Yannis Schumann
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-01 12:04 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-10-31 18:41:52 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 18:42:22 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 30.4 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* 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 9.86 0.487 7.188
* 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 ‘1.6.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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")
2025-10-31 18:42:15.686233 INFO::Formatting Data.
2025-10-31 18:42:15.687792 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:15.691956 INFO::Removing potential empty rows and columns
2025-10-31 18:42:15.804532 INFO::Found 0 missing values.
2025-10-31 18:42:15.805788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:15.805999 INFO::Done
2025-10-31 18:42:15.80618 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:15.811884 INFO::Starting hierarchical adjustment
2025-10-31 18:42:15.812224 INFO::Found 3 batches.
2025-10-31 18:42:15.812434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:15.812884 INFO::Using default BPPARAM
2025-10-31 18:42:15.81308 INFO::Processing subtree level 1
2025-10-31 18:42:15.860506 INFO::Adjusting the last 1 batches sequentially
2025-10-31 18:42:15.861946 INFO::Done
2025-10-31 18:42:15.86231 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:15.863825 INFO::ASW Batch was -0.0359301505442904 prior to batch effect correction and is now -0.0359301505442904 .
2025-10-31 18:42:15.864323 INFO::Total function execution time is 0.178408861160278 s and adjustment time is 0.049793004989624 s ( 27.91 )
2025-10-31 18:42:15.871667 INFO::Formatting Data.
2025-10-31 18:42:15.871927 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:15.872256 INFO::Removing potential empty rows and columns
2025-10-31 18:42:15.8727 INFO::Found 0 missing values.
2025-10-31 18:42:15.873047 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.
2025-10-31 18:42:15.877732 INFO::Formatting Data.
2025-10-31 18:42:15.877941 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:15.878249 INFO::Removing potential empty rows and columns
2025-10-31 18:42:15.878702 INFO::Found 0 missing values.
2025-10-31 18:42:15.878988 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.
2025-10-31 18:42:15.884547 INFO::Formatting Data.
2025-10-31 18:42:15.884777 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:15.885054 INFO::Removing potential empty rows and columns
2025-10-31 18:42:15.885357 INFO::Found 0 missing values.
2025-10-31 18:42:15.885619 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.
2025-10-31 18:42:15.886986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:15.887167 INFO::Done
2025-10-31 18:42:15.887336 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:15.887989 INFO::Starting hierarchical adjustment
2025-10-31 18:42:15.888208 INFO::Found 2 batches.
2025-10-31 18:42:15.88839 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:15.888618 INFO::Using default BPPARAM
2025-10-31 18:42:15.888787 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:15.889049 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-31 18:42:15.898756 INFO::Done
2025-10-31 18:42:15.899004 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:15.89964 INFO::ASW Batch was -0.0712680225292154 prior to batch effect correction and is now -0.110096921726602 .
2025-10-31 18:42:15.899898 INFO::Total function execution time is 0.0153520107269287 s and adjustment time is 0.0105650424957275 s ( 68.82 )
2025-10-31 18:42:15.900891 INFO::Formatting Data.
2025-10-31 18:42:15.901099 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:15.904043 INFO::Formatting Data.
2025-10-31 18:42:15.904269 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:15.904529 INFO::Removing potential empty rows and columns
2025-10-31 18:42:15.904859 INFO::Found 0 missing values.
2025-10-31 18:42:15.905724 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:15.905896 INFO::Done
2025-10-31 18:42:15.906049 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:15.906725 INFO::Starting hierarchical adjustment
2025-10-31 18:42:15.907047 INFO::Found 2 batches.
2025-10-31 18:42:15.907241 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:15.907431 INFO::Using default BPPARAM
2025-10-31 18:42:15.90759 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:15.907863 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:15.92512 INFO::Done
2025-10-31 18:42:15.925337 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:15.925929 INFO::ASW Batch was -0.00285623862509956 prior to batch effect correction and is now -0.123214772817471 .
2025-10-31 18:42:15.926155 INFO::Total function execution time is 0.0221230983734131 s and adjustment time is 0.0181388854980469 s ( 81.99 )
2025-10-31 18:42:15.926449 INFO::Formatting Data.
