Yannis Schumann
| Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 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 2025-09-06 12:07 -0400 (Sat, 06 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
| 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 163/2322 | 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 12.7.1 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: 2025-09-05 04:29:23 -0000 (Fri, 05 Sep 2025) |
| EndedAt: 2025-09-05 04:31:19 -0000 (Fri, 05 Sep 2025) |
| EllapsedTime: 115.8 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_1.5.0.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 27.857 1.356 20.117
* 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")
2025-09-05 04:31:03.329864 INFO::Formatting Data.
2025-09-05 04:31:03.331751 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:03.349371 INFO::Removing potential empty rows and columns
2025-09-05 04:31:03.727829 INFO::Found 0 missing values.
2025-09-05 04:31:03.732615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:03.733536 INFO::Done
2025-09-05 04:31:03.734291 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:03.749637 INFO::Starting hierarchical adjustment
2025-09-05 04:31:03.750846 INFO::Found 3 batches.
2025-09-05 04:31:03.75165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:03.753209 INFO::Using default BPPARAM
2025-09-05 04:31:03.75403 INFO::Processing subtree level 1
2025-09-05 04:31:03.881661 INFO::Adjusting the last 1 batches sequentially
2025-09-05 04:31:03.884008 INFO::Done
2025-09-05 04:31:03.884927 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:03.888447 INFO::ASW Batch was -0.138291228122344 prior to batch effect correction and is now -0.138291228122344 .
2025-09-05 04:31:03.8901 INFO::Total function execution time is 0.56115984916687 s and adjustment time is 0.133398056030273 s ( 23.77 )
2025-09-05 04:31:03.909399 INFO::Formatting Data.
2025-09-05 04:31:03.910388 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:03.911596 INFO::Removing potential empty rows and columns
2025-09-05 04:31:03.913185 INFO::Found 0 missing values.
2025-09-05 04:31:03.914473 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.
2025-09-05 04:31:03.929946 INFO::Formatting Data.
2025-09-05 04:31:03.930946 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:03.932176 INFO::Removing potential empty rows and columns
2025-09-05 04:31:03.933717 INFO::Found 0 missing values.
2025-09-05 04:31:03.934982 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.
2025-09-05 04:31:03.957255 INFO::Formatting Data.
2025-09-05 04:31:03.95823 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:03.959394 INFO::Removing potential empty rows and columns
2025-09-05 04:31:03.960886 INFO::Found 0 missing values.
2025-09-05 04:31:03.962148 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.
2025-09-05 04:31:03.968409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:03.969398 INFO::Done
2025-09-05 04:31:03.970167 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:03.973277 INFO::Starting hierarchical adjustment
2025-09-05 04:31:03.974489 INFO::Found 2 batches.
2025-09-05 04:31:03.975327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:03.976288 INFO::Using default BPPARAM
2025-09-05 04:31:03.977188 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:03.978664 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-05 04:31:04.009903 INFO::Done
2025-09-05 04:31:04.010772 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:04.013509 INFO::ASW Batch was -0.0346364593578811 prior to batch effect correction and is now -0.100861867900678 .
2025-09-05 04:31:04.014615 INFO::Total function execution time is 0.0574276447296143 s and adjustment time is 0.0356526374816895 s ( 62.08 )
2025-09-05 04:31:04.018119 INFO::Formatting Data.
2025-09-05 04:31:04.018995 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:04.030999 INFO::Formatting Data.
2025-09-05 04:31:04.031994 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:04.033409 INFO::Removing potential empty rows and columns
2025-09-05 04:31:04.034912 INFO::Found 0 missing values.
2025-09-05 04:31:04.039937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:04.040952 INFO::Done
2025-09-05 04:31:04.041702 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:04.04468 INFO::Starting hierarchical adjustment
2025-09-05 04:31:04.045864 INFO::Found 2 batches.
2025-09-05 04:31:04.046643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:04.047534 INFO::Using default BPPARAM
2025-09-05 04:31:04.048287 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:04.049679 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-05 04:31:04.104809 INFO::Done
2025-09-05 04:31:04.105675 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:04.108293 INFO::ASW Batch was 0.0140147690192904 prior to batch effect correction and is now -0.115080448225335 .
2025-09-05 04:31:04.109425 INFO::Total function execution time is 0.0784797668457031 s and adjustment time is 0.0591683387756348 s ( 75.39 )
2025-09-05 04:31:04.110842 INFO::Formatting Data.
2025-09-05 04:31:04.111633 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:04.112851 INFO::Removing potential empty rows and columns
2025-09-05 04:31:04.114256 INFO::Found 0 missing values.
2025-09-05 04:31:04.118222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:04.11902 INFO::Done
2025-09-05 04:31:04.119755 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:04.122568 INFO::Starting hierarchical adjustment
2025-09-05 04:31:04.123585 INFO::Found 2 batches.
2025-09-05 04:31:04.12432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:04.125229 INFO::Using default BPPARAM
2025-09-05 04:31:04.125955 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:04.127231 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-05 04:31:04.147887 INFO::Done
2025-09-05 04:31:04.148784 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:04.151468 INFO::ASW Batch was 0.0140147690192904 prior to batch effect correction and is now -0.115080448225335 .
2025-09-05 04:31:04.152572 INFO::Total function execution time is 0.0416672229766846 s and adjustment time is 0.0244765281677246 s ( 58.74 )
2025-09-05 04:31:07.854097 INFO::Formatting Data.
2025-09-05 04:31:07.855072 INFO::Recognized SummarizedExperiment
2025-09-05 04:31:07.855824 INFO::Typecasting input to dataframe.
2025-09-05 04:31:07.90088 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:07.902552 INFO::Removing potential empty rows and columns
2025-09-05 04:31:07.907937 INFO::Found 0 missing values.
2025-09-05 04:31:07.918725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:07.919715 INFO::Done
2025-09-05 04:31:07.920603 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:07.925917 INFO::Starting hierarchical adjustment
2025-09-05 04:31:07.927137 INFO::Found 2 batches.
2025-09-05 04:31:07.927973 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:07.929585 INFO::Using default BPPARAM
2025-09-05 04:31:07.930478 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:07.932001 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-05 04:31:08.014019 INFO::Done
2025-09-05 04:31:08.014997 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:08.020148 INFO::ASW Batch was 0.00307890455706641 prior to batch effect correction and is now -0.0886904092848459 .
2025-09-05 04:31:08.021574 INFO::Total function execution time is 0.167900323867798 s and adjustment time is 0.0871038436889648 s ( 51.88 )
2025-09-05 04:31:08.049896 INFO::Formatting Data.
2025-09-05 04:31:08.050943 INFO::Recognized SummarizedExperiment
2025-09-05 04:31:08.051793 INFO::Typecasting input to dataframe.
2025-09-05 04:31:08.065857 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:08.067544 INFO::Removing potential empty rows and columns
2025-09-05 04:31:08.072861 INFO::Found 0 missing values.
2025-09-05 04:31:08.083519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:08.084482 INFO::Done
2025-09-05 04:31:08.085376 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:08.090503 INFO::Starting hierarchical adjustment
2025-09-05 04:31:08.091736 INFO::Found 2 batches.
2025-09-05 04:31:08.092627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:08.093569 INFO::Using default BPPARAM
2025-09-05 04:31:08.094382 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:08.095868 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-05 04:31:08.1318 INFO::Done
2025-09-05 04:31:08.132826 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:08.137921 INFO::ASW Batch was 0.0201643169323268 prior to batch effect correction and is now 0.0201643169323268 .
2025-09-05 04:31:08.139262 INFO::Total function execution time is 0.0893237590789795 s and adjustment time is 0.0402998924255371 s ( 45.12 )
2025-09-05 04:31:08.166655 INFO::Formatting Data.
2025-09-05 04:31:08.167821 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:08.169343 INFO::Removing potential empty rows and columns
2025-09-05 04:31:08.171074 INFO::Found 0 missing values.
2025-09-05 04:31:08.176064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:08.177122 INFO::Done
2025-09-05 04:31:08.178055 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:08.181317 INFO::Starting hierarchical adjustment
2025-09-05 04:31:08.182612 INFO::Found 3 batches.
2025-09-05 04:31:08.183573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:08.184615 INFO::Using default BPPARAM
2025-09-05 04:31:08.185571 INFO::Processing subtree level 1
2025-09-05 04:31:08.356973 INFO::Adjusting the last 1 batches sequentially
2025-09-05 04:31:08.359327 INFO::Done
2025-09-05 04:31:08.360136 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:08.363622 INFO::ASW Batch was 0.020450757621209 prior to batch effect correction and is now -0.147004517696989 .
2025-09-05 04:31:08.365007 INFO::Total function execution time is 0.198371887207031 s and adjustment time is 0.177036046981812 s ( 89.24 )
2025-09-05 04:31:08.38479 INFO::Skipping initial DF formatting
2025-09-05 04:31:08.385718 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:08.39118 INFO::Starting hierarchical adjustment
2025-09-05 04:31:08.392341 INFO::Found 5 batches.
2025-09-05 04:31:08.393172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:08.394174 INFO::Using default BPPARAM
2025-09-05 04:31:08.394926 INFO::Processing subtree level 1
2025-09-05 04:31:08.648077 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:08.650512 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-05 04:31:08.679325 INFO::Done
2025-09-05 04:31:08.680301 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:08.686413 INFO::ASW Batch was 0.547066647283366 prior to batch effect correction and is now 0.547066647283366 .
2025-09-05 04:31:08.68739 INFO::ASW Label was 0.354881998192229 prior to batch effect correction and is now 0.354881998192229 .
2025-09-05 04:31:08.688676 INFO::Total function execution time is 0.304003238677979 s and adjustment time is 0.287173509597778 s ( 94.46 )
2025-09-05 04:31:08.826438 INFO::Formatting Data.
2025-09-05 04:31:08.827676 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:08.829165 INFO::Removing potential empty rows and columns
2025-09-05 04:31:08.830796 INFO::Found 0 missing values.
2025-09-05 04:31:08.837626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:08.838637 INFO::Done
2025-09-05 04:31:08.839504 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:08.84417 INFO::Starting hierarchical adjustment
2025-09-05 04:31:08.845546 INFO::Found 5 batches.
2025-09-05 04:31:08.846416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:08.847446 INFO::Using default BPPARAM
2025-09-05 04:31:08.848453 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.
2025-09-05 04:31:09.03397 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:09.036223 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-05 04:31:09.062357 INFO::Done
2025-09-05 04:31:09.063453 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:09.068424 INFO::ASW Batch was 0.465781173009476 prior to batch effect correction and is now -0.0700549263327067 .
2025-09-05 04:31:09.069456 INFO::ASW Label was 0.285249315339515 prior to batch effect correction and is now 0.783626990600269 .
2025-09-05 04:31:09.07067 INFO::Total function execution time is 0.244339942932129 s and adjustment time is 0.217041015625 s ( 88.83 )
2025-09-05 04:31:09.071895 INFO::Formatting Data.
2025-09-05 04:31:09.072845 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:09.074171 INFO::Removing potential empty rows and columns
2025-09-05 04:31:09.075779 INFO::Found 0 missing values.
2025-09-05 04:31:09.082815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:09.083767 INFO::Done
2025-09-05 04:31:09.084548 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:09.089009 INFO::Starting hierarchical adjustment
2025-09-05 04:31:09.090144 INFO::Found 5 batches.
2025-09-05 04:31:09.090931 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:09.091833 INFO::Using default BPPARAM
2025-09-05 04:31:09.092703 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.
2025-09-05 04:31:09.26565 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:09.268759 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-05 04:31:09.299187 INFO::Done
2025-09-05 04:31:09.30024 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:09.305448 INFO::ASW Batch was 0.465781173009476 prior to batch effect correction and is now -0.0700549263327067 .
2025-09-05 04:31:09.306496 INFO::ASW Label was 0.285249315339515 prior to batch effect correction and is now 0.783626990600269 .
2025-09-05 04:31:09.307763 INFO::Total function execution time is 0.235796451568604 s and adjustment time is 0.209213972091675 s ( 88.73 )
2025-09-05 04:31:09.330109 INFO::Formatting Data.
2025-09-05 04:31:09.331271 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:09.332818 INFO::Removing potential empty rows and columns
2025-09-05 04:31:09.334631 INFO::Found 0 missing values.
2025-09-05 04:31:09.34157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:09.342575 INFO::Done
2025-09-05 04:31:09.34344 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:09.34861 INFO::Starting hierarchical adjustment
2025-09-05 04:31:09.349959 INFO::Found 5 batches.
2025-09-05 04:31:09.350922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:09.351938 INFO::Using default BPPARAM
2025-09-05 04:31:09.352888 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.
2025-09-05 04:31:09.524275 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:09.526761 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-05 04:31:09.551977 INFO::Done
2025-09-05 04:31:09.553056 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:09.558006 INFO::ASW Batch was 0.312815625170219 prior to batch effect correction and is now -0.0729196400606522 .
2025-09-05 04:31:09.558987 INFO::ASW Label was 0.540947210382294 prior to batch effect correction and is now 0.738672167458002 .
2025-09-05 04:31:09.560184 INFO::Total function execution time is 0.230154752731323 s and adjustment time is 0.202280759811401 s ( 87.89 )
2025-09-05 04:31:09.561483 INFO::Formatting Data.
2025-09-05 04:31:09.562414 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:09.563753 INFO::Removing potential empty rows and columns
2025-09-05 04:31:09.565385 INFO::Found 0 missing values.
2025-09-05 04:31:09.571843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:09.572863 INFO::Done
2025-09-05 04:31:09.573687 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:09.578136 INFO::Starting hierarchical adjustment
2025-09-05 04:31:09.579298 INFO::Found 5 batches.
2025-09-05 04:31:09.580099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:09.581184 INFO::Using default BPPARAM
2025-09-05 04:31:09.582006 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.
2025-09-05 04:31:09.738525 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:09.740864 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-05 04:31:09.766525 INFO::Done
2025-09-05 04:31:09.767601 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:09.773143 INFO::ASW Batch was 0.312815625170219 prior to batch effect correction and is now -0.0729196400606522 .
2025-09-05 04:31:09.774283 INFO::ASW Label was 0.540947210382294 prior to batch effect correction and is now 0.738672167458002 .
2025-09-05 04:31:09.775714 INFO::Total function execution time is 0.214133024215698 s and adjustment time is 0.187405109405518 s ( 87.52 )
2025-09-05 04:31:09.796978 INFO::Formatting Data.
2025-09-05 04:31:09.79811 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:09.799436 INFO::Removing potential empty rows and columns
2025-09-05 04:31:09.80098 INFO::Found 0 missing values.
2025-09-05 04:31:09.805216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:09.806149 INFO::Done
2025-09-05 04:31:09.806939 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:09.811177 INFO::Starting hierarchical adjustment
2025-09-05 04:31:09.812294 INFO::Found 2 batches.
2025-09-05 04:31:09.81319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:09.814155 INFO::Using default BPPARAM
2025-09-05 04:31:09.814951 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:09.816297 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-05 04:31:09.837872 INFO::Done
2025-09-05 04:31:09.838855 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:09.843176 INFO::ASW Batch was 0.520306000132664 prior to batch effect correction and is now -0.0251650794266811 .
2025-09-05 04:31:09.844104 INFO::ASW Label was 0.579338428882159 prior to batch effect correction and is now 0.925351378330237 .
2025-09-05 04:31:09.845283 INFO::Total function execution time is 0.0484147071838379 s and adjustment time is 0.0257740020751953 s ( 53.24 )
2025-09-05 04:31:09.846417 INFO::Formatting Data.
2025-09-05 04:31:09.847296 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:09.848614 INFO::Removing potential empty rows and columns
2025-09-05 04:31:09.850118 INFO::Found 0 missing values.
2025-09-05 04:31:09.854154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:09.855024 INFO::Done
2025-09-05 04:31:09.85578 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:09.859885 INFO::Starting hierarchical adjustment
2025-09-05 04:31:09.861086 INFO::Found 2 batches.
2025-09-05 04:31:09.861876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:09.862733 INFO::Using default BPPARAM
2025-09-05 04:31:09.863481 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:09.864886 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-05 04:31:09.885974 INFO::Done
2025-09-05 04:31:09.886899 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:09.891108 INFO::ASW Batch was 0.520306000132664 prior to batch effect correction and is now -0.0251650794266811 .
2025-09-05 04:31:09.892035 INFO::ASW Label was 0.579338428882159 prior to batch effect correction and is now 0.925351378330237 .
2025-09-05 04:31:09.893196 INFO::Total function execution time is 0.0467815399169922 s and adjustment time is 0.0251052379608154 s ( 53.66 )
2025-09-05 04:31:09.914119 INFO::Formatting Data.
2025-09-05 04:31:09.915402 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:09.916733 INFO::Removing potential empty rows and columns
2025-09-05 04:31:09.918087 INFO::Found 0 missing values.
2025-09-05 04:31:09.921298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:09.92221 INFO::Done
2025-09-05 04:31:09.922992 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:09.926444 INFO::Starting hierarchical adjustment
2025-09-05 04:31:09.927637 INFO::Found 2 batches.
2025-09-05 04:31:09.928424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:09.929431 INFO::Using default BPPARAM
2025-09-05 04:31:09.930204 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:09.931561 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-05 04:31:09.978314 INFO::Done
2025-09-05 04:31:09.979224 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:09.981983 INFO::ASW Batch was -0.0658231758193967 prior to batch effect correction and is now -0.140468383758105 .
2025-09-05 04:31:09.983213 INFO::Total function execution time is 0.0692501068115234 s and adjustment time is 0.0509488582611084 s ( 73.57 )
2025-09-05 04:31:10.000482 INFO::Formatting Data.
2025-09-05 04:31:10.001574 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:10.002763 INFO::Removing potential empty rows and columns
2025-09-05 04:31:10.004222 INFO::Found 0 missing values.
2025-09-05 04:31:10.005967 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.
2025-09-05 04:31:10.012971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:10.013872 INFO::Done
2025-09-05 04:31:10.014623 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:10.018737 INFO::Starting hierarchical adjustment
2025-09-05 04:31:10.019844 INFO::Found 2 batches.
2025-09-05 04:31:10.020663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:10.021569 INFO::Using default BPPARAM
2025-09-05 04:31:10.022317 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:10.023664 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-05 04:31:10.047291 INFO::Done
2025-09-05 04:31:10.048217 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:10.05237 INFO::ASW Batch was 0.415256513712088 prior to batch effect correction and is now 0.265139214875177 .
2025-09-05 04:31:10.053322 INFO::ASW Label was 0.753062476326379 prior to batch effect correction and is now 0.815179015111193 .
2025-09-05 04:31:10.0544 INFO::Total function execution time is 0.0539937019348145 s and adjustment time is 0.0276319980621338 s ( 51.18 )
2025-09-05 04:31:10.055576 INFO::Formatting Data.
2025-09-05 04:31:10.05648 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:10.057848 INFO::Removing potential empty rows and columns
2025-09-05 04:31:10.059267 INFO::Found 0 missing values.
2025-09-05 04:31:10.060583 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.
2025-09-05 04:31:10.067394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:10.068275 INFO::Done
2025-09-05 04:31:10.069101 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:10.073256 INFO::Starting hierarchical adjustment
2025-09-05 04:31:10.074363 INFO::Found 2 batches.
2025-09-05 04:31:10.07512 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:10.075966 INFO::Using default BPPARAM
2025-09-05 04:31:10.076774 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:10.078133 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-05 04:31:10.102037 INFO::Done
2025-09-05 04:31:10.102999 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:10.107203 INFO::ASW Batch was 0.415256513712088 prior to batch effect correction and is now 0.265139214875177 .
2025-09-05 04:31:10.108168 INFO::ASW Label was 0.753062476326379 prior to batch effect correction and is now 0.815179015111193 .
2025-09-05 04:31:10.109436 INFO::Total function execution time is 0.0538578033447266 s and adjustment time is 0.0278706550598145 s ( 51.75 )
2025-09-05 04:31:10.415241 INFO::Formatting Data.
2025-09-05 04:31:10.41627 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:10.417599 INFO::Removing potential empty rows and columns
2025-09-05 04:31:10.419072 INFO::Found 0 missing values.
2025-09-05 04:31:10.423642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:10.424584 INFO::Done
2025-09-05 04:31:10.42543 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:10.428277 INFO::Starting hierarchical adjustment
2025-09-05 04:31:10.429516 INFO::Found 3 batches.
2025-09-05 04:31:10.43032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:10.431247 INFO::Using default BPPARAM
2025-09-05 04:31:10.43203 INFO::Processing subtree level 1
2025-09-05 04:31:10.538521 INFO::Adjusting the last 1 batches sequentially
2025-09-05 04:31:10.540896 INFO::Done
2025-09-05 04:31:10.541755 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:10.545062 INFO::ASW Batch was -0.118016540044711 prior to batch effect correction and is now -0.118016540044711 .
2025-09-05 04:31:10.546433 INFO::Total function execution time is 0.131237268447876 s and adjustment time is 0.111592292785645 s ( 85.03 )
2025-09-05 04:31:10.547844 INFO::Formatting Data.
2025-09-05 04:31:10.54881 INFO::Typecasting input to dataframe.
2025-09-05 04:31:10.549927 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:10.551205 INFO::Removing potential empty rows and columns
2025-09-05 04:31:10.552835 INFO::Found 0 missing values.
2025-09-05 04:31:10.557465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:10.558424 INFO::Done
2025-09-05 04:31:10.559216 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:10.562199 INFO::Starting hierarchical adjustment
2025-09-05 04:31:10.563372 INFO::Found 3 batches.
2025-09-05 04:31:10.56417 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:10.56516 INFO::Using default BPPARAM
2025-09-05 04:31:10.565927 INFO::Processing subtree level 1
2025-09-05 04:31:10.671603 INFO::Adjusting the last 1 batches sequentially
2025-09-05 04:31:10.67394 INFO::Done
2025-09-05 04:31:10.674829 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:10.678234 INFO::ASW Batch was -0.118016540044711 prior to batch effect correction and is now -0.118016540044711 .
2025-09-05 04:31:10.679669 INFO::Total function execution time is 0.131774425506592 s and adjustment time is 0.110810279846191 s ( 84.09 )
2025-09-05 04:31:10.698505 INFO::Formatting Data.
2025-09-05 04:31:10.699533 INFO::Typecasting input to dataframe.
2025-09-05 04:31:10.700729 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:10.701985 INFO::Removing potential empty rows and columns
2025-09-05 04:31:10.703458 INFO::Found 0 missing values.
2025-09-05 04:31:10.707628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:10.708477 INFO::Done
2025-09-05 04:31:10.709273 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:10.711952 INFO::Starting hierarchical adjustment
2025-09-05 04:31:10.713051 INFO::Found 3 batches.
2025-09-05 04:31:10.713828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:10.7147 INFO::Using default BPPARAM
2025-09-05 04:31:10.715517 INFO::Processing subtree level 1
2025-09-05 04:31:10.823359 INFO::Adjusting the last 1 batches sequentially
2025-09-05 04:31:10.825841 INFO::Done
2025-09-05 04:31:10.826813 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:10.830422 INFO::ASW Batch was -0.00888853428314501 prior to batch effect correction and is now -0.00888853428314501 .
2025-09-05 04:31:10.831838 INFO::Total function execution time is 0.133332252502441 s and adjustment time is 0.112982988357544 s ( 84.74 )
2025-09-05 04:31:11.012063 INFO::Formatting Data.
2025-09-05 04:31:11.01322 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:11.014722 INFO::Removing potential empty rows and columns
2025-09-05 04:31:11.018704 INFO::Found 1000 missing values.
2025-09-05 04:31:11.046036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:11.046993 INFO::Done
2025-09-05 04:31:11.047758 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:11.055315 INFO::Starting hierarchical adjustment
2025-09-05 04:31:11.056495 INFO::Found 10 batches.
2025-09-05 04:31:11.057386 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:11.058264 INFO::Using default BPPARAM
2025-09-05 04:31:11.059027 INFO::Processing subtree level 1
2025-09-05 04:31:11.2194 INFO::Processing subtree level 2
2025-09-05 04:31:11.409959 INFO::Adjusting the last 1 batches sequentially
2025-09-05 04:31:11.41243 INFO::Done
2025-09-05 04:31:11.413358 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:11.421092 INFO::ASW Batch was 0.491782463048507 prior to batch effect correction and is now 0.491782463048507 .
2025-09-05 04:31:11.422063 INFO::ASW Label was 0.354089012286713 prior to batch effect correction and is now 0.354089012286713 .
2025-09-05 04:31:11.423374 INFO::Total function execution time is 0.411334037780762 s and adjustment time is 0.356180667877197 s ( 86.59 )
2025-09-05 04:31:11.424598 INFO::Formatting Data.
2025-09-05 04:31:11.425634 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:11.427283 INFO::Removing potential empty rows and columns
2025-09-05 04:31:11.43131 INFO::Found 1000 missing values.
2025-09-05 04:31:11.459008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:11.459955 INFO::Done
2025-09-05 04:31:11.460811 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:11.468298 INFO::Starting hierarchical adjustment
2025-09-05 04:31:11.469506 INFO::Found 10 batches.
2025-09-05 04:31:12.665774 INFO::Set up parallel execution backend with 2 workers
2025-09-05 04:31:12.671156 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-05 04:31:13.958951 INFO::Adjusting the last 2 batches sequentially
2025-09-05 04:31:13.961229 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-05 04:31:13.985083 INFO::Done
2025-09-05 04:31:13.985916 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:13.992342 INFO::ASW Batch was 0.491782463048507 prior to batch effect correction and is now 0.491782463048507 .
2025-09-05 04:31:13.993264 INFO::ASW Label was 0.354089012286713 prior to batch effect correction and is now 0.354089012286713 .
2025-09-05 04:31:13.994271 INFO::Total function execution time is 2.56974792480469 s and adjustment time is 2.51579260826111 s ( 97.9 )
2025-09-05 04:31:14.187961 INFO::Formatting Data.
2025-09-05 04:31:14.189141 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:14.190445 INFO::Removing potential empty rows and columns
2025-09-05 04:31:14.192052 INFO::Found 0 missing values.
2025-09-05 04:31:14.197942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:14.198889 INFO::Done
2025-09-05 04:31:14.199666 INFO::Acquiring quality metrics before batch effect correction.
2025-09-05 04:31:14.203753 INFO::Starting hierarchical adjustment
2025-09-05 04:31:14.205008 INFO::Found 3 batches.
2025-09-05 04:31:14.205806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-05 04:31:14.206811 INFO::Using default BPPARAM
2025-09-05 04:31:14.20763 INFO::Processing subtree level 1
2025-09-05 04:31:14.346912 INFO::Adjusting the last 1 batches sequentially
2025-09-05 04:31:14.349474 INFO::Done
2025-09-05 04:31:14.350386 INFO::Acquiring quality metrics after batch effect correction.
2025-09-05 04:31:14.355076 INFO::ASW Batch was 0.191516238437357 prior to batch effect correction and is now -0.159443176724183 .
2025-09-05 04:31:14.356116 INFO::ASW Label was -0.185010988782348 prior to batch effect correction and is now -0.0595851922387645 .
2025-09-05 04:31:14.357489 INFO::Total function execution time is 0.169637441635132 s and adjustment time is 0.144720554351807 s ( 85.31 )
2025-09-05 04:31:14.533994 INFO::Formatting Data.
2025-09-05 04:31:14.535049 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:14.536298 INFO::Removing potential empty rows and columns
2025-09-05 04:31:14.537887 INFO::Found 2 missing values.
2025-09-05 04:31:14.542263 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:14.543177 INFO::Done
2025-09-05 04:31:14.585187 INFO::Found NA in Reference column
2025-09-05 04:31:14.609715 INFO::Require at least two references per batch.
2025-09-05 04:31:14.650524 INFO::Formatting Data.
2025-09-05 04:31:14.651723 INFO::Recognized SummarizedExperiment
2025-09-05 04:31:14.65271 INFO::Typecasting input to dataframe.
2025-09-05 04:31:14.672104 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:14.674449 INFO::Removing potential empty rows and columns
2025-09-05 04:31:14.681956 INFO::Found 0 missing values.
2025-09-05 04:31:14.696158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:14.69732 INFO::Done
2025-09-05 04:31:14.726579 INFO::Formatting Data.
2025-09-05 04:31:14.727744 INFO::Recognized SummarizedExperiment
2025-09-05 04:31:14.728722 INFO::Typecasting input to dataframe.
2025-09-05 04:31:14.763142 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:14.76531 INFO::Removing potential empty rows and columns
2025-09-05 04:31:14.772488 INFO::Found 0 missing values.
2025-09-05 04:31:14.79594 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:14.797156 INFO::Done
2025-09-05 04:31:14.826642 INFO::Formatting Data.
2025-09-05 04:31:14.827848 INFO::Recognized SummarizedExperiment
2025-09-05 04:31:14.828876 INFO::Typecasting input to dataframe.
2025-09-05 04:31:14.86089 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:14.862574 INFO::Removing potential empty rows and columns
2025-09-05 04:31:14.864496 INFO::Found 0 missing values.
2025-09-05 04:31:14.866202 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.
2025-09-05 04:31:14.874927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:14.876022 INFO::Done
2025-09-05 04:31:14.894443 INFO::Formatting Data.
2025-09-05 04:31:14.895733 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:14.89728 INFO::Removing potential empty rows and columns
2025-09-05 04:31:14.899078 INFO::Found 0 missing values.
2025-09-05 04:31:14.904888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:14.905975 INFO::Done
2025-09-05 04:31:14.927609 INFO::Formatting Data.
2025-09-05 04:31:14.929005 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:14.930533 INFO::Removing potential empty rows and columns
2025-09-05 04:31:14.932453 INFO::Found 0 missing values.
2025-09-05 04:31:14.938435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:14.939548 INFO::Done
2025-09-05 04:31:14.991832 INFO::Formatting Data.
2025-09-05 04:31:14.993207 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:14.994915 INFO::Removing potential empty rows and columns
2025-09-05 04:31:14.997058 INFO::Found 1 missing values.
2025-09-05 04:31:15.002068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:15.003117 INFO::Done
2025-09-05 04:31:15.035571 INFO::Formatting Data.
2025-09-05 04:31:15.036757 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:15.03803 INFO::Removing potential empty rows and columns
2025-09-05 04:31:15.03954 INFO::Found 2 missing values.
2025-09-05 04:31:15.040964 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.
2025-09-05 04:31:15.044691 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:15.045682 INFO::Done
2025-09-05 04:31:15.062204 INFO::Formatting Data.
2025-09-05 04:31:15.063339 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:15.064693 INFO::Removing potential empty rows and columns
2025-09-05 04:31:15.06614 INFO::Found 2 missing values.
2025-09-05 04:31:15.068718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:15.069642 INFO::Done
2025-09-05 04:31:15.086937 INFO::Formatting Data.
2025-09-05 04:31:15.088059 INFO::Typecasting input to dataframe.
2025-09-05 04:31:15.089343 INFO::Replacing NaNs with NAs.
2025-09-05 04:31:15.090629 INFO::Removing potential empty rows and columns
2025-09-05 04:31:15.092278 INFO::Found 0 missing values.
2025-09-05 04:31:15.097026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-05 04:31:15.097975 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.984 5.255 25.916
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.857 | 1.356 | 20.117 | |
| compute_asw | 0.030 | 0.012 | 0.042 | |
| count_existing | 0.019 | 0.000 | 0.019 | |
| generate_data_covariables | 0.007 | 0.008 | 0.015 | |
| generate_dataset | 0.014 | 0.000 | 0.014 | |