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 13:17 -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 18:17:35 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 18:18:09 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 33.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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: aarch64-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 Ventura 13.7.1
* 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 10.118 0.546 7.424
* 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-arm64/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: aarch64-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 18:18:00.602987 INFO::Formatting Data.
2025-04-21 18:18:00.604562 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:00.609172 INFO::Removing potential empty rows and columns
2025-04-21 18:18:00.716897 INFO::Found 0 missing values.
2025-04-21 18:18:00.798715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:00.800893 INFO::Done
2025-04-21 18:18:00.801725 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:00.808301 INFO::Starting hierarchical adjustment
2025-04-21 18:18:00.8087 INFO::Found 3 batches.
2025-04-21 18:18:00.808901 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:00.809616 INFO::Using default BPPARAM
2025-04-21 18:18:00.809873 INFO::Processing subtree level 1
2025-04-21 18:18:00.863404 INFO::Adjusting the last 1 batches sequentially
2025-04-21 18:18:00.864553 INFO::Done
2025-04-21 18:18:00.864789 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:00.866638 INFO::ASW Batch was -0.0709759753663955 prior to batch effect correction and is now -0.0709759753663955 .
2025-04-21 18:18:00.867515 INFO::Total function execution time is 0.26490592956543 s and adjustment time is 0.0559389591217041 s ( 21.12 )
2025-04-21 18:18:00.87764 INFO::Formatting Data.
2025-04-21 18:18:00.877941 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:00.878303 INFO::Removing potential empty rows and columns
2025-04-21 18:18:00.878859 INFO::Found 0 missing values.
2025-04-21 18:18:00.87924 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 18:18:00.883831 INFO::Formatting Data.
2025-04-21 18:18:00.884323 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:00.884833 INFO::Removing potential empty rows and columns
2025-04-21 18:18:00.885228 INFO::Found 0 missing values.
2025-04-21 18:18:00.885537 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 18:18:00.891758 INFO::Formatting Data.
2025-04-21 18:18:00.892019 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:00.8923 INFO::Removing potential empty rows and columns
2025-04-21 18:18:00.892781 INFO::Found 0 missing values.
2025-04-21 18:18:00.893119 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 18:18:00.894846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:00.895174 INFO::Done
2025-04-21 18:18:00.895365 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:00.896202 INFO::Starting hierarchical adjustment
2025-04-21 18:18:00.89643 INFO::Found 2 batches.
2025-04-21 18:18:00.896613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:00.896918 INFO::Using default BPPARAM
2025-04-21 18:18:00.89711 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:00.897411 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:00.907104 INFO::Done
2025-04-21 18:18:00.907369 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:00.908073 INFO::ASW Batch was -0.00674754005735061 prior to batch effect correction and is now -0.11188492812914 .
2025-04-21 18:18:00.908542 INFO::Total function execution time is 0.0166110992431641 s and adjustment time is 0.0107040405273438 s ( 64.44 )
2025-04-21 18:18:00.909737 INFO::Formatting Data.
2025-04-21 18:18:00.909972 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:00.913081 INFO::Formatting Data.
2025-04-21 18:18:00.913334 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:00.928839 INFO::Removing potential empty rows and columns
2025-04-21 18:18:00.929932 INFO::Found 0 missing values.
2025-04-21 18:18:00.930872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:00.931042 INFO::Done
2025-04-21 18:18:00.931201 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:00.931857 INFO::Starting hierarchical adjustment
2025-04-21 18:18:00.932078 INFO::Found 2 batches.
2025-04-21 18:18:00.932238 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:00.932425 INFO::Using default BPPARAM
2025-04-21 18:18:00.93257 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:00.93282 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:00.937308 INFO::Done
2025-04-21 18:18:00.937501 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:00.938093 INFO::ASW Batch was -0.0520131073267866 prior to batch effect correction and is now -0.121318311903925 .
2025-04-21 18:18:00.938323 INFO::Total function execution time is 0.0252549648284912 s and adjustment time is 0.00527405738830566 s ( 20.88 )
2025-04-21 18:18:00.938632 INFO::Formatting Data.
2025-04-21 18:18:00.938802 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:00.939038 INFO::Removing potential empty rows and columns
2025-04-21 18:18:00.939321 INFO::Found 0 missing values.
2025-04-21 18:18:00.940151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:00.940325 INFO::Done
2025-04-21 18:18:00.940484 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:00.941055 INFO::Starting hierarchical adjustment
2025-04-21 18:18:00.941249 INFO::Found 2 batches.
2025-04-21 18:18:00.94142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:00.941609 INFO::Using default BPPARAM
2025-04-21 18:18:00.941761 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:00.942017 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:00.946563 INFO::Done
2025-04-21 18:18:00.946769 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:00.947373 INFO::ASW Batch was -0.0520131073267866 prior to batch effect correction and is now -0.121318311903925 .
2025-04-21 18:18:00.947612 INFO::Total function execution time is 0.00895595550537109 s and adjustment time is 0.00534701347351074 s ( 59.7 )
2025-04-21 18:18:02.149588 INFO::Formatting Data.
2025-04-21 18:18:02.149883 INFO::Recognized SummarizedExperiment
2025-04-21 18:18:02.150058 INFO::Typecasting input to dataframe.
2025-04-21 18:18:02.161068 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.161507 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.162608 INFO::Found 0 missing values.
2025-04-21 18:18:02.164744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.164933 INFO::Done
2025-04-21 18:18:02.165092 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.166399 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.166641 INFO::Found 2 batches.
2025-04-21 18:18:02.166806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.167169 INFO::Using default BPPARAM
2025-04-21 18:18:02.167327 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.167638 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.187241 INFO::Done
2025-04-21 18:18:02.187579 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.189082 INFO::ASW Batch was 0.0132342809291303 prior to batch effect correction and is now -0.0939645643598454 .
2025-04-21 18:18:02.189423 INFO::Total function execution time is 0.0399332046508789 s and adjustment time is 0.0206098556518555 s ( 51.61 )
2025-04-21 18:18:02.198001 INFO::Formatting Data.
2025-04-21 18:18:02.198326 INFO::Recognized SummarizedExperiment
2025-04-21 18:18:02.198503 INFO::Typecasting input to dataframe.
2025-04-21 18:18:02.201566 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.201935 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.203145 INFO::Found 0 missing values.
2025-04-21 18:18:02.205268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.207313 INFO::Done
2025-04-21 18:18:02.207502 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.208817 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.209054 INFO::Found 2 batches.
2025-04-21 18:18:02.209212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.209402 INFO::Using default BPPARAM
2025-04-21 18:18:02.209552 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.209853 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.217907 INFO::Done
2025-04-21 18:18:02.218137 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.219318 INFO::ASW Batch was -0.012507638481988 prior to batch effect correction and is now -0.012507638481988 .
2025-04-21 18:18:02.219583 INFO::Total function execution time is 0.0215930938720703 s and adjustment time is 0.00889110565185547 s ( 41.18 )
2025-04-21 18:18:02.227335 INFO::Formatting Data.
2025-04-21 18:18:02.227598 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.227892 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.228219 INFO::Found 0 missing values.
2025-04-21 18:18:02.22909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.229269 INFO::Done
2025-04-21 18:18:02.229477 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.23014 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.230349 INFO::Found 3 batches.
2025-04-21 18:18:02.2305 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.230686 INFO::Using default BPPARAM
2025-04-21 18:18:02.230833 INFO::Processing subtree level 1
2025-04-21 18:18:02.367255 INFO::Adjusting the last 1 batches sequentially
2025-04-21 18:18:02.371555 INFO::Done
2025-04-21 18:18:02.372225 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.374748 INFO::ASW Batch was -0.131267894522449 prior to batch effect correction and is now -0.180725009348025 .
2025-04-21 18:18:02.376659 INFO::Total function execution time is 0.149057865142822 s and adjustment time is 0.141230821609497 s ( 94.75 )
2025-04-21 18:18:02.417756 INFO::Skipping initial DF formatting
2025-04-21 18:18:02.418229 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.419776 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.420069 INFO::Found 5 batches.
2025-04-21 18:18:02.420254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.420563 INFO::Using default BPPARAM
2025-04-21 18:18:02.420733 INFO::Processing subtree level 1
2025-04-21 18:18:02.51835 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.52071 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.540335 INFO::Done
2025-04-21 18:18:02.540993 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.544359 INFO::ASW Batch was 0.514699593560557 prior to batch effect correction and is now 0.514699593560557 .
2025-04-21 18:18:02.544843 INFO::ASW Label was 0.370762539741547 prior to batch effect correction and is now 0.370762539741547 .
2025-04-21 18:18:02.54564 INFO::Total function execution time is 0.127856969833374 s and adjustment time is 0.120297908782959 s ( 94.09 )
2025-04-21 18:18:02.558614 INFO::Formatting Data.
2025-04-21 18:18:02.55899 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.559404 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.559821 INFO::Found 0 missing values.
2025-04-21 18:18:02.561498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.56172 INFO::Done
2025-04-21 18:18:02.562132 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.563541 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.563852 INFO::Found 5 batches.
2025-04-21 18:18:02.564093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.564419 INFO::Using default BPPARAM
2025-04-21 18:18:02.564703 INFO::Processing subtree level 1
2025-04-21 18:18:02.637962 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.640346 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.654735 INFO::Done
2025-04-21 18:18:02.655398 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.657731 INFO::ASW Batch was 0.40136633497436 prior to batch effect correction and is now -0.0814501953186641 .
2025-04-21 18:18:02.658222 INFO::ASW Label was 0.391249320215034 prior to batch effect correction and is now 0.780543919988382 .
2025-04-21 18:18:02.658987 INFO::Total function execution time is 0.100250959396362 s and adjustment time is 0.0909299850463867 s ( 90.7 )
2025-04-21 18:18:02.659753 INFO::Formatting Data.
2025-04-21 18:18:02.660077 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.660615 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.66111 INFO::Found 0 missing values.
2025-04-21 18:18:02.663239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.663518 INFO::Done
2025-04-21 18:18:02.663922 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.665161 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.665474 INFO::Found 5 batches.
2025-04-21 18:18:02.665883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.666251 INFO::Using default BPPARAM
2025-04-21 18:18:02.666467 INFO::Processing subtree level 1
2025-04-21 18:18:02.725995 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.727741 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.741883 INFO::Done
2025-04-21 18:18:02.742711 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.745355 INFO::ASW Batch was 0.40136633497436 prior to batch effect correction and is now -0.0814501953186641 .
2025-04-21 18:18:02.745684 INFO::ASW Label was 0.391249320215034 prior to batch effect correction and is now 0.780543919988382 .
2025-04-21 18:18:02.746217 INFO::Total function execution time is 0.0864040851593018 s and adjustment time is 0.0764510631561279 s ( 88.48 )
2025-04-21 18:18:02.758355 INFO::Formatting Data.
2025-04-21 18:18:02.758843 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.759355 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.759898 INFO::Found 0 missing values.
2025-04-21 18:18:02.762974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.763362 INFO::Done
2025-04-21 18:18:02.763785 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.765529 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.765872 INFO::Found 5 batches.
2025-04-21 18:18:02.768212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.768851 INFO::Using default BPPARAM
2025-04-21 18:18:02.769175 INFO::Processing subtree level 1
2025-04-21 18:18:02.838592 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.840353 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.850858 INFO::Done
2025-04-21 18:18:02.851204 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.853291 INFO::ASW Batch was 0.57643212599614 prior to batch effect correction and is now -0.09081026400087 .
2025-04-21 18:18:02.853635 INFO::ASW Label was 0.206109268124307 prior to batch effect correction and is now 0.872194807876084 .
2025-04-21 18:18:02.854142 INFO::Total function execution time is 0.0957629680633545 s and adjustment time is 0.0850470066070557 s ( 88.81 )
2025-04-21 18:18:02.854823 INFO::Formatting Data.
2025-04-21 18:18:02.855121 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.855651 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.856203 INFO::Found 0 missing values.
2025-04-21 18:18:02.858017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.85827 INFO::Done
2025-04-21 18:18:02.858518 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.859766 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.860096 INFO::Found 5 batches.
2025-04-21 18:18:02.860315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.860666 INFO::Using default BPPARAM
2025-04-21 18:18:02.860907 INFO::Processing subtree level 1
2025-04-21 18:18:02.932064 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.93376 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.944301 INFO::Done
2025-04-21 18:18:02.944691 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.946625 INFO::ASW Batch was 0.57643212599614 prior to batch effect correction and is now -0.09081026400087 .
2025-04-21 18:18:02.946943 INFO::ASW Label was 0.206109268124307 prior to batch effect correction and is now 0.872194807876084 .
2025-04-21 18:18:02.947393 INFO::Total function execution time is 0.092540979385376 s and adjustment time is 0.0842652320861816 s ( 91.06 )
2025-04-21 18:18:02.956441 INFO::Formatting Data.
2025-04-21 18:18:02.956769 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.957195 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.957765 INFO::Found 0 missing values.
2025-04-21 18:18:02.959186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.959456 INFO::Done
2025-04-21 18:18:02.95972 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.961195 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.961538 INFO::Found 2 batches.
2025-04-21 18:18:02.961771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.96239 INFO::Using default BPPARAM
2025-04-21 18:18:02.962667 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.963148 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.970829 INFO::Done
2025-04-21 18:18:02.971184 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.972453 INFO::ASW Batch was 0.535744315486675 prior to batch effect correction and is now 0.0611245213939462 .
2025-04-21 18:18:02.972705 INFO::ASW Label was 0.54373934850324 prior to batch effect correction and is now 0.88140555590028 .
2025-04-21 18:18:02.97305 INFO::Total function execution time is 0.0166471004486084 s and adjustment time is 0.00933098793029785 s ( 56.05 )
2025-04-21 18:18:02.973344 INFO::Formatting Data.
2025-04-21 18:18:02.973924 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.974249 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.97464 INFO::Found 0 missing values.
2025-04-21 18:18:02.975697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.975898 INFO::Done
2025-04-21 18:18:02.976089 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.9773 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.977593 INFO::Found 2 batches.
2025-04-21 18:18:02.977813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.978077 INFO::Using default BPPARAM
2025-04-21 18:18:02.978279 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.978616 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:02.984553 INFO::Done
2025-04-21 18:18:02.98482 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:02.985979 INFO::ASW Batch was 0.535744315486675 prior to batch effect correction and is now 0.0611245213939462 .
2025-04-21 18:18:02.986215 INFO::ASW Label was 0.54373934850324 prior to batch effect correction and is now 0.88140555590028 .
2025-04-21 18:18:02.986506 INFO::Total function execution time is 0.013153076171875 s and adjustment time is 0.00700807571411133 s ( 53.28 )
2025-04-21 18:18:02.993421 INFO::Formatting Data.
2025-04-21 18:18:02.993807 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:02.994194 INFO::Removing potential empty rows and columns
2025-04-21 18:18:02.994566 INFO::Found 0 missing values.
2025-04-21 18:18:02.995435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:02.995667 INFO::Done
2025-04-21 18:18:02.995879 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:02.996768 INFO::Starting hierarchical adjustment
2025-04-21 18:18:02.997071 INFO::Found 2 batches.
2025-04-21 18:18:02.997253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:02.997503 INFO::Using default BPPARAM
2025-04-21 18:18:02.997687 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:02.998044 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:03.011894 INFO::Done
2025-04-21 18:18:03.012207 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:03.012977 INFO::ASW Batch was -0.00354795298268259 prior to batch effect correction and is now -0.070507949841022 .
2025-04-21 18:18:03.013354 INFO::Total function execution time is 0.0199918746948242 s and adjustment time is 0.0148849487304688 s ( 74.45 )
2025-04-21 18:18:03.019109 INFO::Formatting Data.
2025-04-21 18:18:03.019402 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:03.019766 INFO::Removing potential empty rows and columns
2025-04-21 18:18:03.020174 INFO::Found 0 missing values.
2025-04-21 18:18:03.02065 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 18:18:03.022174 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:03.022377 INFO::Done
2025-04-21 18:18:03.022563 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:03.023724 INFO::Starting hierarchical adjustment
2025-04-21 18:18:03.02399 INFO::Found 2 batches.
2025-04-21 18:18:03.024162 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:03.024384 INFO::Using default BPPARAM
2025-04-21 18:18:03.02457 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:03.024979 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:03.031043 INFO::Done
2025-04-21 18:18:03.031288 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:03.032324 INFO::ASW Batch was 0.289302853541272 prior to batch effect correction and is now -0.0188397510902178 .
2025-04-21 18:18:03.032547 INFO::ASW Label was 0.768188704939189 prior to batch effect correction and is now 0.95079132847403 .
2025-04-21 18:18:03.032915 INFO::Total function execution time is 0.0138349533081055 s and adjustment time is 0.0070948600769043 s ( 51.28 )
2025-04-21 18:18:03.033188 INFO::Formatting Data.
2025-04-21 18:18:03.033411 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:03.033738 INFO::Removing potential empty rows and columns
2025-04-21 18:18:03.034067 INFO::Found 0 missing values.
2025-04-21 18:18:03.034359 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 18:18:03.035864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:03.036053 INFO::Done
2025-04-21 18:18:03.036236 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:03.037183 INFO::Starting hierarchical adjustment
2025-04-21 18:18:03.03746 INFO::Found 2 batches.
2025-04-21 18:18:03.037699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:03.037956 INFO::Using default BPPARAM
2025-04-21 18:18:03.038206 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:03.038588 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:03.044165 INFO::Done
2025-04-21 18:18:03.044366 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:03.045294 INFO::ASW Batch was 0.289302853541272 prior to batch effect correction and is now -0.0188397510902178 .
2025-04-21 18:18:03.045467 INFO::ASW Label was 0.768188704939189 prior to batch effect correction and is now 0.95079132847403 .
2025-04-21 18:18:03.045757 INFO::Total function execution time is 0.0125589370727539 s and adjustment time is 0.00674200057983398 s ( 53.68 )
2025-04-21 18:18:03.118517 INFO::Formatting Data.
2025-04-21 18:18:03.118823 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:03.119144 INFO::Removing potential empty rows and columns
2025-04-21 18:18:03.119499 INFO::Found 0 missing values.
2025-04-21 18:18:03.120609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:03.12086 INFO::Done
2025-04-21 18:18:03.121035 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:03.121825 INFO::Starting hierarchical adjustment
2025-04-21 18:18:03.12206 INFO::Found 3 batches.
2025-04-21 18:18:03.12224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:03.122435 INFO::Using default BPPARAM
2025-04-21 18:18:03.122678 INFO::Processing subtree level 1
2025-04-21 18:18:03.162319 INFO::Adjusting the last 1 batches sequentially
2025-04-21 18:18:03.16439 INFO::Done
2025-04-21 18:18:03.164857 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:03.166183 INFO::ASW Batch was -0.113234032745842 prior to batch effect correction and is now -0.113234032745842 .
2025-04-21 18:18:03.1669 INFO::Total function execution time is 0.0484180450439453 s and adjustment time is 0.042356014251709 s ( 87.48 )
2025-04-21 18:18:03.167484 INFO::Formatting Data.
2025-04-21 18:18:03.167714 INFO::Typecasting input to dataframe.
2025-04-21 18:18:03.167988 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:03.168355 INFO::Removing potential empty rows and columns
2025-04-21 18:18:03.168926 INFO::Found 0 missing values.
2025-04-21 18:18:03.170036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:03.170229 INFO::Done
2025-04-21 18:18:03.170448 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:03.171122 INFO::Starting hierarchical adjustment
2025-04-21 18:18:03.171356 INFO::Found 3 batches.
2025-04-21 18:18:03.171563 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:03.171808 INFO::Using default BPPARAM
2025-04-21 18:18:03.171981 INFO::Processing subtree level 1
2025-04-21 18:18:03.220894 INFO::Adjusting the last 1 batches sequentially
2025-04-21 18:18:03.222461 INFO::Done
2025-04-21 18:18:03.222831 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:03.224689 INFO::ASW Batch was -0.113234032745842 prior to batch effect correction and is now -0.113234032745842 .
2025-04-21 18:18:03.225291 INFO::Total function execution time is 0.0577709674835205 s and adjustment time is 0.0511271953582764 s ( 88.5 )
2025-04-21 18:18:03.233814 INFO::Formatting Data.
2025-04-21 18:18:03.234259 INFO::Typecasting input to dataframe.
2025-04-21 18:18:03.234677 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:03.235134 INFO::Removing potential empty rows and columns
2025-04-21 18:18:03.235671 INFO::Found 0 missing values.
2025-04-21 18:18:03.236625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:03.236803 INFO::Done
2025-04-21 18:18:03.236991 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:03.237635 INFO::Starting hierarchical adjustment
2025-04-21 18:18:03.237906 INFO::Found 3 batches.
2025-04-21 18:18:03.238087 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:03.238307 INFO::Using default BPPARAM
2025-04-21 18:18:03.238468 INFO::Processing subtree level 1
2025-04-21 18:18:03.288579 INFO::Adjusting the last 1 batches sequentially
2025-04-21 18:18:03.290299 INFO::Done
2025-04-21 18:18:03.290734 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:03.292746 INFO::ASW Batch was -0.00937211759787892 prior to batch effect correction and is now -0.00937211759787892 .