2025-10-31 18:42:15.926613 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:15.926856 INFO::Removing potential empty rows and columns
2025-10-31 18:42:15.927138 INFO::Found 0 missing values.
2025-10-31 18:42:15.927911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:15.928063 INFO::Done
2025-10-31 18:42:15.928204 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:15.92874 INFO::Starting hierarchical adjustment
2025-10-31 18:42:15.928943 INFO::Found 2 batches.
2025-10-31 18:42:15.929089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:15.929258 INFO::Using default BPPARAM
2025-10-31 18:42:15.929412 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:15.929662 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:15.933932 INFO::Done
2025-10-31 18:42:15.934117 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:15.934667 INFO::ASW Batch was -0.00285623862509956 prior to batch effect correction and is now -0.123214772817471 .
2025-10-31 18:42:15.934895 INFO::Total function execution time is 0.00843405723571777 s and adjustment time is 0.00502395629882812 s ( 59.57 )
2025-10-31 18:42:17.082962 INFO::Formatting Data.
2025-10-31 18:42:17.08321 INFO::Recognized SummarizedExperiment
2025-10-31 18:42:17.083362 INFO::Typecasting input to dataframe.
2025-10-31 18:42:17.09349 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.093918 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.095082 INFO::Found 0 missing values.
2025-10-31 18:42:17.09724 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.097436 INFO::Done
2025-10-31 18:42:17.097605 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.098815 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.099041 INFO::Found 2 batches.
2025-10-31 18:42:17.099186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.099515 INFO::Using default BPPARAM
2025-10-31 18:42:17.099659 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.099945 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-31 18:42:17.117076 INFO::Done
2025-10-31 18:42:17.117312 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.118513 INFO::ASW Batch was -0.022203598758113 prior to batch effect correction and is now -0.0933609699228598 .
2025-10-31 18:42:17.11878 INFO::Total function execution time is 0.0359160900115967 s and adjustment time is 0.0180659294128418 s ( 50.3 )
2025-10-31 18:42:17.124965 INFO::Formatting Data.
2025-10-31 18:42:17.125207 INFO::Recognized SummarizedExperiment
2025-10-31 18:42:17.12537 INFO::Typecasting input to dataframe.
2025-10-31 18:42:17.128361 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.128718 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.129839 INFO::Found 0 missing values.
2025-10-31 18:42:17.131979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.132145 INFO::Done
2025-10-31 18:42:17.132298 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.133502 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.133749 INFO::Found 2 batches.
2025-10-31 18:42:17.133907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.134094 INFO::Using default BPPARAM
2025-10-31 18:42:17.134241 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.134538 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-31 18:42:17.142416 INFO::Done
2025-10-31 18:42:17.142616 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.143758 INFO::ASW Batch was 0.0184021622186881 prior to batch effect correction and is now 0.0184021622186881 .
2025-10-31 18:42:17.144026 INFO::Total function execution time is 0.0190601348876953 s and adjustment time is 0.00871896743774414 s ( 45.74 )
2025-10-31 18:42:17.150508 INFO::Formatting Data.
2025-10-31 18:42:17.150727 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.150992 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.151297 INFO::Found 0 missing values.
2025-10-31 18:42:17.152127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.152288 INFO::Done
2025-10-31 18:42:17.152438 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.153031 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.15323 INFO::Found 3 batches.
2025-10-31 18:42:17.153373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.153549 INFO::Using default BPPARAM
2025-10-31 18:42:17.153688 INFO::Processing subtree level 1
2025-10-31 18:42:17.206092 INFO::Adjusting the last 1 batches sequentially
2025-10-31 18:42:17.207496 INFO::Done
2025-10-31 18:42:17.207845 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.20942 INFO::ASW Batch was -0.0708665088383777 prior to batch effect correction and is now -0.162127367400128 .
2025-10-31 18:42:17.210183 INFO::Total function execution time is 0.0596680641174316 s and adjustment time is 0.0542981624603271 s ( 91 )
2025-10-31 18:42:17.216651 INFO::Skipping initial DF formatting
2025-10-31 18:42:17.216895 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.218282 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.218529 INFO::Found 5 batches.
2025-10-31 18:42:17.218711 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.218924 INFO::Using default BPPARAM
2025-10-31 18:42:17.219086 INFO::Processing subtree level 1
2025-10-31 18:42:17.323746 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.326318 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-31 18:42:17.334523 INFO::Done
2025-10-31 18:42:17.334926 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.33707 INFO::ASW Batch was 0.544750481832721 prior to batch effect correction and is now 0.544750481832721 .
2025-10-31 18:42:17.337273 INFO::ASW Label was 0.382522294315275 prior to batch effect correction and is now 0.382522294315275 .
2025-10-31 18:42:17.340791 INFO::Total function execution time is 0.124085903167725 s and adjustment time is 0.116040945053101 s ( 93.52 )
2025-10-31 18:42:17.379367 INFO::Formatting Data.
2025-10-31 18:42:17.379712 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.380108 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.380462 INFO::Found 0 missing values.
2025-10-31 18:42:17.381709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.38189 INFO::Done
2025-10-31 18:42:17.382044 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.383037 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.383273 INFO::Found 5 batches.
2025-10-31 18:42:17.383442 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.383666 INFO::Using default BPPARAM
2025-10-31 18:42:17.38386 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.44567 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.447897 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.459419 INFO::Done
2025-10-31 18:42:17.459939 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.462388 INFO::ASW Batch was 0.326687313289217 prior to batch effect correction and is now -0.0764909832214525 .
2025-10-31 18:42:17.46269 INFO::ASW Label was 0.385607397442332 prior to batch effect correction and is now 0.849077800147806 .
2025-10-31 18:42:17.463094 INFO::Total function execution time is 0.0837531089782715 s and adjustment time is 0.076153039932251 s ( 90.93 )
2025-10-31 18:42:17.463502 INFO::Formatting Data.
2025-10-31 18:42:17.46373 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.464102 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.464557 INFO::Found 0 missing values.
2025-10-31 18:42:17.466575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.466861 INFO::Done
2025-10-31 18:42:17.467094 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.468341 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.468966 INFO::Found 5 batches.
2025-10-31 18:42:17.469195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.46944 INFO::Using default BPPARAM
2025-10-31 18:42:17.469624 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.527393 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.530739 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.540527 INFO::Done
2025-10-31 18:42:17.540841 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.542703 INFO::ASW Batch was 0.326687313289217 prior to batch effect correction and is now -0.0764909832214525 .
2025-10-31 18:42:17.542946 INFO::ASW Label was 0.385607397442332 prior to batch effect correction and is now 0.849077800147806 .
2025-10-31 18:42:17.543454 INFO::Total function execution time is 0.0799210071563721 s and adjustment time is 0.0716729164123535 s ( 89.68 )
2025-10-31 18:42:17.550916 INFO::Formatting Data.
2025-10-31 18:42:17.551201 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.551531 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.551912 INFO::Found 0 missing values.
2025-10-31 18:42:17.553299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.553485 INFO::Done
2025-10-31 18:42:17.553663 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.554831 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.555087 INFO::Found 5 batches.
2025-10-31 18:42:17.555278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.555501 INFO::Using default BPPARAM
2025-10-31 18:42:17.555666 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.604409 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.605711 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.617267 INFO::Done
2025-10-31 18:42:17.617676 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.619719 INFO::ASW Batch was 0.411247337862874 prior to batch effect correction and is now -0.105915369325626 .
2025-10-31 18:42:17.620033 INFO::ASW Label was 0.395023780600925 prior to batch effect correction and is now 0.723023587363515 .
2025-10-31 18:42:17.620475 INFO::Total function execution time is 0.0695300102233887 s and adjustment time is 0.0622248649597168 s ( 89.49 )
2025-10-31 18:42:17.620886 INFO::Formatting Data.
2025-10-31 18:42:17.621205 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.621588 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.622097 INFO::Found 0 missing values.
2025-10-31 18:42:17.623954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.624215 INFO::Done
2025-10-31 18:42:17.624443 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.625852 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.626193 INFO::Found 5 batches.
