Yannis Schumann
| Snapshot Date: 2025-11-02 13:45 -0500 (Sun, 02 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 2025-11-03 12:02 -0500 (Mon, 03 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 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 | | ||||||||
| 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-11-02 21:38:29 -0500 (Sun, 02 Nov 2025) |
| EndedAt: 2025-11-02 21:39:59 -0500 (Sun, 02 Nov 2025) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 24.201 1.422 17.682
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
2025-11-02 21:39:21.521672 INFO::Formatting Data.
2025-11-02 21:39:21.523218 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:21.534794 INFO::Removing potential empty rows and columns
2025-11-02 21:39:21.780781 INFO::Found 0 missing values.
2025-11-02 21:39:21.784277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:21.784997 INFO::Done
2025-11-02 21:39:21.785581 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:21.809273 INFO::Starting hierarchical adjustment
2025-11-02 21:39:21.810532 INFO::Found 3 batches.
2025-11-02 21:39:21.811111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:21.812727 INFO::Using default BPPARAM
2025-11-02 21:39:21.813309 INFO::Processing subtree level 1
2025-11-02 21:39:21.923959 INFO::Adjusting the last 1 batches sequentially
2025-11-02 21:39:21.926835 INFO::Done
2025-11-02 21:39:21.928015 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:21.932172 INFO::ASW Batch was 0.117469648940226 prior to batch effect correction and is now 0.117469648940226 .
2025-11-02 21:39:21.934038 INFO::Total function execution time is 0.412914991378784 s and adjustment time is 0.116497039794922 s ( 28.21 )
2025-11-02 21:39:21.961566 INFO::Formatting Data.
2025-11-02 21:39:21.962938 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:21.964151 INFO::Removing potential empty rows and columns
2025-11-02 21:39:21.965426 INFO::Found 0 missing values.
2025-11-02 21:39:21.966522 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.
2025-11-02 21:39:21.979283 INFO::Formatting Data.
2025-11-02 21:39:21.980077 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:21.981067 INFO::Removing potential empty rows and columns
2025-11-02 21:39:21.982203 INFO::Found 0 missing values.
2025-11-02 21:39:21.983166 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.
2025-11-02 21:39:21.999546 INFO::Formatting Data.
2025-11-02 21:39:22.000401 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:22.001343 INFO::Removing potential empty rows and columns
2025-11-02 21:39:22.002409 INFO::Found 0 missing values.
2025-11-02 21:39:22.003349 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.
2025-11-02 21:39:22.007812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:22.008386 INFO::Done
2025-11-02 21:39:22.008909 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:22.011041 INFO::Starting hierarchical adjustment
2025-11-02 21:39:22.011771 INFO::Found 2 batches.
2025-11-02 21:39:22.012314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:22.012944 INFO::Using default BPPARAM
2025-11-02 21:39:22.013501 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:22.014468 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-02 21:39:22.039901 INFO::Done
2025-11-02 21:39:22.040712 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:22.043073 INFO::ASW Batch was 0.0584718004159191 prior to batch effect correction and is now -0.122089208619431 .
2025-11-02 21:39:22.044582 INFO::Total function execution time is 0.0450294017791748 s and adjustment time is 0.0282137393951416 s ( 62.66 )
2025-11-02 21:39:22.0479 INFO::Formatting Data.
2025-11-02 21:39:22.048593 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:22.057902 INFO::Formatting Data.
2025-11-02 21:39:22.058685 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:22.059611 INFO::Removing potential empty rows and columns
2025-11-02 21:39:22.060681 INFO::Found 0 missing values.
2025-11-02 21:39:22.06362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:22.064186 INFO::Done
2025-11-02 21:39:22.064702 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:22.066912 INFO::Starting hierarchical adjustment
2025-11-02 21:39:22.067647 INFO::Found 2 batches.
2025-11-02 21:39:22.068198 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:22.068885 INFO::Using default BPPARAM
2025-11-02 21:39:22.06955 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:22.070568 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-02 21:39:22.118873 INFO::Done
2025-11-02 21:39:22.119536 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:22.121493 INFO::ASW Batch was -0.0337757040096197 prior to batch effect correction and is now -0.101456892525564 .
2025-11-02 21:39:22.122262 INFO::Total function execution time is 0.0644278526306152 s and adjustment time is 0.0513532161712646 s ( 79.71 )
2025-11-02 21:39:22.123306 INFO::Formatting Data.
2025-11-02 21:39:22.123877 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:22.124698 INFO::Removing potential empty rows and columns
2025-11-02 21:39:22.12566 INFO::Found 0 missing values.
2025-11-02 21:39:22.128239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:22.128748 INFO::Done
2025-11-02 21:39:22.129238 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:22.131179 INFO::Starting hierarchical adjustment
2025-11-02 21:39:22.131828 INFO::Found 2 batches.
2025-11-02 21:39:22.132324 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:22.132864 INFO::Using default BPPARAM
2025-11-02 21:39:22.133348 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:22.134209 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-02 21:39:22.148515 INFO::Done
2025-11-02 21:39:22.149155 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:22.151098 INFO::ASW Batch was -0.0337757040096197 prior to batch effect correction and is now -0.101456892525564 .
2025-11-02 21:39:22.151839 INFO::Total function execution time is 0.0285384654998779 s and adjustment time is 0.0167911052703857 s ( 58.84 )
2025-11-02 21:39:25.185972 INFO::Formatting Data.
2025-11-02 21:39:25.186868 INFO::Recognized SummarizedExperiment
2025-11-02 21:39:25.187456 INFO::Typecasting input to dataframe.
2025-11-02 21:39:25.222556 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:25.223901 INFO::Removing potential empty rows and columns
2025-11-02 21:39:25.227741 INFO::Found 0 missing values.
2025-11-02 21:39:25.234849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:25.23552 INFO::Done
2025-11-02 21:39:25.236062 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:25.239733 INFO::Starting hierarchical adjustment
2025-11-02 21:39:25.240476 INFO::Found 2 batches.
2025-11-02 21:39:25.240989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:25.242113 INFO::Using default BPPARAM
2025-11-02 21:39:25.242655 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:25.243641 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-02 21:39:25.301278 INFO::Done
2025-11-02 21:39:25.301986 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:25.305532 INFO::ASW Batch was 0.00508903270519355 prior to batch effect correction and is now -0.105382651589453 .
2025-11-02 21:39:25.30637 INFO::Total function execution time is 0.120774269104004 s and adjustment time is 0.0609402656555176 s ( 50.46 )
2025-11-02 21:39:25.330675 INFO::Formatting Data.
2025-11-02 21:39:25.331473 INFO::Recognized SummarizedExperiment
2025-11-02 21:39:25.332019 INFO::Typecasting input to dataframe.
2025-11-02 21:39:25.341785 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:25.342964 INFO::Removing potential empty rows and columns
2025-11-02 21:39:25.346659 INFO::Found 0 missing values.
2025-11-02 21:39:25.353687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:25.354335 INFO::Done
2025-11-02 21:39:25.354863 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:25.358476 INFO::Starting hierarchical adjustment
2025-11-02 21:39:25.359285 INFO::Found 2 batches.
2025-11-02 21:39:25.359817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:25.360428 INFO::Using default BPPARAM
2025-11-02 21:39:25.360951 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:25.361931 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-02 21:39:25.38762 INFO::Done
2025-11-02 21:39:25.388385 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:25.392014 INFO::ASW Batch was 0.0251569910745279 prior to batch effect correction and is now 0.0251569910745279 .
2025-11-02 21:39:25.392915 INFO::Total function execution time is 0.0622212886810303 s and adjustment time is 0.0284769535064697 s ( 45.77 )
2025-11-02 21:39:25.411855 INFO::Formatting Data.
2025-11-02 21:39:25.412687 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:25.413613 INFO::Removing potential empty rows and columns
2025-11-02 21:39:25.414658 INFO::Found 0 missing values.
2025-11-02 21:39:25.417679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:25.418246 INFO::Done
2025-11-02 21:39:25.418769 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:25.42082 INFO::Starting hierarchical adjustment
2025-11-02 21:39:25.421538 INFO::Found 3 batches.
2025-11-02 21:39:25.422055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:25.422666 INFO::Using default BPPARAM
2025-11-02 21:39:25.423203 INFO::Processing subtree level 1
2025-11-02 21:39:25.556316 INFO::Adjusting the last 1 batches sequentially
2025-11-02 21:39:25.558286 INFO::Done
2025-11-02 21:39:25.558937 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:25.561368 INFO::ASW Batch was 0.0447207059398747 prior to batch effect correction and is now -0.169328594650998 .
2025-11-02 21:39:25.562263 INFO::Total function execution time is 0.150472640991211 s and adjustment time is 0.136887073516846 s ( 90.97 )
2025-11-02 21:39:25.576497 INFO::Skipping initial DF formatting
2025-11-02 21:39:25.577237 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:25.581156 INFO::Starting hierarchical adjustment
2025-11-02 21:39:25.581913 INFO::Found 5 batches.
2025-11-02 21:39:25.582481 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:25.583086 INFO::Using default BPPARAM
2025-11-02 21:39:25.583639 INFO::Processing subtree level 1
2025-11-02 21:39:25.809309 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:25.810897 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-02 21:39:25.83054 INFO::Done
2025-11-02 21:39:25.831265 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:25.886783 INFO::ASW Batch was 0.536802357545108 prior to batch effect correction and is now 0.536802357545108 .
2025-11-02 21:39:25.887505 INFO::ASW Label was 0.390998660593498 prior to batch effect correction and is now 0.390998660593498 .
2025-11-02 21:39:25.888353 INFO::Total function execution time is 0.311927556991577 s and adjustment time is 0.24874472618103 s ( 79.74 )
2025-11-02 21:39:25.905429 INFO::Formatting Data.
2025-11-02 21:39:25.906191 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:25.907111 INFO::Removing potential empty rows and columns
2025-11-02 21:39:25.908157 INFO::Found 0 missing values.
2025-11-02 21:39:25.91247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:25.913057 INFO::Done
2025-11-02 21:39:25.913657 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:25.91669 INFO::Starting hierarchical adjustment
2025-11-02 21:39:25.917457 INFO::Found 5 batches.
2025-11-02 21:39:25.917993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:25.91869 INFO::Using default BPPARAM
2025-11-02 21:39:25.919256 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.
2025-11-02 21:39:26.054738 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.056393 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-02 21:39:26.073699 INFO::Done
2025-11-02 21:39:26.074424 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.077841 INFO::ASW Batch was 0.708735918361607 prior to batch effect correction and is now -0.0874203041259703 .
2025-11-02 21:39:26.078485 INFO::ASW Label was 0.0493139071774081 prior to batch effect correction and is now 0.671163227049457 .
2025-11-02 21:39:26.07931 INFO::Total function execution time is 0.173944711685181 s and adjustment time is 0.156367540359497 s ( 89.89 )
2025-11-02 21:39:26.080215 INFO::Formatting Data.
2025-11-02 21:39:26.080858 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.08176 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.082869 INFO::Found 0 missing values.
2025-11-02 21:39:26.087061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.087631 INFO::Done
2025-11-02 21:39:26.088178 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.091245 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.091965 INFO::Found 5 batches.
2025-11-02 21:39:26.092496 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.093103 INFO::Using default BPPARAM
2025-11-02 21:39:26.09364 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.
2025-11-02 21:39:26.212692 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.21424 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-02 21:39:26.230921 INFO::Done
2025-11-02 21:39:26.231671 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.235109 INFO::ASW Batch was 0.708735918361607 prior to batch effect correction and is now -0.0874203041259703 .
2025-11-02 21:39:26.235754 INFO::ASW Label was 0.0493139071774081 prior to batch effect correction and is now 0.671163227049457 .
2025-11-02 21:39:26.236653 INFO::Total function execution time is 0.156433820724487 s and adjustment time is 0.139074802398682 s ( 88.9 )
2025-11-02 21:39:26.251053 INFO::Formatting Data.
2025-11-02 21:39:26.251885 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.25279 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.253819 INFO::Found 0 missing values.
2025-11-02 21:39:26.25786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.258405 INFO::Done
2025-11-02 21:39:26.258925 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.261998 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.262713 INFO::Found 5 batches.
2025-11-02 21:39:26.263279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.263926 INFO::Using default BPPARAM
2025-11-02 21:39:26.264507 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.
2025-11-02 21:39:26.384077 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.385717 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-02 21:39:26.401203 INFO::Done
2025-11-02 21:39:26.401884 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.405005 INFO::ASW Batch was 0.162248658939792 prior to batch effect correction and is now -0.088971110350945 .
2025-11-02 21:39:26.405586 INFO::ASW Label was 0.649271366690916 prior to batch effect correction and is now 0.84608913851138 .
2025-11-02 21:39:26.406381 INFO::Total function execution time is 0.155410289764404 s and adjustment time is 0.138604402542114 s ( 89.19 )
2025-11-02 21:39:26.407202 INFO::Formatting Data.
2025-11-02 21:39:26.407824 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.40868 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.40966 INFO::Found 0 missing values.
2025-11-02 21:39:26.413587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.414142 INFO::Done
2025-11-02 21:39:26.414653 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.417572 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.418251 INFO::Found 5 batches.
2025-11-02 21:39:26.418762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.41938 INFO::Using default BPPARAM
2025-11-02 21:39:26.419891 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.
2025-11-02 21:39:26.54028 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.542005 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-02 21:39:26.559592 INFO::Done
2025-11-02 21:39:26.560375 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.563908 INFO::ASW Batch was 0.162248658939792 prior to batch effect correction and is now -0.088971110350945 .
2025-11-02 21:39:26.564597 INFO::ASW Label was 0.649271366690916 prior to batch effect correction and is now 0.84608913851138 .
2025-11-02 21:39:26.565489 INFO::Total function execution time is 0.158279895782471 s and adjustment time is 0.14144229888916 s ( 89.36 )
2025-11-02 21:39:26.580175 INFO::Formatting Data.
2025-11-02 21:39:26.581025 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.582016 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.583129 INFO::Found 0 missing values.
2025-11-02 21:39:26.586003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.586568 INFO::Done
2025-11-02 21:39:26.58709 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.590182 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.590933 INFO::Found 2 batches.
2025-11-02 21:39:26.59149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.592128 INFO::Using default BPPARAM
2025-11-02 21:39:26.592675 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.593631 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-02 21:39:26.608863 INFO::Done
2025-11-02 21:39:26.609526 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.612569 INFO::ASW Batch was 0.5452382366639 prior to batch effect correction and is now 0.0260683606718595 .
2025-11-02 21:39:26.613173 INFO::ASW Label was 0.529226163262298 prior to batch effect correction and is now 0.88811621588321 .
2025-11-02 21:39:26.613969 INFO::Total function execution time is 0.0339052677154541 s and adjustment time is 0.0180785655975342 s ( 53.32 )
2025-11-02 21:39:26.614772 INFO::Formatting Data.
2025-11-02 21:39:26.615411 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.616288 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.617287 INFO::Found 0 missing values.
2025-11-02 21:39:26.619988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.620548 INFO::Done
2025-11-02 21:39:26.621054 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.623963 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.624663 INFO::Found 2 batches.
2025-11-02 21:39:26.625209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.625816 INFO::Using default BPPARAM
2025-11-02 21:39:26.626344 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.627238 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-02 21:39:26.642071 INFO::Done
2025-11-02 21:39:26.642732 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.645652 INFO::ASW Batch was 0.5452382366639 prior to batch effect correction and is now 0.0260683606718595 .
2025-11-02 21:39:26.646243 INFO::ASW Label was 0.529226163262298 prior to batch effect correction and is now 0.88811621588321 .
2025-11-02 21:39:26.647008 INFO::Total function execution time is 0.0322659015655518 s and adjustment time is 0.0175356864929199 s ( 54.35 )
2025-11-02 21:39:26.658032 INFO::Formatting Data.
2025-11-02 21:39:26.658772 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.659727 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.660641 INFO::Found 0 missing values.
2025-11-02 21:39:26.662733 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.663272 INFO::Done
2025-11-02 21:39:26.663782 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.665741 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.666451 INFO::Found 2 batches.
2025-11-02 21:39:26.666975 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.667583 INFO::Using default BPPARAM
2025-11-02 21:39:26.668106 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.668999 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-02 21:39:26.699057 INFO::Done
2025-11-02 21:39:26.699744 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.701679 INFO::ASW Batch was 0.0407962406173673 prior to batch effect correction and is now -0.10769526351175 .
2025-11-02 21:39:26.702461 INFO::Total function execution time is 0.0444958209991455 s and adjustment time is 0.0327250957489014 s ( 73.55 )
2025-11-02 21:39:26.713814 INFO::Formatting Data.
2025-11-02 21:39:26.714538 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.715389 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.716353 INFO::Found 0 missing values.
2025-11-02 21:39:26.717448 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.
2025-11-02 21:39:26.72178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.722323 INFO::Done
2025-11-02 21:39:26.722815 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.725696 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.7264 INFO::Found 2 batches.
2025-11-02 21:39:26.726909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.727517 INFO::Using default BPPARAM
2025-11-02 21:39:26.728018 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.728932 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-02 21:39:26.744874 INFO::Done
2025-11-02 21:39:26.745528 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.74837 INFO::ASW Batch was 0.412287233587824 prior to batch effect correction and is now 0.0229828738817948 .
2025-11-02 21:39:26.748924 INFO::ASW Label was 0.662758987233919 prior to batch effect correction and is now 0.90723925109368 .
2025-11-02 21:39:26.749662 INFO::Total function execution time is 0.0359199047088623 s and adjustment time is 0.0186014175415039 s ( 51.79 )
2025-11-02 21:39:26.750415 INFO::Formatting Data.
2025-11-02 21:39:26.751005 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.751884 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.752809 INFO::Found 0 missing values.
2025-11-02 21:39:26.753677 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.
2025-11-02 21:39:26.757912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.758447 INFO::Done
2025-11-02 21:39:26.758936 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.761704 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.762375 INFO::Found 2 batches.
2025-11-02 21:39:26.762876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.763467 INFO::Using default BPPARAM
2025-11-02 21:39:26.763955 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:26.764834 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-02 21:39:26.780331 INFO::Done
2025-11-02 21:39:26.780956 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:26.783738 INFO::ASW Batch was 0.412287233587824 prior to batch effect correction and is now 0.0229828738817948 .
2025-11-02 21:39:26.784318 INFO::ASW Label was 0.662758987233919 prior to batch effect correction and is now 0.90723925109368 .
2025-11-02 21:39:26.785061 INFO::Total function execution time is 0.03466796875 s and adjustment time is 0.018078088760376 s ( 52.15 )
2025-11-02 21:39:26.983911 INFO::Formatting Data.
2025-11-02 21:39:26.984752 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:26.985633 INFO::Removing potential empty rows and columns
2025-11-02 21:39:26.986646 INFO::Found 0 missing values.
2025-11-02 21:39:26.989603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:26.99015 INFO::Done
2025-11-02 21:39:26.990656 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:26.992622 INFO::Starting hierarchical adjustment
2025-11-02 21:39:26.993316 INFO::Found 3 batches.
2025-11-02 21:39:26.993825 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:26.994422 INFO::Using default BPPARAM
2025-11-02 21:39:26.994924 INFO::Processing subtree level 1
2025-11-02 21:39:27.079042 INFO::Adjusting the last 1 batches sequentially
2025-11-02 21:39:27.080797 INFO::Done
2025-11-02 21:39:27.081435 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:27.08383 INFO::ASW Batch was -0.0494183207459793 prior to batch effect correction and is now -0.0494183207459793 .
2025-11-02 21:39:27.084775 INFO::Total function execution time is 0.100898742675781 s and adjustment time is 0.0876092910766602 s ( 86.83 )
2025-11-02 21:39:27.085843 INFO::Formatting Data.
2025-11-02 21:39:27.086513 INFO::Typecasting input to dataframe.
2025-11-02 21:39:27.087256 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:27.08818 INFO::Removing potential empty rows and columns
2025-11-02 21:39:27.089253 INFO::Found 0 missing values.
2025-11-02 21:39:27.092316 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:27.092886 INFO::Done
2025-11-02 21:39:27.093426 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:27.095448 INFO::Starting hierarchical adjustment
2025-11-02 21:39:27.096155 INFO::Found 3 batches.
2025-11-02 21:39:27.096712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:27.097335 INFO::Using default BPPARAM
2025-11-02 21:39:27.097854 INFO::Processing subtree level 1
2025-11-02 21:39:27.181468 INFO::Adjusting the last 1 batches sequentially
2025-11-02 21:39:27.183334 INFO::Done
2025-11-02 21:39:27.184028 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:27.186599 INFO::ASW Batch was -0.0494183207459793 prior to batch effect correction and is now -0.0494183207459793 .
2025-11-02 21:39:27.187638 INFO::Total function execution time is 0.10177206993103 s and adjustment time is 0.0872945785522461 s ( 85.77 )
2025-11-02 21:39:27.200353 INFO::Formatting Data.
2025-11-02 21:39:27.20115 INFO::Typecasting input to dataframe.
2025-11-02 21:39:27.201998 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:27.202904 INFO::Removing potential empty rows and columns
2025-11-02 21:39:27.203965 INFO::Found 0 missing values.
2025-11-02 21:39:27.206959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:27.20751 INFO::Done
2025-11-02 21:39:27.208024 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:27.210043 INFO::Starting hierarchical adjustment
2025-11-02 21:39:27.21075 INFO::Found 3 batches.
2025-11-02 21:39:27.211287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:27.21191 INFO::Using default BPPARAM
2025-11-02 21:39:27.212446 INFO::Processing subtree level 1
2025-11-02 21:39:27.297197 INFO::Adjusting the last 1 batches sequentially
2025-11-02 21:39:27.299158 INFO::Done
2025-11-02 21:39:27.299829 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:27.302599 INFO::ASW Batch was -0.0162170438340186 prior to batch effect correction and is now -0.0162170438340186 .
2025-11-02 21:39:27.303569 INFO::Total function execution time is 0.103340625762939 s and adjustment time is 0.0885007381439209 s ( 85.64 )
2025-11-02 21:39:27.440193 INFO::Formatting Data.
2025-11-02 21:39:27.44098 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:27.442068 INFO::Removing potential empty rows and columns
2025-11-02 21:39:27.444908 INFO::Found 1000 missing values.
2025-11-02 21:39:27.463413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:27.464142 INFO::Done
2025-11-02 21:39:27.4647 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:27.470164 INFO::Starting hierarchical adjustment
2025-11-02 21:39:27.470951 INFO::Found 10 batches.
2025-11-02 21:39:27.47154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:27.472224 INFO::Using default BPPARAM
2025-11-02 21:39:27.472783 INFO::Processing subtree level 1
2025-11-02 21:39:27.627836 INFO::Processing subtree level 2
2025-11-02 21:39:27.762401 INFO::Adjusting the last 1 batches sequentially
2025-11-02 21:39:27.76432 INFO::Done
2025-11-02 21:39:27.764973 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:27.770403 INFO::ASW Batch was 0.545378432134573 prior to batch effect correction and is now 0.545378432134573 .
2025-11-02 21:39:27.771062 INFO::ASW Label was 0.319131886739126 prior to batch effect correction and is now 0.319131886739126 .
2025-11-02 21:39:27.771956 INFO::Total function execution time is 0.33183741569519 s and adjustment time is 0.293517351150513 s ( 88.45 )
2025-11-02 21:39:27.772844 INFO::Formatting Data.
2025-11-02 21:39:27.773506 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:27.774719 INFO::Removing potential empty rows and columns
2025-11-02 21:39:27.777501 INFO::Found 1000 missing values.
2025-11-02 21:39:27.796179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:27.796905 INFO::Done
2025-11-02 21:39:27.797463 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:27.80292 INFO::Starting hierarchical adjustment
2025-11-02 21:39:27.803678 INFO::Found 10 batches.
2025-11-02 21:39:28.753259 INFO::Set up parallel execution backend with 2 workers
2025-11-02 21:39:28.755059 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-02 21:39:29.820799 INFO::Adjusting the last 2 batches sequentially
2025-11-02 21:39:29.822552 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-02 21:39:29.838221 INFO::Done
2025-11-02 21:39:29.838835 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:29.84313 INFO::ASW Batch was 0.545378432134573 prior to batch effect correction and is now 0.545378432134573 .
2025-11-02 21:39:29.843652 INFO::ASW Label was 0.319131886739126 prior to batch effect correction and is now 0.319131886739126 .
2025-11-02 21:39:29.844352 INFO::Total function execution time is 2.07156085968018 s and adjustment time is 2.03467011451721 s ( 98.22 )
2025-11-02 21:39:29.997287 INFO::Formatting Data.
2025-11-02 21:39:29.998862 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.000469 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.002267 INFO::Found 0 missing values.
2025-11-02 21:39:30.00878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.009707 INFO::Done
2025-11-02 21:39:30.010578 INFO::Acquiring quality metrics before batch effect correction.
2025-11-02 21:39:30.016002 INFO::Starting hierarchical adjustment
2025-11-02 21:39:30.017166 INFO::Found 3 batches.
2025-11-02 21:39:30.018017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-02 21:39:30.019024 INFO::Using default BPPARAM
2025-11-02 21:39:30.01988 INFO::Processing subtree level 1
2025-11-02 21:39:30.15141 INFO::Adjusting the last 1 batches sequentially
2025-11-02 21:39:30.153661 INFO::Done
2025-11-02 21:39:30.154449 INFO::Acquiring quality metrics after batch effect correction.
2025-11-02 21:39:30.158754 INFO::ASW Batch was 0.209007755426816 prior to batch effect correction and is now -0.130747632670173 .
2025-11-02 21:39:30.159595 INFO::ASW Label was -0.201942102848094 prior to batch effect correction and is now -0.0602511844050414 .
2025-11-02 21:39:30.160743 INFO::Total function execution time is 0.163718938827515 s and adjustment time is 0.136755704879761 s ( 83.53 )
2025-11-02 21:39:30.286048 INFO::Formatting Data.
2025-11-02 21:39:30.286996 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.287878 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.288893 INFO::Found 2 missing values.
2025-11-02 21:39:30.291636 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.292156 INFO::Done
2025-11-02 21:39:30.31798 INFO::Found NA in Reference column
2025-11-02 21:39:30.327065 INFO::Require at least two references per batch.
2025-11-02 21:39:30.346805 INFO::Formatting Data.
2025-11-02 21:39:30.347595 INFO::Recognized SummarizedExperiment
2025-11-02 21:39:30.348099 INFO::Typecasting input to dataframe.
2025-11-02 21:39:30.35737 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.358603 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.361924 INFO::Found 0 missing values.
2025-11-02 21:39:30.368475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.369134 INFO::Done
2025-11-02 21:39:30.384966 INFO::Formatting Data.
2025-11-02 21:39:30.385834 INFO::Recognized SummarizedExperiment
2025-11-02 21:39:30.386411 INFO::Typecasting input to dataframe.
2025-11-02 21:39:30.404173 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.405467 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.408904 INFO::Found 0 missing values.
2025-11-02 21:39:30.419278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.41999 INFO::Done
2025-11-02 21:39:30.435194 INFO::Formatting Data.
2025-11-02 21:39:30.436033 INFO::Recognized SummarizedExperiment
2025-11-02 21:39:30.436569 INFO::Typecasting input to dataframe.
2025-11-02 21:39:30.452593 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.45365 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.45468 INFO::Found 0 missing values.
2025-11-02 21:39:30.455583 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.
2025-11-02 21:39:30.459706 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.460238 INFO::Done
2025-11-02 21:39:30.469692 INFO::Formatting Data.
2025-11-02 21:39:30.470536 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.471379 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.472339 INFO::Found 0 missing values.
2025-11-02 21:39:30.475022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.475541 INFO::Done
2025-11-02 21:39:30.48593 INFO::Formatting Data.
2025-11-02 21:39:30.486752 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.487594 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.488541 INFO::Found 0 missing values.
2025-11-02 21:39:30.491371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.491868 INFO::Done
2025-11-02 21:39:30.519374 INFO::Formatting Data.
2025-11-02 21:39:30.520227 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.52125 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.522368 INFO::Found 1 missing values.
2025-11-02 21:39:30.524898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.525489 INFO::Done
2025-11-02 21:39:30.543321 INFO::Formatting Data.
2025-11-02 21:39:30.544129 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.544953 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.545842 INFO::Found 2 missing values.
2025-11-02 21:39:30.546724 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.
2025-11-02 21:39:30.548869 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.549418 INFO::Done
2025-11-02 21:39:30.558547 INFO::Formatting Data.
2025-11-02 21:39:30.559291 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.56011 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.561088 INFO::Found 2 missing values.
2025-11-02 21:39:30.562643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.563162 INFO::Done
2025-11-02 21:39:30.572755 INFO::Formatting Data.
2025-11-02 21:39:30.57353 INFO::Typecasting input to dataframe.
2025-11-02 21:39:30.57431 INFO::Replacing NaNs with NAs.
2025-11-02 21:39:30.575107 INFO::Removing potential empty rows and columns
2025-11-02 21:39:30.576092 INFO::Found 0 missing values.
2025-11-02 21:39:30.578771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-02 21:39:30.57927 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.557 3.683 20.904
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.201 | 1.422 | 17.682 | |
| compute_asw | 0.023 | 0.001 | 0.024 | |
| count_existing | 0.012 | 0.001 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.000 | 0.011 | |