Yannis Schumann
| Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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 2025-10-18 12:07 -0400 (Sat, 18 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" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 165/2353 | 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: 2025-10-17 06:21:39 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 06:23:16 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 97.2 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 29.488 1.745 24.522
* 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")
2025-10-17 06:22:56.715902 INFO::Formatting Data.
2025-10-17 06:22:56.71802 INFO::Replacing NaNs with NAs.
2025-10-17 06:22:56.757205 INFO::Removing potential empty rows and columns
2025-10-17 06:22:57.514789 INFO::Found 0 missing values.
2025-10-17 06:22:57.52011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:22:57.521128 INFO::Done
2025-10-17 06:22:57.522099 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:22:57.539997 INFO::Starting hierarchical adjustment
2025-10-17 06:22:57.541971 INFO::Found 3 batches.
2025-10-17 06:22:57.542939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:22:57.544766 INFO::Using default BPPARAM
2025-10-17 06:22:57.545752 INFO::Processing subtree level 1
2025-10-17 06:22:57.706832 INFO::Adjusting the last 1 batches sequentially
2025-10-17 06:22:57.713915 INFO::Done
2025-10-17 06:22:57.715041 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:22:57.723396 INFO::ASW Batch was -0.0439264160020428 prior to batch effect correction and is now -0.0439264160020428 .
2025-10-17 06:22:57.729329 INFO::Total function execution time is 1.01036381721497 s and adjustment time is 0.172240257263184 s ( 17.05 )
2025-10-17 06:22:57.754645 INFO::Formatting Data.
2025-10-17 06:22:57.755762 INFO::Replacing NaNs with NAs.
2025-10-17 06:22:57.757103 INFO::Removing potential empty rows and columns
2025-10-17 06:22:57.758875 INFO::Found 0 missing values.
2025-10-17 06:22:57.760451 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.
2025-10-17 06:22:57.777757 INFO::Formatting Data.
2025-10-17 06:22:57.778914 INFO::Replacing NaNs with NAs.
2025-10-17 06:22:57.780355 INFO::Removing potential empty rows and columns
2025-10-17 06:22:57.782107 INFO::Found 0 missing values.
2025-10-17 06:22:57.783705 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.
2025-10-17 06:22:57.808586 INFO::Formatting Data.
2025-10-17 06:22:57.809753 INFO::Replacing NaNs with NAs.
2025-10-17 06:22:57.811116 INFO::Removing potential empty rows and columns
2025-10-17 06:22:57.812787 INFO::Found 0 missing values.
2025-10-17 06:22:57.814179 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.
2025-10-17 06:22:57.82129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:22:57.822258 INFO::Done
2025-10-17 06:22:57.823069 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:22:57.826238 INFO::Starting hierarchical adjustment
2025-10-17 06:22:57.827486 INFO::Found 2 batches.
2025-10-17 06:22:57.828371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:22:57.829382 INFO::Using default BPPARAM
2025-10-17 06:22:57.830221 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:22:57.831748 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 06:22:57.866994 INFO::Done
2025-10-17 06:22:57.867984 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:22:57.871192 INFO::ASW Batch was 0.0382193490636303 prior to batch effect correction and is now -0.115152851713371 .
2025-10-17 06:22:57.872484 INFO::Total function execution time is 0.0639469623565674 s and adjustment time is 0.0397813320159912 s ( 62.21 )
2025-10-17 06:22:57.876765 INFO::Formatting Data.
2025-10-17 06:22:57.87786 INFO::Replacing NaNs with NAs.
2025-10-17 06:22:57.890865 INFO::Formatting Data.
2025-10-17 06:22:57.891922 INFO::Replacing NaNs with NAs.
2025-10-17 06:22:57.89325 INFO::Removing potential empty rows and columns
2025-10-17 06:22:57.894776 INFO::Found 0 missing values.
2025-10-17 06:22:57.899338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:22:57.900466 INFO::Done
2025-10-17 06:22:57.90135 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:22:57.90454 INFO::Starting hierarchical adjustment
2025-10-17 06:22:57.905651 INFO::Found 2 batches.
2025-10-17 06:22:57.906471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:22:57.907435 INFO::Using default BPPARAM
2025-10-17 06:22:57.908306 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:22:57.90987 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 06:22:57.995352 INFO::Done
2025-10-17 06:22:57.996426 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:22:57.999786 INFO::ASW Batch was 0.0996964950741612 prior to batch effect correction and is now -0.126509378684589 .
2025-10-17 06:22:58.001111 INFO::Total function execution time is 0.110285758972168 s and adjustment time is 0.0898368358612061 s ( 81.46 )
2025-10-17 06:22:58.002725 INFO::Formatting Data.
2025-10-17 06:22:58.003695 INFO::Replacing NaNs with NAs.
2025-10-17 06:22:58.005032 INFO::Removing potential empty rows and columns
2025-10-17 06:22:58.006646 INFO::Found 0 missing values.
2025-10-17 06:22:58.010954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:22:58.01186 INFO::Done
2025-10-17 06:22:58.012623 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:22:58.015661 INFO::Starting hierarchical adjustment
2025-10-17 06:22:58.016799 INFO::Found 2 batches.
2025-10-17 06:22:58.017564 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:22:58.018413 INFO::Using default BPPARAM
2025-10-17 06:22:58.01916 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:22:58.020504 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 06:22:58.043577 INFO::Done
2025-10-17 06:22:58.044501 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:22:58.047481 INFO::ASW Batch was 0.0996964950741612 prior to batch effect correction and is now -0.126509378684589 .
2025-10-17 06:22:58.048668 INFO::Total function execution time is 0.0459563732147217 s and adjustment time is 0.026986837387085 s ( 58.72 )
2025-10-17 06:23:02.271847 INFO::Formatting Data.
2025-10-17 06:23:02.272787 INFO::Recognized SummarizedExperiment
2025-10-17 06:23:02.273468 INFO::Typecasting input to dataframe.
2025-10-17 06:23:02.314786 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:02.316417 INFO::Removing potential empty rows and columns
2025-10-17 06:23:02.321719 INFO::Found 0 missing values.
2025-10-17 06:23:02.332091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:02.333157 INFO::Done
2025-10-17 06:23:02.333901 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:02.338845 INFO::Starting hierarchical adjustment
2025-10-17 06:23:02.339967 INFO::Found 2 batches.
2025-10-17 06:23:02.34071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:02.342168 INFO::Using default BPPARAM
2025-10-17 06:23:02.342926 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:02.344281 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 06:23:02.422138 INFO::Done
2025-10-17 06:23:02.423038 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:02.427908 INFO::ASW Batch was -0.011266491843676 prior to batch effect correction and is now -0.0911564343138708 .
2025-10-17 06:23:02.429143 INFO::Total function execution time is 0.15775990486145 s and adjustment time is 0.0823583602905273 s ( 52.2 )
2025-10-17 06:23:02.454111 INFO::Formatting Data.
2025-10-17 06:23:02.455068 INFO::Recognized SummarizedExperiment
2025-10-17 06:23:02.4558 INFO::Typecasting input to dataframe.
2025-10-17 06:23:02.476404 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:02.478017 INFO::Removing potential empty rows and columns
2025-10-17 06:23:02.483152 INFO::Found 0 missing values.
2025-10-17 06:23:02.493655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:02.494542 INFO::Done
2025-10-17 06:23:02.495312 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:02.500422 INFO::Starting hierarchical adjustment
2025-10-17 06:23:02.501591 INFO::Found 2 batches.
2025-10-17 06:23:02.50233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:02.503158 INFO::Using default BPPARAM
2025-10-17 06:23:02.503914 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:02.505286 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 06:23:02.540581 INFO::Done
2025-10-17 06:23:02.541485 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:02.546322 INFO::ASW Batch was 0.00605204064699828 prior to batch effect correction and is now 0.00605204064699828 .
2025-10-17 06:23:02.547617 INFO::Total function execution time is 0.0934686660766602 s and adjustment time is 0.0392067432403564 s ( 41.95 )
2025-10-17 06:23:02.573061 INFO::Formatting Data.
2025-10-17 06:23:02.574028 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:02.575185 INFO::Removing potential empty rows and columns
2025-10-17 06:23:02.576583 INFO::Found 0 missing values.
2025-10-17 06:23:02.580779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:02.581639 INFO::Done
2025-10-17 06:23:02.582373 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:02.585085 INFO::Starting hierarchical adjustment
2025-10-17 06:23:02.586102 INFO::Found 3 batches.
2025-10-17 06:23:02.586819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:02.587659 INFO::Using default BPPARAM
2025-10-17 06:23:02.588388 INFO::Processing subtree level 1
2025-10-17 06:23:02.816816 INFO::Adjusting the last 1 batches sequentially
2025-10-17 06:23:02.819335 INFO::Done
2025-10-17 06:23:02.820194 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:02.82813 INFO::ASW Batch was 0.156594876176288 prior to batch effect correction and is now -0.190427664335499 .
2025-10-17 06:23:02.833784 INFO::Total function execution time is 0.260676145553589 s and adjustment time is 0.233383655548096 s ( 89.53 )
2025-10-17 06:23:02.870458 INFO::Skipping initial DF formatting
2025-10-17 06:23:02.871449 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:02.878746 INFO::Starting hierarchical adjustment
2025-10-17 06:23:02.88004 INFO::Found 5 batches.
2025-10-17 06:23:02.880913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:02.881854 INFO::Using default BPPARAM
2025-10-17 06:23:02.883372 INFO::Processing subtree level 1
2025-10-17 06:23:03.189647 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:03.191846 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 06:23:03.253314 INFO::Done
2025-10-17 06:23:03.254278 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:03.260233 INFO::ASW Batch was 0.501835631720331 prior to batch effect correction and is now 0.501835631720331 .
2025-10-17 06:23:03.262036 INFO::ASW Label was 0.372858664313912 prior to batch effect correction and is now 0.372858664313912 .
2025-10-17 06:23:03.263385 INFO::Total function execution time is 0.392904281616211 s and adjustment time is 0.373533010482788 s ( 95.07 )
2025-10-17 06:23:03.380613 INFO::Formatting Data.
2025-10-17 06:23:03.381896 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:03.38352 INFO::Removing potential empty rows and columns
2025-10-17 06:23:03.38532 INFO::Found 0 missing values.
2025-10-17 06:23:03.392095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:03.393088 INFO::Done
2025-10-17 06:23:03.393905 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:03.400921 INFO::Starting hierarchical adjustment
2025-10-17 06:23:03.402237 INFO::Found 5 batches.
2025-10-17 06:23:03.403076 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:03.404011 INFO::Using default BPPARAM
2025-10-17 06:23:03.404851 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.
2025-10-17 06:23:03.681473 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:03.684052 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 06:23:03.737563 INFO::Done
2025-10-17 06:23:03.738948 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:03.746035 INFO::ASW Batch was 0.538622488861758 prior to batch effect correction and is now -0.0817806800026257 .
2025-10-17 06:23:03.747195 INFO::ASW Label was 0.147554859226401 prior to batch effect correction and is now 0.698989205154655 .
2025-10-17 06:23:03.748666 INFO::Total function execution time is 0.368088960647583 s and adjustment time is 0.334826707839966 s ( 90.96 )
2025-10-17 06:23:03.751713 INFO::Formatting Data.
2025-10-17 06:23:03.752911 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:03.754595 INFO::Removing potential empty rows and columns
2025-10-17 06:23:03.757501 INFO::Found 0 missing values.
2025-10-17 06:23:03.767574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:03.76865 INFO::Done
2025-10-17 06:23:03.769547 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:03.775121 INFO::Starting hierarchical adjustment
2025-10-17 06:23:03.776471 INFO::Found 5 batches.
2025-10-17 06:23:03.777427 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:03.778431 INFO::Using default BPPARAM
2025-10-17 06:23:03.779348 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.
2025-10-17 06:23:04.054912 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:04.061922 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 06:23:04.120678 INFO::Done
2025-10-17 06:23:04.122129 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:04.127789 INFO::ASW Batch was 0.538622488861758 prior to batch effect correction and is now -0.0817806800026257 .
2025-10-17 06:23:04.128952 INFO::ASW Label was 0.147554859226401 prior to batch effect correction and is now 0.698989205154655 .
2025-10-17 06:23:04.130298 INFO::Total function execution time is 0.378644943237305 s and adjustment time is 0.344443559646606 s ( 90.97 )
2025-10-17 06:23:04.161776 INFO::Formatting Data.
2025-10-17 06:23:04.162975 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:04.164482 INFO::Removing potential empty rows and columns
2025-10-17 06:23:04.166329 INFO::Found 0 missing values.
2025-10-17 06:23:04.173752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:04.174774 INFO::Done
2025-10-17 06:23:04.175703 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:04.180711 INFO::Starting hierarchical adjustment
2025-10-17 06:23:04.182057 INFO::Found 5 batches.
2025-10-17 06:23:04.183044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:04.184108 INFO::Using default BPPARAM
2025-10-17 06:23:04.185023 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.
2025-10-17 06:23:04.501699 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:04.504267 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 06:23:04.555749 INFO::Done
2025-10-17 06:23:04.556808 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:04.561982 INFO::ASW Batch was 0.303744293165939 prior to batch effect correction and is now -0.0353610535189465 .
2025-10-17 06:23:04.562983 INFO::ASW Label was 0.493373353309078 prior to batch effect correction and is now 0.803549769231803 .
2025-10-17 06:23:04.564333 INFO::Total function execution time is 0.40261173248291 s and adjustment time is 0.373945474624634 s ( 92.88 )
2025-10-17 06:23:04.565742 INFO::Formatting Data.
2025-10-17 06:23:04.566741 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:04.568201 INFO::Removing potential empty rows and columns
2025-10-17 06:23:04.569856 INFO::Found 0 missing values.
2025-10-17 06:23:04.576562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:04.580211 INFO::Done
2025-10-17 06:23:04.581095 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:04.588799 INFO::Starting hierarchical adjustment
2025-10-17 06:23:04.59009 INFO::Found 5 batches.
2025-10-17 06:23:04.59093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:04.592554 INFO::Using default BPPARAM
2025-10-17 06:23:04.593483 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.
2025-10-17 06:23:04.911408 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:04.934294 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 06:23:04.995187 INFO::Done
2025-10-17 06:23:04.996407 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:05.01095 INFO::ASW Batch was 0.303744293165939 prior to batch effect correction and is now -0.0353610535189465 .
2025-10-17 06:23:05.012179 INFO::ASW Label was 0.493373353309078 prior to batch effect correction and is now 0.803549769231803 .
2025-10-17 06:23:05.018351 INFO::Total function execution time is 0.452399492263794 s and adjustment time is 0.405292987823486 s ( 89.59 )
2025-10-17 06:23:05.056388 INFO::Formatting Data.
2025-10-17 06:23:05.057591 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:05.05902 INFO::Removing potential empty rows and columns
2025-10-17 06:23:05.060673 INFO::Found 0 missing values.
2025-10-17 06:23:05.065257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:05.066289 INFO::Done
2025-10-17 06:23:05.067144 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:05.071898 INFO::Starting hierarchical adjustment
2025-10-17 06:23:05.073228 INFO::Found 2 batches.
2025-10-17 06:23:05.074081 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:05.075066 INFO::Using default BPPARAM
2025-10-17 06:23:05.075974 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:05.077545 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 06:23:05.104187 INFO::Done
2025-10-17 06:23:05.107248 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:05.112188 INFO::ASW Batch was 0.367876854693626 prior to batch effect correction and is now 0.000423833930510086 .
2025-10-17 06:23:05.113566 INFO::ASW Label was 0.674430193356857 prior to batch effect correction and is now 0.916328782345193 .
2025-10-17 06:23:05.114751 INFO::Total function execution time is 0.0584626197814941 s and adjustment time is 0.0311918258666992 s ( 53.35 )
2025-10-17 06:23:05.115928 INFO::Formatting Data.
2025-10-17 06:23:05.116887 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:05.118244 INFO::Removing potential empty rows and columns
2025-10-17 06:23:05.119776 INFO::Found 0 missing values.
2025-10-17 06:23:05.123934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:05.124799 INFO::Done
2025-10-17 06:23:05.125623 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:05.130082 INFO::Starting hierarchical adjustment
2025-10-17 06:23:05.131242 INFO::Found 2 batches.
2025-10-17 06:23:05.132066 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:05.132988 INFO::Using default BPPARAM
2025-10-17 06:23:05.133818 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:05.135212 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-17 06:23:05.157752 INFO::Done
2025-10-17 06:23:05.158826 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:05.163406 INFO::ASW Batch was 0.367876854693626 prior to batch effect correction and is now 0.000423833930510086 .
2025-10-17 06:23:05.164314 INFO::ASW Label was 0.674430193356857 prior to batch effect correction and is now 0.916328782345193 .
2025-10-17 06:23:05.165537 INFO::Total function execution time is 0.0495824813842773 s and adjustment time is 0.0266892910003662 s ( 53.83 )
2025-10-17 06:23:05.189546 INFO::Formatting Data.
2025-10-17 06:23:05.19064 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:05.191961 INFO::Removing potential empty rows and columns
2025-10-17 06:23:05.193394 INFO::Found 0 missing values.
2025-10-17 06:23:05.196723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:05.19767 INFO::Done
2025-10-17 06:23:05.198481 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:05.201529 INFO::Starting hierarchical adjustment
2025-10-17 06:23:05.202617 INFO::Found 2 batches.
2025-10-17 06:23:05.203444 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:05.204347 INFO::Using default BPPARAM
2025-10-17 06:23:05.20517 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:05.206566 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 06:23:05.256953 INFO::Done
2025-10-17 06:23:05.257918 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:05.260911 INFO::ASW Batch was 0.0147634887125437 prior to batch effect correction and is now -0.182807504557247 .
2025-10-17 06:23:05.262193 INFO::Total function execution time is 0.0727303028106689 s and adjustment time is 0.0545268058776855 s ( 74.97 )
2025-10-17 06:23:05.280625 INFO::Formatting Data.
2025-10-17 06:23:05.281718 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:05.283008 INFO::Removing potential empty rows and columns
2025-10-17 06:23:05.284572 INFO::Found 0 missing values.
2025-10-17 06:23:05.286407 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.
2025-10-17 06:23:05.294276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:05.295373 INFO::Done
2025-10-17 06:23:05.296231 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:05.30106 INFO::Starting hierarchical adjustment
2025-10-17 06:23:05.302427 INFO::Found 2 batches.
2025-10-17 06:23:05.303351 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:05.304306 INFO::Using default BPPARAM
2025-10-17 06:23:05.305201 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:05.306718 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 06:23:05.333423 INFO::Done
2025-10-17 06:23:05.334414 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:05.33887 INFO::ASW Batch was 0.820092768644629 prior to batch effect correction and is now 0.0593852914667316 .
2025-10-17 06:23:05.339859 INFO::ASW Label was 0.189831881165344 prior to batch effect correction and is now 0.691649246704053 .
2025-10-17 06:23:05.341031 INFO::Total function execution time is 0.0604996681213379 s and adjustment time is 0.0312583446502686 s ( 51.67 )
2025-10-17 06:23:05.342203 INFO::Formatting Data.
2025-10-17 06:23:05.343101 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:05.344532 INFO::Removing potential empty rows and columns
2025-10-17 06:23:05.346075 INFO::Found 0 missing values.
2025-10-17 06:23:05.347452 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.
2025-10-17 06:23:05.354796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:05.355757 INFO::Done
2025-10-17 06:23:05.356533 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:05.36113 INFO::Starting hierarchical adjustment
2025-10-17 06:23:05.362354 INFO::Found 2 batches.
2025-10-17 06:23:05.363191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:05.364136 INFO::Using default BPPARAM
2025-10-17 06:23:05.364957 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:05.36639 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 06:23:05.39229 INFO::Done
2025-10-17 06:23:05.39334 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:05.397668 INFO::ASW Batch was 0.820092768644629 prior to batch effect correction and is now 0.0593852914667316 .
2025-10-17 06:23:05.398545 INFO::ASW Label was 0.189831881165344 prior to batch effect correction and is now 0.691649246704053 .
2025-10-17 06:23:05.399793 INFO::Total function execution time is 0.0575788021087646 s and adjustment time is 0.0301432609558105 s ( 52.35 )
2025-10-17 06:23:05.717927 INFO::Formatting Data.
2025-10-17 06:23:05.719011 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:05.720298 INFO::Removing potential empty rows and columns
2025-10-17 06:23:05.721846 INFO::Found 0 missing values.
2025-10-17 06:23:05.726911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:05.727856 INFO::Done
2025-10-17 06:23:05.728618 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:05.731551 INFO::Starting hierarchical adjustment
2025-10-17 06:23:05.732646 INFO::Found 3 batches.
2025-10-17 06:23:05.733473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:05.734355 INFO::Using default BPPARAM
2025-10-17 06:23:05.735102 INFO::Processing subtree level 1
2025-10-17 06:23:05.903525 INFO::Adjusting the last 1 batches sequentially
2025-10-17 06:23:05.915458 INFO::Done
2025-10-17 06:23:05.916514 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:05.924562 INFO::ASW Batch was -0.108885919560922 prior to batch effect correction and is now -0.108885919560922 .
2025-10-17 06:23:05.930809 INFO::Total function execution time is 0.212825536727905 s and adjustment time is 0.182987451553345 s ( 85.98 )
2025-10-17 06:23:05.932581 INFO::Formatting Data.
2025-10-17 06:23:05.937921 INFO::Typecasting input to dataframe.
2025-10-17 06:23:05.939303 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:05.944875 INFO::Removing potential empty rows and columns
2025-10-17 06:23:05.946739 INFO::Found 0 missing values.
2025-10-17 06:23:05.955697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:05.956673 INFO::Done
2025-10-17 06:23:05.96186 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:05.965453 INFO::Starting hierarchical adjustment
2025-10-17 06:23:05.966733 INFO::Found 3 batches.
2025-10-17 06:23:05.967669 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:05.968643 INFO::Using default BPPARAM
2025-10-17 06:23:05.969507 INFO::Processing subtree level 1
2025-10-17 06:23:06.093047 INFO::Adjusting the last 1 batches sequentially
2025-10-17 06:23:06.095795 INFO::Done
2025-10-17 06:23:06.100992 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:06.109115 INFO::ASW Batch was -0.108885919560922 prior to batch effect correction and is now -0.108885919560922 .
2025-10-17 06:23:06.110667 INFO::Total function execution time is 0.178101062774658 s and adjustment time is 0.129308462142944 s ( 72.6 )
2025-10-17 06:23:06.149059 INFO::Formatting Data.
2025-10-17 06:23:06.150162 INFO::Typecasting input to dataframe.
2025-10-17 06:23:06.151473 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:06.152881 INFO::Removing potential empty rows and columns
2025-10-17 06:23:06.154542 INFO::Found 0 missing values.
2025-10-17 06:23:06.159364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:06.160309 INFO::Done
2025-10-17 06:23:06.161156 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:06.164106 INFO::Starting hierarchical adjustment
2025-10-17 06:23:06.165326 INFO::Found 3 batches.
2025-10-17 06:23:06.166216 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:06.167182 INFO::Using default BPPARAM
2025-10-17 06:23:06.168085 INFO::Processing subtree level 1
2025-10-17 06:23:06.295122 INFO::Adjusting the last 1 batches sequentially
2025-10-17 06:23:06.302311 INFO::Done
2025-10-17 06:23:06.303512 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:06.312034 INFO::ASW Batch was -0.0223709356822413 prior to batch effect correction and is now -0.0223709356822413 .
2025-10-17 06:23:06.317741 INFO::Total function execution time is 0.168723344802856 s and adjustment time is 0.137182235717773 s ( 81.31 )
2025-10-17 06:23:06.571757 INFO::Formatting Data.
2025-10-17 06:23:06.572922 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:06.574661 INFO::Removing potential empty rows and columns
2025-10-17 06:23:06.57902 INFO::Found 1000 missing values.
2025-10-17 06:23:06.609103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:06.610103 INFO::Done
2025-10-17 06:23:06.610958 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:06.618911 INFO::Starting hierarchical adjustment
2025-10-17 06:23:06.620194 INFO::Found 10 batches.
2025-10-17 06:23:06.621104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:06.622056 INFO::Using default BPPARAM
2025-10-17 06:23:06.622918 INFO::Processing subtree level 1
2025-10-17 06:23:06.932478 INFO::Processing subtree level 2
2025-10-17 06:23:07.302642 INFO::Adjusting the last 1 batches sequentially
2025-10-17 06:23:07.309914 INFO::Done
2025-10-17 06:23:07.31103 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:07.32798 INFO::ASW Batch was 0.49813427315393 prior to batch effect correction and is now 0.49813427315393 .
2025-10-17 06:23:07.333181 INFO::ASW Label was 0.325899475723826 prior to batch effect correction and is now 0.325899475723826 .
2025-10-17 06:23:07.334744 INFO::Total function execution time is 0.762964487075806 s and adjustment time is 0.689922094345093 s ( 90.43 )
2025-10-17 06:23:07.336206 INFO::Formatting Data.
2025-10-17 06:23:07.341518 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:07.343645 INFO::Removing potential empty rows and columns
2025-10-17 06:23:07.352349 INFO::Found 1000 missing values.
2025-10-17 06:23:07.393965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:07.395067 INFO::Done
2025-10-17 06:23:07.396151 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:07.404799 INFO::Starting hierarchical adjustment
2025-10-17 06:23:07.406178 INFO::Found 10 batches.
2025-10-17 06:23:08.621461 INFO::Set up parallel execution backend with 2 workers
2025-10-17 06:23:08.623944 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-17 06:23:10.146424 INFO::Adjusting the last 2 batches sequentially
2025-10-17 06:23:10.148637 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-17 06:23:10.17247 INFO::Done
2025-10-17 06:23:10.173336 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:10.179904 INFO::ASW Batch was 0.49813427315393 prior to batch effect correction and is now 0.49813427315393 .
2025-10-17 06:23:10.180778 INFO::ASW Label was 0.325899475723826 prior to batch effect correction and is now 0.325899475723826 .
2025-10-17 06:23:10.18183 INFO::Total function execution time is 2.84570169448853 s and adjustment time is 2.766606092453 s ( 97.22 )
2025-10-17 06:23:10.487618 INFO::Formatting Data.
2025-10-17 06:23:10.488817 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:10.490216 INFO::Removing potential empty rows and columns
2025-10-17 06:23:10.491989 INFO::Found 0 missing values.
2025-10-17 06:23:10.498132 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:10.499113 INFO::Done
2025-10-17 06:23:10.500016 INFO::Acquiring quality metrics before batch effect correction.
2025-10-17 06:23:10.504285 INFO::Starting hierarchical adjustment
2025-10-17 06:23:10.505556 INFO::Found 3 batches.
2025-10-17 06:23:10.506418 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-17 06:23:10.507421 INFO::Using default BPPARAM
2025-10-17 06:23:10.508267 INFO::Processing subtree level 1
2025-10-17 06:23:10.681893 INFO::Adjusting the last 1 batches sequentially
2025-10-17 06:23:10.684352 INFO::Done
2025-10-17 06:23:10.689477 INFO::Acquiring quality metrics after batch effect correction.
2025-10-17 06:23:10.69857 INFO::ASW Batch was 0.243118051541861 prior to batch effect correction and is now -0.129471828257114 .
2025-10-17 06:23:10.699679 INFO::ASW Label was -0.224829163026818 prior to batch effect correction and is now -0.0617338390780482 .
2025-10-17 06:23:10.705187 INFO::Total function execution time is 0.217596530914307 s and adjustment time is 0.179038763046265 s ( 82.28 )
2025-10-17 06:23:10.900584 INFO::Formatting Data.
2025-10-17 06:23:10.901839 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:10.903378 INFO::Removing potential empty rows and columns
2025-10-17 06:23:10.905064 INFO::Found 2 missing values.
2025-10-17 06:23:10.90969 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:10.910613 INFO::Done
2025-10-17 06:23:10.956904 INFO::Found NA in Reference column
2025-10-17 06:23:10.972781 INFO::Require at least two references per batch.
2025-10-17 06:23:11.00423 INFO::Formatting Data.
2025-10-17 06:23:11.005285 INFO::Recognized SummarizedExperiment
2025-10-17 06:23:11.006104 INFO::Typecasting input to dataframe.
2025-10-17 06:23:11.020904 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.022511 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.027956 INFO::Found 0 missing values.
2025-10-17 06:23:11.038782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.039755 INFO::Done
2025-10-17 06:23:11.062905 INFO::Formatting Data.
2025-10-17 06:23:11.063934 INFO::Recognized SummarizedExperiment
2025-10-17 06:23:11.064704 INFO::Typecasting input to dataframe.
2025-10-17 06:23:11.092118 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.093886 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.099454 INFO::Found 0 missing values.
2025-10-17 06:23:11.117581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.11855 INFO::Done
2025-10-17 06:23:11.142241 INFO::Formatting Data.
2025-10-17 06:23:11.143241 INFO::Recognized SummarizedExperiment
2025-10-17 06:23:11.144071 INFO::Typecasting input to dataframe.
2025-10-17 06:23:11.169772 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.171139 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.172736 INFO::Found 0 missing values.
2025-10-17 06:23:11.174076 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.
2025-10-17 06:23:11.181188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.182137 INFO::Done
2025-10-17 06:23:11.196945 INFO::Formatting Data.
2025-10-17 06:23:11.197986 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.199198 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.200664 INFO::Found 0 missing values.
2025-10-17 06:23:11.205019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.205964 INFO::Done
2025-10-17 06:23:11.222387 INFO::Formatting Data.
2025-10-17 06:23:11.223453 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.224624 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.226138 INFO::Found 0 missing values.
2025-10-17 06:23:11.230567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.231519 INFO::Done
2025-10-17 06:23:11.277857 INFO::Formatting Data.
2025-10-17 06:23:11.279039 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.280626 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.282496 INFO::Found 1 missing values.
2025-10-17 06:23:11.286637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.287598 INFO::Done
2025-10-17 06:23:11.316765 INFO::Formatting Data.
2025-10-17 06:23:11.317837 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.319031 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.320482 INFO::Found 2 missing values.
2025-10-17 06:23:11.321798 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.
2025-10-17 06:23:11.32528 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.326157 INFO::Done
2025-10-17 06:23:11.341667 INFO::Formatting Data.
2025-10-17 06:23:11.342794 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.344147 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.345749 INFO::Found 2 missing values.
2025-10-17 06:23:11.348275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.349213 INFO::Done
2025-10-17 06:23:11.36553 INFO::Formatting Data.
2025-10-17 06:23:11.366609 INFO::Typecasting input to dataframe.
2025-10-17 06:23:11.367956 INFO::Replacing NaNs with NAs.
2025-10-17 06:23:11.369299 INFO::Removing potential empty rows and columns
2025-10-17 06:23:11.370886 INFO::Found 0 missing values.
2025-10-17 06:23:11.375524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-17 06:23:11.376442 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.070 5.203 31.447
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.488 | 1.745 | 24.522 | |
| compute_asw | 0.035 | 0.000 | 0.035 | |
| count_existing | 0.018 | 0.000 | 0.020 | |
| generate_data_covariables | 0.016 | 0.000 | 0.016 | |
| generate_dataset | 0.014 | 0.000 | 0.014 | |