2025-10-31 18:42:17.626477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.626828 INFO::Using default BPPARAM
2025-10-31 18:42:17.627051 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.690806 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.69226 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.70279 INFO::Done
2025-10-31 18:42:17.703136 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.705339 INFO::ASW Batch was 0.411247337862874 prior to batch effect correction and is now -0.105915369325626 .
2025-10-31 18:42:17.705783 INFO::ASW Label was 0.395023780600925 prior to batch effect correction and is now 0.723023587363515 .
2025-10-31 18:42:17.706235 INFO::Total function execution time is 0.085291862487793 s and adjustment time is 0.0766539573669434 s ( 89.87 )
2025-10-31 18:42:17.718318 INFO::Formatting Data.
2025-10-31 18:42:17.718669 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.719045 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.719554 INFO::Found 0 missing values.
2025-10-31 18:42:17.720723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.720939 INFO::Done
2025-10-31 18:42:17.721171 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.72248 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.722778 INFO::Found 2 batches.
2025-10-31 18:42:17.722985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.723261 INFO::Using default BPPARAM
2025-10-31 18:42:17.723457 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.723785 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.729904 INFO::Done
2025-10-31 18:42:17.730166 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.731316 INFO::ASW Batch was 0.288753724567355 prior to batch effect correction and is now -0.0272679155623563 .
2025-10-31 18:42:17.731531 INFO::ASW Label was 0.697408882858354 prior to batch effect correction and is now 0.910935851932345 .
2025-10-31 18:42:17.731806 INFO::Total function execution time is 0.0135488510131836 s and adjustment time is 0.00718402862548828 s ( 53.02 )
2025-10-31 18:42:17.732087 INFO::Formatting Data.
2025-10-31 18:42:17.732286 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.732581 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.732928 INFO::Found 0 missing values.
2025-10-31 18:42:17.733826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.734029 INFO::Done
2025-10-31 18:42:17.734208 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.735179 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.735439 INFO::Found 2 batches.
2025-10-31 18:42:17.735618 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.735837 INFO::Using default BPPARAM
2025-10-31 18:42:17.735998 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.7363 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-31 18:42:17.741663 INFO::Done
2025-10-31 18:42:17.741882 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.742869 INFO::ASW Batch was 0.288753724567355 prior to batch effect correction and is now -0.0272679155623563 .
2025-10-31 18:42:17.743077 INFO::ASW Label was 0.697408882858354 prior to batch effect correction and is now 0.910935851932345 .
2025-10-31 18:42:17.743343 INFO::Total function execution time is 0.0112419128417969 s and adjustment time is 0.00626802444458008 s ( 55.76 )
2025-10-31 18:42:17.748077 INFO::Formatting Data.
2025-10-31 18:42:17.74832 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.748605 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.748914 INFO::Found 0 missing values.
2025-10-31 18:42:17.749621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.749799 INFO::Done
2025-10-31 18:42:17.749978 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.750559 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.75078 INFO::Found 2 batches.
2025-10-31 18:42:17.750966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.751165 INFO::Using default BPPARAM
2025-10-31 18:42:17.751336 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.751621 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-31 18:42:17.763972 INFO::Done
2025-10-31 18:42:17.764249 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.764959 INFO::ASW Batch was 0.119061216431515 prior to batch effect correction and is now -0.126799277285625 .
2025-10-31 18:42:17.765253 INFO::Total function execution time is 0.0171880722045898 s and adjustment time is 0.0132210254669189 s ( 76.92 )
2025-10-31 18:42:17.772084 INFO::Formatting Data.
2025-10-31 18:42:17.772422 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.772746 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.773163 INFO::Found 0 missing values.
2025-10-31 18:42:17.77371 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.
2025-10-31 18:42:17.775501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.775743 INFO::Done
2025-10-31 18:42:17.775924 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.777079 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.777356 INFO::Found 2 batches.
2025-10-31 18:42:17.777541 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.777789 INFO::Using default BPPARAM
2025-10-31 18:42:17.777971 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.778334 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-31 18:42:17.785172 INFO::Done
2025-10-31 18:42:17.785434 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.78652 INFO::ASW Batch was 0.661830782818765 prior to batch effect correction and is now 0.0563395856628861 .
