Yannis Schumann
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:07 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-10-21 04:50:11 -0000 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 04:52:11 -0000 (Tue, 21 Oct 2025) |
| EllapsedTime: 119.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* 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 26.964 1.518 19.672
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-10-21 04:51:54.85428 INFO::Formatting Data.
2025-10-21 04:51:54.856297 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:54.87447 INFO::Removing potential empty rows and columns
2025-10-21 04:51:55.396921 INFO::Found 0 missing values.
2025-10-21 04:51:55.401682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:51:55.40258 INFO::Done
2025-10-21 04:51:55.403365 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:51:55.418837 INFO::Starting hierarchical adjustment
2025-10-21 04:51:55.420085 INFO::Found 3 batches.
2025-10-21 04:51:55.420895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:51:55.422431 INFO::Using default BPPARAM
2025-10-21 04:51:55.42322 INFO::Processing subtree level 1
2025-10-21 04:51:55.558269 INFO::Adjusting the last 1 batches sequentially
2025-10-21 04:51:55.560653 INFO::Done
2025-10-21 04:51:55.561546 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:51:55.565156 INFO::ASW Batch was -0.0119329784102977 prior to batch effect correction and is now -0.0119329784102977 .
2025-10-21 04:51:55.566708 INFO::Total function execution time is 0.713305950164795 s and adjustment time is 0.140820026397705 s ( 19.74 )
2025-10-21 04:51:55.586302 INFO::Formatting Data.
2025-10-21 04:51:55.587291 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:55.588531 INFO::Removing potential empty rows and columns
2025-10-21 04:51:55.590142 INFO::Found 0 missing values.
2025-10-21 04:51:55.591508 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-21 04:51:55.607556 INFO::Formatting Data.
2025-10-21 04:51:55.608663 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:55.609966 INFO::Removing potential empty rows and columns
2025-10-21 04:51:55.611494 INFO::Found 0 missing values.
2025-10-21 04:51:55.612844 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-21 04:51:55.636 INFO::Formatting Data.
2025-10-21 04:51:55.637029 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:55.638286 INFO::Removing potential empty rows and columns
2025-10-21 04:51:55.639809 INFO::Found 0 missing values.
2025-10-21 04:51:55.641125 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-21 04:51:55.647535 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:51:55.648466 INFO::Done
2025-10-21 04:51:55.649237 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:51:55.652088 INFO::Starting hierarchical adjustment
2025-10-21 04:51:55.653247 INFO::Found 2 batches.
2025-10-21 04:51:55.654017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:51:55.654884 INFO::Using default BPPARAM
2025-10-21 04:51:55.655659 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:51:55.657009 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 04:51:55.688528 INFO::Done
2025-10-21 04:51:55.689449 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:51:55.692198 INFO::ASW Batch was 0.0418291494989033 prior to batch effect correction and is now -0.111237684618644 .
2025-10-21 04:51:55.693409 INFO::Total function execution time is 0.0574719905853271 s and adjustment time is 0.035489559173584 s ( 61.75 )
2025-10-21 04:51:55.697074 INFO::Formatting Data.
2025-10-21 04:51:55.698019 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:55.710384 INFO::Formatting Data.
2025-10-21 04:51:55.711349 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:55.712626 INFO::Removing potential empty rows and columns
2025-10-21 04:51:55.714067 INFO::Found 0 missing values.
2025-10-21 04:51:55.7182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:51:55.719069 INFO::Done
2025-10-21 04:51:55.719863 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:51:55.722758 INFO::Starting hierarchical adjustment
2025-10-21 04:51:55.723859 INFO::Found 2 batches.
2025-10-21 04:51:55.724633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:51:55.725549 INFO::Using default BPPARAM
2025-10-21 04:51:55.726315 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:51:55.727695 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:51:55.789959 INFO::Done
2025-10-21 04:51:55.790861 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:51:55.793775 INFO::ASW Batch was 0.0700463635976849 prior to batch effect correction and is now -0.107452523007263 .
2025-10-21 04:51:55.794996 INFO::Total function execution time is 0.0846624374389648 s and adjustment time is 0.0663273334503174 s ( 78.34 )
2025-10-21 04:51:55.796558 INFO::Formatting Data.
2025-10-21 04:51:55.797482 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:55.79871 INFO::Removing potential empty rows and columns
2025-10-21 04:51:55.800213 INFO::Found 0 missing values.
2025-10-21 04:51:55.80442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:51:55.805351 INFO::Done
2025-10-21 04:51:55.806106 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:51:55.809039 INFO::Starting hierarchical adjustment
2025-10-21 04:51:55.810153 INFO::Found 2 batches.
2025-10-21 04:51:55.810905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:51:55.811795 INFO::Using default BPPARAM
2025-10-21 04:51:55.812543 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:51:55.813888 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:51:55.835675 INFO::Done
2025-10-21 04:51:55.836577 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:51:55.8394 INFO::ASW Batch was 0.0700463635976849 prior to batch effect correction and is now -0.107452523007263 .
2025-10-21 04:51:55.840578 INFO::Total function execution time is 0.0440263748168945 s and adjustment time is 0.0256679058074951 s ( 58.3 )
2025-10-21 04:51:59.701823 INFO::Formatting Data.
2025-10-21 04:51:59.702672 INFO::Recognized SummarizedExperiment
2025-10-21 04:51:59.703313 INFO::Typecasting input to dataframe.
2025-10-21 04:51:59.742389 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:59.743858 INFO::Removing potential empty rows and columns
2025-10-21 04:51:59.74899 INFO::Found 0 missing values.
2025-10-21 04:51:59.75874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:51:59.759661 INFO::Done
2025-10-21 04:51:59.760384 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:51:59.765095 INFO::Starting hierarchical adjustment
2025-10-21 04:51:59.766156 INFO::Found 2 batches.
2025-10-21 04:51:59.766895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:51:59.768317 INFO::Using default BPPARAM
2025-10-21 04:51:59.769116 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:51:59.770438 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 04:51:59.846733 INFO::Done
2025-10-21 04:51:59.847579 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:51:59.860277 INFO::ASW Batch was 0.00589390594901991 prior to batch effect correction and is now -0.0948448615886372 .
2025-10-21 04:51:59.861791 INFO::Total function execution time is 0.160319805145264 s and adjustment time is 0.0807747840881348 s ( 50.38 )
2025-10-21 04:51:59.888402 INFO::Formatting Data.
2025-10-21 04:51:59.889326 INFO::Recognized SummarizedExperiment
2025-10-21 04:51:59.890039 INFO::Typecasting input to dataframe.
2025-10-21 04:51:59.90354 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:59.905092 INFO::Removing potential empty rows and columns
2025-10-21 04:51:59.910094 INFO::Found 0 missing values.
2025-10-21 04:51:59.919964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:51:59.920857 INFO::Done
2025-10-21 04:51:59.921598 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:51:59.926466 INFO::Starting hierarchical adjustment
2025-10-21 04:51:59.927545 INFO::Found 2 batches.
2025-10-21 04:51:59.928346 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:51:59.929262 INFO::Using default BPPARAM
2025-10-21 04:51:59.930005 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:51:59.931307 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 04:51:59.965927 INFO::Done
2025-10-21 04:51:59.96678 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:51:59.971363 INFO::ASW Batch was -0.0185415609390753 prior to batch effect correction and is now -0.0185415609390753 .
2025-10-21 04:51:59.972524 INFO::Total function execution time is 0.0840888023376465 s and adjustment time is 0.0385804176330566 s ( 45.88 )
2025-10-21 04:51:59.996259 INFO::Formatting Data.
2025-10-21 04:51:59.997231 INFO::Replacing NaNs with NAs.
2025-10-21 04:51:59.99837 INFO::Removing potential empty rows and columns
2025-10-21 04:51:59.999846 INFO::Found 0 missing values.
2025-10-21 04:52:00.003991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:00.004882 INFO::Done
2025-10-21 04:52:00.00565 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:00.008423 INFO::Starting hierarchical adjustment
2025-10-21 04:52:00.00959 INFO::Found 3 batches.
2025-10-21 04:52:00.010378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:00.01123 INFO::Using default BPPARAM
2025-10-21 04:52:00.012053 INFO::Processing subtree level 1
2025-10-21 04:52:00.177799 INFO::Adjusting the last 1 batches sequentially
2025-10-21 04:52:00.180138 INFO::Done
2025-10-21 04:52:00.181041 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:00.184276 INFO::ASW Batch was 0.0595442875214541 prior to batch effect correction and is now -0.173858565983095 .
2025-10-21 04:52:00.18562 INFO::Total function execution time is 0.18935489654541 s and adjustment time is 0.170774936676025 s ( 90.19 )
2025-10-21 04:52:00.204644 INFO::Skipping initial DF formatting
2025-10-21 04:52:00.205562 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:00.210898 INFO::Starting hierarchical adjustment
2025-10-21 04:52:00.212044 INFO::Found 5 batches.
2025-10-21 04:52:00.212863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:00.213746 INFO::Using default BPPARAM
2025-10-21 04:52:00.214508 INFO::Processing subtree level 1
2025-10-21 04:52:00.459939 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:00.461986 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 04:52:00.489091 INFO::Done
2025-10-21 04:52:00.489963 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:00.495645 INFO::ASW Batch was 0.485418050243483 prior to batch effect correction and is now 0.485418050243483 .
2025-10-21 04:52:00.496539 INFO::ASW Label was 0.370519755732695 prior to batch effect correction and is now 0.370519755732695 .
2025-10-21 04:52:00.497735 INFO::Total function execution time is 0.293120622634888 s and adjustment time is 0.27724027633667 s ( 94.58 )
2025-10-21 04:52:00.589242 INFO::Formatting Data.
2025-10-21 04:52:00.590309 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:00.591539 INFO::Removing potential empty rows and columns
2025-10-21 04:52:00.593006 INFO::Found 0 missing values.
2025-10-21 04:52:00.598784 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:00.599707 INFO::Done
2025-10-21 04:52:00.60048 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:00.604713 INFO::Starting hierarchical adjustment
2025-10-21 04:52:00.60589 INFO::Found 5 batches.
2025-10-21 04:52:00.606658 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:00.607507 INFO::Using default BPPARAM
2025-10-21 04:52:00.608399 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:00.766375 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:00.768783 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:00.794923 INFO::Done
2025-10-21 04:52:00.795959 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:00.801008 INFO::ASW Batch was 0.291310413076281 prior to batch effect correction and is now -0.0583814871301979 .
2025-10-21 04:52:00.802005 INFO::ASW Label was 0.571638715716199 prior to batch effect correction and is now 0.725695090497145 .
2025-10-21 04:52:00.803252 INFO::Total function execution time is 0.214019060134888 s and adjustment time is 0.18924617767334 s ( 88.42 )
2025-10-21 04:52:00.804518 INFO::Formatting Data.
2025-10-21 04:52:00.805497 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:00.806895 INFO::Removing potential empty rows and columns
2025-10-21 04:52:00.808499 INFO::Found 0 missing values.
2025-10-21 04:52:00.815723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:00.816698 INFO::Done
2025-10-21 04:52:00.817566 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:00.822046 INFO::Starting hierarchical adjustment
2025-10-21 04:52:00.823249 INFO::Found 5 batches.
2025-10-21 04:52:00.824173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:00.825199 INFO::Using default BPPARAM
2025-10-21 04:52:00.82606 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:00.976224 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:00.978271 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:01.001715 INFO::Done
2025-10-21 04:52:01.002702 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:01.007542 INFO::ASW Batch was 0.291310413076281 prior to batch effect correction and is now -0.0583814871301979 .
2025-10-21 04:52:01.008587 INFO::ASW Label was 0.571638715716199 prior to batch effect correction and is now 0.725695090497145 .
2025-10-21 04:52:01.009881 INFO::Total function execution time is 0.205312967300415 s and adjustment time is 0.17868185043335 s ( 87.03 )
2025-10-21 04:52:01.029795 INFO::Formatting Data.
2025-10-21 04:52:01.030843 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:01.032104 INFO::Removing potential empty rows and columns
2025-10-21 04:52:01.033525 INFO::Found 0 missing values.
2025-10-21 04:52:01.039526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:01.040478 INFO::Done
2025-10-21 04:52:01.041324 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:01.045556 INFO::Starting hierarchical adjustment
2025-10-21 04:52:01.04663 INFO::Found 5 batches.
2025-10-21 04:52:01.047395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:01.048312 INFO::Using default BPPARAM
2025-10-21 04:52:01.049127 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:01.199494 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:01.201676 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:01.225559 INFO::Done
2025-10-21 04:52:01.226647 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:01.231708 INFO::ASW Batch was 0.206284050540531 prior to batch effect correction and is now -0.0541583383166411 .
2025-10-21 04:52:01.232709 INFO::ASW Label was 0.572999872202606 prior to batch effect correction and is now 0.793281456732536 .
2025-10-21 04:52:01.234029 INFO::Total function execution time is 0.204253673553467 s and adjustment time is 0.179103374481201 s ( 87.69 )
2025-10-21 04:52:01.23532 INFO::Formatting Data.
2025-10-21 04:52:01.23637 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:01.237928 INFO::Removing potential empty rows and columns
2025-10-21 04:52:01.239536 INFO::Found 0 missing values.
2025-10-21 04:52:01.246147 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:01.247108 INFO::Done
2025-10-21 04:52:01.248003 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:01.252336 INFO::Starting hierarchical adjustment
2025-10-21 04:52:01.253437 INFO::Found 5 batches.
2025-10-21 04:52:01.254238 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:01.255179 INFO::Using default BPPARAM
2025-10-21 04:52:01.25604 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:01.415076 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:01.417441 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:01.44396 INFO::Done
2025-10-21 04:52:01.445188 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:01.450689 INFO::ASW Batch was 0.206284050540531 prior to batch effect correction and is now -0.0541583383166411 .
2025-10-21 04:52:01.452024 INFO::ASW Label was 0.572999872202606 prior to batch effect correction and is now 0.793281456732536 .
2025-10-21 04:52:01.45366 INFO::Total function execution time is 0.218291997909546 s and adjustment time is 0.19063401222229 s ( 87.33 )
2025-10-21 04:52:01.474585 INFO::Formatting Data.
2025-10-21 04:52:01.475794 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:01.477248 INFO::Removing potential empty rows and columns
2025-10-21 04:52:01.478845 INFO::Found 0 missing values.
2025-10-21 04:52:01.48341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:01.484442 INFO::Done
2025-10-21 04:52:01.485437 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:01.489968 INFO::Starting hierarchical adjustment
2025-10-21 04:52:01.491129 INFO::Found 2 batches.
2025-10-21 04:52:01.492004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:01.493072 INFO::Using default BPPARAM
2025-10-21 04:52:01.493999 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:01.495482 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:01.523824 INFO::Done
2025-10-21 04:52:01.52485 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:01.529252 INFO::ASW Batch was 0.685420195615089 prior to batch effect correction and is now -0.00147594476859278 .
2025-10-21 04:52:01.530152 INFO::ASW Label was 0.409236059034508 prior to batch effect correction and is now 0.892312715549554 .
2025-10-21 04:52:01.531317 INFO::Total function execution time is 0.0568034648895264 s and adjustment time is 0.0329053401947021 s ( 57.93 )
2025-10-21 04:52:01.532524 INFO::Formatting Data.
2025-10-21 04:52:01.533486 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:01.534781 INFO::Removing potential empty rows and columns
2025-10-21 04:52:01.536317 INFO::Found 0 missing values.
2025-10-21 04:52:01.540446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:01.541289 INFO::Done
2025-10-21 04:52:01.542099 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:01.546492 INFO::Starting hierarchical adjustment
2025-10-21 04:52:01.547645 INFO::Found 2 batches.
2025-10-21 04:52:01.548476 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:01.549432 INFO::Using default BPPARAM
2025-10-21 04:52:01.550276 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:01.551674 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 04:52:01.573471 INFO::Done
2025-10-21 04:52:01.57439 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:01.578569 INFO::ASW Batch was 0.685420195615089 prior to batch effect correction and is now -0.00147594476859278 .
2025-10-21 04:52:01.579439 INFO::ASW Label was 0.409236059034508 prior to batch effect correction and is now 0.892312715549554 .
2025-10-21 04:52:01.580594 INFO::Total function execution time is 0.0480766296386719 s and adjustment time is 0.0260820388793945 s ( 54.25 )
2025-10-21 04:52:01.597187 INFO::Formatting Data.
2025-10-21 04:52:01.5983 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:01.599758 INFO::Removing potential empty rows and columns
2025-10-21 04:52:01.601237 INFO::Found 0 missing values.
2025-10-21 04:52:01.604534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:01.605426 INFO::Done
2025-10-21 04:52:01.606285 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:01.609058 INFO::Starting hierarchical adjustment
2025-10-21 04:52:01.610121 INFO::Found 2 batches.
2025-10-21 04:52:01.610931 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:01.611902 INFO::Using default BPPARAM
2025-10-21 04:52:01.612715 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:01.614234 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 04:52:01.661176 INFO::Done
2025-10-21 04:52:01.662126 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:01.664911 INFO::ASW Batch was -0.173023322013301 prior to batch effect correction and is now -0.178037413849758 .
2025-10-21 04:52:01.666106 INFO::Total function execution time is 0.0689783096313477 s and adjustment time is 0.0512456893920898 s ( 74.29 )
2025-10-21 04:52:01.683197 INFO::Formatting Data.
2025-10-21 04:52:01.684492 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:01.685737 INFO::Removing potential empty rows and columns
2025-10-21 04:52:01.687205 INFO::Found 0 missing values.
2025-10-21 04:52:01.688915 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-21 04:52:01.69592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:01.696905 INFO::Done
2025-10-21 04:52:01.697686 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:01.702027 INFO::Starting hierarchical adjustment
2025-10-21 04:52:01.703242 INFO::Found 2 batches.
2025-10-21 04:52:01.704079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:01.705 INFO::Using default BPPARAM
2025-10-21 04:52:01.705807 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:01.707214 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 04:52:01.731674 INFO::Done
2025-10-21 04:52:01.732652 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:01.737014 INFO::ASW Batch was 0.431485702108945 prior to batch effect correction and is now 0.0153235609269297 .
2025-10-21 04:52:01.737931 INFO::ASW Label was 0.651103604917932 prior to batch effect correction and is now 0.906929391623703 .
2025-10-21 04:52:01.739038 INFO::Total function execution time is 0.0558962821960449 s and adjustment time is 0.0286035537719727 s ( 51.17 )
2025-10-21 04:52:01.740167 INFO::Formatting Data.
2025-10-21 04:52:01.741116 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:01.742411 INFO::Removing potential empty rows and columns
2025-10-21 04:52:01.743859 INFO::Found 0 missing values.
2025-10-21 04:52:01.745193 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-21 04:52:01.752832 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:01.753758 INFO::Done
2025-10-21 04:52:01.754545 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:01.75877 INFO::Starting hierarchical adjustment
2025-10-21 04:52:01.759993 INFO::Found 2 batches.
2025-10-21 04:52:01.760844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:01.761752 INFO::Using default BPPARAM
2025-10-21 04:52:01.762543 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:01.763928 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 04:52:01.787943 INFO::Done
2025-10-21 04:52:01.788889 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:01.79307 INFO::ASW Batch was 0.431485702108945 prior to batch effect correction and is now 0.0153235609269297 .
2025-10-21 04:52:01.793993 INFO::ASW Label was 0.651103604917932 prior to batch effect correction and is now 0.906929391623703 .
2025-10-21 04:52:01.795128 INFO::Total function execution time is 0.0549511909484863 s and adjustment time is 0.0282204151153564 s ( 51.36 )
2025-10-21 04:52:02.106207 INFO::Formatting Data.
2025-10-21 04:52:02.107416 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:02.10886 INFO::Removing potential empty rows and columns
2025-10-21 04:52:02.110359 INFO::Found 0 missing values.
2025-10-21 04:52:02.114805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:02.115782 INFO::Done
2025-10-21 04:52:02.116616 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:02.119824 INFO::Starting hierarchical adjustment
2025-10-21 04:52:02.120964 INFO::Found 3 batches.
2025-10-21 04:52:02.12177 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:02.122672 INFO::Using default BPPARAM
2025-10-21 04:52:02.123459 INFO::Processing subtree level 1
2025-10-21 04:52:02.230699 INFO::Adjusting the last 1 batches sequentially
2025-10-21 04:52:02.233118 INFO::Done
2025-10-21 04:52:02.233956 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:02.237465 INFO::ASW Batch was -0.120806032912346 prior to batch effect correction and is now -0.120806032912346 .
2025-10-21 04:52:02.238945 INFO::Total function execution time is 0.132914304733276 s and adjustment time is 0.112426280975342 s ( 84.59 )
2025-10-21 04:52:02.240514 INFO::Formatting Data.
2025-10-21 04:52:02.24149 INFO::Typecasting input to dataframe.
2025-10-21 04:52:02.242596 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:02.243939 INFO::Removing potential empty rows and columns
2025-10-21 04:52:02.245525 INFO::Found 0 missing values.
2025-10-21 04:52:02.250263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:02.251144 INFO::Done
2025-10-21 04:52:02.251966 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:02.254778 INFO::Starting hierarchical adjustment
2025-10-21 04:52:02.255922 INFO::Found 3 batches.
2025-10-21 04:52:02.256726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:02.257676 INFO::Using default BPPARAM
2025-10-21 04:52:02.258481 INFO::Processing subtree level 1
2025-10-21 04:52:02.363401 INFO::Adjusting the last 1 batches sequentially
2025-10-21 04:52:02.365768 INFO::Done
2025-10-21 04:52:02.366605 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:02.36995 INFO::ASW Batch was -0.120806032912346 prior to batch effect correction and is now -0.120806032912346 .
2025-10-21 04:52:02.371242 INFO::Total function execution time is 0.130708932876587 s and adjustment time is 0.11011791229248 s ( 84.25 )
2025-10-21 04:52:02.389132 INFO::Formatting Data.
2025-10-21 04:52:02.390135 INFO::Typecasting input to dataframe.
2025-10-21 04:52:02.391306 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:02.392632 INFO::Removing potential empty rows and columns
2025-10-21 04:52:02.394215 INFO::Found 0 missing values.
2025-10-21 04:52:02.398677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:02.399633 INFO::Done
2025-10-21 04:52:02.400426 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:02.4033 INFO::Starting hierarchical adjustment
2025-10-21 04:52:02.404397 INFO::Found 3 batches.
2025-10-21 04:52:02.405227 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:02.406107 INFO::Using default BPPARAM
2025-10-21 04:52:02.406914 INFO::Processing subtree level 1
2025-10-21 04:52:02.511227 INFO::Adjusting the last 1 batches sequentially
2025-10-21 04:52:02.513628 INFO::Done
2025-10-21 04:52:02.514472 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:02.518124 INFO::ASW Batch was -0.0135850166655796 prior to batch effect correction and is now -0.0135850166655796 .
2025-10-21 04:52:02.519506 INFO::Total function execution time is 0.130378246307373 s and adjustment time is 0.109447956085205 s ( 83.95 )
2025-10-21 04:52:02.697345 INFO::Formatting Data.
2025-10-21 04:52:02.698446 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:02.699979 INFO::Removing potential empty rows and columns
2025-10-21 04:52:02.704295 INFO::Found 1000 missing values.
2025-10-21 04:52:02.733759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:02.734798 INFO::Done
2025-10-21 04:52:02.735728 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:02.74371 INFO::Starting hierarchical adjustment
2025-10-21 04:52:02.744998 INFO::Found 10 batches.
2025-10-21 04:52:02.745911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:02.746869 INFO::Using default BPPARAM
2025-10-21 04:52:02.747769 INFO::Processing subtree level 1
2025-10-21 04:52:02.917525 INFO::Processing subtree level 2
2025-10-21 04:52:03.100958 INFO::Adjusting the last 1 batches sequentially
2025-10-21 04:52:03.103637 INFO::Done
2025-10-21 04:52:03.104478 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:03.113255 INFO::ASW Batch was 0.546081530963828 prior to batch effect correction and is now 0.546081530963828 .
2025-10-21 04:52:03.114251 INFO::ASW Label was 0.294935010819586 prior to batch effect correction and is now 0.294935010819586 .
2025-10-21 04:52:03.115757 INFO::Total function execution time is 0.418363571166992 s and adjustment time is 0.358944654464722 s ( 85.8 )
2025-10-21 04:52:03.117171 INFO::Formatting Data.
2025-10-21 04:52:03.118115 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:03.119948 INFO::Removing potential empty rows and columns
2025-10-21 04:52:03.124125 INFO::Found 1000 missing values.
2025-10-21 04:52:03.15128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:03.152249 INFO::Done
2025-10-21 04:52:03.153077 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:03.160554 INFO::Starting hierarchical adjustment
2025-10-21 04:52:03.161727 INFO::Found 10 batches.
2025-10-21 04:52:04.476164 INFO::Set up parallel execution backend with 2 workers
2025-10-21 04:52:04.478677 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-21 04:52:05.83387 INFO::Adjusting the last 2 batches sequentially
2025-10-21 04:52:05.836054 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 04:52:05.859775 INFO::Done
2025-10-21 04:52:05.86065 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:05.867508 INFO::ASW Batch was 0.546081530963828 prior to batch effect correction and is now 0.546081530963828 .
2025-10-21 04:52:05.868421 INFO::ASW Label was 0.294935010819586 prior to batch effect correction and is now 0.294935010819586 .
2025-10-21 04:52:05.869519 INFO::Total function execution time is 2.75237083435059 s and adjustment time is 2.69821834564209 s ( 98.03 )
2025-10-21 04:52:06.066771 INFO::Formatting Data.
2025-10-21 04:52:06.068036 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.069465 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.07109 INFO::Found 0 missing values.
2025-10-21 04:52:06.07669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.077685 INFO::Done
2025-10-21 04:52:06.078564 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 04:52:06.082846 INFO::Starting hierarchical adjustment
2025-10-21 04:52:06.084099 INFO::Found 3 batches.
2025-10-21 04:52:06.084933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 04:52:06.085834 INFO::Using default BPPARAM
2025-10-21 04:52:06.086602 INFO::Processing subtree level 1
2025-10-21 04:52:06.225407 INFO::Adjusting the last 1 batches sequentially
2025-10-21 04:52:06.228071 INFO::Done
2025-10-21 04:52:06.229064 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 04:52:06.233901 INFO::ASW Batch was 0.13244119900359 prior to batch effect correction and is now -0.147887691644106 .
2025-10-21 04:52:06.234904 INFO::ASW Label was -0.141740065919262 prior to batch effect correction and is now 0.0698544009765548 .
2025-10-21 04:52:06.236288 INFO::Total function execution time is 0.169572353363037 s and adjustment time is 0.144192934036255 s ( 85.03 )
2025-10-21 04:52:06.442637 INFO::Formatting Data.
2025-10-21 04:52:06.444028 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.445357 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.446968 INFO::Found 2 missing values.
2025-10-21 04:52:06.45129 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.45222 INFO::Done
2025-10-21 04:52:06.492847 INFO::Found NA in Reference column
2025-10-21 04:52:06.506883 INFO::Require at least two references per batch.
2025-10-21 04:52:06.538554 INFO::Formatting Data.
2025-10-21 04:52:06.539569 INFO::Recognized SummarizedExperiment
2025-10-21 04:52:06.540408 INFO::Typecasting input to dataframe.
2025-10-21 04:52:06.555682 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.557323 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.562824 INFO::Found 0 missing values.
2025-10-21 04:52:06.573972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.575245 INFO::Done
2025-10-21 04:52:06.597994 INFO::Formatting Data.
2025-10-21 04:52:06.598943 INFO::Recognized SummarizedExperiment
2025-10-21 04:52:06.599737 INFO::Typecasting input to dataframe.
2025-10-21 04:52:06.625543 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.627217 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.633002 INFO::Found 0 missing values.
2025-10-21 04:52:06.651635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.652694 INFO::Done
2025-10-21 04:52:06.678984 INFO::Formatting Data.
2025-10-21 04:52:06.68014 INFO::Recognized SummarizedExperiment
2025-10-21 04:52:06.681047 INFO::Typecasting input to dataframe.
2025-10-21 04:52:06.70966 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.711233 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.713077 INFO::Found 0 missing values.
2025-10-21 04:52:06.714577 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-21 04:52:06.72192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.722921 INFO::Done
2025-10-21 04:52:06.7397 INFO::Formatting Data.
2025-10-21 04:52:06.740984 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.742476 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.744269 INFO::Found 0 missing values.
2025-10-21 04:52:06.749234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.75026 INFO::Done
2025-10-21 04:52:06.768982 INFO::Formatting Data.
2025-10-21 04:52:06.770201 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.77163 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.773344 INFO::Found 0 missing values.
2025-10-21 04:52:06.778651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.779629 INFO::Done
2025-10-21 04:52:06.829921 INFO::Formatting Data.
2025-10-21 04:52:06.83119 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.832937 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.834962 INFO::Found 1 missing values.
2025-10-21 04:52:06.839457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.840481 INFO::Done
2025-10-21 04:52:06.885293 INFO::Formatting Data.
2025-10-21 04:52:06.886966 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.88852 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.890297 INFO::Found 2 missing values.
2025-10-21 04:52:06.891892 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-21 04:52:06.896068 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.897171 INFO::Done
2025-10-21 04:52:06.914896 INFO::Formatting Data.
2025-10-21 04:52:06.916188 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.917764 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.919528 INFO::Found 2 missing values.
2025-10-21 04:52:06.922446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.923412 INFO::Done
2025-10-21 04:52:06.941761 INFO::Formatting Data.
2025-10-21 04:52:06.942807 INFO::Typecasting input to dataframe.
2025-10-21 04:52:06.944063 INFO::Replacing NaNs with NAs.
2025-10-21 04:52:06.945407 INFO::Removing potential empty rows and columns
2025-10-21 04:52:06.946938 INFO::Found 0 missing values.
2025-10-21 04:52:06.951302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 04:52:06.952237 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.503 4.944 25.121
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.964 | 1.518 | 19.672 | |
| compute_asw | 0.036 | 0.007 | 0.043 | |
| count_existing | 0.021 | 0.000 | 0.021 | |
| generate_data_covariables | 0.006 | 0.011 | 0.017 | |
| generate_dataset | 0.016 | 0.001 | 0.015 | |