Yannis Schumann
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 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 2025-12-22 12:06 -0500 (Mon, 22 Dec 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" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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: 2025-12-19 07:01:59 -0000 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 07:03:34 -0000 (Fri, 19 Dec 2025) |
| EllapsedTime: 95.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.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 28.421 1.656 22.728
* 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")
2025-12-19 07:03:15.190257 INFO::Formatting Data.
2025-12-19 07:03:15.192075 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:15.208794 INFO::Removing potential empty rows and columns
2025-12-19 07:03:15.615757 INFO::Found 0 missing values.
2025-12-19 07:03:15.620587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:15.621525 INFO::Done
2025-12-19 07:03:15.622307 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:15.639225 INFO::Starting hierarchical adjustment
2025-12-19 07:03:15.64054 INFO::Found 3 batches.
2025-12-19 07:03:15.641459 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:15.64316 INFO::Using default BPPARAM
2025-12-19 07:03:15.644088 INFO::Processing subtree level 1
2025-12-19 07:03:15.778985 INFO::Adjusting the last 1 batches sequentially
2025-12-19 07:03:15.781648 INFO::Done
2025-12-19 07:03:15.782768 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:15.786991 INFO::ASW Batch was -0.0607120206123547 prior to batch effect correction and is now -0.0607120206123547 .
2025-12-19 07:03:15.788806 INFO::Total function execution time is 0.599249124526978 s and adjustment time is 0.141362428665161 s ( 23.59 )
2025-12-19 07:03:15.81085 INFO::Formatting Data.
2025-12-19 07:03:15.811996 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:15.813426 INFO::Removing potential empty rows and columns
2025-12-19 07:03:15.815307 INFO::Found 0 missing values.
2025-12-19 07:03:15.816899 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.
2025-12-19 07:03:15.833938 INFO::Formatting Data.
2025-12-19 07:03:15.835076 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:15.836454 INFO::Removing potential empty rows and columns
2025-12-19 07:03:15.838168 INFO::Found 0 missing values.
2025-12-19 07:03:15.839683 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.
2025-12-19 07:03:15.863897 INFO::Formatting Data.
2025-12-19 07:03:15.865019 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:15.866386 INFO::Removing potential empty rows and columns
2025-12-19 07:03:15.868067 INFO::Found 0 missing values.
2025-12-19 07:03:15.869493 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.
2025-12-19 07:03:15.876505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:15.877494 INFO::Done
2025-12-19 07:03:15.87829 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:15.881311 INFO::Starting hierarchical adjustment
2025-12-19 07:03:15.882482 INFO::Found 2 batches.
2025-12-19 07:03:15.883316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:15.884252 INFO::Using default BPPARAM
2025-12-19 07:03:15.885122 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:15.886664 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 07:03:15.920207 INFO::Done
2025-12-19 07:03:15.921241 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:15.92447 INFO::ASW Batch was -0.0338555122028427 prior to batch effect correction and is now -0.128902651946435 .
2025-12-19 07:03:15.925789 INFO::Total function execution time is 0.0619339942932129 s and adjustment time is 0.0379176139831543 s ( 61.22 )
2025-12-19 07:03:15.929877 INFO::Formatting Data.
2025-12-19 07:03:15.931024 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:15.943997 INFO::Formatting Data.
2025-12-19 07:03:15.945083 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:15.946458 INFO::Removing potential empty rows and columns
2025-12-19 07:03:15.948109 INFO::Found 0 missing values.
2025-12-19 07:03:15.952693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:15.953668 INFO::Done
2025-12-19 07:03:15.954497 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:15.957591 INFO::Starting hierarchical adjustment
2025-12-19 07:03:15.95887 INFO::Found 2 batches.
2025-12-19 07:03:15.959732 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:15.96087 INFO::Using default BPPARAM
2025-12-19 07:03:15.961792 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:15.963371 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 07:03:16.026062 INFO::Done
2025-12-19 07:03:16.027047 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:16.030028 INFO::ASW Batch was -0.0293953465077083 prior to batch effect correction and is now -0.0890403384168086 .
