Yannis Schumann
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| 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 162/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 2025-08-01 04:26:46 -0000 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 04:28:04 -0000 (Fri, 01 Aug 2025) |
| EllapsedTime: 78.9 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 28.128 1.257 20.409
* 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")
2025-08-01 04:27:47.379435 INFO::Formatting Data.
2025-08-01 04:27:47.382102 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:47.402609 INFO::Removing potential empty rows and columns
2025-08-01 04:27:47.796982 INFO::Found 0 missing values.
2025-08-01 04:27:47.802405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:47.803396 INFO::Done
2025-08-01 04:27:47.804206 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:47.820822 INFO::Starting hierarchical adjustment
2025-08-01 04:27:47.822221 INFO::Found 3 batches.
2025-08-01 04:27:47.82329 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:47.824996 INFO::Using default BPPARAM
2025-08-01 04:27:47.825881 INFO::Processing subtree level 1
2025-08-01 04:27:47.958008 INFO::Adjusting the last 1 batches sequentially
2025-08-01 04:27:47.960561 INFO::Done
2025-08-01 04:27:47.96152 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:47.965861 INFO::ASW Batch was -0.0857064510971367 prior to batch effect correction and is now -0.0857064510971367 .
2025-08-01 04:27:47.967591 INFO::Total function execution time is 0.589163780212402 s and adjustment time is 0.138679504394531 s ( 23.54 )
2025-08-01 04:27:47.988679 INFO::Formatting Data.
2025-08-01 04:27:47.989752 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:47.991099 INFO::Removing potential empty rows and columns
2025-08-01 04:27:47.992759 INFO::Found 0 missing values.
2025-08-01 04:27:47.994151 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-01 04:27:48.010652 INFO::Formatting Data.
2025-08-01 04:27:48.011735 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:48.013077 INFO::Removing potential empty rows and columns
2025-08-01 04:27:48.014672 INFO::Found 0 missing values.
2025-08-01 04:27:48.016025 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-01 04:27:48.039468 INFO::Formatting Data.
2025-08-01 04:27:48.040504 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:48.041782 INFO::Removing potential empty rows and columns
2025-08-01 04:27:48.043545 INFO::Found 0 missing values.
2025-08-01 04:27:48.045 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-01 04:27:48.052205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:48.05317 INFO::Done
2025-08-01 04:27:48.05415 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:48.057252 INFO::Starting hierarchical adjustment
2025-08-01 04:27:48.0585 INFO::Found 2 batches.
2025-08-01 04:27:48.059341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:48.060289 INFO::Using default BPPARAM
2025-08-01 04:27:48.061119 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:48.06262 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 04:27:48.096208 INFO::Done
2025-08-01 04:27:48.097208 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:48.100158 INFO::ASW Batch was 0.0378775140816462 prior to batch effect correction and is now -0.0972806428867309 .
2025-08-01 04:27:48.101418 INFO::Total function execution time is 0.0620105266571045 s and adjustment time is 0.0379881858825684 s ( 61.26 )
2025-08-01 04:27:48.105295 INFO::Formatting Data.
2025-08-01 04:27:48.106305 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:48.118809 INFO::Formatting Data.
2025-08-01 04:27:48.11985 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:48.121165 INFO::Removing potential empty rows and columns
2025-08-01 04:27:48.122815 INFO::Found 0 missing values.
2025-08-01 04:27:48.127207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:48.128105 INFO::Done
2025-08-01 04:27:48.128912 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:48.132194 INFO::Starting hierarchical adjustment
2025-08-01 04:27:48.133314 INFO::Found 2 batches.
2025-08-01 04:27:48.13411 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:48.135048 INFO::Using default BPPARAM
2025-08-01 04:27:48.135862 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:48.137423 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:48.200851 INFO::Done
2025-08-01 04:27:48.201763 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:48.204644 INFO::ASW Batch was -0.00180800616077658 prior to batch effect correction and is now -0.100495207454765 .
2025-08-01 04:27:48.205779 INFO::Total function execution time is 0.0870420932769775 s and adjustment time is 0.0677089691162109 s ( 77.79 )
2025-08-01 04:27:48.207284 INFO::Formatting Data.
2025-08-01 04:27:48.208125 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:48.209346 INFO::Removing potential empty rows and columns
2025-08-01 04:27:48.211099 INFO::Found 0 missing values.
2025-08-01 04:27:48.215333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:48.216294 INFO::Done
2025-08-01 04:27:48.21716 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:48.220264 INFO::Starting hierarchical adjustment
2025-08-01 04:27:48.221488 INFO::Found 2 batches.
2025-08-01 04:27:48.222355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:48.223295 INFO::Using default BPPARAM
2025-08-01 04:27:48.224051 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:48.225442 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:48.247867 INFO::Done
2025-08-01 04:27:48.249317 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:48.252084 INFO::ASW Batch was -0.00180800616077658 prior to batch effect correction and is now -0.100495207454765 .
2025-08-01 04:27:48.253222 INFO::Total function execution time is 0.0459136962890625 s and adjustment time is 0.026613712310791 s ( 57.96 )
2025-08-01 04:27:51.966546 INFO::Formatting Data.
2025-08-01 04:27:51.967554 INFO::Recognized SummarizedExperiment
2025-08-01 04:27:51.968246 INFO::Typecasting input to dataframe.
2025-08-01 04:27:52.009909 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:52.011562 INFO::Removing potential empty rows and columns
2025-08-01 04:27:52.016862 INFO::Found 0 missing values.
2025-08-01 04:27:52.027359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:52.028277 INFO::Done
2025-08-01 04:27:52.02907 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:52.034144 INFO::Starting hierarchical adjustment
2025-08-01 04:27:52.035225 INFO::Found 2 batches.
2025-08-01 04:27:52.035977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:52.037477 INFO::Using default BPPARAM
2025-08-01 04:27:52.038259 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:52.039667 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 04:27:52.118294 INFO::Done
2025-08-01 04:27:52.119226 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:52.123904 INFO::ASW Batch was 0.037944197365138 prior to batch effect correction and is now -0.100295934886464 .
2025-08-01 04:27:52.125041 INFO::Total function execution time is 0.159014463424683 s and adjustment time is 0.0832769870758057 s ( 52.37 )
2025-08-01 04:27:52.150362 INFO::Formatting Data.
2025-08-01 04:27:52.151321 INFO::Recognized SummarizedExperiment
2025-08-01 04:27:52.152058 INFO::Typecasting input to dataframe.
2025-08-01 04:27:52.164514 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:52.166018 INFO::Removing potential empty rows and columns
2025-08-01 04:27:52.171095 INFO::Found 0 missing values.
2025-08-01 04:27:52.180866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:52.181768 INFO::Done
2025-08-01 04:27:52.182527 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:52.187269 INFO::Starting hierarchical adjustment
2025-08-01 04:27:52.18827 INFO::Found 2 batches.
2025-08-01 04:27:52.189051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:52.189883 INFO::Using default BPPARAM
2025-08-01 04:27:52.190661 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:52.191976 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 04:27:52.225957 INFO::Done
2025-08-01 04:27:52.226869 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:52.231736 INFO::ASW Batch was 0.00519053336368932 prior to batch effect correction and is now 0.00519053336368932 .
2025-08-01 04:27:52.232863 INFO::Total function execution time is 0.0824534893035889 s and adjustment time is 0.0378732681274414 s ( 45.93 )
2025-08-01 04:27:52.256814 INFO::Formatting Data.
2025-08-01 04:27:52.257791 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:52.25899 INFO::Removing potential empty rows and columns
2025-08-01 04:27:52.26039 INFO::Found 0 missing values.
2025-08-01 04:27:52.26458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:52.265358 INFO::Done
2025-08-01 04:27:52.266085 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:52.268693 INFO::Starting hierarchical adjustment
2025-08-01 04:27:52.269692 INFO::Found 3 batches.
2025-08-01 04:27:52.270431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:52.271261 INFO::Using default BPPARAM
2025-08-01 04:27:52.271997 INFO::Processing subtree level 1
2025-08-01 04:27:52.440336 INFO::Adjusting the last 1 batches sequentially
2025-08-01 04:27:52.442891 INFO::Done
2025-08-01 04:27:52.443682 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:52.447164 INFO::ASW Batch was -0.0734337196698771 prior to batch effect correction and is now -0.16967532255031 .
2025-08-01 04:27:52.448447 INFO::Total function execution time is 0.191679954528809 s and adjustment time is 0.173402786254883 s ( 90.46 )
2025-08-01 04:27:52.468436 INFO::Skipping initial DF formatting
2025-08-01 04:27:52.469393 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:52.475147 INFO::Starting hierarchical adjustment
2025-08-01 04:27:52.476298 INFO::Found 5 batches.
2025-08-01 04:27:52.477088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:52.477946 INFO::Using default BPPARAM
2025-08-01 04:27:52.4787 INFO::Processing subtree level 1
2025-08-01 04:27:53.955396 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:53.958642 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 04:27:53.988304 INFO::Done
2025-08-01 04:27:53.989266 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:54.066104 INFO::ASW Batch was 0.54502121913515 prior to batch effect correction and is now 0.54502121913515 .
2025-08-01 04:27:54.067102 INFO::ASW Label was 0.356302357028975 prior to batch effect correction and is now 0.356302357028975 .
2025-08-01 04:27:54.068325 INFO::Total function execution time is 1.59996342658997 s and adjustment time is 1.51218485832214 s ( 94.51 )
2025-08-01 04:27:54.095619 INFO::Formatting Data.
2025-08-01 04:27:54.106609 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:54.109815 INFO::Removing potential empty rows and columns
2025-08-01 04:27:54.112347 INFO::Found 0 missing values.
2025-08-01 04:27:54.12311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:54.125292 INFO::Done
2025-08-01 04:27:54.127179 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:54.135244 INFO::Starting hierarchical adjustment
2025-08-01 04:27:54.136994 INFO::Found 5 batches.
2025-08-01 04:27:54.138277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:54.13982 INFO::Using default BPPARAM
2025-08-01 04:27:54.14109 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:54.331538 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:54.334159 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:54.361956 INFO::Done
2025-08-01 04:27:54.363081 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:54.368584 INFO::ASW Batch was 0.444273589491456 prior to batch effect correction and is now -0.100384793364011 .
2025-08-01 04:27:54.369809 INFO::ASW Label was 0.331924969377186 prior to batch effect correction and is now 0.822810325597331 .
2025-08-01 04:27:54.371348 INFO::Total function execution time is 0.275723218917847 s and adjustment time is 0.225400686264038 s ( 81.75 )
2025-08-01 04:27:54.372944 INFO::Formatting Data.
2025-08-01 04:27:54.373998 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:54.375487 INFO::Removing potential empty rows and columns
2025-08-01 04:27:54.377279 INFO::Found 0 missing values.
2025-08-01 04:27:54.384411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:54.385465 INFO::Done
2025-08-01 04:27:54.386305 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:54.391279 INFO::Starting hierarchical adjustment
2025-08-01 04:27:54.392519 INFO::Found 5 batches.
2025-08-01 04:27:54.393432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:54.394362 INFO::Using default BPPARAM
2025-08-01 04:27:54.395228 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:54.571558 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:54.574063 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:54.600338 INFO::Done
2025-08-01 04:27:54.601443 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:54.606698 INFO::ASW Batch was 0.444273589491456 prior to batch effect correction and is now -0.100384793364011 .
2025-08-01 04:27:54.607713 INFO::ASW Label was 0.331924969377186 prior to batch effect correction and is now 0.822810325597331 .
2025-08-01 04:27:54.609067 INFO::Total function execution time is 0.236072778701782 s and adjustment time is 0.208018064498901 s ( 88.12 )
2025-08-01 04:27:54.632479 INFO::Formatting Data.
2025-08-01 04:27:54.633649 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:54.635229 INFO::Removing potential empty rows and columns
2025-08-01 04:27:54.636923 INFO::Found 0 missing values.
2025-08-01 04:27:54.643748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:54.644708 INFO::Done
2025-08-01 04:27:54.645606 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:54.650214 INFO::Starting hierarchical adjustment
2025-08-01 04:27:54.651556 INFO::Found 5 batches.
2025-08-01 04:27:54.652341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:54.65332 INFO::Using default BPPARAM
2025-08-01 04:27:54.654144 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:54.836145 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:54.838925 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:54.871307 INFO::Done
2025-08-01 04:27:54.872616 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:54.878735 INFO::ASW Batch was 0.370802131407393 prior to batch effect correction and is now -0.0561589025344615 .
2025-08-01 04:27:54.879928 INFO::ASW Label was 0.375466742379978 prior to batch effect correction and is now 0.803462772350516 .
2025-08-01 04:27:54.881466 INFO::Total function execution time is 0.248977899551392 s and adjustment time is 0.219936370849609 s ( 88.34 )
2025-08-01 04:27:54.883193 INFO::Formatting Data.
2025-08-01 04:27:54.884549 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:54.886365 INFO::Removing potential empty rows and columns
2025-08-01 04:27:54.888814 INFO::Found 0 missing values.
2025-08-01 04:27:54.898188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:54.899602 INFO::Done
2025-08-01 04:27:54.90085 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:54.907173 INFO::Starting hierarchical adjustment
2025-08-01 04:27:54.909803 INFO::Found 5 batches.
2025-08-01 04:27:54.911041 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:54.912372 INFO::Using default BPPARAM
2025-08-01 04:27:54.913627 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:55.083996 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:55.086367 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:55.112274 INFO::Done
2025-08-01 04:27:55.113288 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:55.11812 INFO::ASW Batch was 0.370802131407393 prior to batch effect correction and is now -0.0561589025344615 .
2025-08-01 04:27:55.119134 INFO::ASW Label was 0.375466742379978 prior to batch effect correction and is now 0.803462772350516 .
2025-08-01 04:27:55.120344 INFO::Total function execution time is 0.237221956253052 s and adjustment time is 0.203030824661255 s ( 85.59 )
2025-08-01 04:27:55.141298 INFO::Formatting Data.
2025-08-01 04:27:55.142448 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:55.143803 INFO::Removing potential empty rows and columns
2025-08-01 04:27:55.145356 INFO::Found 0 missing values.
2025-08-01 04:27:55.149734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:55.15074 INFO::Done
2025-08-01 04:27:55.151565 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:55.155995 INFO::Starting hierarchical adjustment
2025-08-01 04:27:55.157238 INFO::Found 2 batches.
2025-08-01 04:27:55.158049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:55.159029 INFO::Using default BPPARAM
2025-08-01 04:27:55.159827 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:55.16127 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:55.191475 INFO::Done
2025-08-01 04:27:55.1927 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:55.197861 INFO::ASW Batch was 0.666012121332274 prior to batch effect correction and is now -0.0360792423595489 .
2025-08-01 04:27:55.198954 INFO::ASW Label was 0.402879078218553 prior to batch effect correction and is now 0.928033867990164 .
2025-08-01 04:27:55.200291 INFO::Total function execution time is 0.0590291023254395 s and adjustment time is 0.0344254970550537 s ( 58.32 )
2025-08-01 04:27:55.201614 INFO::Formatting Data.
2025-08-01 04:27:55.202632 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:55.204064 INFO::Removing potential empty rows and columns
2025-08-01 04:27:55.205695 INFO::Found 0 missing values.
2025-08-01 04:27:55.210265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:55.211311 INFO::Done
2025-08-01 04:27:55.212174 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:55.216801 INFO::Starting hierarchical adjustment
2025-08-01 04:27:55.218007 INFO::Found 2 batches.
2025-08-01 04:27:55.218913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:55.219857 INFO::Using default BPPARAM
2025-08-01 04:27:55.220683 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:55.222151 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 04:27:55.245054 INFO::Done
2025-08-01 04:27:55.246023 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:55.250699 INFO::ASW Batch was 0.666012121332274 prior to batch effect correction and is now -0.0360792423595489 .
2025-08-01 04:27:55.251721 INFO::ASW Label was 0.402879078218553 prior to batch effect correction and is now 0.928033867990164 .
2025-08-01 04:27:55.252953 INFO::Total function execution time is 0.0513265132904053 s and adjustment time is 0.0272502899169922 s ( 53.09 )
2025-08-01 04:27:55.270715 INFO::Formatting Data.
2025-08-01 04:27:55.271872 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:55.273275 INFO::Removing potential empty rows and columns
2025-08-01 04:27:55.274744 INFO::Found 0 missing values.
2025-08-01 04:27:55.278297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:55.279247 INFO::Done
2025-08-01 04:27:55.28008 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:55.2833 INFO::Starting hierarchical adjustment
2025-08-01 04:27:55.284455 INFO::Found 2 batches.
2025-08-01 04:27:55.285417 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:55.286379 INFO::Using default BPPARAM
2025-08-01 04:27:55.287252 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:55.288649 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 04:27:55.339097 INFO::Done
2025-08-01 04:27:55.340116 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:55.343197 INFO::ASW Batch was -0.128622129017872 prior to batch effect correction and is now -0.182906278873631 .
2025-08-01 04:27:55.344542 INFO::Total function execution time is 0.0739226341247559 s and adjustment time is 0.0548436641693115 s ( 74.19 )
2025-08-01 04:27:55.363627 INFO::Formatting Data.
2025-08-01 04:27:55.364798 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:55.366235 INFO::Removing potential empty rows and columns
2025-08-01 04:27:55.368013 INFO::Found 0 missing values.
2025-08-01 04:27:55.370094 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-01 04:27:55.378045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:55.379138 INFO::Done
2025-08-01 04:27:55.380033 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:55.384906 INFO::Starting hierarchical adjustment
2025-08-01 04:27:55.386185 INFO::Found 2 batches.
2025-08-01 04:27:55.387177 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:55.388171 INFO::Using default BPPARAM
2025-08-01 04:27:55.389116 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:55.390636 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 04:27:55.415525 INFO::Done
2025-08-01 04:27:55.416463 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:55.42097 INFO::ASW Batch was 0.42578583068336 prior to batch effect correction and is now 0.060886503476764 .
2025-08-01 04:27:55.421957 INFO::ASW Label was 0.438754679434644 prior to batch effect correction and is now 0.917793946655647 .
2025-08-01 04:27:55.423173 INFO::Total function execution time is 0.0596439838409424 s and adjustment time is 0.0295839309692383 s ( 49.6 )
2025-08-01 04:27:55.424394 INFO::Formatting Data.
2025-08-01 04:27:55.425373 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:55.426872 INFO::Removing potential empty rows and columns
2025-08-01 04:27:55.428456 INFO::Found 0 missing values.
2025-08-01 04:27:55.429905 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-01 04:27:55.437521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:55.438582 INFO::Done
2025-08-01 04:27:55.439571 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:55.444186 INFO::Starting hierarchical adjustment
2025-08-01 04:27:55.445455 INFO::Found 2 batches.
2025-08-01 04:27:55.446326 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:55.447345 INFO::Using default BPPARAM
2025-08-01 04:27:55.448176 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:55.44972 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 04:27:55.475857 INFO::Done
2025-08-01 04:27:55.476877 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:55.481419 INFO::ASW Batch was 0.42578583068336 prior to batch effect correction and is now 0.060886503476764 .
2025-08-01 04:27:55.482469 INFO::ASW Label was 0.438754679434644 prior to batch effect correction and is now 0.917793946655647 .
2025-08-01 04:27:55.483858 INFO::Total function execution time is 0.059354305267334 s and adjustment time is 0.0306365489959717 s ( 51.62 )
2025-08-01 04:27:55.803259 INFO::Formatting Data.
2025-08-01 04:27:55.804264 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:55.805476 INFO::Removing potential empty rows and columns
2025-08-01 04:27:55.806919 INFO::Found 0 missing values.
2025-08-01 04:27:55.811193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:55.812068 INFO::Done
2025-08-01 04:27:55.812839 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:55.815587 INFO::Starting hierarchical adjustment
2025-08-01 04:27:55.816638 INFO::Found 3 batches.
2025-08-01 04:27:55.817441 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:55.818294 INFO::Using default BPPARAM
2025-08-01 04:27:55.819083 INFO::Processing subtree level 1
2025-08-01 04:27:55.93804 INFO::Adjusting the last 1 batches sequentially
2025-08-01 04:27:55.940833 INFO::Done
2025-08-01 04:27:55.941828 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:55.945815 INFO::ASW Batch was -0.0412405461507111 prior to batch effect correction and is now -0.0412405461507111 .
2025-08-01 04:27:55.947425 INFO::Total function execution time is 0.14411187171936 s and adjustment time is 0.124356269836426 s ( 86.29 )
2025-08-01 04:27:55.949101 INFO::Formatting Data.
2025-08-01 04:27:55.95015 INFO::Typecasting input to dataframe.
