Back to Multiple platform build/check report for BioC 3.21:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4658
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4455
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R 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

Package 159/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.3.6  (landing page)
Yannis Schumann
Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: devel
git_last_commit: ac84667
git_last_commit_date: 2025-01-22 02:25:44 -0500 (Wed, 22 Jan 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for BERT on nebbiolo1

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

raw results


Summary

Package: BERT
Version: 1.3.6
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.6.tar.gz
StartedAt: 2025-01-24 20:16:49 -0500 (Fri, 24 Jan 2025)
EndedAt: 2025-01-24 20:18:24 -0500 (Fri, 24 Jan 2025)
EllapsedTime: 95.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BERT.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 26.111  1.744   19.49
* 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:
  2025-01-24 20:17:53.986055 INFO::Typecasting input to dataframe.
  2025-01-24 20:17:53.986928 INFO::Replacing NaNs with NAs.
  2025-01-24 20:17:53.987885 INFO::Removing potential empty rows and columns
  2025-01-24 20:17:53.989054 INFO::Found  0  missing values.
  2025-01-24 20:17:53.99252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
  2025-01-24 20:17:53.993155 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 re-building of vignette outputs ... OK
* 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/bbs-3.21-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.3.6’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
2025-01-24 20:17:43.932096 INFO::Formatting Data.
2025-01-24 20:17:43.933429 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:43.944216 INFO::Removing potential empty rows and columns
2025-01-24 20:17:44.216197 INFO::Found  0  missing values.
2025-01-24 20:17:44.220683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:44.221612 INFO::Done
2025-01-24 20:17:44.222362 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:44.237514 INFO::Starting hierarchical adjustment
2025-01-24 20:17:44.238844 INFO::Found  3  batches.
2025-01-24 20:17:44.23959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:44.241124 INFO::Using default BPPARAM
2025-01-24 20:17:44.241807 INFO::Processing subtree level 1
2025-01-24 20:17:44.358373 INFO::Adjusting the last 1 batches sequentially
2025-01-24 20:17:44.360428 INFO::Done
2025-01-24 20:17:44.361229 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:44.364138 INFO::ASW Batch was -0.0808602022889864 prior to batch effect correction and is now -0.0808602022889864 .
2025-01-24 20:17:44.365413 INFO::Total function execution time is  0.433851957321167  s and adjustment time is  0.121905088424683 s ( 28.1 )
2025-01-24 20:17:44.379841 INFO::Formatting Data.
2025-01-24 20:17:44.380687 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:44.381663 INFO::Removing potential empty rows and columns
2025-01-24 20:17:44.382846 INFO::Found  0  missing values.
2025-01-24 20:17:44.383887 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.
2025-01-24 20:17:44.395141 INFO::Formatting Data.
2025-01-24 20:17:44.395926 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:44.396863 INFO::Removing potential empty rows and columns
2025-01-24 20:17:44.397956 INFO::Found  0  missing values.
2025-01-24 20:17:44.398919 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.
2025-01-24 20:17:44.415688 INFO::Formatting Data.
2025-01-24 20:17:44.416535 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:44.417495 INFO::Removing potential empty rows and columns
2025-01-24 20:17:44.418598 INFO::Found  0  missing values.
2025-01-24 20:17:44.419595 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.
2025-01-24 20:17:44.424178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:44.424769 INFO::Done
2025-01-24 20:17:44.425322 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:44.427398 INFO::Starting hierarchical adjustment
2025-01-24 20:17:44.42813 INFO::Found  2  batches.
2025-01-24 20:17:44.4287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:44.429392 INFO::Using default BPPARAM
2025-01-24 20:17:44.429949 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:44.430904 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:44.45362 INFO::Done
2025-01-24 20:17:44.454396 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:44.456594 INFO::ASW Batch was 0.0538195619662387 prior to batch effect correction and is now -0.112544255316871 .
2025-01-24 20:17:44.457459 INFO::Total function execution time is  0.0418524742126465  s and adjustment time is  0.0255937576293945 s ( 61.15 )
2025-01-24 20:17:44.460302 INFO::Formatting Data.
2025-01-24 20:17:44.460968 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:44.469977 INFO::Formatting Data.
2025-01-24 20:17:44.470758 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:44.471687 INFO::Removing potential empty rows and columns
2025-01-24 20:17:44.472763 INFO::Found  0  missing values.
2025-01-24 20:17:44.500807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:44.501886 INFO::Done
2025-01-24 20:17:44.502448 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:44.504492 INFO::Starting hierarchical adjustment
2025-01-24 20:17:44.505254 INFO::Found  2  batches.
2025-01-24 20:17:44.505775 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:44.506393 INFO::Using default BPPARAM
2025-01-24 20:17:44.506896 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:44.507815 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:44.521872 INFO::Done
2025-01-24 20:17:44.522573 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:44.524597 INFO::ASW Batch was 0.0158074646949027 prior to batch effect correction and is now -0.111512982434259 .
2025-01-24 20:17:44.525391 INFO::Total function execution time is  0.0554745197296143  s and adjustment time is  0.0167779922485352 s ( 30.24 )
2025-01-24 20:17:44.526451 INFO::Formatting Data.
2025-01-24 20:17:44.527047 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:44.52791 INFO::Removing potential empty rows and columns
2025-01-24 20:17:44.528949 INFO::Found  0  missing values.
2025-01-24 20:17:44.531791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:44.532345 INFO::Done
2025-01-24 20:17:44.532884 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:44.535058 INFO::Starting hierarchical adjustment
2025-01-24 20:17:44.535788 INFO::Found  2  batches.
2025-01-24 20:17:44.536319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:44.536929 INFO::Using default BPPARAM
2025-01-24 20:17:44.537465 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:44.53842 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:44.553667 INFO::Done
2025-01-24 20:17:44.554424 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:44.5566 INFO::ASW Batch was 0.0158074646949027 prior to batch effect correction and is now -0.111512982434259 .
2025-01-24 20:17:44.557472 INFO::Total function execution time is  0.030998706817627  s and adjustment time is  0.0179920196533203 s ( 58.04 )
2025-01-24 20:17:47.594141 INFO::Formatting Data.
2025-01-24 20:17:47.595064 INFO::Recognized SummarizedExperiment
2025-01-24 20:17:47.595623 INFO::Typecasting input to dataframe.
2025-01-24 20:17:47.625673 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:47.627259 INFO::Removing potential empty rows and columns
2025-01-24 20:17:47.631065 INFO::Found  0  missing values.
2025-01-24 20:17:47.638763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:47.639752 INFO::Done
2025-01-24 20:17:47.640386 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:47.644102 INFO::Starting hierarchical adjustment
2025-01-24 20:17:47.644824 INFO::Found  2  batches.
2025-01-24 20:17:47.645335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:47.646472 INFO::Using default BPPARAM
2025-01-24 20:17:47.646986 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:47.647963 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:47.707226 INFO::Done
2025-01-24 20:17:47.708036 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:47.711791 INFO::ASW Batch was 0.0406923382023358 prior to batch effect correction and is now -0.0903127072630824 .
2025-01-24 20:17:47.712663 INFO::Total function execution time is  0.118839740753174  s and adjustment time is  0.0624990463256836 s ( 52.59 )
2025-01-24 20:17:47.732183 INFO::Formatting Data.
2025-01-24 20:17:47.733033 INFO::Recognized SummarizedExperiment
2025-01-24 20:17:47.73366 INFO::Typecasting input to dataframe.
2025-01-24 20:17:47.743183 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:47.744394 INFO::Removing potential empty rows and columns
2025-01-24 20:17:47.748342 INFO::Found  0  missing values.
2025-01-24 20:17:47.755662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:47.756294 INFO::Done
2025-01-24 20:17:47.756837 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:47.760561 INFO::Starting hierarchical adjustment
2025-01-24 20:17:47.761361 INFO::Found  2  batches.