2025-12-19 07:03:16.031289 INFO::Total function execution time is 0.0873363018035889 s and adjustment time is 0.0674800872802734 s ( 77.26 )
2025-12-19 07:03:16.032894 INFO::Formatting Data.
2025-12-19 07:03:16.033832 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:16.035151 INFO::Removing potential empty rows and columns
2025-12-19 07:03:16.036668 INFO::Found 0 missing values.
2025-12-19 07:03:16.042117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:16.043091 INFO::Done
2025-12-19 07:03:16.043888 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:16.046895 INFO::Starting hierarchical adjustment
2025-12-19 07:03:16.048048 INFO::Found 2 batches.
2025-12-19 07:03:16.048865 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:16.049769 INFO::Using default BPPARAM
2025-12-19 07:03:16.050556 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:16.051934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 07:03:16.074238 INFO::Done
2025-12-19 07:03:16.075242 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:16.078154 INFO::ASW Batch was -0.0293953465077083 prior to batch effect correction and is now -0.0890403384168086 .
2025-12-19 07:03:16.079438 INFO::Total function execution time is 0.0465431213378906 s and adjustment time is 0.0263979434967041 s ( 56.72 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-19 07:03:20.153948 INFO::Formatting Data.
2025-12-19 07:03:20.154998 INFO::Recognized SummarizedExperiment
2025-12-19 07:03:20.155844 INFO::Typecasting input to dataframe.
2025-12-19 07:03:20.199843 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:20.201538 INFO::Removing potential empty rows and columns
2025-12-19 07:03:20.206912 INFO::Found 0 missing values.
2025-12-19 07:03:20.217372 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:20.218292 INFO::Done
2025-12-19 07:03:20.21913 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:20.224272 INFO::Starting hierarchical adjustment
2025-12-19 07:03:20.225512 INFO::Found 2 batches.
2025-12-19 07:03:20.226352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:20.227903 INFO::Using default BPPARAM
2025-12-19 07:03:20.228806 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:20.230286 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 07:03:20.325233 INFO::Done
2025-12-19 07:03:20.326342 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:20.331594 INFO::ASW Batch was -0.0154985026145598 prior to batch effect correction and is now -0.100054432611233 .
2025-12-19 07:03:20.332942 INFO::Total function execution time is 0.179435729980469 s and adjustment time is 0.0998375415802002 s ( 55.64 )
Warning: stack imbalance in '{', 73 then 75
2025-12-19 07:03:20.36521 INFO::Formatting Data.
2025-12-19 07:03:20.366219 INFO::Recognized SummarizedExperiment
2025-12-19 07:03:20.367107 INFO::Typecasting input to dataframe.
2025-12-19 07:03:20.383817 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:20.385495 INFO::Removing potential empty rows and columns
2025-12-19 07:03:20.390903 INFO::Found 0 missing values.
2025-12-19 07:03:20.401693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:20.402641 INFO::Done
2025-12-19 07:03:20.403519 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:20.408665 INFO::Starting hierarchical adjustment
2025-12-19 07:03:20.409924 INFO::Found 2 batches.
2025-12-19 07:03:20.410839 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:20.411825 INFO::Using default BPPARAM
2025-12-19 07:03:20.412626 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:20.414141 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 07:03:20.450711 INFO::Done
2025-12-19 07:03:20.451647 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:20.456595 INFO::ASW Batch was -0.0100862366368531 prior to batch effect correction and is now -0.0100862366368531 .
2025-12-19 07:03:20.457965 INFO::Total function execution time is 0.092689037322998 s and adjustment time is 0.041008472442627 s ( 44.24 )
2025-12-19 07:03:20.485375 INFO::Formatting Data.
2025-12-19 07:03:20.486495 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:20.487902 INFO::Removing potential empty rows and columns
2025-12-19 07:03:20.489516 INFO::Found 0 missing values.
2025-12-19 07:03:20.494221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:20.495248 INFO::Done
2025-12-19 07:03:20.496383 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:20.499546 INFO::Starting hierarchical adjustment
2025-12-19 07:03:20.500778 INFO::Found 3 batches.
2025-12-19 07:03:20.501695 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:20.502661 INFO::Using default BPPARAM
2025-12-19 07:03:20.503567 INFO::Processing subtree level 1
2025-12-19 07:03:20.680536 INFO::Adjusting the last 1 batches sequentially
2025-12-19 07:03:20.691098 INFO::Done
2025-12-19 07:03:20.692021 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:20.699772 INFO::ASW Batch was -0.0720659421910119 prior to batch effect correction and is now -0.167616930574738 .
2025-12-19 07:03:20.70537 INFO::Total function execution time is 0.219949007034302 s and adjustment time is 0.190596342086792 s ( 86.65 )
2025-12-19 07:03:20.744604 INFO::Skipping initial DF formatting
2025-12-19 07:03:20.745626 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:20.751746 INFO::Starting hierarchical adjustment
2025-12-19 07:03:20.753057 INFO::Found 5 batches.
2025-12-19 07:03:20.753964 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:20.754965 INFO::Using default BPPARAM
2025-12-19 07:03:20.755836 INFO::Processing subtree level 1
2025-12-19 07:03:21.107894 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:21.11019 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 07:03:21.138184 INFO::Done
2025-12-19 07:03:21.139182 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:21.213956 INFO::ASW Batch was 0.506558738891657 prior to batch effect correction and is now 0.506558738891657 .
2025-12-19 07:03:21.214964 INFO::ASW Label was 0.3518206120664 prior to batch effect correction and is now 0.3518206120664 .
2025-12-19 07:03:21.216202 INFO::Total function execution time is 0.471650123596191 s and adjustment time is 0.385409355163574 s ( 81.72 )
2025-12-19 07:03:21.24193 INFO::Formatting Data.
2025-12-19 07:03:21.242974 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:21.244241 INFO::Removing potential empty rows and columns
2025-12-19 07:03:21.245709 INFO::Found 0 missing values.
2025-12-19 07:03:21.252213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:21.253205 INFO::Done
2025-12-19 07:03:21.254134 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:21.258453 INFO::Starting hierarchical adjustment
2025-12-19 07:03:21.259537 INFO::Found 5 batches.
2025-12-19 07:03:21.260327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:21.261268 INFO::Using default BPPARAM
2025-12-19 07:03:21.262052 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.
2025-12-19 07:03:21.55877 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:21.573974 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 07:03:21.630496 INFO::Done
2025-12-19 07:03:21.631688 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:21.637807 INFO::ASW Batch was 0.457534911417745 prior to batch effect correction and is now -0.0308043814925126 .
2025-12-19 07:03:21.638924 INFO::ASW Label was 0.414817250708159 prior to batch effect correction and is now 0.736096279236555 .
2025-12-19 07:03:21.640301 INFO::Total function execution time is 0.398355007171631 s and adjustment time is 0.371131658554077 s ( 93.17 )
2025-12-19 07:03:21.641723 INFO::Formatting Data.
2025-12-19 07:03:21.642885 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:21.644311 INFO::Removing potential empty rows and columns
2025-12-19 07:03:21.646092 INFO::Found 0 missing values.
2025-12-19 07:03:21.653414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:21.654429 INFO::Done
2025-12-19 07:03:21.655364 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:21.66022 INFO::Starting hierarchical adjustment
2025-12-19 07:03:21.66154 INFO::Found 5 batches.
2025-12-19 07:03:21.662404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:21.663409 INFO::Using default BPPARAM
2025-12-19 07:03:21.6643 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.
2025-12-19 07:03:21.830381 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:21.836993 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 07:03:21.866903 INFO::Done
2025-12-19 07:03:21.867924 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:21.872967 INFO::ASW Batch was 0.457534911417745 prior to batch effect correction and is now -0.0308043814925126 .
2025-12-19 07:03:21.873965 INFO::ASW Label was 0.414817250708159 prior to batch effect correction and is now 0.736096279236555 .
2025-12-19 07:03:21.87531 INFO::Total function execution time is 0.23357105255127 s and adjustment time is 0.205625057220459 s ( 88.04 )
2025-12-19 07:03:21.896414 INFO::Formatting Data.
2025-12-19 07:03:21.89766 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:21.899182 INFO::Removing potential empty rows and columns
2025-12-19 07:03:21.900917 INFO::Found 0 missing values.
2025-12-19 07:03:21.914758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:21.915777 INFO::Done
2025-12-19 07:03:21.916667 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:21.930321 INFO::Starting hierarchical adjustment
2025-12-19 07:03:21.931738 INFO::Found 5 batches.
2025-12-19 07:03:21.936899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:21.938265 INFO::Using default BPPARAM
2025-12-19 07:03:21.93935 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.
2025-12-19 07:03:22.152294 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:22.154796 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 07:03:22.181495 INFO::Done
2025-12-19 07:03:22.182528 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:22.187801 INFO::ASW Batch was 0.499550677030742 prior to batch effect correction and is now -0.0177402079611896 .
2025-12-19 07:03:22.188882 INFO::ASW Label was 0.284816307552327 prior to batch effect correction and is now 0.754926462023118 .
2025-12-19 07:03:22.190253 INFO::Total function execution time is 0.293855667114258 s and adjustment time is 0.250054359436035 s ( 85.09 )
2025-12-19 07:03:22.191678 INFO::Formatting Data.
2025-12-19 07:03:22.192695 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:22.194224 INFO::Removing potential empty rows and columns
2025-12-19 07:03:22.19608 INFO::Found 0 missing values.
2025-12-19 07:03:22.203257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:22.204309 INFO::Done
2025-12-19 07:03:22.205208 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:22.210199 INFO::Starting hierarchical adjustment
2025-12-19 07:03:22.211635 INFO::Found 5 batches.
2025-12-19 07:03:22.212581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:22.213706 INFO::Using default BPPARAM
2025-12-19 07:03:22.214566 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.
2025-12-19 07:03:22.419229 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:22.429658 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 07:03:22.483556 INFO::Done
2025-12-19 07:03:22.484645 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:22.489874 INFO::ASW Batch was 0.499550677030742 prior to batch effect correction and is now -0.0177402079611896 .
2025-12-19 07:03:22.490959 INFO::ASW Label was 0.284816307552327 prior to batch effect correction and is now 0.754926462023118 .
2025-12-19 07:03:22.492295 INFO::Total function execution time is 0.300601482391357 s and adjustment time is 0.272170782089233 s ( 90.54 )
2025-12-19 07:03:22.513877 INFO::Formatting Data.
2025-12-19 07:03:22.515135 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:22.516633 INFO::Removing potential empty rows and columns
2025-12-19 07:03:22.518409 INFO::Found 0 missing values.
2025-12-19 07:03:22.523223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:22.524233 INFO::Done
2025-12-19 07:03:22.525155 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:22.529876 INFO::Starting hierarchical adjustment
2025-12-19 07:03:22.531183 INFO::Found 2 batches.
2025-12-19 07:03:22.532074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:22.533113 INFO::Using default BPPARAM
2025-12-19 07:03:22.534 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:22.53556 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 07:03:22.567414 INFO::Done
2025-12-19 07:03:22.568567 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:22.573469 INFO::ASW Batch was 0.901031853156361 prior to batch effect correction and is now -0.0245635266751055 .
2025-12-19 07:03:22.574523 INFO::ASW Label was 0.064414158484281 prior to batch effect correction and is now 0.704644969608355 .
2025-12-19 07:03:22.575842 INFO::Total function execution time is 0.0620224475860596 s and adjustment time is 0.0364563465118408 s ( 58.78 )
2025-12-19 07:03:22.57717 INFO::Formatting Data.
2025-12-19 07:03:22.578223 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:22.579717 INFO::Removing potential empty rows and columns
2025-12-19 07:03:22.581382 INFO::Found 0 missing values.
2025-12-19 07:03:22.586163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:22.587211 INFO::Done
2025-12-19 07:03:22.588109 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:22.593174 INFO::Starting hierarchical adjustment
2025-12-19 07:03:22.594474 INFO::Found 2 batches.
2025-12-19 07:03:22.595504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:22.596551 INFO::Using default BPPARAM
2025-12-19 07:03:22.597501 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:22.599101 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 07:03:22.622992 INFO::Done
2025-12-19 07:03:22.624056 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:22.629062 INFO::ASW Batch was 0.901031853156361 prior to batch effect correction and is now -0.0245635266751055 .
2025-12-19 07:03:22.630164 INFO::ASW Label was 0.064414158484281 prior to batch effect correction and is now 0.704644969608355 .
2025-12-19 07:03:22.631499 INFO::Total function execution time is 0.0543441772460938 s and adjustment time is 0.028754711151123 s ( 52.91 )
2025-12-19 07:03:22.650812 INFO::Formatting Data.
2025-12-19 07:03:22.652107 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:22.653752 INFO::Removing potential empty rows and columns
2025-12-19 07:03:22.655454 INFO::Found 0 missing values.
2025-12-19 07:03:22.659415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:22.66048 INFO::Done
2025-12-19 07:03:22.661497 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:22.664736 INFO::Starting hierarchical adjustment
2025-12-19 07:03:22.666054 INFO::Found 2 batches.
2025-12-19 07:03:22.667048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:22.668063 INFO::Using default BPPARAM
2025-12-19 07:03:22.669034 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:22.670606 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 07:03:22.721561 INFO::Done
2025-12-19 07:03:22.722597 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:22.725796 INFO::ASW Batch was -0.0976020528749991 prior to batch effect correction and is now -0.154624426437111 .
2025-12-19 07:03:22.727257 INFO::Total function execution time is 0.0765345096588135 s and adjustment time is 0.055753231048584 s ( 72.85 )
2025-12-19 07:03:22.747226 INFO::Formatting Data.
2025-12-19 07:03:22.748463 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:22.750001 INFO::Removing potential empty rows and columns
2025-12-19 07:03:22.751787 INFO::Found 0 missing values.
2025-12-19 07:03:22.753754 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.
2025-12-19 07:03:22.761946 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:22.763035 INFO::Done
2025-12-19 07:03:22.76395 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:22.768673 INFO::Starting hierarchical adjustment
2025-12-19 07:03:22.770031 INFO::Found 2 batches.
2025-12-19 07:03:22.771013 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:22.772024 INFO::Using default BPPARAM
2025-12-19 07:03:22.772924 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:22.774518 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 07:03:22.801007 INFO::Done
2025-12-19 07:03:22.802072 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:22.8071 INFO::ASW Batch was 0.686145459828974 prior to batch effect correction and is now 0.0700171592810336 .
2025-12-19 07:03:22.808158 INFO::ASW Label was 0.369646801411931 prior to batch effect correction and is now 0.806634717566797 .
2025-12-19 07:03:22.809474 INFO::Total function execution time is 0.0622906684875488 s and adjustment time is 0.0312201976776123 s ( 50.12 )
2025-12-19 07:03:22.81085 INFO::Formatting Data.
2025-12-19 07:03:22.811959 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:22.813562 INFO::Removing potential empty rows and columns
2025-12-19 07:03:22.815555 INFO::Found 0 missing values.
2025-12-19 07:03:22.81725 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.
2025-12-19 07:03:22.825462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:22.826482 INFO::Done
2025-12-19 07:03:22.827452 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:22.832297 INFO::Starting hierarchical adjustment
2025-12-19 07:03:22.833611 INFO::Found 2 batches.
2025-12-19 07:03:22.834578 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:22.835646 INFO::Using default BPPARAM
2025-12-19 07:03:22.836563 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:22.838188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 07:03:22.865195 INFO::Done
2025-12-19 07:03:22.866236 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:22.871145 INFO::ASW Batch was 0.686145459828974 prior to batch effect correction and is now 0.0700171592810336 .
2025-12-19 07:03:22.872193 INFO::ASW Label was 0.369646801411931 prior to batch effect correction and is now 0.806634717566797 .
2025-12-19 07:03:22.87355 INFO::Total function execution time is 0.06276535987854 s and adjustment time is 0.0318150520324707 s ( 50.69 )
2025-12-19 07:03:23.20056 INFO::Formatting Data.
2025-12-19 07:03:23.201729 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:23.203025 INFO::Removing potential empty rows and columns
2025-12-19 07:03:23.204519 INFO::Found 0 missing values.
2025-12-19 07:03:23.208972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:23.209842 INFO::Done
2025-12-19 07:03:23.210592 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:23.21369 INFO::Starting hierarchical adjustment
2025-12-19 07:03:23.214871 INFO::Found 3 batches.
2025-12-19 07:03:23.215648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:23.216568 INFO::Using default BPPARAM
2025-12-19 07:03:23.217366 INFO::Processing subtree level 1
2025-12-19 07:03:23.328262 INFO::Adjusting the last 1 batches sequentially
2025-12-19 07:03:23.338836 INFO::Done
2025-12-19 07:03:23.33975 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:23.347509 INFO::ASW Batch was -0.0209870191393318 prior to batch effect correction and is now -0.0209870191393318 .
2025-12-19 07:03:23.353169 INFO::Total function execution time is 0.148572206497192 s and adjustment time is 0.124168395996094 s ( 83.57 )
2025-12-19 07:03:23.355037 INFO::Formatting Data.
2025-12-19 07:03:23.356145 INFO::Typecasting input to dataframe.
2025-12-19 07:03:23.3616 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:23.363209 INFO::Removing potential empty rows and columns
2025-12-19 07:03:23.369106 INFO::Found 0 missing values.
2025-12-19 07:03:23.378471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:23.379473 INFO::Done
2025-12-19 07:03:23.380332 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:23.387582 INFO::Starting hierarchical adjustment
2025-12-19 07:03:23.392448 INFO::Found 3 batches.
2025-12-19 07:03:23.393521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:23.39452 INFO::Using default BPPARAM
2025-12-19 07:03:23.395396 INFO::Processing subtree level 1
2025-12-19 07:03:23.504628 INFO::Adjusting the last 1 batches sequentially
2025-12-19 07:03:23.515139 INFO::Done
2025-12-19 07:03:23.515946 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:23.523443 INFO::ASW Batch was -0.0209870191393318 prior to batch effect correction and is now -0.0209870191393318 .
2025-12-19 07:03:23.528908 INFO::Total function execution time is 0.169880867004395 s and adjustment time is 0.126599550247192 s ( 74.52 )
2025-12-19 07:03:23.563616 INFO::Formatting Data.
2025-12-19 07:03:23.564617 INFO::Typecasting input to dataframe.
2025-12-19 07:03:23.56622 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:23.5675 INFO::Removing potential empty rows and columns
2025-12-19 07:03:23.569017 INFO::Found 0 missing values.
2025-12-19 07:03:23.573261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:23.574145 INFO::Done
2025-12-19 07:03:23.574932 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:23.577627 INFO::Starting hierarchical adjustment
2025-12-19 07:03:23.578643 INFO::Found 3 batches.
2025-12-19 07:03:23.579449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:23.580297 INFO::Using default BPPARAM
2025-12-19 07:03:23.581076 INFO::Processing subtree level 1
2025-12-19 07:03:23.688427 INFO::Adjusting the last 1 batches sequentially
2025-12-19 07:03:23.699102 INFO::Done
2025-12-19 07:03:23.699936 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:23.708428 INFO::ASW Batch was -0.00962276288741068 prior to batch effect correction and is now -0.00962276288741068 .
2025-12-19 07:03:23.714133 INFO::Total function execution time is 0.150494813919067 s and adjustment time is 0.120618343353271 s ( 80.15 )
2025-12-19 07:03:23.953507 INFO::Formatting Data.
2025-12-19 07:03:23.954653 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:23.956149 INFO::Removing potential empty rows and columns
2025-12-19 07:03:23.960059 INFO::Found 1000 missing values.
2025-12-19 07:03:23.98698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:23.987917 INFO::Done
2025-12-19 07:03:23.988667 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:23.996328 INFO::Starting hierarchical adjustment
2025-12-19 07:03:23.997554 INFO::Found 10 batches.
2025-12-19 07:03:23.998316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:23.999209 INFO::Using default BPPARAM
2025-12-19 07:03:23.999949 INFO::Processing subtree level 1
2025-12-19 07:03:24.287072 INFO::Processing subtree level 2
2025-12-19 07:03:24.464542 INFO::Adjusting the last 1 batches sequentially
2025-12-19 07:03:24.475303 INFO::Done
2025-12-19 07:03:24.476129 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:24.492023 INFO::ASW Batch was 0.454784968847695 prior to batch effect correction and is now 0.454784968847695 .
2025-12-19 07:03:24.497133 INFO::ASW Label was 0.345379954282876 prior to batch effect correction and is now 0.345379954282876 .
2025-12-19 07:03:24.498546 INFO::Total function execution time is 0.545122623443604 s and adjustment time is 0.477982044219971 s ( 87.68 )
2025-12-19 07:03:24.499728 INFO::Formatting Data.
2025-12-19 07:03:24.500577 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:24.506516 INFO::Removing potential empty rows and columns
2025-12-19 07:03:24.514827 INFO::Found 1000 missing values.
2025-12-19 07:03:24.549667 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:24.550543 INFO::Done
2025-12-19 07:03:24.551301 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:24.558449 INFO::Starting hierarchical adjustment
2025-12-19 07:03:24.559577 INFO::Found 10 batches.
2025-12-19 07:03:25.742716 INFO::Set up parallel execution backend with 2 workers
2025-12-19 07:03:25.745912 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-19 07:03:27.197922 INFO::Adjusting the last 2 batches sequentially
2025-12-19 07:03:27.20048 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 07:03:27.226846 INFO::Done
2025-12-19 07:03:27.227805 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:27.235093 INFO::ASW Batch was 0.454784968847695 prior to batch effect correction and is now 0.454784968847695 .
2025-12-19 07:03:27.236053 INFO::ASW Label was 0.345379954282876 prior to batch effect correction and is now 0.345379954282876 .
2025-12-19 07:03:27.237309 INFO::Total function execution time is 2.73753428459167 s and adjustment time is 2.6674337387085 s ( 97.44 )
2025-12-19 07:03:27.475837 INFO::Formatting Data.
2025-12-19 07:03:27.478824 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:27.485663 INFO::Removing potential empty rows and columns
2025-12-19 07:03:27.487642 INFO::Found 0 missing values.
2025-12-19 07:03:27.498353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:27.49942 INFO::Done
2025-12-19 07:03:27.500313 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 07:03:27.504765 INFO::Starting hierarchical adjustment
2025-12-19 07:03:27.506079 INFO::Found 3 batches.
2025-12-19 07:03:27.507025 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 07:03:27.508006 INFO::Using default BPPARAM
2025-12-19 07:03:27.508867 INFO::Processing subtree level 1
2025-12-19 07:03:27.661652 INFO::Adjusting the last 1 batches sequentially
2025-12-19 07:03:27.664218 INFO::Done
2025-12-19 07:03:27.669399 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 07:03:27.678746 INFO::ASW Batch was 0.178641670677361 prior to batch effect correction and is now -0.136370695799511 .
2025-12-19 07:03:27.679836 INFO::ASW Label was -0.236604480609343 prior to batch effect correction and is now -0.0151022626158752 .
2025-12-19 07:03:27.685401 INFO::Total function execution time is 0.209546804428101 s and adjustment time is 0.158385038375854 s ( 75.58 )
2025-12-19 07:03:27.891562 INFO::Formatting Data.
2025-12-19 07:03:27.892727 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:27.894212 INFO::Removing potential empty rows and columns
2025-12-19 07:03:27.896007 INFO::Found 2 missing values.
2025-12-19 07:03:27.900952 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:27.901924 INFO::Done
2025-12-19 07:03:27.947081 INFO::Found NA in Reference column
2025-12-19 07:03:27.961973 INFO::Require at least two references per batch.
2025-12-19 07:03:27.994107 INFO::Formatting Data.
2025-12-19 07:03:27.995167 INFO::Recognized SummarizedExperiment
2025-12-19 07:03:27.996001 INFO::Typecasting input to dataframe.
2025-12-19 07:03:28.010922 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.012604 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.018273 INFO::Found 0 missing values.
2025-12-19 07:03:28.029207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.030161 INFO::Done
2025-12-19 07:03:28.064853 INFO::Formatting Data.
2025-12-19 07:03:28.066131 INFO::Recognized SummarizedExperiment
2025-12-19 07:03:28.067017 INFO::Typecasting input to dataframe.
2025-12-19 07:03:28.096233 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.098096 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.103848 INFO::Found 0 missing values.
2025-12-19 07:03:28.121699 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.122656 INFO::Done
2025-12-19 07:03:28.147512 INFO::Formatting Data.
2025-12-19 07:03:28.14852 INFO::Recognized SummarizedExperiment
2025-12-19 07:03:28.149389 INFO::Typecasting input to dataframe.
2025-12-19 07:03:28.175529 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.17698 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.178638 INFO::Found 0 missing values.
2025-12-19 07:03:28.180091 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.
2025-12-19 07:03:28.187175 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.188091 INFO::Done
2025-12-19 07:03:28.203432 INFO::Formatting Data.
2025-12-19 07:03:28.204484 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.205833 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.207428 INFO::Found 0 missing values.
2025-12-19 07:03:28.212036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.213032 INFO::Done
2025-12-19 07:03:28.230918 INFO::Formatting Data.
2025-12-19 07:03:28.232067 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.233471 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.23519 INFO::Found 0 missing values.
2025-12-19 07:03:28.240199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.241177 INFO::Done
2025-12-19 07:03:28.290171 INFO::Formatting Data.
2025-12-19 07:03:28.291471 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.293231 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.295322 INFO::Found 1 missing values.
2025-12-19 07:03:28.300119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.301256 INFO::Done
2025-12-19 07:03:28.333818 INFO::Formatting Data.
2025-12-19 07:03:28.335139 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.336679 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.338438 INFO::Found 2 missing values.
2025-12-19 07:03:28.34001 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.
2025-12-19 07:03:28.343982 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.345087 INFO::Done
2025-12-19 07:03:28.361792 INFO::Formatting Data.
2025-12-19 07:03:28.363018 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.364465 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.366122 INFO::Found 2 missing values.
2025-12-19 07:03:28.368934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.36996 INFO::Done
2025-12-19 07:03:28.387862 INFO::Formatting Data.
2025-12-19 07:03:28.389053 INFO::Typecasting input to dataframe.
2025-12-19 07:03:28.390722 INFO::Replacing NaNs with NAs.
2025-12-19 07:03:28.392277 INFO::Removing potential empty rows and columns
2025-12-19 07:03:28.394128 INFO::Found 0 missing values.
2025-12-19 07:03:28.399055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 07:03:28.400066 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.467 4.765 26.910
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.421 | 1.656 | 22.728 | |
| compute_asw | 0.035 | 0.000 | 0.035 | |
| count_existing | 0.018 | 0.000 | 0.018 | |
| generate_data_covariables | 0.016 | 0.000 | 0.016 | |
| generate_dataset | 0.010 | 0.004 | 0.014 | |