Yannis Schumann
| Snapshot Date: 2025-11-26 13:40 -0500 (Wed, 26 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 2025-11-27 11:37 -0500 (Thu, 27 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" | 4865 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| 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 167/2328 | 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-11-26 21:21:21 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 21:22:49 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 23.864 1.112 16.815
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
2025-11-26 21:22:10.888237 INFO::Formatting Data.
2025-11-26 21:22:10.889728 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:10.901342 INFO::Removing potential empty rows and columns
2025-11-26 21:22:11.142666 INFO::Found 0 missing values.
2025-11-26 21:22:11.14613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:11.146778 INFO::Done
2025-11-26 21:22:11.147345 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:11.15856 INFO::Starting hierarchical adjustment
2025-11-26 21:22:11.159423 INFO::Found 3 batches.
2025-11-26 21:22:11.159981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:11.161086 INFO::Using default BPPARAM
2025-11-26 21:22:11.161636 INFO::Processing subtree level 1
2025-11-26 21:22:11.262727 INFO::Adjusting the last 1 batches sequentially
2025-11-26 21:22:11.264604 INFO::Done
2025-11-26 21:22:11.265392 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:11.268257 INFO::ASW Batch was 0.0366547251349904 prior to batch effect correction and is now 0.0366547251349904 .
2025-11-26 21:22:11.269515 INFO::Total function execution time is 0.382043123245239 s and adjustment time is 0.105311393737793 s ( 27.57 )
2025-11-26 21:22:11.284216 INFO::Formatting Data.
2025-11-26 21:22:11.285052 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:11.286049 INFO::Removing potential empty rows and columns
2025-11-26 21:22:11.287259 INFO::Found 0 missing values.
2025-11-26 21:22:11.28827 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.
2025-11-26 21:22:11.299724 INFO::Formatting Data.
2025-11-26 21:22:11.300535 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:11.301541 INFO::Removing potential empty rows and columns
2025-11-26 21:22:11.302773 INFO::Found 0 missing values.
2025-11-26 21:22:11.303832 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.
2025-11-26 21:22:11.320291 INFO::Formatting Data.
2025-11-26 21:22:11.321045 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:11.321923 INFO::Removing potential empty rows and columns
2025-11-26 21:22:11.32297 INFO::Found 0 missing values.
2025-11-26 21:22:11.323907 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.
2025-11-26 21:22:11.328398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:11.328989 INFO::Done
2025-11-26 21:22:11.329549 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:11.331598 INFO::Starting hierarchical adjustment
2025-11-26 21:22:11.33233 INFO::Found 2 batches.
2025-11-26 21:22:11.332895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:11.333565 INFO::Using default BPPARAM
2025-11-26 21:22:11.334129 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:11.335089 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 21:22:11.355648 INFO::Done
2025-11-26 21:22:11.356342 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:11.358366 INFO::ASW Batch was -0.0487341613519641 prior to batch effect correction and is now -0.129281556905695 .
2025-11-26 21:22:11.359182 INFO::Total function execution time is 0.0389504432678223 s and adjustment time is 0.0234472751617432 s ( 60.2 )
2025-11-26 21:22:11.361995 INFO::Formatting Data.
2025-11-26 21:22:11.362622 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:11.37139 INFO::Formatting Data.
2025-11-26 21:22:11.37208 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:11.372979 INFO::Removing potential empty rows and columns
2025-11-26 21:22:11.374022 INFO::Found 0 missing values.
2025-11-26 21:22:11.376869 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:11.377416 INFO::Done
2025-11-26 21:22:11.378078 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:11.380094 INFO::Starting hierarchical adjustment
2025-11-26 21:22:11.380807 INFO::Found 2 batches.
2025-11-26 21:22:11.381348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:11.381999 INFO::Using default BPPARAM
2025-11-26 21:22:11.382533 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:11.383473 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 21:22:11.419146 INFO::Done
2025-11-26 21:22:11.419807 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:11.421652 INFO::ASW Batch was -0.025099036137948 prior to batch effect correction and is now -0.126240299200694 .
2025-11-26 21:22:11.422403 INFO::Total function execution time is 0.0510401725769043 s and adjustment time is 0.0384726524353027 s ( 75.38 )
2025-11-26 21:22:11.423369 INFO::Formatting Data.
2025-11-26 21:22:11.42395 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:11.424745 INFO::Removing potential empty rows and columns
2025-11-26 21:22:11.425694 INFO::Found 0 missing values.
2025-11-26 21:22:11.428231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:11.428743 INFO::Done
2025-11-26 21:22:11.429245 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:11.431 INFO::Starting hierarchical adjustment
2025-11-26 21:22:11.431642 INFO::Found 2 batches.
2025-11-26 21:22:11.432146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:11.432711 INFO::Using default BPPARAM
2025-11-26 21:22:11.433208 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:11.434043 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 21:22:11.447198 INFO::Done
2025-11-26 21:22:11.447772 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:11.449572 INFO::ASW Batch was -0.025099036137948 prior to batch effect correction and is now -0.126240299200694 .
2025-11-26 21:22:11.450299 INFO::Total function execution time is 0.0269265174865723 s and adjustment time is 0.0156822204589844 s ( 58.24 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-26 21:22:14.325992 INFO::Formatting Data.
2025-11-26 21:22:14.326764 INFO::Recognized SummarizedExperiment
2025-11-26 21:22:14.327276 INFO::Typecasting input to dataframe.
2025-11-26 21:22:14.356526 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:14.357688 INFO::Removing potential empty rows and columns
2025-11-26 21:22:14.360703 INFO::Found 0 missing values.
2025-11-26 21:22:14.366488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:14.367128 INFO::Done
2025-11-26 21:22:14.367619 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:14.370723 INFO::Starting hierarchical adjustment
2025-11-26 21:22:14.371407 INFO::Found 2 batches.
2025-11-26 21:22:14.371898 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:14.372935 INFO::Using default BPPARAM
2025-11-26 21:22:14.373412 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:14.374289 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 21:22:14.421253 INFO::Done
2025-11-26 21:22:14.421941 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:14.424996 INFO::ASW Batch was 0.015719177843671 prior to batch effect correction and is now -0.0894047427291473 .
2025-11-26 21:22:14.425749 INFO::Total function execution time is 0.100098848342896 s and adjustment time is 0.0499584674835205 s ( 49.91 )
Warning: stack imbalance in '{', 73 then 75
2025-11-26 21:22:14.442183 INFO::Formatting Data.
2025-11-26 21:22:14.442953 INFO::Recognized SummarizedExperiment
2025-11-26 21:22:14.443469 INFO::Typecasting input to dataframe.
2025-11-26 21:22:14.451642 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:14.452765 INFO::Removing potential empty rows and columns
2025-11-26 21:22:14.455764 INFO::Found 0 missing values.
2025-11-26 21:22:14.461552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:14.462139 INFO::Done
2025-11-26 21:22:14.462622 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:14.46571 INFO::Starting hierarchical adjustment
2025-11-26 21:22:14.4664 INFO::Found 2 batches.
2025-11-26 21:22:14.466933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:14.467592 INFO::Using default BPPARAM
2025-11-26 21:22:14.468152 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:14.469174 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 21:22:14.494389 INFO::Done
2025-11-26 21:22:14.495155 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:14.498846 INFO::ASW Batch was -0.000103530995943283 prior to batch effect correction and is now -0.000103530995943283 .
2025-11-26 21:22:14.49977 INFO::Total function execution time is 0.0575621128082275 s and adjustment time is 0.0280776023864746 s ( 48.78 )
2025-11-26 21:22:14.518126 INFO::Formatting Data.
2025-11-26 21:22:14.518949 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:14.519891 INFO::Removing potential empty rows and columns
2025-11-26 21:22:14.520918 INFO::Found 0 missing values.
2025-11-26 21:22:14.523889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:14.524448 INFO::Done
2025-11-26 21:22:14.52498 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:14.527053 INFO::Starting hierarchical adjustment
2025-11-26 21:22:14.527781 INFO::Found 3 batches.
2025-11-26 21:22:14.528339 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:14.528966 INFO::Using default BPPARAM
2025-11-26 21:22:14.529491 INFO::Processing subtree level 1
2025-11-26 21:22:14.676578 INFO::Adjusting the last 1 batches sequentially
2025-11-26 21:22:14.678774 INFO::Done
2025-11-26 21:22:14.679493 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:14.682397 INFO::ASW Batch was -0.060530309625837 prior to batch effect correction and is now -0.15866277730709 .
2025-11-26 21:22:14.683418 INFO::Total function execution time is 0.16531229019165 s and adjustment time is 0.151090383529663 s ( 91.4 )
2025-11-26 21:22:14.699458 INFO::Skipping initial DF formatting
2025-11-26 21:22:14.700281 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:14.704628 INFO::Starting hierarchical adjustment
2025-11-26 21:22:14.705505 INFO::Found 5 batches.
2025-11-26 21:22:14.7061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:14.706806 INFO::Using default BPPARAM
2025-11-26 21:22:14.707356 INFO::Processing subtree level 1
2025-11-26 21:22:14.842022 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:14.843958 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 21:22:14.864219 INFO::Done
2025-11-26 21:22:14.865044 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:14.869599 INFO::ASW Batch was 0.49717409098495 prior to batch effect correction and is now 0.49717409098495 .
2025-11-26 21:22:14.870319 INFO::ASW Label was 0.408823100423569 prior to batch effect correction and is now 0.408823100423569 .
2025-11-26 21:22:14.871265 INFO::Total function execution time is 0.171920299530029 s and adjustment time is 0.158863067626953 s ( 92.41 )
2025-11-26 21:22:14.890289 INFO::Formatting Data.
2025-11-26 21:22:14.89121 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:14.892223 INFO::Removing potential empty rows and columns
2025-11-26 21:22:14.893447 INFO::Found 0 missing values.
2025-11-26 21:22:14.897845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:14.898514 INFO::Done
2025-11-26 21:22:14.899103 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:14.902424 INFO::Starting hierarchical adjustment
2025-11-26 21:22:14.903225 INFO::Found 5 batches.
2025-11-26 21:22:14.903793 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:14.904444 INFO::Using default BPPARAM
2025-11-26 21:22:14.905015 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.
2025-11-26 21:22:15.019213 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.020985 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 21:22:15.038324 INFO::Done
2025-11-26 21:22:15.039225 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.04274 INFO::ASW Batch was 0.221445905287407 prior to batch effect correction and is now 0.0531714964258315 .
2025-11-26 21:22:15.043437 INFO::ASW Label was 0.503704580182287 prior to batch effect correction and is now 0.71874473267511 .
2025-11-26 21:22:15.044335 INFO::Total function execution time is 0.154130220413208 s and adjustment time is 0.135198831558228 s ( 87.72 )
2025-11-26 21:22:15.045477 INFO::Formatting Data.
2025-11-26 21:22:15.046141 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:15.047063 INFO::Removing potential empty rows and columns
2025-11-26 21:22:15.048109 INFO::Found 0 missing values.
2025-11-26 21:22:15.05225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:15.052818 INFO::Done
2025-11-26 21:22:15.053354 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:15.056476 INFO::Starting hierarchical adjustment
2025-11-26 21:22:15.057258 INFO::Found 5 batches.
2025-11-26 21:22:15.05782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:15.058491 INFO::Using default BPPARAM
2025-11-26 21:22:15.059065 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.
2025-11-26 21:22:15.179115 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.180818 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 21:22:15.196995 INFO::Done
2025-11-26 21:22:15.197748 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.201265 INFO::ASW Batch was 0.221445905287407 prior to batch effect correction and is now 0.0531714964258315 .
2025-11-26 21:22:15.20192 INFO::ASW Label was 0.503704580182287 prior to batch effect correction and is now 0.71874473267511 .
2025-11-26 21:22:15.202803 INFO::Total function execution time is 0.157316207885742 s and adjustment time is 0.139866590499878 s ( 88.91 )
2025-11-26 21:22:15.217152 INFO::Formatting Data.
2025-11-26 21:22:15.218009 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:15.219 INFO::Removing potential empty rows and columns
2025-11-26 21:22:15.220061 INFO::Found 0 missing values.
2025-11-26 21:22:15.224206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:15.224835 INFO::Done
2025-11-26 21:22:15.225387 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:15.228441 INFO::Starting hierarchical adjustment
2025-11-26 21:22:15.229191 INFO::Found 5 batches.
2025-11-26 21:22:15.229737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:15.230422 INFO::Using default BPPARAM
2025-11-26 21:22:15.230974 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.
2025-11-26 21:22:15.345097 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.346983 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 21:22:15.364029 INFO::Done
2025-11-26 21:22:15.364954 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.368804 INFO::ASW Batch was 0.58310630067175 prior to batch effect correction and is now -0.0836356596288972 .
2025-11-26 21:22:15.369505 INFO::ASW Label was 0.164445065225191 prior to batch effect correction and is now 0.828998413971713 .
2025-11-26 21:22:15.370402 INFO::Total function execution time is 0.153333425521851 s and adjustment time is 0.134922504425049 s ( 87.99 )
2025-11-26 21:22:15.3713 INFO::Formatting Data.
2025-11-26 21:22:15.371957 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:15.372949 INFO::Removing potential empty rows and columns
2025-11-26 21:22:15.374225 INFO::Found 0 missing values.
2025-11-26 21:22:15.378436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:15.378997 INFO::Done
2025-11-26 21:22:15.379525 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:15.382633 INFO::Starting hierarchical adjustment
2025-11-26 21:22:15.383369 INFO::Found 5 batches.
2025-11-26 21:22:15.383942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:15.384596 INFO::Using default BPPARAM
2025-11-26 21:22:15.385166 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.
2025-11-26 21:22:15.514334 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.516279 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 21:22:15.534649 INFO::Done
2025-11-26 21:22:15.535603 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.539605 INFO::ASW Batch was 0.58310630067175 prior to batch effect correction and is now -0.0836356596288972 .
2025-11-26 21:22:15.540463 INFO::ASW Label was 0.164445065225191 prior to batch effect correction and is now 0.828998413971713 .
2025-11-26 21:22:15.541579 INFO::Total function execution time is 0.17022442817688 s and adjustment time is 0.151340484619141 s ( 88.91 )
2025-11-26 21:22:15.55969 INFO::Formatting Data.
2025-11-26 21:22:15.560872 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:15.562102 INFO::Removing potential empty rows and columns
2025-11-26 21:22:15.563271 INFO::Found 0 missing values.
2025-11-26 21:22:15.566285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:15.56694 INFO::Done
2025-11-26 21:22:15.567497 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:15.570976 INFO::Starting hierarchical adjustment
2025-11-26 21:22:15.571831 INFO::Found 2 batches.
2025-11-26 21:22:15.572402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:15.573092 INFO::Using default BPPARAM
2025-11-26 21:22:15.573698 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.574811 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 21:22:15.592576 INFO::Done
2025-11-26 21:22:15.593474 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.597021 INFO::ASW Batch was 0.658252441378885 prior to batch effect correction and is now 0.0668745903208223 .
2025-11-26 21:22:15.597719 INFO::ASW Label was 0.458320573440203 prior to batch effect correction and is now 0.874015988589853 .
2025-11-26 21:22:15.598667 INFO::Total function execution time is 0.0392444133758545 s and adjustment time is 0.0208704471588135 s ( 53.18 )
2025-11-26 21:22:15.599555 INFO::Formatting Data.
2025-11-26 21:22:15.60023 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:15.601186 INFO::Removing potential empty rows and columns
2025-11-26 21:22:15.602263 INFO::Found 0 missing values.
2025-11-26 21:22:15.605186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:15.605792 INFO::Done
2025-11-26 21:22:15.606319 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:15.609615 INFO::Starting hierarchical adjustment
2025-11-26 21:22:15.610396 INFO::Found 2 batches.
2025-11-26 21:22:15.610946 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:15.611592 INFO::Using default BPPARAM
2025-11-26 21:22:15.612179 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.613236 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 21:22:15.631195 INFO::Done
2025-11-26 21:22:15.632115 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.63552 INFO::ASW Batch was 0.658252441378885 prior to batch effect correction and is now 0.0668745903208223 .
2025-11-26 21:22:15.636188 INFO::ASW Label was 0.458320573440203 prior to batch effect correction and is now 0.874015988589853 .
2025-11-26 21:22:15.637177 INFO::Total function execution time is 0.0376324653625488 s and adjustment time is 0.0208840370178223 s ( 55.49 )
2025-11-26 21:22:15.652247 INFO::Formatting Data.
2025-11-26 21:22:15.653446 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:15.654667 INFO::Removing potential empty rows and columns
2025-11-26 21:22:15.655773 INFO::Found 0 missing values.
2025-11-26 21:22:15.658444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:15.65902 INFO::Done
2025-11-26 21:22:15.659563 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:15.661951 INFO::Starting hierarchical adjustment
2025-11-26 21:22:15.66272 INFO::Found 2 batches.
2025-11-26 21:22:15.663282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:15.664194 INFO::Using default BPPARAM
2025-11-26 21:22:15.664773 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.665907 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 21:22:15.702979 INFO::Done
2025-11-26 21:22:15.70387 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.70643 INFO::ASW Batch was -0.010470951352917 prior to batch effect correction and is now -0.137589709503256 .
2025-11-26 21:22:15.707377 INFO::Total function execution time is 0.0554511547088623 s and adjustment time is 0.0403537750244141 s ( 72.77 )
2025-11-26 21:22:15.721305 INFO::Formatting Data.
2025-11-26 21:22:15.722349 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:15.723499 INFO::Removing potential empty rows and columns
2025-11-26 21:22:15.72461 INFO::Found 0 missing values.
2025-11-26 21:22:15.725935 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.
2025-11-26 21:22:15.731249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:15.731943 INFO::Done
2025-11-26 21:22:15.732508 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:15.735721 INFO::Starting hierarchical adjustment
2025-11-26 21:22:15.736493 INFO::Found 2 batches.
2025-11-26 21:22:15.737051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:15.737712 INFO::Using default BPPARAM
2025-11-26 21:22:15.738257 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.739271 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 21:22:15.757274 INFO::Done
2025-11-26 21:22:15.758121 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.761371 INFO::ASW Batch was 0.51296515625975 prior to batch effect correction and is now -0.0282644815629017 .
2025-11-26 21:22:15.76206 INFO::ASW Label was 0.556348439845778 prior to batch effect correction and is now 0.943105829750001 .
2025-11-26 21:22:15.762932 INFO::Total function execution time is 0.0417804718017578 s and adjustment time is 0.0208885669708252 s ( 50 )
2025-11-26 21:22:15.763988 INFO::Formatting Data.
2025-11-26 21:22:15.764632 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:15.765645 INFO::Removing potential empty rows and columns
2025-11-26 21:22:15.766695 INFO::Found 0 missing values.
2025-11-26 21:22:15.767703 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.
2025-11-26 21:22:15.772525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:15.773152 INFO::Done
2025-11-26 21:22:15.773685 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:15.77685 INFO::Starting hierarchical adjustment
2025-11-26 21:22:15.777573 INFO::Found 2 batches.
2025-11-26 21:22:15.77815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:15.778762 INFO::Using default BPPARAM
2025-11-26 21:22:15.779305 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:15.780301 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 21:22:15.798482 INFO::Done
2025-11-26 21:22:15.799308 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:15.802513 INFO::ASW Batch was 0.51296515625975 prior to batch effect correction and is now -0.0282644815629017 .
2025-11-26 21:22:15.803193 INFO::ASW Label was 0.556348439845778 prior to batch effect correction and is now 0.943105829750001 .
2025-11-26 21:22:15.804044 INFO::Total function execution time is 0.0400881767272949 s and adjustment time is 0.0209908485412598 s ( 52.36 )
2025-11-26 21:22:16.081715 INFO::Formatting Data.
2025-11-26 21:22:16.083493 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:16.084904 INFO::Removing potential empty rows and columns
2025-11-26 21:22:16.086416 INFO::Found 0 missing values.
2025-11-26 21:22:16.090104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:16.09073 INFO::Done
2025-11-26 21:22:16.09128 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:16.094803 INFO::Starting hierarchical adjustment
2025-11-26 21:22:16.095613 INFO::Found 3 batches.
2025-11-26 21:22:16.096178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:16.097059 INFO::Using default BPPARAM
2025-11-26 21:22:16.097622 INFO::Processing subtree level 1
2025-11-26 21:22:16.20319 INFO::Adjusting the last 1 batches sequentially
2025-11-26 21:22:16.205288 INFO::Done
2025-11-26 21:22:16.20602 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:16.208835 INFO::ASW Batch was 0.072208586507816 prior to batch effect correction and is now 0.072208586507816 .
2025-11-26 21:22:16.209903 INFO::Total function execution time is 0.129334688186646 s and adjustment time is 0.109834432601929 s ( 84.92 )
2025-11-26 21:22:16.211009 INFO::Formatting Data.
2025-11-26 21:22:16.211686 INFO::Typecasting input to dataframe.
2025-11-26 21:22:16.212521 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:16.213513 INFO::Removing potential empty rows and columns
2025-11-26 21:22:16.214684 INFO::Found 0 missing values.
2025-11-26 21:22:16.218018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:16.218691 INFO::Done
2025-11-26 21:22:16.219281 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:16.221545 INFO::Starting hierarchical adjustment
2025-11-26 21:22:16.222325 INFO::Found 3 batches.
2025-11-26 21:22:16.222905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:16.223556 INFO::Using default BPPARAM
2025-11-26 21:22:16.224146 INFO::Processing subtree level 1
2025-11-26 21:22:16.321669 INFO::Adjusting the last 1 batches sequentially
2025-11-26 21:22:16.323677 INFO::Done
2025-11-26 21:22:16.324426 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:16.327163 INFO::ASW Batch was 0.072208586507816 prior to batch effect correction and is now 0.072208586507816 .
2025-11-26 21:22:16.328228 INFO::Total function execution time is 0.117218017578125 s and adjustment time is 0.101484537124634 s ( 86.58 )
2025-11-26 21:22:16.342518 INFO::Formatting Data.
2025-11-26 21:22:16.343485 INFO::Typecasting input to dataframe.
2025-11-26 21:22:16.344431 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:16.34543 INFO::Removing potential empty rows and columns
2025-11-26 21:22:16.346583 INFO::Found 0 missing values.
2025-11-26 21:22:16.349679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:16.350255 INFO::Done
2025-11-26 21:22:16.350807 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:16.353007 INFO::Starting hierarchical adjustment
2025-11-26 21:22:16.353746 INFO::Found 3 batches.
2025-11-26 21:22:16.354321 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:16.354993 INFO::Using default BPPARAM
2025-11-26 21:22:16.355552 INFO::Processing subtree level 1
2025-11-26 21:22:16.450164 INFO::Adjusting the last 1 batches sequentially
2025-11-26 21:22:16.452183 INFO::Done
2025-11-26 21:22:16.452963 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:16.455678 INFO::ASW Batch was 0.0746494342515923 prior to batch effect correction and is now 0.0746494342515923 .
2025-11-26 21:22:16.456687 INFO::Total function execution time is 0.114248514175415 s and adjustment time is 0.0985591411590576 s ( 86.27 )
2025-11-26 21:22:16.612039 INFO::Formatting Data.
2025-11-26 21:22:16.613022 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:16.614245 INFO::Removing potential empty rows and columns
2025-11-26 21:22:16.61741 INFO::Found 1000 missing values.
2025-11-26 21:22:16.637514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:16.638448 INFO::Done
2025-11-26 21:22:16.639086 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:16.644921 INFO::Starting hierarchical adjustment
2025-11-26 21:22:16.645807 INFO::Found 10 batches.
2025-11-26 21:22:16.646393 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:16.647112 INFO::Using default BPPARAM
2025-11-26 21:22:16.647681 INFO::Processing subtree level 1
2025-11-26 21:22:16.819368 INFO::Processing subtree level 2
2025-11-26 21:22:17.13988 INFO::Adjusting the last 1 batches sequentially
2025-11-26 21:22:17.141971 INFO::Done
2025-11-26 21:22:17.142658 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:17.148412 INFO::ASW Batch was 0.47582265212288 prior to batch effect correction and is now 0.47582265212288 .
2025-11-26 21:22:17.149219 INFO::ASW Label was 0.351453012097768 prior to batch effect correction and is now 0.351453012097768 .
2025-11-26 21:22:17.150196 INFO::Total function execution time is 0.538241863250732 s and adjustment time is 0.496338367462158 s ( 92.21 )
2025-11-26 21:22:17.151098 INFO::Formatting Data.
2025-11-26 21:22:17.15175 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:17.152945 INFO::Removing potential empty rows and columns
2025-11-26 21:22:17.201536 INFO::Found 1000 missing values.
2025-11-26 21:22:17.22125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:17.22211 INFO::Done
2025-11-26 21:22:17.222753 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:17.228262 INFO::Starting hierarchical adjustment
2025-11-26 21:22:17.229053 INFO::Found 10 batches.
2025-11-26 21:22:18.759264 INFO::Set up parallel execution backend with 2 workers
2025-11-26 21:22:18.761222 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-26 21:22:20.56156 INFO::Adjusting the last 2 batches sequentially
2025-11-26 21:22:20.564917 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 21:22:20.582132 INFO::Done
2025-11-26 21:22:20.582853 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:20.587774 INFO::ASW Batch was 0.47582265212288 prior to batch effect correction and is now 0.47582265212288 .
2025-11-26 21:22:20.588498 INFO::ASW Label was 0.351453012097768 prior to batch effect correction and is now 0.351453012097768 .
2025-11-26 21:22:20.589353 INFO::Total function execution time is 3.43828415870667 s and adjustment time is 3.35320544242859 s ( 97.53 )
2025-11-26 21:22:20.745041 INFO::Formatting Data.
2025-11-26 21:22:20.745908 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:20.746917 INFO::Removing potential empty rows and columns
2025-11-26 21:22:20.748037 INFO::Found 0 missing values.
2025-11-26 21:22:20.751755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:20.752314 INFO::Done
2025-11-26 21:22:20.75285 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 21:22:20.75564 INFO::Starting hierarchical adjustment
2025-11-26 21:22:20.756361 INFO::Found 3 batches.
2025-11-26 21:22:20.75695 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 21:22:20.757571 INFO::Using default BPPARAM
2025-11-26 21:22:20.75818 INFO::Processing subtree level 1
2025-11-26 21:22:20.874374 INFO::Adjusting the last 1 batches sequentially
2025-11-26 21:22:20.876359 INFO::Done
2025-11-26 21:22:20.877055 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 21:22:20.880474 INFO::ASW Batch was 0.24081028081074 prior to batch effect correction and is now -0.160832450553083 .
2025-11-26 21:22:20.881129 INFO::ASW Label was -0.184515277086409 prior to batch effect correction and is now -0.00498949631741259 .
2025-11-26 21:22:20.882134 INFO::Total function execution time is 0.137146234512329 s and adjustment time is 0.12010645866394 s ( 87.58 )
2025-11-26 21:22:21.002652 INFO::Formatting Data.
2025-11-26 21:22:21.003569 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.00452 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.005597 INFO::Found 2 missing values.
2025-11-26 21:22:21.008469 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.009042 INFO::Done
2025-11-26 21:22:21.035722 INFO::Found NA in Reference column
2025-11-26 21:22:21.045165 INFO::Require at least two references per batch.
2025-11-26 21:22:21.065802 INFO::Formatting Data.
2025-11-26 21:22:21.066652 INFO::Recognized SummarizedExperiment
2025-11-26 21:22:21.06725 INFO::Typecasting input to dataframe.
2025-11-26 21:22:21.090196 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.091936 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.096966 INFO::Found 0 missing values.
2025-11-26 21:22:21.106992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.107938 INFO::Done
2025-11-26 21:22:21.129971 INFO::Formatting Data.
2025-11-26 21:22:21.131011 INFO::Recognized SummarizedExperiment
2025-11-26 21:22:21.131732 INFO::Typecasting input to dataframe.
2025-11-26 21:22:21.155054 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.156741 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.162291 INFO::Found 0 missing values.
2025-11-26 21:22:21.178037 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.178994 INFO::Done
2025-11-26 21:22:21.200333 INFO::Formatting Data.
2025-11-26 21:22:21.201371 INFO::Recognized SummarizedExperiment
2025-11-26 21:22:21.202085 INFO::Typecasting input to dataframe.
2025-11-26 21:22:21.224597 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.225982 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.227465 INFO::Found 0 missing values.
2025-11-26 21:22:21.228643 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.
2025-11-26 21:22:21.234822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.235538 INFO::Done
2025-11-26 21:22:21.248549 INFO::Formatting Data.
2025-11-26 21:22:21.24957 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.250726 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.251984 INFO::Found 0 missing values.
2025-11-26 21:22:21.25557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.256246 INFO::Done
2025-11-26 21:22:21.269601 INFO::Formatting Data.
2025-11-26 21:22:21.27064 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.271762 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.272925 INFO::Found 0 missing values.
2025-11-26 21:22:21.276191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.27681 INFO::Done
2025-11-26 21:22:21.311795 INFO::Formatting Data.
2025-11-26 21:22:21.312798 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.314054 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.315379 INFO::Found 1 missing values.
2025-11-26 21:22:21.318259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.318916 INFO::Done
2025-11-26 21:22:21.34131 INFO::Formatting Data.
2025-11-26 21:22:21.342272 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.343269 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.344305 INFO::Found 2 missing values.
2025-11-26 21:22:21.345304 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.
2025-11-26 21:22:21.347979 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.348558 INFO::Done
2025-11-26 21:22:21.360723 INFO::Formatting Data.
2025-11-26 21:22:21.361692 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.362739 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.363774 INFO::Found 2 missing values.
2025-11-26 21:22:21.365525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.36613 INFO::Done
2025-11-26 21:22:21.377731 INFO::Formatting Data.
2025-11-26 21:22:21.378627 INFO::Typecasting input to dataframe.
2025-11-26 21:22:21.379544 INFO::Replacing NaNs with NAs.
2025-11-26 21:22:21.380476 INFO::Removing potential empty rows and columns
2025-11-26 21:22:21.38156 INFO::Found 0 missing values.
2025-11-26 21:22:21.384657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 21:22:21.385262 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.698 4.953 21.212
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.864 | 1.112 | 16.815 | |
| compute_asw | 0.024 | 0.000 | 0.023 | |
| count_existing | 0.013 | 0.001 | 0.013 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |