Yannis Schumann
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-21 11:38 -0500 (Fri, 21 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 167/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2025-11-20 19:37:14 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 19:38:46 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 92.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 28.095 1.596 20.381
* 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/4.6-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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")
2025-11-20 19:38:24.393369 INFO::Formatting Data.
2025-11-20 19:38:24.397808 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:24.412516 INFO::Removing potential empty rows and columns
2025-11-20 19:38:24.730669 INFO::Found 0 missing values.
2025-11-20 19:38:24.73523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:24.735963 INFO::Done
2025-11-20 19:38:24.736856 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:24.754626 INFO::Starting hierarchical adjustment
2025-11-20 19:38:24.755786 INFO::Found 3 batches.
2025-11-20 19:38:24.756649 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:24.758212 INFO::Using default BPPARAM
2025-11-20 19:38:24.758981 INFO::Processing subtree level 1
2025-11-20 19:38:24.93506 INFO::Adjusting the last 1 batches sequentially
2025-11-20 19:38:24.941072 INFO::Done
2025-11-20 19:38:24.942121 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:24.945922 INFO::ASW Batch was -0.0328958866603829 prior to batch effect correction and is now -0.0328958866603829 .
2025-11-20 19:38:24.94696 INFO::Total function execution time is 0.554715156555176 s and adjustment time is 0.185505151748657 s ( 33.44 )
2025-11-20 19:38:24.967988 INFO::Formatting Data.
2025-11-20 19:38:24.969194 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:24.970333 INFO::Removing potential empty rows and columns
2025-11-20 19:38:24.971497 INFO::Found 0 missing values.
2025-11-20 19:38:24.972451 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-20 19:38:24.987808 INFO::Formatting Data.
2025-11-20 19:38:24.98896 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:24.990315 INFO::Removing potential empty rows and columns
2025-11-20 19:38:24.991998 INFO::Found 0 missing values.
2025-11-20 19:38:24.993389 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-20 19:38:25.016766 INFO::Formatting Data.
2025-11-20 19:38:25.017614 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:25.018902 INFO::Removing potential empty rows and columns
2025-11-20 19:38:25.020327 INFO::Found 0 missing values.
2025-11-20 19:38:25.021362 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-20 19:38:25.02712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:25.027764 INFO::Done
2025-11-20 19:38:25.028305 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:25.03052 INFO::Starting hierarchical adjustment
2025-11-20 19:38:25.03126 INFO::Found 2 batches.
2025-11-20 19:38:25.03194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:25.032848 INFO::Using default BPPARAM
2025-11-20 19:38:25.033556 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:25.034835 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 19:38:25.061846 INFO::Done
2025-11-20 19:38:25.062553 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:25.065341 INFO::ASW Batch was 0.00970091722574334 prior to batch effect correction and is now -0.118933939290354 .
2025-11-20 19:38:25.066452 INFO::Total function execution time is 0.0496900081634521 s and adjustment time is 0.0307021141052246 s ( 61.79 )
2025-11-20 19:38:25.069835 INFO::Formatting Data.
2025-11-20 19:38:25.070792 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:25.080183 INFO::Formatting Data.
2025-11-20 19:38:25.081126 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:25.082355 INFO::Removing potential empty rows and columns
2025-11-20 19:38:25.083346 INFO::Found 0 missing values.
2025-11-20 19:38:25.086605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:25.087215 INFO::Done
2025-11-20 19:38:25.087868 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:25.091103 INFO::Starting hierarchical adjustment
2025-11-20 19:38:25.09305 INFO::Found 2 batches.
2025-11-20 19:38:25.093933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:25.094747 INFO::Using default BPPARAM
2025-11-20 19:38:25.095434 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:25.096674 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:25.149944 INFO::Done
2025-11-20 19:38:25.150937 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:25.153099 INFO::ASW Batch was 0.127618606228154 prior to batch effect correction and is now -0.116893223811194 .
2025-11-20 19:38:25.153872 INFO::Total function execution time is 0.0737731456756592 s and adjustment time is 0.0572619438171387 s ( 77.62 )
2025-11-20 19:38:25.154813 INFO::Formatting Data.
2025-11-20 19:38:25.15536 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:25.156141 INFO::Removing potential empty rows and columns
2025-11-20 19:38:25.157014 INFO::Found 0 missing values.
2025-11-20 19:38:25.160372 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:25.161126 INFO::Done
2025-11-20 19:38:25.161829 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:25.164297 INFO::Starting hierarchical adjustment
2025-11-20 19:38:25.16496 INFO::Found 2 batches.
2025-11-20 19:38:25.165688 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:25.166262 INFO::Using default BPPARAM
2025-11-20 19:38:25.166887 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:25.168112 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:25.18774 INFO::Done
2025-11-20 19:38:25.188489 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:25.190444 INFO::ASW Batch was 0.127618606228154 prior to batch effect correction and is now -0.116893223811194 .
2025-11-20 19:38:25.191329 INFO::Total function execution time is 0.0363650321960449 s and adjustment time is 0.0228800773620605 s ( 62.92 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-20 19:38:28.508675 INFO::Formatting Data.
2025-11-20 19:38:28.509702 INFO::Recognized SummarizedExperiment
2025-11-20 19:38:28.510275 INFO::Typecasting input to dataframe.
2025-11-20 19:38:28.549522 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:28.55064 INFO::Removing potential empty rows and columns
2025-11-20 19:38:28.553238 INFO::Found 0 missing values.
2025-11-20 19:38:28.56027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:28.560838 INFO::Done
2025-11-20 19:38:28.561282 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:28.564617 INFO::Starting hierarchical adjustment
2025-11-20 19:38:28.565385 INFO::Found 2 batches.
2025-11-20 19:38:28.565829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:28.566751 INFO::Using default BPPARAM
2025-11-20 19:38:28.567194 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:28.568027 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 19:38:28.618227 INFO::Done
2025-11-20 19:38:28.618956 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:28.622618 INFO::ASW Batch was 0.0263782304088582 prior to batch effect correction and is now -0.0880892270407305 .
2025-11-20 19:38:28.623431 INFO::Total function execution time is 0.115084886550903 s and adjustment time is 0.052872896194458 s ( 45.94 )
Warning: stack imbalance in '{', 73 then 74
2025-11-20 19:38:28.648728 INFO::Formatting Data.
2025-11-20 19:38:28.649836 INFO::Recognized SummarizedExperiment
2025-11-20 19:38:28.650681 INFO::Typecasting input to dataframe.
2025-11-20 19:38:28.66302 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:28.664507 INFO::Removing potential empty rows and columns
2025-11-20 19:38:28.66881 INFO::Found 0 missing values.
2025-11-20 19:38:28.676551 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:28.677247 INFO::Done
2025-11-20 19:38:28.677718 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:28.681267 INFO::Starting hierarchical adjustment
2025-11-20 19:38:28.682383 INFO::Found 2 batches.
2025-11-20 19:38:28.683324 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:28.684282 INFO::Using default BPPARAM
2025-11-20 19:38:28.685061 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:28.68641 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 19:38:28.718906 INFO::Done
2025-11-20 19:38:28.720061 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:28.725617 INFO::ASW Batch was 0.0124184918964968 prior to batch effect correction and is now 0.0124184918964968 .
2025-11-20 19:38:28.727136 INFO::Total function execution time is 0.0783529281616211 s and adjustment time is 0.0367369651794434 s ( 46.89 )
2025-11-20 19:38:28.75831 INFO::Formatting Data.
2025-11-20 19:38:28.75942 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:28.760389 INFO::Removing potential empty rows and columns
2025-11-20 19:38:28.761381 INFO::Found 0 missing values.
2025-11-20 19:38:28.764666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:28.76524 INFO::Done
2025-11-20 19:38:28.765746 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:28.767593 INFO::Starting hierarchical adjustment
2025-11-20 19:38:28.768515 INFO::Found 3 batches.
2025-11-20 19:38:28.769275 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:28.770133 INFO::Using default BPPARAM
2025-11-20 19:38:28.770851 INFO::Processing subtree level 1
2025-11-20 19:38:28.965211 INFO::Adjusting the last 1 batches sequentially
2025-11-20 19:38:28.973311 INFO::Done
2025-11-20 19:38:28.974032 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:28.979763 INFO::ASW Batch was -0.0905465936635253 prior to batch effect correction and is now -0.179074962269499 .
2025-11-20 19:38:28.981416 INFO::Total function execution time is 0.223201990127563 s and adjustment time is 0.205151796340942 s ( 91.91 )
2025-11-20 19:38:29.002146 INFO::Skipping initial DF formatting
2025-11-20 19:38:29.002872 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:29.007825 INFO::Starting hierarchical adjustment
2025-11-20 19:38:29.009335 INFO::Found 5 batches.
2025-11-20 19:38:29.010239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:29.011152 INFO::Using default BPPARAM
2025-11-20 19:38:29.011932 INFO::Processing subtree level 1
2025-11-20 19:38:29.156443 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:29.162889 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 19:38:29.185037 INFO::Done
2025-11-20 19:38:29.185803 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:29.192302 INFO::ASW Batch was 0.499786417704388 prior to batch effect correction and is now 0.499786417704388 .
2025-11-20 19:38:29.193028 INFO::ASW Label was 0.394770808277687 prior to batch effect correction and is now 0.394770808277687 .
2025-11-20 19:38:29.194801 INFO::Total function execution time is 0.192247152328491 s and adjustment time is 0.175980091094971 s ( 91.54 )
2025-11-20 19:38:29.222794 INFO::Formatting Data.
2025-11-20 19:38:29.223877 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:29.225504 INFO::Removing potential empty rows and columns
2025-11-20 19:38:29.226776 INFO::Found 0 missing values.
2025-11-20 19:38:29.231018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:29.231648 INFO::Done
2025-11-20 19:38:29.232149 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:29.23614 INFO::Starting hierarchical adjustment
2025-11-20 19:38:29.237211 INFO::Found 5 batches.
2025-11-20 19:38:29.237945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:29.238794 INFO::Using default BPPARAM
2025-11-20 19:38:29.239517 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:29.386823 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:29.394396 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:29.419032 INFO::Done
2025-11-20 19:38:29.419728 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:29.424812 INFO::ASW Batch was 0.259836844552542 prior to batch effect correction and is now -0.0596632170527395 .
2025-11-20 19:38:29.426104 INFO::ASW Label was 0.435449452053832 prior to batch effect correction and is now 0.797713726730643 .
2025-11-20 19:38:29.427282 INFO::Total function execution time is 0.204545021057129 s and adjustment time is 0.182037115097046 s ( 89 )
2025-11-20 19:38:29.428405 INFO::Formatting Data.
2025-11-20 19:38:29.429386 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:29.430397 INFO::Removing potential empty rows and columns
2025-11-20 19:38:29.431404 INFO::Found 0 missing values.
2025-11-20 19:38:29.435627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:29.436488 INFO::Done
2025-11-20 19:38:29.437587 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:29.44048 INFO::Starting hierarchical adjustment
2025-11-20 19:38:29.441669 INFO::Found 5 batches.
2025-11-20 19:38:29.442443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:29.443338 INFO::Using default BPPARAM
2025-11-20 19:38:29.444243 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:29.577366 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:29.586614 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:29.617687 INFO::Done
2025-11-20 19:38:29.618731 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:29.623486 INFO::ASW Batch was 0.259836844552542 prior to batch effect correction and is now -0.0596632170527395 .
2025-11-20 19:38:29.624416 INFO::ASW Label was 0.435449452053832 prior to batch effect correction and is now 0.797713726730643 .
2025-11-20 19:38:29.625624 INFO::Total function execution time is 0.197158098220825 s and adjustment time is 0.176202774047852 s ( 89.37 )
2025-11-20 19:38:29.649232 INFO::Formatting Data.
2025-11-20 19:38:29.650507 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:29.651893 INFO::Removing potential empty rows and columns
2025-11-20 19:38:29.653417 INFO::Found 0 missing values.
2025-11-20 19:38:29.658878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:29.660147 INFO::Done
2025-11-20 19:38:29.661046 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:29.66507 INFO::Starting hierarchical adjustment
2025-11-20 19:38:29.666268 INFO::Found 5 batches.
2025-11-20 19:38:29.667089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:29.667918 INFO::Using default BPPARAM
2025-11-20 19:38:29.668433 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:29.794768 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:29.810484 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:29.841164 INFO::Done
2025-11-20 19:38:29.8422 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:29.847169 INFO::ASW Batch was 0.397925299732997 prior to batch effect correction and is now 0.0448586839850523 .
2025-11-20 19:38:29.847827 INFO::ASW Label was 0.456647953397414 prior to batch effect correction and is now 0.722141137212947 .
2025-11-20 19:38:29.849829 INFO::Total function execution time is 0.200546979904175 s and adjustment time is 0.17509913444519 s ( 87.31 )
2025-11-20 19:38:29.851164 INFO::Formatting Data.
2025-11-20 19:38:29.85179 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:29.852687 INFO::Removing potential empty rows and columns
2025-11-20 19:38:29.853599 INFO::Found 0 missing values.
2025-11-20 19:38:29.859042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:29.860017 INFO::Done
2025-11-20 19:38:29.860838 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:29.864157 INFO::Starting hierarchical adjustment
2025-11-20 19:38:29.864839 INFO::Found 5 batches.
2025-11-20 19:38:29.865556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:29.866489 INFO::Using default BPPARAM
2025-11-20 19:38:29.867297 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:29.999554 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:30.013543 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:30.039064 INFO::Done
2025-11-20 19:38:30.039744 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:30.044132 INFO::ASW Batch was 0.397925299732997 prior to batch effect correction and is now 0.0448586839850523 .
2025-11-20 19:38:30.045105 INFO::ASW Label was 0.456647953397414 prior to batch effect correction and is now 0.722141137212947 .
2025-11-20 19:38:30.046719 INFO::Total function execution time is 0.195465087890625 s and adjustment time is 0.174338102340698 s ( 89.19 )
2025-11-20 19:38:30.069477 INFO::Formatting Data.
2025-11-20 19:38:30.070638 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:30.072034 INFO::Removing potential empty rows and columns
2025-11-20 19:38:30.073408 INFO::Found 0 missing values.
2025-11-20 19:38:30.077414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:30.078304 INFO::Done
2025-11-20 19:38:30.078967 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:30.081791 INFO::Starting hierarchical adjustment
2025-11-20 19:38:30.082491 INFO::Found 2 batches.
2025-11-20 19:38:30.082986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:30.083553 INFO::Using default BPPARAM
2025-11-20 19:38:30.084039 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:30.084925 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:30.105518 INFO::Done
2025-11-20 19:38:30.106215 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:30.109179 INFO::ASW Batch was 0.599430281181698 prior to batch effect correction and is now -0.0328813569929853 .
2025-11-20 19:38:30.110093 INFO::ASW Label was 0.492303423039474 prior to batch effect correction and is now 0.935843836928215 .
2025-11-20 19:38:30.111056 INFO::Total function execution time is 0.0417640209197998 s and adjustment time is 0.0231242179870605 s ( 55.37 )
2025-11-20 19:38:30.111805 INFO::Formatting Data.
2025-11-20 19:38:30.112389 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:30.113756 INFO::Removing potential empty rows and columns
2025-11-20 19:38:30.115052 INFO::Found 0 missing values.
2025-11-20 19:38:30.117518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:30.118056 INFO::Done
2025-11-20 19:38:30.118549 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:30.121609 INFO::Starting hierarchical adjustment
2025-11-20 19:38:30.122572 INFO::Found 2 batches.
2025-11-20 19:38:30.123129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:30.123702 INFO::Using default BPPARAM
2025-11-20 19:38:30.124193 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:30.125112 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-20 19:38:30.141246 INFO::Done
2025-11-20 19:38:30.142249 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:30.146119 INFO::ASW Batch was 0.599430281181698 prior to batch effect correction and is now -0.0328813569929853 .
2025-11-20 19:38:30.146729 INFO::ASW Label was 0.492303423039474 prior to batch effect correction and is now 0.935843836928215 .
2025-11-20 19:38:30.147468 INFO::Total function execution time is 0.0356810092926025 s and adjustment time is 0.0187530517578125 s ( 52.56 )
2025-11-20 19:38:30.164852 INFO::Formatting Data.
2025-11-20 19:38:30.165835 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:30.167297 INFO::Removing potential empty rows and columns
2025-11-20 19:38:30.168678 INFO::Found 0 missing values.
2025-11-20 19:38:30.17137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:30.17191 INFO::Done
2025-11-20 19:38:30.172395 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:30.17457 INFO::Starting hierarchical adjustment
2025-11-20 19:38:30.17522 INFO::Found 2 batches.
2025-11-20 19:38:30.176013 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:30.176887 INFO::Using default BPPARAM
2025-11-20 19:38:30.177838 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:30.179144 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 19:38:30.214337 INFO::Done
2025-11-20 19:38:30.215488 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:30.218482 INFO::ASW Batch was 0.139769463637889 prior to batch effect correction and is now -0.0676642459720252 .
2025-11-20 19:38:30.219631 INFO::Total function execution time is 0.0548160076141357 s and adjustment time is 0.0391960144042969 s ( 71.5 )
2025-11-20 19:38:30.240321 INFO::Formatting Data.
2025-11-20 19:38:30.241486 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:30.242873 INFO::Removing potential empty rows and columns
2025-11-20 19:38:30.244341 INFO::Found 0 missing values.
2025-11-20 19:38:30.24595 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-20 19:38:30.250902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:30.2518 INFO::Done
2025-11-20 19:38:30.252604 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:30.256141 INFO::Starting hierarchical adjustment
2025-11-20 19:38:30.256847 INFO::Found 2 batches.
2025-11-20 19:38:30.257335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:30.257887 INFO::Using default BPPARAM
2025-11-20 19:38:30.258353 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:30.259218 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 19:38:30.273537 INFO::Done
2025-11-20 19:38:30.274186 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:30.278067 INFO::ASW Batch was 0.481869621322734 prior to batch effect correction and is now 0.10625726729769 .
2025-11-20 19:38:30.279013 INFO::ASW Label was 0.635085240295057 prior to batch effect correction and is now 0.8914636732537 .
2025-11-20 19:38:30.280127 INFO::Total function execution time is 0.0399031639099121 s and adjustment time is 0.0168020725250244 s ( 42.11 )
2025-11-20 19:38:30.281256 INFO::Formatting Data.
2025-11-20 19:38:30.282154 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:30.283501 INFO::Removing potential empty rows and columns
2025-11-20 19:38:30.284934 INFO::Found 0 missing values.
2025-11-20 19:38:30.285999 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-20 19:38:30.290719 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:30.291277 INFO::Done
2025-11-20 19:38:30.291968 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:30.29459 INFO::Starting hierarchical adjustment
2025-11-20 19:38:30.295293 INFO::Found 2 batches.
2025-11-20 19:38:30.295805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:30.296351 INFO::Using default BPPARAM
2025-11-20 19:38:30.296845 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:30.297983 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 19:38:30.318895 INFO::Done
2025-11-20 19:38:30.319905 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:30.323708 INFO::ASW Batch was 0.481869621322734 prior to batch effect correction and is now 0.10625726729769 .
2025-11-20 19:38:30.324292 INFO::ASW Label was 0.635085240295057 prior to batch effect correction and is now 0.8914636732537 .
2025-11-20 19:38:30.325029 INFO::Total function execution time is 0.0438799858093262 s and adjustment time is 0.0236539840698242 s ( 53.91 )
2025-11-20 19:38:30.576328 INFO::Formatting Data.
2025-11-20 19:38:30.577504 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:30.578799 INFO::Removing potential empty rows and columns
2025-11-20 19:38:30.579879 INFO::Found 0 missing values.
2025-11-20 19:38:30.583274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:30.583961 INFO::Done
2025-11-20 19:38:30.584873 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:30.587585 INFO::Starting hierarchical adjustment
2025-11-20 19:38:30.588583 INFO::Found 3 batches.
2025-11-20 19:38:30.589307 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:30.590097 INFO::Using default BPPARAM
2025-11-20 19:38:30.590821 INFO::Processing subtree level 1
2025-11-20 19:38:30.708346 INFO::Adjusting the last 1 batches sequentially
2025-11-20 19:38:30.717897 INFO::Done
2025-11-20 19:38:30.721149 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:30.730218 INFO::ASW Batch was -0.102396095375962 prior to batch effect correction and is now -0.102396095375962 .
2025-11-20 19:38:30.732659 INFO::Total function execution time is 0.156213045120239 s and adjustment time is 0.129482984542847 s ( 82.89 )
2025-11-20 19:38:30.734694 INFO::Formatting Data.
2025-11-20 19:38:30.735951 INFO::Typecasting input to dataframe.
2025-11-20 19:38:30.737637 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:30.738816 INFO::Removing potential empty rows and columns
2025-11-20 19:38:30.740186 INFO::Found 0 missing values.
2025-11-20 19:38:30.743588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:30.744299 INFO::Done
2025-11-20 19:38:30.744836 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:30.746999 INFO::Starting hierarchical adjustment
2025-11-20 19:38:30.748033 INFO::Found 3 batches.
2025-11-20 19:38:30.748531 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:30.749612 INFO::Using default BPPARAM
2025-11-20 19:38:30.750351 INFO::Processing subtree level 1
2025-11-20 19:38:30.875018 INFO::Adjusting the last 1 batches sequentially
2025-11-20 19:38:30.880973 INFO::Done
2025-11-20 19:38:30.882368 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:30.889213 INFO::ASW Batch was -0.102396095375962 prior to batch effect correction and is now -0.102396095375962 .
2025-11-20 19:38:30.890466 INFO::Total function execution time is 0.155724048614502 s and adjustment time is 0.133031129837036 s ( 85.43 )
2025-11-20 19:38:30.916127 INFO::Formatting Data.
2025-11-20 19:38:30.916982 INFO::Typecasting input to dataframe.
2025-11-20 19:38:30.917803 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:30.91871 INFO::Removing potential empty rows and columns
2025-11-20 19:38:30.919707 INFO::Found 0 missing values.
2025-11-20 19:38:30.922355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:30.922865 INFO::Done
2025-11-20 19:38:30.923346 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:30.925137 INFO::Starting hierarchical adjustment
2025-11-20 19:38:30.92592 INFO::Found 3 batches.
2025-11-20 19:38:30.926419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:30.926994 INFO::Using default BPPARAM
2025-11-20 19:38:30.927493 INFO::Processing subtree level 1
2025-11-20 19:38:31.042269 INFO::Adjusting the last 1 batches sequentially
2025-11-20 19:38:31.050301 INFO::Done
2025-11-20 19:38:31.051593 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:31.060859 INFO::ASW Batch was 0.0359202955745056 prior to batch effect correction and is now 0.0359202955745056 .
2025-11-20 19:38:31.063998 INFO::Total function execution time is 0.147302865982056 s and adjustment time is 0.124563217163086 s ( 84.56 )
2025-11-20 19:38:31.269262 INFO::Formatting Data.
2025-11-20 19:38:31.270346 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:31.271618 INFO::Removing potential empty rows and columns
2025-11-20 19:38:31.275182 INFO::Found 1000 missing values.
2025-11-20 19:38:31.296176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:31.296888 INFO::Done
2025-11-20 19:38:31.297415 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:31.304253 INFO::Starting hierarchical adjustment
2025-11-20 19:38:31.305517 INFO::Found 10 batches.
2025-11-20 19:38:31.306413 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:31.307329 INFO::Using default BPPARAM
2025-11-20 19:38:31.308127 INFO::Processing subtree level 1
2025-11-20 19:38:31.458422 INFO::Processing subtree level 2
2025-11-20 19:38:31.836572 INFO::Adjusting the last 1 batches sequentially
2025-11-20 19:38:31.839652 INFO::Done
2025-11-20 19:38:31.84039 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:31.848712 INFO::ASW Batch was 0.48630782921437 prior to batch effect correction and is now 0.48630782921437 .
2025-11-20 19:38:31.850159 INFO::ASW Label was 0.32901828696066 prior to batch effect correction and is now 0.32901828696066 .
2025-11-20 19:38:31.852087 INFO::Total function execution time is 0.58276891708374 s and adjustment time is 0.53443717956543 s ( 91.71 )
2025-11-20 19:38:31.853695 INFO::Formatting Data.
2025-11-20 19:38:31.854962 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:31.856448 INFO::Removing potential empty rows and columns
2025-11-20 19:38:31.859815 INFO::Found 1000 missing values.
2025-11-20 19:38:31.998331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:31.999323 INFO::Done
2025-11-20 19:38:32.000043 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:32.006641 INFO::Starting hierarchical adjustment
2025-11-20 19:38:32.007738 INFO::Found 10 batches.
2025-11-20 19:38:33.505795 INFO::Set up parallel execution backend with 2 workers
2025-11-20 19:38:33.506465 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-20 19:38:34.877686 INFO::Adjusting the last 2 batches sequentially
2025-11-20 19:38:34.879649 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-20 19:38:34.896489 INFO::Done
2025-11-20 19:38:34.897156 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:34.901108 INFO::ASW Batch was 0.48630782921437 prior to batch effect correction and is now 0.48630782921437 .
2025-11-20 19:38:34.901742 INFO::ASW Label was 0.32901828696066 prior to batch effect correction and is now 0.32901828696066 .
2025-11-20 19:38:34.902794 INFO::Total function execution time is 3.04920983314514 s and adjustment time is 2.8889319896698 s ( 94.74 )
2025-11-20 19:38:35.136447 INFO::Formatting Data.
2025-11-20 19:38:35.137702 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.139031 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.141188 INFO::Found 0 missing values.
2025-11-20 19:38:35.146738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.148013 INFO::Done
2025-11-20 19:38:35.148549 INFO::Acquiring quality metrics before batch effect correction.
2025-11-20 19:38:35.151377 INFO::Starting hierarchical adjustment
2025-11-20 19:38:35.152125 INFO::Found 3 batches.
2025-11-20 19:38:35.152641 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-20 19:38:35.153214 INFO::Using default BPPARAM
2025-11-20 19:38:35.153714 INFO::Processing subtree level 1
2025-11-20 19:38:35.337085 INFO::Adjusting the last 1 batches sequentially
2025-11-20 19:38:35.344595 INFO::Done
2025-11-20 19:38:35.345996 INFO::Acquiring quality metrics after batch effect correction.
2025-11-20 19:38:35.354352 INFO::ASW Batch was 0.19596807532819 prior to batch effect correction and is now -0.120441911073211 .
2025-11-20 19:38:35.356365 INFO::ASW Label was -0.194522243123273 prior to batch effect correction and is now -0.0850925914181995 .
2025-11-20 19:38:35.358877 INFO::Total function execution time is 0.222413063049316 s and adjustment time is 0.192539930343628 s ( 86.57 )
2025-11-20 19:38:35.542517 INFO::Formatting Data.
2025-11-20 19:38:35.543655 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.544957 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.546458 INFO::Found 2 missing values.
2025-11-20 19:38:35.550657 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.55121 INFO::Done
2025-11-20 19:38:35.596508 INFO::Found NA in Reference column
2025-11-20 19:38:35.61337 INFO::Require at least two references per batch.
2025-11-20 19:38:35.644257 INFO::Formatting Data.
2025-11-20 19:38:35.645316 INFO::Recognized SummarizedExperiment
2025-11-20 19:38:35.646009 INFO::Typecasting input to dataframe.
2025-11-20 19:38:35.660244 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.661795 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.66659 INFO::Found 0 missing values.
2025-11-20 19:38:35.674874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.675988 INFO::Done
2025-11-20 19:38:35.698892 INFO::Formatting Data.
2025-11-20 19:38:35.699795 INFO::Recognized SummarizedExperiment
2025-11-20 19:38:35.700664 INFO::Typecasting input to dataframe.
2025-11-20 19:38:35.726306 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.728111 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.73339 INFO::Found 0 missing values.
2025-11-20 19:38:35.745092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.746073 INFO::Done
2025-11-20 19:38:35.767882 INFO::Formatting Data.
2025-11-20 19:38:35.768862 INFO::Recognized SummarizedExperiment
2025-11-20 19:38:35.769618 INFO::Typecasting input to dataframe.
2025-11-20 19:38:35.791172 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.792636 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.794223 INFO::Found 0 missing values.
2025-11-20 19:38:35.795141 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-20 19:38:35.800004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.800924 INFO::Done
2025-11-20 19:38:35.818306 INFO::Formatting Data.
2025-11-20 19:38:35.819079 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.819929 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.820854 INFO::Found 0 missing values.
2025-11-20 19:38:35.825212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.826066 INFO::Done
2025-11-20 19:38:35.84346 INFO::Formatting Data.
2025-11-20 19:38:35.844569 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.84591 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.847388 INFO::Found 0 missing values.
2025-11-20 19:38:35.851735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.852534 INFO::Done
2025-11-20 19:38:35.900477 INFO::Formatting Data.
2025-11-20 19:38:35.901776 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.903432 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.905278 INFO::Found 1 missing values.
2025-11-20 19:38:35.909012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.909831 INFO::Done
2025-11-20 19:38:35.941615 INFO::Formatting Data.
2025-11-20 19:38:35.942832 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.944112 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.945431 INFO::Found 2 missing values.
2025-11-20 19:38:35.946777 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-20 19:38:35.949975 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.950768 INFO::Done
2025-11-20 19:38:35.967195 INFO::Formatting Data.
2025-11-20 19:38:35.968514 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.969591 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.970719 INFO::Found 2 missing values.
2025-11-20 19:38:35.972632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:35.973529 INFO::Done
2025-11-20 19:38:35.991139 INFO::Formatting Data.
2025-11-20 19:38:35.992228 INFO::Typecasting input to dataframe.
2025-11-20 19:38:35.993419 INFO::Replacing NaNs with NAs.
2025-11-20 19:38:35.994428 INFO::Removing potential empty rows and columns
2025-11-20 19:38:35.995772 INFO::Found 0 missing values.
2025-11-20 19:38:35.999768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-20 19:38:36.000544 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.023 4.377 26.158
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.095 | 1.596 | 20.381 | |
| compute_asw | 0.023 | 0.002 | 0.025 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.013 | 0.001 | 0.015 | |