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:29.045452 INFO::Using default BPPARAM
2025-01-28 03:48:29.046206 INFO::Processing subtree level 1
2025-01-28 03:48:29.205797 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:29.208343 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:29.235698 INFO::Done
2025-01-28 03:48:29.236853 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:29.242694 INFO::ASW Batch was 0.482303049816466 prior to batch effect correction and is now 0.482303049816466 .
2025-01-28 03:48:29.243591 INFO::ASW Label was 0.390251042876037 prior to batch effect correction and is now 0.390251042876037 .
2025-01-28 03:48:29.244795 INFO::Total function execution time is  0.208375453948975  s and adjustment time is  0.192117929458618 s ( 92.2 )
2025-01-28 03:48:29.269253 INFO::Formatting Data.
2025-01-28 03:48:29.270296 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:29.27161 INFO::Removing potential empty rows and columns
2025-01-28 03:48:29.273063 INFO::Found  0  missing values.
2025-01-28 03:48:29.279159 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:29.280011 INFO::Done
2025-01-28 03:48:29.280798 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:29.284782 INFO::Starting hierarchical adjustment
2025-01-28 03:48:29.285876 INFO::Found  5  batches.
2025-01-28 03:48:29.286673 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:29.287575 INFO::Using default BPPARAM
2025-01-28 03:48:29.288332 INFO::Processing subtree level 1
2025-01-28 03:48:29.422835 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:29.425404 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:29.447537 INFO::Done
2025-01-28 03:48:29.448454 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:29.45286 INFO::ASW Batch was 0.28098763913977 prior to batch effect correction and is now -0.0877971773277059 .
2025-01-28 03:48:29.453771 INFO::ASW Label was 0.389578232697029 prior to batch effect correction and is now 0.874060773106853 .
2025-01-28 03:48:29.454931 INFO::Total function execution time is  0.185714721679688  s and adjustment time is  0.161861419677734 s ( 87.16 )
2025-01-28 03:48:29.456105 INFO::Formatting Data.
2025-01-28 03:48:29.457005 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:29.45824 INFO::Removing potential empty rows and columns
2025-01-28 03:48:29.459721 INFO::Found  0  missing values.
2025-01-28 03:48:29.465536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:29.466431 INFO::Done
2025-01-28 03:48:29.467185 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:29.471513 INFO::Starting hierarchical adjustment
2025-01-28 03:48:29.472939 INFO::Found  5  batches.
2025-01-28 03:48:29.47375 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:29.474656 INFO::Using default BPPARAM
2025-01-28 03:48:29.475404 INFO::Processing subtree level 1
2025-01-28 03:48:29.607832 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:29.618283 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:29.639375 INFO::Done
2025-01-28 03:48:29.640282 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:29.644683 INFO::ASW Batch was 0.28098763913977 prior to batch effect correction and is now -0.0877971773277059 .
2025-01-28 03:48:29.645615 INFO::ASW Label was 0.389578232697029 prior to batch effect correction and is now 0.874060773106853 .
2025-01-28 03:48:29.646846 INFO::Total function execution time is  0.190712928771973  s and adjustment time is  0.166683197021484 s ( 87.4 )
2025-01-28 03:48:29.665596 INFO::Formatting Data.
2025-01-28 03:48:29.666631 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:29.667851 INFO::Removing potential empty rows and columns
2025-01-28 03:48:29.669228 INFO::Found  0  missing values.
2025-01-28 03:48:29.675036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:29.675912 INFO::Done
2025-01-28 03:48:29.676691 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:29.680577 INFO::Starting hierarchical adjustment
2025-01-28 03:48:29.681688 INFO::Found  5  batches.
2025-01-28 03:48:29.68247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:29.68333 INFO::Using default BPPARAM
2025-01-28 03:48:29.684076 INFO::Processing subtree level 1
2025-01-28 03:48:29.819876 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:29.822741 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:29.843542 INFO::Done
2025-01-28 03:48:29.844559 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:29.848982 INFO::ASW Batch was 0.378635939320999 prior to batch effect correction and is now -0.0413386000627619 .
2025-01-28 03:48:29.8499 INFO::ASW Label was 0.322967175572302 prior to batch effect correction and is now 0.815328348366248 .
2025-01-28 03:48:29.851093 INFO::Total function execution time is  0.185513019561768  s and adjustment time is  0.162042140960693 s ( 87.35 )
2025-01-28 03:48:29.852278 INFO::Formatting Data.
2025-01-28 03:48:29.853181 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:29.854452 INFO::Removing potential empty rows and columns
2025-01-28 03:48:29.855922 INFO::Found  0  missing values.
2025-01-28 03:48:29.861969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:29.862831 INFO::Done
2025-01-28 03:48:29.863595 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:29.86759 INFO::Starting hierarchical adjustment
2025-01-28 03:48:29.86868 INFO::Found  5  batches.
2025-01-28 03:48:29.869478 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:29.870389 INFO::Using default BPPARAM
2025-01-28 03:48:29.871222 INFO::Processing subtree level 1
2025-01-28 03:48:30.008474 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:30.010607 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:30.032892 INFO::Done
2025-01-28 03:48:30.033812 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:30.038197 INFO::ASW Batch was 0.378635939320999 prior to batch effect correction and is now -0.0413386000627619 .
2025-01-28 03:48:30.039184 INFO::ASW Label was 0.322967175572302 prior to batch effect correction and is now 0.815328348366248 .
2025-01-28 03:48:30.040405 INFO::Total function execution time is  0.188064813613892  s and adjustment time is  0.164422750473022 s ( 87.43 )
2025-01-28 03:48:30.059503 INFO::Formatting Data.
2025-01-28 03:48:30.060556 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:30.061865 INFO::Removing potential empty rows and columns
2025-01-28 03:48:30.063351 INFO::Found  0  missing values.
2025-01-28 03:48:30.067372 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:30.068204 INFO::Done
2025-01-28 03:48:30.069008 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:30.073041 INFO::Starting hierarchical adjustment
2025-01-28 03:48:30.074102 INFO::Found  2  batches.
2025-01-28 03:48:30.074908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:30.075793 INFO::Using default BPPARAM
2025-01-28 03:48:30.076575 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:30.077919 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:30.097844 INFO::Done
2025-01-28 03:48:30.098763 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:30.102899 INFO::ASW Batch was 0.590162215313362 prior to batch effect correction and is now 0.0345706715267976 .
2025-01-28 03:48:30.103787 INFO::ASW Label was 0.513458926977302 prior to batch effect correction and is now 0.898335339928224 .
2025-01-28 03:48:30.1049 INFO::Total function execution time is  0.0454897880554199  s and adjustment time is  0.0239400863647461 s ( 52.63 )
2025-01-28 03:48:30.106001 INFO::Formatting Data.
2025-01-28 03:48:30.106878 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:30.108087 INFO::Removing potential empty rows and columns
2025-01-28 03:48:30.109503 INFO::Found  0  missing values.
2025-01-28 03:48:30.113451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:30.114278 INFO::Done
2025-01-28 03:48:30.11506 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:30.308222 INFO::Starting hierarchical adjustment
2025-01-28 03:48:30.309426 INFO::Found  2  batches.
2025-01-28 03:48:30.310309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:30.311267 INFO::Using default BPPARAM
2025-01-28 03:48:30.312109 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:30.313584 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:30.335868 INFO::Done
2025-01-28 03:48:30.345225 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:30.350227 INFO::ASW Batch was 0.590162215313362 prior to batch effect correction and is now 0.0345706715267976 .
2025-01-28 03:48:30.351255 INFO::ASW Label was 0.513458926977302 prior to batch effect correction and is now 0.898335339928224 .
2025-01-28 03:48:30.352529 INFO::Total function execution time is  0.246491193771362  s and adjustment time is  0.0266687870025635 s ( 10.82 )
2025-01-28 03:48:30.37047 INFO::Formatting Data.
2025-01-28 03:48:30.371578 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:30.373001 INFO::Removing potential empty rows and columns
2025-01-28 03:48:30.374532 INFO::Found  0  missing values.
2025-01-28 03:48:30.377908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:30.378808 INFO::Done
2025-01-28 03:48:30.379637 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:30.382453 INFO::Starting hierarchical adjustment
2025-01-28 03:48:30.383537 INFO::Found  2  batches.
2025-01-28 03:48:30.384377 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:30.385353 INFO::Using default BPPARAM
2025-01-28 03:48:30.386246 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:30.387686 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:30.436155 INFO::Done
2025-01-28 03:48:30.437145 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:30.439849 INFO::ASW Batch was -0.0675579811304256 prior to batch effect correction and is now -0.172551547391934 .
2025-01-28 03:48:30.440974 INFO::Total function execution time is  0.0706052780151367  s and adjustment time is  0.0528213977813721 s ( 74.81 )
2025-01-28 03:48:30.457978 INFO::Formatting Data.
2025-01-28 03:48:30.459014 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:30.460224 INFO::Removing potential empty rows and columns
2025-01-28 03:48:30.461731 INFO::Found  0  missing values.
2025-01-28 03:48:30.463377 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.
2025-01-28 03:48:30.470387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:30.471306 INFO::Done
2025-01-28 03:48:30.472064 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:30.476239 INFO::Starting hierarchical adjustment
2025-01-28 03:48:30.477367 INFO::Found  2  batches.
2025-01-28 03:48:30.478114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:30.478956 INFO::Using default BPPARAM
2025-01-28 03:48:30.479668 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:30.481088 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:30.505096 INFO::Done
2025-01-28 03:48:30.505958 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:30.509917 INFO::ASW Batch was 0.557092704139573 prior to batch effect correction and is now 0.103789210084549 .
2025-01-28 03:48:30.510835 INFO::ASW Label was 0.552170746228713 prior to batch effect correction and is now 0.850458519514286 .
2025-01-28 03:48:30.512004 INFO::Total function execution time is  0.0541861057281494  s and adjustment time is  0.0279369354248047 s ( 51.56 )
2025-01-28 03:48:30.513055 INFO::Formatting Data.
2025-01-28 03:48:30.513861 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:30.515116 INFO::Removing potential empty rows and columns
2025-01-28 03:48:30.516494 INFO::Found  0  missing values.
2025-01-28 03:48:30.517794 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.
2025-01-28 03:48:30.524711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:30.525567 INFO::Done
2025-01-28 03:48:30.526315 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:30.530296 INFO::Starting hierarchical adjustment
2025-01-28 03:48:30.531337 INFO::Found  2  batches.
2025-01-28 03:48:30.532079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:30.533 INFO::Using default BPPARAM
2025-01-28 03:48:30.533754 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:30.535076 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:30.559385 INFO::Done
2025-01-28 03:48:30.5603 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:30.564728 INFO::ASW Batch was 0.557092704139573 prior to batch effect correction and is now 0.103789210084549 .
2025-01-28 03:48:30.565624 INFO::ASW Label was 0.552170746228713 prior to batch effect correction and is now 0.850458519514286 .
2025-01-28 03:48:30.566787 INFO::Total function execution time is  0.0537040233612061  s and adjustment time is  0.0282237529754639 s ( 52.55 )
2025-01-28 03:48:30.891126 INFO::Formatting Data.
2025-01-28 03:48:30.89233 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:30.893718 INFO::Removing potential empty rows and columns
2025-01-28 03:48:30.895394 INFO::Found  0  missing values.
2025-01-28 03:48:30.900172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:30.90516 INFO::Done
2025-01-28 03:48:30.906122 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:30.909529 INFO::Starting hierarchical adjustment
2025-01-28 03:48:30.910727 INFO::Found  3  batches.
2025-01-28 03:48:30.911592 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:30.912619 INFO::Using default BPPARAM
2025-01-28 03:48:30.913416 INFO::Processing subtree level 1
2025-01-28 03:48:31.043639 INFO::Adjusting the last 1 batches sequentially
2025-01-28 03:48:31.046123 INFO::Done
2025-01-28 03:48:31.04709 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:31.050604 INFO::ASW Batch was -0.0216452406682546 prior to batch effect correction and is now -0.0216452406682546 .
2025-01-28 03:48:31.052042 INFO::Total function execution time is  0.160910606384277  s and adjustment time is  0.135676622390747 s ( 84.32 )
2025-01-28 03:48:31.053684 INFO::Formatting Data.
2025-01-28 03:48:31.054682 INFO::Typecasting input to dataframe.
2025-01-28 03:48:31.055816 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:31.057236 INFO::Removing potential empty rows and columns
2025-01-28 03:48:31.059045 INFO::Found  0  missing values.
2025-01-28 03:48:31.063892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:31.064824 INFO::Done
2025-01-28 03:48:31.065647 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:31.068573 INFO::Starting hierarchical adjustment
2025-01-28 03:48:31.069746 INFO::Found  3  batches.
2025-01-28 03:48:31.070577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:31.071523 INFO::Using default BPPARAM
2025-01-28 03:48:31.072324 INFO::Processing subtree level 1
2025-01-28 03:48:31.220066 INFO::Adjusting the last 1 batches sequentially
2025-01-28 03:48:31.222566 INFO::Done
2025-01-28 03:48:31.223477 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:31.226901 INFO::ASW Batch was -0.0216452406682546 prior to batch effect correction and is now -0.0216452406682546 .
2025-01-28 03:48:31.228325 INFO::Total function execution time is  0.174654006958008  s and adjustment time is  0.153050184249878 s ( 87.63 )
2025-01-28 03:48:31.249297 INFO::Formatting Data.
2025-01-28 03:48:31.250409 INFO::Typecasting input to dataframe.
2025-01-28 03:48:31.251717 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:31.253116 INFO::Removing potential empty rows and columns
2025-01-28 03:48:31.254839 INFO::Found  0  missing values.
2025-01-28 03:48:31.259649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:31.260571 INFO::Done
2025-01-28 03:48:31.261401 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:31.264338 INFO::Starting hierarchical adjustment
2025-01-28 03:48:31.265512 INFO::Found  3  batches.
2025-01-28 03:48:31.266347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:31.267307 INFO::Using default BPPARAM
2025-01-28 03:48:31.268124 INFO::Processing subtree level 1
2025-01-28 03:48:31.402368 INFO::Adjusting the last 1 batches sequentially
2025-01-28 03:48:31.407601 INFO::Done
2025-01-28 03:48:31.408684 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:31.416579 INFO::ASW Batch was 0.0398048492281878 prior to batch effect correction and is now 0.0398048492281878 .
2025-01-28 03:48:31.418271 INFO::Total function execution time is  0.168951511383057  s and adjustment time is  0.142272233963013 s ( 84.21 )
2025-01-28 03:48:31.655786 INFO::Formatting Data.
2025-01-28 03:48:31.657083 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:31.659144 INFO::Removing potential empty rows and columns
2025-01-28 03:48:31.664642 INFO::Found  1000  missing values.
2025-01-28 03:48:31.700889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:31.701976 INFO::Done
2025-01-28 03:48:31.702878 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:31.711756 INFO::Starting hierarchical adjustment
2025-01-28 03:48:31.713074 INFO::Found  10  batches.
2025-01-28 03:48:31.713933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:31.715055 INFO::Using default BPPARAM
2025-01-28 03:48:31.715876 INFO::Processing subtree level 1
2025-01-28 03:48:31.923408 INFO::Processing subtree level 2
2025-01-28 03:48:32.161882 INFO::Adjusting the last 1 batches sequentially
2025-01-28 03:48:32.164846 INFO::Done
2025-01-28 03:48:32.165871 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:32.174657 INFO::ASW Batch was 0.431573354873693 prior to batch effect correction and is now 0.431573354873693 .
2025-01-28 03:48:32.17573 INFO::ASW Label was 0.373601655993848 prior to batch effect correction and is now 0.373601655993848 .
2025-01-28 03:48:32.177208 INFO::Total function execution time is  0.521515130996704  s and adjustment time is  0.452015399932861 s ( 86.67 )
2025-01-28 03:48:32.178518 INFO::Formatting Data.
2025-01-28 03:48:32.179486 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:32.181361 INFO::Removing potential empty rows and columns
2025-01-28 03:48:32.186035 INFO::Found  1000  missing values.
2025-01-28 03:48:32.217537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:32.218504 INFO::Done
2025-01-28 03:48:32.219331 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:32.227335 INFO::Starting hierarchical adjustment
2025-01-28 03:48:32.228497 INFO::Found  10  batches.
2025-01-28 03:48:33.609039 INFO::Set up parallel execution backend with 2 workers
2025-01-28 03:48:33.611791 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-28 03:48:35.055891 INFO::Adjusting the last 2 batches sequentially
2025-01-28 03:48:35.057804 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-28 03:48:35.083896 INFO::Done
2025-01-28 03:48:35.084783 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:35.091846 INFO::ASW Batch was 0.431573354873693 prior to batch effect correction and is now 0.431573354873693 .
2025-01-28 03:48:35.092721 INFO::ASW Label was 0.373601655993848 prior to batch effect correction and is now 0.373601655993848 .
2025-01-28 03:48:35.093764 INFO::Total function execution time is  2.91532397270203  s and adjustment time is  2.85562610626221 s ( 97.95 )
2025-01-28 03:48:35.287145 INFO::Formatting Data.
2025-01-28 03:48:35.288277 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:35.289637 INFO::Removing potential empty rows and columns
2025-01-28 03:48:35.291263 INFO::Found  0  missing values.
2025-01-28 03:48:35.297135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:35.298062 INFO::Done
2025-01-28 03:48:35.298885 INFO::Acquiring quality metrics before batch effect correction.
2025-01-28 03:48:35.302941 INFO::Starting hierarchical adjustment
2025-01-28 03:48:35.304133 INFO::Found  3  batches.
2025-01-28 03:48:35.304986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-28 03:48:35.305883 INFO::Using default BPPARAM
2025-01-28 03:48:35.306695 INFO::Processing subtree level 1
2025-01-28 03:48:35.440307 INFO::Adjusting the last 1 batches sequentially
2025-01-28 03:48:35.442672 INFO::Done
2025-01-28 03:48:35.443566 INFO::Acquiring quality metrics after batch effect correction.
2025-01-28 03:48:35.44808 INFO::ASW Batch was 0.150139164915023 prior to batch effect correction and is now -0.157012546047896 .
2025-01-28 03:48:35.449086 INFO::ASW Label was -0.134828249275797 prior to batch effect correction and is now 0.160338923861365 .
2025-01-28 03:48:35.450353 INFO::Total function execution time is  0.163249015808105  s and adjustment time is  0.138752698898315 s ( 84.99 )
2025-01-28 03:48:35.64078 INFO::Formatting Data.
2025-01-28 03:48:35.641961 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:35.643319 INFO::Removing potential empty rows and columns
2025-01-28 03:48:35.644937 INFO::Found  2  missing values.
2025-01-28 03:48:35.649544 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:35.650475 INFO::Done
2025-01-28 03:48:35.694859 INFO::Found NA in Reference column
2025-01-28 03:48:35.709883 INFO::Require at least two references per batch.
