Yannis Schumann
| Snapshot Date: 2025-11-11 13:45 -0500 (Tue, 11 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-12 11:58 -0500 (Wed, 12 Nov 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" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-11-11 07:20:54 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 07:22:13 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 79.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 27.929 1.779 20.528
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-11-11 07:21:56.621625 INFO::Formatting Data.
2025-11-11 07:21:56.623486 INFO::Replacing NaNs with NAs.
2025-11-11 07:21:56.640594 INFO::Removing potential empty rows and columns
2025-11-11 07:21:57.35273 INFO::Found 0 missing values.
2025-11-11 07:21:57.357737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:21:57.358561 INFO::Done
2025-11-11 07:21:57.359408 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:21:57.375999 INFO::Starting hierarchical adjustment
2025-11-11 07:21:57.377255 INFO::Found 3 batches.
2025-11-11 07:21:57.378107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:21:57.379707 INFO::Using default BPPARAM
2025-11-11 07:21:57.38053 INFO::Processing subtree level 1
2025-11-11 07:21:57.539813 INFO::Adjusting the last 1 batches sequentially
2025-11-11 07:21:57.542527 INFO::Done
2025-11-11 07:21:57.5435 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:21:57.547602 INFO::ASW Batch was -0.02008749419616 prior to batch effect correction and is now -0.02008749419616 .
2025-11-11 07:21:57.549386 INFO::Total function execution time is 0.928561925888062 s and adjustment time is 0.165522575378418 s ( 17.83 )
2025-11-11 07:21:57.571488 INFO::Formatting Data.
2025-11-11 07:21:57.572563 INFO::Replacing NaNs with NAs.
2025-11-11 07:21:57.573945 INFO::Removing potential empty rows and columns
2025-11-11 07:21:57.575688 INFO::Found 0 missing values.
2025-11-11 07:21:57.57713 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.
2025-11-11 07:21:57.593415 INFO::Formatting Data.
2025-11-11 07:21:57.594502 INFO::Replacing NaNs with NAs.
2025-11-11 07:21:57.595849 INFO::Removing potential empty rows and columns
2025-11-11 07:21:57.597436 INFO::Found 0 missing values.
2025-11-11 07:21:57.598881 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.
2025-11-11 07:21:57.624141 INFO::Formatting Data.
2025-11-11 07:21:57.625305 INFO::Replacing NaNs with NAs.
2025-11-11 07:21:57.626676 INFO::Removing potential empty rows and columns
2025-11-11 07:21:57.628302 INFO::Found 0 missing values.
2025-11-11 07:21:57.629755 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.
2025-11-11 07:21:57.636824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:21:57.63782 INFO::Done
2025-11-11 07:21:57.638705 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:21:57.642742 INFO::Starting hierarchical adjustment
2025-11-11 07:21:57.644044 INFO::Found 2 batches.
2025-11-11 07:21:57.644913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:21:57.645902 INFO::Using default BPPARAM
2025-11-11 07:21:57.646778 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:21:57.648231 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 07:21:57.682384 INFO::Done
2025-11-11 07:21:57.683415 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:21:57.686703 INFO::ASW Batch was -0.0342552974140753 prior to batch effect correction and is now -0.111134477619657 .
2025-11-11 07:21:57.688007 INFO::Total function execution time is 0.0639421939849854 s and adjustment time is 0.0385642051696777 s ( 60.31 )
2025-11-11 07:21:57.692102 INFO::Formatting Data.
2025-11-11 07:21:57.693211 INFO::Replacing NaNs with NAs.
2025-11-11 07:21:57.706542 INFO::Formatting Data.
2025-11-11 07:21:57.707625 INFO::Replacing NaNs with NAs.
2025-11-11 07:21:57.709015 INFO::Removing potential empty rows and columns
2025-11-11 07:21:57.710793 INFO::Found 0 missing values.
2025-11-11 07:21:57.715542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:21:57.716511 INFO::Done
2025-11-11 07:21:57.717371 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:21:57.720396 INFO::Starting hierarchical adjustment
2025-11-11 07:21:57.721627 INFO::Found 2 batches.
2025-11-11 07:21:57.722455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:21:57.723507 INFO::Using default BPPARAM
2025-11-11 07:21:57.72447 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:21:57.726126 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 07:21:57.794565 INFO::Done
2025-11-11 07:21:57.795521 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:21:57.7984 INFO::ASW Batch was -0.0114907659310668 prior to batch effect correction and is now -0.110852222004658 .
2025-11-11 07:21:57.799591 INFO::Total function execution time is 0.0931160449981689 s and adjustment time is 0.0731644630432129 s ( 78.57 )
2025-11-11 07:21:57.801136 INFO::Formatting Data.
2025-11-11 07:21:57.802042 INFO::Replacing NaNs with NAs.
2025-11-11 07:21:57.803346 INFO::Removing potential empty rows and columns
2025-11-11 07:21:57.804895 INFO::Found 0 missing values.
2025-11-11 07:21:57.809249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:21:57.810152 INFO::Done
2025-11-11 07:21:57.811002 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:21:57.813895 INFO::Starting hierarchical adjustment
2025-11-11 07:21:57.815094 INFO::Found 2 batches.
2025-11-11 07:21:57.815904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:21:57.816857 INFO::Using default BPPARAM
2025-11-11 07:21:57.817673 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:21:57.819074 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 07:21:57.841249 INFO::Done
2025-11-11 07:21:57.842202 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:21:57.845216 INFO::ASW Batch was -0.0114907659310668 prior to batch effect correction and is now -0.110852222004658 .
2025-11-11 07:21:57.846412 INFO::Total function execution time is 0.0452620983123779 s and adjustment time is 0.0263712406158447 s ( 58.26 )
2025-11-11 07:22:01.754739 INFO::Formatting Data.
2025-11-11 07:22:01.755641 INFO::Recognized SummarizedExperiment
2025-11-11 07:22:01.756291 INFO::Typecasting input to dataframe.
2025-11-11 07:22:01.796865 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:01.798435 INFO::Removing potential empty rows and columns
2025-11-11 07:22:01.80371 INFO::Found 0 missing values.
2025-11-11 07:22:01.813968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:01.814938 INFO::Done
2025-11-11 07:22:01.815671 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:01.820883 INFO::Starting hierarchical adjustment
2025-11-11 07:22:01.821982 INFO::Found 2 batches.
2025-11-11 07:22:01.822759 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:01.824166 INFO::Using default BPPARAM
2025-11-11 07:22:01.824957 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:01.826303 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 07:22:01.905579 INFO::Done
2025-11-11 07:22:01.906515 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:01.91139 INFO::ASW Batch was -0.00701029148083244 prior to batch effect correction and is now -0.0965594987995954 .
2025-11-11 07:22:01.9126 INFO::Total function execution time is 0.158261775970459 s and adjustment time is 0.0837891101837158 s ( 52.94 )
2025-11-11 07:22:01.938207 INFO::Formatting Data.
2025-11-11 07:22:01.939196 INFO::Recognized SummarizedExperiment
2025-11-11 07:22:01.939928 INFO::Typecasting input to dataframe.
2025-11-11 07:22:01.952801 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:01.954333 INFO::Removing potential empty rows and columns
2025-11-11 07:22:01.959817 INFO::Found 0 missing values.
2025-11-11 07:22:01.970122 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:01.971076 INFO::Done
2025-11-11 07:22:01.971821 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:01.976777 INFO::Starting hierarchical adjustment
2025-11-11 07:22:01.977953 INFO::Found 2 batches.
2025-11-11 07:22:01.97878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:01.9796 INFO::Using default BPPARAM
2025-11-11 07:22:01.980338 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:01.981772 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 07:22:02.016716 INFO::Done
2025-11-11 07:22:02.01763 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:02.022399 INFO::ASW Batch was 0.00240042446731091 prior to batch effect correction and is now 0.00240042446731091 .
2025-11-11 07:22:02.023642 INFO::Total function execution time is 0.0854041576385498 s and adjustment time is 0.0389807224273682 s ( 45.64 )
2025-11-11 07:22:02.048702 INFO::Formatting Data.
2025-11-11 07:22:02.049708 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:02.050887 INFO::Removing potential empty rows and columns
2025-11-11 07:22:02.05226 INFO::Found 0 missing values.
2025-11-11 07:22:02.056477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:02.057363 INFO::Done
2025-11-11 07:22:02.058104 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:02.060897 INFO::Starting hierarchical adjustment
2025-11-11 07:22:02.062011 INFO::Found 3 batches.
2025-11-11 07:22:02.062819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:02.063653 INFO::Using default BPPARAM
2025-11-11 07:22:02.064391 INFO::Processing subtree level 1
2025-11-11 07:22:02.234943 INFO::Adjusting the last 1 batches sequentially
2025-11-11 07:22:02.237674 INFO::Done
2025-11-11 07:22:02.238669 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:02.242466 INFO::ASW Batch was -0.0408075066774755 prior to batch effect correction and is now -0.149808799824327 .
2025-11-11 07:22:02.243958 INFO::Total function execution time is 0.195262432098389 s and adjustment time is 0.17586612701416 s ( 90.07 )
2025-11-11 07:22:02.264815 INFO::Skipping initial DF formatting
2025-11-11 07:22:02.265793 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:02.271374 INFO::Starting hierarchical adjustment
2025-11-11 07:22:02.272552 INFO::Found 5 batches.
2025-11-11 07:22:02.273447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:02.274334 INFO::Using default BPPARAM
2025-11-11 07:22:02.275127 INFO::Processing subtree level 1
2025-11-11 07:22:02.563391 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:02.567945 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 07:22:02.602038 INFO::Done
2025-11-11 07:22:02.603038 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:02.610407 INFO::ASW Batch was 0.562230348987069 prior to batch effect correction and is now 0.562230348987069 .
2025-11-11 07:22:02.611453 INFO::ASW Label was 0.390247374160889 prior to batch effect correction and is now 0.390247374160889 .
2025-11-11 07:22:02.613226 INFO::Total function execution time is 0.348473787307739 s and adjustment time is 0.329696893692017 s ( 94.61 )
2025-11-11 07:22:02.7407 INFO::Formatting Data.
2025-11-11 07:22:02.741827 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:02.743243 INFO::Removing potential empty rows and columns
2025-11-11 07:22:02.744889 INFO::Found 0 missing values.
2025-11-11 07:22:02.751483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:02.752433 INFO::Done
2025-11-11 07:22:02.753316 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:02.757946 INFO::Starting hierarchical adjustment
2025-11-11 07:22:02.759261 INFO::Found 5 batches.
2025-11-11 07:22:02.760097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:02.761198 INFO::Using default BPPARAM
2025-11-11 07:22:02.762065 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.
2025-11-11 07:22:02.943911 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:02.946535 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 07:22:02.975506 INFO::Done
2025-11-11 07:22:02.97665 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:02.982582 INFO::ASW Batch was 0.478942538855865 prior to batch effect correction and is now -0.0984067402164602 .
2025-11-11 07:22:02.983673 INFO::ASW Label was 0.22327516067235 prior to batch effect correction and is now 0.865219861418739 .
2025-11-11 07:22:02.985078 INFO::Total function execution time is 0.244326114654541 s and adjustment time is 0.216490745544434 s ( 88.61 )
2025-11-11 07:22:02.986557 INFO::Formatting Data.
2025-11-11 07:22:02.987683 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:02.989392 INFO::Removing potential empty rows and columns
2025-11-11 07:22:02.991298 INFO::Found 0 missing values.
2025-11-11 07:22:02.99907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:03.000107 INFO::Done
2025-11-11 07:22:03.00109 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:03.006091 INFO::Starting hierarchical adjustment
2025-11-11 07:22:03.00749 INFO::Found 5 batches.
2025-11-11 07:22:03.008456 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:03.009658 INFO::Using default BPPARAM
2025-11-11 07:22:03.010717 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.
2025-11-11 07:22:03.173674 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:03.176183 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 07:22:03.202873 INFO::Done
2025-11-11 07:22:03.203961 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:03.209412 INFO::ASW Batch was 0.478942538855865 prior to batch effect correction and is now -0.0984067402164602 .
2025-11-11 07:22:03.210486 INFO::ASW Label was 0.22327516067235 prior to batch effect correction and is now 0.865219861418739 .
2025-11-11 07:22:03.211886 INFO::Total function execution time is 0.225296258926392 s and adjustment time is 0.195642232894897 s ( 86.84 )
2025-11-11 07:22:03.234819 INFO::Formatting Data.
2025-11-11 07:22:03.23603 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:03.23764 INFO::Removing potential empty rows and columns
2025-11-11 07:22:03.239386 INFO::Found 0 missing values.
2025-11-11 07:22:03.246898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:03.247905 INFO::Done
2025-11-11 07:22:03.248819 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:03.25385 INFO::Starting hierarchical adjustment
2025-11-11 07:22:03.255242 INFO::Found 5 batches.
2025-11-11 07:22:03.256226 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:03.257352 INFO::Using default BPPARAM
2025-11-11 07:22:03.258328 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.
2025-11-11 07:22:03.428555 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:03.431192 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 07:22:03.458557 INFO::Done
2025-11-11 07:22:03.459714 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:03.465522 INFO::ASW Batch was 0.561424639926917 prior to batch effect correction and is now 0.00130471221112732 .
2025-11-11 07:22:03.466704 INFO::ASW Label was 0.260107687976456 prior to batch effect correction and is now 0.710831214241766 .
2025-11-11 07:22:03.468212 INFO::Total function execution time is 0.233417272567749 s and adjustment time is 0.2035813331604 s ( 87.22 )
2025-11-11 07:22:03.469761 INFO::Formatting Data.
2025-11-11 07:22:03.470998 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:03.472597 INFO::Removing potential empty rows and columns
2025-11-11 07:22:03.474534 INFO::Found 0 missing values.
2025-11-11 07:22:03.482267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:03.483391 INFO::Done
2025-11-11 07:22:03.484397 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:03.489814 INFO::Starting hierarchical adjustment
2025-11-11 07:22:03.49132 INFO::Found 5 batches.
2025-11-11 07:22:03.492421 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:03.493639 INFO::Using default BPPARAM
2025-11-11 07:22:03.494724 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.
2025-11-11 07:22:03.655106 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:03.657854 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 07:22:03.686339 INFO::Done
2025-11-11 07:22:03.687622 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:03.693661 INFO::ASW Batch was 0.561424639926917 prior to batch effect correction and is now 0.00130471221112732 .
2025-11-11 07:22:03.695111 INFO::ASW Label was 0.260107687976456 prior to batch effect correction and is now 0.710831214241766 .
2025-11-11 07:22:03.696818 INFO::Total function execution time is 0.227007627487183 s and adjustment time is 0.195317029953003 s ( 86.04 )
2025-11-11 07:22:03.720454 INFO::Formatting Data.
2025-11-11 07:22:03.721675 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:03.723179 INFO::Removing potential empty rows and columns
2025-11-11 07:22:03.724878 INFO::Found 0 missing values.
2025-11-11 07:22:03.729672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:03.730666 INFO::Done
2025-11-11 07:22:03.731547 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:03.736288 INFO::Starting hierarchical adjustment
2025-11-11 07:22:03.737596 INFO::Found 2 batches.
2025-11-11 07:22:03.738521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:03.739582 INFO::Using default BPPARAM
2025-11-11 07:22:03.740447 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:03.741982 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 07:22:03.764912 INFO::Done
2025-11-11 07:22:03.765879 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:03.770361 INFO::ASW Batch was 0.740376037724836 prior to batch effect correction and is now 0.0345258751700435 .
2025-11-11 07:22:03.771403 INFO::ASW Label was 0.318200321451196 prior to batch effect correction and is now 0.836530052936142 .
2025-11-11 07:22:03.772612 INFO::Total function execution time is 0.0522282123565674 s and adjustment time is 0.027543306350708 s ( 52.74 )
2025-11-11 07:22:03.773891 INFO::Formatting Data.
2025-11-11 07:22:03.774906 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:03.776269 INFO::Removing potential empty rows and columns
2025-11-11 07:22:03.77788 INFO::Found 0 missing values.
2025-11-11 07:22:03.782269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:03.783235 INFO::Done
2025-11-11 07:22:03.784066 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:03.788532 INFO::Starting hierarchical adjustment
2025-11-11 07:22:03.789763 INFO::Found 2 batches.
2025-11-11 07:22:03.790665 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:03.79165 INFO::Using default BPPARAM
2025-11-11 07:22:03.792505 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:03.794015 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-11 07:22:03.816609 INFO::Done
2025-11-11 07:22:03.817601 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:03.822069 INFO::ASW Batch was 0.740376037724836 prior to batch effect correction and is now 0.0345258751700435 .
2025-11-11 07:22:03.823082 INFO::ASW Label was 0.318200321451196 prior to batch effect correction and is now 0.836530052936142 .
2025-11-11 07:22:03.824259 INFO::Total function execution time is 0.0503768920898438 s and adjustment time is 0.0270605087280273 s ( 53.72 )
2025-11-11 07:22:03.841795 INFO::Formatting Data.
2025-11-11 07:22:03.842925 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:03.844273 INFO::Removing potential empty rows and columns
2025-11-11 07:22:03.845754 INFO::Found 0 missing values.
2025-11-11 07:22:03.849198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:03.850134 INFO::Done
2025-11-11 07:22:03.85102 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:03.853965 INFO::Starting hierarchical adjustment
2025-11-11 07:22:03.855215 INFO::Found 2 batches.
2025-11-11 07:22:03.856055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:03.856999 INFO::Using default BPPARAM
2025-11-11 07:22:03.857831 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:03.859271 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 07:22:03.908737 INFO::Done
2025-11-11 07:22:03.909832 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:03.913006 INFO::ASW Batch was -0.0063707886419288 prior to batch effect correction and is now -0.120252719629792 .
2025-11-11 07:22:03.914432 INFO::Total function execution time is 0.0726604461669922 s and adjustment time is 0.05373215675354 s ( 73.95 )
2025-11-11 07:22:03.933932 INFO::Formatting Data.
2025-11-11 07:22:03.935174 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:03.936666 INFO::Removing potential empty rows and columns
2025-11-11 07:22:03.938448 INFO::Found 0 missing values.
2025-11-11 07:22:03.940437 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.
2025-11-11 07:22:03.955782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:03.956996 INFO::Done
2025-11-11 07:22:03.958026 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:03.963375 INFO::Starting hierarchical adjustment
2025-11-11 07:22:03.964792 INFO::Found 2 batches.
2025-11-11 07:22:03.965852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:03.967017 INFO::Using default BPPARAM
2025-11-11 07:22:03.968048 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:03.969818 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 07:22:03.999736 INFO::Done
2025-11-11 07:22:04.000957 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:04.006325 INFO::ASW Batch was 0.543666511107274 prior to batch effect correction and is now 0.0733498031018025 .
2025-11-11 07:22:04.007559 INFO::ASW Label was 0.580627932889505 prior to batch effect correction and is now 0.881902303431822 .
2025-11-11 07:22:04.009038 INFO::Total function execution time is 0.0751094818115234 s and adjustment time is 0.0352137088775635 s ( 46.88 )
2025-11-11 07:22:04.010521 INFO::Formatting Data.
2025-11-11 07:22:04.01178 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:04.013588 INFO::Removing potential empty rows and columns
2025-11-11 07:22:04.015597 INFO::Found 0 missing values.
2025-11-11 07:22:04.017434 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.
2025-11-11 07:22:04.026288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:04.027474 INFO::Done
2025-11-11 07:22:04.028575 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:04.033969 INFO::Starting hierarchical adjustment
2025-11-11 07:22:04.035513 INFO::Found 2 batches.
2025-11-11 07:22:04.036588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:04.03781 INFO::Using default BPPARAM
2025-11-11 07:22:04.03887 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:04.040672 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 07:22:04.069113 INFO::Done
2025-11-11 07:22:04.0701 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:04.074532 INFO::ASW Batch was 0.543666511107274 prior to batch effect correction and is now 0.0733498031018025 .
2025-11-11 07:22:04.07555 INFO::ASW Label was 0.580627932889505 prior to batch effect correction and is now 0.881902303431822 .
2025-11-11 07:22:04.076808 INFO::Total function execution time is 0.0663337707519531 s and adjustment time is 0.0339324474334717 s ( 51.15 )
2025-11-11 07:22:04.423484 INFO::Formatting Data.
2025-11-11 07:22:04.42455 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:04.425881 INFO::Removing potential empty rows and columns
2025-11-11 07:22:04.42753 INFO::Found 0 missing values.
2025-11-11 07:22:04.432348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:04.433533 INFO::Done
2025-11-11 07:22:04.434355 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:04.437772 INFO::Starting hierarchical adjustment
2025-11-11 07:22:04.439018 INFO::Found 3 batches.
2025-11-11 07:22:04.439799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:04.440722 INFO::Using default BPPARAM
2025-11-11 07:22:04.441559 INFO::Processing subtree level 1
2025-11-11 07:22:04.55029 INFO::Adjusting the last 1 batches sequentially
2025-11-11 07:22:04.552949 INFO::Done
2025-11-11 07:22:04.55388 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:04.557601 INFO::ASW Batch was -0.0752397472272318 prior to batch effect correction and is now -0.0752397472272318 .
2025-11-11 07:22:04.55901 INFO::Total function execution time is 0.135555267333984 s and adjustment time is 0.114251852035522 s ( 84.28 )
2025-11-11 07:22:04.560615 INFO::Formatting Data.
2025-11-11 07:22:04.561625 INFO::Typecasting input to dataframe.
2025-11-11 07:22:04.562799 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:04.564165 INFO::Removing potential empty rows and columns
2025-11-11 07:22:04.566043 INFO::Found 0 missing values.
2025-11-11 07:22:04.57105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:04.572046 INFO::Done
2025-11-11 07:22:04.572876 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:04.576174 INFO::Starting hierarchical adjustment
2025-11-11 07:22:04.577412 INFO::Found 3 batches.
2025-11-11 07:22:04.578248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:04.579259 INFO::Using default BPPARAM
2025-11-11 07:22:04.58008 INFO::Processing subtree level 1
2025-11-11 07:22:04.69086 INFO::Adjusting the last 1 batches sequentially
2025-11-11 07:22:04.693633 INFO::Done
2025-11-11 07:22:04.694579 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:04.698394 INFO::ASW Batch was -0.0752397472272318 prior to batch effect correction and is now -0.0752397472272318 .
2025-11-11 07:22:04.699985 INFO::Total function execution time is 0.139262199401855 s and adjustment time is 0.116464853286743 s ( 83.63 )
2025-11-11 07:22:04.721005 INFO::Formatting Data.
2025-11-11 07:22:04.722288 INFO::Typecasting input to dataframe.
2025-11-11 07:22:04.723683 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:04.725085 INFO::Removing potential empty rows and columns
2025-11-11 07:22:04.726851 INFO::Found 0 missing values.
2025-11-11 07:22:04.73158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:04.732516 INFO::Done
2025-11-11 07:22:04.733388 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:04.736385 INFO::Starting hierarchical adjustment
2025-11-11 07:22:04.737563 INFO::Found 3 batches.
2025-11-11 07:22:04.738373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:04.739338 INFO::Using default BPPARAM
2025-11-11 07:22:04.740137 INFO::Processing subtree level 1
2025-11-11 07:22:04.847501 INFO::Adjusting the last 1 batches sequentially
2025-11-11 07:22:04.850098 INFO::Done
2025-11-11 07:22:04.851087 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:04.854792 INFO::ASW Batch was -0.0973359193609679 prior to batch effect correction and is now -0.0973359193609679 .
2025-11-11 07:22:04.856244 INFO::Total function execution time is 0.135299921035767 s and adjustment time is 0.112736225128174 s ( 83.32 )
2025-11-11 07:22:05.037658 INFO::Formatting Data.
2025-11-11 07:22:05.038793 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:05.040294 INFO::Removing potential empty rows and columns
2025-11-11 07:22:05.0444 INFO::Found 1000 missing values.
2025-11-11 07:22:05.083896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:05.085875 INFO::Done
2025-11-11 07:22:05.086812 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:05.09633 INFO::Starting hierarchical adjustment
2025-11-11 07:22:05.097692 INFO::Found 10 batches.
2025-11-11 07:22:05.098494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:05.099631 INFO::Using default BPPARAM
2025-11-11 07:22:05.100431 INFO::Processing subtree level 1
2025-11-11 07:22:05.272534 INFO::Processing subtree level 2
2025-11-11 07:22:05.457133 INFO::Adjusting the last 1 batches sequentially
2025-11-11 07:22:05.460008 INFO::Done
2025-11-11 07:22:05.461017 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:05.46939 INFO::ASW Batch was 0.54105055524297 prior to batch effect correction and is now 0.54105055524297 .
2025-11-11 07:22:05.470446 INFO::ASW Label was 0.302697702660332 prior to batch effect correction and is now 0.302697702660332 .
2025-11-11 07:22:05.471931 INFO::Total function execution time is 0.434325218200684 s and adjustment time is 0.362583875656128 s ( 83.48 )
2025-11-11 07:22:05.473365 INFO::Formatting Data.
2025-11-11 07:22:05.474286 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:05.476173 INFO::Removing potential empty rows and columns
2025-11-11 07:22:05.480608 INFO::Found 1000 missing values.
2025-11-11 07:22:05.510755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:05.511804 INFO::Done
2025-11-11 07:22:05.512649 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:05.52029 INFO::Starting hierarchical adjustment
2025-11-11 07:22:05.521492 INFO::Found 10 batches.
2025-11-11 07:22:06.721052 INFO::Set up parallel execution backend with 2 workers
2025-11-11 07:22:06.723516 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-11 07:22:08.060177 INFO::Adjusting the last 2 batches sequentially
2025-11-11 07:22:08.062811 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-11 07:22:08.089173 INFO::Done
2025-11-11 07:22:08.090034 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:08.097125 INFO::ASW Batch was 0.54105055524297 prior to batch effect correction and is now 0.54105055524297 .
2025-11-11 07:22:08.098022 INFO::ASW Label was 0.302697702660332 prior to batch effect correction and is now 0.302697702660332 .
2025-11-11 07:22:08.099163 INFO::Total function execution time is 2.62583065032959 s and adjustment time is 2.56789898872375 s ( 97.79 )
2025-11-11 07:22:08.289304 INFO::Formatting Data.
2025-11-11 07:22:08.29045 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:08.29187 INFO::Removing potential empty rows and columns
2025-11-11 07:22:08.293541 INFO::Found 0 missing values.
2025-11-11 07:22:08.299527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:08.300363 INFO::Done
2025-11-11 07:22:08.30124 INFO::Acquiring quality metrics before batch effect correction.
2025-11-11 07:22:08.305334 INFO::Starting hierarchical adjustment
2025-11-11 07:22:08.306428 INFO::Found 3 batches.
2025-11-11 07:22:08.307279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-11 07:22:08.308261 INFO::Using default BPPARAM
2025-11-11 07:22:08.309125 INFO::Processing subtree level 1
2025-11-11 07:22:08.444622 INFO::Adjusting the last 1 batches sequentially
2025-11-11 07:22:08.44728 INFO::Done
2025-11-11 07:22:08.448191 INFO::Acquiring quality metrics after batch effect correction.
2025-11-11 07:22:08.453035 INFO::ASW Batch was 0.169450233492928 prior to batch effect correction and is now -0.132721784278502 .
2025-11-11 07:22:08.454114 INFO::ASW Label was -0.201588490728389 prior to batch effect correction and is now -0.143314227496022 .
2025-11-11 07:22:08.455513 INFO::Total function execution time is 0.166293621063232 s and adjustment time is 0.141076803207397 s ( 84.84 )
2025-11-11 07:22:08.636093 INFO::Formatting Data.
2025-11-11 07:22:08.637225 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:08.638517 INFO::Removing potential empty rows and columns
2025-11-11 07:22:08.640122 INFO::Found 2 missing values.