2025-10-31 18:42:17.786785 INFO::ASW Label was 0.397039648465532 prior to batch effect correction and is now 0.869713394390334 .
2025-10-31 18:42:17.78707 INFO::Total function execution time is 0.0150229930877686 s and adjustment time is 0.00786805152893066 s ( 52.37 )
2025-10-31 18:42:17.78737 INFO::Formatting Data.
2025-10-31 18:42:17.787568 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.787918 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.788305 INFO::Found 0 missing values.
2025-10-31 18:42:17.788615 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.
2025-10-31 18:42:17.79027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.790513 INFO::Done
2025-10-31 18:42:17.790702 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.791829 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.792081 INFO::Found 2 batches.
2025-10-31 18:42:17.792265 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.792475 INFO::Using default BPPARAM
2025-10-31 18:42:17.792642 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:17.792981 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-31 18:42:17.799641 INFO::Done
2025-10-31 18:42:17.799916 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.800987 INFO::ASW Batch was 0.661830782818765 prior to batch effect correction and is now 0.0563395856628861 .
2025-10-31 18:42:17.801195 INFO::ASW Label was 0.397039648465532 prior to batch effect correction and is now 0.869713394390334 .
2025-10-31 18:42:17.801519 INFO::Total function execution time is 0.0141348838806152 s and adjustment time is 0.00760197639465332 s ( 53.78 )
2025-10-31 18:42:17.873064 INFO::Formatting Data.
2025-10-31 18:42:17.87333 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.873608 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.873939 INFO::Found 0 missing values.
2025-10-31 18:42:17.874803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.874996 INFO::Done
2025-10-31 18:42:17.87518 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.875835 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.876042 INFO::Found 3 batches.
2025-10-31 18:42:17.876199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.876376 INFO::Using default BPPARAM
2025-10-31 18:42:17.876525 INFO::Processing subtree level 1
2025-10-31 18:42:17.925681 INFO::Adjusting the last 1 batches sequentially
2025-10-31 18:42:17.926975 INFO::Done
2025-10-31 18:42:17.927234 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.928726 INFO::ASW Batch was -0.0823908365568674 prior to batch effect correction and is now -0.0823908365568674 .
2025-10-31 18:42:17.929339 INFO::Total function execution time is 0.0562629699707031 s and adjustment time is 0.0509638786315918 s ( 90.58 )
2025-10-31 18:42:17.929855 INFO::Formatting Data.
2025-10-31 18:42:17.930124 INFO::Typecasting input to dataframe.
2025-10-31 18:42:17.930404 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.930746 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.931159 INFO::Found 0 missing values.
2025-10-31 18:42:17.932109 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:17.932291 INFO::Done
2025-10-31 18:42:17.932455 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:17.933122 INFO::Starting hierarchical adjustment
2025-10-31 18:42:17.933361 INFO::Found 3 batches.
2025-10-31 18:42:17.933521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:17.933779 INFO::Using default BPPARAM
2025-10-31 18:42:17.933985 INFO::Processing subtree level 1
2025-10-31 18:42:17.987205 INFO::Adjusting the last 1 batches sequentially
2025-10-31 18:42:17.988574 INFO::Done
2025-10-31 18:42:17.988859 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:17.990279 INFO::ASW Batch was -0.0823908365568674 prior to batch effect correction and is now -0.0823908365568674 .
2025-10-31 18:42:17.990738 INFO::Total function execution time is 0.0608680248260498 s and adjustment time is 0.0552499294281006 s ( 90.77 )
2025-10-31 18:42:17.998132 INFO::Formatting Data.
2025-10-31 18:42:17.99845 INFO::Typecasting input to dataframe.
2025-10-31 18:42:17.998781 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:17.999135 INFO::Removing potential empty rows and columns
2025-10-31 18:42:17.999642 INFO::Found 0 missing values.
2025-10-31 18:42:18.000854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:18.001089 INFO::Done
2025-10-31 18:42:18.001305 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:18.002154 INFO::Starting hierarchical adjustment
2025-10-31 18:42:18.002447 INFO::Found 3 batches.
2025-10-31 18:42:18.002654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:18.002958 INFO::Using default BPPARAM
2025-10-31 18:42:18.003188 INFO::Processing subtree level 1
2025-10-31 18:42:18.053859 INFO::Adjusting the last 1 batches sequentially
2025-10-31 18:42:18.055811 INFO::Done
2025-10-31 18:42:18.056106 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:18.058466 INFO::ASW Batch was -0.13529497870801 prior to batch effect correction and is now -0.13529497870801 .
2025-10-31 18:42:18.059687 INFO::Total function execution time is 0.0615341663360596 s and adjustment time is 0.0534219741821289 s ( 86.82 )
2025-10-31 18:42:18.135856 INFO::Formatting Data.
2025-10-31 18:42:18.136217 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:18.136615 INFO::Removing potential empty rows and columns
2025-10-31 18:42:18.137672 INFO::Found 1000 missing values.
2025-10-31 18:42:18.14347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:18.143693 INFO::Done
2025-10-31 18:42:18.143879 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:18.146049 INFO::Starting hierarchical adjustment
2025-10-31 18:42:18.146303 INFO::Found 10 batches.
2025-10-31 18:42:18.146484 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:18.14673 INFO::Using default BPPARAM
2025-10-31 18:42:18.146892 INFO::Processing subtree level 1
2025-10-31 18:42:18.20669 INFO::Processing subtree level 2
2025-10-31 18:42:18.260704 INFO::Adjusting the last 1 batches sequentially
2025-10-31 18:42:18.262233 INFO::Done
2025-10-31 18:42:18.262572 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:18.265212 INFO::ASW Batch was 0.477413120977305 prior to batch effect correction and is now 0.477413120977305 .
2025-10-31 18:42:18.265455 INFO::ASW Label was 0.329064750424509 prior to batch effect correction and is now 0.329064750424509 .
2025-10-31 18:42:18.265819 INFO::Total function execution time is 0.129969120025635 s and adjustment time is 0.115978956222534 s ( 89.24 )
2025-10-31 18:42:18.266098 INFO::Formatting Data.
2025-10-31 18:42:18.266288 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:18.266721 INFO::Removing potential empty rows and columns
2025-10-31 18:42:18.267672 INFO::Found 1000 missing values.
2025-10-31 18:42:18.273477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:18.273726 INFO::Done
2025-10-31 18:42:18.273894 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:18.27592 INFO::Starting hierarchical adjustment
2025-10-31 18:42:18.276177 INFO::Found 10 batches.
2025-10-31 18:42:18.752965 INFO::Set up parallel execution backend with 2 workers
2025-10-31 18:42:18.753261 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-31 18:42:19.198085 INFO::Adjusting the last 2 batches sequentially
2025-10-31 18:42:19.198614 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-31 18:42:19.203855 INFO::Done
2025-10-31 18:42:19.20405 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:19.205753 INFO::ASW Batch was 0.477413120977305 prior to batch effect correction and is now 0.477413120977305 .
2025-10-31 18:42:19.205918 INFO::ASW Label was 0.329064750424509 prior to batch effect correction and is now 0.329064750424509 .
2025-10-31 18:42:19.206144 INFO::Total function execution time is 0.940046072006226 s and adjustment time is 0.927738189697266 s ( 98.69 )
2025-10-31 18:42:19.264664 INFO::Formatting Data.
2025-10-31 18:42:19.264946 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.265512 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.266021 INFO::Found 0 missing values.
2025-10-31 18:42:19.267369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.267563 INFO::Done
2025-10-31 18:42:19.267735 INFO::Acquiring quality metrics before batch effect correction.
2025-10-31 18:42:19.268674 INFO::Starting hierarchical adjustment
2025-10-31 18:42:19.268898 INFO::Found 3 batches.
2025-10-31 18:42:19.269065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-31 18:42:19.269285 INFO::Using default BPPARAM
2025-10-31 18:42:19.269449 INFO::Processing subtree level 1
2025-10-31 18:42:19.32153 INFO::Adjusting the last 1 batches sequentially
2025-10-31 18:42:19.323084 INFO::Done
2025-10-31 18:42:19.323312 INFO::Acquiring quality metrics after batch effect correction.
2025-10-31 18:42:19.325481 INFO::ASW Batch was 0.145539168829291 prior to batch effect correction and is now -0.174864277448523 .
2025-10-31 18:42:19.325706 INFO::ASW Label was -0.185391046648525 prior to batch effect correction and is now 0.0041529107217422 .
2025-10-31 18:42:19.326418 INFO::Total function execution time is 0.0617489814758301 s and adjustment time is 0.0542311668395996 s ( 87.83 )
2025-10-31 18:42:19.378547 INFO::Formatting Data.
2025-10-31 18:42:19.378881 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.379232 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.379655 INFO::Found 2 missing values.
2025-10-31 18:42:19.380637 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.380825 INFO::Done
2025-10-31 18:42:19.391029 INFO::Found NA in Reference column
2025-10-31 18:42:19.394557 INFO::Require at least two references per batch.
2025-10-31 18:42:19.402491 INFO::Formatting Data.
2025-10-31 18:42:19.402728 INFO::Recognized SummarizedExperiment
2025-10-31 18:42:19.402898 INFO::Typecasting input to dataframe.
2025-10-31 18:42:19.406677 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.407049 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.408326 INFO::Found 0 missing values.
2025-10-31 18:42:19.410637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.410811 INFO::Done
2025-10-31 18:42:19.416017 INFO::Formatting Data.
2025-10-31 18:42:19.41623 INFO::Recognized SummarizedExperiment
2025-10-31 18:42:19.416401 INFO::Typecasting input to dataframe.
2025-10-31 18:42:19.421745 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.42215 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.423386 INFO::Found 0 missing values.
2025-10-31 18:42:19.427019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.427209 INFO::Done
2025-10-31 18:42:19.432508 INFO::Formatting Data.
2025-10-31 18:42:19.432748 INFO::Recognized SummarizedExperiment
2025-10-31 18:42:19.432926 INFO::Typecasting input to dataframe.
2025-10-31 18:42:19.438518 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.438844 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.439199 INFO::Found 0 missing values.
2025-10-31 18:42:19.4395 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.
2025-10-31 18:42:19.440957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.441145 INFO::Done
2025-10-31 18:42:19.444713 INFO::Formatting Data.
2025-10-31 18:42:19.444923 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.445185 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.445471 INFO::Found 0 missing values.
2025-10-31 18:42:19.446328 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.446489 INFO::Done
2025-10-31 18:42:19.450539 INFO::Formatting Data.
2025-10-31 18:42:19.450768 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.451068 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.452078 INFO::Found 0 missing values.
2025-10-31 18:42:19.453456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.453687 INFO::Done
2025-10-31 18:42:19.466606 INFO::Formatting Data.
2025-10-31 18:42:19.466904 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.467236 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.467643 INFO::Found 1 missing values.
2025-10-31 18:42:19.468595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.468854 INFO::Done
2025-10-31 18:42:19.477534 INFO::Formatting Data.
2025-10-31 18:42:19.477819 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.47814 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.478442 INFO::Found 2 missing values.
2025-10-31 18:42:19.478773 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.
2025-10-31 18:42:19.47957 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.479787 INFO::Done
2025-10-31 18:42:19.484021 INFO::Formatting Data.
2025-10-31 18:42:19.484258 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.484569 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.484909 INFO::Found 2 missing values.
2025-10-31 18:42:19.4855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.485717 INFO::Done
2025-10-31 18:42:19.489964 INFO::Formatting Data.
2025-10-31 18:42:19.490205 INFO::Typecasting input to dataframe.
2025-10-31 18:42:19.490449 INFO::Replacing NaNs with NAs.
2025-10-31 18:42:19.490716 INFO::Removing potential empty rows and columns
2025-10-31 18:42:19.491072 INFO::Found 0 missing values.
2025-10-31 18:42:19.491958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-31 18:42:19.492162 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.634 1.637 8.484
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.860 | 0.487 | 7.188 | |
| compute_asw | 0.009 | 0.000 | 0.009 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.004 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |