Yannis Schumann
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:35 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 170/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-04-17 21:40:12 -0400 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 21:41:49 -0400 (Fri, 17 Apr 2026) |
| EllapsedTime: 96.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-18 01:40:13 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.667 1.375 17.846
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 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")
2026-04-17 21:41:05.410296 INFO::Formatting Data.
2026-04-17 21:41:05.411772 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:05.423264 INFO::Removing potential empty rows and columns
2026-04-17 21:41:05.672586 INFO::Found 0 missing values.
2026-04-17 21:41:05.675984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:05.676729 INFO::Done
2026-04-17 21:41:05.677339 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:05.690571 INFO::Starting hierarchical adjustment
2026-04-17 21:41:05.691662 INFO::Found 3 batches.
2026-04-17 21:41:05.692293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:05.693467 INFO::Using default BPPARAM
2026-04-17 21:41:05.694085 INFO::Processing subtree level 1
2026-04-17 21:41:05.812384 INFO::Adjusting the last 1 batches sequentially
2026-04-17 21:41:05.81441 INFO::Done
2026-04-17 21:41:05.815197 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:05.817927 INFO::ASW Batch was -0.0465073664652424 prior to batch effect correction and is now -0.0465073664652424 .
2026-04-17 21:41:05.819054 INFO::Total function execution time is 0.40948224067688 s and adjustment time is 0.122940301895142 s ( 30.02 )
2026-04-17 21:41:05.833133 INFO::Formatting Data.
2026-04-17 21:41:05.834062 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:05.835098 INFO::Removing potential empty rows and columns
2026-04-17 21:41:05.83627 INFO::Found 0 missing values.
2026-04-17 21:41:05.837278 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.
2026-04-17 21:41:05.848739 INFO::Formatting Data.
2026-04-17 21:41:05.849632 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:05.850657 INFO::Removing potential empty rows and columns
2026-04-17 21:41:05.851876 INFO::Found 0 missing values.
2026-04-17 21:41:05.852907 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.
2026-04-17 21:41:05.869891 INFO::Formatting Data.
2026-04-17 21:41:05.87085 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:05.871904 INFO::Removing potential empty rows and columns
2026-04-17 21:41:05.873057 INFO::Found 0 missing values.
2026-04-17 21:41:05.874077 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.
2026-04-17 21:41:05.878804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:05.879455 INFO::Done
2026-04-17 21:41:05.880042 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:05.882308 INFO::Starting hierarchical adjustment
2026-04-17 21:41:05.883081 INFO::Found 2 batches.
2026-04-17 21:41:05.883692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:05.884407 INFO::Using default BPPARAM
2026-04-17 21:41:05.885029 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:05.886089 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 21:41:05.908149 INFO::Done
2026-04-17 21:41:05.908964 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:05.911149 INFO::ASW Batch was -0.00398976099744956 prior to batch effect correction and is now -0.106283981385998 .
2026-04-17 21:41:05.912022 INFO::Total function execution time is 0.0422251224517822 s and adjustment time is 0.0252010822296143 s ( 59.68 )
2026-04-17 21:41:05.915059 INFO::Formatting Data.
2026-04-17 21:41:05.915781 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:05.925379 INFO::Formatting Data.
2026-04-17 21:41:05.926138 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:05.9272 INFO::Removing potential empty rows and columns
2026-04-17 21:41:05.928436 INFO::Found 0 missing values.
2026-04-17 21:41:05.931694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:05.932348 INFO::Done
2026-04-17 21:41:05.932938 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:05.9352 INFO::Starting hierarchical adjustment
2026-04-17 21:41:05.935995 INFO::Found 2 batches.
2026-04-17 21:41:05.936612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:05.937379 INFO::Using default BPPARAM
2026-04-17 21:41:05.938018 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:05.939065 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 21:41:05.956476 INFO::Done
2026-04-17 21:41:05.957507 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:05.959966 INFO::ASW Batch was -0.0274430939119442 prior to batch effect correction and is now -0.116370567526301 .
