Yannis Schumann
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_21 |
| git_last_commit: dedce04 |
| git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:15 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: BERT |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz |
| StartedAt: 2025-04-21 19:14:32 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 19:15:55 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 83.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 25.436 1.412 18.406
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.4.0’ ** 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)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-04-21 19:15:33.268731 INFO::Formatting Data.
2025-04-21 19:15:33.272327 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:33.284286 INFO::Removing potential empty rows and columns
2025-04-21 19:15:33.561107 INFO::Found 0 missing values.
2025-04-21 19:15:33.565876 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:33.566852 INFO::Done
2025-04-21 19:15:33.567755 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:33.583281 INFO::Starting hierarchical adjustment
2025-04-21 19:15:33.584533 INFO::Found 3 batches.
2025-04-21 19:15:33.585392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:33.586943 INFO::Using default BPPARAM
2025-04-21 19:15:33.587671 INFO::Processing subtree level 1
2025-04-21 19:15:33.752755 INFO::Adjusting the last 1 batches sequentially
2025-04-21 19:15:33.758681 INFO::Done
2025-04-21 19:15:33.759917 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:33.765181 INFO::ASW Batch was -0.0400962928733784 prior to batch effect correction and is now -0.0400962928733784 .
2025-04-21 19:15:33.767609 INFO::Total function execution time is 0.498944044113159 s and adjustment time is 0.17438006401062 s ( 34.95 )
2025-04-21 19:15:33.79005 INFO::Formatting Data.
2025-04-21 19:15:33.791393 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:33.792949 INFO::Removing potential empty rows and columns
2025-04-21 19:15:33.794786 INFO::Found 0 missing values.
2025-04-21 19:15:33.796226 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.
2025-04-21 19:15:33.812196 INFO::Formatting Data.
2025-04-21 19:15:33.8134 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:33.814799 INFO::Removing potential empty rows and columns
2025-04-21 19:15:33.816329 INFO::Found 0 missing values.
2025-04-21 19:15:33.817689 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.
2025-04-21 19:15:33.836023 INFO::Formatting Data.
2025-04-21 19:15:33.836861 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:33.837957 INFO::Removing potential empty rows and columns
2025-04-21 19:15:33.839449 INFO::Found 0 missing values.
2025-04-21 19:15:33.840363 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.
2025-04-21 19:15:33.84422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:33.844914 INFO::Done
2025-04-21 19:15:33.84566 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:33.848298 INFO::Starting hierarchical adjustment
2025-04-21 19:15:33.849519 INFO::Found 2 batches.
2025-04-21 19:15:33.850064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:33.850707 INFO::Using default BPPARAM
2025-04-21 19:15:33.851201 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:33.852299 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:33.878249 INFO::Done
2025-04-21 19:15:33.878948 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:33.880892 INFO::ASW Batch was -0.013164289377109 prior to batch effect correction and is now -0.12649318104251 .
2025-04-21 19:15:33.88185 INFO::Total function execution time is 0.0458369255065918 s and adjustment time is 0.0289380550384521 s ( 63.13 )
2025-04-21 19:15:33.88609 INFO::Formatting Data.
2025-04-21 19:15:33.887049 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:33.898542 INFO::Formatting Data.
2025-04-21 19:15:33.899635 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:33.936787 INFO::Removing potential empty rows and columns
2025-04-21 19:15:33.939578 INFO::Found 0 missing values.
2025-04-21 19:15:33.943712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:33.944543 INFO::Done
2025-04-21 19:15:33.945323 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:33.948053 INFO::Starting hierarchical adjustment
2025-04-21 19:15:33.948924 INFO::Found 2 batches.
2025-04-21 19:15:33.949407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:33.949932 INFO::Using default BPPARAM
2025-04-21 19:15:33.950396 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:33.951212 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:33.967827 INFO::Done
2025-04-21 19:15:33.968557 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:33.970807 INFO::ASW Batch was 0.149246055070806 prior to batch effect correction and is now -0.108480840562437 .
