Yannis Schumann
| Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 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 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 163/2334 | 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. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-09-26 19:37:28 -0400 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 19:38:55 -0400 (Fri, 26 Sep 2025) |
| EllapsedTime: 86.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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 28.362 1.601 20.323
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
2025-09-26 19:38:33.870082 INFO::Formatting Data.
2025-09-26 19:38:33.874635 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:33.88785 INFO::Removing potential empty rows and columns
2025-09-26 19:38:34.21278 INFO::Found 0 missing values.
2025-09-26 19:38:34.217572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:34.218618 INFO::Done
2025-09-26 19:38:34.21948 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:34.238696 INFO::Starting hierarchical adjustment
2025-09-26 19:38:34.239842 INFO::Found 3 batches.
2025-09-26 19:38:34.240592 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:34.242107 INFO::Using default BPPARAM
2025-09-26 19:38:34.242826 INFO::Processing subtree level 1
2025-09-26 19:38:34.41458 INFO::Adjusting the last 1 batches sequentially
2025-09-26 19:38:34.419564 INFO::Done
2025-09-26 19:38:34.420568 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:34.426205 INFO::ASW Batch was -0.11347727932089 prior to batch effect correction and is now -0.11347727932089 .
2025-09-26 19:38:34.428427 INFO::Total function execution time is 0.55899715423584 s and adjustment time is 0.17992901802063 s ( 32.19 )
2025-09-26 19:38:34.451587 INFO::Formatting Data.
2025-09-26 19:38:34.452376 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:34.453289 INFO::Removing potential empty rows and columns
2025-09-26 19:38:34.454619 INFO::Found 0 missing values.
2025-09-26 19:38:34.45559 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.
2025-09-26 19:38:34.468132 INFO::Formatting Data.
2025-09-26 19:38:34.468988 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:34.469894 INFO::Removing potential empty rows and columns
2025-09-26 19:38:34.470851 INFO::Found 0 missing values.
2025-09-26 19:38:34.471711 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.
2025-09-26 19:38:34.496311 INFO::Formatting Data.
2025-09-26 19:38:34.497434 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:34.498652 INFO::Removing potential empty rows and columns
2025-09-26 19:38:34.499951 INFO::Found 0 missing values.
2025-09-26 19:38:34.500816 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.
2025-09-26 19:38:34.507333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:34.508161 INFO::Done
2025-09-26 19:38:34.508752 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:34.511843 INFO::Starting hierarchical adjustment
2025-09-26 19:38:34.512604 INFO::Found 2 batches.
2025-09-26 19:38:34.513125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:34.513885 INFO::Using default BPPARAM
2025-09-26 19:38:34.514634 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:34.51571 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 19:38:34.545284 INFO::Done
2025-09-26 19:38:34.546025 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:34.548424 INFO::ASW Batch was -0.0486961586698623 prior to batch effect correction and is now -0.127671223615086 .
2025-09-26 19:38:34.549277 INFO::Total function execution time is 0.0531008243560791 s and adjustment time is 0.0327908992767334 s ( 61.75 )
2025-09-26 19:38:34.553195 INFO::Formatting Data.
2025-09-26 19:38:34.553966 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:34.565367 INFO::Formatting Data.
2025-09-26 19:38:34.566177 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:34.567109 INFO::Removing potential empty rows and columns
2025-09-26 19:38:34.568497 INFO::Found 0 missing values.
2025-09-26 19:38:34.572524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:34.573125 INFO::Done
2025-09-26 19:38:34.573648 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:34.576367 INFO::Starting hierarchical adjustment
2025-09-26 19:38:34.57704 INFO::Found 2 batches.
2025-09-26 19:38:34.57769 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:34.578565 INFO::Using default BPPARAM
2025-09-26 19:38:34.57949 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:34.580693 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 19:38:34.632302 INFO::Done
2025-09-26 19:38:34.632965 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:34.634947 INFO::ASW Batch was 0.00272084580369146 prior to batch effect correction and is now -0.117527762501687 .
2025-09-26 19:38:34.636077 INFO::Total function execution time is 0.0707418918609619 s and adjustment time is 0.0553631782531738 s ( 78.26 )
2025-09-26 19:38:34.637581 INFO::Formatting Data.
2025-09-26 19:38:34.638424 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:34.639616 INFO::Removing potential empty rows and columns
2025-09-26 19:38:34.641018 INFO::Found 0 missing values.
2025-09-26 19:38:34.644958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:34.645728 INFO::Done
2025-09-26 19:38:34.646446 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:34.64908 INFO::Starting hierarchical adjustment
2025-09-26 19:38:34.649993 INFO::Found 2 batches.
2025-09-26 19:38:34.650755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:34.651743 INFO::Using default BPPARAM
2025-09-26 19:38:34.652479 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:34.653748 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 19:38:34.672895 INFO::Done
2025-09-26 19:38:34.674015 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:34.677631 INFO::ASW Batch was 0.00272084580369146 prior to batch effect correction and is now -0.117527762501687 .
2025-09-26 19:38:34.678517 INFO::Total function execution time is 0.0409870147705078 s and adjustment time is 0.0230100154876709 s ( 56.14 )
2025-09-26 19:38:38.155083 INFO::Formatting Data.
2025-09-26 19:38:38.156004 INFO::Recognized SummarizedExperiment
2025-09-26 19:38:38.156695 INFO::Typecasting input to dataframe.
2025-09-26 19:38:38.19555 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:38.196801 INFO::Removing potential empty rows and columns
2025-09-26 19:38:38.200221 INFO::Found 0 missing values.
2025-09-26 19:38:38.208954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:38.209712 INFO::Done
2025-09-26 19:38:38.210234 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:38.214706 INFO::Starting hierarchical adjustment
2025-09-26 19:38:38.215804 INFO::Found 2 batches.
2025-09-26 19:38:38.216582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:38.218044 INFO::Using default BPPARAM
2025-09-26 19:38:38.21878 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:38.220287 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 19:38:38.285401 INFO::Done
2025-09-26 19:38:38.286496 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:38.291494 INFO::ASW Batch was -0.00175236716917928 prior to batch effect correction and is now -0.0912686955634012 .
2025-09-26 19:38:38.29242 INFO::Total function execution time is 0.137764930725098 s and adjustment time is 0.0697920322418213 s ( 50.66 )
2025-09-26 19:38:38.31626 INFO::Formatting Data.
2025-09-26 19:38:38.317277 INFO::Recognized SummarizedExperiment
2025-09-26 19:38:38.318046 INFO::Typecasting input to dataframe.
2025-09-26 19:38:38.331853 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:38.333457 INFO::Removing potential empty rows and columns
2025-09-26 19:38:38.338243 INFO::Found 0 missing values.
2025-09-26 19:38:38.347666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:38.348603 INFO::Done
2025-09-26 19:38:38.3494 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:38.354652 INFO::Starting hierarchical adjustment
2025-09-26 19:38:38.355826 INFO::Found 2 batches.
2025-09-26 19:38:38.356646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:38.357508 INFO::Using default BPPARAM
2025-09-26 19:38:38.35821 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:38.359797 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 19:38:38.390953 INFO::Done
2025-09-26 19:38:38.391622 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:38.394902 INFO::ASW Batch was 0.00294016253364299 prior to batch effect correction and is now 0.00294016253364299 .
2025-09-26 19:38:38.396155 INFO::Total function execution time is 0.0798349380493164 s and adjustment time is 0.0353691577911377 s ( 44.3 )
2025-09-26 19:38:38.424449 INFO::Formatting Data.
2025-09-26 19:38:38.425686 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:38.427044 INFO::Removing potential empty rows and columns
2025-09-26 19:38:38.428456 INFO::Found 0 missing values.
2025-09-26 19:38:38.432564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:38.43336 INFO::Done
2025-09-26 19:38:38.434093 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:38.436692 INFO::Starting hierarchical adjustment
2025-09-26 19:38:38.437487 INFO::Found 3 batches.
2025-09-26 19:38:38.43831 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:38.438944 INFO::Using default BPPARAM
2025-09-26 19:38:38.439428 INFO::Processing subtree level 1
2025-09-26 19:38:38.671652 INFO::Adjusting the last 1 batches sequentially
2025-09-26 19:38:38.681188 INFO::Done
2025-09-26 19:38:38.68231 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:38.689072 INFO::ASW Batch was -0.0018592247992033 prior to batch effect correction and is now -0.165289380379636 .
2025-09-26 19:38:38.691806 INFO::Total function execution time is 0.267282962799072 s and adjustment time is 0.243832111358643 s ( 91.23 )
2025-09-26 19:38:38.717347 INFO::Skipping initial DF formatting
2025-09-26 19:38:38.718438 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:38.724161 INFO::Starting hierarchical adjustment
2025-09-26 19:38:38.72642 INFO::Found 5 batches.
2025-09-26 19:38:38.727189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:38.727809 INFO::Using default BPPARAM
2025-09-26 19:38:38.728319 INFO::Processing subtree level 1
2025-09-26 19:38:39.09641 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:39.100303 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 19:38:39.167288 INFO::Done
2025-09-26 19:38:39.169202 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:39.179593 INFO::ASW Batch was 0.471333749991036 prior to batch effect correction and is now 0.471333749991036 .
2025-09-26 19:38:39.180777 INFO::ASW Label was 0.389169765275662 prior to batch effect correction and is now 0.389169765275662 .
2025-09-26 19:38:39.183933 INFO::Total function execution time is 0.466267824172974 s and adjustment time is 0.442172050476074 s ( 94.83 )
2025-09-26 19:38:39.287905 INFO::Formatting Data.
2025-09-26 19:38:39.288701 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:39.289728 INFO::Removing potential empty rows and columns
2025-09-26 19:38:39.291113 INFO::Found 0 missing values.
2025-09-26 19:38:39.296773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:39.297577 INFO::Done
2025-09-26 19:38:39.298217 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:39.302083 INFO::Starting hierarchical adjustment
2025-09-26 19:38:39.30309 INFO::Found 5 batches.
2025-09-26 19:38:39.303961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:39.304931 INFO::Using default BPPARAM
2025-09-26 19:38:39.305681 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.
2025-09-26 19:38:39.55313 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:39.56363 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 19:38:39.598999 INFO::Done
2025-09-26 19:38:39.600294 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:39.606313 INFO::ASW Batch was 0.246819886375531 prior to batch effect correction and is now -0.0773002759290347 .
2025-09-26 19:38:39.607104 INFO::ASW Label was 0.374596096523168 prior to batch effect correction and is now 0.884408209523584 .
2025-09-26 19:38:39.607984 INFO::Total function execution time is 0.320132970809937 s and adjustment time is 0.29605507850647 s ( 92.48 )
2025-09-26 19:38:39.609253 INFO::Formatting Data.
2025-09-26 19:38:39.609945 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:39.611339 INFO::Removing potential empty rows and columns
2025-09-26 19:38:39.612808 INFO::Found 0 missing values.
2025-09-26 19:38:39.617953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:39.619402 INFO::Done
2025-09-26 19:38:39.620625 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:39.625586 INFO::Starting hierarchical adjustment
2025-09-26 19:38:39.626813 INFO::Found 5 batches.
2025-09-26 19:38:39.6274 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:39.628034 INFO::Using default BPPARAM
2025-09-26 19:38:39.628902 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.
2025-09-26 19:38:39.839744 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:39.847747 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 19:38:39.882303 INFO::Done
2025-09-26 19:38:39.88309 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:39.889899 INFO::ASW Batch was 0.246819886375531 prior to batch effect correction and is now -0.0773002759290347 .
2025-09-26 19:38:39.890957 INFO::ASW Label was 0.374596096523168 prior to batch effect correction and is now 0.884408209523584 .
2025-09-26 19:38:39.892246 INFO::Total function execution time is 0.2829270362854 s and adjustment time is 0.255688905715942 s ( 90.37 )
2025-09-26 19:38:39.918182 INFO::Formatting Data.
2025-09-26 19:38:39.919716 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:39.920739 INFO::Removing potential empty rows and columns
2025-09-26 19:38:39.922322 INFO::Found 0 missing values.
2025-09-26 19:38:39.927778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:39.928723 INFO::Done
2025-09-26 19:38:39.929404 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:39.933353 INFO::Starting hierarchical adjustment
2025-09-26 19:38:39.934478 INFO::Found 5 batches.
2025-09-26 19:38:39.935302 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:39.936183 INFO::Using default BPPARAM
2025-09-26 19:38:39.936932 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.
2025-09-26 19:38:40.154763 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:40.168587 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 19:38:40.200708 INFO::Done
2025-09-26 19:38:40.202026 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:40.21002 INFO::ASW Batch was 0.289596868956027 prior to batch effect correction and is now -0.0833669207048187 .
2025-09-26 19:38:40.211058 INFO::ASW Label was 0.461516850129397 prior to batch effect correction and is now 0.782129304164632 .
2025-09-26 19:38:40.212554 INFO::Total function execution time is 0.294229030609131 s and adjustment time is 0.266448974609375 s ( 90.56 )
2025-09-26 19:38:40.213801 INFO::Formatting Data.
2025-09-26 19:38:40.214718 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:40.215983 INFO::Removing potential empty rows and columns
2025-09-26 19:38:40.217382 INFO::Found 0 missing values.
2025-09-26 19:38:40.222775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:40.224153 INFO::Done
2025-09-26 19:38:40.224915 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:40.228909 INFO::Starting hierarchical adjustment
2025-09-26 19:38:40.229655 INFO::Found 5 batches.
2025-09-26 19:38:40.230162 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:40.230734 INFO::Using default BPPARAM
2025-09-26 19:38:40.231742 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.
2025-09-26 19:38:40.451277 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:40.465208 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 19:38:40.495858 INFO::Done
2025-09-26 19:38:40.497374 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:40.503397 INFO::ASW Batch was 0.289596868956027 prior to batch effect correction and is now -0.0833669207048187 .
2025-09-26 19:38:40.504579 INFO::ASW Label was 0.461516850129397 prior to batch effect correction and is now 0.782129304164632 .
2025-09-26 19:38:40.506016 INFO::Total function execution time is 0.292294025421143 s and adjustment time is 0.266220092773438 s ( 91.08 )
2025-09-26 19:38:40.529025 INFO::Formatting Data.
2025-09-26 19:38:40.530172 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:40.53154 INFO::Removing potential empty rows and columns
2025-09-26 19:38:40.533019 INFO::Found 0 missing values.
2025-09-26 19:38:40.536752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:40.537377 INFO::Done
2025-09-26 19:38:40.538005 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:40.5423 INFO::Starting hierarchical adjustment
2025-09-26 19:38:40.543426 INFO::Found 2 batches.
2025-09-26 19:38:40.544223 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:40.545351 INFO::Using default BPPARAM
2025-09-26 19:38:40.546197 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:40.547629 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 19:38:40.566568 INFO::Done
2025-09-26 19:38:40.567441 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:40.571154 INFO::ASW Batch was 0.437406404188436 prior to batch effect correction and is now 0.0404560003820354 .
2025-09-26 19:38:40.571918 INFO::ASW Label was 0.670035957514928 prior to batch effect correction and is now 0.901883177638704 .
2025-09-26 19:38:40.572909 INFO::Total function execution time is 0.0440261363983154 s and adjustment time is 0.0233139991760254 s ( 52.95 )
2025-09-26 19:38:40.57386 INFO::Formatting Data.
2025-09-26 19:38:40.574457 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:40.575815 INFO::Removing potential empty rows and columns
2025-09-26 19:38:40.577293 INFO::Found 0 missing values.
2025-09-26 19:38:40.581202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:40.582017 INFO::Done
2025-09-26 19:38:40.582764 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:40.586755 INFO::Starting hierarchical adjustment
2025-09-26 19:38:40.587846 INFO::Found 2 batches.
2025-09-26 19:38:40.58843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:40.589016 INFO::Using default BPPARAM
2025-09-26 19:38:40.589765 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:40.591066 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-26 19:38:40.61206 INFO::Done
2025-09-26 19:38:40.613581 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:40.618547 INFO::ASW Batch was 0.437406404188436 prior to batch effect correction and is now 0.0404560003820354 .
2025-09-26 19:38:40.61958 INFO::ASW Label was 0.670035957514928 prior to batch effect correction and is now 0.901883177638704 .
2025-09-26 19:38:40.620789 INFO::Total function execution time is 0.046846866607666 s and adjustment time is 0.0243771076202393 s ( 52.04 )
2025-09-26 19:38:40.640317 INFO::Formatting Data.
2025-09-26 19:38:40.641094 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:40.642344 INFO::Removing potential empty rows and columns
2025-09-26 19:38:40.643643 INFO::Found 0 missing values.
2025-09-26 19:38:40.646456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:40.647264 INFO::Done
2025-09-26 19:38:40.647932 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:40.650448 INFO::Starting hierarchical adjustment
2025-09-26 19:38:40.651474 INFO::Found 2 batches.
2025-09-26 19:38:40.652211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:40.652872 INFO::Using default BPPARAM
2025-09-26 19:38:40.653653 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:40.655142 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 19:38:40.695766 INFO::Done
2025-09-26 19:38:40.696835 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:40.699253 INFO::ASW Batch was -0.0340204060368584 prior to batch effect correction and is now -0.128004591910741 .
2025-09-26 19:38:40.700158 INFO::Total function execution time is 0.0598409175872803 s and adjustment time is 0.0444490909576416 s ( 74.28 )
2025-09-26 19:38:40.719572 INFO::Formatting Data.
2025-09-26 19:38:40.72078 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:40.72191 INFO::Removing potential empty rows and columns
2025-09-26 19:38:40.723462 INFO::Found 0 missing values.
2025-09-26 19:38:40.725174 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.
2025-09-26 19:38:40.731531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:40.732525 INFO::Done
2025-09-26 19:38:40.733385 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:40.73764 INFO::Starting hierarchical adjustment
2025-09-26 19:38:40.738919 INFO::Found 2 batches.
2025-09-26 19:38:40.739854 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:40.740584 INFO::Using default BPPARAM
2025-09-26 19:38:40.741188 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:40.742597 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 19:38:40.764365 INFO::Done
2025-09-26 19:38:40.765438 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:40.769478 INFO::ASW Batch was 0.521169438324132 prior to batch effect correction and is now -0.0353007238653474 .
2025-09-26 19:38:40.770523 INFO::ASW Label was 0.537018107998509 prior to batch effect correction and is now 0.912663661075881 .
2025-09-26 19:38:40.771687 INFO::Total function execution time is 0.0522580146789551 s and adjustment time is 0.025709867477417 s ( 49.2 )
2025-09-26 19:38:40.772838 INFO::Formatting Data.
2025-09-26 19:38:40.773725 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:40.77466 INFO::Removing potential empty rows and columns
2025-09-26 19:38:40.775764 INFO::Found 0 missing values.
2025-09-26 19:38:40.777055 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.
2025-09-26 19:38:40.783522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:40.784441 INFO::Done
2025-09-26 19:38:40.785229 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:40.789226 INFO::Starting hierarchical adjustment
2025-09-26 19:38:40.790253 INFO::Found 2 batches.
2025-09-26 19:38:40.791094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:40.792002 INFO::Using default BPPARAM
2025-09-26 19:38:40.792762 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:40.794096 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 19:38:40.81381 INFO::Done
2025-09-26 19:38:40.814715 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:40.818346 INFO::ASW Batch was 0.521169438324132 prior to batch effect correction and is now -0.0353007238653474 .
2025-09-26 19:38:40.819107 INFO::ASW Label was 0.537018107998509 prior to batch effect correction and is now 0.912663661075881 .
2025-09-26 19:38:40.820153 INFO::Total function execution time is 0.0472919940948486 s and adjustment time is 0.0236630439758301 s ( 50.04 )
2025-09-26 19:38:41.091669 INFO::Formatting Data.
2025-09-26 19:38:41.092581 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:41.093458 INFO::Removing potential empty rows and columns
2025-09-26 19:38:41.094535 INFO::Found 0 missing values.
2025-09-26 19:38:41.099056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:41.100091 INFO::Done
2025-09-26 19:38:41.100911 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:41.103424 INFO::Starting hierarchical adjustment
2025-09-26 19:38:41.104705 INFO::Found 3 batches.
2025-09-26 19:38:41.105473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:41.106343 INFO::Using default BPPARAM
2025-09-26 19:38:41.107132 INFO::Processing subtree level 1
2025-09-26 19:38:41.254183 INFO::Adjusting the last 1 batches sequentially
2025-09-26 19:38:41.279018 INFO::Done
2025-09-26 19:38:41.281571 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:41.293805 INFO::ASW Batch was -0.0434521877455194 prior to batch effect correction and is now -0.0434521877455194 .
2025-09-26 19:38:41.29609 INFO::Total function execution time is 0.204056978225708 s and adjustment time is 0.174463987350464 s ( 85.5 )
2025-09-26 19:38:41.298722 INFO::Formatting Data.
2025-09-26 19:38:41.300112 INFO::Typecasting input to dataframe.
2025-09-26 19:38:41.301341 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:41.303883 INFO::Removing potential empty rows and columns
2025-09-26 19:38:41.305105 INFO::Found 0 missing values.
2025-09-26 19:38:41.310336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:41.312348 INFO::Done
2025-09-26 19:38:41.313229 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:41.316388 INFO::Starting hierarchical adjustment
2025-09-26 19:38:41.317815 INFO::Found 3 batches.
2025-09-26 19:38:41.31861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:41.320145 INFO::Using default BPPARAM
2025-09-26 19:38:41.321347 INFO::Processing subtree level 1
2025-09-26 19:38:41.462748 INFO::Adjusting the last 1 batches sequentially
2025-09-26 19:38:41.480148 INFO::Done
2025-09-26 19:38:41.481222 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:41.491102 INFO::ASW Batch was -0.0434521877455194 prior to batch effect correction and is now -0.0434521877455194 .
2025-09-26 19:38:41.493432 INFO::Total function execution time is 0.194453001022339 s and adjustment time is 0.162512063980103 s ( 83.57 )
2025-09-26 19:38:41.51646 INFO::Formatting Data.
2025-09-26 19:38:41.517334 INFO::Typecasting input to dataframe.
2025-09-26 19:38:41.51864 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:41.521006 INFO::Removing potential empty rows and columns
2025-09-26 19:38:41.523671 INFO::Found 0 missing values.
2025-09-26 19:38:41.527801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:41.528838 INFO::Done
2025-09-26 19:38:41.529692 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:41.532668 INFO::Starting hierarchical adjustment
2025-09-26 19:38:41.533919 INFO::Found 3 batches.
2025-09-26 19:38:41.534802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:41.535493 INFO::Using default BPPARAM
2025-09-26 19:38:41.537684 INFO::Processing subtree level 1
2025-09-26 19:38:41.707033 INFO::Adjusting the last 1 batches sequentially
2025-09-26 19:38:41.718455 INFO::Done
2025-09-26 19:38:41.720025 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:41.729281 INFO::ASW Batch was 0.0377645644437217 prior to batch effect correction and is now 0.0377645644437217 .
2025-09-26 19:38:41.733197 INFO::Total function execution time is 0.216186046600342 s and adjustment time is 0.18480396270752 s ( 85.48 )
2025-09-26 19:38:42.050419 INFO::Formatting Data.
2025-09-26 19:38:42.051512 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:42.054655 INFO::Removing potential empty rows and columns
2025-09-26 19:38:42.059925 INFO::Found 1000 missing values.
2025-09-26 19:38:42.085336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:42.086346 INFO::Done
2025-09-26 19:38:42.087306 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:42.094519 INFO::Starting hierarchical adjustment
2025-09-26 19:38:42.095773 INFO::Found 10 batches.
2025-09-26 19:38:42.096821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:42.0978 INFO::Using default BPPARAM
2025-09-26 19:38:42.099186 INFO::Processing subtree level 1
2025-09-26 19:38:42.283389 INFO::Processing subtree level 2
2025-09-26 19:38:42.538876 INFO::Adjusting the last 1 batches sequentially
2025-09-26 19:38:42.554493 INFO::Done
2025-09-26 19:38:42.562679 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:42.577497 INFO::ASW Batch was 0.461557832499523 prior to batch effect correction and is now 0.461557832499523 .
2025-09-26 19:38:42.5792 INFO::ASW Label was 0.357311396845896 prior to batch effect correction and is now 0.357311396845896 .
2025-09-26 19:38:42.58298 INFO::Total function execution time is 0.532562017440796 s and adjustment time is 0.45894193649292 s ( 86.18 )
2025-09-26 19:38:42.584624 INFO::Formatting Data.
2025-09-26 19:38:42.586553 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:42.589098 INFO::Removing potential empty rows and columns
2025-09-26 19:38:42.593071 INFO::Found 1000 missing values.
2025-09-26 19:38:42.618734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:42.619718 INFO::Done
2025-09-26 19:38:42.620476 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:42.627906 INFO::Starting hierarchical adjustment
2025-09-26 19:38:42.629152 INFO::Found 10 batches.
2025-09-26 19:38:43.75278 INFO::Set up parallel execution backend with 2 workers
2025-09-26 19:38:43.753537 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-26 19:38:45.044099 INFO::Adjusting the last 2 batches sequentially
2025-09-26 19:38:45.045671 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-26 19:38:45.064922 INFO::Done
2025-09-26 19:38:45.065798 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:45.070946 INFO::ASW Batch was 0.461557832499523 prior to batch effect correction and is now 0.461557832499523 .
2025-09-26 19:38:45.071559 INFO::ASW Label was 0.357311396845896 prior to batch effect correction and is now 0.357311396845896 .
2025-09-26 19:38:45.072222 INFO::Total function execution time is 2.48785185813904 s and adjustment time is 2.4360499382019 s ( 97.92 )
2025-09-26 19:38:45.3522 INFO::Formatting Data.
2025-09-26 19:38:45.353586 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:45.35594 INFO::Removing potential empty rows and columns
2025-09-26 19:38:45.357116 INFO::Found 0 missing values.
2025-09-26 19:38:45.363044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:45.364032 INFO::Done
2025-09-26 19:38:45.365042 INFO::Acquiring quality metrics before batch effect correction.
2025-09-26 19:38:45.369082 INFO::Starting hierarchical adjustment
2025-09-26 19:38:45.370051 INFO::Found 3 batches.
2025-09-26 19:38:45.371066 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-26 19:38:45.372095 INFO::Using default BPPARAM
2025-09-26 19:38:45.372925 INFO::Processing subtree level 1
2025-09-26 19:38:45.53673 INFO::Adjusting the last 1 batches sequentially
2025-09-26 19:38:45.560542 INFO::Done
2025-09-26 19:38:45.564003 INFO::Acquiring quality metrics after batch effect correction.
2025-09-26 19:38:45.57882 INFO::ASW Batch was 0.210894951302052 prior to batch effect correction and is now -0.141972033113361 .
2025-09-26 19:38:45.579867 INFO::ASW Label was -0.188656593401141 prior to batch effect correction and is now 0.00370578365386657 .
2025-09-26 19:38:45.584584 INFO::Total function execution time is 0.232361078262329 s and adjustment time is 0.190254926681519 s ( 81.88 )
2025-09-26 19:38:45.775592 INFO::Formatting Data.
2025-09-26 19:38:45.777486 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:45.78036 INFO::Removing potential empty rows and columns
2025-09-26 19:38:45.782106 INFO::Found 2 missing values.
2025-09-26 19:38:45.786208 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:45.787014 INFO::Done
2025-09-26 19:38:45.826994 INFO::Found NA in Reference column
2025-09-26 19:38:45.843145 INFO::Require at least two references per batch.
2025-09-26 19:38:45.873596 INFO::Formatting Data.
2025-09-26 19:38:45.874303 INFO::Recognized SummarizedExperiment
2025-09-26 19:38:45.874802 INFO::Typecasting input to dataframe.
2025-09-26 19:38:45.88713 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:45.888633 INFO::Removing potential empty rows and columns
2025-09-26 19:38:45.89372 INFO::Found 0 missing values.
2025-09-26 19:38:45.901981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:45.902761 INFO::Done
2025-09-26 19:38:45.922065 INFO::Formatting Data.
2025-09-26 19:38:45.923144 INFO::Recognized SummarizedExperiment
2025-09-26 19:38:45.923859 INFO::Typecasting input to dataframe.
2025-09-26 19:38:45.94693 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:45.948763 INFO::Removing potential empty rows and columns
2025-09-26 19:38:45.953714 INFO::Found 0 missing values.
2025-09-26 19:38:45.968875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:45.969952 INFO::Done
2025-09-26 19:38:45.992162 INFO::Formatting Data.
2025-09-26 19:38:45.993161 INFO::Recognized SummarizedExperiment
2025-09-26 19:38:45.993958 INFO::Typecasting input to dataframe.
2025-09-26 19:38:46.014527 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:46.015967 INFO::Removing potential empty rows and columns
2025-09-26 19:38:46.017542 INFO::Found 0 missing values.
2025-09-26 19:38:46.019048 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.
2025-09-26 19:38:46.025228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:46.026103 INFO::Done
2025-09-26 19:38:46.040069 INFO::Formatting Data.
2025-09-26 19:38:46.041188 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:46.042466 INFO::Removing potential empty rows and columns
2025-09-26 19:38:46.04344 INFO::Found 0 missing values.
2025-09-26 19:38:46.04705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:46.047878 INFO::Done
2025-09-26 19:38:46.066459 INFO::Formatting Data.
2025-09-26 19:38:46.067618 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:46.068906 INFO::Removing potential empty rows and columns
2025-09-26 19:38:46.070343 INFO::Found 0 missing values.
2025-09-26 19:38:46.073298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:46.0741 INFO::Done
2025-09-26 19:38:46.118278 INFO::Formatting Data.
2025-09-26 19:38:46.119473 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:46.121087 INFO::Removing potential empty rows and columns
2025-09-26 19:38:46.122839 INFO::Found 1 missing values.
2025-09-26 19:38:46.126949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:46.127865 INFO::Done
2025-09-26 19:38:46.157167 INFO::Formatting Data.
2025-09-26 19:38:46.158306 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:46.159276 INFO::Removing potential empty rows and columns
2025-09-26 19:38:46.160144 INFO::Found 2 missing values.
2025-09-26 19:38:46.160969 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.
2025-09-26 19:38:46.162972 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:46.163479 INFO::Done
2025-09-26 19:38:46.178904 INFO::Formatting Data.
2025-09-26 19:38:46.180053 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:46.181411 INFO::Removing potential empty rows and columns
2025-09-26 19:38:46.182365 INFO::Found 2 missing values.
2025-09-26 19:38:46.183781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:46.184275 INFO::Done
2025-09-26 19:38:46.199604 INFO::Formatting Data.
2025-09-26 19:38:46.200695 INFO::Typecasting input to dataframe.
2025-09-26 19:38:46.201919 INFO::Replacing NaNs with NAs.
2025-09-26 19:38:46.203181 INFO::Removing potential empty rows and columns
2025-09-26 19:38:46.204677 INFO::Found 0 missing values.
2025-09-26 19:38:46.209126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-26 19:38:46.20994 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.674 4.577 25.533
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.362 | 1.601 | 20.323 | |
| compute_asw | 0.028 | 0.001 | 0.030 | |
| count_existing | 0.016 | 0.001 | 0.017 | |
| generate_data_covariables | 0.014 | 0.000 | 0.014 | |
| generate_dataset | 0.015 | 0.001 | 0.015 | |