2025-11-11 07:22:08.644564 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:08.645425 INFO::Done
2025-11-11 07:22:08.68675 INFO::Found NA in Reference column
2025-11-11 07:22:08.701436 INFO::Require at least two references per batch.
2025-11-11 07:22:08.735112 INFO::Formatting Data.
2025-11-11 07:22:08.736099 INFO::Recognized SummarizedExperiment
2025-11-11 07:22:08.737213 INFO::Typecasting input to dataframe.
2025-11-11 07:22:08.752694 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:08.754574 INFO::Removing potential empty rows and columns
2025-11-11 07:22:08.76897 INFO::Found 0 missing values.
2025-11-11 07:22:08.781139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:08.782187 INFO::Done
2025-11-11 07:22:08.806775 INFO::Formatting Data.
2025-11-11 07:22:08.807758 INFO::Recognized SummarizedExperiment
2025-11-11 07:22:08.808504 INFO::Typecasting input to dataframe.
2025-11-11 07:22:08.836879 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:08.838572 INFO::Removing potential empty rows and columns
2025-11-11 07:22:08.844366 INFO::Found 0 missing values.
2025-11-11 07:22:08.863265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:08.864181 INFO::Done
2025-11-11 07:22:08.888192 INFO::Formatting Data.
2025-11-11 07:22:08.889298 INFO::Recognized SummarizedExperiment
2025-11-11 07:22:08.89016 INFO::Typecasting input to dataframe.
2025-11-11 07:22:08.91694 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:08.918351 INFO::Removing potential empty rows and columns
2025-11-11 07:22:08.920054 INFO::Found 0 missing values.
2025-11-11 07:22:08.921474 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.
2025-11-11 07:22:08.928451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:08.929408 INFO::Done
2025-11-11 07:22:08.944989 INFO::Formatting Data.
2025-11-11 07:22:08.946104 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:08.94739 INFO::Removing potential empty rows and columns
2025-11-11 07:22:08.948916 INFO::Found 0 missing values.
2025-11-11 07:22:08.953571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:08.954433 INFO::Done
2025-11-11 07:22:08.971009 INFO::Formatting Data.
2025-11-11 07:22:08.972099 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:08.973436 INFO::Removing potential empty rows and columns
2025-11-11 07:22:08.975046 INFO::Found 0 missing values.
2025-11-11 07:22:08.979983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:08.980967 INFO::Done
2025-11-11 07:22:09.03039 INFO::Formatting Data.
2025-11-11 07:22:09.031571 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:09.033292 INFO::Removing potential empty rows and columns
2025-11-11 07:22:09.035172 INFO::Found 1 missing values.
2025-11-11 07:22:09.039741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:09.040862 INFO::Done
2025-11-11 07:22:09.072343 INFO::Formatting Data.
2025-11-11 07:22:09.073541 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:09.074796 INFO::Removing potential empty rows and columns
2025-11-11 07:22:09.076152 INFO::Found 2 missing values.
2025-11-11 07:22:09.077495 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.
2025-11-11 07:22:09.080974 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:09.08183 INFO::Done
2025-11-11 07:22:09.097775 INFO::Formatting Data.
2025-11-11 07:22:09.098879 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:09.100152 INFO::Removing potential empty rows and columns
2025-11-11 07:22:09.101661 INFO::Found 2 missing values.
2025-11-11 07:22:09.104083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:09.105109 INFO::Done
2025-11-11 07:22:09.1216 INFO::Formatting Data.
2025-11-11 07:22:09.122748 INFO::Typecasting input to dataframe.
2025-11-11 07:22:09.123998 INFO::Replacing NaNs with NAs.
2025-11-11 07:22:09.125287 INFO::Removing potential empty rows and columns
2025-11-11 07:22:09.12701 INFO::Found 0 missing values.
2025-11-11 07:22:09.131701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-11 07:22:09.132689 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.007 4.776 25.842
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.929 | 1.779 | 20.528 | |
| compute_asw | 0.034 | 0.000 | 0.034 | |
| count_existing | 0.017 | 0.000 | 0.017 | |
| generate_data_covariables | 0.016 | 0.000 | 0.016 | |
| generate_dataset | 0.012 | 0.004 | 0.015 | |