2025-04-21 18:18:03.293496 INFO::Total function execution time is 0.0596919059753418 s and adjustment time is 0.0524828433990479 s ( 87.92 )
2025-04-21 18:18:03.368052 INFO::Formatting Data.
2025-04-21 18:18:03.368468 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:03.368986 INFO::Removing potential empty rows and columns
2025-04-21 18:18:03.370148 INFO::Found 1000 missing values.
2025-04-21 18:18:03.376562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:03.376802 INFO::Done
2025-04-21 18:18:03.377 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:03.379085 INFO::Starting hierarchical adjustment
2025-04-21 18:18:03.379357 INFO::Found 10 batches.
2025-04-21 18:18:03.379542 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:03.379796 INFO::Using default BPPARAM
2025-04-21 18:18:03.380054 INFO::Processing subtree level 1
2025-04-21 18:18:03.450093 INFO::Processing subtree level 2
2025-04-21 18:18:03.515304 INFO::Adjusting the last 1 batches sequentially
2025-04-21 18:18:03.51725 INFO::Done
2025-04-21 18:18:03.517596 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:03.52115 INFO::ASW Batch was 0.487466990552415 prior to batch effect correction and is now 0.487466990552415 .
2025-04-21 18:18:03.52145 INFO::ASW Label was 0.337524863276083 prior to batch effect correction and is now 0.337524863276083 .
2025-04-21 18:18:03.522153 INFO::Total function execution time is 0.154460906982422 s and adjustment time is 0.137923955917358 s ( 89.29 )
2025-04-21 18:18:03.522517 INFO::Formatting Data.
2025-04-21 18:18:03.522753 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:03.523215 INFO::Removing potential empty rows and columns
2025-04-21 18:18:03.524227 INFO::Found 1000 missing values.
2025-04-21 18:18:03.530029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:03.53028 INFO::Done
2025-04-21 18:18:03.530471 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:03.532596 INFO::Starting hierarchical adjustment
2025-04-21 18:18:03.532869 INFO::Found 10 batches.
2025-04-21 18:18:04.148989 INFO::Set up parallel execution backend with 2 workers
2025-04-21 18:18:04.149312 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-04-21 18:18:04.691121 INFO::Adjusting the last 2 batches sequentially
2025-04-21 18:18:04.691699 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-21 18:18:04.697183 INFO::Done
2025-04-21 18:18:04.697404 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:04.699268 INFO::ASW Batch was 0.487466990552415 prior to batch effect correction and is now 0.487466990552415 .
2025-04-21 18:18:04.699448 INFO::ASW Label was 0.337524863276083 prior to batch effect correction and is now 0.337524863276083 .
2025-04-21 18:18:04.699694 INFO::Total function execution time is 1.17718505859375 s and adjustment time is 1.16436910629272 s ( 98.91 )
2025-04-21 18:18:04.811532 INFO::Formatting Data.
2025-04-21 18:18:04.812208 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:04.812771 INFO::Removing potential empty rows and columns
2025-04-21 18:18:04.813464 INFO::Found 0 missing values.
2025-04-21 18:18:04.815437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:04.815695 INFO::Done
2025-04-21 18:18:04.815936 INFO::Acquiring quality metrics before batch effect correction.
2025-04-21 18:18:04.817251 INFO::Starting hierarchical adjustment
2025-04-21 18:18:04.817591 INFO::Found 3 batches.
2025-04-21 18:18:04.817849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-21 18:18:04.818198 INFO::Using default BPPARAM
2025-04-21 18:18:04.818442 INFO::Processing subtree level 1
2025-04-21 18:18:04.882431 INFO::Adjusting the last 1 batches sequentially
2025-04-21 18:18:04.883791 INFO::Done
2025-04-21 18:18:04.884004 INFO::Acquiring quality metrics after batch effect correction.
2025-04-21 18:18:04.886111 INFO::ASW Batch was 0.235506858725134 prior to batch effect correction and is now -0.156963106487865 .
2025-04-21 18:18:04.887156 INFO::ASW Label was -0.176492444286164 prior to batch effect correction and is now 0.0759678127519086 .
2025-04-21 18:18:04.888332 INFO::Total function execution time is 0.0768749713897705 s and adjustment time is 0.0662648677825928 s ( 86.2 )
2025-04-21 18:18:04.949002 INFO::Formatting Data.
2025-04-21 18:18:04.949344 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:04.949671 INFO::Removing potential empty rows and columns
2025-04-21 18:18:04.950083 INFO::Found 2 missing values.
2025-04-21 18:18:04.951019 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:04.951202 INFO::Done
2025-04-21 18:18:04.964339 INFO::Found NA in Reference column
2025-04-21 18:18:04.971142 INFO::Require at least two references per batch.
2025-04-21 18:18:04.980874 INFO::Formatting Data.
2025-04-21 18:18:04.981242 INFO::Recognized SummarizedExperiment
2025-04-21 18:18:04.981431 INFO::Typecasting input to dataframe.
2025-04-21 18:18:04.985411 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:04.985815 INFO::Removing potential empty rows and columns
2025-04-21 18:18:04.987057 INFO::Found 0 missing values.
2025-04-21 18:18:04.989789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:04.990036 INFO::Done
2025-04-21 18:18:04.995898 INFO::Formatting Data.
2025-04-21 18:18:04.996162 INFO::Recognized SummarizedExperiment
2025-04-21 18:18:04.996339 INFO::Typecasting input to dataframe.
2025-04-21 18:18:05.001925 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:05.002333 INFO::Removing potential empty rows and columns
2025-04-21 18:18:05.003576 INFO::Found 0 missing values.
2025-04-21 18:18:05.007158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:05.007334 INFO::Done
2025-04-21 18:18:05.012655 INFO::Formatting Data.
2025-04-21 18:18:05.012854 INFO::Recognized SummarizedExperiment
2025-04-21 18:18:05.013007 INFO::Typecasting input to dataframe.
2025-04-21 18:18:05.018036 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:05.01835 INFO::Removing potential empty rows and columns
2025-04-21 18:18:05.018704 INFO::Found 0 missing values.
2025-04-21 18:18:05.018988 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 18:18:05.020302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:05.02047 INFO::Done
2025-04-21 18:18:05.024475 INFO::Formatting Data.
2025-04-21 18:18:05.024692 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:05.024938 INFO::Removing potential empty rows and columns
2025-04-21 18:18:05.025228 INFO::Found 0 missing values.
2025-04-21 18:18:05.026034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:05.0262 INFO::Done
2025-04-21 18:18:05.030627 INFO::Formatting Data.
2025-04-21 18:18:05.030859 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:05.03111 INFO::Removing potential empty rows and columns
2025-04-21 18:18:05.031395 INFO::Found 0 missing values.
2025-04-21 18:18:05.032287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:05.032475 INFO::Done
2025-04-21 18:18:05.04537 INFO::Formatting Data.
2025-04-21 18:18:05.045652 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:05.046001 INFO::Removing potential empty rows and columns
2025-04-21 18:18:05.046551 INFO::Found 1 missing values.
2025-04-21 18:18:05.047566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:05.047745 INFO::Done
2025-04-21 18:18:05.056705 INFO::Formatting Data.
2025-04-21 18:18:05.056983 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:05.057286 INFO::Removing potential empty rows and columns
2025-04-21 18:18:05.057814 INFO::Found 2 missing values.
2025-04-21 18:18:05.058162 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 18:18:05.05906 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:05.059249 INFO::Done
2025-04-21 18:18:05.065588 INFO::Formatting Data.
2025-04-21 18:18:05.065909 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:05.066224 INFO::Removing potential empty rows and columns
2025-04-21 18:18:05.066566 INFO::Found 2 missing values.
2025-04-21 18:18:05.067157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:05.06737 INFO::Done
2025-04-21 18:18:05.072259 INFO::Formatting Data.
2025-04-21 18:18:05.072507 INFO::Typecasting input to dataframe.
2025-04-21 18:18:05.072755 INFO::Replacing NaNs with NAs.
2025-04-21 18:18:05.073044 INFO::Removing potential empty rows and columns
2025-04-21 18:18:05.073368 INFO::Found 0 missing values.
2025-04-21 18:18:05.074364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-21 18:18:05.074532 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.987 2.029 9.326
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.118 | 0.546 | 7.424 | |
| compute_asw | 0.009 | 0.000 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.006 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |