Yannis Schumann
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-19 10:13 -0500 (Wed, 19 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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 166/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | 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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2025-11-18 19:33:32 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 19:35:03 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 90.5 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 26.386 1.497 19.159
* 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/4.6-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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")
2025-11-18 19:34:41.953942 INFO::Formatting Data.
2025-11-18 19:34:41.957912 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:41.974624 INFO::Removing potential empty rows and columns
2025-11-18 19:34:42.281495 INFO::Found 0 missing values.
2025-11-18 19:34:42.286077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:42.286771 INFO::Done
2025-11-18 19:34:42.287303 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:42.304542 INFO::Starting hierarchical adjustment
2025-11-18 19:34:42.305583 INFO::Found 3 batches.
2025-11-18 19:34:42.306163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:42.307363 INFO::Using default BPPARAM
2025-11-18 19:34:42.308143 INFO::Processing subtree level 1
2025-11-18 19:34:42.480716 INFO::Adjusting the last 1 batches sequentially
2025-11-18 19:34:42.486832 INFO::Done
2025-11-18 19:34:42.488739 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:42.492914 INFO::ASW Batch was -0.125850752162286 prior to batch effect correction and is now -0.125850752162286 .
2025-11-18 19:34:42.49402 INFO::Total function execution time is 0.54125714302063 s and adjustment time is 0.181407928466797 s ( 33.52 )
2025-11-18 19:34:42.514296 INFO::Formatting Data.
2025-11-18 19:34:42.515118 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:42.516209 INFO::Removing potential empty rows and columns
2025-11-18 19:34:42.517607 INFO::Found 0 missing values.
2025-11-18 19:34:42.519118 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.
2025-11-18 19:34:42.533402 INFO::Formatting Data.
2025-11-18 19:34:42.534601 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:42.535991 INFO::Removing potential empty rows and columns
2025-11-18 19:34:42.537253 INFO::Found 0 missing values.
2025-11-18 19:34:42.538227 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.
2025-11-18 19:34:42.562432 INFO::Formatting Data.
2025-11-18 19:34:42.563462 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:42.564815 INFO::Removing potential empty rows and columns
2025-11-18 19:34:42.566366 INFO::Found 0 missing values.
2025-11-18 19:34:42.56734 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.
2025-11-18 19:34:42.572337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:42.573023 INFO::Done
2025-11-18 19:34:42.573703 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:42.577026 INFO::Starting hierarchical adjustment
2025-11-18 19:34:42.57823 INFO::Found 2 batches.
2025-11-18 19:34:42.57909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:42.580183 INFO::Using default BPPARAM
2025-11-18 19:34:42.580994 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:42.582462 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 19:34:42.611921 INFO::Done
2025-11-18 19:34:42.612651 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:42.615045 INFO::ASW Batch was -0.0115129449873316 prior to batch effect correction and is now -0.126710945352049 .
2025-11-18 19:34:42.616322 INFO::Total function execution time is 0.0540380477905273 s and adjustment time is 0.0339460372924805 s ( 62.82 )
2025-11-18 19:34:42.619832 INFO::Formatting Data.
2025-11-18 19:34:42.620852 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:42.631817 INFO::Formatting Data.
2025-11-18 19:34:42.632616 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:42.633939 INFO::Removing potential empty rows and columns
2025-11-18 19:34:42.634989 INFO::Found 0 missing values.
2025-11-18 19:34:42.638649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:42.639536 INFO::Done
2025-11-18 19:34:42.640182 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:42.643436 INFO::Starting hierarchical adjustment
2025-11-18 19:34:42.644495 INFO::Found 2 batches.
2025-11-18 19:34:42.645266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:42.646128 INFO::Using default BPPARAM
2025-11-18 19:34:42.646873 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:42.648256 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 19:34:42.704497 INFO::Done
2025-11-18 19:34:42.705483 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:42.708574 INFO::ASW Batch was 0.0619445072196844 prior to batch effect correction and is now -0.11227233574327 .
2025-11-18 19:34:42.709511 INFO::Total function execution time is 0.0776669979095459 s and adjustment time is 0.0601778030395508 s ( 77.48 )
2025-11-18 19:34:42.711032 INFO::Formatting Data.
2025-11-18 19:34:42.711901 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:42.713077 INFO::Removing potential empty rows and columns
2025-11-18 19:34:42.714475 INFO::Found 0 missing values.
2025-11-18 19:34:42.718688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:42.719618 INFO::Done
2025-11-18 19:34:42.720402 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:42.723123 INFO::Starting hierarchical adjustment
2025-11-18 19:34:42.724113 INFO::Found 2 batches.
2025-11-18 19:34:42.724846 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:42.725685 INFO::Using default BPPARAM
2025-11-18 19:34:42.726534 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:42.727872 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 19:34:42.747399 INFO::Done
2025-11-18 19:34:42.748348 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:42.751025 INFO::ASW Batch was 0.0619445072196844 prior to batch effect correction and is now -0.11227233574327 .
2025-11-18 19:34:42.752082 INFO::Total function execution time is 0.0410740375518799 s and adjustment time is 0.0234460830688477 s ( 57.08 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-18 19:34:46.196707 INFO::Formatting Data.
2025-11-18 19:34:46.197638 INFO::Recognized SummarizedExperiment
2025-11-18 19:34:46.198334 INFO::Typecasting input to dataframe.
2025-11-18 19:34:46.233811 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:46.235443 INFO::Removing potential empty rows and columns
2025-11-18 19:34:46.240343 INFO::Found 0 missing values.
2025-11-18 19:34:46.248709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:46.249619 INFO::Done
2025-11-18 19:34:46.25021 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:46.253307 INFO::Starting hierarchical adjustment
2025-11-18 19:34:46.253992 INFO::Found 2 batches.
2025-11-18 19:34:46.254448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:46.255629 INFO::Using default BPPARAM
2025-11-18 19:34:46.256341 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:46.257645 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 19:34:46.311536 INFO::Done
2025-11-18 19:34:46.312484 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:46.317759 INFO::ASW Batch was -0.0122201159309312 prior to batch effect correction and is now -0.089455675639379 .
2025-11-18 19:34:46.318985 INFO::Total function execution time is 0.122664928436279 s and adjustment time is 0.0576250553131104 s ( 46.98 )
Warning: stack imbalance in '{', 73 then 74
2025-11-18 19:34:46.342625 INFO::Formatting Data.
2025-11-18 19:34:46.34333 INFO::Recognized SummarizedExperiment
2025-11-18 19:34:46.343838 INFO::Typecasting input to dataframe.
2025-11-18 19:34:46.353499 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:46.355139 INFO::Removing potential empty rows and columns
2025-11-18 19:34:46.359936 INFO::Found 0 missing values.
2025-11-18 19:34:46.368187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:46.369162 INFO::Done
2025-11-18 19:34:46.370094 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:46.374836 INFO::Starting hierarchical adjustment
2025-11-18 19:34:46.375613 INFO::Found 2 batches.
2025-11-18 19:34:46.376322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:46.377134 INFO::Using default BPPARAM
2025-11-18 19:34:46.37761 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:46.378797 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 19:34:46.407387 INFO::Done
2025-11-18 19:34:46.408106 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:46.411816 INFO::ASW Batch was 0.0127153908082914 prior to batch effect correction and is now 0.0127153908082914 .
2025-11-18 19:34:46.412962 INFO::Total function execution time is 0.070228099822998 s and adjustment time is 0.0318870544433594 s ( 45.4 )
2025-11-18 19:34:46.440004 INFO::Formatting Data.
2025-11-18 19:34:46.441148 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:46.442635 INFO::Removing potential empty rows and columns
2025-11-18 19:34:46.443713 INFO::Found 0 missing values.
2025-11-18 19:34:46.447881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:46.448733 INFO::Done
2025-11-18 19:34:46.449824 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:46.451958 INFO::Starting hierarchical adjustment
2025-11-18 19:34:46.452633 INFO::Found 3 batches.
2025-11-18 19:34:46.453111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:46.453782 INFO::Using default BPPARAM
2025-11-18 19:34:46.454533 INFO::Processing subtree level 1
2025-11-18 19:34:46.657149 INFO::Adjusting the last 1 batches sequentially
2025-11-18 19:34:46.660697 INFO::Done
2025-11-18 19:34:46.661514 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:46.66623 INFO::ASW Batch was -0.0925489189097561 prior to batch effect correction and is now -0.159699315982583 .
2025-11-18 19:34:46.667464 INFO::Total function execution time is 0.227500200271606 s and adjustment time is 0.20816707611084 s ( 91.5 )
2025-11-18 19:34:46.692718 INFO::Skipping initial DF formatting
2025-11-18 19:34:46.693577 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:46.697594 INFO::Starting hierarchical adjustment
2025-11-18 19:34:46.698567 INFO::Found 5 batches.
2025-11-18 19:34:46.699139 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:46.700362 INFO::Using default BPPARAM
2025-11-18 19:34:46.701257 INFO::Processing subtree level 1
2025-11-18 19:34:46.835096 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:46.837953 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 19:34:46.870367 INFO::Done
2025-11-18 19:34:46.87181 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:46.878055 INFO::ASW Batch was 0.531934445927969 prior to batch effect correction and is now 0.531934445927969 .
2025-11-18 19:34:46.879155 INFO::ASW Label was 0.348331402845561 prior to batch effect correction and is now 0.348331402845561 .
2025-11-18 19:34:46.880621 INFO::Total function execution time is 0.187873125076294 s and adjustment time is 0.171914100646973 s ( 91.51 )
2025-11-18 19:34:46.912152 INFO::Formatting Data.
2025-11-18 19:34:46.913236 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:46.914531 INFO::Removing potential empty rows and columns
2025-11-18 19:34:46.916721 INFO::Found 0 missing values.
2025-11-18 19:34:46.923385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:46.924435 INFO::Done
2025-11-18 19:34:46.925277 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:46.929948 INFO::Starting hierarchical adjustment
2025-11-18 19:34:46.9312 INFO::Found 5 batches.
2025-11-18 19:34:46.932082 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:46.933032 INFO::Using default BPPARAM
2025-11-18 19:34:46.933685 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.
2025-11-18 19:34:47.061348 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.066601 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 19:34:47.090882 INFO::Done
2025-11-18 19:34:47.091889 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:47.095932 INFO::ASW Batch was 0.353498206913309 prior to batch effect correction and is now -0.0802218073855453 .
2025-11-18 19:34:47.096782 INFO::ASW Label was 0.430808582061703 prior to batch effect correction and is now 0.789134095522826 .
2025-11-18 19:34:47.097716 INFO::Total function execution time is 0.185657978057861 s and adjustment time is 0.159885883331299 s ( 86.12 )
2025-11-18 19:34:47.09875 INFO::Formatting Data.
2025-11-18 19:34:47.09953 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:47.100673 INFO::Removing potential empty rows and columns
2025-11-18 19:34:47.102297 INFO::Found 0 missing values.
2025-11-18 19:34:47.105988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:47.106552 INFO::Done
2025-11-18 19:34:47.107471 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:47.11247 INFO::Starting hierarchical adjustment
2025-11-18 19:34:47.113973 INFO::Found 5 batches.
2025-11-18 19:34:47.114796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:47.115691 INFO::Using default BPPARAM
2025-11-18 19:34:47.116447 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.
2025-11-18 19:34:47.239899 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.246471 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 19:34:47.268771 INFO::Done
2025-11-18 19:34:47.269643 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:47.274017 INFO::ASW Batch was 0.353498206913309 prior to batch effect correction and is now -0.0802218073855453 .
2025-11-18 19:34:47.275068 INFO::ASW Label was 0.430808582061703 prior to batch effect correction and is now 0.789134095522826 .
2025-11-18 19:34:47.27669 INFO::Total function execution time is 0.17775297164917 s and adjustment time is 0.15522289276123 s ( 87.33 )
2025-11-18 19:34:47.30007 INFO::Formatting Data.
2025-11-18 19:34:47.300886 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:47.302046 INFO::Removing potential empty rows and columns
2025-11-18 19:34:47.303555 INFO::Found 0 missing values.
2025-11-18 19:34:47.309263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:47.310304 INFO::Done
2025-11-18 19:34:47.311153 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:47.314063 INFO::Starting hierarchical adjustment
2025-11-18 19:34:47.315211 INFO::Found 5 batches.
2025-11-18 19:34:47.316088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:47.317075 INFO::Using default BPPARAM
2025-11-18 19:34:47.317827 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.
2025-11-18 19:34:47.459274 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.466831 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 19:34:47.488415 INFO::Done
2025-11-18 19:34:47.489709 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:47.494419 INFO::ASW Batch was 0.213255668938322 prior to batch effect correction and is now -0.0672962599241423 .
2025-11-18 19:34:47.495344 INFO::ASW Label was 0.502228054293885 prior to batch effect correction and is now 0.859075359212689 .
2025-11-18 19:34:47.496266 INFO::Total function execution time is 0.196182012557983 s and adjustment time is 0.173451900482178 s ( 88.41 )
2025-11-18 19:34:47.497593 INFO::Formatting Data.
2025-11-18 19:34:47.49847 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:47.49968 INFO::Removing potential empty rows and columns
2025-11-18 19:34:47.501038 INFO::Found 0 missing values.
2025-11-18 19:34:47.507586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:47.508431 INFO::Done
2025-11-18 19:34:47.509504 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:47.513478 INFO::Starting hierarchical adjustment
2025-11-18 19:34:47.51463 INFO::Found 5 batches.
2025-11-18 19:34:47.515254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:47.515884 INFO::Using default BPPARAM
2025-11-18 19:34:47.516412 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.
2025-11-18 19:34:47.658773 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.664632 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 19:34:47.686306 INFO::Done
2025-11-18 19:34:47.687258 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:47.692187 INFO::ASW Batch was 0.213255668938322 prior to batch effect correction and is now -0.0672962599241423 .
2025-11-18 19:34:47.693201 INFO::ASW Label was 0.502228054293885 prior to batch effect correction and is now 0.859075359212689 .
2025-11-18 19:34:47.694627 INFO::Total function execution time is 0.197036027908325 s and adjustment time is 0.171904802322388 s ( 87.25 )
2025-11-18 19:34:47.717129 INFO::Formatting Data.
2025-11-18 19:34:47.718111 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:47.719072 INFO::Removing potential empty rows and columns
2025-11-18 19:34:47.720029 INFO::Found 0 missing values.
2025-11-18 19:34:47.723688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:47.724525 INFO::Done
2025-11-18 19:34:47.725334 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:47.72988 INFO::Starting hierarchical adjustment
2025-11-18 19:34:47.730783 INFO::Found 2 batches.
2025-11-18 19:34:47.731318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:47.732302 INFO::Using default BPPARAM
2025-11-18 19:34:47.732886 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.733811 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 19:34:47.750342 INFO::Done
2025-11-18 19:34:47.751422 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:47.754781 INFO::ASW Batch was 0.415884661388755 prior to batch effect correction and is now -0.0375570472621412 .
2025-11-18 19:34:47.755599 INFO::ASW Label was 0.66760571255004 prior to batch effect correction and is now 0.954911446335921 .
2025-11-18 19:34:47.756409 INFO::Total function execution time is 0.0393640995025635 s and adjustment time is 0.0196878910064697 s ( 50.01 )
2025-11-18 19:34:47.757154 INFO::Formatting Data.
2025-11-18 19:34:47.757756 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:47.758561 INFO::Removing potential empty rows and columns
2025-11-18 19:34:47.760251 INFO::Found 0 missing values.
2025-11-18 19:34:47.764066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:47.764864 INFO::Done
2025-11-18 19:34:47.765548 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:47.769059 INFO::Starting hierarchical adjustment
2025-11-18 19:34:47.769779 INFO::Found 2 batches.
2025-11-18 19:34:47.770355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:47.77123 INFO::Using default BPPARAM
2025-11-18 19:34:47.771995 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.773347 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-18 19:34:47.796313 INFO::Done
2025-11-18 19:34:47.803207 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:47.808542 INFO::ASW Batch was 0.415884661388755 prior to batch effect correction and is now -0.0375570472621412 .
2025-11-18 19:34:47.809753 INFO::ASW Label was 0.66760571255004 prior to batch effect correction and is now 0.954911446335921 .
2025-11-18 19:34:47.810752 INFO::Total function execution time is 0.0535941123962402 s and adjustment time is 0.0266389846801758 s ( 49.71 )
2025-11-18 19:34:47.832716 INFO::Formatting Data.
2025-11-18 19:34:47.834964 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:47.835895 INFO::Removing potential empty rows and columns
2025-11-18 19:34:47.837771 INFO::Found 0 missing values.
2025-11-18 19:34:47.840524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:47.841687 INFO::Done
2025-11-18 19:34:47.843999 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:47.84772 INFO::Starting hierarchical adjustment
2025-11-18 19:34:47.849073 INFO::Found 2 batches.
2025-11-18 19:34:47.850158 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:47.851014 INFO::Using default BPPARAM
2025-11-18 19:34:47.851741 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.852692 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 19:34:47.906988 INFO::Done
2025-11-18 19:34:47.907716 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:47.909504 INFO::ASW Batch was 0.124852955370821 prior to batch effect correction and is now -0.0898814759491341 .
2025-11-18 19:34:47.910529 INFO::Total function execution time is 0.0779261589050293 s and adjustment time is 0.0581610202789307 s ( 74.64 )
2025-11-18 19:34:47.931384 INFO::Formatting Data.
2025-11-18 19:34:47.932141 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:47.932961 INFO::Removing potential empty rows and columns
2025-11-18 19:34:47.935095 INFO::Found 0 missing values.
2025-11-18 19:34:47.937528 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.
2025-11-18 19:34:47.942687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:47.943287 INFO::Done
2025-11-18 19:34:47.943834 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:47.947395 INFO::Starting hierarchical adjustment
2025-11-18 19:34:47.948636 INFO::Found 2 batches.
2025-11-18 19:34:47.949588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:47.950782 INFO::Using default BPPARAM
2025-11-18 19:34:47.95144 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.952345 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 19:34:47.971937 INFO::Done
2025-11-18 19:34:47.972634 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:47.975868 INFO::ASW Batch was 0.653004994301721 prior to batch effect correction and is now 0.0545338826471837 .
2025-11-18 19:34:47.976708 INFO::ASW Label was 0.430103855262909 prior to batch effect correction and is now 0.881679640999192 .
2025-11-18 19:34:47.977809 INFO::Total function execution time is 0.0464468002319336 s and adjustment time is 0.0236399173736572 s ( 50.9 )
2025-11-18 19:34:47.978853 INFO::Formatting Data.
2025-11-18 19:34:47.97969 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:47.980978 INFO::Removing potential empty rows and columns
2025-11-18 19:34:47.982165 INFO::Found 0 missing values.
2025-11-18 19:34:47.983028 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.
2025-11-18 19:34:47.987247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:47.987822 INFO::Done
2025-11-18 19:34:47.988328 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:47.991441 INFO::Starting hierarchical adjustment
2025-11-18 19:34:47.992158 INFO::Found 2 batches.
2025-11-18 19:34:47.9932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:47.994086 INFO::Using default BPPARAM
2025-11-18 19:34:47.996088 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:47.997206 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 19:34:48.016518 INFO::Done
2025-11-18 19:34:48.017201 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:48.020261 INFO::ASW Batch was 0.653004994301721 prior to batch effect correction and is now 0.0545338826471837 .
2025-11-18 19:34:48.020863 INFO::ASW Label was 0.430103855262909 prior to batch effect correction and is now 0.881679640999192 .
2025-11-18 19:34:48.022852 INFO::Total function execution time is 0.0440709590911865 s and adjustment time is 0.0244700908660889 s ( 55.52 )
2025-11-18 19:34:48.271429 INFO::Formatting Data.
2025-11-18 19:34:48.272196 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:48.273404 INFO::Removing potential empty rows and columns
2025-11-18 19:34:48.274788 INFO::Found 0 missing values.
2025-11-18 19:34:48.278873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:48.279495 INFO::Done
2025-11-18 19:34:48.279986 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:48.281805 INFO::Starting hierarchical adjustment
2025-11-18 19:34:48.282441 INFO::Found 3 batches.
2025-11-18 19:34:48.282911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:48.283453 INFO::Using default BPPARAM
2025-11-18 19:34:48.283925 INFO::Processing subtree level 1
2025-11-18 19:34:48.418728 INFO::Adjusting the last 1 batches sequentially
2025-11-18 19:34:48.425387 INFO::Done
2025-11-18 19:34:48.42734 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:48.434085 INFO::ASW Batch was -0.0295232121297083 prior to batch effect correction and is now -0.0295232121297083 .
2025-11-18 19:34:48.43649 INFO::Total function execution time is 0.164973020553589 s and adjustment time is 0.142900228500366 s ( 86.62 )
2025-11-18 19:34:48.438149 INFO::Formatting Data.
2025-11-18 19:34:48.439145 INFO::Typecasting input to dataframe.
2025-11-18 19:34:48.440113 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:48.441124 INFO::Removing potential empty rows and columns
2025-11-18 19:34:48.442236 INFO::Found 0 missing values.
2025-11-18 19:34:48.446495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:48.447625 INFO::Done
2025-11-18 19:34:48.44888 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:48.451793 INFO::Starting hierarchical adjustment
2025-11-18 19:34:48.453063 INFO::Found 3 batches.
2025-11-18 19:34:48.453724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:48.454277 INFO::Using default BPPARAM
2025-11-18 19:34:48.454777 INFO::Processing subtree level 1
2025-11-18 19:34:48.576976 INFO::Adjusting the last 1 batches sequentially
2025-11-18 19:34:48.582696 INFO::Done
2025-11-18 19:34:48.583835 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:48.5909 INFO::ASW Batch was -0.0295232121297083 prior to batch effect correction and is now -0.0295232121297083 .
2025-11-18 19:34:48.592527 INFO::Total function execution time is 0.154486894607544 s and adjustment time is 0.129827976226807 s ( 84.04 )
2025-11-18 19:34:48.611021 INFO::Formatting Data.
2025-11-18 19:34:48.61211 INFO::Typecasting input to dataframe.
2025-11-18 19:34:48.613292 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:48.614535 INFO::Removing potential empty rows and columns
2025-11-18 19:34:48.61601 INFO::Found 0 missing values.
2025-11-18 19:34:48.619208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:48.619764 INFO::Done
2025-11-18 19:34:48.620775 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:48.622719 INFO::Starting hierarchical adjustment
2025-11-18 19:34:48.623554 INFO::Found 3 batches.
2025-11-18 19:34:48.624048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:48.62462 INFO::Using default BPPARAM
2025-11-18 19:34:48.625109 INFO::Processing subtree level 1
2025-11-18 19:34:48.748556 INFO::Adjusting the last 1 batches sequentially
2025-11-18 19:34:48.762591 INFO::Done
2025-11-18 19:34:48.764552 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:48.772619 INFO::ASW Batch was 0.00134057396140109 prior to batch effect correction and is now 0.00134057396140109 .
2025-11-18 19:34:48.77684 INFO::Total function execution time is 0.165449142456055 s and adjustment time is 0.138762950897217 s ( 83.87 )
2025-11-18 19:34:48.996764 INFO::Formatting Data.
2025-11-18 19:34:48.998003 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:48.999714 INFO::Removing potential empty rows and columns
2025-11-18 19:34:49.003111 INFO::Found 1000 missing values.
2025-11-18 19:34:49.027632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:49.028665 INFO::Done
2025-11-18 19:34:49.02935 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:49.036263 INFO::Starting hierarchical adjustment
2025-11-18 19:34:49.037535 INFO::Found 10 batches.
2025-11-18 19:34:49.038489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:49.039463 INFO::Using default BPPARAM
2025-11-18 19:34:49.040524 INFO::Processing subtree level 1
2025-11-18 19:34:49.215411 INFO::Processing subtree level 2
2025-11-18 19:34:49.65682 INFO::Adjusting the last 1 batches sequentially
2025-11-18 19:34:49.661166 INFO::Done
2025-11-18 19:34:49.662246 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:49.70385 INFO::ASW Batch was 0.533177742859843 prior to batch effect correction and is now 0.533177742859843 .
2025-11-18 19:34:49.705454 INFO::ASW Label was 0.325398786889953 prior to batch effect correction and is now 0.325398786889953 .
2025-11-18 19:34:49.710836 INFO::Total function execution time is 0.71300482749939 s and adjustment time is 0.623900890350342 s ( 87.5 )
2025-11-18 19:34:49.714115 INFO::Formatting Data.
2025-11-18 19:34:49.715621 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:49.718712 INFO::Removing potential empty rows and columns
2025-11-18 19:34:49.723503 INFO::Found 1000 missing values.
2025-11-18 19:34:49.804467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:49.805545 INFO::Done
2025-11-18 19:34:49.80644 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:49.813133 INFO::Starting hierarchical adjustment
2025-11-18 19:34:49.814015 INFO::Found 10 batches.
2025-11-18 19:34:50.889643 INFO::Set up parallel execution backend with 2 workers
2025-11-18 19:34:50.890294 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-18 19:34:52.272529 INFO::Adjusting the last 2 batches sequentially
2025-11-18 19:34:52.274106 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-18 19:34:52.292911 INFO::Done
2025-11-18 19:34:52.293517 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:52.297816 INFO::ASW Batch was 0.533177742859843 prior to batch effect correction and is now 0.533177742859843 .
2025-11-18 19:34:52.298387 INFO::ASW Label was 0.325398786889953 prior to batch effect correction and is now 0.325398786889953 .
2025-11-18 19:34:52.299405 INFO::Total function execution time is 2.58536505699158 s and adjustment time is 2.47905707359314 s ( 95.89 )
2025-11-18 19:34:52.538865 INFO::Formatting Data.
2025-11-18 19:34:52.540049 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:52.54099 INFO::Removing potential empty rows and columns
2025-11-18 19:34:52.542009 INFO::Found 0 missing values.
2025-11-18 19:34:52.546032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:52.546616 INFO::Done
2025-11-18 19:34:52.547127 INFO::Acquiring quality metrics before batch effect correction.
2025-11-18 19:34:52.550844 INFO::Starting hierarchical adjustment
2025-11-18 19:34:52.551953 INFO::Found 3 batches.
2025-11-18 19:34:52.552713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-18 19:34:52.553618 INFO::Using default BPPARAM
2025-11-18 19:34:52.554379 INFO::Processing subtree level 1
2025-11-18 19:34:52.714801 INFO::Adjusting the last 1 batches sequentially
2025-11-18 19:34:52.736174 INFO::Done
2025-11-18 19:34:52.737573 INFO::Acquiring quality metrics after batch effect correction.
2025-11-18 19:34:52.745907 INFO::ASW Batch was 0.213346931325419 prior to batch effect correction and is now -0.118036000629923 .
2025-11-18 19:34:52.746661 INFO::ASW Label was -0.211423265404315 prior to batch effect correction and is now -0.133019967310882 .
2025-11-18 19:34:52.749813 INFO::Total function execution time is 0.210981845855713 s and adjustment time is 0.184384822845459 s ( 87.39 )
2025-11-18 19:34:52.945078 INFO::Formatting Data.
2025-11-18 19:34:52.946185 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:52.947213 INFO::Removing potential empty rows and columns
2025-11-18 19:34:52.948233 INFO::Found 2 missing values.
2025-11-18 19:34:52.950793 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:52.951377 INFO::Done
2025-11-18 19:34:52.99708 INFO::Found NA in Reference column
2025-11-18 19:34:53.011848 INFO::Require at least two references per batch.
2025-11-18 19:34:53.038859 INFO::Formatting Data.
2025-11-18 19:34:53.039714 INFO::Recognized SummarizedExperiment
2025-11-18 19:34:53.040351 INFO::Typecasting input to dataframe.
2025-11-18 19:34:53.052782 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.054431 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.059786 INFO::Found 0 missing values.
2025-11-18 19:34:53.069494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.070544 INFO::Done
2025-11-18 19:34:53.091041 INFO::Formatting Data.
2025-11-18 19:34:53.091755 INFO::Recognized SummarizedExperiment
2025-11-18 19:34:53.092248 INFO::Typecasting input to dataframe.
2025-11-18 19:34:53.113546 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.115164 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.120417 INFO::Found 0 missing values.
2025-11-18 19:34:53.134039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.13509 INFO::Done
2025-11-18 19:34:53.157639 INFO::Formatting Data.
2025-11-18 19:34:53.158352 INFO::Recognized SummarizedExperiment
2025-11-18 19:34:53.159138 INFO::Typecasting input to dataframe.
2025-11-18 19:34:53.179215 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.180316 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.181582 INFO::Found 0 missing values.
2025-11-18 19:34:53.182732 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.
2025-11-18 19:34:53.18901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.189992 INFO::Done
2025-11-18 19:34:53.207381 INFO::Formatting Data.
2025-11-18 19:34:53.208149 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.209027 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.21007 INFO::Found 0 missing values.
2025-11-18 19:34:53.214031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.214984 INFO::Done
2025-11-18 19:34:53.231993 INFO::Formatting Data.
2025-11-18 19:34:53.23307 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.234064 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.235536 INFO::Found 0 missing values.
2025-11-18 19:34:53.238523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.239165 INFO::Done
2025-11-18 19:34:53.285797 INFO::Formatting Data.
2025-11-18 19:34:53.286966 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.28851 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.290436 INFO::Found 1 missing values.
2025-11-18 19:34:53.294436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.295011 INFO::Done
2025-11-18 19:34:53.322339 INFO::Formatting Data.
2025-11-18 19:34:53.323464 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.324719 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.32599 INFO::Found 2 missing values.
2025-11-18 19:34:53.327203 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.
2025-11-18 19:34:53.329406 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.329906 INFO::Done
2025-11-18 19:34:53.345714 INFO::Formatting Data.
2025-11-18 19:34:53.347118 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.348503 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.349909 INFO::Found 2 missing values.
2025-11-18 19:34:53.35183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.352321 INFO::Done
2025-11-18 19:34:53.367792 INFO::Formatting Data.
2025-11-18 19:34:53.368678 INFO::Typecasting input to dataframe.
2025-11-18 19:34:53.369481 INFO::Replacing NaNs with NAs.
2025-11-18 19:34:53.3703 INFO::Removing potential empty rows and columns
2025-11-18 19:34:53.371575 INFO::Found 0 missing values.
2025-11-18 19:34:53.375766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-18 19:34:53.376603 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.405 3.859 24.857
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.386 | 1.497 | 19.159 | |
| compute_asw | 0.023 | 0.001 | 0.024 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.014 | 0.001 | 0.015 | |
| generate_dataset | 0.014 | 0.001 | 0.015 | |