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"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4464
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4418
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for BERT on 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: 2025-01-27 04:37:04 -0000 (Mon, 27 Jan 2025)

EndedAt: 2025-01-27 04:38:27 -0000 (Mon, 27 Jan 2025)

EllapsedTime: 83.1 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 31.488  1.554  22.877
* 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:
  2025-01-27 04:38:23.692427 INFO::Typecasting input to dataframe.
  2025-01-27 04:38:23.69363 INFO::Replacing NaNs with NAs.
  2025-01-27 04:38:23.694881 INFO::Removing potential empty rows and columns
  2025-01-27 04:38:23.696398 INFO::Found  0  missing values.
  2025-01-27 04:38:23.700884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
  2025-01-27 04:38:23.701787 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")
2025-01-27 04:38:11.532454 INFO::Formatting Data.
2025-01-27 04:38:11.534236 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:11.552455 INFO::Removing potential empty rows and columns
2025-01-27 04:38:11.941315 INFO::Found  0  missing values.
2025-01-27 04:38:11.94612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:11.947031 INFO::Done
2025-01-27 04:38:11.947787 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:11.963287 INFO::Starting hierarchical adjustment
2025-01-27 04:38:11.964545 INFO::Found  3  batches.
2025-01-27 04:38:11.965397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:11.966979 INFO::Using default BPPARAM
2025-01-27 04:38:11.967857 INFO::Processing subtree level 1
2025-01-27 04:38:12.097205 INFO::Adjusting the last 1 batches sequentially
2025-01-27 04:38:12.099676 INFO::Done
2025-01-27 04:38:12.100638 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:12.104365 INFO::ASW Batch was -0.0556370596434996 prior to batch effect correction and is now -0.0556370596434996 .
2025-01-27 04:38:12.106061 INFO::Total function execution time is  0.574430227279663  s and adjustment time is  0.135421514511108 s ( 23.57 )
2025-01-27 04:38:12.125876 INFO::Formatting Data.
2025-01-27 04:38:12.126927 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:12.128226 INFO::Removing potential empty rows and columns
2025-01-27 04:38:12.129869 INFO::Found  0  missing values.
2025-01-27 04:38:12.13122 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.
2025-01-27 04:38:12.146954 INFO::Formatting Data.
2025-01-27 04:38:12.14798 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:12.149241 INFO::Removing potential empty rows and columns
2025-01-27 04:38:12.150782 INFO::Found  0  missing values.
2025-01-27 04:38:12.152128 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.
2025-01-27 04:38:12.175141 INFO::Formatting Data.
2025-01-27 04:38:12.176175 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:12.177441 INFO::Removing potential empty rows and columns
2025-01-27 04:38:12.178957 INFO::Found  0  missing values.
2025-01-27 04:38:12.180234 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.
2025-01-27 04:38:12.186756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:12.187673 INFO::Done
2025-01-27 04:38:12.188497 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:12.191402 INFO::Starting hierarchical adjustment
2025-01-27 04:38:12.192532 INFO::Found  2  batches.
2025-01-27 04:38:12.193357 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:12.194294 INFO::Using default BPPARAM
2025-01-27 04:38:12.195062 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:12.19656 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:12.228392 INFO::Done
2025-01-27 04:38:12.22933 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:12.232141 INFO::ASW Batch was 0.0249577630843086 prior to batch effect correction and is now -0.121034502972087 .
2025-01-27 04:38:12.233326 INFO::Total function execution time is  0.0582511425018311  s and adjustment time is  0.0361034870147705 s ( 61.98 )
2025-01-27 04:38:12.237061 INFO::Formatting Data.
2025-01-27 04:38:12.238039 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:12.250418 INFO::Formatting Data.
2025-01-27 04:38:12.251411 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:12.25267 INFO::Removing potential empty rows and columns
2025-01-27 04:38:12.254147 INFO::Found  0  missing values.
2025-01-27 04:38:12.258412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:12.259325 INFO::Done
2025-01-27 04:38:12.260069 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:12.263031 INFO::Starting hierarchical adjustment
2025-01-27 04:38:12.264204 INFO::Found  2  batches.
2025-01-27 04:38:12.265064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:12.303388 INFO::Using default BPPARAM
2025-01-27 04:38:12.30419 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:12.305557 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:12.327098 INFO::Done
2025-01-27 04:38:12.327978 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:12.33082 INFO::ASW Batch was -0.0588281529839878 prior to batch effect correction and is now -0.128119228610621 .
2025-01-27 04:38:12.331962 INFO::Total function execution time is  0.0815935134887695  s and adjustment time is  0.0631186962127686 s ( 77.36 )
2025-01-27 04:38:12.333496 INFO::Formatting Data.
2025-01-27 04:38:12.334342 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:12.33553 INFO::Removing potential empty rows and columns
2025-01-27 04:38:12.337042 INFO::Found  0  missing values.
2025-01-27 04:38:12.34139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:12.342426 INFO::Done
2025-01-27 04:38:12.343211 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:12.346174 INFO::Starting hierarchical adjustment
2025-01-27 04:38:12.347334 INFO::Found  2  batches.
2025-01-27 04:38:12.348099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:12.349017 INFO::Using default BPPARAM
2025-01-27 04:38:12.349747 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:12.351083 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:12.372753 INFO::Done
2025-01-27 04:38:12.373648 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:12.376387 INFO::ASW Batch was -0.0588281529839878 prior to batch effect correction and is now -0.128119228610621 .
2025-01-27 04:38:12.377515 INFO::Total function execution time is  0.0440311431884766  s and adjustment time is  0.0256204605102539 s ( 58.19 )
2025-01-27 04:38:16.294318 INFO::Formatting Data.
2025-01-27 04:38:16.295192 INFO::Recognized SummarizedExperiment
2025-01-27 04:38:16.295837 INFO::Typecasting input to dataframe.
2025-01-27 04:38:16.337133 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:16.338664 INFO::Removing potential empty rows and columns
2025-01-27 04:38:16.343812 INFO::Found  0  missing values.
2025-01-27 04:38:16.353719 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:16.354583 INFO::Done
2025-01-27 04:38:16.355279 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:16.360005 INFO::Starting hierarchical adjustment
2025-01-27 04:38:16.361091 INFO::Found  2  batches.
2025-01-27 04:38:16.361842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:16.363318 INFO::Using default BPPARAM
2025-01-27 04:38:16.364128 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:16.365553 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:16.443472 INFO::Done
2025-01-27 04:38:16.444366 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:16.449271 INFO::ASW Batch was 0.00155923578048791 prior to batch effect correction and is now -0.0924663045425311 .
2025-01-27 04:38:16.450546 INFO::Total function execution time is  0.156628847122192  s and adjustment time is  0.0825691223144531 s ( 52.72 )
2025-01-27 04:38:16.475517 INFO::Formatting Data.
2025-01-27 04:38:16.476521 INFO::Recognized SummarizedExperiment
2025-01-27 04:38:16.477271 INFO::Typecasting input to dataframe.
2025-01-27 04:38:16.490616 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:16.492211 INFO::Removing potential empty rows and columns
2025-01-27 04:38:16.497417 INFO::Found  0  missing values.
2025-01-27 04:38:16.50773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:16.508679 INFO::Done
2025-01-27 04:38:16.509423 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:16.514374 INFO::Starting hierarchical adjustment
2025-01-27 04:38:16.51553 INFO::Found  2  batches.
2025-01-27 04:38:16.516296 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:16.517157 INFO::Using default BPPARAM
2025-01-27 04:38:16.517862 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:16.519239 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:16.555475 INFO::Done
2025-01-27 04:38:16.556383 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:16.561549 INFO::ASW Batch was -0.0174378739113108 prior to batch effect correction and is now -0.0174378739113108 .
2025-01-27 04:38:16.562839 INFO::Total function execution time is  0.0872795581817627  s and adjustment time is  0.0401577949523926 s ( 46.01 )
2025-01-27 04:38:16.58816 INFO::Formatting Data.
2025-01-27 04:38:16.589272 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:16.590531 INFO::Removing potential empty rows and columns
2025-01-27 04:38:16.591969 INFO::Found  0  missing values.
2025-01-27 04:38:16.596255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:16.597205 INFO::Done
2025-01-27 04:38:16.597951 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:16.600817 INFO::Starting hierarchical adjustment
2025-01-27 04:38:16.601944 INFO::Found  3  batches.
2025-01-27 04:38:16.602741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:16.603605 INFO::Using default BPPARAM
2025-01-27 04:38:16.604334 INFO::Processing subtree level 1
2025-01-27 04:38:16.77909 INFO::Adjusting the last 1 batches sequentially
2025-01-27 04:38:16.781671 INFO::Done
2025-01-27 04:38:16.782652 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:16.78625 INFO::ASW Batch was -0.0300218611520514 prior to batch effect correction and is now -0.153513358282754 .
2025-01-27 04:38:16.787707 INFO::Total function execution time is  0.199546337127686  s and adjustment time is  0.17989706993103 s ( 90.15 )
2025-01-27 04:38:16.808378 INFO::Skipping initial DF formatting
2025-01-27 04:38:16.80938 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:16.815192 INFO::Starting hierarchical adjustment
2025-01-27 04:38:16.816426 INFO::Found  5  batches.
2025-01-27 04:38:16.817271 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:16.818164 INFO::Using default BPPARAM
2025-01-27 04:38:16.818946 INFO::Processing subtree level 1
2025-01-27 04:38:16.977826 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:16.980254 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:17.01009 INFO::Done
2025-01-27 04:38:17.011198 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:17.018234 INFO::ASW Batch was 0.466824597975804 prior to batch effect correction and is now 0.466824597975804 .
2025-01-27 04:38:17.01935 INFO::ASW Label was 0.432252112221225 prior to batch effect correction and is now 0.432252112221225 .
2025-01-27 04:38:17.02088 INFO::Total function execution time is  0.212568998336792  s and adjustment time is  0.193886518478394 s ( 91.21 )
2025-01-27 04:38:17.047059 INFO::Formatting Data.
2025-01-27 04:38:17.048189 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:17.049602 INFO::Removing potential empty rows and columns
2025-01-27 04:38:17.051126 INFO::Found  0  missing values.
2025-01-27 04:38:17.057552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:17.0586 INFO::Done
2025-01-27 04:38:17.059419 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:17.063834 INFO::Starting hierarchical adjustment
2025-01-27 04:38:17.065098 INFO::Found  5  batches.
2025-01-27 04:38:17.065913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:17.066831 INFO::Using default BPPARAM
2025-01-27 04:38:17.067662 INFO::Processing subtree level 1
2025-01-27 04:38:17.198866 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:17.201065 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:17.224182 INFO::Done
2025-01-27 04:38:17.225208 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:17.229707 INFO::ASW Batch was 0.499537945336398 prior to batch effect correction and is now -0.110799481032762 .
2025-01-27 04:38:17.230667 INFO::ASW Label was 0.169611553528828 prior to batch effect correction and is now 0.849027053718608 .
2025-01-27 04:38:17.231813 INFO::Total function execution time is  0.184798240661621  s and adjustment time is  0.159327268600464 s ( 86.22 )
2025-01-27 04:38:17.232965 INFO::Formatting Data.
2025-01-27 04:38:17.233836 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:17.235102 INFO::Removing potential empty rows and columns
2025-01-27 04:38:17.236561 INFO::Found  0  missing values.
2025-01-27 04:38:17.242681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:17.24361 INFO::Done
2025-01-27 04:38:17.244397 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:17.248593 INFO::Starting hierarchical adjustment
2025-01-27 04:38:17.249772 INFO::Found  5  batches.
2025-01-27 04:38:17.250628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:17.251538 INFO::Using default BPPARAM
2025-01-27 04:38:17.252296 INFO::Processing subtree level 1
2025-01-27 04:38:17.383063 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:17.385167 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:17.407513 INFO::Done
2025-01-27 04:38:17.408602 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:17.413087 INFO::ASW Batch was 0.499537945336398 prior to batch effect correction and is now -0.110799481032762 .
2025-01-27 04:38:17.413999 INFO::ASW Label was 0.169611553528828 prior to batch effect correction and is now 0.849027053718608 .
2025-01-27 04:38:17.415154 INFO::Total function execution time is  0.182169675827026  s and adjustment time is  0.157965421676636 s ( 86.71 )
2025-01-27 04:38:17.433886 INFO::Formatting Data.
2025-01-27 04:38:17.43495 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:17.436249 INFO::Removing potential empty rows and columns
2025-01-27 04:38:17.437722 INFO::Found  0  missing values.
2025-01-27 04:38:17.443797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:17.44477 INFO::Done
2025-01-27 04:38:17.445512 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:17.449708 INFO::Starting hierarchical adjustment
2025-01-27 04:38:17.450968 INFO::Found  5  batches.
2025-01-27 04:38:17.451723 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:17.452596 INFO::Using default BPPARAM
2025-01-27 04:38:17.453347 INFO::Processing subtree level 1
2025-01-27 04:38:17.588344 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:17.590513 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:17.62322 INFO::Done
2025-01-27 04:38:17.624259 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:17.629049 INFO::ASW Batch was 0.540428549599635 prior to batch effect correction and is now 0.0220011231481431 .
2025-01-27 04:38:17.629971 INFO::ASW Label was 0.354212250522217 prior to batch effect correction and is now 0.715316757805959 .
2025-01-27 04:38:17.631199 INFO::Total function execution time is  0.197354078292847  s and adjustment time is  0.17245626449585 s ( 87.38 )
2025-01-27 04:38:17.632402 INFO::Formatting Data.
2025-01-27 04:38:17.633341 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:17.634671 INFO::Removing potential empty rows and columns
2025-01-27 04:38:17.636154 INFO::Found  0  missing values.
2025-01-27 04:38:17.642381 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:17.64327 INFO::Done
2025-01-27 04:38:17.644034 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:17.648355 INFO::Starting hierarchical adjustment
2025-01-27 04:38:17.649606 INFO::Found  5  batches.
2025-01-27 04:38:17.65055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:17.65163 INFO::Using default BPPARAM
2025-01-27 04:38:17.652488 INFO::Processing subtree level 1
2025-01-27 04:38:17.783711 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:17.785767 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:17.806594 INFO::Done
2025-01-27 04:38:17.807507 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:17.811889 INFO::ASW Batch was 0.540428549599635 prior to batch effect correction and is now 0.0220011231481431 .
2025-01-27 04:38:17.812825 INFO::ASW Label was 0.354212250522217 prior to batch effect correction and is now 0.715316757805959 .
2025-01-27 04:38:17.813948 INFO::Total function execution time is  0.181530475616455  s and adjustment time is  0.157259225845337 s ( 86.63 )
2025-01-27 04:38:17.833253 INFO::Formatting Data.
2025-01-27 04:38:17.834277 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:17.835518 INFO::Removing potential empty rows and columns
2025-01-27 04:38:17.836935 INFO::Found  0  missing values.
2025-01-27 04:38:17.840961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:17.841824 INFO::Done
2025-01-27 04:38:17.842594 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:17.846533 INFO::Starting hierarchical adjustment
2025-01-27 04:38:17.847625 INFO::Found  2  batches.
2025-01-27 04:38:17.848361 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:17.849235 INFO::Using default BPPARAM
2025-01-27 04:38:17.849948 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:17.851244 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:17.870664 INFO::Done
2025-01-27 04:38:17.871554 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:17.875538 INFO::ASW Batch was 0.818044933158366 prior to batch effect correction and is now 0.0176015698682931 .
2025-01-27 04:38:17.87644 INFO::ASW Label was 0.234159326054676 prior to batch effect correction and is now 0.864422132613766 .
2025-01-27 04:38:17.877563 INFO::Total function execution time is  0.0443689823150635  s and adjustment time is  0.0232381820678711 s ( 52.37 )
2025-01-27 04:38:17.878603 INFO::Formatting Data.
2025-01-27 04:38:17.879421 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:17.880623 INFO::Removing potential empty rows and columns
2025-01-27 04:38:17.88198 INFO::Found  0  missing values.
2025-01-27 04:38:17.959391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:17.961132 INFO::Done
2025-01-27 04:38:17.961886 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:17.965926 INFO::Starting hierarchical adjustment
2025-01-27 04:38:17.967061 INFO::Found  2  batches.
2025-01-27 04:38:17.967829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:17.968693 INFO::Using default BPPARAM
2025-01-27 04:38:17.969437 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:17.970777 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:17.992377 INFO::Done
2025-01-27 04:38:17.993367 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:17.997628 INFO::ASW Batch was 0.818044933158366 prior to batch effect correction and is now 0.0176015698682931 .
2025-01-27 04:38:17.998556 INFO::ASW Label was 0.234159326054676 prior to batch effect correction and is now 0.864422132613766 .
2025-01-27 04:38:17.999688 INFO::Total function execution time is  0.121082305908203  s and adjustment time is  0.0255222320556641 s ( 21.08 )
2025-01-27 04:38:18.0163 INFO::Formatting Data.
2025-01-27 04:38:18.017363 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:18.018578 INFO::Removing potential empty rows and columns
2025-01-27 04:38:18.01983 INFO::Found  0  missing values.
2025-01-27 04:38:18.022858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:18.023686 INFO::Done
2025-01-27 04:38:18.024438 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:18.027102 INFO::Starting hierarchical adjustment
2025-01-27 04:38:18.028172 INFO::Found  2  batches.
2025-01-27 04:38:18.028958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:18.029793 INFO::Using default BPPARAM
2025-01-27 04:38:18.030569 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:18.031852 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:18.076921 INFO::Done
2025-01-27 04:38:18.077786 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:18.080377 INFO::ASW Batch was 0.00347860477657686 prior to batch effect correction and is now -0.0837603443079579 .
2025-01-27 04:38:18.081552 INFO::Total function execution time is  0.065326452255249  s and adjustment time is  0.0489532947540283 s ( 74.94 )
2025-01-27 04:38:18.098468 INFO::Formatting Data.
2025-01-27 04:38:18.099497 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:18.100788 INFO::Removing potential empty rows and columns
2025-01-27 04:38:18.102207 INFO::Found  0  missing values.
2025-01-27 04:38:18.10378 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.
2025-01-27 04:38:18.110604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:18.111539 INFO::Done
2025-01-27 04:38:18.112309 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:18.119657 INFO::Starting hierarchical adjustment
2025-01-27 04:38:18.120845 INFO::Found  2  batches.
2025-01-27 04:38:18.121633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:18.122515 INFO::Using default BPPARAM
2025-01-27 04:38:18.123233 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:18.12464 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:18.148816 INFO::Done
2025-01-27 04:38:18.149719 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:18.154098 INFO::ASW Batch was 0.286872941125885 prior to batch effect correction and is now 0.0190200171827059 .
2025-01-27 04:38:18.155093 INFO::ASW Label was 0.783709368670393 prior to batch effect correction and is now 0.930581576835259 .
2025-01-27 04:38:18.156259 INFO::Total function execution time is  0.057849645614624  s and adjustment time is  0.0282256603240967 s ( 48.79 )
2025-01-27 04:38:18.157577 INFO::Formatting Data.
2025-01-27 04:38:18.158508 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:18.159943 INFO::Removing potential empty rows and columns
2025-01-27 04:38:18.16154 INFO::Found  0  missing values.
2025-01-27 04:38:18.163042 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.
2025-01-27 04:38:18.170126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:18.171051 INFO::Done
2025-01-27 04:38:18.171799 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:18.175888 INFO::Starting hierarchical adjustment
2025-01-27 04:38:18.177027 INFO::Found  2  batches.
2025-01-27 04:38:18.17778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:18.178624 INFO::Using default BPPARAM
2025-01-27 04:38:18.179336 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:18.180703 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:18.204901 INFO::Done
2025-01-27 04:38:18.205798 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:18.209872 INFO::ASW Batch was 0.286872941125885 prior to batch effect correction and is now 0.0190200171827059 .
2025-01-27 04:38:18.210814 INFO::ASW Label was 0.783709368670393 prior to batch effect correction and is now 0.930581576835259 .
2025-01-27 04:38:18.21195 INFO::Total function execution time is  0.0544037818908691  s and adjustment time is  0.0280754566192627 s ( 51.61 )
2025-01-27 04:38:18.540137 INFO::Formatting Data.
2025-01-27 04:38:18.541253 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:18.542532 INFO::Removing potential empty rows and columns
2025-01-27 04:38:18.544096 INFO::Found  0  missing values.
2025-01-27 04:38:18.548645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:18.549541 INFO::Done
2025-01-27 04:38:18.550317 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:18.55373 INFO::Starting hierarchical adjustment
2025-01-27 04:38:18.554842 INFO::Found  3  batches.
2025-01-27 04:38:18.555588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:18.556451 INFO::Using default BPPARAM
2025-01-27 04:38:18.557238 INFO::Processing subtree level 1
2025-01-27 04:38:18.683773 INFO::Adjusting the last 1 batches sequentially
2025-01-27 04:38:18.686143 INFO::Done
2025-01-27 04:38:18.68708 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:18.690533 INFO::ASW Batch was -0.0672811124908734 prior to batch effect correction and is now -0.0672811124908734 .
2025-01-27 04:38:18.69198 INFO::Total function execution time is  0.151911497116089  s and adjustment time is  0.131522417068481 s ( 86.58 )
2025-01-27 04:38:18.693558 INFO::Formatting Data.
2025-01-27 04:38:18.694553 INFO::Typecasting input to dataframe.
2025-01-27 04:38:18.695646 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:18.697038 INFO::Removing potential empty rows and columns
2025-01-27 04:38:18.698726 INFO::Found  0  missing values.
2025-01-27 04:38:18.703391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:18.704349 INFO::Done
2025-01-27 04:38:18.705159 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:18.708055 INFO::Starting hierarchical adjustment
2025-01-27 04:38:18.709246 INFO::Found  3  batches.
2025-01-27 04:38:18.710064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:18.711007 INFO::Using default BPPARAM
2025-01-27 04:38:18.71182 INFO::Processing subtree level 1
2025-01-27 04:38:18.84196 INFO::Adjusting the last 1 batches sequentially
2025-01-27 04:38:18.844401 INFO::Done
2025-01-27 04:38:18.845345 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:18.848889 INFO::ASW Batch was -0.0672811124908734 prior to batch effect correction and is now -0.0672811124908734 .
2025-01-27 04:38:18.850391 INFO::Total function execution time is  0.156779527664185  s and adjustment time is  0.135386228561401 s ( 86.35 )
2025-01-27 04:38:18.869485 INFO::Formatting Data.
2025-01-27 04:38:18.870592 INFO::Typecasting input to dataframe.
2025-01-27 04:38:18.871828 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:18.873119 INFO::Removing potential empty rows and columns
2025-01-27 04:38:18.874719 INFO::Found  0  missing values.
2025-01-27 04:38:18.879196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:18.880082 INFO::Done
2025-01-27 04:38:18.880878 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:18.883668 INFO::Starting hierarchical adjustment
2025-01-27 04:38:18.884783 INFO::Found  3  batches.
2025-01-27 04:38:18.885566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:18.886483 INFO::Using default BPPARAM
2025-01-27 04:38:18.887271 INFO::Processing subtree level 1
2025-01-27 04:38:19.010268 INFO::Adjusting the last 1 batches sequentially
2025-01-27 04:38:19.012846 INFO::Done
2025-01-27 04:38:19.013855 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:19.017669 INFO::ASW Batch was -0.105561743786992 prior to batch effect correction and is now -0.105561743786992 .
2025-01-27 04:38:19.019194 INFO::Total function execution time is  0.149714946746826  s and adjustment time is  0.128281116485596 s ( 85.68 )
2025-01-27 04:38:19.213806 INFO::Formatting Data.
2025-01-27 04:38:19.214931 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:19.216555 INFO::Removing potential empty rows and columns
2025-01-27 04:38:19.221137 INFO::Found  1000  missing values.
2025-01-27 04:38:19.262045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:19.263106 INFO::Done
2025-01-27 04:38:19.263947 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:19.272333 INFO::Starting hierarchical adjustment
2025-01-27 04:38:19.273592 INFO::Found  10  batches.
2025-01-27 04:38:19.274481 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:19.275419 INFO::Using default BPPARAM
2025-01-27 04:38:19.276232 INFO::Processing subtree level 1
2025-01-27 04:38:19.484553 INFO::Processing subtree level 2
2025-01-27 04:38:19.707055 INFO::Adjusting the last 1 batches sequentially
2025-01-27 04:38:19.709663 INFO::Done
2025-01-27 04:38:19.710597 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:19.719106 INFO::ASW Batch was 0.536139592325518 prior to batch effect correction and is now 0.536139592325518 .
2025-01-27 04:38:19.720124 INFO::ASW Label was 0.295253794638173 prior to batch effect correction and is now 0.295253794638173 .
2025-01-27 04:38:19.721497 INFO::Total function execution time is  0.507728576660156  s and adjustment time is  0.436315298080444 s ( 85.93 )
2025-01-27 04:38:19.722778 INFO::Formatting Data.
2025-01-27 04:38:19.723696 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:19.72569 INFO::Removing potential empty rows and columns
2025-01-27 04:38:19.730511 INFO::Found  1000  missing values.
2025-01-27 04:38:19.762737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:19.76371 INFO::Done
2025-01-27 04:38:19.76455 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:19.772673 INFO::Starting hierarchical adjustment
2025-01-27 04:38:19.773903 INFO::Found  10  batches.
2025-01-27 04:38:21.118755 INFO::Set up parallel execution backend with 2 workers
2025-01-27 04:38:21.122725 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-27 04:38:22.632012 INFO::Adjusting the last 2 batches sequentially
2025-01-27 04:38:22.634824 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-27 04:38:22.662259 INFO::Done
2025-01-27 04:38:22.663184 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:22.670277 INFO::ASW Batch was 0.536139592325518 prior to batch effect correction and is now 0.536139592325518 .
2025-01-27 04:38:22.671203 INFO::ASW Label was 0.295253794638173 prior to batch effect correction and is now 0.295253794638173 .
2025-01-27 04:38:22.672303 INFO::Total function execution time is  2.9495701789856  s and adjustment time is  2.88859701156616 s ( 97.93 )
2025-01-27 04:38:22.865274 INFO::Formatting Data.
2025-01-27 04:38:22.866539 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:22.868074 INFO::Removing potential empty rows and columns
2025-01-27 04:38:22.870026 INFO::Found  0  missing values.
2025-01-27 04:38:22.876714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:22.877715 INFO::Done
2025-01-27 04:38:22.878647 INFO::Acquiring quality metrics before batch effect correction.
2025-01-27 04:38:22.883052 INFO::Starting hierarchical adjustment
2025-01-27 04:38:22.884321 INFO::Found  3  batches.
2025-01-27 04:38:22.885258 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-27 04:38:22.886258 INFO::Using default BPPARAM
2025-01-27 04:38:22.887134 INFO::Processing subtree level 1
2025-01-27 04:38:23.024004 INFO::Adjusting the last 1 batches sequentially
2025-01-27 04:38:23.026588 INFO::Done
2025-01-27 04:38:23.027591 INFO::Acquiring quality metrics after batch effect correction.
2025-01-27 04:38:23.03259 INFO::ASW Batch was 0.200870310638433 prior to batch effect correction and is now -0.13507733366272 .
2025-01-27 04:38:23.033631 INFO::ASW Label was -0.201114606983816 prior to batch effect correction and is now 0.0885864129946978 .
2025-01-27 04:38:23.035065 INFO::Total function execution time is  0.169831037521362  s and adjustment time is  0.142516136169434 s ( 83.92 )
2025-01-27 04:38:23.222993 INFO::Formatting Data.
2025-01-27 04:38:23.22406 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.22538 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.22699 INFO::Found  2  missing values.
2025-01-27 04:38:23.231476 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.232364 INFO::Done
2025-01-27 04:38:23.274742 INFO::Found NA in Reference column
2025-01-27 04:38:23.289401 INFO::Require at least two references per batch.
2025-01-27 04:38:23.319712 INFO::Formatting Data.
2025-01-27 04:38:23.32071 INFO::Recognized SummarizedExperiment
2025-01-27 04:38:23.321472 INFO::Typecasting input to dataframe.
2025-01-27 04:38:23.336066 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.337837 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.343936 INFO::Found  0  missing values.
2025-01-27 04:38:23.355388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.356296 INFO::Done
2025-01-27 04:38:23.37923 INFO::Formatting Data.
2025-01-27 04:38:23.380253 INFO::Recognized SummarizedExperiment
2025-01-27 04:38:23.381083 INFO::Typecasting input to dataframe.
2025-01-27 04:38:23.408559 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.410318 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.416469 INFO::Found  0  missing values.
2025-01-27 04:38:23.435328 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.436247 INFO::Done
2025-01-27 04:38:23.458732 INFO::Formatting Data.
2025-01-27 04:38:23.459745 INFO::Recognized SummarizedExperiment
2025-01-27 04:38:23.460588 INFO::Typecasting input to dataframe.
2025-01-27 04:38:23.48645 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.487893 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.489565 INFO::Found  0  missing values.
2025-01-27 04:38:23.490922 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.
2025-01-27 04:38:23.497892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.498842 INFO::Done
2025-01-27 04:38:23.525375 INFO::Formatting Data.
2025-01-27 04:38:23.526663 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.527991 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.52955 INFO::Found  0  missing values.
2025-01-27 04:38:23.534023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.53494 INFO::Done
2025-01-27 04:38:23.552435 INFO::Formatting Data.
2025-01-27 04:38:23.553525 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.554768 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.556195 INFO::Found  0  missing values.
2025-01-27 04:38:23.560563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.561464 INFO::Done
2025-01-27 04:38:23.605832 INFO::Formatting Data.
2025-01-27 04:38:23.606906 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.608377 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.610159 INFO::Found  1  missing values.
2025-01-27 04:38:23.614063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.614987 INFO::Done
2025-01-27 04:38:23.643118 INFO::Formatting Data.
2025-01-27 04:38:23.644171 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.645492 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.646877 INFO::Found  2  missing values.
2025-01-27 04:38:23.648163 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.
2025-01-27 04:38:23.651628 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.652494 INFO::Done
2025-01-27 04:38:23.668242 INFO::Formatting Data.
2025-01-27 04:38:23.669335 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.670602 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.671967 INFO::Found  2  missing values.
2025-01-27 04:38:23.674473 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.675307 INFO::Done
2025-01-27 04:38:23.691373 INFO::Formatting Data.
2025-01-27 04:38:23.692427 INFO::Typecasting input to dataframe.
2025-01-27 04:38:23.69363 INFO::Replacing NaNs with NAs.
2025-01-27 04:38:23.694881 INFO::Removing potential empty rows and columns
2025-01-27 04:38:23.696398 INFO::Found  0  missing values.
2025-01-27 04:38:23.700884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-27 04:38:23.701787 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	31.488	1.554	22.877
compute_asw	0.033	0.004	0.038
count_existing	0.020	0.000	0.021
generate_data_covariables	0.017	0.000	0.017
generate_dataset	0.012	0.004	0.016