2025-04-21 19:15:33.971904 INFO::Total function execution time is 0.0734169483184814 s and adjustment time is 0.0189919471740723 s ( 25.87 )
2025-04-21 19:15:33.973329 INFO::Formatting Data.
2025-04-21 19:15:33.973911 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:33.974713 INFO::Removing potential empty rows and columns
2025-04-21 19:15:33.975602 INFO::Found 0 missing values.
2025-04-21 19:15:33.97802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:33.978502 INFO::Done
2025-04-21 19:15:33.978978 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:33.980796 INFO::Starting hierarchical adjustment
2025-04-21 19:15:33.981512 INFO::Found 2 batches.
2025-04-21 19:15:33.982224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:33.983028 INFO::Using default BPPARAM
2025-04-21 19:15:33.983738 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:33.984958 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:33.998025 INFO::Done
2025-04-21 19:15:33.998739 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:34.000688 INFO::ASW Batch was 0.149246055070806 prior to batch effect correction and is now -0.108480840562437 .
2025-04-21 19:15:34.001462 INFO::Total function execution time is 0.0281388759613037 s and adjustment time is 0.0166850090026855 s ( 59.3 )
2025-04-21 19:15:37.190483 INFO::Formatting Data.
2025-04-21 19:15:37.191459 INFO::Recognized SummarizedExperiment
2025-04-21 19:15:37.19228 INFO::Typecasting input to dataframe.
2025-04-21 19:15:37.228367 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:37.229484 INFO::Removing potential empty rows and columns
2025-04-21 19:15:37.233029 INFO::Found 0 missing values.
2025-04-21 19:15:37.241379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:37.242267 INFO::Done
2025-04-21 19:15:37.242954 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:37.247161 INFO::Starting hierarchical adjustment
2025-04-21 19:15:37.248005 INFO::Found 2 batches.
2025-04-21 19:15:37.248912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:37.249897 INFO::Using default BPPARAM
2025-04-21 19:15:37.250386 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:37.251915 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:37.315623 INFO::Done
2025-04-21 19:15:37.316635 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:37.321581 INFO::ASW Batch was 0.00822870564506407 prior to batch effect correction and is now -0.0951121655413293 .
2025-04-21 19:15:37.32274 INFO::Total function execution time is 0.132659196853638 s and adjustment time is 0.0677981376647949 s ( 51.11 )
2025-04-21 19:15:37.345502 INFO::Formatting Data.
2025-04-21 19:15:37.346614 INFO::Recognized SummarizedExperiment
2025-04-21 19:15:37.347512 INFO::Typecasting input to dataframe.
2025-04-21 19:15:37.359297 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:37.360514 INFO::Removing potential empty rows and columns
2025-04-21 19:15:37.364307 INFO::Found 0 missing values.
2025-04-21 19:15:37.371756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:37.372506 INFO::Done
2025-04-21 19:15:37.373311 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:37.377526 INFO::Starting hierarchical adjustment
2025-04-21 19:15:37.378363 INFO::Found 2 batches.
2025-04-21 19:15:37.37894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:37.379752 INFO::Using default BPPARAM
2025-04-21 19:15:37.380478 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:37.382097 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:37.40986 INFO::Done
2025-04-21 19:15:37.410865 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:37.414858 INFO::ASW Batch was 0.00743436466434231 prior to batch effect correction and is now 0.00743436466434231 .
2025-04-21 19:15:37.416092 INFO::Total function execution time is 0.0706009864807129 s and adjustment time is 0.0316390991210938 s ( 44.81 )
2025-04-21 19:15:37.441461 INFO::Formatting Data.
2025-04-21 19:15:37.442223 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:37.44349 INFO::Removing potential empty rows and columns
2025-04-21 19:15:37.444454 INFO::Found 0 missing values.
2025-04-21 19:15:37.447045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:37.447563 INFO::Done
2025-04-21 19:15:37.448046 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:37.450486 INFO::Starting hierarchical adjustment
2025-04-21 19:15:37.451443 INFO::Found 3 batches.
2025-04-21 19:15:37.452201 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:37.452966 INFO::Using default BPPARAM
2025-04-21 19:15:37.453503 INFO::Processing subtree level 1
2025-04-21 19:15:37.872562 INFO::Adjusting the last 1 batches sequentially
2025-04-21 19:15:37.875455 INFO::Done
2025-04-21 19:15:37.87646 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:37.884465 INFO::ASW Batch was -0.123169042140814 prior to batch effect correction and is now -0.165119081012923 .
2025-04-21 19:15:37.904006 INFO::Total function execution time is 0.458817958831787 s and adjustment time is 0.424207925796509 s ( 92.46 )
2025-04-21 19:15:38.020452 INFO::Skipping initial DF formatting
2025-04-21 19:15:38.021471 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:38.026977 INFO::Starting hierarchical adjustment
2025-04-21 19:15:38.027797 INFO::Found 5 batches.
2025-04-21 19:15:38.028313 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:38.028899 INFO::Using default BPPARAM
2025-04-21 19:15:38.029393 INFO::Processing subtree level 1
2025-04-21 19:15:38.29661 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:38.32362 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:38.368801 INFO::Done
2025-04-21 19:15:38.369602 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:38.375892 INFO::ASW Batch was 0.507411038628715 prior to batch effect correction and is now 0.507411038628715 .
2025-04-21 19:15:38.376745 INFO::ASW Label was 0.355735589582304 prior to batch effect correction and is now 0.355735589582304 .
2025-04-21 19:15:38.378933 INFO::Total function execution time is 0.358567953109741 s and adjustment time is 0.341133117675781 s ( 95.14 )
2025-04-21 19:15:38.409267 INFO::Formatting Data.
2025-04-21 19:15:38.410484 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:38.412314 INFO::Removing potential empty rows and columns
2025-04-21 19:15:38.41397 INFO::Found 0 missing values.
2025-04-21 19:15:38.420593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:38.42143 INFO::Done
2025-04-21 19:15:38.422368 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:38.426245 INFO::Starting hierarchical adjustment
2025-04-21 19:15:38.427378 INFO::Found 5 batches.
2025-04-21 19:15:38.428423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:38.429418 INFO::Using default BPPARAM
2025-04-21 19:15:38.430192 INFO::Processing subtree level 1
2025-04-21 19:15:38.61836 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:38.644315 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:38.686563 INFO::Done
2025-04-21 19:15:38.68734 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:38.692465 INFO::ASW Batch was 0.453423933428084 prior to batch effect correction and is now -0.0569053393455499 .
2025-04-21 19:15:38.693706 INFO::ASW Label was 0.250981773095544 prior to batch effect correction and is now 0.732953426241459 .
2025-04-21 19:15:38.694971 INFO::Total function execution time is 0.285819053649902 s and adjustment time is 0.259371995925903 s ( 90.75 )
2025-04-21 19:15:38.696055 INFO::Formatting Data.
2025-04-21 19:15:38.696916 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:38.698144 INFO::Removing potential empty rows and columns
2025-04-21 19:15:38.699217 INFO::Found 0 missing values.
2025-04-21 19:15:38.703515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:38.704132 INFO::Done
2025-04-21 19:15:38.704657 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:38.707974 INFO::Starting hierarchical adjustment
2025-04-21 19:15:38.708757 INFO::Found 5 batches.
2025-04-21 19:15:38.709293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:38.70995 INFO::Using default BPPARAM
2025-04-21 19:15:38.710689 INFO::Processing subtree level 1
2025-04-21 19:15:38.894756 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:38.923 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:38.962593 INFO::Done
2025-04-21 19:15:38.963582 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:38.969117 INFO::ASW Batch was 0.453423933428084 prior to batch effect correction and is now -0.0569053393455499 .
2025-04-21 19:15:38.970135 INFO::ASW Label was 0.250981773095544 prior to batch effect correction and is now 0.732953426241459 .
2025-04-21 19:15:38.971869 INFO::Total function execution time is 0.275753974914551 s and adjustment time is 0.253911972045898 s ( 92.08 )
2025-04-21 19:15:38.995378 INFO::Formatting Data.
2025-04-21 19:15:38.996234 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:38.997345 INFO::Removing potential empty rows and columns
2025-04-21 19:15:38.998724 INFO::Found 0 missing values.
2025-04-21 19:15:39.00554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:39.006627 INFO::Done
2025-04-21 19:15:39.00752 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:39.011626 INFO::Starting hierarchical adjustment
2025-04-21 19:15:39.013241 INFO::Found 5 batches.
2025-04-21 19:15:39.014261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:39.015289 INFO::Using default BPPARAM
2025-04-21 19:15:39.015938 INFO::Processing subtree level 1
2025-04-21 19:15:39.209475 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:39.222366 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:39.25682 INFO::Done
2025-04-21 19:15:39.258383 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:39.262573 INFO::ASW Batch was 0.328720424443131 prior to batch effect correction and is now -0.0839725213843878 .
2025-04-21 19:15:39.26326 INFO::ASW Label was 0.340827246163823 prior to batch effect correction and is now 0.896438678135944 .
2025-04-21 19:15:39.264834 INFO::Total function execution time is 0.269411087036133 s and adjustment time is 0.243927001953125 s ( 90.54 )
2025-04-21 19:15:39.265934 INFO::Formatting Data.
2025-04-21 19:15:39.266645 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:39.267575 INFO::Removing potential empty rows and columns
2025-04-21 19:15:39.268641 INFO::Found 0 missing values.
2025-04-21 19:15:39.273751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:39.274797 INFO::Done
2025-04-21 19:15:39.275415 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:39.279473 INFO::Starting hierarchical adjustment
2025-04-21 19:15:39.28065 INFO::Found 5 batches.
2025-04-21 19:15:39.281628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:39.282383 INFO::Using default BPPARAM
2025-04-21 19:15:39.283012 INFO::Processing subtree level 1
2025-04-21 19:15:39.456958 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:39.472471 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:39.507698 INFO::Done
2025-04-21 19:15:39.508774 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:39.514547 INFO::ASW Batch was 0.328720424443131 prior to batch effect correction and is now -0.0839725213843878 .
2025-04-21 19:15:39.515219 INFO::ASW Label was 0.340827246163823 prior to batch effect correction and is now 0.896438678135944 .
2025-04-21 19:15:39.516692 INFO::Total function execution time is 0.250830888748169 s and adjustment time is 0.227257966995239 s ( 90.6 )
2025-04-21 19:15:39.53672 INFO::Formatting Data.
2025-04-21 19:15:39.53765 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:39.538585 INFO::Removing potential empty rows and columns
2025-04-21 19:15:39.539786 INFO::Found 0 missing values.
2025-04-21 19:15:39.54445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:39.545058 INFO::Done
2025-04-21 19:15:39.545743 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:39.55003 INFO::Starting hierarchical adjustment
2025-04-21 19:15:39.551107 INFO::Found 2 batches.
2025-04-21 19:15:39.551977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:39.552989 INFO::Using default BPPARAM
2025-04-21 19:15:39.55397 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:39.554916 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:39.573488 INFO::Done
2025-04-21 19:15:39.574588 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:39.578843 INFO::ASW Batch was 0.682719754467807 prior to batch effect correction and is now 0.113517416513995 .
2025-04-21 19:15:39.579545 INFO::ASW Label was 0.462059490725859 prior to batch effect correction and is now 0.864223159470325 .
2025-04-21 19:15:39.580613 INFO::Total function execution time is 0.0439009666442871 s and adjustment time is 0.022536039352417 s ( 51.33 )
2025-04-21 19:15:39.581983 INFO::Formatting Data.
2025-04-21 19:15:39.583017 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:39.584061 INFO::Removing potential empty rows and columns
2025-04-21 19:15:39.585037 INFO::Found 0 missing values.
2025-04-21 19:15:39.588046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:39.588599 INFO::Done
2025-04-21 19:15:39.589104 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:39.592557 INFO::Starting hierarchical adjustment
2025-04-21 19:15:39.593336 INFO::Found 2 batches.
2025-04-21 19:15:39.593909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:39.59479 INFO::Using default BPPARAM
2025-04-21 19:15:39.595567 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:39.596481 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:39.614731 INFO::Done
2025-04-21 19:15:39.615749 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:39.620313 INFO::ASW Batch was 0.682719754467807 prior to batch effect correction and is now 0.113517416513995 .
2025-04-21 19:15:39.62125 INFO::ASW Label was 0.462059490725859 prior to batch effect correction and is now 0.864223159470325 .
2025-04-21 19:15:39.62243 INFO::Total function execution time is 0.0405209064483643 s and adjustment time is 0.0214800834655762 s ( 53.01 )
2025-04-21 19:15:39.639639 INFO::Formatting Data.
2025-04-21 19:15:39.640478 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:39.641361 INFO::Removing potential empty rows and columns
2025-04-21 19:15:39.642229 INFO::Found 0 missing values.
2025-04-21 19:15:39.644406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:39.645024 INFO::Done
2025-04-21 19:15:39.645695 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:39.64756 INFO::Starting hierarchical adjustment
2025-04-21 19:15:39.648585 INFO::Found 2 batches.
2025-04-21 19:15:39.649128 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:39.649972 INFO::Using default BPPARAM
2025-04-21 19:15:39.650719 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:39.651991 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:39.695555 INFO::Done
2025-04-21 19:15:39.6965 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:39.699057 INFO::ASW Batch was -0.048217592873453 prior to batch effect correction and is now -0.109159323114185 .
2025-04-21 19:15:39.700172 INFO::Total function execution time is 0.0606658458709717 s and adjustment time is 0.0471508502960205 s ( 77.72 )
2025-04-21 19:15:39.717942 INFO::Formatting Data.
2025-04-21 19:15:39.719178 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:39.720225 INFO::Removing potential empty rows and columns
2025-04-21 19:15:39.721377 INFO::Found 0 missing values.
2025-04-21 19:15:39.722742 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.
2025-04-21 19:15:39.729437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:39.730421 INFO::Done
2025-04-21 19:15:39.7312 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:39.735277 INFO::Starting hierarchical adjustment
2025-04-21 19:15:39.736332 INFO::Found 2 batches.
2025-04-21 19:15:39.737103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:39.737943 INFO::Using default BPPARAM
2025-04-21 19:15:39.738669 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:39.740036 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:39.759616 INFO::Done
2025-04-21 19:15:39.760642 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:39.764813 INFO::ASW Batch was 0.564925981380849 prior to batch effect correction and is now -0.0356346228036407 .
2025-04-21 19:15:39.765822 INFO::ASW Label was 0.524684212222145 prior to batch effect correction and is now 0.922197364844885 .
2025-04-21 19:15:39.767009 INFO::Total function execution time is 0.0491499900817871 s and adjustment time is 0.0234420299530029 s ( 47.69 )
2025-04-21 19:15:39.768151 INFO::Formatting Data.
2025-04-21 19:15:39.769081 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:39.770437 INFO::Removing potential empty rows and columns
2025-04-21 19:15:39.771933 INFO::Found 0 missing values.
2025-04-21 19:15:39.773218 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.
2025-04-21 19:15:39.780015 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:39.780982 INFO::Done
2025-04-21 19:15:39.781773 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:39.785733 INFO::Starting hierarchical adjustment
2025-04-21 19:15:39.786941 INFO::Found 2 batches.
2025-04-21 19:15:39.787922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:39.78862 INFO::Using default BPPARAM
2025-04-21 19:15:39.789149 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:39.790275 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:39.808995 INFO::Done
2025-04-21 19:15:39.809789 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:39.813413 INFO::ASW Batch was 0.564925981380849 prior to batch effect correction and is now -0.0356346228036407 .
2025-04-21 19:15:39.814105 INFO::ASW Label was 0.524684212222145 prior to batch effect correction and is now 0.922197364844885 .
2025-04-21 19:15:39.814966 INFO::Total function execution time is 0.0468959808349609 s and adjustment time is 0.0222878456115723 s ( 47.53 )
2025-04-21 19:15:40.087774 INFO::Formatting Data.
2025-04-21 19:15:40.088922 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:40.090294 INFO::Removing potential empty rows and columns
2025-04-21 19:15:40.091816 INFO::Found 0 missing values.
2025-04-21 19:15:40.095794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:40.096688 INFO::Done
2025-04-21 19:15:40.098542 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:40.101016 INFO::Starting hierarchical adjustment
2025-04-21 19:15:40.102075 INFO::Found 3 batches.
2025-04-21 19:15:40.102813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:40.103653 INFO::Using default BPPARAM
2025-04-21 19:15:40.10438 INFO::Processing subtree level 1
2025-04-21 19:15:40.239768 INFO::Adjusting the last 1 batches sequentially
2025-04-21 19:15:40.24949 INFO::Done
2025-04-21 19:15:40.251523 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:40.258946 INFO::ASW Batch was 0.0202690685520213 prior to batch effect correction and is now 0.0202690685520213 .
2025-04-21 19:15:40.26253 INFO::Total function execution time is 0.173896074295044 s and adjustment time is 0.147567987442017 s ( 84.86 )
2025-04-21 19:15:40.265207 INFO::Formatting Data.
2025-04-21 19:15:40.267029 INFO::Typecasting input to dataframe.
2025-04-21 19:15:40.268317 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:40.269667 INFO::Removing potential empty rows and columns
2025-04-21 19:15:40.271241 INFO::Found 0 missing values.
2025-04-21 19:15:40.276226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:40.276854 INFO::Done
2025-04-21 19:15:40.277382 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:40.279235 INFO::Starting hierarchical adjustment
2025-04-21 19:15:40.279906 INFO::Found 3 batches.
2025-04-21 19:15:40.280676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:40.28206 INFO::Using default BPPARAM
2025-04-21 19:15:40.282816 INFO::Processing subtree level 1
2025-04-21 19:15:40.412941 INFO::Adjusting the last 1 batches sequentially
2025-04-21 19:15:40.425345 INFO::Done
2025-04-21 19:15:40.42649 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:40.434093 INFO::ASW Batch was 0.0202690685520213 prior to batch effect correction and is now 0.0202690685520213 .
2025-04-21 19:15:40.436966 INFO::Total function execution time is 0.171993970870972 s and adjustment time is 0.145473957061768 s ( 84.58 )
2025-04-21 19:15:40.463255 INFO::Formatting Data.
2025-04-21 19:15:40.464424 INFO::Typecasting input to dataframe.
2025-04-21 19:15:40.465672 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:40.468167 INFO::Removing potential empty rows and columns
2025-04-21 19:15:40.46924 INFO::Found 0 missing values.
2025-04-21 19:15:40.473855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:40.474803 INFO::Done
2025-04-21 19:15:40.475787 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:40.478304 INFO::Starting hierarchical adjustment
2025-04-21 19:15:40.47932 INFO::Found 3 batches.
2025-04-21 19:15:40.480067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:40.4809 INFO::Using default BPPARAM
2025-04-21 19:15:40.481706 INFO::Processing subtree level 1
2025-04-21 19:15:40.615838 INFO::Adjusting the last 1 batches sequentially
2025-04-21 19:15:40.623638 INFO::Done
2025-04-21 19:15:40.626411 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:40.634029 INFO::ASW Batch was -0.0765899835732451 prior to batch effect correction and is now -0.0765899835732451 .
2025-04-21 19:15:40.637251 INFO::Total function execution time is 0.173742055892944 s and adjustment time is 0.144503116607666 s ( 83.17 )
2025-04-21 19:15:40.882811 INFO::Formatting Data.
2025-04-21 19:15:40.88377 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:40.886443 INFO::Removing potential empty rows and columns
2025-04-21 19:15:40.889674 INFO::Found 1000 missing values.
2025-04-21 19:15:40.916017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:40.917647 INFO::Done
2025-04-21 19:15:40.918323 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:40.925054 INFO::Starting hierarchical adjustment
2025-04-21 19:15:40.927005 INFO::Found 10 batches.
2025-04-21 19:15:40.928016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:40.929099 INFO::Using default BPPARAM
2025-04-21 19:15:40.929998 INFO::Processing subtree level 1
2025-04-21 19:15:41.100951 INFO::Processing subtree level 2
2025-04-21 19:15:41.3094 INFO::Adjusting the last 1 batches sequentially
2025-04-21 19:15:41.32648 INFO::Done
2025-04-21 19:15:41.328459 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:41.342342 INFO::ASW Batch was 0.518552074314545 prior to batch effect correction and is now 0.518552074314545 .
2025-04-21 19:15:41.343416 INFO::ASW Label was 0.312702125877453 prior to batch effect correction and is now 0.312702125877453 .
2025-04-21 19:15:41.346445 INFO::Total function execution time is 0.463262796401978 s and adjustment time is 0.400206804275513 s ( 86.39 )
2025-04-21 19:15:41.347878 INFO::Formatting Data.
2025-04-21 19:15:41.350958 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:41.353994 INFO::Removing potential empty rows and columns
2025-04-21 19:15:41.359181 INFO::Found 1000 missing values.
2025-04-21 19:15:41.377442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:41.378473 INFO::Done
2025-04-21 19:15:41.379412 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:41.384371 INFO::Starting hierarchical adjustment
2025-04-21 19:15:41.3855 INFO::Found 10 batches.
2025-04-21 19:15:42.489213 INFO::Set up parallel execution backend with 2 workers
2025-04-21 19:15:42.490302 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-04-21 19:15:43.825988 INFO::Adjusting the last 2 batches sequentially
2025-04-21 19:15:43.827958 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 19:15:43.850547 INFO::Done
2025-04-21 19:15:43.851216 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:43.855967 INFO::ASW Batch was 0.518552074314545 prior to batch effect correction and is now 0.518552074314545 .
2025-04-21 19:15:43.856585 INFO::ASW Label was 0.312702125877453 prior to batch effect correction and is now 0.312702125877453 .
2025-04-21 19:15:43.857268 INFO::Total function execution time is 2.50948596000671 s and adjustment time is 2.46517896652222 s ( 98.23 )
2025-04-21 19:15:44.157363 INFO::Formatting Data.
2025-04-21 19:15:44.159122 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.160157 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.161181 INFO::Found 0 missing values.
2025-04-21 19:15:44.166792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.167721 INFO::Done
2025-04-21 19:15:44.168502 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 19:15:44.172294 INFO::Starting hierarchical adjustment
2025-04-21 19:15:44.173298 INFO::Found 3 batches.
2025-04-21 19:15:44.175488 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 19:15:44.176687 INFO::Using default BPPARAM
2025-04-21 19:15:44.177732 INFO::Processing subtree level 1
2025-04-21 19:15:44.35221 INFO::Adjusting the last 1 batches sequentially
2025-04-21 19:15:44.368441 INFO::Done
2025-04-21 19:15:44.370257 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 19:15:44.381585 INFO::ASW Batch was 0.250460093088552 prior to batch effect correction and is now -0.146117325449196 .
2025-04-21 19:15:44.383307 INFO::ASW Label was -0.209725823481286 prior to batch effect correction and is now -0.0960413079224953 .
2025-04-21 19:15:44.386477 INFO::Total function execution time is 0.228539943695068 s and adjustment time is 0.195313930511475 s ( 85.46 )
2025-04-21 19:15:44.576516 INFO::Formatting Data.
2025-04-21 19:15:44.577763 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.57921 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.580864 INFO::Found 2 missing values.
2025-04-21 19:15:44.583634 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.584248 INFO::Done
2025-04-21 19:15:44.627595 INFO::Found NA in Reference column
2025-04-21 19:15:44.641481 INFO::Require at least two references per batch.
2025-04-21 19:15:44.669284 INFO::Formatting Data.
2025-04-21 19:15:44.6703 INFO::Recognized SummarizedExperiment
2025-04-21 19:15:44.670859 INFO::Typecasting input to dataframe.
2025-04-21 19:15:44.684059 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.685841 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.690223 INFO::Found 0 missing values.
2025-04-21 19:15:44.696919 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.698077 INFO::Done
2025-04-21 19:15:44.718372 INFO::Formatting Data.
2025-04-21 19:15:44.71929 INFO::Recognized SummarizedExperiment
2025-04-21 19:15:44.720187 INFO::Typecasting input to dataframe.
2025-04-21 19:15:44.743622 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.745403 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.748932 INFO::Found 0 missing values.
2025-04-21 19:15:44.758969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.759724 INFO::Done
2025-04-21 19:15:44.781445 INFO::Formatting Data.
2025-04-21 19:15:44.782554 INFO::Recognized SummarizedExperiment
2025-04-21 19:15:44.783408 INFO::Typecasting input to dataframe.
2025-04-21 19:15:44.802526 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.804038 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.805194 INFO::Found 0 missing values.
2025-04-21 19:15:44.806684 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.
2025-04-21 19:15:44.810682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.811292 INFO::Done
2025-04-21 19:15:44.827347 INFO::Formatting Data.
2025-04-21 19:15:44.828118 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.828957 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.829868 INFO::Found 0 missing values.
2025-04-21 19:15:44.832391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.83291 INFO::Done
2025-04-21 19:15:44.848237 INFO::Formatting Data.
2025-04-21 19:15:44.849052 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.849919 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.850826 INFO::Found 0 missing values.
2025-04-21 19:15:44.853376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.853886 INFO::Done
2025-04-21 19:15:44.896639 INFO::Formatting Data.
2025-04-21 19:15:44.897459 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.898708 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.899895 INFO::Found 1 missing values.
2025-04-21 19:15:44.902804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.903444 INFO::Done
2025-04-21 19:15:44.931583 INFO::Formatting Data.
2025-04-21 19:15:44.932371 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.933737 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.935057 INFO::Found 2 missing values.
2025-04-21 19:15:44.936 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.
2025-04-21 19:15:44.938231 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.938994 INFO::Done
2025-04-21 19:15:44.95366 INFO::Formatting Data.
2025-04-21 19:15:44.954467 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.955306 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.95618 INFO::Found 2 missing values.
2025-04-21 19:15:44.957692 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.958215 INFO::Done
2025-04-21 19:15:44.974523 INFO::Formatting Data.
2025-04-21 19:15:44.975324 INFO::Typecasting input to dataframe.
2025-04-21 19:15:44.976281 INFO::Replacing NaNs with NAs.
2025-04-21 19:15:44.978078 INFO::Removing potential empty rows and columns
2025-04-21 19:15:44.979176 INFO::Found 0 missing values.
2025-04-21 19:15:44.983378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 19:15:44.984226 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.850 4.293 24.407
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.436 | 1.412 | 18.406 | |
| compute_asw | 0.030 | 0.002 | 0.032 | |
| count_existing | 0.015 | 0.002 | 0.016 | |
| generate_data_covariables | 0.012 | 0.001 | 0.012 | |
| generate_dataset | 0.014 | 0.001 | 0.015 | |