2026-04-17 21:41:05.96096 INFO::Total function execution time is 0.0355739593505859 s and adjustment time is 0.0206005573272705 s ( 57.91 )
2026-04-17 21:41:05.962167 INFO::Formatting Data.
2026-04-17 21:41:05.962887 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:05.963916 INFO::Removing potential empty rows and columns
2026-04-17 21:41:05.965215 INFO::Found 0 missing values.
2026-04-17 21:41:05.968726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:05.969411 INFO::Done
2026-04-17 21:41:05.97002 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:05.97241 INFO::Starting hierarchical adjustment
2026-04-17 21:41:05.973282 INFO::Found 2 batches.
2026-04-17 21:41:05.973916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:05.974637 INFO::Using default BPPARAM
2026-04-17 21:41:05.975282 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:05.97633 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 21:41:05.993038 INFO::Done
2026-04-17 21:41:05.993916 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:05.996299 INFO::ASW Batch was -0.0274430939119442 prior to batch effect correction and is now -0.116370567526301 .
2026-04-17 21:41:05.997182 INFO::Total function execution time is 0.0349993705749512 s and adjustment time is 0.0199189186096191 s ( 56.91 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-17 21:41:09.549901 INFO::Formatting Data.
2026-04-17 21:41:09.550763 INFO::Recognized SummarizedExperiment
2026-04-17 21:41:09.551366 INFO::Typecasting input to dataframe.
2026-04-17 21:41:09.582979 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:09.584265 INFO::Removing potential empty rows and columns
2026-04-17 21:41:09.587758 INFO::Found 0 missing values.
2026-04-17 21:41:09.594288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:09.594903 INFO::Done
2026-04-17 21:41:09.595521 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:09.598943 INFO::Starting hierarchical adjustment
2026-04-17 21:41:09.599706 INFO::Found 2 batches.
2026-04-17 21:41:09.600244 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:09.601349 INFO::Using default BPPARAM
2026-04-17 21:41:09.601948 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:09.602963 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 21:41:09.6559 INFO::Done
2026-04-17 21:41:09.656676 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:09.660047 INFO::ASW Batch was 0.0231885972746498 prior to batch effect correction and is now -0.0926848462700714 .
2026-04-17 21:41:09.660871 INFO::Total function execution time is 0.111294507980347 s and adjustment time is 0.0563106536865234 s ( 50.6 )
Warning: stack imbalance in '{', 73 then 75
2026-04-17 21:41:09.677435 INFO::Formatting Data.
2026-04-17 21:41:09.678184 INFO::Recognized SummarizedExperiment
2026-04-17 21:41:09.678723 INFO::Typecasting input to dataframe.
2026-04-17 21:41:09.687052 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:09.68812 INFO::Removing potential empty rows and columns
2026-04-17 21:41:09.691405 INFO::Found 0 missing values.
2026-04-17 21:41:09.697703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:09.698274 INFO::Done
2026-04-17 21:41:09.698802 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:09.702083 INFO::Starting hierarchical adjustment
2026-04-17 21:41:09.702776 INFO::Found 2 batches.
2026-04-17 21:41:09.70331 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:09.703888 INFO::Using default BPPARAM
2026-04-17 21:41:09.704429 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:09.705346 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 21:41:09.731409 INFO::Done
2026-04-17 21:41:09.732251 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:09.736391 INFO::ASW Batch was 0.00364040101059437 prior to batch effect correction and is now 0.00364040101059437 .
2026-04-17 21:41:09.737365 INFO::Total function execution time is 0.0598647594451904 s and adjustment time is 0.0286970138549805 s ( 47.94 )
2026-04-17 21:41:09.758476 INFO::Formatting Data.
2026-04-17 21:41:09.759469 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:09.760518 INFO::Removing potential empty rows and columns
2026-04-17 21:41:09.761826 INFO::Found 0 missing values.
2026-04-17 21:41:09.765029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:09.765646 INFO::Done
2026-04-17 21:41:09.766211 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:09.768354 INFO::Starting hierarchical adjustment
2026-04-17 21:41:09.769087 INFO::Found 3 batches.
2026-04-17 21:41:09.769669 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:09.770319 INFO::Using default BPPARAM
2026-04-17 21:41:09.77088 INFO::Processing subtree level 1
2026-04-17 21:41:09.923242 INFO::Adjusting the last 1 batches sequentially
2026-04-17 21:41:09.925179 INFO::Done
2026-04-17 21:41:09.92592 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:09.928537 INFO::ASW Batch was -0.058059928072905 prior to batch effect correction and is now -0.161606407586441 .
2026-04-17 21:41:09.929576 INFO::Total function execution time is 0.171178579330444 s and adjustment time is 0.156230211257935 s ( 91.27 )
2026-04-17 21:41:09.945131 INFO::Skipping initial DF formatting
2026-04-17 21:41:09.945987 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:09.950189 INFO::Starting hierarchical adjustment
2026-04-17 21:41:09.951016 INFO::Found 5 batches.
2026-04-17 21:41:09.951648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:09.952347 INFO::Using default BPPARAM
2026-04-17 21:41:09.952929 INFO::Processing subtree level 1
2026-04-17 21:41:10.083822 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.085964 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 21:41:10.10823 INFO::Done
2026-04-17 21:41:10.109282 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:10.114182 INFO::ASW Batch was 0.533036672865175 prior to batch effect correction and is now 0.533036672865175 .
2026-04-17 21:41:10.114904 INFO::ASW Label was 0.376962341033396 prior to batch effect correction and is now 0.376962341033396 .
2026-04-17 21:41:10.115933 INFO::Total function execution time is 0.170873641967773 s and adjustment time is 0.15731143951416 s ( 92.06 )
2026-04-17 21:41:10.135732 INFO::Formatting Data.
2026-04-17 21:41:10.136752 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:10.137837 INFO::Removing potential empty rows and columns
2026-04-17 21:41:10.139318 INFO::Found 0 missing values.
2026-04-17 21:41:10.144567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:10.145452 INFO::Done
2026-04-17 21:41:10.146144 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:10.150137 INFO::Starting hierarchical adjustment
2026-04-17 21:41:10.15108 INFO::Found 5 batches.
2026-04-17 21:41:10.151763 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:10.152575 INFO::Using default BPPARAM
2026-04-17 21:41:10.153242 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.
2026-04-17 21:41:10.27702 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.279029 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 21:41:10.297673 INFO::Done
2026-04-17 21:41:10.298691 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:10.302652 INFO::ASW Batch was 0.371105121202425 prior to batch effect correction and is now 0.00223586532480255 .
2026-04-17 21:41:10.303422 INFO::ASW Label was 0.408035391006488 prior to batch effect correction and is now 0.772874500338742 .
2026-04-17 21:41:10.304397 INFO::Total function execution time is 0.168781518936157 s and adjustment time is 0.146716594696045 s ( 86.93 )
2026-04-17 21:41:10.305403 INFO::Formatting Data.
2026-04-17 21:41:10.306138 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:10.307195 INFO::Removing potential empty rows and columns
2026-04-17 21:41:10.308411 INFO::Found 0 missing values.
2026-04-17 21:41:10.313136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:10.313841 INFO::Done
2026-04-17 21:41:10.314469 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:10.317993 INFO::Starting hierarchical adjustment
2026-04-17 21:41:10.318902 INFO::Found 5 batches.
2026-04-17 21:41:10.319577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:10.320397 INFO::Using default BPPARAM
2026-04-17 21:41:10.321052 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.
2026-04-17 21:41:10.45701 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.459152 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 21:41:10.478211 INFO::Done
2026-04-17 21:41:10.479165 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:10.482959 INFO::ASW Batch was 0.371105121202425 prior to batch effect correction and is now 0.00223586532480255 .
2026-04-17 21:41:10.483708 INFO::ASW Label was 0.408035391006488 prior to batch effect correction and is now 0.772874500338742 .
2026-04-17 21:41:10.484723 INFO::Total function execution time is 0.179321765899658 s and adjustment time is 0.159462451934814 s ( 88.93 )
2026-04-17 21:41:10.501598 INFO::Formatting Data.
2026-04-17 21:41:10.50268 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:10.503806 INFO::Removing potential empty rows and columns
2026-04-17 21:41:10.50505 INFO::Found 0 missing values.
2026-04-17 21:41:10.509871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:10.510543 INFO::Done
2026-04-17 21:41:10.511221 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:10.514931 INFO::Starting hierarchical adjustment
2026-04-17 21:41:10.515804 INFO::Found 5 batches.
2026-04-17 21:41:10.516496 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:10.517236 INFO::Using default BPPARAM
2026-04-17 21:41:10.51792 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.
2026-04-17 21:41:10.630899 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.632676 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 21:41:10.649451 INFO::Done
2026-04-17 21:41:10.650274 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:10.653734 INFO::ASW Batch was 0.381899446991725 prior to batch effect correction and is now -0.101944700311616 .
2026-04-17 21:41:10.654398 INFO::ASW Label was 0.433631257514819 prior to batch effect correction and is now 0.813971303028449 .
2026-04-17 21:41:10.655251 INFO::Total function execution time is 0.153780698776245 s and adjustment time is 0.133764743804932 s ( 86.98 )
2026-04-17 21:41:10.65614 INFO::Formatting Data.
2026-04-17 21:41:10.656823 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:10.657816 INFO::Removing potential empty rows and columns
2026-04-17 21:41:10.658894 INFO::Found 0 missing values.
2026-04-17 21:41:10.663027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:10.663631 INFO::Done
2026-04-17 21:41:10.664207 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:10.667346 INFO::Starting hierarchical adjustment
2026-04-17 21:41:10.668338 INFO::Found 5 batches.
2026-04-17 21:41:10.66893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:10.669616 INFO::Using default BPPARAM
2026-04-17 21:41:10.670185 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.
2026-04-17 21:41:10.778876 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.780679 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 21:41:10.797304 INFO::Done
2026-04-17 21:41:10.798197 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:10.801678 INFO::ASW Batch was 0.381899446991725 prior to batch effect correction and is now -0.101944700311616 .
2026-04-17 21:41:10.802361 INFO::ASW Label was 0.433631257514819 prior to batch effect correction and is now 0.813971303028449 .
2026-04-17 21:41:10.803296 INFO::Total function execution time is 0.147131443023682 s and adjustment time is 0.129069566726685 s ( 87.72 )
2026-04-17 21:41:10.819023 INFO::Formatting Data.
2026-04-17 21:41:10.820042 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:10.821133 INFO::Removing potential empty rows and columns
2026-04-17 21:41:10.822385 INFO::Found 0 missing values.
2026-04-17 21:41:10.825558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:10.826243 INFO::Done
2026-04-17 21:41:10.826894 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:10.830373 INFO::Starting hierarchical adjustment
2026-04-17 21:41:10.831227 INFO::Found 2 batches.
2026-04-17 21:41:10.831875 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:10.832621 INFO::Using default BPPARAM
2026-04-17 21:41:10.833265 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.834356 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 21:41:10.852198 INFO::Done
2026-04-17 21:41:10.853176 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:10.856884 INFO::ASW Batch was 0.384547890170435 prior to batch effect correction and is now -0.0374425831335812 .
2026-04-17 21:41:10.857637 INFO::ASW Label was 0.591491515046178 prior to batch effect correction and is now 0.941883238573753 .
2026-04-17 21:41:10.85866 INFO::Total function execution time is 0.0397460460662842 s and adjustment time is 0.0211119651794434 s ( 53.12 )
2026-04-17 21:41:10.859661 INFO::Formatting Data.
2026-04-17 21:41:10.860443 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:10.861519 INFO::Removing potential empty rows and columns
2026-04-17 21:41:10.862746 INFO::Found 0 missing values.
2026-04-17 21:41:10.865981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:10.866666 INFO::Done
2026-04-17 21:41:10.867321 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:10.870746 INFO::Starting hierarchical adjustment
2026-04-17 21:41:10.871602 INFO::Found 2 batches.
2026-04-17 21:41:10.87223 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:10.872958 INFO::Using default BPPARAM
2026-04-17 21:41:10.873593 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.874651 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-17 21:41:10.891723 INFO::Done
2026-04-17 21:41:10.892635 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:10.896044 INFO::ASW Batch was 0.384547890170435 prior to batch effect correction and is now -0.0374425831335812 .
2026-04-17 21:41:10.896765 INFO::ASW Label was 0.591491515046178 prior to batch effect correction and is now 0.941883238573753 .
2026-04-17 21:41:10.897709 INFO::Total function execution time is 0.0380992889404297 s and adjustment time is 0.0202531814575195 s ( 53.16 )
2026-04-17 21:41:10.911266 INFO::Formatting Data.
2026-04-17 21:41:10.912276 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:10.913339 INFO::Removing potential empty rows and columns
2026-04-17 21:41:10.914468 INFO::Found 0 missing values.
2026-04-17 21:41:10.916944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:10.917624 INFO::Done
2026-04-17 21:41:10.918277 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:10.920589 INFO::Starting hierarchical adjustment
2026-04-17 21:41:10.921441 INFO::Found 2 batches.
2026-04-17 21:41:10.922089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:10.922829 INFO::Using default BPPARAM
2026-04-17 21:41:10.923487 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.924564 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 21:41:10.959535 INFO::Done
2026-04-17 21:41:10.960425 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:10.962608 INFO::ASW Batch was -0.13336142186338 prior to batch effect correction and is now -0.16958650240687 .
2026-04-17 21:41:10.963521 INFO::Total function execution time is 0.0523920059204102 s and adjustment time is 0.0382392406463623 s ( 72.99 )
2026-04-17 21:41:10.976209 INFO::Formatting Data.
2026-04-17 21:41:10.977206 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:10.978187 INFO::Removing potential empty rows and columns
2026-04-17 21:41:10.97928 INFO::Found 0 missing values.
2026-04-17 21:41:10.980481 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.
2026-04-17 21:41:10.985425 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:10.986101 INFO::Done
2026-04-17 21:41:10.986691 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:10.989814 INFO::Starting hierarchical adjustment
2026-04-17 21:41:10.990611 INFO::Found 2 batches.
2026-04-17 21:41:10.991184 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:10.991841 INFO::Using default BPPARAM
2026-04-17 21:41:10.992439 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:10.993418 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 21:41:11.010218 INFO::Done
2026-04-17 21:41:11.011025 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:11.014213 INFO::ASW Batch was 0.596898042556997 prior to batch effect correction and is now 0.11366219189976 .
2026-04-17 21:41:11.014874 INFO::ASW Label was 0.421144371660942 prior to batch effect correction and is now 0.809642511657953 .
2026-04-17 21:41:11.015735 INFO::Total function execution time is 0.0396595001220703 s and adjustment time is 0.0197277069091797 s ( 49.74 )
2026-04-17 21:41:11.016599 INFO::Formatting Data.
2026-04-17 21:41:11.017266 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:11.018215 INFO::Removing potential empty rows and columns
2026-04-17 21:41:11.019274 INFO::Found 0 missing values.
2026-04-17 21:41:11.020207 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.
2026-04-17 21:41:11.024849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:11.025475 INFO::Done
2026-04-17 21:41:11.026029 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:11.029019 INFO::Starting hierarchical adjustment
2026-04-17 21:41:11.029769 INFO::Found 2 batches.
2026-04-17 21:41:11.030349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:11.031025 INFO::Using default BPPARAM
2026-04-17 21:41:11.031605 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:11.032567 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 21:41:11.049036 INFO::Done
2026-04-17 21:41:11.049821 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:11.052819 INFO::ASW Batch was 0.596898042556997 prior to batch effect correction and is now 0.11366219189976 .
2026-04-17 21:41:11.053489 INFO::ASW Label was 0.421144371660942 prior to batch effect correction and is now 0.809642511657953 .
2026-04-17 21:41:11.054335 INFO::Total function execution time is 0.0377390384674072 s and adjustment time is 0.0193755626678467 s ( 51.34 )
2026-04-17 21:41:11.282382 INFO::Formatting Data.
2026-04-17 21:41:11.283446 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:11.292876 INFO::Removing potential empty rows and columns
2026-04-17 21:41:11.294993 INFO::Found 0 missing values.
2026-04-17 21:41:11.298975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:11.299758 INFO::Done
2026-04-17 21:41:11.300411 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:11.303174 INFO::Starting hierarchical adjustment
2026-04-17 21:41:11.304021 INFO::Found 3 batches.
2026-04-17 21:41:11.304685 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:11.3055 INFO::Using default BPPARAM
2026-04-17 21:41:11.306156 INFO::Processing subtree level 1
2026-04-17 21:41:11.420196 INFO::Adjusting the last 1 batches sequentially
2026-04-17 21:41:11.422244 INFO::Done
2026-04-17 21:41:11.423026 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:11.425936 INFO::ASW Batch was -0.0179384788045823 prior to batch effect correction and is now -0.0179384788045823 .
2026-04-17 21:41:11.427199 INFO::Total function execution time is 0.144892454147339 s and adjustment time is 0.118375062942505 s ( 81.7 )
2026-04-17 21:41:11.428455 INFO::Formatting Data.
2026-04-17 21:41:11.429227 INFO::Typecasting input to dataframe.
2026-04-17 21:41:11.430171 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:11.43128 INFO::Removing potential empty rows and columns
2026-04-17 21:41:11.43251 INFO::Found 0 missing values.
2026-04-17 21:41:11.435953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:11.436783 INFO::Done
2026-04-17 21:41:11.43748 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:11.439958 INFO::Starting hierarchical adjustment
2026-04-17 21:41:11.440828 INFO::Found 3 batches.
2026-04-17 21:41:11.441485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:11.442198 INFO::Using default BPPARAM
2026-04-17 21:41:11.442861 INFO::Processing subtree level 1
2026-04-17 21:41:11.544433 INFO::Adjusting the last 1 batches sequentially
2026-04-17 21:41:11.546597 INFO::Done
2026-04-17 21:41:11.547391 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:11.550367 INFO::ASW Batch was -0.0179384788045823 prior to batch effect correction and is now -0.0179384788045823 .
2026-04-17 21:41:11.551514 INFO::Total function execution time is 0.123050928115845 s and adjustment time is 0.105939865112305 s ( 86.09 )
2026-04-17 21:41:11.567928 INFO::Formatting Data.
2026-04-17 21:41:11.568952 INFO::Typecasting input to dataframe.
2026-04-17 21:41:11.569963 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:11.571049 INFO::Removing potential empty rows and columns
2026-04-17 21:41:11.572336 INFO::Found 0 missing values.
2026-04-17 21:41:11.575677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:11.57634 INFO::Done
2026-04-17 21:41:11.576972 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:11.579309 INFO::Starting hierarchical adjustment
2026-04-17 21:41:11.580128 INFO::Found 3 batches.
2026-04-17 21:41:11.580748 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:11.58148 INFO::Using default BPPARAM
2026-04-17 21:41:11.582133 INFO::Processing subtree level 1
2026-04-17 21:41:11.683405 INFO::Adjusting the last 1 batches sequentially
2026-04-17 21:41:11.685611 INFO::Done
2026-04-17 21:41:11.68645 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:11.689537 INFO::ASW Batch was -0.0483114788343396 prior to batch effect correction and is now -0.0483114788343396 .
2026-04-17 21:41:11.690718 INFO::Total function execution time is 0.122856140136719 s and adjustment time is 0.105618238449097 s ( 85.97 )
2026-04-17 21:41:11.850854 INFO::Formatting Data.
2026-04-17 21:41:11.851912 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:11.853289 INFO::Removing potential empty rows and columns
2026-04-17 21:41:11.856749 INFO::Found 1000 missing values.
2026-04-17 21:41:11.880299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:11.881215 INFO::Done
2026-04-17 21:41:11.881932 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:11.888267 INFO::Starting hierarchical adjustment
2026-04-17 21:41:11.889297 INFO::Found 10 batches.
2026-04-17 21:41:11.889969 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:11.890766 INFO::Using default BPPARAM
2026-04-17 21:41:11.891416 INFO::Processing subtree level 1
2026-04-17 21:41:12.058798 INFO::Processing subtree level 2
2026-04-17 21:41:12.230393 INFO::Adjusting the last 1 batches sequentially
2026-04-17 21:41:12.232921 INFO::Done
2026-04-17 21:41:12.233843 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:12.240813 INFO::ASW Batch was 0.474598945767958 prior to batch effect correction and is now 0.474598945767958 .
2026-04-17 21:41:12.24183 INFO::ASW Label was 0.31955177148216 prior to batch effect correction and is now 0.31955177148216 .
2026-04-17 21:41:12.243061 INFO::Total function execution time is 0.392250537872314 s and adjustment time is 0.343821287155151 s ( 87.65 )
2026-04-17 21:41:12.244153 INFO::Formatting Data.
2026-04-17 21:41:12.245048 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:12.246583 INFO::Removing potential empty rows and columns
2026-04-17 21:41:12.250407 INFO::Found 1000 missing values.
2026-04-17 21:41:12.27657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:12.277551 INFO::Done
2026-04-17 21:41:12.278293 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:12.28477 INFO::Starting hierarchical adjustment
2026-04-17 21:41:12.285752 INFO::Found 10 batches.
2026-04-17 21:41:13.499151 INFO::Set up parallel execution backend with 2 workers
2026-04-17 21:41:13.507937 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-17 21:41:14.979048 INFO::Adjusting the last 2 batches sequentially
2026-04-17 21:41:14.983591 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-17 21:41:15.002379 INFO::Done
2026-04-17 21:41:15.003237 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:15.008478 INFO::ASW Batch was 0.474598945767958 prior to batch effect correction and is now 0.474598945767958 .
2026-04-17 21:41:15.009729 INFO::ASW Label was 0.31955177148216 prior to batch effect correction and is now 0.31955177148216 .
2026-04-17 21:41:15.010639 INFO::Total function execution time is 2.76653242111206 s and adjustment time is 2.71676635742188 s ( 98.2 )
2026-04-17 21:41:15.204127 INFO::Formatting Data.
2026-04-17 21:41:15.20524 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.206463 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.207728 INFO::Found 0 missing values.
2026-04-17 21:41:15.211814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.212539 INFO::Done
2026-04-17 21:41:15.213188 INFO::Acquiring quality metrics before batch effect correction.
2026-04-17 21:41:15.216604 INFO::Starting hierarchical adjustment
2026-04-17 21:41:15.217464 INFO::Found 3 batches.
2026-04-17 21:41:15.2181 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-17 21:41:15.218821 INFO::Using default BPPARAM
2026-04-17 21:41:15.219494 INFO::Processing subtree level 1
2026-04-17 21:41:15.363618 INFO::Adjusting the last 1 batches sequentially
2026-04-17 21:41:15.365915 INFO::Done
2026-04-17 21:41:15.366777 INFO::Acquiring quality metrics after batch effect correction.
2026-04-17 21:41:15.370826 INFO::ASW Batch was 0.186664593589102 prior to batch effect correction and is now -0.171972652084348 .
2026-04-17 21:41:15.371685 INFO::ASW Label was -0.179861084455983 prior to batch effect correction and is now -0.0586539604062156 .
2026-04-17 21:41:15.372868 INFO::Total function execution time is 0.168802499771118 s and adjustment time is 0.148613691329956 s ( 88.04 )
2026-04-17 21:41:15.509881 INFO::Formatting Data.
2026-04-17 21:41:15.51086 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.511897 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.513052 INFO::Found 2 missing values.
2026-04-17 21:41:15.516109 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.516804 INFO::Done
2026-04-17 21:41:15.545658 INFO::Found NA in Reference column
2026-04-17 21:41:15.555828 INFO::Require at least two references per batch.
2026-04-17 21:41:15.576578 INFO::Formatting Data.
2026-04-17 21:41:15.577554 INFO::Recognized SummarizedExperiment
2026-04-17 21:41:15.578217 INFO::Typecasting input to dataframe.
2026-04-17 21:41:15.588555 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.589951 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.593811 INFO::Found 0 missing values.
2026-04-17 21:41:15.600889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.601703 INFO::Done
2026-04-17 21:41:15.627354 INFO::Formatting Data.
2026-04-17 21:41:15.628363 INFO::Recognized SummarizedExperiment
2026-04-17 21:41:15.628976 INFO::Typecasting input to dataframe.
2026-04-17 21:41:15.650938 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.652604 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.657194 INFO::Found 0 missing values.
2026-04-17 21:41:15.670369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.671277 INFO::Done
2026-04-17 21:41:15.689692 INFO::Formatting Data.
2026-04-17 21:41:15.690653 INFO::Recognized SummarizedExperiment
2026-04-17 21:41:15.691306 INFO::Typecasting input to dataframe.
2026-04-17 21:41:15.710681 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.712052 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.713443 INFO::Found 0 missing values.
2026-04-17 21:41:15.714515 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.
2026-04-17 21:41:15.719282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.71994 INFO::Done
2026-04-17 21:41:15.731246 INFO::Formatting Data.
2026-04-17 21:41:15.732287 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.733545 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.734779 INFO::Found 0 missing values.
2026-04-17 21:41:15.738371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.739063 INFO::Done
2026-04-17 21:41:15.75286 INFO::Formatting Data.
2026-04-17 21:41:15.753831 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.755036 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.756244 INFO::Found 0 missing values.
2026-04-17 21:41:15.759861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.760666 INFO::Done
2026-04-17 21:41:15.797507 INFO::Formatting Data.
2026-04-17 21:41:15.798568 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.799906 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.801396 INFO::Found 1 missing values.
2026-04-17 21:41:15.804801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.805531 INFO::Done
2026-04-17 21:41:15.829659 INFO::Formatting Data.
2026-04-17 21:41:15.83066 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.831751 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.832883 INFO::Found 2 missing values.
2026-04-17 21:41:15.833993 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.
2026-04-17 21:41:15.836636 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.837305 INFO::Done
2026-04-17 21:41:15.849502 INFO::Formatting Data.
2026-04-17 21:41:15.850611 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.85174 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.85293 INFO::Found 2 missing values.
2026-04-17 21:41:15.854851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.855594 INFO::Done
2026-04-17 21:41:15.868612 INFO::Formatting Data.
2026-04-17 21:41:15.869786 INFO::Typecasting input to dataframe.
2026-04-17 21:41:15.870837 INFO::Replacing NaNs with NAs.
2026-04-17 21:41:15.871975 INFO::Removing potential empty rows and columns
2026-04-17 21:41:15.873287 INFO::Found 0 missing values.
2026-04-17 21:41:15.876576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-17 21:41:15.877296 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.886 4.143 22.989
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.667 | 1.375 | 17.846 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.012 | 0.000 | 0.013 | |
| generate_dataset | 0.010 | 0.002 | 0.012 | |