Yannis Schumann
| Snapshot Date: 2025-11-03 13:45 -0500 (Mon, 03 Nov 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-04 12:03 -0500 (Tue, 04 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" | 4902 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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: 2025-11-03 19:41:32 -0500 (Mon, 03 Nov 2025) |
| EndedAt: 2025-11-03 19:42:54 -0500 (Mon, 03 Nov 2025) |
| EllapsedTime: 82.5 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_1.6.0.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: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* 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 26.357 1.404 18.902
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** 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: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-11-03 19:42:33.827121 INFO::Formatting Data.
2025-11-03 19:42:33.831025 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:33.845529 INFO::Removing potential empty rows and columns
2025-11-03 19:42:34.172263 INFO::Found 0 missing values.
2025-11-03 19:42:34.175729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:34.176615 INFO::Done
2025-11-03 19:42:34.177265 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:34.194975 INFO::Starting hierarchical adjustment
2025-11-03 19:42:34.196195 INFO::Found 3 batches.
2025-11-03 19:42:34.197049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:34.1988 INFO::Using default BPPARAM
2025-11-03 19:42:34.199425 INFO::Processing subtree level 1
2025-11-03 19:42:34.366354 INFO::Adjusting the last 1 batches sequentially
2025-11-03 19:42:34.370945 INFO::Done
2025-11-03 19:42:34.373314 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:34.378367 INFO::ASW Batch was -0.103100267705285 prior to batch effect correction and is now -0.103100267705285 .
2025-11-03 19:42:34.380331 INFO::Total function execution time is 0.553498029708862 s and adjustment time is 0.174949884414673 s ( 31.61 )
2025-11-03 19:42:34.409452 INFO::Formatting Data.
2025-11-03 19:42:34.410616 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:34.411952 INFO::Removing potential empty rows and columns
2025-11-03 19:42:34.413542 INFO::Found 0 missing values.
2025-11-03 19:42:34.415422 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.
2025-11-03 19:42:34.430893 INFO::Formatting Data.
2025-11-03 19:42:34.432164 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:34.433666 INFO::Removing potential empty rows and columns
2025-11-03 19:42:34.435301 INFO::Found 0 missing values.
2025-11-03 19:42:34.436678 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.
2025-11-03 19:42:34.457905 INFO::Formatting Data.
2025-11-03 19:42:34.459017 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:34.460434 INFO::Removing potential empty rows and columns
2025-11-03 19:42:34.462031 INFO::Found 0 missing values.
2025-11-03 19:42:34.463423 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.
2025-11-03 19:42:34.469594 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:34.47047 INFO::Done
2025-11-03 19:42:34.471385 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:34.473624 INFO::Starting hierarchical adjustment
2025-11-03 19:42:34.474572 INFO::Found 2 batches.
2025-11-03 19:42:34.475071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:34.475942 INFO::Using default BPPARAM
2025-11-03 19:42:34.476496 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:34.47739 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-03 19:42:34.500407 INFO::Done
2025-11-03 19:42:34.501054 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:34.503249 INFO::ASW Batch was -0.0403359993189856 prior to batch effect correction and is now -0.113945093658624 .
2025-11-03 19:42:34.504404 INFO::Total function execution time is 0.0465810298919678 s and adjustment time is 0.0260169506072998 s ( 55.85 )
2025-11-03 19:42:34.508343 INFO::Formatting Data.
2025-11-03 19:42:34.5094 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:34.520765 INFO::Formatting Data.
2025-11-03 19:42:34.521551 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:34.522734 INFO::Removing potential empty rows and columns
2025-11-03 19:42:34.5241 INFO::Found 0 missing values.
2025-11-03 19:42:34.527759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:34.528283 INFO::Done
2025-11-03 19:42:34.529138 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:34.531565 INFO::Starting hierarchical adjustment
2025-11-03 19:42:34.532354 INFO::Found 2 batches.
2025-11-03 19:42:34.532873 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:34.53352 INFO::Using default BPPARAM
2025-11-03 19:42:34.534439 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:34.535928 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-03 19:42:34.555798 INFO::Done
2025-11-03 19:42:34.556772 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:34.559637 INFO::ASW Batch was -0.0159723706885249 prior to batch effect correction and is now -0.121704278672095 .
2025-11-03 19:42:34.560836 INFO::Total function execution time is 0.0400350093841553 s and adjustment time is 0.0235450267791748 s ( 58.81 )
2025-11-03 19:42:34.562408 INFO::Formatting Data.
2025-11-03 19:42:34.563103 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:34.563903 INFO::Removing potential empty rows and columns
2025-11-03 19:42:34.564819 INFO::Found 0 missing values.
2025-11-03 19:42:34.567685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:34.568452 INFO::Done
2025-11-03 19:42:34.569475 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:34.571843 INFO::Starting hierarchical adjustment
2025-11-03 19:42:34.572621 INFO::Found 2 batches.
2025-11-03 19:42:34.57333 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:34.573941 INFO::Using default BPPARAM
2025-11-03 19:42:34.574412 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:34.575239 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-03 19:42:34.59397 INFO::Done
2025-11-03 19:42:34.594765 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:34.597118 INFO::ASW Batch was -0.0159723706885249 prior to batch effect correction and is now -0.121704278672095 .
2025-11-03 19:42:34.598149 INFO::Total function execution time is 0.0358061790466309 s and adjustment time is 0.0214900970458984 s ( 60.02 )
2025-11-03 19:42:38.026436 INFO::Formatting Data.
2025-11-03 19:42:38.02729 INFO::Recognized SummarizedExperiment
2025-11-03 19:42:38.027961 INFO::Typecasting input to dataframe.
2025-11-03 19:42:38.059536 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:38.060646 INFO::Removing potential empty rows and columns
2025-11-03 19:42:38.064304 INFO::Found 0 missing values.
2025-11-03 19:42:38.070562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:38.071232 INFO::Done
2025-11-03 19:42:38.071918 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:38.076319 INFO::Starting hierarchical adjustment
2025-11-03 19:42:38.077289 INFO::Found 2 batches.
2025-11-03 19:42:38.077967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:38.079285 INFO::Using default BPPARAM
2025-11-03 19:42:38.079935 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:38.08125 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-03 19:42:38.143922 INFO::Done
2025-11-03 19:42:38.144576 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:38.148865 INFO::ASW Batch was -0.00958560625103757 prior to batch effect correction and is now -0.0951922773947102 .
2025-11-03 19:42:38.150236 INFO::Total function execution time is 0.123950004577637 s and adjustment time is 0.0668280124664307 s ( 53.92 )
2025-11-03 19:42:38.174491 INFO::Formatting Data.
2025-11-03 19:42:38.175517 INFO::Recognized SummarizedExperiment
2025-11-03 19:42:38.176309 INFO::Typecasting input to dataframe.
2025-11-03 19:42:38.187961 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:38.18969 INFO::Removing potential empty rows and columns
2025-11-03 19:42:38.19465 INFO::Found 0 missing values.
2025-11-03 19:42:38.203808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:38.204728 INFO::Done
2025-11-03 19:42:38.20545 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:38.209479 INFO::Starting hierarchical adjustment
2025-11-03 19:42:38.210543 INFO::Found 2 batches.
2025-11-03 19:42:38.211314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:38.212143 INFO::Using default BPPARAM
2025-11-03 19:42:38.212845 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:38.213855 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-03 19:42:38.245349 INFO::Done
2025-11-03 19:42:38.246227 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:38.249996 INFO::ASW Batch was -0.00811381564121983 prior to batch effect correction and is now -0.00811381564121983 .
2025-11-03 19:42:38.250849 INFO::Total function execution time is 0.0763950347900391 s and adjustment time is 0.0350069999694824 s ( 45.82 )
2025-11-03 19:42:38.274271 INFO::Formatting Data.
2025-11-03 19:42:38.275304 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:38.276175 INFO::Removing potential empty rows and columns
2025-11-03 19:42:38.277079 INFO::Found 0 missing values.
2025-11-03 19:42:38.280405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:38.280994 INFO::Done
2025-11-03 19:42:38.281684 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:38.284171 INFO::Starting hierarchical adjustment
2025-11-03 19:42:38.284765 INFO::Found 3 batches.
2025-11-03 19:42:38.285179 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:38.285982 INFO::Using default BPPARAM
2025-11-03 19:42:38.286714 INFO::Processing subtree level 1
2025-11-03 19:42:38.504544 INFO::Adjusting the last 1 batches sequentially
2025-11-03 19:42:38.512704 INFO::Done
2025-11-03 19:42:38.513411 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:38.520765 INFO::ASW Batch was -0.0397447686932244 prior to batch effect correction and is now -0.148851132841168 .
2025-11-03 19:42:38.52563 INFO::Total function execution time is 0.249025106430054 s and adjustment time is 0.227999925613403 s ( 91.56 )
2025-11-03 19:42:38.55248 INFO::Skipping initial DF formatting
2025-11-03 19:42:38.554169 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:38.559924 INFO::Starting hierarchical adjustment
2025-11-03 19:42:38.561115 INFO::Found 5 batches.
2025-11-03 19:42:38.561986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:38.563224 INFO::Using default BPPARAM
2025-11-03 19:42:38.563788 INFO::Processing subtree level 1
2025-11-03 19:42:38.729975 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:38.742207 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-03 19:42:38.775875 INFO::Done
2025-11-03 19:42:38.776911 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:38.785211 INFO::ASW Batch was 0.493970669235498 prior to batch effect correction and is now 0.493970669235498 .
2025-11-03 19:42:38.785958 INFO::ASW Label was 0.394252312736633 prior to batch effect correction and is now 0.394252312736633 .
2025-11-03 19:42:38.789127 INFO::Total function execution time is 0.23548698425293 s and adjustment time is 0.214977025985718 s ( 91.29 )
2025-11-03 19:42:38.817267 INFO::Formatting Data.
2025-11-03 19:42:38.81903 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:38.82088 INFO::Removing potential empty rows and columns
2025-11-03 19:42:38.822893 INFO::Found 0 missing values.
2025-11-03 19:42:38.829291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:38.830328 INFO::Done
2025-11-03 19:42:38.831275 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:38.835567 INFO::Starting hierarchical adjustment
2025-11-03 19:42:38.836727 INFO::Found 5 batches.
2025-11-03 19:42:38.83753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:38.838192 INFO::Using default BPPARAM
2025-11-03 19:42:38.838717 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.
2025-11-03 19:42:38.99958 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:39.012298 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-03 19:42:39.051085 INFO::Done
2025-11-03 19:42:39.051845 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:39.056034 INFO::ASW Batch was 0.337521158032839 prior to batch effect correction and is now -0.0591649352612345 .
2025-11-03 19:42:39.056665 INFO::ASW Label was 0.468780167220091 prior to batch effect correction and is now 0.85799034947718 .
2025-11-03 19:42:39.057884 INFO::Total function execution time is 0.240761995315552 s and adjustment time is 0.214498996734619 s ( 89.09 )
2025-11-03 19:42:39.059034 INFO::Formatting Data.
2025-11-03 19:42:39.059646 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:39.0609 INFO::Removing potential empty rows and columns
2025-11-03 19:42:39.062111 INFO::Found 0 missing values.
2025-11-03 19:42:39.067683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:39.068665 INFO::Done
2025-11-03 19:42:39.070072 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:39.074221 INFO::Starting hierarchical adjustment
2025-11-03 19:42:39.075295 INFO::Found 5 batches.
2025-11-03 19:42:39.075913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:39.076492 INFO::Using default BPPARAM
2025-11-03 19:42:39.076981 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.
2025-11-03 19:42:39.232415 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:39.244369 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-03 19:42:39.276754 INFO::Done
2025-11-03 19:42:39.277827 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:39.28168 INFO::ASW Batch was 0.337521158032839 prior to batch effect correction and is now -0.0591649352612345 .
2025-11-03 19:42:39.282716 INFO::ASW Label was 0.468780167220091 prior to batch effect correction and is now 0.85799034947718 .
2025-11-03 19:42:39.284279 INFO::Total function execution time is 0.22520112991333 s and adjustment time is 0.201711893081665 s ( 89.57 )
2025-11-03 19:42:39.306922 INFO::Formatting Data.
2025-11-03 19:42:39.308045 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:39.30942 INFO::Removing potential empty rows and columns
2025-11-03 19:42:39.310892 INFO::Found 0 missing values.
2025-11-03 19:42:39.316065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:39.317018 INFO::Done
2025-11-03 19:42:39.317804 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:39.322228 INFO::Starting hierarchical adjustment
2025-11-03 19:42:39.323601 INFO::Found 5 batches.
2025-11-03 19:42:39.324453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:39.325308 INFO::Using default BPPARAM
2025-11-03 19:42:39.326232 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.
2025-11-03 19:42:39.456837 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:39.48286 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-03 19:42:39.519945 INFO::Done
2025-11-03 19:42:39.521014 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:39.526541 INFO::ASW Batch was 0.484535154502922 prior to batch effect correction and is now -0.0533692036063656 .
2025-11-03 19:42:39.527706 INFO::ASW Label was 0.16001121905079 prior to batch effect correction and is now 0.763103855191738 .
2025-11-03 19:42:39.529385 INFO::Total function execution time is 0.22261381149292 s and adjustment time is 0.19654393196106 s ( 88.29 )
2025-11-03 19:42:39.530423 INFO::Formatting Data.
2025-11-03 19:42:39.531263 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:39.532589 INFO::Removing potential empty rows and columns
2025-11-03 19:42:39.533567 INFO::Found 0 missing values.
2025-11-03 19:42:39.537985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:39.539137 INFO::Done
2025-11-03 19:42:39.539889 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:39.543329 INFO::Starting hierarchical adjustment
2025-11-03 19:42:39.544053 INFO::Found 5 batches.
2025-11-03 19:42:39.544566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:39.545158 INFO::Using default BPPARAM
2025-11-03 19:42:39.54564 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.
2025-11-03 19:42:39.678935 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:39.703603 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-03 19:42:39.743739 INFO::Done
2025-11-03 19:42:39.744765 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:39.750325 INFO::ASW Batch was 0.484535154502922 prior to batch effect correction and is now -0.0533692036063656 .
2025-11-03 19:42:39.75197 INFO::ASW Label was 0.16001121905079 prior to batch effect correction and is now 0.763103855191738 .
2025-11-03 19:42:39.753571 INFO::Total function execution time is 0.222928047180176 s and adjustment time is 0.199769020080566 s ( 89.61 )
2025-11-03 19:42:39.776542 INFO::Formatting Data.
2025-11-03 19:42:39.777671 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:39.779035 INFO::Removing potential empty rows and columns
2025-11-03 19:42:39.780561 INFO::Found 0 missing values.
2025-11-03 19:42:39.78501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:39.785955 INFO::Done
2025-11-03 19:42:39.786769 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:39.790218 INFO::Starting hierarchical adjustment
2025-11-03 19:42:39.791374 INFO::Found 2 batches.
2025-11-03 19:42:39.79189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:39.792582 INFO::Using default BPPARAM
2025-11-03 19:42:39.793209 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:39.794093 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-03 19:42:39.810849 INFO::Done
2025-11-03 19:42:39.81199 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:39.816151 INFO::ASW Batch was 0.482102540814096 prior to batch effect correction and is now -0.0262759333102993 .
2025-11-03 19:42:39.816969 INFO::ASW Label was 0.577412170353855 prior to batch effect correction and is now 0.904863047962011 .
2025-11-03 19:42:39.818006 INFO::Total function execution time is 0.0415871143341064 s and adjustment time is 0.0195009708404541 s ( 46.89 )
2025-11-03 19:42:39.819051 INFO::Formatting Data.
2025-11-03 19:42:39.819901 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:39.821191 INFO::Removing potential empty rows and columns
2025-11-03 19:42:39.822497 INFO::Found 0 missing values.
2025-11-03 19:42:39.827172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:39.828037 INFO::Done
2025-11-03 19:42:39.828608 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:39.831335 INFO::Starting hierarchical adjustment
2025-11-03 19:42:39.832352 INFO::Found 2 batches.
2025-11-03 19:42:39.833101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:39.833937 INFO::Using default BPPARAM
2025-11-03 19:42:39.834658 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:39.835947 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-03 19:42:39.8573 INFO::Done
2025-11-03 19:42:39.858357 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:39.863375 INFO::ASW Batch was 0.482102540814096 prior to batch effect correction and is now -0.0262759333102993 .
2025-11-03 19:42:39.864399 INFO::ASW Label was 0.577412170353855 prior to batch effect correction and is now 0.904863047962011 .
2025-11-03 19:42:39.8653 INFO::Total function execution time is 0.0463089942932129 s and adjustment time is 0.0250868797302246 s ( 54.17 )
2025-11-03 19:42:39.882566 INFO::Formatting Data.
2025-11-03 19:42:39.88338 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:39.884246 INFO::Removing potential empty rows and columns
2025-11-03 19:42:39.885376 INFO::Found 0 missing values.
2025-11-03 19:42:39.888412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:39.889218 INFO::Done
2025-11-03 19:42:39.88995 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:39.892245 INFO::Starting hierarchical adjustment
2025-11-03 19:42:39.892905 INFO::Found 2 batches.
2025-11-03 19:42:39.893411 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:39.894147 INFO::Using default BPPARAM
2025-11-03 19:42:39.894896 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:39.89619 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-03 19:42:39.936487 INFO::Done
2025-11-03 19:42:39.937207 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:39.940115 INFO::ASW Batch was -0.0438878681939965 prior to batch effect correction and is now -0.0873105018989708 .
2025-11-03 19:42:39.941358 INFO::Total function execution time is 0.0589718818664551 s and adjustment time is 0.0436899662017822 s ( 74.09 )
2025-11-03 19:42:39.959506 INFO::Formatting Data.
2025-11-03 19:42:39.96031 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:39.96122 INFO::Removing potential empty rows and columns
2025-11-03 19:42:39.962596 INFO::Found 0 missing values.
2025-11-03 19:42:39.963735 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.
2025-11-03 19:42:39.968541 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:39.969463 INFO::Done
2025-11-03 19:42:39.97028 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:39.97334 INFO::Starting hierarchical adjustment
2025-11-03 19:42:39.974062 INFO::Found 2 batches.
2025-11-03 19:42:39.974843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:39.975451 INFO::Using default BPPARAM
2025-11-03 19:42:39.975938 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:39.977009 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-03 19:42:39.998981 INFO::Done
2025-11-03 19:42:40.000777 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:40.004743 INFO::ASW Batch was 0.628468700744968 prior to batch effect correction and is now -0.0252703160749583 .
2025-11-03 19:42:40.0054 INFO::ASW Label was 0.432951787597453 prior to batch effect correction and is now 0.882742613102477 .
2025-11-03 19:42:40.00616 INFO::Total function execution time is 0.046727180480957 s and adjustment time is 0.0249600410461426 s ( 53.42 )
2025-11-03 19:42:40.007181 INFO::Formatting Data.
2025-11-03 19:42:40.008013 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:40.009216 INFO::Removing potential empty rows and columns
2025-11-03 19:42:40.010547 INFO::Found 0 missing values.
2025-11-03 19:42:40.011871 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.
2025-11-03 19:42:40.079486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:40.080544 INFO::Done
2025-11-03 19:42:40.081408 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:40.084535 INFO::Starting hierarchical adjustment
2025-11-03 19:42:40.085459 INFO::Found 2 batches.
2025-11-03 19:42:40.086193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:40.087052 INFO::Using default BPPARAM
2025-11-03 19:42:40.087597 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:40.088774 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-03 19:42:40.110846 INFO::Done
2025-11-03 19:42:40.11158 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:40.114326 INFO::ASW Batch was 0.628468700744968 prior to batch effect correction and is now -0.0252703160749583 .
2025-11-03 19:42:40.115202 INFO::ASW Label was 0.432951787597453 prior to batch effect correction and is now 0.882742613102477 .
2025-11-03 19:42:40.116115 INFO::Total function execution time is 0.109009981155396 s and adjustment time is 0.0256190299987793 s ( 23.5 )
2025-11-03 19:42:40.352902 INFO::Formatting Data.
2025-11-03 19:42:40.353697 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:40.354565 INFO::Removing potential empty rows and columns
2025-11-03 19:42:40.355831 INFO::Found 0 missing values.
2025-11-03 19:42:40.35891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:40.359572 INFO::Done
2025-11-03 19:42:40.360352 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:40.362856 INFO::Starting hierarchical adjustment
2025-11-03 19:42:40.363562 INFO::Found 3 batches.
2025-11-03 19:42:40.364051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:40.364625 INFO::Using default BPPARAM
2025-11-03 19:42:40.36511 INFO::Processing subtree level 1
2025-11-03 19:42:40.508712 INFO::Adjusting the last 1 batches sequentially
2025-11-03 19:42:40.512788 INFO::Done
2025-11-03 19:42:40.513677 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:40.518671 INFO::ASW Batch was -0.0941486310978874 prior to batch effect correction and is now -0.0941486310978874 .
2025-11-03 19:42:40.520721 INFO::Total function execution time is 0.167654037475586 s and adjustment time is 0.149338006973267 s ( 89.08 )
2025-11-03 19:42:40.522768 INFO::Formatting Data.
2025-11-03 19:42:40.524003 INFO::Typecasting input to dataframe.
2025-11-03 19:42:40.525422 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:40.527102 INFO::Removing potential empty rows and columns
2025-11-03 19:42:40.529124 INFO::Found 0 missing values.
2025-11-03 19:42:40.533725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:40.534512 INFO::Done
2025-11-03 19:42:40.535318 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:40.538285 INFO::Starting hierarchical adjustment
2025-11-03 19:42:40.539262 INFO::Found 3 batches.
2025-11-03 19:42:40.539912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:40.540758 INFO::Using default BPPARAM
2025-11-03 19:42:40.541395 INFO::Processing subtree level 1
2025-11-03 19:42:40.676438 INFO::Adjusting the last 1 batches sequentially
2025-11-03 19:42:40.681636 INFO::Done
2025-11-03 19:42:40.683123 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:40.687857 INFO::ASW Batch was -0.0941486310978874 prior to batch effect correction and is now -0.0941486310978874 .
2025-11-03 19:42:40.68984 INFO::Total function execution time is 0.167131185531616 s and adjustment time is 0.142523050308228 s ( 85.28 )
2025-11-03 19:42:40.714471 INFO::Formatting Data.
2025-11-03 19:42:40.715618 INFO::Typecasting input to dataframe.
2025-11-03 19:42:40.716712 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:40.718425 INFO::Removing potential empty rows and columns
2025-11-03 19:42:40.720271 INFO::Found 0 missing values.
2025-11-03 19:42:40.723925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:40.724612 INFO::Done
2025-11-03 19:42:40.725283 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:40.728644 INFO::Starting hierarchical adjustment
2025-11-03 19:42:40.729907 INFO::Found 3 batches.
2025-11-03 19:42:40.730827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:40.732121 INFO::Using default BPPARAM
2025-11-03 19:42:40.733077 INFO::Processing subtree level 1
2025-11-03 19:42:40.866649 INFO::Adjusting the last 1 batches sequentially
2025-11-03 19:42:40.874515 INFO::Done
2025-11-03 19:42:40.875575 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:40.879168 INFO::ASW Batch was 0.0208267513596592 prior to batch effect correction and is now 0.0208267513596592 .
2025-11-03 19:42:40.880877 INFO::Total function execution time is 0.166409015655518 s and adjustment time is 0.144835948944092 s ( 87.04 )
2025-11-03 19:42:41.096541 INFO::Formatting Data.
2025-11-03 19:42:41.097566 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:41.099475 INFO::Removing potential empty rows and columns
2025-11-03 19:42:41.10463 INFO::Found 1000 missing values.
2025-11-03 19:42:41.137564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:41.138484 INFO::Done
2025-11-03 19:42:41.13919 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:41.146624 INFO::Starting hierarchical adjustment
2025-11-03 19:42:41.148068 INFO::Found 10 batches.
2025-11-03 19:42:41.149094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:41.150218 INFO::Using default BPPARAM
2025-11-03 19:42:41.151151 INFO::Processing subtree level 1
2025-11-03 19:42:41.335554 INFO::Processing subtree level 2
2025-11-03 19:42:41.558102 INFO::Adjusting the last 1 batches sequentially
2025-11-03 19:42:41.562729 INFO::Done
2025-11-03 19:42:41.563904 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:41.573678 INFO::ASW Batch was 0.475023175525149 prior to batch effect correction and is now 0.475023175525149 .
2025-11-03 19:42:41.574965 INFO::ASW Label was 0.357617180293211 prior to batch effect correction and is now 0.357617180293211 .
2025-11-03 19:42:41.576577 INFO::Total function execution time is 0.480014085769653 s and adjustment time is 0.4148850440979 s ( 86.43 )
2025-11-03 19:42:41.578132 INFO::Formatting Data.
2025-11-03 19:42:41.578995 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:41.580411 INFO::Removing potential empty rows and columns
2025-11-03 19:42:41.584409 INFO::Found 1000 missing values.
2025-11-03 19:42:41.620309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:41.621592 INFO::Done
2025-11-03 19:42:41.622671 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:41.631058 INFO::Starting hierarchical adjustment
2025-11-03 19:42:41.632677 INFO::Found 10 batches.
2025-11-03 19:42:42.759935 INFO::Set up parallel execution backend with 2 workers
2025-11-03 19:42:42.760878 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-03 19:42:44.019145 INFO::Adjusting the last 2 batches sequentially
2025-11-03 19:42:44.020676 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-03 19:42:44.04067 INFO::Done
2025-11-03 19:42:44.041558 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:44.04801 INFO::ASW Batch was 0.475023175525149 prior to batch effect correction and is now 0.475023175525149 .
2025-11-03 19:42:44.048906 INFO::ASW Label was 0.357617180293211 prior to batch effect correction and is now 0.357617180293211 .
2025-11-03 19:42:44.049933 INFO::Total function execution time is 2.4719340801239 s and adjustment time is 2.40831208229065 s ( 97.43 )
2025-11-03 19:42:44.309355 INFO::Formatting Data.
2025-11-03 19:42:44.310241 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:44.311852 INFO::Removing potential empty rows and columns
2025-11-03 19:42:44.312959 INFO::Found 0 missing values.
2025-11-03 19:42:44.317413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:44.318819 INFO::Done
2025-11-03 19:42:44.319374 INFO::Acquiring quality metrics before batch effect correction.
2025-11-03 19:42:44.323803 INFO::Starting hierarchical adjustment
2025-11-03 19:42:44.325006 INFO::Found 3 batches.
2025-11-03 19:42:44.325683 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-03 19:42:44.326729 INFO::Using default BPPARAM
2025-11-03 19:42:44.327494 INFO::Processing subtree level 1
2025-11-03 19:42:44.496127 INFO::Adjusting the last 1 batches sequentially
2025-11-03 19:42:44.509333 INFO::Done
2025-11-03 19:42:44.516319 INFO::Acquiring quality metrics after batch effect correction.
2025-11-03 19:42:44.525389 INFO::ASW Batch was 0.200930165503859 prior to batch effect correction and is now -0.14408149015715 .
2025-11-03 19:42:44.526475 INFO::ASW Label was -0.219135656290538 prior to batch effect correction and is now -0.0872548799474197 .
2025-11-03 19:42:44.529718 INFO::Total function execution time is 0.219207048416138 s and adjustment time is 0.18464183807373 s ( 84.23 )
2025-11-03 19:42:44.710338 INFO::Formatting Data.
2025-11-03 19:42:44.711155 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:44.712141 INFO::Removing potential empty rows and columns
2025-11-03 19:42:44.713508 INFO::Found 2 missing values.
2025-11-03 19:42:44.717676 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:44.718512 INFO::Done
2025-11-03 19:42:44.760957 INFO::Found NA in Reference column
2025-11-03 19:42:44.776708 INFO::Require at least two references per batch.
2025-11-03 19:42:44.802709 INFO::Formatting Data.
2025-11-03 19:42:44.803629 INFO::Recognized SummarizedExperiment
2025-11-03 19:42:44.80417 INFO::Typecasting input to dataframe.
2025-11-03 19:42:44.814235 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:44.815492 INFO::Removing potential empty rows and columns
2025-11-03 19:42:44.819292 INFO::Found 0 missing values.
2025-11-03 19:42:44.826518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:44.827649 INFO::Done
2025-11-03 19:42:44.848979 INFO::Formatting Data.
2025-11-03 19:42:44.85005 INFO::Recognized SummarizedExperiment
2025-11-03 19:42:44.850935 INFO::Typecasting input to dataframe.
2025-11-03 19:42:44.875822 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:44.877734 INFO::Removing potential empty rows and columns
2025-11-03 19:42:44.881453 INFO::Found 0 missing values.
2025-11-03 19:42:44.896731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:44.897442 INFO::Done
2025-11-03 19:42:44.916491 INFO::Formatting Data.
2025-11-03 19:42:44.917249 INFO::Recognized SummarizedExperiment
2025-11-03 19:42:44.917918 INFO::Typecasting input to dataframe.
2025-11-03 19:42:44.943411 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:44.944734 INFO::Removing potential empty rows and columns
2025-11-03 19:42:44.946047 INFO::Found 0 missing values.
2025-11-03 19:42:44.946967 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.
2025-11-03 19:42:44.951681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:44.952317 INFO::Done
2025-11-03 19:42:44.968468 INFO::Formatting Data.
2025-11-03 19:42:44.969267 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:44.970114 INFO::Removing potential empty rows and columns
2025-11-03 19:42:44.971689 INFO::Found 0 missing values.
2025-11-03 19:42:44.974541 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:44.975074 INFO::Done
2025-11-03 19:42:44.990617 INFO::Formatting Data.
2025-11-03 19:42:44.991844 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:44.992967 INFO::Removing potential empty rows and columns
2025-11-03 19:42:44.994166 INFO::Found 0 missing values.
2025-11-03 19:42:44.99704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:44.997625 INFO::Done
2025-11-03 19:42:45.045317 INFO::Formatting Data.
2025-11-03 19:42:45.04629 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:45.047599 INFO::Removing potential empty rows and columns
2025-11-03 19:42:45.049384 INFO::Found 1 missing values.
2025-11-03 19:42:45.052991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:45.053852 INFO::Done
2025-11-03 19:42:45.081266 INFO::Formatting Data.
2025-11-03 19:42:45.082029 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:45.082843 INFO::Removing potential empty rows and columns
2025-11-03 19:42:45.083695 INFO::Found 2 missing values.
2025-11-03 19:42:45.084518 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.
2025-11-03 19:42:45.087271 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:45.088032 INFO::Done
2025-11-03 19:42:45.102312 INFO::Formatting Data.
2025-11-03 19:42:45.10353 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:45.104597 INFO::Removing potential empty rows and columns
2025-11-03 19:42:45.105506 INFO::Found 2 missing values.
2025-11-03 19:42:45.106989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:45.107741 INFO::Done
2025-11-03 19:42:45.123839 INFO::Formatting Data.
2025-11-03 19:42:45.12487 INFO::Typecasting input to dataframe.
2025-11-03 19:42:45.125912 INFO::Replacing NaNs with NAs.
2025-11-03 19:42:45.127001 INFO::Removing potential empty rows and columns
2025-11-03 19:42:45.128206 INFO::Found 0 missing values.
2025-11-03 19:42:45.132021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-03 19:42:45.1329 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.245 3.881 24.609
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.357 | 1.404 | 18.902 | |
| compute_asw | 0.026 | 0.002 | 0.027 | |
| count_existing | 0.017 | 0.001 | 0.019 | |
| generate_data_covariables | 0.014 | 0.001 | 0.016 | |
| generate_dataset | 0.011 | 0.002 | 0.013 | |