Yannis Schumann
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-27 12:05 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-11-25 06:50:39 -0000 (Tue, 25 Nov 2025) |
| EndedAt: 2025-11-25 06:52:11 -0000 (Tue, 25 Nov 2025) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.6.0.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 ‘1.6.0’
* 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 28.76 1.672 22.474
* 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 ‘1.6.0’ ** 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")
2025-11-25 06:51:52.702239 INFO::Formatting Data.
2025-11-25 06:51:52.703961 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:52.72083 INFO::Removing potential empty rows and columns
2025-11-25 06:51:53.519981 INFO::Found 0 missing values.
2025-11-25 06:51:53.525114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:53.526081 INFO::Done
2025-11-25 06:51:53.526929 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:53.543017 INFO::Starting hierarchical adjustment
2025-11-25 06:51:53.544281 INFO::Found 3 batches.
2025-11-25 06:51:53.545253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:53.546904 INFO::Using default BPPARAM
2025-11-25 06:51:53.54781 INFO::Processing subtree level 1
2025-11-25 06:51:53.683127 INFO::Adjusting the last 1 batches sequentially
2025-11-25 06:51:53.68608 INFO::Done
2025-11-25 06:51:53.68721 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:53.691874 INFO::ASW Batch was -0.0330589145798564 prior to batch effect correction and is now -0.0330589145798564 .
2025-11-25 06:51:53.694345 INFO::Total function execution time is 0.992692232131958 s and adjustment time is 0.142029285430908 s ( 14.31 )
2025-11-25 06:51:53.721429 INFO::Formatting Data.
2025-11-25 06:51:53.722759 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:53.724406 INFO::Removing potential empty rows and columns
2025-11-25 06:51:53.726511 INFO::Found 0 missing values.
2025-11-25 06:51:53.728278 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 06:51:53.745759 INFO::Formatting Data.
2025-11-25 06:51:53.746979 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:53.748645 INFO::Removing potential empty rows and columns
2025-11-25 06:51:53.750587 INFO::Found 0 missing values.
2025-11-25 06:51:53.752283 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 06:51:53.778066 INFO::Formatting Data.
2025-11-25 06:51:53.779274 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:53.780923 INFO::Removing potential empty rows and columns
2025-11-25 06:51:53.782806 INFO::Found 0 missing values.
2025-11-25 06:51:53.784493 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 06:51:53.792087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:53.793207 INFO::Done
2025-11-25 06:51:53.794216 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:53.797666 INFO::Starting hierarchical adjustment
2025-11-25 06:51:53.799033 INFO::Found 2 batches.
2025-11-25 06:51:53.800067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:53.801298 INFO::Using default BPPARAM
2025-11-25 06:51:53.802344 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:51:53.804056 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 06:51:53.836576 INFO::Done
2025-11-25 06:51:53.837586 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:53.840703 INFO::ASW Batch was -0.0491015346304586 prior to batch effect correction and is now -0.120290292153549 .
2025-11-25 06:51:53.841965 INFO::Total function execution time is 0.063992977142334 s and adjustment time is 0.0378313064575195 s ( 59.12 )
2025-11-25 06:51:53.845746 INFO::Formatting Data.
2025-11-25 06:51:53.846701 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:53.85897 INFO::Formatting Data.
2025-11-25 06:51:53.85994 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:53.861242 INFO::Removing potential empty rows and columns
2025-11-25 06:51:53.863017 INFO::Found 0 missing values.
2025-11-25 06:51:53.867277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:53.868157 INFO::Done
2025-11-25 06:51:53.868982 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:53.871745 INFO::Starting hierarchical adjustment
2025-11-25 06:51:53.87291 INFO::Found 2 batches.
2025-11-25 06:51:53.873698 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:53.874626 INFO::Using default BPPARAM
2025-11-25 06:51:53.875478 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:51:53.876983 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:51:53.933388 INFO::Done
2025-11-25 06:51:53.934276 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:53.937052 INFO::ASW Batch was 0.0645164848994119 prior to batch effect correction and is now -0.12658294327054 .
2025-11-25 06:51:53.938186 INFO::Total function execution time is 0.0792863368988037 s and adjustment time is 0.0607523918151855 s ( 76.62 )
2025-11-25 06:51:53.939675 INFO::Formatting Data.
2025-11-25 06:51:53.940575 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:53.941844 INFO::Removing potential empty rows and columns
2025-11-25 06:51:53.943272 INFO::Found 0 missing values.
2025-11-25 06:51:53.947351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:53.948224 INFO::Done
2025-11-25 06:51:53.949046 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:53.951802 INFO::Starting hierarchical adjustment
2025-11-25 06:51:53.952947 INFO::Found 2 batches.
2025-11-25 06:51:53.953728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:53.95457 INFO::Using default BPPARAM
2025-11-25 06:51:53.955294 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:51:53.956581 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:51:53.977642 INFO::Done
2025-11-25 06:51:53.978528 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:53.981329 INFO::ASW Batch was 0.0645164848994119 prior to batch effect correction and is now -0.12658294327054 .
2025-11-25 06:51:53.982473 INFO::Total function execution time is 0.0427825450897217 s and adjustment time is 0.0249612331390381 s ( 58.34 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-25 06:51:58.001062 INFO::Formatting Data.
2025-11-25 06:51:58.002101 INFO::Recognized SummarizedExperiment
2025-11-25 06:51:58.002977 INFO::Typecasting input to dataframe.
2025-11-25 06:51:58.052521 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:58.054323 INFO::Removing potential empty rows and columns
2025-11-25 06:51:58.059853 INFO::Found 0 missing values.
2025-11-25 06:51:58.070763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:58.07175 INFO::Done
2025-11-25 06:51:58.072862 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:58.078199 INFO::Starting hierarchical adjustment
2025-11-25 06:51:58.079465 INFO::Found 2 batches.
2025-11-25 06:51:58.080327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:58.082001 INFO::Using default BPPARAM
2025-11-25 06:51:58.082941 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:51:58.084513 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 06:51:58.167187 INFO::Done
2025-11-25 06:51:58.168159 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:58.173385 INFO::ASW Batch was -0.0131854776845391 prior to batch effect correction and is now -0.0916210685885286 .
2025-11-25 06:51:58.17475 INFO::Total function execution time is 0.174291133880615 s and adjustment time is 0.0879614353179932 s ( 50.47 )
Warning: stack imbalance in '{', 73 then 75
2025-11-25 06:51:58.202686 INFO::Formatting Data.
2025-11-25 06:51:58.203688 INFO::Recognized SummarizedExperiment
2025-11-25 06:51:58.204505 INFO::Typecasting input to dataframe.
2025-11-25 06:51:58.218423 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:58.220088 INFO::Removing potential empty rows and columns
2025-11-25 06:51:58.22561 INFO::Found 0 missing values.
2025-11-25 06:51:58.236434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:58.237514 INFO::Done
2025-11-25 06:51:58.238414 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:58.243747 INFO::Starting hierarchical adjustment
2025-11-25 06:51:58.245221 INFO::Found 2 batches.
2025-11-25 06:51:58.246252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:58.247334 INFO::Using default BPPARAM
2025-11-25 06:51:58.248294 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:51:58.250127 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 06:51:58.288546 INFO::Done
2025-11-25 06:51:58.289682 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:58.295202 INFO::ASW Batch was -0.00866512067870886 prior to batch effect correction and is now -0.00866512067870886 .
2025-11-25 06:51:58.296769 INFO::Total function execution time is 0.0939202308654785 s and adjustment time is 0.0436553955078125 s ( 46.48 )
2025-11-25 06:51:58.323573 INFO::Formatting Data.
2025-11-25 06:51:58.324564 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:58.325818 INFO::Removing potential empty rows and columns
2025-11-25 06:51:58.327282 INFO::Found 0 missing values.
2025-11-25 06:51:58.331582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:58.332474 INFO::Done
2025-11-25 06:51:58.33329 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:58.336047 INFO::Starting hierarchical adjustment
2025-11-25 06:51:58.337219 INFO::Found 3 batches.
2025-11-25 06:51:58.337979 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:58.338811 INFO::Using default BPPARAM
2025-11-25 06:51:58.339538 INFO::Processing subtree level 1
2025-11-25 06:51:58.54065 INFO::Adjusting the last 1 batches sequentially
2025-11-25 06:51:58.551488 INFO::Done
2025-11-25 06:51:58.552693 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:58.564945 INFO::ASW Batch was 0.0373739469380377 prior to batch effect correction and is now -0.177493211668565 .
2025-11-25 06:51:58.56658 INFO::Total function execution time is 0.242995977401733 s and adjustment time is 0.214414119720459 s ( 88.24 )
2025-11-25 06:51:58.597358 INFO::Skipping initial DF formatting
2025-11-25 06:51:58.598328 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:58.604015 INFO::Starting hierarchical adjustment
2025-11-25 06:51:58.605234 INFO::Found 5 batches.
2025-11-25 06:51:58.606024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:58.606928 INFO::Using default BPPARAM
2025-11-25 06:51:58.607714 INFO::Processing subtree level 1
2025-11-25 06:51:58.913595 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:51:58.915941 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 06:51:58.979229 INFO::Done
2025-11-25 06:51:58.980271 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:58.995315 INFO::ASW Batch was 0.484984900970484 prior to batch effect correction and is now 0.484984900970484 .
2025-11-25 06:51:58.996361 INFO::ASW Label was 0.450624009917747 prior to batch effect correction and is now 0.450624009917747 .
2025-11-25 06:51:59.002028 INFO::Total function execution time is 0.404640913009644 s and adjustment time is 0.374206304550171 s ( 92.48 )
2025-11-25 06:51:59.202289 INFO::Formatting Data.
2025-11-25 06:51:59.203528 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:59.209243 INFO::Removing potential empty rows and columns
2025-11-25 06:51:59.211144 INFO::Found 0 missing values.
2025-11-25 06:51:59.226799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:59.227782 INFO::Done
2025-11-25 06:51:59.228642 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:59.242229 INFO::Starting hierarchical adjustment
2025-11-25 06:51:59.243748 INFO::Found 5 batches.
2025-11-25 06:51:59.248881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:59.25024 INFO::Using default BPPARAM
2025-11-25 06:51:59.251204 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:51:59.518411 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:51:59.522085 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:51:59.553557 INFO::Done
2025-11-25 06:51:59.554674 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:59.56048 INFO::ASW Batch was 0.347392073214331 prior to batch effect correction and is now -0.0465379035705994 .
2025-11-25 06:51:59.561891 INFO::ASW Label was 0.403176714781173 prior to batch effect correction and is now 0.818788959407869 .
2025-11-25 06:51:59.563178 INFO::Total function execution time is 0.360970258712769 s and adjustment time is 0.310068368911743 s ( 85.9 )
2025-11-25 06:51:59.564567 INFO::Formatting Data.
2025-11-25 06:51:59.565778 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:59.567295 INFO::Removing potential empty rows and columns
2025-11-25 06:51:59.570141 INFO::Found 0 missing values.
2025-11-25 06:51:59.587009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:59.58808 INFO::Done
2025-11-25 06:51:59.593259 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:59.602946 INFO::Starting hierarchical adjustment
2025-11-25 06:51:59.604264 INFO::Found 5 batches.
2025-11-25 06:51:59.605391 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:59.606501 INFO::Using default BPPARAM
2025-11-25 06:51:59.607454 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:51:59.781982 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:51:59.784385 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:51:59.830793 INFO::Done
2025-11-25 06:51:59.831862 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:51:59.837183 INFO::ASW Batch was 0.347392073214331 prior to batch effect correction and is now -0.0465379035705994 .
2025-11-25 06:51:59.83816 INFO::ASW Label was 0.403176714781173 prior to batch effect correction and is now 0.818788959407869 .
2025-11-25 06:51:59.839422 INFO::Total function execution time is 0.274825811386108 s and adjustment time is 0.226769685745239 s ( 82.51 )
2025-11-25 06:51:59.860943 INFO::Formatting Data.
2025-11-25 06:51:59.862046 INFO::Replacing NaNs with NAs.
2025-11-25 06:51:59.863346 INFO::Removing potential empty rows and columns
2025-11-25 06:51:59.864905 INFO::Found 0 missing values.
2025-11-25 06:51:59.871289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:51:59.872303 INFO::Done
2025-11-25 06:51:59.873165 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:51:59.877717 INFO::Starting hierarchical adjustment
2025-11-25 06:51:59.878868 INFO::Found 5 batches.
2025-11-25 06:51:59.879625 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:51:59.880557 INFO::Using default BPPARAM
2025-11-25 06:51:59.881386 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:52:00.076026 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:52:00.08271 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:52:00.119106 INFO::Done
2025-11-25 06:52:00.120193 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:00.125753 INFO::ASW Batch was 0.323197395695597 prior to batch effect correction and is now -0.0972278427328915 .
2025-11-25 06:52:00.126854 INFO::ASW Label was 0.319811630808488 prior to batch effect correction and is now 0.917688699021316 .
2025-11-25 06:52:00.128328 INFO::Total function execution time is 0.267443895339966 s and adjustment time is 0.240418910980225 s ( 89.9 )
2025-11-25 06:52:00.130024 INFO::Formatting Data.
2025-11-25 06:52:00.131305 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:00.134194 INFO::Removing potential empty rows and columns
2025-11-25 06:52:00.136115 INFO::Found 0 missing values.
2025-11-25 06:52:00.143653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:00.144767 INFO::Done
2025-11-25 06:52:00.145844 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:00.151079 INFO::Starting hierarchical adjustment
2025-11-25 06:52:00.152481 INFO::Found 5 batches.
2025-11-25 06:52:00.153653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:00.15483 INFO::Using default BPPARAM
2025-11-25 06:52:00.155895 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:52:00.327766 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:52:00.338562 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:52:00.387841 INFO::Done
2025-11-25 06:52:00.38907 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:00.394764 INFO::ASW Batch was 0.323197395695597 prior to batch effect correction and is now -0.0972278427328915 .
2025-11-25 06:52:00.395914 INFO::ASW Label was 0.319811630808488 prior to batch effect correction and is now 0.917688699021316 .
2025-11-25 06:52:00.397515 INFO::Total function execution time is 0.26749587059021 s and adjustment time is 0.235644817352295 s ( 88.09 )
2025-11-25 06:52:00.427284 INFO::Formatting Data.
2025-11-25 06:52:00.428642 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:00.430317 INFO::Removing potential empty rows and columns
2025-11-25 06:52:00.432239 INFO::Found 0 missing values.
2025-11-25 06:52:00.437696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:00.438883 INFO::Done
2025-11-25 06:52:00.439986 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:00.445557 INFO::Starting hierarchical adjustment
2025-11-25 06:52:00.44699 INFO::Found 2 batches.
2025-11-25 06:52:00.44807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:00.449322 INFO::Using default BPPARAM
2025-11-25 06:52:00.450369 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:52:00.452098 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:52:00.476978 INFO::Done
2025-11-25 06:52:00.478012 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:00.482864 INFO::ASW Batch was 0.46451733125707 prior to batch effect correction and is now -0.0252026437629973 .
2025-11-25 06:52:00.483897 INFO::ASW Label was 0.615212094560458 prior to batch effect correction and is now 0.932897141431327 .
2025-11-25 06:52:00.485303 INFO::Total function execution time is 0.0581150054931641 s and adjustment time is 0.0302917957305908 s ( 52.12 )
2025-11-25 06:52:00.486641 INFO::Formatting Data.
2025-11-25 06:52:00.487756 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:00.489253 INFO::Removing potential empty rows and columns
2025-11-25 06:52:00.491483 INFO::Found 0 missing values.
2025-11-25 06:52:00.496387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:00.497523 INFO::Done
2025-11-25 06:52:00.498448 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:00.503478 INFO::Starting hierarchical adjustment
2025-11-25 06:52:00.504947 INFO::Found 2 batches.
2025-11-25 06:52:00.505968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:00.507007 INFO::Using default BPPARAM
2025-11-25 06:52:00.507938 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:52:00.509722 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 06:52:00.534553 INFO::Done
2025-11-25 06:52:00.535687 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:00.540947 INFO::ASW Batch was 0.46451733125707 prior to batch effect correction and is now -0.0252026437629973 .
2025-11-25 06:52:00.542063 INFO::ASW Label was 0.615212094560458 prior to batch effect correction and is now 0.932897141431327 .
2025-11-25 06:52:00.54349 INFO::Total function execution time is 0.0568206310272217 s and adjustment time is 0.0299453735351562 s ( 52.7 )
2025-11-25 06:52:00.563567 INFO::Formatting Data.
2025-11-25 06:52:00.564961 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:00.566626 INFO::Removing potential empty rows and columns
2025-11-25 06:52:00.568422 INFO::Found 0 missing values.
2025-11-25 06:52:00.572652 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:00.573814 INFO::Done
2025-11-25 06:52:00.574796 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:00.578155 INFO::Starting hierarchical adjustment
2025-11-25 06:52:00.579548 INFO::Found 2 batches.
2025-11-25 06:52:00.580561 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:00.581762 INFO::Using default BPPARAM
2025-11-25 06:52:00.582778 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:52:00.584428 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 06:52:00.636889 INFO::Done
2025-11-25 06:52:00.637976 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:00.641311 INFO::ASW Batch was -0.024105604153906 prior to batch effect correction and is now -0.171617277625672 .
2025-11-25 06:52:00.642763 INFO::Total function execution time is 0.0792741775512695 s and adjustment time is 0.0575919151306152 s ( 72.65 )
2025-11-25 06:52:00.670644 INFO::Formatting Data.
2025-11-25 06:52:00.672024 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:00.673762 INFO::Removing potential empty rows and columns
2025-11-25 06:52:00.675649 INFO::Found 0 missing values.
2025-11-25 06:52:00.677763 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 06:52:00.686074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:00.687171 INFO::Done
2025-11-25 06:52:00.688189 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:00.693423 INFO::Starting hierarchical adjustment
2025-11-25 06:52:00.69486 INFO::Found 2 batches.
2025-11-25 06:52:00.695894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:00.697039 INFO::Using default BPPARAM
2025-11-25 06:52:00.698099 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:52:00.699816 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 06:52:00.728719 INFO::Done
2025-11-25 06:52:00.729896 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:00.735001 INFO::ASW Batch was 0.70199138848115 prior to batch effect correction and is now -0.0043146158669808 .
2025-11-25 06:52:00.736097 INFO::ASW Label was 0.383373023229972 prior to batch effect correction and is now 0.914941194664982 .
2025-11-25 06:52:00.737569 INFO::Total function execution time is 0.0669872760772705 s and adjustment time is 0.0340971946716309 s ( 50.9 )
2025-11-25 06:52:00.738999 INFO::Formatting Data.
2025-11-25 06:52:00.74016 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:00.741833 INFO::Removing potential empty rows and columns
2025-11-25 06:52:00.743661 INFO::Found 0 missing values.
2025-11-25 06:52:00.745447 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 06:52:00.753756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:00.754846 INFO::Done
2025-11-25 06:52:00.755887 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:00.761232 INFO::Starting hierarchical adjustment
2025-11-25 06:52:00.762643 INFO::Found 2 batches.
2025-11-25 06:52:00.763661 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:00.764871 INFO::Using default BPPARAM
2025-11-25 06:52:00.765921 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:52:00.767687 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 06:52:00.797252 INFO::Done
2025-11-25 06:52:00.798418 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:00.8038 INFO::ASW Batch was 0.70199138848115 prior to batch effect correction and is now -0.0043146158669808 .
2025-11-25 06:52:00.805019 INFO::ASW Label was 0.383373023229972 prior to batch effect correction and is now 0.914941194664982 .
2025-11-25 06:52:00.806553 INFO::Total function execution time is 0.0675549507141113 s and adjustment time is 0.0348551273345947 s ( 51.6 )
2025-11-25 06:52:01.128943 INFO::Formatting Data.
2025-11-25 06:52:01.130028 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:01.131399 INFO::Removing potential empty rows and columns
2025-11-25 06:52:01.133084 INFO::Found 0 missing values.
2025-11-25 06:52:01.137879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:01.138858 INFO::Done
2025-11-25 06:52:01.13968 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:01.142728 INFO::Starting hierarchical adjustment
2025-11-25 06:52:01.143954 INFO::Found 3 batches.
2025-11-25 06:52:01.144888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:01.145824 INFO::Using default BPPARAM
2025-11-25 06:52:01.14665 INFO::Processing subtree level 1
2025-11-25 06:52:01.26 INFO::Adjusting the last 1 batches sequentially
2025-11-25 06:52:01.262674 INFO::Done
2025-11-25 06:52:01.263819 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:01.267547 INFO::ASW Batch was -0.12665161320238 prior to batch effect correction and is now -0.12665161320238 .
2025-11-25 06:52:01.269198 INFO::Total function execution time is 0.140322685241699 s and adjustment time is 0.118956089019775 s ( 84.77 )
2025-11-25 06:52:01.270949 INFO::Formatting Data.
2025-11-25 06:52:01.271987 INFO::Typecasting input to dataframe.
2025-11-25 06:52:01.273291 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:01.274981 INFO::Removing potential empty rows and columns
2025-11-25 06:52:01.277097 INFO::Found 0 missing values.
2025-11-25 06:52:01.282537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:01.283579 INFO::Done
2025-11-25 06:52:01.284446 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:01.28773 INFO::Starting hierarchical adjustment
2025-11-25 06:52:01.28914 INFO::Found 3 batches.
2025-11-25 06:52:01.290054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:01.291022 INFO::Using default BPPARAM
2025-11-25 06:52:01.291861 INFO::Processing subtree level 1
2025-11-25 06:52:01.437403 INFO::Adjusting the last 1 batches sequentially
2025-11-25 06:52:01.439799 INFO::Done
2025-11-25 06:52:01.440731 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:01.446802 INFO::ASW Batch was -0.12665161320238 prior to batch effect correction and is now -0.12665161320238 .
2025-11-25 06:52:01.453887 INFO::Total function execution time is 0.182898044586182 s and adjustment time is 0.1509690284729 s ( 82.54 )
2025-11-25 06:52:01.477236 INFO::Formatting Data.
2025-11-25 06:52:01.478257 INFO::Typecasting input to dataframe.
2025-11-25 06:52:01.479448 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:01.480844 INFO::Removing potential empty rows and columns
2025-11-25 06:52:01.482383 INFO::Found 0 missing values.
2025-11-25 06:52:01.486803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:01.487736 INFO::Done
2025-11-25 06:52:01.488507 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:01.491431 INFO::Starting hierarchical adjustment
2025-11-25 06:52:01.492568 INFO::Found 3 batches.
2025-11-25 06:52:01.49346 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:01.494416 INFO::Using default BPPARAM
2025-11-25 06:52:01.495202 INFO::Processing subtree level 1
2025-11-25 06:52:01.625626 INFO::Adjusting the last 1 batches sequentially
2025-11-25 06:52:01.627976 INFO::Done
2025-11-25 06:52:01.633076 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:01.636649 INFO::ASW Batch was -0.110183166421552 prior to batch effect correction and is now -0.110183166421552 .
2025-11-25 06:52:01.642279 INFO::Total function execution time is 0.165052890777588 s and adjustment time is 0.135624647140503 s ( 82.17 )
2025-11-25 06:52:01.868032 INFO::Formatting Data.
2025-11-25 06:52:01.869294 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:01.870978 INFO::Removing potential empty rows and columns
2025-11-25 06:52:01.875328 INFO::Found 1000 missing values.
2025-11-25 06:52:01.913512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:01.914785 INFO::Done
2025-11-25 06:52:01.915737 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:01.9243 INFO::Starting hierarchical adjustment
2025-11-25 06:52:01.925694 INFO::Found 10 batches.
2025-11-25 06:52:01.926609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:01.927682 INFO::Using default BPPARAM
2025-11-25 06:52:01.928587 INFO::Processing subtree level 1
2025-11-25 06:52:02.190842 INFO::Processing subtree level 2
2025-11-25 06:52:02.420216 INFO::Adjusting the last 1 batches sequentially
2025-11-25 06:52:02.422988 INFO::Done
2025-11-25 06:52:02.423865 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:02.431782 INFO::ASW Batch was 0.533259026548675 prior to batch effect correction and is now 0.533259026548675 .
2025-11-25 06:52:02.432829 INFO::ASW Label was 0.3242644144462 prior to batch effect correction and is now 0.3242644144462 .
2025-11-25 06:52:02.434194 INFO::Total function execution time is 0.566195487976074 s and adjustment time is 0.497601509094238 s ( 87.89 )
2025-11-25 06:52:02.435396 INFO::Formatting Data.
2025-11-25 06:52:02.436262 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:02.438042 INFO::Removing potential empty rows and columns
2025-11-25 06:52:02.442111 INFO::Found 1000 missing values.
2025-11-25 06:52:02.470123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:02.471054 INFO::Done
2025-11-25 06:52:02.471817 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:02.479484 INFO::Starting hierarchical adjustment
2025-11-25 06:52:02.48069 INFO::Found 10 batches.
2025-11-25 06:52:03.671358 INFO::Set up parallel execution backend with 2 workers
2025-11-25 06:52:03.674039 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-25 06:52:05.303954 INFO::Adjusting the last 2 batches sequentially
2025-11-25 06:52:05.306556 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 06:52:05.334045 INFO::Done
2025-11-25 06:52:05.335069 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:05.342664 INFO::ASW Batch was 0.533259026548675 prior to batch effect correction and is now 0.533259026548675 .
2025-11-25 06:52:05.343664 INFO::ASW Label was 0.3242644144462 prior to batch effect correction and is now 0.3242644144462 .
2025-11-25 06:52:05.345008 INFO::Total function execution time is 2.90954566001892 s and adjustment time is 2.85358881950378 s ( 98.08 )
2025-11-25 06:52:05.579794 INFO::Formatting Data.
2025-11-25 06:52:05.585204 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:05.586796 INFO::Removing potential empty rows and columns
2025-11-25 06:52:05.588564 INFO::Found 0 missing values.
2025-11-25 06:52:05.60351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:05.604534 INFO::Done
2025-11-25 06:52:05.609101 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 06:52:05.617759 INFO::Starting hierarchical adjustment
2025-11-25 06:52:05.619041 INFO::Found 3 batches.
2025-11-25 06:52:05.619925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 06:52:05.625118 INFO::Using default BPPARAM
2025-11-25 06:52:05.626183 INFO::Processing subtree level 1
2025-11-25 06:52:05.909554 INFO::Adjusting the last 1 batches sequentially
2025-11-25 06:52:05.912078 INFO::Done
2025-11-25 06:52:05.917284 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 06:52:05.926674 INFO::ASW Batch was 0.107413042025737 prior to batch effect correction and is now -0.154367097394714 .
2025-11-25 06:52:05.927703 INFO::ASW Label was -0.194011744021586 prior to batch effect correction and is now -0.119721941634271 .
2025-11-25 06:52:05.933294 INFO::Total function execution time is 0.353483438491821 s and adjustment time is 0.293306827545166 s ( 82.98 )
2025-11-25 06:52:06.214811 INFO::Formatting Data.
2025-11-25 06:52:06.216084 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.217394 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.2189 INFO::Found 2 missing values.
2025-11-25 06:52:06.223212 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.224091 INFO::Done
2025-11-25 06:52:06.277357 INFO::Found NA in Reference column
2025-11-25 06:52:06.292303 INFO::Require at least two references per batch.
2025-11-25 06:52:06.3255 INFO::Formatting Data.
2025-11-25 06:52:06.326557 INFO::Recognized SummarizedExperiment
2025-11-25 06:52:06.327356 INFO::Typecasting input to dataframe.
2025-11-25 06:52:06.343279 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.345175 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.351229 INFO::Found 0 missing values.
2025-11-25 06:52:06.363444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.364467 INFO::Done
2025-11-25 06:52:06.390719 INFO::Formatting Data.
2025-11-25 06:52:06.39185 INFO::Recognized SummarizedExperiment
2025-11-25 06:52:06.392725 INFO::Typecasting input to dataframe.
2025-11-25 06:52:06.430177 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.431949 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.443023 INFO::Found 0 missing values.
2025-11-25 06:52:06.462965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.464058 INFO::Done
2025-11-25 06:52:06.49114 INFO::Formatting Data.
2025-11-25 06:52:06.492269 INFO::Recognized SummarizedExperiment
2025-11-25 06:52:06.493189 INFO::Typecasting input to dataframe.
2025-11-25 06:52:06.52256 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.524144 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.526067 INFO::Found 0 missing values.
2025-11-25 06:52:06.527672 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 06:52:06.535237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.536249 INFO::Done
2025-11-25 06:52:06.55331 INFO::Formatting Data.
2025-11-25 06:52:06.554554 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.556157 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.558076 INFO::Found 0 missing values.
2025-11-25 06:52:06.563529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.564669 INFO::Done
2025-11-25 06:52:06.582751 INFO::Formatting Data.
2025-11-25 06:52:06.583822 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.58516 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.586811 INFO::Found 0 missing values.
2025-11-25 06:52:06.591638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.592631 INFO::Done
2025-11-25 06:52:06.639416 INFO::Formatting Data.
2025-11-25 06:52:06.64053 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.642053 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.643833 INFO::Found 1 missing values.
2025-11-25 06:52:06.647903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.648989 INFO::Done
2025-11-25 06:52:06.678349 INFO::Formatting Data.
2025-11-25 06:52:06.67943 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.680658 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.682009 INFO::Found 2 missing values.
2025-11-25 06:52:06.683265 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-25 06:52:06.686581 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.687413 INFO::Done
2025-11-25 06:52:06.702368 INFO::Formatting Data.
2025-11-25 06:52:06.703381 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.704571 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.70605 INFO::Found 2 missing values.
2025-11-25 06:52:06.708324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.70921 INFO::Done
2025-11-25 06:52:06.724083 INFO::Formatting Data.
2025-11-25 06:52:06.725168 INFO::Typecasting input to dataframe.
2025-11-25 06:52:06.726243 INFO::Replacing NaNs with NAs.
2025-11-25 06:52:06.727393 INFO::Removing potential empty rows and columns
2025-11-25 06:52:06.728926 INFO::Found 0 missing values.
2025-11-25 06:52:06.733193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 06:52:06.734033 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.721 4.146 28.353
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.760 | 1.672 | 22.474 | |
| compute_asw | 0.034 | 0.000 | 0.034 | |
| count_existing | 0.018 | 0.000 | 0.017 | |
| generate_data_covariables | 0.015 | 0.000 | 0.015 | |
| generate_dataset | 0.014 | 0.000 | 0.014 | |