Yannis Schumann
| Snapshot Date: 2025-10-21 13:45 -0400 (Tue, 21 Oct 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 2025-10-22 12:03 -0400 (Wed, 22 Oct 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" | 4890 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4680 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4625 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 165/2355 | 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 12.7.6 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: 2025-10-21 21:25:30 -0400 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 21:27:00 -0400 (Tue, 21 Oct 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 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 ‘1.5.0’
* 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 23.08 1.607 17.274
* 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 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")
2025-10-21 21:26:20.79661 INFO::Formatting Data.
2025-10-21 21:26:20.798109 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:20.810136 INFO::Removing potential empty rows and columns
2025-10-21 21:26:21.063135 INFO::Found 0 missing values.
2025-10-21 21:26:21.066665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:21.067428 INFO::Done
2025-10-21 21:26:21.067996 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:21.080532 INFO::Starting hierarchical adjustment
2025-10-21 21:26:21.081566 INFO::Found 3 batches.
2025-10-21 21:26:21.082199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:21.083549 INFO::Using default BPPARAM
2025-10-21 21:26:21.084148 INFO::Processing subtree level 1
2025-10-21 21:26:21.203387 INFO::Adjusting the last 1 batches sequentially
2025-10-21 21:26:21.205666 INFO::Done
2025-10-21 21:26:21.206529 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:21.209855 INFO::ASW Batch was -0.0606198261404757 prior to batch effect correction and is now -0.0606198261404757 .
2025-10-21 21:26:21.21125 INFO::Total function execution time is 0.415297985076904 s and adjustment time is 0.124289751052856 s ( 29.93 )
2025-10-21 21:26:21.226894 INFO::Formatting Data.
2025-10-21 21:26:21.228037 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:21.229139 INFO::Removing potential empty rows and columns
2025-10-21 21:26:21.230393 INFO::Found 0 missing values.
2025-10-21 21:26:21.231496 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.
2025-10-21 21:26:21.24363 INFO::Formatting Data.
2025-10-21 21:26:21.244541 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:21.245548 INFO::Removing potential empty rows and columns
2025-10-21 21:26:21.246711 INFO::Found 0 missing values.
2025-10-21 21:26:21.247744 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.
2025-10-21 21:26:21.265055 INFO::Formatting Data.
2025-10-21 21:26:21.265882 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:21.266904 INFO::Removing potential empty rows and columns
2025-10-21 21:26:21.26807 INFO::Found 0 missing values.
2025-10-21 21:26:21.269088 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.
2025-10-21 21:26:21.273942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:21.274555 INFO::Done
2025-10-21 21:26:21.275084 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:21.277296 INFO::Starting hierarchical adjustment
2025-10-21 21:26:21.278048 INFO::Found 2 batches.
2025-10-21 21:26:21.27863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:21.279314 INFO::Using default BPPARAM
2025-10-21 21:26:21.279875 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:21.280859 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 21:26:21.305212 INFO::Done
2025-10-21 21:26:21.305998 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:21.308309 INFO::ASW Batch was 0.0869090515332261 prior to batch effect correction and is now -0.0672108199154684 .
2025-10-21 21:26:21.30919 INFO::Total function execution time is 0.0442101955413818 s and adjustment time is 0.0272583961486816 s ( 61.66 )
2025-10-21 21:26:21.312207 INFO::Formatting Data.
2025-10-21 21:26:21.312878 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:21.322366 INFO::Formatting Data.
2025-10-21 21:26:21.323237 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:21.324269 INFO::Removing potential empty rows and columns
2025-10-21 21:26:21.325408 INFO::Found 0 missing values.
2025-10-21 21:26:21.328589 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:21.32917 INFO::Done
2025-10-21 21:26:21.329738 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:21.332177 INFO::Starting hierarchical adjustment
2025-10-21 21:26:21.332943 INFO::Found 2 batches.
2025-10-21 21:26:21.333521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:21.334179 INFO::Using default BPPARAM
2025-10-21 21:26:21.334809 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:21.335835 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 21:26:21.392137 INFO::Done
2025-10-21 21:26:21.392909 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:21.394962 INFO::ASW Batch was 0.0389275429669971 prior to batch effect correction and is now -0.110146692816457 .
2025-10-21 21:26:21.395815 INFO::Total function execution time is 0.0735645294189453 s and adjustment time is 0.0593085289001465 s ( 80.62 )
2025-10-21 21:26:21.396964 INFO::Formatting Data.
2025-10-21 21:26:21.397652 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:21.398657 INFO::Removing potential empty rows and columns
2025-10-21 21:26:21.399875 INFO::Found 0 missing values.
2025-10-21 21:26:21.403288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:21.403941 INFO::Done
2025-10-21 21:26:21.404541 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:21.407022 INFO::Starting hierarchical adjustment
2025-10-21 21:26:21.407835 INFO::Found 2 batches.
2025-10-21 21:26:21.408412 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:21.409037 INFO::Using default BPPARAM
2025-10-21 21:26:21.409585 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:21.41057 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 21:26:21.427021 INFO::Done
2025-10-21 21:26:21.427771 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:21.429936 INFO::ASW Batch was 0.0389275429669971 prior to batch effect correction and is now -0.110146692816457 .
2025-10-21 21:26:21.430773 INFO::Total function execution time is 0.0338277816772461 s and adjustment time is 0.0193383693695068 s ( 57.17 )
2025-10-21 21:26:24.424712 INFO::Formatting Data.
2025-10-21 21:26:24.42546 INFO::Recognized SummarizedExperiment
2025-10-21 21:26:24.425954 INFO::Typecasting input to dataframe.
2025-10-21 21:26:24.456015 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:24.457321 INFO::Removing potential empty rows and columns
2025-10-21 21:26:24.461106 INFO::Found 0 missing values.
2025-10-21 21:26:24.468273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:24.469011 INFO::Done
2025-10-21 21:26:24.469572 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:24.473234 INFO::Starting hierarchical adjustment
2025-10-21 21:26:24.473983 INFO::Found 2 batches.
2025-10-21 21:26:24.474515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:24.47561 INFO::Using default BPPARAM
2025-10-21 21:26:24.476173 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:24.477185 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 21:26:24.536017 INFO::Done
2025-10-21 21:26:24.536788 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:24.540842 INFO::ASW Batch was -0.0057331512158996 prior to batch effect correction and is now -0.0874877894834557 .
2025-10-21 21:26:24.541789 INFO::Total function execution time is 0.117332458496094 s and adjustment time is 0.0621564388275146 s ( 52.97 )
2025-10-21 21:26:24.571515 INFO::Formatting Data.
2025-10-21 21:26:24.572629 INFO::Recognized SummarizedExperiment
2025-10-21 21:26:24.573238 INFO::Typecasting input to dataframe.
2025-10-21 21:26:24.584703 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:24.586029 INFO::Removing potential empty rows and columns
2025-10-21 21:26:24.589919 INFO::Found 0 missing values.
2025-10-21 21:26:24.597303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:24.597905 INFO::Done
2025-10-21 21:26:24.598453 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:24.602423 INFO::Starting hierarchical adjustment
2025-10-21 21:26:24.603206 INFO::Found 2 batches.
2025-10-21 21:26:24.603723 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:24.604378 INFO::Using default BPPARAM
2025-10-21 21:26:24.604902 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:24.60594 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 21:26:24.633305 INFO::Done
2025-10-21 21:26:24.634149 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:24.637983 INFO::ASW Batch was -0.0176550312614847 prior to batch effect correction and is now -0.0176550312614847 .
2025-10-21 21:26:24.638993 INFO::Total function execution time is 0.0676181316375732 s and adjustment time is 0.0302350521087646 s ( 44.71 )
2025-10-21 21:26:24.660113 INFO::Formatting Data.
2025-10-21 21:26:24.66114 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:24.662049 INFO::Removing potential empty rows and columns
2025-10-21 21:26:24.663131 INFO::Found 0 missing values.
2025-10-21 21:26:24.666463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:24.667048 INFO::Done
2025-10-21 21:26:24.667634 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:24.669855 INFO::Starting hierarchical adjustment
2025-10-21 21:26:24.670642 INFO::Found 3 batches.
2025-10-21 21:26:24.67125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:24.671903 INFO::Using default BPPARAM
2025-10-21 21:26:24.672497 INFO::Processing subtree level 1
2025-10-21 21:26:24.822589 INFO::Adjusting the last 1 batches sequentially
2025-10-21 21:26:24.824758 INFO::Done
2025-10-21 21:26:24.825553 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:24.828453 INFO::ASW Batch was -0.133562498468269 prior to batch effect correction and is now -0.175041392751848 .
2025-10-21 21:26:24.829549 INFO::Total function execution time is 0.169437646865845 s and adjustment time is 0.154251337051392 s ( 91.04 )
2025-10-21 21:26:24.844437 INFO::Skipping initial DF formatting
2025-10-21 21:26:24.845165 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:24.849292 INFO::Starting hierarchical adjustment
2025-10-21 21:26:24.850086 INFO::Found 5 batches.
2025-10-21 21:26:24.850671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:24.851325 INFO::Using default BPPARAM
2025-10-21 21:26:24.851863 INFO::Processing subtree level 1
2025-10-21 21:26:25.095371 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:25.097057 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 21:26:25.117403 INFO::Done
2025-10-21 21:26:25.118355 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:25.123276 INFO::ASW Batch was 0.510732042300471 prior to batch effect correction and is now 0.510732042300471 .
2025-10-21 21:26:25.124003 INFO::ASW Label was 0.426415498957607 prior to batch effect correction and is now 0.426415498957607 .
2025-10-21 21:26:25.124905 INFO::Total function execution time is 0.280632734298706 s and adjustment time is 0.26740550994873 s ( 95.29 )
2025-10-21 21:26:25.200507 INFO::Formatting Data.
2025-10-21 21:26:25.201369 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:25.202306 INFO::Removing potential empty rows and columns
2025-10-21 21:26:25.203337 INFO::Found 0 missing values.
2025-10-21 21:26:25.207333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:25.207867 INFO::Done
2025-10-21 21:26:25.208395 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:25.211563 INFO::Starting hierarchical adjustment
2025-10-21 21:26:25.212291 INFO::Found 5 batches.
2025-10-21 21:26:25.212821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:25.213428 INFO::Using default BPPARAM
2025-10-21 21:26:25.213928 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.
2025-10-21 21:26:25.35552 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:25.357437 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 21:26:25.37559 INFO::Done
2025-10-21 21:26:25.376401 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:25.380228 INFO::ASW Batch was 0.483354894957085 prior to batch effect correction and is now -0.0216123919815399 .
2025-10-21 21:26:25.380928 INFO::ASW Label was 0.339127381453353 prior to batch effect correction and is now 0.775474423194549 .
2025-10-21 21:26:25.381835 INFO::Total function execution time is 0.181425094604492 s and adjustment time is 0.1634202003479 s ( 90.08 )
2025-10-21 21:26:25.382763 INFO::Formatting Data.
2025-10-21 21:26:25.383463 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:25.384406 INFO::Removing potential empty rows and columns
2025-10-21 21:26:25.385568 INFO::Found 0 missing values.
2025-10-21 21:26:25.390271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:25.39087 INFO::Done
2025-10-21 21:26:25.391425 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:25.394579 INFO::Starting hierarchical adjustment
2025-10-21 21:26:25.395339 INFO::Found 5 batches.
2025-10-21 21:26:25.395875 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:25.396534 INFO::Using default BPPARAM
2025-10-21 21:26:25.397069 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.
2025-10-21 21:26:25.532928 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:25.534866 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 21:26:25.554396 INFO::Done
2025-10-21 21:26:25.555387 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:25.55942 INFO::ASW Batch was 0.483354894957085 prior to batch effect correction and is now -0.0216123919815399 .
2025-10-21 21:26:25.560185 INFO::ASW Label was 0.339127381453353 prior to batch effect correction and is now 0.775474423194549 .
2025-10-21 21:26:25.572074 INFO::Total function execution time is 0.178339719772339 s and adjustment time is 0.159117221832275 s ( 89.22 )
2025-10-21 21:26:25.596367 INFO::Formatting Data.
2025-10-21 21:26:25.597818 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:25.599448 INFO::Removing potential empty rows and columns
2025-10-21 21:26:25.601185 INFO::Found 0 missing values.
2025-10-21 21:26:25.607457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:25.60832 INFO::Done
2025-10-21 21:26:25.609066 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:25.61503 INFO::Starting hierarchical adjustment
2025-10-21 21:26:25.616135 INFO::Found 5 batches.
2025-10-21 21:26:25.616911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:25.617866 INFO::Using default BPPARAM
2025-10-21 21:26:25.618651 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.
2025-10-21 21:26:25.781858 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:25.783767 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 21:26:25.80125 INFO::Done
2025-10-21 21:26:25.802069 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:25.805861 INFO::ASW Batch was 0.318408295540177 prior to batch effect correction and is now -0.0767794669470198 .
2025-10-21 21:26:25.80658 INFO::ASW Label was 0.33395708678685 prior to batch effect correction and is now 0.854732230096688 .
2025-10-21 21:26:25.807507 INFO::Total function execution time is 0.211505889892578 s and adjustment time is 0.185371875762939 s ( 87.64 )
2025-10-21 21:26:25.808451 INFO::Formatting Data.
2025-10-21 21:26:25.809138 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:25.810147 INFO::Removing potential empty rows and columns
2025-10-21 21:26:25.811277 INFO::Found 0 missing values.
2025-10-21 21:26:25.815555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:25.816187 INFO::Done
2025-10-21 21:26:25.816726 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:25.820095 INFO::Starting hierarchical adjustment
2025-10-21 21:26:25.820899 INFO::Found 5 batches.
2025-10-21 21:26:25.821494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:25.822145 INFO::Using default BPPARAM
2025-10-21 21:26:25.822756 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.
2025-10-21 21:26:25.962552 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:25.964564 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 21:26:25.983086 INFO::Done
2025-10-21 21:26:25.984017 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:25.988148 INFO::ASW Batch was 0.318408295540177 prior to batch effect correction and is now -0.0767794669470198 .
2025-10-21 21:26:25.988933 INFO::ASW Label was 0.33395708678685 prior to batch effect correction and is now 0.854732230096688 .
2025-10-21 21:26:25.989914 INFO::Total function execution time is 0.181458473205566 s and adjustment time is 0.162297010421753 s ( 89.44 )
2025-10-21 21:26:26.006567 INFO::Formatting Data.
2025-10-21 21:26:26.007633 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:26.008745 INFO::Removing potential empty rows and columns
2025-10-21 21:26:26.009887 INFO::Found 0 missing values.
2025-10-21 21:26:26.012951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:26.013552 INFO::Done
2025-10-21 21:26:26.014139 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:26.017543 INFO::Starting hierarchical adjustment
2025-10-21 21:26:26.018353 INFO::Found 2 batches.
2025-10-21 21:26:26.018929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:26.019639 INFO::Using default BPPARAM
2025-10-21 21:26:26.020227 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:26.021236 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 21:26:26.038113 INFO::Done
2025-10-21 21:26:26.039011 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:26.042555 INFO::ASW Batch was 0.299908811720136 prior to batch effect correction and is now 0.0692256212133686 .
2025-10-21 21:26:26.043259 INFO::ASW Label was 0.485338692914232 prior to batch effect correction and is now 0.882559465741099 .
2025-10-21 21:26:26.044183 INFO::Total function execution time is 0.0377480983734131 s and adjustment time is 0.0198783874511719 s ( 52.66 )
2025-10-21 21:26:26.045073 INFO::Formatting Data.
2025-10-21 21:26:26.045799 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:26.046805 INFO::Removing potential empty rows and columns
2025-10-21 21:26:26.047911 INFO::Found 0 missing values.
2025-10-21 21:26:26.050867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:26.051458 INFO::Done
2025-10-21 21:26:26.051997 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:26.055217 INFO::Starting hierarchical adjustment
2025-10-21 21:26:26.055996 INFO::Found 2 batches.
2025-10-21 21:26:26.056589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:26.057243 INFO::Using default BPPARAM
2025-10-21 21:26:26.0578 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:26.058806 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-21 21:26:26.075243 INFO::Done
2025-10-21 21:26:26.076042 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:26.079354 INFO::ASW Batch was 0.299908811720136 prior to batch effect correction and is now 0.0692256212133686 .
2025-10-21 21:26:26.080018 INFO::ASW Label was 0.485338692914232 prior to batch effect correction and is now 0.882559465741099 .
2025-10-21 21:26:26.080878 INFO::Total function execution time is 0.0358290672302246 s and adjustment time is 0.0193526744842529 s ( 54.01 )
2025-10-21 21:26:26.093391 INFO::Formatting Data.
2025-10-21 21:26:26.094351 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:26.095369 INFO::Removing potential empty rows and columns
2025-10-21 21:26:26.096367 INFO::Found 0 missing values.
2025-10-21 21:26:26.098661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:26.099237 INFO::Done
2025-10-21 21:26:26.099762 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:26.101965 INFO::Starting hierarchical adjustment
2025-10-21 21:26:26.10273 INFO::Found 2 batches.
2025-10-21 21:26:26.103289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:26.103893 INFO::Using default BPPARAM
2025-10-21 21:26:26.104439 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:26.105442 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 21:26:26.141822 INFO::Done
2025-10-21 21:26:26.142685 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:26.144955 INFO::ASW Batch was -0.0422082375643381 prior to batch effect correction and is now -0.124347486798982 .
2025-10-21 21:26:26.145924 INFO::Total function execution time is 0.0527093410491943 s and adjustment time is 0.0391948223114014 s ( 74.36 )
2025-10-21 21:26:26.159542 INFO::Formatting Data.
2025-10-21 21:26:26.160506 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:26.161534 INFO::Removing potential empty rows and columns
2025-10-21 21:26:26.162674 INFO::Found 0 missing values.
2025-10-21 21:26:26.164267 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.
2025-10-21 21:26:26.169729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:26.170379 INFO::Done
2025-10-21 21:26:26.170927 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:26.174233 INFO::Starting hierarchical adjustment
2025-10-21 21:26:26.174984 INFO::Found 2 batches.
2025-10-21 21:26:26.17556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:26.176189 INFO::Using default BPPARAM
2025-10-21 21:26:26.176748 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:26.177828 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 21:26:26.196559 INFO::Done
2025-10-21 21:26:26.197434 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:26.200947 INFO::ASW Batch was 0.48407795145051 prior to batch effect correction and is now 0.0172830953796923 .
2025-10-21 21:26:26.201695 INFO::ASW Label was 0.509214890791655 prior to batch effect correction and is now 0.871816271603613 .
2025-10-21 21:26:26.202578 INFO::Total function execution time is 0.0432000160217285 s and adjustment time is 0.0216686725616455 s ( 50.16 )
2025-10-21 21:26:26.203466 INFO::Formatting Data.
2025-10-21 21:26:26.204175 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:26.205233 INFO::Removing potential empty rows and columns
2025-10-21 21:26:26.206352 INFO::Found 0 missing values.
2025-10-21 21:26:26.207433 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.
2025-10-21 21:26:26.212329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:26.212926 INFO::Done
2025-10-21 21:26:26.21347 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:26.216778 INFO::Starting hierarchical adjustment
2025-10-21 21:26:26.21755 INFO::Found 2 batches.
2025-10-21 21:26:26.21809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:26.218747 INFO::Using default BPPARAM
2025-10-21 21:26:26.219288 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:26.220336 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 21:26:26.238659 INFO::Done
2025-10-21 21:26:26.23955 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:26.243034 INFO::ASW Batch was 0.48407795145051 prior to batch effect correction and is now 0.0172830953796923 .
2025-10-21 21:26:26.243758 INFO::ASW Label was 0.509214890791655 prior to batch effect correction and is now 0.871816271603613 .
2025-10-21 21:26:26.244678 INFO::Total function execution time is 0.0412216186523438 s and adjustment time is 0.0212008953094482 s ( 51.43 )
2025-10-21 21:26:26.491596 INFO::Formatting Data.
2025-10-21 21:26:26.49255 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:26.493607 INFO::Removing potential empty rows and columns
2025-10-21 21:26:26.494798 INFO::Found 0 missing values.
2025-10-21 21:26:26.49826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:26.498838 INFO::Done
2025-10-21 21:26:26.499414 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:26.501734 INFO::Starting hierarchical adjustment
2025-10-21 21:26:26.502491 INFO::Found 3 batches.
2025-10-21 21:26:26.503069 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:26.503725 INFO::Using default BPPARAM
2025-10-21 21:26:26.504293 INFO::Processing subtree level 1
2025-10-21 21:26:26.603991 INFO::Adjusting the last 1 batches sequentially
2025-10-21 21:26:26.606073 INFO::Done
2025-10-21 21:26:26.606881 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:26.609746 INFO::ASW Batch was 0.00736013936097614 prior to batch effect correction and is now 0.00736013936097614 .
2025-10-21 21:26:26.610825 INFO::Total function execution time is 0.119331836700439 s and adjustment time is 0.10368275642395 s ( 86.89 )
2025-10-21 21:26:26.612016 INFO::Formatting Data.
2025-10-21 21:26:26.612768 INFO::Typecasting input to dataframe.
2025-10-21 21:26:26.613595 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:26.614595 INFO::Removing potential empty rows and columns
2025-10-21 21:26:26.615737 INFO::Found 0 missing values.
2025-10-21 21:26:26.619004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:26.619605 INFO::Done
2025-10-21 21:26:26.620153 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:26.622366 INFO::Starting hierarchical adjustment
2025-10-21 21:26:26.623109 INFO::Found 3 batches.
2025-10-21 21:26:26.623678 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:26.624378 INFO::Using default BPPARAM
2025-10-21 21:26:26.62492 INFO::Processing subtree level 1
2025-10-21 21:26:26.718689 INFO::Adjusting the last 1 batches sequentially
2025-10-21 21:26:26.720701 INFO::Done
2025-10-21 21:26:26.721442 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:26.72411 INFO::ASW Batch was 0.00736013936097614 prior to batch effect correction and is now 0.00736013936097614 .
2025-10-21 21:26:26.725155 INFO::Total function execution time is 0.113101482391357 s and adjustment time is 0.097705602645874 s ( 86.39 )
2025-10-21 21:26:26.740514 INFO::Formatting Data.
2025-10-21 21:26:26.741631 INFO::Typecasting input to dataframe.
2025-10-21 21:26:26.742677 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:26.743752 INFO::Removing potential empty rows and columns
2025-10-21 21:26:26.744994 INFO::Found 0 missing values.
2025-10-21 21:26:26.748668 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:26.74932 INFO::Done
2025-10-21 21:26:26.749917 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:26.752401 INFO::Starting hierarchical adjustment
2025-10-21 21:26:26.753284 INFO::Found 3 batches.
2025-10-21 21:26:26.75392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:26.754655 INFO::Using default BPPARAM
2025-10-21 21:26:26.755291 INFO::Processing subtree level 1
2025-10-21 21:26:26.852739 INFO::Adjusting the last 1 batches sequentially
2025-10-21 21:26:26.854917 INFO::Done
2025-10-21 21:26:26.855702 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:26.858684 INFO::ASW Batch was 0.00911325693765965 prior to batch effect correction and is now 0.00911325693765965 .
2025-10-21 21:26:26.859752 INFO::Total function execution time is 0.119386672973633 s and adjustment time is 0.101824998855591 s ( 85.29 )
2025-10-21 21:26:27.020413 INFO::Formatting Data.
2025-10-21 21:26:27.02148 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:27.023005 INFO::Removing potential empty rows and columns
2025-10-21 21:26:27.027035 INFO::Found 1000 missing values.
2025-10-21 21:26:27.051938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:27.052915 INFO::Done
2025-10-21 21:26:27.053643 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:27.060337 INFO::Starting hierarchical adjustment
2025-10-21 21:26:27.061256 INFO::Found 10 batches.
2025-10-21 21:26:27.061841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:27.062527 INFO::Using default BPPARAM
2025-10-21 21:26:27.063066 INFO::Processing subtree level 1
2025-10-21 21:26:27.219567 INFO::Processing subtree level 2
2025-10-21 21:26:27.373308 INFO::Adjusting the last 1 batches sequentially
2025-10-21 21:26:27.375779 INFO::Done
2025-10-21 21:26:27.376611 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:27.382956 INFO::ASW Batch was 0.475248415754452 prior to batch effect correction and is now 0.475248415754452 .
2025-10-21 21:26:27.383801 INFO::ASW Label was 0.351638061560294 prior to batch effect correction and is now 0.351638061560294 .
2025-10-21 21:26:27.384922 INFO::Total function execution time is 0.364610910415649 s and adjustment time is 0.314693212509155 s ( 86.31 )
2025-10-21 21:26:27.386029 INFO::Formatting Data.
2025-10-21 21:26:27.386801 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:27.388318 INFO::Removing potential empty rows and columns
2025-10-21 21:26:27.391435 INFO::Found 1000 missing values.
2025-10-21 21:26:27.411155 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:27.412159 INFO::Done
2025-10-21 21:26:27.412792 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:27.418906 INFO::Starting hierarchical adjustment
2025-10-21 21:26:27.419778 INFO::Found 10 batches.
2025-10-21 21:26:29.361425 INFO::Set up parallel execution backend with 2 workers
2025-10-21 21:26:29.364552 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-21 21:26:30.634835 INFO::Adjusting the last 2 batches sequentially
2025-10-21 21:26:30.636717 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-21 21:26:30.653018 INFO::Done
2025-10-21 21:26:30.653702 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:30.658337 INFO::ASW Batch was 0.475248415754452 prior to batch effect correction and is now 0.475248415754452 .
2025-10-21 21:26:30.65891 INFO::ASW Label was 0.351638061560294 prior to batch effect correction and is now 0.351638061560294 .
2025-10-21 21:26:30.659621 INFO::Total function execution time is 3.27367496490479 s and adjustment time is 3.23339247703552 s ( 98.77 )
2025-10-21 21:26:30.821497 INFO::Formatting Data.
2025-10-21 21:26:30.822979 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:30.824619 INFO::Removing potential empty rows and columns
2025-10-21 21:26:30.826553 INFO::Found 0 missing values.
2025-10-21 21:26:30.833269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:30.834319 INFO::Done
2025-10-21 21:26:30.835258 INFO::Acquiring quality metrics before batch effect correction.
2025-10-21 21:26:30.840161 INFO::Starting hierarchical adjustment
2025-10-21 21:26:30.84138 INFO::Found 3 batches.
2025-10-21 21:26:30.842231 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-21 21:26:30.84323 INFO::Using default BPPARAM
2025-10-21 21:26:30.844084 INFO::Processing subtree level 1
2025-10-21 21:26:30.977038 INFO::Adjusting the last 1 batches sequentially
2025-10-21 21:26:30.978892 INFO::Done
2025-10-21 21:26:30.979541 INFO::Acquiring quality metrics after batch effect correction.
2025-10-21 21:26:30.982852 INFO::ASW Batch was 0.275429187352122 prior to batch effect correction and is now -0.136744404443223 .
2025-10-21 21:26:30.983481 INFO::ASW Label was -0.224780879890849 prior to batch effect correction and is now 0.0487365090052002 .
2025-10-21 21:26:30.984398 INFO::Total function execution time is 0.163177967071533 s and adjustment time is 0.137833595275879 s ( 84.47 )
2025-10-21 21:26:31.109146 INFO::Formatting Data.
2025-10-21 21:26:31.110161 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.111186 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.112319 INFO::Found 2 missing values.
2025-10-21 21:26:31.115298 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.115883 INFO::Done
2025-10-21 21:26:31.144655 INFO::Found NA in Reference column
2025-10-21 21:26:31.154516 INFO::Require at least two references per batch.
2025-10-21 21:26:31.176436 INFO::Formatting Data.
2025-10-21 21:26:31.177323 INFO::Recognized SummarizedExperiment
2025-10-21 21:26:31.177868 INFO::Typecasting input to dataframe.
2025-10-21 21:26:31.188581 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.190011 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.193575 INFO::Found 0 missing values.
2025-10-21 21:26:31.20046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.201145 INFO::Done
2025-10-21 21:26:31.218541 INFO::Formatting Data.
2025-10-21 21:26:31.219485 INFO::Recognized SummarizedExperiment
2025-10-21 21:26:31.220063 INFO::Typecasting input to dataframe.
2025-10-21 21:26:31.239897 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.241616 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.245601 INFO::Found 0 missing values.
2025-10-21 21:26:31.256691 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.257511 INFO::Done
2025-10-21 21:26:31.290811 INFO::Formatting Data.
2025-10-21 21:26:31.292004 INFO::Recognized SummarizedExperiment
2025-10-21 21:26:31.292546 INFO::Typecasting input to dataframe.
2025-10-21 21:26:31.311178 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.312398 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.313624 INFO::Found 0 missing values.
2025-10-21 21:26:31.314553 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.
2025-10-21 21:26:31.318908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.319472 INFO::Done
2025-10-21 21:26:31.330838 INFO::Formatting Data.
2025-10-21 21:26:31.331748 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.332685 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.333665 INFO::Found 0 missing values.
2025-10-21 21:26:31.336482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.336978 INFO::Done
2025-10-21 21:26:31.348043 INFO::Formatting Data.
2025-10-21 21:26:31.348882 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.349727 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.350709 INFO::Found 0 missing values.
2025-10-21 21:26:31.353529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.354105 INFO::Done
2025-10-21 21:26:31.383344 INFO::Formatting Data.
2025-10-21 21:26:31.38422 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.385309 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.386504 INFO::Found 1 missing values.
2025-10-21 21:26:31.389133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.389675 INFO::Done
2025-10-21 21:26:31.409195 INFO::Formatting Data.
2025-10-21 21:26:31.410022 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.410912 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.411864 INFO::Found 2 missing values.
2025-10-21 21:26:31.412771 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.
2025-10-21 21:26:31.415021 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.415573 INFO::Done
2025-10-21 21:26:31.425033 INFO::Formatting Data.
2025-10-21 21:26:31.42583 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.42668 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.427578 INFO::Found 2 missing values.
2025-10-21 21:26:31.429137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.429656 INFO::Done
2025-10-21 21:26:31.440218 INFO::Formatting Data.
2025-10-21 21:26:31.441039 INFO::Typecasting input to dataframe.
2025-10-21 21:26:31.441858 INFO::Replacing NaNs with NAs.
2025-10-21 21:26:31.44275 INFO::Removing potential empty rows and columns
2025-10-21 21:26:31.443797 INFO::Found 0 missing values.
2025-10-21 21:26:31.446695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-21 21:26:31.447217 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.044 4.504 22.146
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.080 | 1.607 | 17.274 | |
| compute_asw | 0.023 | 0.003 | 0.026 | |
| count_existing | 0.013 | 0.001 | 0.015 | |
| generate_data_covariables | 0.009 | 0.004 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |