Yannis Schumann
| Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 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 2025-11-28 11:37 -0500 (Fri, 28 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" | 4866 |
| 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: 2025-11-27 21:20:58 -0500 (Thu, 27 Nov 2025) |
| EndedAt: 2025-11-27 21:22:24 -0500 (Thu, 27 Nov 2025) |
| EllapsedTime: 86.1 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 22.808 1.096 16.158
* 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")
2025-11-27 21:21:48.139755 INFO::Formatting Data.
2025-11-27 21:21:48.141123 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:48.15197 INFO::Removing potential empty rows and columns
2025-11-27 21:21:48.382143 INFO::Found 0 missing values.
2025-11-27 21:21:48.385233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:48.385833 INFO::Done
2025-11-27 21:21:48.386352 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:48.396913 INFO::Starting hierarchical adjustment
2025-11-27 21:21:48.397716 INFO::Found 3 batches.
2025-11-27 21:21:48.398262 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:48.399307 INFO::Using default BPPARAM
2025-11-27 21:21:48.39984 INFO::Processing subtree level 1
2025-11-27 21:21:48.498264 INFO::Adjusting the last 1 batches sequentially
2025-11-27 21:21:48.500254 INFO::Done
2025-11-27 21:21:48.500958 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:48.504016 INFO::ASW Batch was -0.0662082699876627 prior to batch effect correction and is now -0.0662082699876627 .
2025-11-27 21:21:48.505081 INFO::Total function execution time is 0.365980863571167 s and adjustment time is 0.102667331695557 s ( 28.05 )
2025-11-27 21:21:48.520185 INFO::Formatting Data.
2025-11-27 21:21:48.520936 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:48.521879 INFO::Removing potential empty rows and columns
2025-11-27 21:21:48.523054 INFO::Found 0 missing values.
2025-11-27 21:21:48.524019 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.
2025-11-27 21:21:48.534858 INFO::Formatting Data.
2025-11-27 21:21:48.535549 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:48.536434 INFO::Removing potential empty rows and columns
2025-11-27 21:21:48.537539 INFO::Found 0 missing values.
2025-11-27 21:21:48.538464 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.
2025-11-27 21:21:48.553677 INFO::Formatting Data.
2025-11-27 21:21:48.554391 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:48.555298 INFO::Removing potential empty rows and columns
2025-11-27 21:21:48.556436 INFO::Found 0 missing values.
2025-11-27 21:21:48.557412 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.
2025-11-27 21:21:48.562412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:48.56303 INFO::Done
2025-11-27 21:21:48.563716 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:48.56597 INFO::Starting hierarchical adjustment
2025-11-27 21:21:48.566778 INFO::Found 2 batches.
2025-11-27 21:21:48.567392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:48.568159 INFO::Using default BPPARAM
2025-11-27 21:21:48.568771 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:48.569845 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 21:21:48.59372 INFO::Done
2025-11-27 21:21:48.594493 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:48.596644 INFO::ASW Batch was -0.0325465165226156 prior to batch effect correction and is now -0.111562496729479 .
2025-11-27 21:21:48.597516 INFO::Total function execution time is 0.0438668727874756 s and adjustment time is 0.0270869731903076 s ( 61.75 )
2025-11-27 21:21:48.600431 INFO::Formatting Data.
2025-11-27 21:21:48.601115 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:48.610813 INFO::Formatting Data.
2025-11-27 21:21:48.611571 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:48.612538 INFO::Removing potential empty rows and columns
2025-11-27 21:21:48.613668 INFO::Found 0 missing values.
2025-11-27 21:21:48.61679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:48.617369 INFO::Done
2025-11-27 21:21:48.617935 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:48.620121 INFO::Starting hierarchical adjustment
2025-11-27 21:21:48.620865 INFO::Found 2 batches.
2025-11-27 21:21:48.621446 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:48.622123 INFO::Using default BPPARAM
2025-11-27 21:21:48.622697 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:48.62372 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 21:21:48.679074 INFO::Done
2025-11-27 21:21:48.679777 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:48.681792 INFO::ASW Batch was 0.0658196695302737 prior to batch effect correction and is now -0.128366525830065 .
2025-11-27 21:21:48.682585 INFO::Total function execution time is 0.0718288421630859 s and adjustment time is 0.0583503246307373 s ( 81.24 )
2025-11-27 21:21:48.683621 INFO::Formatting Data.
2025-11-27 21:21:48.68425 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:48.685139 INFO::Removing potential empty rows and columns
2025-11-27 21:21:48.68618 INFO::Found 0 missing values.
2025-11-27 21:21:48.689167 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:48.689752 INFO::Done
2025-11-27 21:21:48.69029 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:48.692209 INFO::Starting hierarchical adjustment
2025-11-27 21:21:48.692927 INFO::Found 2 batches.
2025-11-27 21:21:48.693462 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:48.694087 INFO::Using default BPPARAM
2025-11-27 21:21:48.694617 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:48.695571 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 21:21:48.711333 INFO::Done
2025-11-27 21:21:48.712054 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:48.71416 INFO::ASW Batch was 0.0658196695302737 prior to batch effect correction and is now -0.128366525830065 .
2025-11-27 21:21:48.71499 INFO::Total function execution time is 0.0313518047332764 s and adjustment time is 0.0185329914093018 s ( 59.11 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-27 21:21:51.583529 INFO::Formatting Data.
2025-11-27 21:21:51.584314 INFO::Recognized SummarizedExperiment
2025-11-27 21:21:51.584848 INFO::Typecasting input to dataframe.
2025-11-27 21:21:51.616006 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:51.617304 INFO::Removing potential empty rows and columns
2025-11-27 21:21:51.621067 INFO::Found 0 missing values.
2025-11-27 21:21:51.627774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:51.628494 INFO::Done
2025-11-27 21:21:51.629074 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:51.632611 INFO::Starting hierarchical adjustment
2025-11-27 21:21:51.633401 INFO::Found 2 batches.
2025-11-27 21:21:51.633982 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:51.635121 INFO::Using default BPPARAM
2025-11-27 21:21:51.635628 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:51.636576 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 21:21:51.687957 INFO::Done
2025-11-27 21:21:51.688669 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:51.691875 INFO::ASW Batch was 0.000409084621364199 prior to batch effect correction and is now -0.0936450104988595 .
2025-11-27 21:21:51.692699 INFO::Total function execution time is 0.109497308731079 s and adjustment time is 0.0547027587890625 s ( 49.96 )
Warning: stack imbalance in '{', 73 then 75
2025-11-27 21:21:51.709715 INFO::Formatting Data.
2025-11-27 21:21:51.710431 INFO::Recognized SummarizedExperiment
2025-11-27 21:21:51.71095 INFO::Typecasting input to dataframe.
2025-11-27 21:21:51.719388 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:51.720443 INFO::Removing potential empty rows and columns
2025-11-27 21:21:51.723464 INFO::Found 0 missing values.
2025-11-27 21:21:51.729477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:51.730018 INFO::Done
2025-11-27 21:21:51.730486 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:51.733555 INFO::Starting hierarchical adjustment
2025-11-27 21:21:51.73422 INFO::Found 2 batches.
2025-11-27 21:21:51.735008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:51.735653 INFO::Using default BPPARAM
2025-11-27 21:21:51.736187 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:51.737172 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 21:21:51.762812 INFO::Done
2025-11-27 21:21:51.763598 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:51.767248 INFO::ASW Batch was 0.0307493728627015 prior to batch effect correction and is now 0.0307493728627015 .
2025-11-27 21:21:51.768129 INFO::Total function execution time is 0.0583798885345459 s and adjustment time is 0.028658390045166 s ( 49.09 )
2025-11-27 21:21:51.786955 INFO::Formatting Data.
2025-11-27 21:21:51.787872 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:51.78915 INFO::Removing potential empty rows and columns
2025-11-27 21:21:51.790244 INFO::Found 0 missing values.
2025-11-27 21:21:51.793311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:51.793872 INFO::Done
2025-11-27 21:21:51.794401 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:51.796516 INFO::Starting hierarchical adjustment
2025-11-27 21:21:51.797245 INFO::Found 3 batches.
2025-11-27 21:21:51.797774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:51.798389 INFO::Using default BPPARAM
2025-11-27 21:21:51.798934 INFO::Processing subtree level 1
2025-11-27 21:21:51.935923 INFO::Adjusting the last 1 batches sequentially
2025-11-27 21:21:51.937778 INFO::Done
2025-11-27 21:21:51.938489 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:51.941074 INFO::ASW Batch was -0.0530056668175061 prior to batch effect correction and is now -0.168346840315638 .
2025-11-27 21:21:51.942054 INFO::Total function execution time is 0.155188083648682 s and adjustment time is 0.140668392181396 s ( 90.64 )
2025-11-27 21:21:51.956969 INFO::Skipping initial DF formatting
2025-11-27 21:21:51.957688 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:51.961727 INFO::Starting hierarchical adjustment
2025-11-27 21:21:51.962527 INFO::Found 5 batches.
2025-11-27 21:21:51.963084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:51.963707 INFO::Using default BPPARAM
2025-11-27 21:21:51.964263 INFO::Processing subtree level 1
2025-11-27 21:21:52.086833 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.08915 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 21:21:52.109521 INFO::Done
2025-11-27 21:21:52.110301 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.114587 INFO::ASW Batch was 0.557609420279638 prior to batch effect correction and is now 0.557609420279638 .
2025-11-27 21:21:52.115256 INFO::ASW Label was 0.345513599617142 prior to batch effect correction and is now 0.345513599617141 .
2025-11-27 21:21:52.116151 INFO::Total function execution time is 0.159256219863892 s and adjustment time is 0.147111415863037 s ( 92.37 )
2025-11-27 21:21:52.134298 INFO::Formatting Data.
2025-11-27 21:21:52.135142 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.136109 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.13714 INFO::Found 0 missing values.
2025-11-27 21:21:52.141279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.141875 INFO::Done
2025-11-27 21:21:52.142415 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.145472 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.146222 INFO::Found 5 batches.
2025-11-27 21:21:52.146764 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.147424 INFO::Using default BPPARAM
2025-11-27 21:21:52.147985 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.
2025-11-27 21:21:52.25993 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.261667 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 21:21:52.278699 INFO::Done
2025-11-27 21:21:52.279581 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.283155 INFO::ASW Batch was 0.404519621989363 prior to batch effect correction and is now -0.0836881328493703 .
2025-11-27 21:21:52.283896 INFO::ASW Label was 0.296697971754193 prior to batch effect correction and is now 0.876386169537757 .
2025-11-27 21:21:52.284814 INFO::Total function execution time is 0.150566101074219 s and adjustment time is 0.132577419281006 s ( 88.05 )
2025-11-27 21:21:52.285706 INFO::Formatting Data.
2025-11-27 21:21:52.286364 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.287286 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.288317 INFO::Found 0 missing values.
2025-11-27 21:21:52.292494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.293102 INFO::Done
2025-11-27 21:21:52.293644 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.29665 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.297382 INFO::Found 5 batches.
2025-11-27 21:21:52.29794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.298583 INFO::Using default BPPARAM
2025-11-27 21:21:52.299145 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.
2025-11-27 21:21:52.40804 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.409831 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 21:21:52.426975 INFO::Done
2025-11-27 21:21:52.428109 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.431616 INFO::ASW Batch was 0.404519621989363 prior to batch effect correction and is now -0.0836881328493703 .
2025-11-27 21:21:52.432266 INFO::ASW Label was 0.296697971754193 prior to batch effect correction and is now 0.876386169537757 .
2025-11-27 21:21:52.433145 INFO::Total function execution time is 0.14744234085083 s and adjustment time is 0.129675149917603 s ( 87.95 )
2025-11-27 21:21:52.446888 INFO::Formatting Data.
2025-11-27 21:21:52.447712 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.448682 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.449709 INFO::Found 0 missing values.
2025-11-27 21:21:52.453838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.454451 INFO::Done
2025-11-27 21:21:52.455012 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.458025 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.45876 INFO::Found 5 batches.
2025-11-27 21:21:52.459322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.459976 INFO::Using default BPPARAM
2025-11-27 21:21:52.460518 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.
2025-11-27 21:21:52.569447 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.571133 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 21:21:52.587166 INFO::Done
2025-11-27 21:21:52.587953 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.591331 INFO::ASW Batch was 0.442468599268212 prior to batch effect correction and is now -0.1151487423828 .
2025-11-27 21:21:52.591993 INFO::ASW Label was 0.331783481123197 prior to batch effect correction and is now 0.903333442415931 .
2025-11-27 21:21:52.592885 INFO::Total function execution time is 0.146078586578369 s and adjustment time is 0.128522396087646 s ( 87.98 )
2025-11-27 21:21:52.593772 INFO::Formatting Data.
2025-11-27 21:21:52.594438 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.595371 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.596382 INFO::Found 0 missing values.
2025-11-27 21:21:52.600562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.601201 INFO::Done
2025-11-27 21:21:52.601751 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.604831 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.605582 INFO::Found 5 batches.
2025-11-27 21:21:52.606161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.60682 INFO::Using default BPPARAM
2025-11-27 21:21:52.607381 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.
2025-11-27 21:21:52.721352 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.722948 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 21:21:52.738728 INFO::Done
2025-11-27 21:21:52.739506 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.742682 INFO::ASW Batch was 0.442468599268212 prior to batch effect correction and is now -0.1151487423828 .
2025-11-27 21:21:52.74329 INFO::ASW Label was 0.331783481123197 prior to batch effect correction and is now 0.903333442415931 .
2025-11-27 21:21:52.744146 INFO::Total function execution time is 0.150377750396729 s and adjustment time is 0.133262634277344 s ( 88.62 )
2025-11-27 21:21:52.757575 INFO::Formatting Data.
2025-11-27 21:21:52.758375 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.759321 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.760339 INFO::Found 0 missing values.
2025-11-27 21:21:52.763085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.76365 INFO::Done
2025-11-27 21:21:52.764193 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.767201 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.767965 INFO::Found 2 batches.
2025-11-27 21:21:52.768521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.769163 INFO::Using default BPPARAM
2025-11-27 21:21:52.769728 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.770663 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 21:21:52.785374 INFO::Done
2025-11-27 21:21:52.786082 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.789059 INFO::ASW Batch was 0.714737001116099 prior to batch effect correction and is now -0.00750461904591394 .
2025-11-27 21:21:52.789656 INFO::ASW Label was 0.303541379058331 prior to batch effect correction and is now 0.90102436314635 .
2025-11-27 21:21:52.790487 INFO::Total function execution time is 0.0330040454864502 s and adjustment time is 0.0175583362579346 s ( 53.2 )
2025-11-27 21:21:52.791292 INFO::Formatting Data.
2025-11-27 21:21:52.791942 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.792814 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.793811 INFO::Found 0 missing values.
2025-11-27 21:21:52.796519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.797098 INFO::Done
2025-11-27 21:21:52.797631 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.800554 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.801275 INFO::Found 2 batches.
2025-11-27 21:21:52.801822 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.802432 INFO::Using default BPPARAM
2025-11-27 21:21:52.802999 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.80391 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 21:21:52.818509 INFO::Done
2025-11-27 21:21:52.819207 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.822122 INFO::ASW Batch was 0.714737001116099 prior to batch effect correction and is now -0.00750461904591394 .
2025-11-27 21:21:52.822754 INFO::ASW Label was 0.303541379058331 prior to batch effect correction and is now 0.90102436314635 .
2025-11-27 21:21:52.823555 INFO::Total function execution time is 0.0322723388671875 s and adjustment time is 0.0173604488372803 s ( 53.79 )
2025-11-27 21:21:52.834853 INFO::Formatting Data.
2025-11-27 21:21:52.835624 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.836533 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.837441 INFO::Found 0 missing values.
2025-11-27 21:21:52.839597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.840143 INFO::Done
2025-11-27 21:21:52.840668 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.842593 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.843292 INFO::Found 2 batches.
2025-11-27 21:21:52.843839 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.84444 INFO::Using default BPPARAM
2025-11-27 21:21:52.845006 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.845941 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 21:21:52.877198 INFO::Done
2025-11-27 21:21:52.877942 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.879954 INFO::ASW Batch was -0.0321226313395443 prior to batch effect correction and is now -0.0916470757568258 .
2025-11-27 21:21:52.880766 INFO::Total function execution time is 0.0459969043731689 s and adjustment time is 0.0340187549591064 s ( 73.96 )
2025-11-27 21:21:52.892847 INFO::Formatting Data.
2025-11-27 21:21:52.893654 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.894554 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.895544 INFO::Found 0 missing values.
2025-11-27 21:21:52.896705 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.
2025-11-27 21:21:52.901397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.901973 INFO::Done
2025-11-27 21:21:52.902514 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.905499 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.906224 INFO::Found 2 batches.
2025-11-27 21:21:52.906773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.907434 INFO::Using default BPPARAM
2025-11-27 21:21:52.907974 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.90894 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 21:21:52.925428 INFO::Done
2025-11-27 21:21:52.926166 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.929115 INFO::ASW Batch was 0.365547850224266 prior to batch effect correction and is now 0.152040981338162 .
2025-11-27 21:21:52.929719 INFO::ASW Label was 0.728157384248875 prior to batch effect correction and is now 0.813123863779163 .
2025-11-27 21:21:52.930547 INFO::Total function execution time is 0.0378134250640869 s and adjustment time is 0.0193188190460205 s ( 51.09 )
2025-11-27 21:21:52.93137 INFO::Formatting Data.
2025-11-27 21:21:52.932017 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:52.932973 INFO::Removing potential empty rows and columns
2025-11-27 21:21:52.933965 INFO::Found 0 missing values.
2025-11-27 21:21:52.934898 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.
2025-11-27 21:21:52.939632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:52.940299 INFO::Done
2025-11-27 21:21:52.940864 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:52.943902 INFO::Starting hierarchical adjustment
2025-11-27 21:21:52.94463 INFO::Found 2 batches.
2025-11-27 21:21:52.945225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:52.945851 INFO::Using default BPPARAM
2025-11-27 21:21:52.946389 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:52.947358 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 21:21:52.964257 INFO::Done
2025-11-27 21:21:52.965013 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:52.968051 INFO::ASW Batch was 0.365547850224266 prior to batch effect correction and is now 0.152040981338162 .
2025-11-27 21:21:52.968693 INFO::ASW Label was 0.728157384248875 prior to batch effect correction and is now 0.813123863779163 .
2025-11-27 21:21:52.969519 INFO::Total function execution time is 0.0381665229797363 s and adjustment time is 0.019728422164917 s ( 51.69 )
2025-11-27 21:21:53.185898 INFO::Formatting Data.
2025-11-27 21:21:53.186885 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:53.187903 INFO::Removing potential empty rows and columns
2025-11-27 21:21:53.189054 INFO::Found 0 missing values.
2025-11-27 21:21:53.192255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:53.192844 INFO::Done
2025-11-27 21:21:53.193393 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:53.195599 INFO::Starting hierarchical adjustment
2025-11-27 21:21:53.196336 INFO::Found 3 batches.
2025-11-27 21:21:53.196886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:53.197548 INFO::Using default BPPARAM
2025-11-27 21:21:53.1981 INFO::Processing subtree level 1
2025-11-27 21:21:53.298915 INFO::Adjusting the last 1 batches sequentially
2025-11-27 21:21:53.301831 INFO::Done
2025-11-27 21:21:53.303012 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:53.307224 INFO::ASW Batch was 0.0276639245167941 prior to batch effect correction and is now 0.0276639245167941 .
2025-11-27 21:21:53.309167 INFO::Total function execution time is 0.123189449310303 s and adjustment time is 0.105533599853516 s ( 85.67 )
2025-11-27 21:21:53.310536 INFO::Formatting Data.
2025-11-27 21:21:53.311313 INFO::Typecasting input to dataframe.
2025-11-27 21:21:53.312222 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:53.313347 INFO::Removing potential empty rows and columns
2025-11-27 21:21:53.314594 INFO::Found 0 missing values.
2025-11-27 21:21:53.317961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:53.318578 INFO::Done
2025-11-27 21:21:53.319145 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:53.321598 INFO::Starting hierarchical adjustment
2025-11-27 21:21:53.322397 INFO::Found 3 batches.
2025-11-27 21:21:53.32298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:53.323647 INFO::Using default BPPARAM
2025-11-27 21:21:53.324236 INFO::Processing subtree level 1
2025-11-27 21:21:53.41902 INFO::Adjusting the last 1 batches sequentially
2025-11-27 21:21:53.421067 INFO::Done
2025-11-27 21:21:53.421834 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:53.424616 INFO::ASW Batch was 0.0276639245167941 prior to batch effect correction and is now 0.0276639245167941 .
2025-11-27 21:21:53.425653 INFO::Total function execution time is 0.115116119384766 s and adjustment time is 0.0987966060638428 s ( 85.82 )
2025-11-27 21:21:53.440108 INFO::Formatting Data.
2025-11-27 21:21:53.441043 INFO::Typecasting input to dataframe.
2025-11-27 21:21:53.441976 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:53.442974 INFO::Removing potential empty rows and columns
2025-11-27 21:21:53.444164 INFO::Found 0 missing values.
2025-11-27 21:21:53.447304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:53.447906 INFO::Done
2025-11-27 21:21:53.448435 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:53.450669 INFO::Starting hierarchical adjustment
2025-11-27 21:21:53.451419 INFO::Found 3 batches.
2025-11-27 21:21:53.45198 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:53.452626 INFO::Using default BPPARAM
2025-11-27 21:21:53.453182 INFO::Processing subtree level 1
2025-11-27 21:21:53.546774 INFO::Adjusting the last 1 batches sequentially
2025-11-27 21:21:53.54889 INFO::Done
2025-11-27 21:21:53.549605 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:53.55234 INFO::ASW Batch was -0.148685485046738 prior to batch effect correction and is now -0.148685485046738 .
2025-11-27 21:21:53.553357 INFO::Total function execution time is 0.113385200500488 s and adjustment time is 0.0975809097290039 s ( 86.06 )
2025-11-27 21:21:53.694811 INFO::Formatting Data.
2025-11-27 21:21:53.695644 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:53.696819 INFO::Removing potential empty rows and columns
2025-11-27 21:21:53.699586 INFO::Found 1000 missing values.
2025-11-27 21:21:53.718595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:53.719347 INFO::Done
2025-11-27 21:21:53.719919 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:53.725349 INFO::Starting hierarchical adjustment
2025-11-27 21:21:53.726163 INFO::Found 10 batches.
2025-11-27 21:21:53.726711 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:53.72738 INFO::Using default BPPARAM
2025-11-27 21:21:53.727942 INFO::Processing subtree level 1
2025-11-27 21:21:53.862669 INFO::Processing subtree level 2
2025-11-27 21:21:54.107589 INFO::Adjusting the last 1 batches sequentially
2025-11-27 21:21:54.109847 INFO::Done
2025-11-27 21:21:54.110659 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:54.117343 INFO::ASW Batch was 0.430935225537102 prior to batch effect correction and is now 0.430935225537102 .
2025-11-27 21:21:54.118186 INFO::ASW Label was 0.392845595850055 prior to batch effect correction and is now 0.392845595850055 .
2025-11-27 21:21:54.119307 INFO::Total function execution time is 0.424520969390869 s and adjustment time is 0.38377857208252 s ( 90.4 )
2025-11-27 21:21:54.120314 INFO::Formatting Data.
2025-11-27 21:21:54.121131 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:54.122535 INFO::Removing potential empty rows and columns
2025-11-27 21:21:54.174562 INFO::Found 1000 missing values.
2025-11-27 21:21:54.193631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:54.194479 INFO::Done
2025-11-27 21:21:54.195325 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:54.200667 INFO::Starting hierarchical adjustment
2025-11-27 21:21:54.20144 INFO::Found 10 batches.
2025-11-27 21:21:55.217937 INFO::Set up parallel execution backend with 2 workers
2025-11-27 21:21:55.219448 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-27 21:21:56.378254 INFO::Adjusting the last 2 batches sequentially
2025-11-27 21:21:56.381497 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 21:21:56.397243 INFO::Done
2025-11-27 21:21:56.397909 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:56.402267 INFO::ASW Batch was 0.430935225537102 prior to batch effect correction and is now 0.430935225537102 .
2025-11-27 21:21:56.402858 INFO::ASW Label was 0.392845595850055 prior to batch effect correction and is now 0.392845595850055 .
2025-11-27 21:21:56.40356 INFO::Total function execution time is 2.28332018852234 s and adjustment time is 2.19593167304993 s ( 96.17 )
2025-11-27 21:21:56.554892 INFO::Formatting Data.
2025-11-27 21:21:56.555736 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:56.556693 INFO::Removing potential empty rows and columns
2025-11-27 21:21:56.557802 INFO::Found 0 missing values.
2025-11-27 21:21:56.561415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:56.561956 INFO::Done
2025-11-27 21:21:56.562471 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 21:21:56.565184 INFO::Starting hierarchical adjustment
2025-11-27 21:21:56.565897 INFO::Found 3 batches.
2025-11-27 21:21:56.566419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 21:21:56.567073 INFO::Using default BPPARAM
2025-11-27 21:21:56.567619 INFO::Processing subtree level 1
2025-11-27 21:21:56.674403 INFO::Adjusting the last 1 batches sequentially
2025-11-27 21:21:56.676116 INFO::Done
2025-11-27 21:21:56.676727 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 21:21:56.679898 INFO::ASW Batch was 0.273299561866984 prior to batch effect correction and is now -0.143893266238038 .
2025-11-27 21:21:56.680511 INFO::ASW Label was -0.198304890445313 prior to batch effect correction and is now 0.0113020307556374 .
2025-11-27 21:21:56.681436 INFO::Total function execution time is 0.126602172851562 s and adjustment time is 0.110357761383057 s ( 87.17 )
2025-11-27 21:21:56.799385 INFO::Formatting Data.
2025-11-27 21:21:56.800185 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:56.801094 INFO::Removing potential empty rows and columns
2025-11-27 21:21:56.802133 INFO::Found 2 missing values.
2025-11-27 21:21:56.804895 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:56.805438 INFO::Done
2025-11-27 21:21:56.831818 INFO::Found NA in Reference column
2025-11-27 21:21:56.841002 INFO::Require at least two references per batch.
2025-11-27 21:21:56.860559 INFO::Formatting Data.
2025-11-27 21:21:56.861328 INFO::Recognized SummarizedExperiment
2025-11-27 21:21:56.861882 INFO::Typecasting input to dataframe.
2025-11-27 21:21:56.871007 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:56.872131 INFO::Removing potential empty rows and columns
2025-11-27 21:21:56.875493 INFO::Found 0 missing values.
2025-11-27 21:21:56.881918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:56.882476 INFO::Done
2025-11-27 21:21:56.898099 INFO::Formatting Data.
2025-11-27 21:21:56.898911 INFO::Recognized SummarizedExperiment
2025-11-27 21:21:56.899473 INFO::Typecasting input to dataframe.
2025-11-27 21:21:56.917877 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:56.919196 INFO::Removing potential empty rows and columns
2025-11-27 21:21:56.922758 INFO::Found 0 missing values.
2025-11-27 21:21:56.933159 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:56.933815 INFO::Done
2025-11-27 21:21:56.949156 INFO::Formatting Data.
2025-11-27 21:21:56.94987 INFO::Recognized SummarizedExperiment
2025-11-27 21:21:56.950393 INFO::Typecasting input to dataframe.
2025-11-27 21:21:56.966392 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:56.967432 INFO::Removing potential empty rows and columns
2025-11-27 21:21:56.968506 INFO::Found 0 missing values.
2025-11-27 21:21:56.969436 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.
2025-11-27 21:21:56.973747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:56.974318 INFO::Done
2025-11-27 21:21:56.984831 INFO::Formatting Data.
2025-11-27 21:21:56.985608 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:56.98648 INFO::Removing potential empty rows and columns
2025-11-27 21:21:56.987453 INFO::Found 0 missing values.
2025-11-27 21:21:56.990235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:56.990765 INFO::Done
2025-11-27 21:21:57.001965 INFO::Formatting Data.
2025-11-27 21:21:57.002819 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:57.003683 INFO::Removing potential empty rows and columns
2025-11-27 21:21:57.004695 INFO::Found 0 missing values.
2025-11-27 21:21:57.00754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:57.008083 INFO::Done
2025-11-27 21:21:57.038001 INFO::Formatting Data.
2025-11-27 21:21:57.038905 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:57.04003 INFO::Removing potential empty rows and columns
2025-11-27 21:21:57.041229 INFO::Found 1 missing values.
2025-11-27 21:21:57.043727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:57.044309 INFO::Done
2025-11-27 21:21:57.063554 INFO::Formatting Data.
2025-11-27 21:21:57.064459 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:57.0654 INFO::Removing potential empty rows and columns
2025-11-27 21:21:57.066389 INFO::Found 2 missing values.
2025-11-27 21:21:57.067325 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.
2025-11-27 21:21:57.069695 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:57.070257 INFO::Done
2025-11-27 21:21:57.081128 INFO::Formatting Data.
2025-11-27 21:21:57.082132 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:57.083183 INFO::Removing potential empty rows and columns
2025-11-27 21:21:57.084213 INFO::Found 2 missing values.
2025-11-27 21:21:57.085936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:57.086529 INFO::Done
2025-11-27 21:21:57.097295 INFO::Formatting Data.
2025-11-27 21:21:57.098089 INFO::Typecasting input to dataframe.
2025-11-27 21:21:57.098904 INFO::Replacing NaNs with NAs.
2025-11-27 21:21:57.099765 INFO::Removing potential empty rows and columns
2025-11-27 21:21:57.100778 INFO::Found 0 missing values.
2025-11-27 21:21:57.103744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 21:21:57.104308 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.303 3.583 19.548
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 22.808 | 1.096 | 16.158 | |
| compute_asw | 0.024 | 0.001 | 0.023 | |
| count_existing | 0.011 | 0.002 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |