Yannis Schumann
| Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 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 2025-10-04 12:07 -0400 (Sat, 04 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" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 164/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-10-03 04:56:14 -0000 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 04:57:40 -0000 (Fri, 03 Oct 2025) |
| EllapsedTime: 86.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* 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 29.912 1.439 21.527
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-10-03 04:57:22.343573 INFO::Formatting Data.
2025-10-03 04:57:22.34586 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:22.366167 INFO::Removing potential empty rows and columns
2025-10-03 04:57:22.819745 INFO::Found 0 missing values.
2025-10-03 04:57:22.825258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:22.826311 INFO::Done
2025-10-03 04:57:22.827171 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:22.845005 INFO::Starting hierarchical adjustment
2025-10-03 04:57:22.846367 INFO::Found 3 batches.
2025-10-03 04:57:22.847252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:22.84908 INFO::Using default BPPARAM
2025-10-03 04:57:22.850017 INFO::Processing subtree level 1
2025-10-03 04:57:23.001736 INFO::Adjusting the last 1 batches sequentially
2025-10-03 04:57:23.004735 INFO::Done
2025-10-03 04:57:23.005822 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:23.010376 INFO::ASW Batch was -0.0756479802184751 prior to batch effect correction and is now -0.0756479802184751 .
2025-10-03 04:57:23.012418 INFO::Total function execution time is 0.669697999954224 s and adjustment time is 0.158650398254395 s ( 23.69 )
2025-10-03 04:57:23.036235 INFO::Formatting Data.
2025-10-03 04:57:23.037416 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:23.038738 INFO::Removing potential empty rows and columns
2025-10-03 04:57:23.040484 INFO::Found 0 missing values.
2025-10-03 04:57:23.041969 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.
2025-10-03 04:57:23.061226 INFO::Formatting Data.
2025-10-03 04:57:23.062432 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:23.064057 INFO::Removing potential empty rows and columns
2025-10-03 04:57:23.065981 INFO::Found 0 missing values.
2025-10-03 04:57:23.06755 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.
2025-10-03 04:57:23.095371 INFO::Formatting Data.
2025-10-03 04:57:23.096646 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:23.098028 INFO::Removing potential empty rows and columns
2025-10-03 04:57:23.099883 INFO::Found 0 missing values.
2025-10-03 04:57:23.10155 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.
2025-10-03 04:57:23.109909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:23.111044 INFO::Done
2025-10-03 04:57:23.112025 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:23.115651 INFO::Starting hierarchical adjustment
2025-10-03 04:57:23.11702 INFO::Found 2 batches.
2025-10-03 04:57:23.118026 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:23.119313 INFO::Using default BPPARAM
2025-10-03 04:57:23.12017 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:23.121683 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 04:57:23.155345 INFO::Done
2025-10-03 04:57:23.156358 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:23.159537 INFO::ASW Batch was -0.0277097697713102 prior to batch effect correction and is now -0.105449232129483 .
2025-10-03 04:57:23.160806 INFO::Total function execution time is 0.0654585361480713 s and adjustment time is 0.0386347770690918 s ( 59.02 )
2025-10-03 04:57:23.164717 INFO::Formatting Data.
2025-10-03 04:57:23.165758 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:23.179242 INFO::Formatting Data.
2025-10-03 04:57:23.180335 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:23.181776 INFO::Removing potential empty rows and columns
2025-10-03 04:57:23.183392 INFO::Found 0 missing values.
2025-10-03 04:57:23.188178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:23.189208 INFO::Done
2025-10-03 04:57:23.190101 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:23.193431 INFO::Starting hierarchical adjustment
2025-10-03 04:57:23.194535 INFO::Found 2 batches.
2025-10-03 04:57:23.195396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:23.196336 INFO::Using default BPPARAM
2025-10-03 04:57:23.197495 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:23.199127 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 04:57:23.282196 INFO::Done
2025-10-03 04:57:23.283222 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:23.286633 INFO::ASW Batch was -0.0464463902692462 prior to batch effect correction and is now -0.10508953681033 .
2025-10-03 04:57:23.288082 INFO::Total function execution time is 0.108862638473511 s and adjustment time is 0.0878603458404541 s ( 80.71 )
2025-10-03 04:57:23.289978 INFO::Formatting Data.
2025-10-03 04:57:23.290974 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:23.292488 INFO::Removing potential empty rows and columns
2025-10-03 04:57:23.294302 INFO::Found 0 missing values.
2025-10-03 04:57:23.299282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:23.300381 INFO::Done
2025-10-03 04:57:23.301348 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:23.304712 INFO::Starting hierarchical adjustment
2025-10-03 04:57:23.305967 INFO::Found 2 batches.
2025-10-03 04:57:23.306867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:23.307899 INFO::Using default BPPARAM
2025-10-03 04:57:23.308817 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:23.310315 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 04:57:23.336709 INFO::Done
2025-10-03 04:57:23.337824 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:23.341184 INFO::ASW Batch was -0.0464463902692462 prior to batch effect correction and is now -0.10508953681033 .
2025-10-03 04:57:23.342527 INFO::Total function execution time is 0.0525405406951904 s and adjustment time is 0.0309579372406006 s ( 58.92 )
2025-10-03 04:57:27.952487 INFO::Formatting Data.
2025-10-03 04:57:27.953504 INFO::Recognized SummarizedExperiment
2025-10-03 04:57:27.954243 INFO::Typecasting input to dataframe.
2025-10-03 04:57:27.999863 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:28.001601 INFO::Removing potential empty rows and columns
2025-10-03 04:57:28.007125 INFO::Found 0 missing values.
2025-10-03 04:57:28.01796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:28.019042 INFO::Done
2025-10-03 04:57:28.019916 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:28.025188 INFO::Starting hierarchical adjustment
2025-10-03 04:57:28.026433 INFO::Found 2 batches.
2025-10-03 04:57:28.027313 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:28.02901 INFO::Using default BPPARAM
2025-10-03 04:57:28.029974 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:28.031497 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 04:57:28.11233 INFO::Done
2025-10-03 04:57:28.113321 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:28.118433 INFO::ASW Batch was -0.0070245683483491 prior to batch effect correction and is now -0.0939582429086528 .
2025-10-03 04:57:28.119886 INFO::Total function execution time is 0.167809963226318 s and adjustment time is 0.0861330032348633 s ( 51.33 )
2025-10-03 04:57:28.147337 INFO::Formatting Data.
2025-10-03 04:57:28.148411 INFO::Recognized SummarizedExperiment
2025-10-03 04:57:28.149309 INFO::Typecasting input to dataframe.
2025-10-03 04:57:28.163542 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:28.165367 INFO::Removing potential empty rows and columns
2025-10-03 04:57:28.170949 INFO::Found 0 missing values.
2025-10-03 04:57:28.181836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:28.182854 INFO::Done
2025-10-03 04:57:28.183751 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:28.189028 INFO::Starting hierarchical adjustment
2025-10-03 04:57:28.19032 INFO::Found 2 batches.
2025-10-03 04:57:28.191221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:28.192163 INFO::Using default BPPARAM
2025-10-03 04:57:28.193038 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:28.194552 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 04:57:28.24013 INFO::Done
2025-10-03 04:57:28.241239 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:28.246815 INFO::ASW Batch was 0.0238146047535787 prior to batch effect correction and is now 0.0238146047535787 .
2025-10-03 04:57:28.248218 INFO::Total function execution time is 0.100819826126099 s and adjustment time is 0.0500261783599854 s ( 49.62 )
2025-10-03 04:57:28.278353 INFO::Formatting Data.
2025-10-03 04:57:28.279582 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:28.281204 INFO::Removing potential empty rows and columns
2025-10-03 04:57:28.283107 INFO::Found 0 missing values.
2025-10-03 04:57:28.288443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:28.289515 INFO::Done
2025-10-03 04:57:28.290466 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:28.293805 INFO::Starting hierarchical adjustment
2025-10-03 04:57:28.295129 INFO::Found 3 batches.
2025-10-03 04:57:28.296107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:28.297196 INFO::Using default BPPARAM
2025-10-03 04:57:28.298111 INFO::Processing subtree level 1
2025-10-03 04:57:28.484197 INFO::Adjusting the last 1 batches sequentially
2025-10-03 04:57:28.487222 INFO::Done
2025-10-03 04:57:28.488387 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:28.492773 INFO::ASW Batch was -0.110214827864324 prior to batch effect correction and is now -0.157818482638094 .
2025-10-03 04:57:28.494449 INFO::Total function execution time is 0.216071844100952 s and adjustment time is 0.192338943481445 s ( 89.02 )
2025-10-03 04:57:28.517841 INFO::Skipping initial DF formatting
2025-10-03 04:57:28.51895 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:28.525549 INFO::Starting hierarchical adjustment
2025-10-03 04:57:28.526951 INFO::Found 5 batches.
2025-10-03 04:57:28.528055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:28.529302 INFO::Using default BPPARAM
2025-10-03 04:57:28.530301 INFO::Processing subtree level 1
2025-10-03 04:57:28.891382 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:28.894099 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 04:57:28.92504 INFO::Done
2025-10-03 04:57:28.926275 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:28.933156 INFO::ASW Batch was 0.491701144112557 prior to batch effect correction and is now 0.491701144112557 .
2025-10-03 04:57:28.934174 INFO::ASW Label was 0.434653595072177 prior to batch effect correction and is now 0.434653595072177 .
2025-10-03 04:57:28.935487 INFO::Total function execution time is 0.417709350585938 s and adjustment time is 0.398343324661255 s ( 95.36 )
2025-10-03 04:57:29.049855 INFO::Formatting Data.
2025-10-03 04:57:29.050997 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:29.052737 INFO::Removing potential empty rows and columns
2025-10-03 04:57:29.054691 INFO::Found 0 missing values.
2025-10-03 04:57:29.062999 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:29.064359 INFO::Done
2025-10-03 04:57:29.065552 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:29.071683 INFO::Starting hierarchical adjustment
2025-10-03 04:57:29.073287 INFO::Found 5 batches.
2025-10-03 04:57:29.074385 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:29.075982 INFO::Using default BPPARAM
2025-10-03 04:57:29.077602 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.
2025-10-03 04:57:29.258772 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:29.261598 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 04:57:29.290845 INFO::Done
2025-10-03 04:57:29.292016 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:29.297652 INFO::ASW Batch was 0.323061472808606 prior to batch effect correction and is now -0.00971712769018059 .
2025-10-03 04:57:29.298721 INFO::ASW Label was 0.356853326530947 prior to batch effect correction and is now 0.830201444817651 .
2025-10-03 04:57:29.300092 INFO::Total function execution time is 0.250237703323364 s and adjustment time is 0.217915296554565 s ( 87.08 )
2025-10-03 04:57:29.30149 INFO::Formatting Data.
2025-10-03 04:57:29.302512 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:29.304066 INFO::Removing potential empty rows and columns
2025-10-03 04:57:29.306068 INFO::Found 0 missing values.
2025-10-03 04:57:29.313818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:29.314828 INFO::Done
2025-10-03 04:57:29.315725 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:29.320616 INFO::Starting hierarchical adjustment
2025-10-03 04:57:29.321877 INFO::Found 5 batches.
2025-10-03 04:57:29.322767 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:29.323808 INFO::Using default BPPARAM
2025-10-03 04:57:29.324641 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.
2025-10-03 04:57:29.489784 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:29.492307 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 04:57:29.519526 INFO::Done
2025-10-03 04:57:29.520606 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:29.526111 INFO::ASW Batch was 0.323061472808606 prior to batch effect correction and is now -0.00971712769018059 .
2025-10-03 04:57:29.527142 INFO::ASW Label was 0.356853326530947 prior to batch effect correction and is now 0.830201444817651 .
2025-10-03 04:57:29.52847 INFO::Total function execution time is 0.226962566375732 s and adjustment time is 0.197863578796387 s ( 87.18 )
2025-10-03 04:57:29.551704 INFO::Formatting Data.
2025-10-03 04:57:29.552905 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:29.554302 INFO::Removing potential empty rows and columns
2025-10-03 04:57:29.555944 INFO::Found 0 missing values.
2025-10-03 04:57:29.562725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:29.563731 INFO::Done
2025-10-03 04:57:29.564582 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:29.569646 INFO::Starting hierarchical adjustment
2025-10-03 04:57:29.570965 INFO::Found 5 batches.
2025-10-03 04:57:29.571833 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:29.572913 INFO::Using default BPPARAM
2025-10-03 04:57:29.573833 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.
2025-10-03 04:57:29.740338 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:29.742886 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 04:57:29.769857 INFO::Done
2025-10-03 04:57:29.770881 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:29.776284 INFO::ASW Batch was 0.226536568660995 prior to batch effect correction and is now -0.0343190370936797 .
2025-10-03 04:57:29.777377 INFO::ASW Label was 0.556770601813255 prior to batch effect correction and is now 0.823240456616266 .
2025-10-03 04:57:29.778681 INFO::Total function execution time is 0.227072954177856 s and adjustment time is 0.199150562286377 s ( 87.7 )
2025-10-03 04:57:29.780047 INFO::Formatting Data.
2025-10-03 04:57:29.781105 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:29.782528 INFO::Removing potential empty rows and columns
2025-10-03 04:57:29.784312 INFO::Found 0 missing values.
2025-10-03 04:57:29.791239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:29.792316 INFO::Done
2025-10-03 04:57:29.793244 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:29.798069 INFO::Starting hierarchical adjustment
2025-10-03 04:57:29.799342 INFO::Found 5 batches.
2025-10-03 04:57:29.800246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:29.801351 INFO::Using default BPPARAM
2025-10-03 04:57:29.802196 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.
2025-10-03 04:57:29.978929 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:29.981835 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 04:57:30.012873 INFO::Done
2025-10-03 04:57:30.014028 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:30.020351 INFO::ASW Batch was 0.226536568660995 prior to batch effect correction and is now -0.0343190370936797 .
2025-10-03 04:57:30.021661 INFO::ASW Label was 0.556770601813255 prior to batch effect correction and is now 0.823240456616266 .
2025-10-03 04:57:30.02387 INFO::Total function execution time is 0.243628263473511 s and adjustment time is 0.213682174682617 s ( 87.71 )
2025-10-03 04:57:30.049472 INFO::Formatting Data.
2025-10-03 04:57:30.05082 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:30.052538 INFO::Removing potential empty rows and columns
2025-10-03 04:57:30.054625 INFO::Found 0 missing values.
2025-10-03 04:57:30.059689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:30.060704 INFO::Done
2025-10-03 04:57:30.066847 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:30.071977 INFO::Starting hierarchical adjustment
2025-10-03 04:57:30.073333 INFO::Found 2 batches.
2025-10-03 04:57:30.074264 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:30.075289 INFO::Using default BPPARAM
2025-10-03 04:57:30.076269 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:30.077787 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 04:57:30.10319 INFO::Done
2025-10-03 04:57:30.104286 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:30.109358 INFO::ASW Batch was 0.607031780867824 prior to batch effect correction and is now 0.0821799454407443 .
2025-10-03 04:57:30.110389 INFO::ASW Label was 0.453634270103547 prior to batch effect correction and is now 0.847703741798894 .
2025-10-03 04:57:30.111665 INFO::Total function execution time is 0.0622828006744385 s and adjustment time is 0.0300989151000977 s ( 48.33 )
2025-10-03 04:57:30.113274 INFO::Formatting Data.
2025-10-03 04:57:30.114345 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:30.115755 INFO::Removing potential empty rows and columns
2025-10-03 04:57:30.117517 INFO::Found 0 missing values.
2025-10-03 04:57:30.122229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:30.123431 INFO::Done
2025-10-03 04:57:30.124511 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:30.129812 INFO::Starting hierarchical adjustment
2025-10-03 04:57:30.131197 INFO::Found 2 batches.
2025-10-03 04:57:30.132138 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:30.133159 INFO::Using default BPPARAM
2025-10-03 04:57:30.133996 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:30.135697 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-03 04:57:30.160975 INFO::Done
2025-10-03 04:57:30.161994 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:30.166712 INFO::ASW Batch was 0.607031780867824 prior to batch effect correction and is now 0.0821799454407443 .
2025-10-03 04:57:30.167762 INFO::ASW Label was 0.453634270103547 prior to batch effect correction and is now 0.847703741798894 .
2025-10-03 04:57:30.169394 INFO::Total function execution time is 0.0560719966888428 s and adjustment time is 0.0299227237701416 s ( 53.36 )
2025-10-03 04:57:30.1879 INFO::Formatting Data.
2025-10-03 04:57:30.189028 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:30.190355 INFO::Removing potential empty rows and columns
2025-10-03 04:57:30.19183 INFO::Found 0 missing values.
2025-10-03 04:57:30.19532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:30.196345 INFO::Done
2025-10-03 04:57:30.197387 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:30.200782 INFO::Starting hierarchical adjustment
2025-10-03 04:57:30.201993 INFO::Found 2 batches.
2025-10-03 04:57:30.202844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:30.203882 INFO::Using default BPPARAM
2025-10-03 04:57:30.204729 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:30.206205 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 04:57:30.26006 INFO::Done
2025-10-03 04:57:30.261168 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:30.264286 INFO::ASW Batch was -0.0910745664260336 prior to batch effect correction and is now -0.146111565633891 .
2025-10-03 04:57:30.265672 INFO::Total function execution time is 0.0778913497924805 s and adjustment time is 0.0582571029663086 s ( 74.79 )
2025-10-03 04:57:30.285292 INFO::Formatting Data.
2025-10-03 04:57:30.286552 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:30.288131 INFO::Removing potential empty rows and columns
2025-10-03 04:57:30.290022 INFO::Found 0 missing values.
2025-10-03 04:57:30.292109 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.
2025-10-03 04:57:30.300703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:30.30177 INFO::Done
2025-10-03 04:57:30.302758 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:30.307444 INFO::Starting hierarchical adjustment
2025-10-03 04:57:30.308845 INFO::Found 2 batches.
2025-10-03 04:57:30.30985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:30.310905 INFO::Using default BPPARAM
2025-10-03 04:57:30.31181 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:30.313472 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 04:57:30.344355 INFO::Done
2025-10-03 04:57:30.345692 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:30.350925 INFO::ASW Batch was 0.54850216863832 prior to batch effect correction and is now 0.116057777296767 .
2025-10-03 04:57:30.352022 INFO::ASW Label was 0.548043544632677 prior to batch effect correction and is now 0.854236127517747 .
2025-10-03 04:57:30.353298 INFO::Total function execution time is 0.0681154727935791 s and adjustment time is 0.0356540679931641 s ( 52.34 )
2025-10-03 04:57:30.354761 INFO::Formatting Data.
2025-10-03 04:57:30.355782 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:30.357361 INFO::Removing potential empty rows and columns
2025-10-03 04:57:30.359178 INFO::Found 0 missing values.
2025-10-03 04:57:30.361076 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.
2025-10-03 04:57:30.370691 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:30.371774 INFO::Done
2025-10-03 04:57:30.37266 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:30.377816 INFO::Starting hierarchical adjustment
2025-10-03 04:57:30.379149 INFO::Found 2 batches.
2025-10-03 04:57:30.380146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:30.381176 INFO::Using default BPPARAM
2025-10-03 04:57:30.382076 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:30.383689 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 04:57:30.412843 INFO::Done
2025-10-03 04:57:30.41385 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:30.418632 INFO::ASW Batch was 0.54850216863832 prior to batch effect correction and is now 0.116057777296767 .
2025-10-03 04:57:30.419838 INFO::ASW Label was 0.548043544632677 prior to batch effect correction and is now 0.854236127517747 .
2025-10-03 04:57:30.421241 INFO::Total function execution time is 0.0664706230163574 s and adjustment time is 0.0339112281799316 s ( 51.02 )
2025-10-03 04:57:30.778866 INFO::Formatting Data.
2025-10-03 04:57:30.779986 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:30.781231 INFO::Removing potential empty rows and columns
2025-10-03 04:57:30.782707 INFO::Found 0 missing values.
2025-10-03 04:57:30.78713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:30.788166 INFO::Done
2025-10-03 04:57:30.788973 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:30.791985 INFO::Starting hierarchical adjustment
2025-10-03 04:57:30.793238 INFO::Found 3 batches.
2025-10-03 04:57:30.794036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:30.794856 INFO::Using default BPPARAM
2025-10-03 04:57:30.79561 INFO::Processing subtree level 1
2025-10-03 04:57:30.911738 INFO::Adjusting the last 1 batches sequentially
2025-10-03 04:57:30.914765 INFO::Done
2025-10-03 04:57:30.915964 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:30.920331 INFO::ASW Batch was -0.102580904335993 prior to batch effect correction and is now -0.102580904335993 .
2025-10-03 04:57:30.922144 INFO::Total function execution time is 0.143182516098022 s and adjustment time is 0.12180233001709 s ( 85.07 )
2025-10-03 04:57:30.92407 INFO::Formatting Data.
2025-10-03 04:57:30.925232 INFO::Typecasting input to dataframe.
2025-10-03 04:57:30.92646 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:30.928019 INFO::Removing potential empty rows and columns
2025-10-03 04:57:30.929916 INFO::Found 0 missing values.
2025-10-03 04:57:30.934792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:30.935816 INFO::Done
2025-10-03 04:57:30.93665 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:30.939767 INFO::Starting hierarchical adjustment
2025-10-03 04:57:30.941072 INFO::Found 3 batches.
2025-10-03 04:57:30.941971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:30.942921 INFO::Using default BPPARAM
2025-10-03 04:57:30.943823 INFO::Processing subtree level 1
2025-10-03 04:57:31.079363 INFO::Adjusting the last 1 batches sequentially
2025-10-03 04:57:31.082154 INFO::Done
2025-10-03 04:57:31.083062 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:31.086957 INFO::ASW Batch was -0.102580904335993 prior to batch effect correction and is now -0.102580904335993 .
2025-10-03 04:57:31.08847 INFO::Total function execution time is 0.164410591125488 s and adjustment time is 0.141350746154785 s ( 85.97 )
2025-10-03 04:57:31.108974 INFO::Formatting Data.
2025-10-03 04:57:31.110112 INFO::Typecasting input to dataframe.
2025-10-03 04:57:31.111457 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:31.113044 INFO::Removing potential empty rows and columns
2025-10-03 04:57:31.114778 INFO::Found 0 missing values.
2025-10-03 04:57:31.1196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:31.120683 INFO::Done
2025-10-03 04:57:31.121622 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:31.124631 INFO::Starting hierarchical adjustment
2025-10-03 04:57:31.125912 INFO::Found 3 batches.
2025-10-03 04:57:31.126783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:31.127803 INFO::Using default BPPARAM
2025-10-03 04:57:31.128682 INFO::Processing subtree level 1
2025-10-03 04:57:31.244826 INFO::Adjusting the last 1 batches sequentially
2025-10-03 04:57:31.248021 INFO::Done
2025-10-03 04:57:31.24916 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:31.253484 INFO::ASW Batch was -0.0502395476281099 prior to batch effect correction and is now -0.0502395476281099 .
2025-10-03 04:57:31.255134 INFO::Total function execution time is 0.146171092987061 s and adjustment time is 0.122329711914062 s ( 83.69 )
2025-10-03 04:57:31.462798 INFO::Formatting Data.
2025-10-03 04:57:31.464196 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:31.466235 INFO::Removing potential empty rows and columns
2025-10-03 04:57:31.471436 INFO::Found 1000 missing values.
2025-10-03 04:57:31.504346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:31.505537 INFO::Done
2025-10-03 04:57:31.506634 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:31.51549 INFO::Starting hierarchical adjustment
2025-10-03 04:57:31.516785 INFO::Found 10 batches.
2025-10-03 04:57:31.517601 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:31.518486 INFO::Using default BPPARAM
2025-10-03 04:57:31.519259 INFO::Processing subtree level 1
2025-10-03 04:57:31.701949 INFO::Processing subtree level 2
2025-10-03 04:57:31.918366 INFO::Adjusting the last 1 batches sequentially
2025-10-03 04:57:31.921575 INFO::Done
2025-10-03 04:57:31.922588 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:31.931355 INFO::ASW Batch was 0.485723578686428 prior to batch effect correction and is now 0.485723578686428 .
2025-10-03 04:57:31.932445 INFO::ASW Label was 0.340789607377992 prior to batch effect correction and is now 0.340789607377992 .
2025-10-03 04:57:31.933963 INFO::Total function execution time is 0.471229314804077 s and adjustment time is 0.405013799667358 s ( 85.95 )
2025-10-03 04:57:31.935241 INFO::Formatting Data.
2025-10-03 04:57:31.936258 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:31.938185 INFO::Removing potential empty rows and columns
2025-10-03 04:57:31.942657 INFO::Found 1000 missing values.
2025-10-03 04:57:31.972523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:31.973628 INFO::Done
2025-10-03 04:57:31.974522 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:31.982682 INFO::Starting hierarchical adjustment
2025-10-03 04:57:31.984003 INFO::Found 10 batches.
2025-10-03 04:57:33.432265 INFO::Set up parallel execution backend with 2 workers
2025-10-03 04:57:33.434934 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-03 04:57:34.960119 INFO::Adjusting the last 2 batches sequentially
2025-10-03 04:57:34.962778 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-03 04:57:34.989472 INFO::Done
2025-10-03 04:57:34.99043 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:34.997704 INFO::ASW Batch was 0.485723578686428 prior to batch effect correction and is now 0.485723578686428 .
2025-10-03 04:57:34.998646 INFO::ASW Label was 0.340789607377992 prior to batch effect correction and is now 0.340789607377992 .
2025-10-03 04:57:34.999848 INFO::Total function execution time is 3.06456780433655 s and adjustment time is 3.00574326515198 s ( 98.08 )
2025-10-03 04:57:35.197532 INFO::Formatting Data.
2025-10-03 04:57:35.198752 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:35.200229 INFO::Removing potential empty rows and columns
2025-10-03 04:57:35.202044 INFO::Found 0 missing values.
2025-10-03 04:57:35.208592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:35.209617 INFO::Done
2025-10-03 04:57:35.210468 INFO::Acquiring quality metrics before batch effect correction.
2025-10-03 04:57:35.21484 INFO::Starting hierarchical adjustment
2025-10-03 04:57:35.216134 INFO::Found 3 batches.
2025-10-03 04:57:35.217061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-03 04:57:35.218048 INFO::Using default BPPARAM
2025-10-03 04:57:35.21891 INFO::Processing subtree level 1
2025-10-03 04:57:35.361348 INFO::Adjusting the last 1 batches sequentially
2025-10-03 04:57:35.364246 INFO::Done
2025-10-03 04:57:35.365438 INFO::Acquiring quality metrics after batch effect correction.
2025-10-03 04:57:35.37102 INFO::ASW Batch was 0.197540118205192 prior to batch effect correction and is now -0.143395558140049 .
2025-10-03 04:57:35.372219 INFO::ASW Label was -0.182721445471768 prior to batch effect correction and is now -0.0449076779484547 .
2025-10-03 04:57:35.373855 INFO::Total function execution time is 0.176305770874023 s and adjustment time is 0.148322105407715 s ( 84.13 )
2025-10-03 04:57:35.568978 INFO::Formatting Data.
2025-10-03 04:57:35.570139 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:35.571494 INFO::Removing potential empty rows and columns
2025-10-03 04:57:35.573271 INFO::Found 2 missing values.
2025-10-03 04:57:35.578126 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:35.579123 INFO::Done
2025-10-03 04:57:35.627254 INFO::Found NA in Reference column
2025-10-03 04:57:35.643179 INFO::Require at least two references per batch.
2025-10-03 04:57:35.676908 INFO::Formatting Data.
2025-10-03 04:57:35.677949 INFO::Recognized SummarizedExperiment
2025-10-03 04:57:35.678779 INFO::Typecasting input to dataframe.
2025-10-03 04:57:35.694578 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:35.696385 INFO::Removing potential empty rows and columns
2025-10-03 04:57:35.702325 INFO::Found 0 missing values.
2025-10-03 04:57:35.713885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:35.714863 INFO::Done
2025-10-03 04:57:35.739714 INFO::Formatting Data.
2025-10-03 04:57:35.740807 INFO::Recognized SummarizedExperiment
2025-10-03 04:57:35.741654 INFO::Typecasting input to dataframe.
2025-10-03 04:57:35.770349 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:35.772209 INFO::Removing potential empty rows and columns
2025-10-03 04:57:35.778147 INFO::Found 0 missing values.
2025-10-03 04:57:35.796945 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:35.79792 INFO::Done
2025-10-03 04:57:35.822865 INFO::Formatting Data.
2025-10-03 04:57:35.823983 INFO::Recognized SummarizedExperiment
2025-10-03 04:57:35.824858 INFO::Typecasting input to dataframe.
2025-10-03 04:57:35.853026 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:35.854617 INFO::Removing potential empty rows and columns
2025-10-03 04:57:35.856472 INFO::Found 0 missing values.
2025-10-03 04:57:35.858059 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.
2025-10-03 04:57:35.865158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:35.86612 INFO::Done
2025-10-03 04:57:35.881567 INFO::Formatting Data.
2025-10-03 04:57:35.88269 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:35.884043 INFO::Removing potential empty rows and columns
2025-10-03 04:57:35.885643 INFO::Found 0 missing values.
2025-10-03 04:57:35.890352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:35.891309 INFO::Done
2025-10-03 04:57:35.909178 INFO::Formatting Data.
2025-10-03 04:57:35.910308 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:35.911769 INFO::Removing potential empty rows and columns
2025-10-03 04:57:35.913435 INFO::Found 0 missing values.
2025-10-03 04:57:35.918498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:35.919466 INFO::Done
2025-10-03 04:57:35.967387 INFO::Formatting Data.
2025-10-03 04:57:35.968558 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:35.970132 INFO::Removing potential empty rows and columns
2025-10-03 04:57:35.971956 INFO::Found 1 missing values.
2025-10-03 04:57:35.976247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:35.977304 INFO::Done
2025-10-03 04:57:36.007377 INFO::Formatting Data.
2025-10-03 04:57:36.008595 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:36.009974 INFO::Removing potential empty rows and columns
2025-10-03 04:57:36.011492 INFO::Found 2 missing values.
2025-10-03 04:57:36.012998 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.
2025-10-03 04:57:36.016789 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:36.01781 INFO::Done
2025-10-03 04:57:36.034214 INFO::Formatting Data.
2025-10-03 04:57:36.035349 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:36.036785 INFO::Removing potential empty rows and columns
2025-10-03 04:57:36.038273 INFO::Found 2 missing values.
2025-10-03 04:57:36.040961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:36.041925 INFO::Done
2025-10-03 04:57:36.059073 INFO::Formatting Data.
2025-10-03 04:57:36.060248 INFO::Typecasting input to dataframe.
2025-10-03 04:57:36.061555 INFO::Replacing NaNs with NAs.
2025-10-03 04:57:36.062933 INFO::Removing potential empty rows and columns
2025-10-03 04:57:36.064583 INFO::Found 0 missing values.
2025-10-03 04:57:36.069471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-03 04:57:36.070451 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.619 6.129 28.337
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.912 | 1.439 | 21.527 | |
| compute_asw | 0.036 | 0.000 | 0.036 | |
| count_existing | 0.018 | 0.000 | 0.018 | |
| generate_data_covariables | 0.016 | 0.000 | 0.016 | |
| generate_dataset | 0.015 | 0.000 | 0.015 | |