Yannis Schumann
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 163/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /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_1.5.0.tar.gz |
| StartedAt: 2025-08-29 20:36:35 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 20:38:05 -0400 (Fri, 29 Aug 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 23.535 1.081 16.849
* 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 ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "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")
2025-08-29 20:37:25.689262 INFO::Formatting Data.
2025-08-29 20:37:25.690611 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:25.701731 INFO::Removing potential empty rows and columns
2025-08-29 20:37:25.94293 INFO::Found 0 missing values.
2025-08-29 20:37:25.946484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:25.94714 INFO::Done
2025-08-29 20:37:25.947716 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:25.959505 INFO::Starting hierarchical adjustment
2025-08-29 20:37:25.960521 INFO::Found 3 batches.
2025-08-29 20:37:25.96113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:25.962418 INFO::Using default BPPARAM
2025-08-29 20:37:25.963016 INFO::Processing subtree level 1
2025-08-29 20:37:26.067782 INFO::Adjusting the last 1 batches sequentially
2025-08-29 20:37:26.070006 INFO::Done
2025-08-29 20:37:26.070849 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:26.07385 INFO::ASW Batch was -0.0846726828320728 prior to batch effect correction and is now -0.0846726828320728 .
2025-08-29 20:37:26.075119 INFO::Total function execution time is 0.386543750762939 s and adjustment time is 0.109703540802002 s ( 28.38 )
2025-08-29 20:37:26.090197 INFO::Formatting Data.
2025-08-29 20:37:26.091116 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:26.092247 INFO::Removing potential empty rows and columns
2025-08-29 20:37:26.093471 INFO::Found 0 missing values.
2025-08-29 20:37:26.094495 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.
2025-08-29 20:37:26.106454 INFO::Formatting Data.
2025-08-29 20:37:26.107286 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:26.108306 INFO::Removing potential empty rows and columns
2025-08-29 20:37:26.109433 INFO::Found 0 missing values.
2025-08-29 20:37:26.110445 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.
2025-08-29 20:37:26.127983 INFO::Formatting Data.
2025-08-29 20:37:26.128872 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:26.129846 INFO::Removing potential empty rows and columns
2025-08-29 20:37:26.130987 INFO::Found 0 missing values.
2025-08-29 20:37:26.132023 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.
2025-08-29 20:37:26.13666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:26.137235 INFO::Done
2025-08-29 20:37:26.137762 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:26.139927 INFO::Starting hierarchical adjustment
2025-08-29 20:37:26.140681 INFO::Found 2 batches.
2025-08-29 20:37:26.141235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:26.141885 INFO::Using default BPPARAM
2025-08-29 20:37:26.142451 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:26.143483 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 20:37:26.167193 INFO::Done
2025-08-29 20:37:26.168192 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:26.170449 INFO::ASW Batch was -0.0431281775460191 prior to batch effect correction and is now -0.122118355966071 .
2025-08-29 20:37:26.171316 INFO::Total function execution time is 0.043433666229248 s and adjustment time is 0.0266187191009521 s ( 61.29 )
2025-08-29 20:37:26.174248 INFO::Formatting Data.
2025-08-29 20:37:26.174915 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:26.183974 INFO::Formatting Data.
2025-08-29 20:37:26.184688 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:26.185626 INFO::Removing potential empty rows and columns
2025-08-29 20:37:26.186975 INFO::Found 0 missing values.
2025-08-29 20:37:26.190036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:26.190616 INFO::Done
2025-08-29 20:37:26.191149 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:26.193523 INFO::Starting hierarchical adjustment
2025-08-29 20:37:26.194284 INFO::Found 2 batches.
2025-08-29 20:37:26.194837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:26.195491 INFO::Using default BPPARAM
2025-08-29 20:37:26.196045 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:26.197045 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 20:37:26.248569 INFO::Done
2025-08-29 20:37:26.249474 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:26.25192 INFO::ASW Batch was 0.0236672949967539 prior to batch effect correction and is now -0.0802444293644051 .
2025-08-29 20:37:26.252865 INFO::Total function execution time is 0.0688884258270264 s and adjustment time is 0.0544109344482422 s ( 78.98 )
2025-08-29 20:37:26.254063 INFO::Formatting Data.
2025-08-29 20:37:26.254717 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:26.255673 INFO::Removing potential empty rows and columns
2025-08-29 20:37:26.256808 INFO::Found 0 missing values.
2025-08-29 20:37:26.259877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:26.260458 INFO::Done
2025-08-29 20:37:26.260992 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:26.26312 INFO::Starting hierarchical adjustment
2025-08-29 20:37:26.263854 INFO::Found 2 batches.
2025-08-29 20:37:26.264395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:26.265032 INFO::Using default BPPARAM
2025-08-29 20:37:26.265577 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:26.266561 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 20:37:26.282501 INFO::Done
2025-08-29 20:37:26.283191 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:26.285268 INFO::ASW Batch was 0.0236672949967539 prior to batch effect correction and is now -0.0802444293644051 .
2025-08-29 20:37:26.286063 INFO::Total function execution time is 0.032024621963501 s and adjustment time is 0.0187773704528809 s ( 58.63 )
2025-08-29 20:37:29.305443 INFO::Formatting Data.
2025-08-29 20:37:29.306232 INFO::Recognized SummarizedExperiment
2025-08-29 20:37:29.306742 INFO::Typecasting input to dataframe.
2025-08-29 20:37:29.337233 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:29.338506 INFO::Removing potential empty rows and columns
2025-08-29 20:37:29.342412 INFO::Found 0 missing values.
2025-08-29 20:37:29.349983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:29.350645 INFO::Done
2025-08-29 20:37:29.3512 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:29.354902 INFO::Starting hierarchical adjustment
2025-08-29 20:37:29.355644 INFO::Found 2 batches.
2025-08-29 20:37:29.356181 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:29.357288 INFO::Using default BPPARAM
2025-08-29 20:37:29.357833 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:29.358849 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 20:37:29.416944 INFO::Done
2025-08-29 20:37:29.417701 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:29.421458 INFO::ASW Batch was 0.00649680073093186 prior to batch effect correction and is now -0.0881695594234305 .
2025-08-29 20:37:29.422361 INFO::Total function execution time is 0.117214679718018 s and adjustment time is 0.0614111423492432 s ( 52.39 )
2025-08-29 20:37:29.441817 INFO::Formatting Data.
2025-08-29 20:37:29.442656 INFO::Recognized SummarizedExperiment
2025-08-29 20:37:29.443249 INFO::Typecasting input to dataframe.
2025-08-29 20:37:29.454015 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:29.455528 INFO::Removing potential empty rows and columns
2025-08-29 20:37:29.460058 INFO::Found 0 missing values.
2025-08-29 20:37:29.467974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:29.468793 INFO::Done
2025-08-29 20:37:29.469426 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:29.473393 INFO::Starting hierarchical adjustment
2025-08-29 20:37:29.474216 INFO::Found 2 batches.
2025-08-29 20:37:29.474769 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:29.475414 INFO::Using default BPPARAM
2025-08-29 20:37:29.475959 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:29.477038 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 20:37:29.503104 INFO::Done
2025-08-29 20:37:29.503871 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:29.507866 INFO::ASW Batch was -0.000701825489277552 prior to batch effect correction and is now -0.000701825489277552 .
2025-08-29 20:37:29.508782 INFO::Total function execution time is 0.0669713020324707 s and adjustment time is 0.0290391445159912 s ( 43.36 )
2025-08-29 20:37:29.528795 INFO::Formatting Data.
2025-08-29 20:37:29.52973 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:29.530712 INFO::Removing potential empty rows and columns
2025-08-29 20:37:29.531788 INFO::Found 0 missing values.
2025-08-29 20:37:29.534934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:29.535488 INFO::Done
2025-08-29 20:37:29.535999 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:29.538216 INFO::Starting hierarchical adjustment
2025-08-29 20:37:29.538936 INFO::Found 3 batches.
2025-08-29 20:37:29.53979 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:29.540424 INFO::Using default BPPARAM
2025-08-29 20:37:29.540945 INFO::Processing subtree level 1
2025-08-29 20:37:29.686861 INFO::Adjusting the last 1 batches sequentially
2025-08-29 20:37:29.688862 INFO::Done
2025-08-29 20:37:29.689562 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:29.692204 INFO::ASW Batch was -0.0396718702558984 prior to batch effect correction and is now -0.155825906521625 .
2025-08-29 20:37:29.693154 INFO::Total function execution time is 0.164435863494873 s and adjustment time is 0.15004825592041 s ( 91.25 )
2025-08-29 20:37:29.707743 INFO::Skipping initial DF formatting
2025-08-29 20:37:29.708544 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:29.712845 INFO::Starting hierarchical adjustment
2025-08-29 20:37:29.713802 INFO::Found 5 batches.
2025-08-29 20:37:29.714448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:29.715093 INFO::Using default BPPARAM
2025-08-29 20:37:29.715681 INFO::Processing subtree level 1
2025-08-29 20:37:29.966065 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:29.968244 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 20:37:29.990657 INFO::Done
2025-08-29 20:37:29.991606 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:29.99657 INFO::ASW Batch was 0.461028834252165 prior to batch effect correction and is now 0.461028834252165 .
2025-08-29 20:37:29.997334 INFO::ASW Label was 0.40595240713903 prior to batch effect correction and is now 0.40595240713903 .
2025-08-29 20:37:29.998296 INFO::Total function execution time is 0.290613889694214 s and adjustment time is 0.276982545852661 s ( 95.31 )
2025-08-29 20:37:30.085048 INFO::Formatting Data.
2025-08-29 20:37:30.086011 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:30.087071 INFO::Removing potential empty rows and columns
2025-08-29 20:37:30.088225 INFO::Found 0 missing values.
2025-08-29 20:37:30.092654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:30.093247 INFO::Done
2025-08-29 20:37:30.093803 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:30.097037 INFO::Starting hierarchical adjustment
2025-08-29 20:37:30.097914 INFO::Found 5 batches.
2025-08-29 20:37:30.098549 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:30.099226 INFO::Using default BPPARAM
2025-08-29 20:37:30.099775 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.
2025-08-29 20:37:30.237526 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:30.239134 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 20:37:30.256578 INFO::Done
2025-08-29 20:37:30.257336 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:30.26081 INFO::ASW Batch was 0.268276847777344 prior to batch effect correction and is now 0.00016528741760713 .
2025-08-29 20:37:30.261452 INFO::ASW Label was 0.343892805808179 prior to batch effect correction and is now 0.786946890665552 .
2025-08-29 20:37:30.262303 INFO::Total function execution time is 0.177342176437378 s and adjustment time is 0.158818483352661 s ( 89.55 )
2025-08-29 20:37:30.26316 INFO::Formatting Data.
2025-08-29 20:37:30.26382 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:30.264756 INFO::Removing potential empty rows and columns
2025-08-29 20:37:30.265889 INFO::Found 0 missing values.
2025-08-29 20:37:30.270247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:30.27081 INFO::Done
2025-08-29 20:37:30.271373 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:30.274488 INFO::Starting hierarchical adjustment
2025-08-29 20:37:30.275243 INFO::Found 5 batches.
2025-08-29 20:37:30.275763 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:30.276393 INFO::Using default BPPARAM
2025-08-29 20:37:30.276921 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.
2025-08-29 20:37:30.4009 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:30.402861 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 20:37:30.43007 INFO::Done
2025-08-29 20:37:30.431158 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:30.435266 INFO::ASW Batch was 0.268276847777344 prior to batch effect correction and is now 0.00016528741760713 .
2025-08-29 20:37:30.435994 INFO::ASW Label was 0.343892805808179 prior to batch effect correction and is now 0.786946890665552 .
2025-08-29 20:37:30.436958 INFO::Total function execution time is 0.173762559890747 s and adjustment time is 0.154894828796387 s ( 89.14 )
2025-08-29 20:37:30.452918 INFO::Formatting Data.
2025-08-29 20:37:30.453874 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:30.45496 INFO::Removing potential empty rows and columns
2025-08-29 20:37:30.456218 INFO::Found 0 missing values.
2025-08-29 20:37:30.460973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:30.46172 INFO::Done
2025-08-29 20:37:30.462356 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:30.46599 INFO::Starting hierarchical adjustment
2025-08-29 20:37:30.466842 INFO::Found 5 batches.
2025-08-29 20:37:30.467477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:30.468247 INFO::Using default BPPARAM
2025-08-29 20:37:30.468857 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.
2025-08-29 20:37:30.605319 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:30.607024 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 20:37:30.623621 INFO::Done
2025-08-29 20:37:30.624347 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:30.627746 INFO::ASW Batch was 0.402383394699795 prior to batch effect correction and is now -0.0379049549054074 .
2025-08-29 20:37:30.62842 INFO::ASW Label was 0.376948906911458 prior to batch effect correction and is now 0.79716512552577 .
2025-08-29 20:37:30.629274 INFO::Total function execution time is 0.176455020904541 s and adjustment time is 0.156942129135132 s ( 88.94 )
2025-08-29 20:37:30.630142 INFO::Formatting Data.
2025-08-29 20:37:30.6308 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:30.631738 INFO::Removing potential empty rows and columns
2025-08-29 20:37:30.632807 INFO::Found 0 missing values.
2025-08-29 20:37:30.63712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:30.637752 INFO::Done
2025-08-29 20:37:30.638338 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:30.641563 INFO::Starting hierarchical adjustment
2025-08-29 20:37:30.642384 INFO::Found 5 batches.
2025-08-29 20:37:30.642962 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:30.643642 INFO::Using default BPPARAM
2025-08-29 20:37:30.644232 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.
2025-08-29 20:37:30.772292 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:30.774241 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 20:37:30.793787 INFO::Done
2025-08-29 20:37:30.794697 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:30.798957 INFO::ASW Batch was 0.402383394699795 prior to batch effect correction and is now -0.0379049549054074 .
2025-08-29 20:37:30.799827 INFO::ASW Label was 0.376948906911458 prior to batch effect correction and is now 0.79716512552577 .
2025-08-29 20:37:30.800833 INFO::Total function execution time is 0.170679330825806 s and adjustment time is 0.15153980255127 s ( 88.79 )
2025-08-29 20:37:30.816507 INFO::Formatting Data.
2025-08-29 20:37:30.817421 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:30.818503 INFO::Removing potential empty rows and columns
2025-08-29 20:37:30.819697 INFO::Found 0 missing values.
2025-08-29 20:37:30.823019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:30.823686 INFO::Done
2025-08-29 20:37:30.824338 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:30.828135 INFO::Starting hierarchical adjustment
2025-08-29 20:37:30.829007 INFO::Found 2 batches.
2025-08-29 20:37:30.829675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:30.830432 INFO::Using default BPPARAM
2025-08-29 20:37:30.83106 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:30.832214 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 20:37:30.850736 INFO::Done
2025-08-29 20:37:30.85166 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:30.855623 INFO::ASW Batch was 0.634348776434709 prior to batch effect correction and is now 0.0243547258444802 .
2025-08-29 20:37:30.856346 INFO::ASW Label was 0.435979259248599 prior to batch effect correction and is now 0.873011681740161 .
2025-08-29 20:37:30.85731 INFO::Total function execution time is 0.0408861637115479 s and adjustment time is 0.0218579769134521 s ( 53.46 )
2025-08-29 20:37:30.858291 INFO::Formatting Data.
2025-08-29 20:37:30.859024 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:30.860053 INFO::Removing potential empty rows and columns
2025-08-29 20:37:30.861252 INFO::Found 0 missing values.
2025-08-29 20:37:30.864376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:30.864974 INFO::Done
2025-08-29 20:37:30.865605 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:30.869163 INFO::Starting hierarchical adjustment
2025-08-29 20:37:30.870042 INFO::Found 2 batches.
2025-08-29 20:37:30.870674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:30.871374 INFO::Using default BPPARAM
2025-08-29 20:37:30.871964 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:30.872993 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 20:37:30.889518 INFO::Done
2025-08-29 20:37:30.890299 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:30.893609 INFO::ASW Batch was 0.634348776434709 prior to batch effect correction and is now 0.0243547258444802 .
2025-08-29 20:37:30.894245 INFO::ASW Label was 0.435979259248599 prior to batch effect correction and is now 0.873011681740161 .
2025-08-29 20:37:30.895101 INFO::Total function execution time is 0.0368828773498535 s and adjustment time is 0.0196497440338135 s ( 53.28 )
2025-08-29 20:37:30.907837 INFO::Formatting Data.
2025-08-29 20:37:30.908676 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:30.909638 INFO::Removing potential empty rows and columns
2025-08-29 20:37:30.910617 INFO::Found 0 missing values.
2025-08-29 20:37:30.912863 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:30.913439 INFO::Done
2025-08-29 20:37:30.913982 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:30.916069 INFO::Starting hierarchical adjustment
2025-08-29 20:37:30.916833 INFO::Found 2 batches.
2025-08-29 20:37:30.917404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:30.918048 INFO::Using default BPPARAM
2025-08-29 20:37:30.91864 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:30.919603 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 20:37:30.955138 INFO::Done
2025-08-29 20:37:30.955928 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:30.95818 INFO::ASW Batch was 0.165146521453234 prior to batch effect correction and is now -0.0897929594685279 .
2025-08-29 20:37:30.959079 INFO::Total function execution time is 0.05133056640625 s and adjustment time is 0.0384235382080078 s ( 74.86 )
2025-08-29 20:37:30.97176 INFO::Formatting Data.
2025-08-29 20:37:30.972563 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:30.973533 INFO::Removing potential empty rows and columns
2025-08-29 20:37:30.974594 INFO::Found 0 missing values.
2025-08-29 20:37:30.975891 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.
2025-08-29 20:37:30.980726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:30.981307 INFO::Done
2025-08-29 20:37:30.981838 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:30.98507 INFO::Starting hierarchical adjustment
2025-08-29 20:37:30.985816 INFO::Found 2 batches.
2025-08-29 20:37:30.98638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:30.987014 INFO::Using default BPPARAM
2025-08-29 20:37:30.987559 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:30.988573 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 20:37:31.006403 INFO::Done
2025-08-29 20:37:31.007188 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:31.010493 INFO::ASW Batch was 0.576696055365884 prior to batch effect correction and is now -0.00481404718008305 .
2025-08-29 20:37:31.011156 INFO::ASW Label was 0.501573105222549 prior to batch effect correction and is now 0.903498136086548 .
2025-08-29 20:37:31.012035 INFO::Total function execution time is 0.0403780937194824 s and adjustment time is 0.0206935405731201 s ( 51.25 )
2025-08-29 20:37:31.012888 INFO::Formatting Data.
2025-08-29 20:37:31.013549 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:31.01455 INFO::Removing potential empty rows and columns
2025-08-29 20:37:31.015603 INFO::Found 0 missing values.
2025-08-29 20:37:31.016634 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.
2025-08-29 20:37:31.021306 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:31.021891 INFO::Done
2025-08-29 20:37:31.022459 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:31.025647 INFO::Starting hierarchical adjustment
2025-08-29 20:37:31.026383 INFO::Found 2 batches.
2025-08-29 20:37:31.026926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:31.027574 INFO::Using default BPPARAM
2025-08-29 20:37:31.028117 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:31.029096 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 20:37:31.04656 INFO::Done
2025-08-29 20:37:31.047306 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:31.050629 INFO::ASW Batch was 0.576696055365884 prior to batch effect correction and is now -0.00481404718008305 .
2025-08-29 20:37:31.051264 INFO::ASW Label was 0.501573105222549 prior to batch effect correction and is now 0.903498136086548 .
2025-08-29 20:37:31.052094 INFO::Total function execution time is 0.0392210483551025 s and adjustment time is 0.020315408706665 s ( 51.8 )
2025-08-29 20:37:31.314048 INFO::Formatting Data.
2025-08-29 20:37:31.314995 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:31.315959 INFO::Removing potential empty rows and columns
2025-08-29 20:37:31.317025 INFO::Found 0 missing values.
2025-08-29 20:37:31.320185 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:31.320747 INFO::Done
2025-08-29 20:37:31.321279 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:31.323458 INFO::Starting hierarchical adjustment
2025-08-29 20:37:31.324213 INFO::Found 3 batches.
2025-08-29 20:37:31.324755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:31.325423 INFO::Using default BPPARAM
2025-08-29 20:37:31.325941 INFO::Processing subtree level 1
2025-08-29 20:37:31.419884 INFO::Adjusting the last 1 batches sequentially
2025-08-29 20:37:31.421834 INFO::Done
2025-08-29 20:37:31.422562 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:31.425271 INFO::ASW Batch was -0.0694849335517073 prior to batch effect correction and is now -0.0694849335517073 .
2025-08-29 20:37:31.426269 INFO::Total function execution time is 0.112295627593994 s and adjustment time is 0.0977547168731689 s ( 87.05 )
2025-08-29 20:37:31.427367 INFO::Formatting Data.
2025-08-29 20:37:31.428062 INFO::Typecasting input to dataframe.
2025-08-29 20:37:31.428861 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:31.429855 INFO::Removing potential empty rows and columns
2025-08-29 20:37:31.431002 INFO::Found 0 missing values.
2025-08-29 20:37:31.434197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:31.434803 INFO::Done
2025-08-29 20:37:31.435363 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:31.437524 INFO::Starting hierarchical adjustment
2025-08-29 20:37:31.438244 INFO::Found 3 batches.
2025-08-29 20:37:31.438808 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:31.439448 INFO::Using default BPPARAM
2025-08-29 20:37:31.439978 INFO::Processing subtree level 1
2025-08-29 20:37:31.526436 INFO::Adjusting the last 1 batches sequentially
2025-08-29 20:37:31.528741 INFO::Done
2025-08-29 20:37:31.529669 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:31.532476 INFO::ASW Batch was -0.0694849335517073 prior to batch effect correction and is now -0.0694849335517073 .
2025-08-29 20:37:31.533465 INFO::Total function execution time is 0.106098175048828 s and adjustment time is 0.0905594825744629 s ( 85.35 )
2025-08-29 20:37:31.546783 INFO::Formatting Data.
2025-08-29 20:37:31.547635 INFO::Typecasting input to dataframe.
2025-08-29 20:37:31.548513 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:31.549475 INFO::Removing potential empty rows and columns
2025-08-29 20:37:31.550588 INFO::Found 0 missing values.
2025-08-29 20:37:31.553592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:31.554134 INFO::Done
2025-08-29 20:37:31.554671 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:31.556717 INFO::Starting hierarchical adjustment
2025-08-29 20:37:31.557462 INFO::Found 3 batches.
2025-08-29 20:37:31.557989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:31.558627 INFO::Using default BPPARAM
2025-08-29 20:37:31.55916 INFO::Processing subtree level 1
2025-08-29 20:37:31.646561 INFO::Adjusting the last 1 batches sequentially
2025-08-29 20:37:31.648731 INFO::Done
2025-08-29 20:37:31.649542 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:31.652493 INFO::ASW Batch was -0.0288171163926832 prior to batch effect correction and is now -0.0288171163926832 .
2025-08-29 20:37:31.653616 INFO::Total function execution time is 0.106875658035278 s and adjustment time is 0.0913810729980469 s ( 85.5 )
2025-08-29 20:37:31.794105 INFO::Formatting Data.
2025-08-29 20:37:31.794989 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:31.796165 INFO::Removing potential empty rows and columns
2025-08-29 20:37:31.799022 INFO::Found 1000 missing values.
2025-08-29 20:37:31.818054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:31.818969 INFO::Done
2025-08-29 20:37:31.819577 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:31.82532 INFO::Starting hierarchical adjustment
2025-08-29 20:37:31.826114 INFO::Found 10 batches.
2025-08-29 20:37:31.826702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:31.827349 INFO::Using default BPPARAM
2025-08-29 20:37:31.827877 INFO::Processing subtree level 1
2025-08-29 20:37:31.964039 INFO::Processing subtree level 2
2025-08-29 20:37:32.10767 INFO::Adjusting the last 1 batches sequentially
2025-08-29 20:37:32.109791 INFO::Done
2025-08-29 20:37:32.11059 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:32.116402 INFO::ASW Batch was 0.467003104835462 prior to batch effect correction and is now 0.467003104835462 .
2025-08-29 20:37:32.117122 INFO::ASW Label was 0.371299170226465 prior to batch effect correction and is now 0.371299170226465 .
2025-08-29 20:37:32.118146 INFO::Total function execution time is 0.324121952056885 s and adjustment time is 0.283825397491455 s ( 87.57 )
2025-08-29 20:37:32.119105 INFO::Formatting Data.
2025-08-29 20:37:32.119796 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:32.121134 INFO::Removing potential empty rows and columns
2025-08-29 20:37:32.123979 INFO::Found 1000 missing values.
2025-08-29 20:37:32.142987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:32.143871 INFO::Done
2025-08-29 20:37:32.144518 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:32.150342 INFO::Starting hierarchical adjustment
2025-08-29 20:37:32.151218 INFO::Found 10 batches.
2025-08-29 20:37:33.797664 INFO::Set up parallel execution backend with 2 workers
2025-08-29 20:37:33.800917 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-29 20:37:35.128159 INFO::Adjusting the last 2 batches sequentially
2025-08-29 20:37:35.130047 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 20:37:35.146264 INFO::Done
2025-08-29 20:37:35.146919 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:35.151516 INFO::ASW Batch was 0.467003104835462 prior to batch effect correction and is now 0.467003104835462 .
2025-08-29 20:37:35.152077 INFO::ASW Label was 0.371299170226465 prior to batch effect correction and is now 0.371299170226465 .
2025-08-29 20:37:35.152817 INFO::Total function execution time is 3.03376293182373 s and adjustment time is 2.99520206451416 s ( 98.73 )
2025-08-29 20:37:35.307278 INFO::Formatting Data.
2025-08-29 20:37:35.30822 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.309234 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.3104 INFO::Found 0 missing values.
2025-08-29 20:37:35.314179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.314774 INFO::Done
2025-08-29 20:37:35.315334 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 20:37:35.31842 INFO::Starting hierarchical adjustment
2025-08-29 20:37:35.319165 INFO::Found 3 batches.
2025-08-29 20:37:35.319737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 20:37:35.320405 INFO::Using default BPPARAM
2025-08-29 20:37:35.320983 INFO::Processing subtree level 1
2025-08-29 20:37:35.430331 INFO::Adjusting the last 1 batches sequentially
2025-08-29 20:37:35.432217 INFO::Done
2025-08-29 20:37:35.432914 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 20:37:35.43633 INFO::ASW Batch was 0.144920534453987 prior to batch effect correction and is now -0.142988799470651 .
2025-08-29 20:37:35.436989 INFO::ASW Label was -0.146987495006643 prior to batch effect correction and is now 0.139476831564103 .
2025-08-29 20:37:35.4379 INFO::Total function execution time is 0.130843639373779 s and adjustment time is 0.113158226013184 s ( 86.48 )
2025-08-29 20:37:35.558568 INFO::Formatting Data.
2025-08-29 20:37:35.559434 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.560395 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.561478 INFO::Found 2 missing values.
2025-08-29 20:37:35.564465 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.565027 INFO::Done
2025-08-29 20:37:35.593728 INFO::Found NA in Reference column
2025-08-29 20:37:35.603658 INFO::Require at least two references per batch.
2025-08-29 20:37:35.624946 INFO::Formatting Data.
2025-08-29 20:37:35.625725 INFO::Recognized SummarizedExperiment
2025-08-29 20:37:35.626299 INFO::Typecasting input to dataframe.
2025-08-29 20:37:35.636431 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.637691 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.641418 INFO::Found 0 missing values.
2025-08-29 20:37:35.648666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.649307 INFO::Done
2025-08-29 20:37:35.665915 INFO::Formatting Data.
2025-08-29 20:37:35.666681 INFO::Recognized SummarizedExperiment
2025-08-29 20:37:35.667245 INFO::Typecasting input to dataframe.
2025-08-29 20:37:35.685979 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.687417 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.691402 INFO::Found 0 missing values.
2025-08-29 20:37:35.70319 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.703922 INFO::Done
2025-08-29 20:37:35.721241 INFO::Formatting Data.
2025-08-29 20:37:35.722072 INFO::Recognized SummarizedExperiment
2025-08-29 20:37:35.722659 INFO::Typecasting input to dataframe.
2025-08-29 20:37:35.741057 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.742249 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.743446 INFO::Found 0 missing values.
2025-08-29 20:37:35.744488 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.
2025-08-29 20:37:35.749266 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.749878 INFO::Done
2025-08-29 20:37:35.760042 INFO::Formatting Data.
2025-08-29 20:37:35.760919 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.761812 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.76282 INFO::Found 0 missing values.
2025-08-29 20:37:35.765712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.766248 INFO::Done
2025-08-29 20:37:35.777289 INFO::Formatting Data.
2025-08-29 20:37:35.778053 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.778938 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.779982 INFO::Found 0 missing values.
2025-08-29 20:37:35.782976 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.783525 INFO::Done
2025-08-29 20:37:35.812418 INFO::Formatting Data.
2025-08-29 20:37:35.81325 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.814311 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.815462 INFO::Found 1 missing values.
2025-08-29 20:37:35.818009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.818557 INFO::Done
2025-08-29 20:37:35.837632 INFO::Formatting Data.
2025-08-29 20:37:35.838419 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.839307 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.840261 INFO::Found 2 missing values.
2025-08-29 20:37:35.841129 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.
2025-08-29 20:37:35.843327 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.843858 INFO::Done
2025-08-29 20:37:35.853346 INFO::Formatting Data.
2025-08-29 20:37:35.85413 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.854991 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.855911 INFO::Found 2 missing values.
2025-08-29 20:37:35.8575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.858008 INFO::Done
2025-08-29 20:37:35.868245 INFO::Formatting Data.
2025-08-29 20:37:35.868999 INFO::Typecasting input to dataframe.
2025-08-29 20:37:35.869804 INFO::Replacing NaNs with NAs.
2025-08-29 20:37:35.870651 INFO::Removing potential empty rows and columns
2025-08-29 20:37:35.871644 INFO::Found 0 missing values.
2025-08-29 20:37:35.874378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 20:37:35.874883 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.684 4.072 21.459
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.535 | 1.081 | 16.849 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.012 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.011 | |