2025-01-24 20:17:47.761911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:47.76253 INFO::Using default BPPARAM
2025-01-24 20:17:47.763056 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:47.764081 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:47.789968 INFO::Done
2025-01-24 20:17:47.790779 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:47.794567 INFO::ASW Batch was 0.0460817004747777 prior to batch effect correction and is now 0.0460817004747777 .
2025-01-24 20:17:47.795675 INFO::Total function execution time is  0.0634589195251465  s and adjustment time is  0.0287415981292725 s ( 45.29 )
2025-01-24 20:17:47.815968 INFO::Formatting Data.
2025-01-24 20:17:47.81694 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:47.818027 INFO::Removing potential empty rows and columns
2025-01-24 20:17:47.819251 INFO::Found  0  missing values.
2025-01-24 20:17:47.822644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:47.823305 INFO::Done
2025-01-24 20:17:47.823857 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:47.826131 INFO::Starting hierarchical adjustment
2025-01-24 20:17:47.826886 INFO::Found  3  batches.
2025-01-24 20:17:47.82744 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:47.828079 INFO::Using default BPPARAM
2025-01-24 20:17:47.828633 INFO::Processing subtree level 1
2025-01-24 20:17:47.979582 INFO::Adjusting the last 1 batches sequentially
2025-01-24 20:17:47.982159 INFO::Done
2025-01-24 20:17:47.983087 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:47.986423 INFO::ASW Batch was 0.0191846710188708 prior to batch effect correction and is now -0.139022160700655 .
2025-01-24 20:17:47.987657 INFO::Total function execution time is  0.171727418899536  s and adjustment time is  0.155359745025635 s ( 90.47 )
2025-01-24 20:17:48.005294 INFO::Skipping initial DF formatting
2025-01-24 20:17:48.006323 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:48.011135 INFO::Starting hierarchical adjustment
2025-01-24 20:17:48.012023 INFO::Found  5  batches.
2025-01-24 20:17:48.012608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:48.013325 INFO::Using default BPPARAM
2025-01-24 20:17:48.013885 INFO::Processing subtree level 1
2025-01-24 20:17:48.168716 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:48.170852 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:48.192985 INFO::Done
2025-01-24 20:17:48.194081 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:48.199049 INFO::ASW Batch was 0.554449797168841 prior to batch effect correction and is now 0.554449797168841 .
2025-01-24 20:17:48.199874 INFO::ASW Label was 0.352982931519239 prior to batch effect correction and is now 0.352982931519239 .
2025-01-24 20:17:48.200905 INFO::Total function execution time is  0.195807218551636  s and adjustment time is  0.181063413619995 s ( 92.47 )
2025-01-24 20:17:48.221278 INFO::Formatting Data.
2025-01-24 20:17:48.222271 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:48.223316 INFO::Removing potential empty rows and columns
2025-01-24 20:17:48.224412 INFO::Found  0  missing values.
2025-01-24 20:17:48.229061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:48.229692 INFO::Done
2025-01-24 20:17:48.230264 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:48.23346 INFO::Starting hierarchical adjustment
2025-01-24 20:17:48.234253 INFO::Found  5  batches.
2025-01-24 20:17:48.234815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:48.235508 INFO::Using default BPPARAM
2025-01-24 20:17:48.236056 INFO::Processing subtree level 1
2025-01-24 20:17:48.361422 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:48.363296 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:48.380086 INFO::Done
2025-01-24 20:17:48.38092 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:48.38445 INFO::ASW Batch was 0.33793181818867 prior to batch effect correction and is now -0.0375326803430514 .
2025-01-24 20:17:48.38514 INFO::ASW Label was 0.50790312050974 prior to batch effect correction and is now 0.750056216346258 .
2025-01-24 20:17:48.38601 INFO::Total function execution time is  0.164901733398438  s and adjustment time is  0.145980596542358 s ( 88.53 )
2025-01-24 20:17:48.386923 INFO::Formatting Data.
2025-01-24 20:17:48.387596 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:48.388568 INFO::Removing potential empty rows and columns
2025-01-24 20:17:48.3896 INFO::Found  0  missing values.
2025-01-24 20:17:48.393781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:48.394376 INFO::Done
2025-01-24 20:17:48.394915 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:48.397969 INFO::Starting hierarchical adjustment
2025-01-24 20:17:48.398708 INFO::Found  5  batches.
2025-01-24 20:17:48.399268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:48.399924 INFO::Using default BPPARAM
2025-01-24 20:17:48.40063 INFO::Processing subtree level 1
2025-01-24 20:17:48.516952 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:48.518624 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:48.535355 INFO::Done
2025-01-24 20:17:48.536301 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:48.539816 INFO::ASW Batch was 0.33793181818867 prior to batch effect correction and is now -0.0375326803430514 .
2025-01-24 20:17:48.540532 INFO::ASW Label was 0.50790312050974 prior to batch effect correction and is now 0.750056216346258 .
2025-01-24 20:17:48.541437 INFO::Total function execution time is  0.154526472091675  s and adjustment time is  0.136727094650269 s ( 88.48 )
2025-01-24 20:17:48.555842 INFO::Formatting Data.
2025-01-24 20:17:48.55678 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:48.557775 INFO::Removing potential empty rows and columns
2025-01-24 20:17:48.558821 INFO::Found  0  missing values.
2025-01-24 20:17:48.563305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:48.5639 INFO::Done
2025-01-24 20:17:48.564453 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:48.567747 INFO::Starting hierarchical adjustment
2025-01-24 20:17:48.568536 INFO::Found  5  batches.
2025-01-24 20:17:48.56908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:48.569757 INFO::Using default BPPARAM
2025-01-24 20:17:48.570332 INFO::Processing subtree level 1
2025-01-24 20:17:48.699166 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:48.701285 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:48.718162 INFO::Done
2025-01-24 20:17:48.718962 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:48.722303 INFO::ASW Batch was 0.256553417257209 prior to batch effect correction and is now -0.0757641138695152 .
2025-01-24 20:17:48.722974 INFO::ASW Label was 0.404233564198949 prior to batch effect correction and is now 0.755221343942112 .
2025-01-24 20:17:48.723856 INFO::Total function execution time is  0.168116569519043  s and adjustment time is  0.149763107299805 s ( 89.08 )
2025-01-24 20:17:48.724736 INFO::Formatting Data.
2025-01-24 20:17:48.725372 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:48.726309 INFO::Removing potential empty rows and columns
2025-01-24 20:17:48.727317 INFO::Found  0  missing values.
2025-01-24 20:17:48.731595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:48.732166 INFO::Done
2025-01-24 20:17:48.732714 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:48.735845 INFO::Starting hierarchical adjustment
2025-01-24 20:17:48.736571 INFO::Found  5  batches.
2025-01-24 20:17:48.737115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:48.737781 INFO::Using default BPPARAM
2025-01-24 20:17:48.738336 INFO::Processing subtree level 1
2025-01-24 20:17:48.860704 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:48.862302 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:48.878012 INFO::Done
2025-01-24 20:17:48.878778 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:48.881963 INFO::ASW Batch was 0.256553417257209 prior to batch effect correction and is now -0.0757641138695152 .
2025-01-24 20:17:48.882609 INFO::ASW Label was 0.404233564198949 prior to batch effect correction and is now 0.755221343942112 .
2025-01-24 20:17:48.883434 INFO::Total function execution time is  0.15871262550354  s and adjustment time is  0.141562223434448 s ( 89.19 )
2025-01-24 20:17:48.896738 INFO::Formatting Data.
2025-01-24 20:17:48.897522 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:48.898471 INFO::Removing potential empty rows and columns
2025-01-24 20:17:48.8995 INFO::Found  0  missing values.
2025-01-24 20:17:48.902251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:48.902802 INFO::Done
2025-01-24 20:17:48.903339 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:48.90645 INFO::Starting hierarchical adjustment
2025-01-24 20:17:48.907174 INFO::Found  2  batches.
2025-01-24 20:17:48.907711 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:48.908379 INFO::Using default BPPARAM
2025-01-24 20:17:48.908919 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:48.909842 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:48.92428 INFO::Done
2025-01-24 20:17:48.924963 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:49.060638 INFO::ASW Batch was 0.655389779546458 prior to batch effect correction and is now 0.0115841372965455 .
2025-01-24 20:17:49.062343 INFO::ASW Label was 0.412119752782526 prior to batch effect correction and is now 0.866462110460418 .
2025-01-24 20:17:49.063193 INFO::Total function execution time is  0.166527271270752  s and adjustment time is  0.0172348022460938 s ( 10.35 )
2025-01-24 20:17:49.063944 INFO::Formatting Data.
2025-01-24 20:17:49.064542 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:49.065454 INFO::Removing potential empty rows and columns
2025-01-24 20:17:49.066443 INFO::Found  0  missing values.
2025-01-24 20:17:49.06907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:49.069675 INFO::Done
2025-01-24 20:17:49.070187 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:49.073014 INFO::Starting hierarchical adjustment
2025-01-24 20:17:49.073764 INFO::Found  2  batches.
2025-01-24 20:17:49.074326 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:49.07493 INFO::Using default BPPARAM
2025-01-24 20:17:49.07554 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:49.076576 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:49.091883 INFO::Done
2025-01-24 20:17:49.092597 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:49.095508 INFO::ASW Batch was 0.655389779546458 prior to batch effect correction and is now 0.0115841372965455 .
2025-01-24 20:17:49.096064 INFO::ASW Label was 0.412119752782526 prior to batch effect correction and is now 0.866462110460418 .
2025-01-24 20:17:49.096848 INFO::Total function execution time is  0.0329034328460693  s and adjustment time is  0.0182967185974121 s ( 55.61 )
2025-01-24 20:17:49.107422 INFO::Formatting Data.
2025-01-24 20:17:49.108122 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:49.108964 INFO::Removing potential empty rows and columns
2025-01-24 20:17:49.109812 INFO::Found  0  missing values.
2025-01-24 20:17:49.11176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:49.112321 INFO::Done
2025-01-24 20:17:49.112802 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:49.114507 INFO::Starting hierarchical adjustment
2025-01-24 20:17:49.115147 INFO::Found  2  batches.
2025-01-24 20:17:49.115639 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:49.116209 INFO::Using default BPPARAM
2025-01-24 20:17:49.116695 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:49.117555 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:49.146378 INFO::Done
2025-01-24 20:17:49.147054 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:49.148906 INFO::ASW Batch was 0.0822542972866885 prior to batch effect correction and is now -0.169770179662368 .
2025-01-24 20:17:49.149674 INFO::Total function execution time is  0.0423209667205811  s and adjustment time is  0.0313320159912109 s ( 74.03 )
2025-01-24 20:17:49.16075 INFO::Formatting Data.
2025-01-24 20:17:49.161474 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:49.162322 INFO::Removing potential empty rows and columns
2025-01-24 20:17:49.163267 INFO::Found  0  missing values.
2025-01-24 20:17:49.164342 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.
2025-01-24 20:17:49.168605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:49.169196 INFO::Done
2025-01-24 20:17:49.169779 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:49.172526 INFO::Starting hierarchical adjustment
2025-01-24 20:17:49.173189 INFO::Found  2  batches.
2025-01-24 20:17:49.173703 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:49.174285 INFO::Using default BPPARAM
2025-01-24 20:17:49.174774 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:49.17569 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:49.190862 INFO::Done
2025-01-24 20:17:49.191506 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:49.194277 INFO::ASW Batch was 0.410741752028069 prior to batch effect correction and is now -0.0342095384877348 .
2025-01-24 20:17:49.194869 INFO::ASW Label was 0.554604219222781 prior to batch effect correction and is now 0.92073330336463 .
2025-01-24 20:17:49.195735 INFO::Total function execution time is  0.0350179672241211  s and adjustment time is  0.0178022384643555 s ( 50.84 )
2025-01-24 20:17:49.196535 INFO::Formatting Data.
2025-01-24 20:17:49.197156 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:49.198022 INFO::Removing potential empty rows and columns
2025-01-24 20:17:49.198956 INFO::Found  0  missing values.
2025-01-24 20:17:49.199796 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.
2025-01-24 20:17:49.20393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:49.204448 INFO::Done
2025-01-24 20:17:49.204936 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:49.207586 INFO::Starting hierarchical adjustment
2025-01-24 20:17:49.208249 INFO::Found  2  batches.
2025-01-24 20:17:49.208752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:49.209363 INFO::Using default BPPARAM
2025-01-24 20:17:49.209864 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:49.210727 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:49.225925 INFO::Done
2025-01-24 20:17:49.226607 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:49.229461 INFO::ASW Batch was 0.410741752028069 prior to batch effect correction and is now -0.0342095384877348 .
2025-01-24 20:17:49.230089 INFO::ASW Label was 0.554604219222781 prior to batch effect correction and is now 0.92073330336463 .
2025-01-24 20:17:49.230982 INFO::Total function execution time is  0.0344524383544922  s and adjustment time is  0.0178012847900391 s ( 51.67 )
2025-01-24 20:17:49.423135 INFO::Formatting Data.
2025-01-24 20:17:49.423976 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:49.424892 INFO::Removing potential empty rows and columns
2025-01-24 20:17:49.425887 INFO::Found  0  missing values.
2025-01-24 20:17:49.428781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:49.429318 INFO::Done
2025-01-24 20:17:49.429817 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:49.431776 INFO::Starting hierarchical adjustment
2025-01-24 20:17:49.432476 INFO::Found  3  batches.
2025-01-24 20:17:49.432992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:49.433631 INFO::Using default BPPARAM
2025-01-24 20:17:49.434156 INFO::Processing subtree level 1
2025-01-24 20:17:49.542959 INFO::Adjusting the last 1 batches sequentially
2025-01-24 20:17:49.545212 INFO::Done
2025-01-24 20:17:49.545917 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:49.548768 INFO::ASW Batch was -0.0526426613825111 prior to batch effect correction and is now -0.0526426613825111 .
2025-01-24 20:17:49.549839 INFO::Total function execution time is  0.126720190048218  s and adjustment time is  0.112848281860352 s ( 89.05 )
2025-01-24 20:17:49.551049 INFO::Formatting Data.
2025-01-24 20:17:49.551807 INFO::Typecasting input to dataframe.
2025-01-24 20:17:49.552667 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:49.553699 INFO::Removing potential empty rows and columns
2025-01-24 20:17:49.554979 INFO::Found  0  missing values.
2025-01-24 20:17:49.558355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:49.558985 INFO::Done
2025-01-24 20:17:49.55963 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:49.561919 INFO::Starting hierarchical adjustment
2025-01-24 20:17:49.562738 INFO::Found  3  batches.
2025-01-24 20:17:49.563364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:49.56405 INFO::Using default BPPARAM
2025-01-24 20:17:49.564707 INFO::Processing subtree level 1
2025-01-24 20:17:49.669638 INFO::Adjusting the last 1 batches sequentially
2025-01-24 20:17:49.671873 INFO::Done
2025-01-24 20:17:49.672701 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:49.675568 INFO::ASW Batch was -0.0526426613825111 prior to batch effect correction and is now -0.0526426613825111 .
2025-01-24 20:17:49.676682 INFO::Total function execution time is  0.125602006912231  s and adjustment time is  0.109260320663452 s ( 86.99 )
2025-01-24 20:17:49.691823 INFO::Formatting Data.
2025-01-24 20:17:49.692754 INFO::Typecasting input to dataframe.
2025-01-24 20:17:49.693803 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:49.694871 INFO::Removing potential empty rows and columns
2025-01-24 20:17:49.696135 INFO::Found  0  missing values.
2025-01-24 20:17:49.699477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:49.700109 INFO::Done
2025-01-24 20:17:49.70072 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:49.702932 INFO::Starting hierarchical adjustment
2025-01-24 20:17:49.703762 INFO::Found  3  batches.
2025-01-24 20:17:49.704355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:49.705046 INFO::Using default BPPARAM
2025-01-24 20:17:49.705654 INFO::Processing subtree level 1
2025-01-24 20:17:49.808998 INFO::Adjusting the last 1 batches sequentially
2025-01-24 20:17:49.811384 INFO::Done
2025-01-24 20:17:49.81224 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:49.815472 INFO::ASW Batch was -0.120501663619121 prior to batch effect correction and is now -0.120501663619121 .
2025-01-24 20:17:49.816763 INFO::Total function execution time is  0.124936819076538  s and adjustment time is  0.107733964920044 s ( 86.23 )
2025-01-24 20:17:49.991809 INFO::Formatting Data.
2025-01-24 20:17:49.992798 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:49.994071 INFO::Removing potential empty rows and columns
2025-01-24 20:17:49.996991 INFO::Found  1000  missing values.
2025-01-24 20:17:50.017266 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:50.018096 INFO::Done
2025-01-24 20:17:50.01874 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:50.024496 INFO::Starting hierarchical adjustment
2025-01-24 20:17:50.025377 INFO::Found  10  batches.
2025-01-24 20:17:50.025983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:50.026707 INFO::Using default BPPARAM
2025-01-24 20:17:50.027312 INFO::Processing subtree level 1
2025-01-24 20:17:50.188254 INFO::Processing subtree level 2
2025-01-24 20:17:50.373789 INFO::Adjusting the last 1 batches sequentially
2025-01-24 20:17:50.37688 INFO::Done
2025-01-24 20:17:50.377946 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:50.386144 INFO::ASW Batch was 0.525037108985076 prior to batch effect correction and is now 0.525037108985076 .
2025-01-24 20:17:50.387273 INFO::ASW Label was 0.294091450305242 prior to batch effect correction and is now 0.294091450305242 .
2025-01-24 20:17:50.388783 INFO::Total function execution time is  0.396942377090454  s and adjustment time is  0.351621150970459 s ( 88.58 )
2025-01-24 20:17:50.39017 INFO::Formatting Data.
2025-01-24 20:17:50.391184 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:50.39329 INFO::Removing potential empty rows and columns
2025-01-24 20:17:50.397347 INFO::Found  1000  missing values.
2025-01-24 20:17:50.423074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:50.424095 INFO::Done
2025-01-24 20:17:50.42479 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:50.431168 INFO::Starting hierarchical adjustment
2025-01-24 20:17:50.432156 INFO::Found  10  batches.
2025-01-24 20:17:51.838798 INFO::Set up parallel execution backend with 2 workers
2025-01-24 20:17:51.840824 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-24 20:17:53.249249 INFO::Adjusting the last 2 batches sequentially
2025-01-24 20:17:53.2513 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 20:17:53.268649 INFO::Done
2025-01-24 20:17:53.269396 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:53.27477 INFO::ASW Batch was 0.525037108985076 prior to batch effect correction and is now 0.525037108985076 .
2025-01-24 20:17:53.275389 INFO::ASW Label was 0.294091450305242 prior to batch effect correction and is now 0.294091450305242 .
2025-01-24 20:17:53.276238 INFO::Total function execution time is  2.88618397712708  s and adjustment time is  2.83669090270996 s ( 98.29 )
2025-01-24 20:17:53.420143 INFO::Formatting Data.
2025-01-24 20:17:53.420996 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.421927 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.423024 INFO::Found  0  missing values.
2025-01-24 20:17:53.42661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.427185 INFO::Done
2025-01-24 20:17:53.42773 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 20:17:53.430421 INFO::Starting hierarchical adjustment
2025-01-24 20:17:53.43112 INFO::Found  3  batches.
2025-01-24 20:17:53.431657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 20:17:53.432283 INFO::Using default BPPARAM
2025-01-24 20:17:53.432821 INFO::Processing subtree level 1
2025-01-24 20:17:53.543886 INFO::Adjusting the last 1 batches sequentially
2025-01-24 20:17:53.545969 INFO::Done
2025-01-24 20:17:53.547142 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 20:17:53.550984 INFO::ASW Batch was 0.156747482641981 prior to batch effect correction and is now -0.125169421761052 .
2025-01-24 20:17:53.551756 INFO::ASW Label was -0.187319142045692 prior to batch effect correction and is now -0.0604115392320706 .
2025-01-24 20:17:53.552788 INFO::Total function execution time is  0.13267970085144  s and adjustment time is  0.114932537078857 s ( 86.62 )
2025-01-24 20:17:53.669606 INFO::Formatting Data.
2025-01-24 20:17:53.670502 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.671425 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.672471 INFO::Found  2  missing values.
2025-01-24 20:17:53.675238 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.675767 INFO::Done
2025-01-24 20:17:53.701921 INFO::Found NA in Reference column
2025-01-24 20:17:53.710895 INFO::Require at least two references per batch.
2025-01-24 20:17:53.731139 INFO::Formatting Data.
2025-01-24 20:17:53.731913 INFO::Recognized SummarizedExperiment
2025-01-24 20:17:53.732462 INFO::Typecasting input to dataframe.
2025-01-24 20:17:53.742583 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.743745 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.747006 INFO::Found  0  missing values.
2025-01-24 20:17:53.753438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.754048 INFO::Done
2025-01-24 20:17:53.768282 INFO::Formatting Data.
2025-01-24 20:17:53.76901 INFO::Recognized SummarizedExperiment
2025-01-24 20:17:53.769531 INFO::Typecasting input to dataframe.
2025-01-24 20:17:53.786144 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.787377 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.790745 INFO::Found  0  missing values.
2025-01-24 20:17:53.800925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.801547 INFO::Done
2025-01-24 20:17:53.815903 INFO::Formatting Data.
2025-01-24 20:17:53.816619 INFO::Recognized SummarizedExperiment
2025-01-24 20:17:53.817144 INFO::Typecasting input to dataframe.
2025-01-24 20:17:53.833154 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.834248 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.835297 INFO::Found  0  missing values.
2025-01-24 20:17:53.836251 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.
2025-01-24 20:17:53.840642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.841235 INFO::Done
2025-01-24 20:17:53.850844 INFO::Formatting Data.
2025-01-24 20:17:53.851626 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.852485 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.853482 INFO::Found  0  missing values.
2025-01-24 20:17:53.856151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.856675 INFO::Done
2025-01-24 20:17:53.868539 INFO::Formatting Data.
2025-01-24 20:17:53.869449 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.87043 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.871617 INFO::Found  0  missing values.
2025-01-24 20:17:53.87492 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.875582 INFO::Done
2025-01-24 20:17:53.909019 INFO::Formatting Data.
2025-01-24 20:17:53.910052 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.911251 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.912548 INFO::Found  1  missing values.
2025-01-24 20:17:53.915384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.91597 INFO::Done
2025-01-24 20:17:53.947226 INFO::Formatting Data.
2025-01-24 20:17:53.948285 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.949276 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.950368 INFO::Found  2  missing values.
2025-01-24 20:17:53.951396 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.
2025-01-24 20:17:53.954651 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.955451 INFO::Done
2025-01-24 20:17:53.967751 INFO::Formatting Data.
2025-01-24 20:17:53.968658 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.969594 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.970634 INFO::Found  2  missing values.
2025-01-24 20:17:53.972418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.973048 INFO::Done
2025-01-24 20:17:53.98513 INFO::Formatting Data.
2025-01-24 20:17:53.986055 INFO::Typecasting input to dataframe.
2025-01-24 20:17:53.986928 INFO::Replacing NaNs with NAs.
2025-01-24 20:17:53.987885 INFO::Removing potential empty rows and columns
2025-01-24 20:17:53.989054 INFO::Found  0  missing values.
2025-01-24 20:17:53.99252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 20:17:53.993155 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

nameusersystemelapsed
BERT26.111 1.74419.490
compute_asw0.0270.0020.028
count_existing0.0160.0010.016
generate_data_covariables0.0120.0020.014
generate_dataset0.0130.0000.013