2025-01-28 03:48:35.742657 INFO::Formatting Data.
2025-01-28 03:48:35.743684 INFO::Recognized SummarizedExperiment
2025-01-28 03:48:35.744559 INFO::Typecasting input to dataframe.
2025-01-28 03:48:35.75956 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:35.761267 INFO::Removing potential empty rows and columns
2025-01-28 03:48:35.767175 INFO::Found  0  missing values.
2025-01-28 03:48:35.778635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:35.779611 INFO::Done
2025-01-28 03:48:35.802599 INFO::Formatting Data.
2025-01-28 03:48:35.803624 INFO::Recognized SummarizedExperiment
2025-01-28 03:48:35.804466 INFO::Typecasting input to dataframe.
2025-01-28 03:48:35.832217 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:35.833965 INFO::Removing potential empty rows and columns
2025-01-28 03:48:35.839806 INFO::Found  0  missing values.
2025-01-28 03:48:35.858502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:35.859502 INFO::Done
2025-01-28 03:48:35.882667 INFO::Formatting Data.
2025-01-28 03:48:35.883711 INFO::Recognized SummarizedExperiment
2025-01-28 03:48:35.884556 INFO::Typecasting input to dataframe.
2025-01-28 03:48:35.912156 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:35.913715 INFO::Removing potential empty rows and columns
2025-01-28 03:48:35.91594 INFO::Found  0  missing values.
2025-01-28 03:48:35.917655 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.
2025-01-28 03:48:35.925239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:35.926213 INFO::Done
2025-01-28 03:48:35.94249 INFO::Formatting Data.
2025-01-28 03:48:35.943664 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:35.945122 INFO::Removing potential empty rows and columns
2025-01-28 03:48:35.94679 INFO::Found  0  missing values.
2025-01-28 03:48:35.951632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:35.952571 INFO::Done
2025-01-28 03:48:35.971202 INFO::Formatting Data.
2025-01-28 03:48:35.972392 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:35.973924 INFO::Removing potential empty rows and columns
2025-01-28 03:48:35.975671 INFO::Found  0  missing values.
2025-01-28 03:48:35.980811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:35.981784 INFO::Done
2025-01-28 03:48:36.032386 INFO::Formatting Data.
2025-01-28 03:48:36.033636 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:36.035387 INFO::Removing potential empty rows and columns
2025-01-28 03:48:36.037494 INFO::Found  1  missing values.
2025-01-28 03:48:36.042057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:36.043105 INFO::Done
2025-01-28 03:48:36.075813 INFO::Formatting Data.
2025-01-28 03:48:36.077033 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:36.078624 INFO::Removing potential empty rows and columns
2025-01-28 03:48:36.080241 INFO::Found  2  missing values.
2025-01-28 03:48:36.08178 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.
2025-01-28 03:48:36.085736 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:36.086725 INFO::Done
2025-01-28 03:48:36.104985 INFO::Formatting Data.
2025-01-28 03:48:36.106154 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:36.107506 INFO::Removing potential empty rows and columns
2025-01-28 03:48:36.108934 INFO::Found  2  missing values.
2025-01-28 03:48:36.111381 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:36.112197 INFO::Done
2025-01-28 03:48:36.129698 INFO::Formatting Data.
2025-01-28 03:48:36.130882 INFO::Typecasting input to dataframe.
2025-01-28 03:48:36.132183 INFO::Replacing NaNs with NAs.
2025-01-28 03:48:36.133617 INFO::Removing potential empty rows and columns
2025-01-28 03:48:36.135298 INFO::Found  0  missing values.
2025-01-28 03:48:36.140137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-28 03:48:36.141093 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	32.215	1.268	22.675
compute_asw	0.030	0.004	0.035
count_existing	0.018	0.000	0.018
generate_data_covariables	0.016	0.000	0.015
generate_dataset	0.014	0.000	0.015