2025-08-01 04:27:55.951397 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:55.952844 INFO::Removing potential empty rows and columns
2025-08-01 04:27:55.954643 INFO::Found 0 missing values.
2025-08-01 04:27:55.95964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:55.960768 INFO::Done
2025-08-01 04:27:55.961644 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:55.964584 INFO::Starting hierarchical adjustment
2025-08-01 04:27:55.965686 INFO::Found 3 batches.
2025-08-01 04:27:55.966526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:55.967446 INFO::Using default BPPARAM
2025-08-01 04:27:55.96824 INFO::Processing subtree level 1
2025-08-01 04:27:56.089219 INFO::Adjusting the last 1 batches sequentially
2025-08-01 04:27:56.091819 INFO::Done
2025-08-01 04:27:56.096944 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:56.104997 INFO::ASW Batch was -0.0412405461507111 prior to batch effect correction and is now -0.0412405461507111 .
2025-08-01 04:27:56.10675 INFO::Total function execution time is 0.157436370849609 s and adjustment time is 0.126324415206909 s ( 80.24 )
2025-08-01 04:27:56.126074 INFO::Formatting Data.
2025-08-01 04:27:56.12721 INFO::Typecasting input to dataframe.
2025-08-01 04:27:56.128464 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:56.129896 INFO::Removing potential empty rows and columns
2025-08-01 04:27:56.131645 INFO::Found 0 missing values.
2025-08-01 04:27:56.136532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:56.137609 INFO::Done
2025-08-01 04:27:56.138595 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:56.141721 INFO::Starting hierarchical adjustment
2025-08-01 04:27:56.14295 INFO::Found 3 batches.
2025-08-01 04:27:56.143812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:56.144793 INFO::Using default BPPARAM
2025-08-01 04:27:56.145665 INFO::Processing subtree level 1
2025-08-01 04:27:56.259766 INFO::Adjusting the last 1 batches sequentially
2025-08-01 04:27:56.262396 INFO::Done
2025-08-01 04:27:56.263429 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:56.267427 INFO::ASW Batch was -0.0973525426325167 prior to batch effect correction and is now -0.0973525426325167 .
2025-08-01 04:27:56.269026 INFO::Total function execution time is 0.142943382263184 s and adjustment time is 0.119656085968018 s ( 83.71 )
2025-08-01 04:27:56.462299 INFO::Formatting Data.
2025-08-01 04:27:56.463594 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:56.465334 INFO::Removing potential empty rows and columns
2025-08-01 04:27:56.469943 INFO::Found 1000 missing values.
2025-08-01 04:27:56.500384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:56.501429 INFO::Done
2025-08-01 04:27:56.502262 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:56.51023 INFO::Starting hierarchical adjustment
2025-08-01 04:27:56.511574 INFO::Found 10 batches.
2025-08-01 04:27:56.512468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:56.513494 INFO::Using default BPPARAM
2025-08-01 04:27:56.514357 INFO::Processing subtree level 1
2025-08-01 04:27:56.700866 INFO::Processing subtree level 2
2025-08-01 04:27:56.889366 INFO::Adjusting the last 1 batches sequentially
2025-08-01 04:27:56.891934 INFO::Done
2025-08-01 04:27:56.892833 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:56.90083 INFO::ASW Batch was 0.516599045236436 prior to batch effect correction and is now 0.516599045236436 .
2025-08-01 04:27:56.901783 INFO::ASW Label was 0.312377557755943 prior to batch effect correction and is now 0.312377557755943 .
2025-08-01 04:27:56.90311 INFO::Total function execution time is 0.440858125686646 s and adjustment time is 0.380659341812134 s ( 86.35 )
2025-08-01 04:27:56.904278 INFO::Formatting Data.
2025-08-01 04:27:56.905218 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:56.906938 INFO::Removing potential empty rows and columns
2025-08-01 04:27:56.911153 INFO::Found 1000 missing values.
2025-08-01 04:27:56.939049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:56.939958 INFO::Done
2025-08-01 04:27:56.940778 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:56.948271 INFO::Starting hierarchical adjustment
2025-08-01 04:27:56.949492 INFO::Found 10 batches.
2025-08-01 04:27:58.285128 INFO::Set up parallel execution backend with 2 workers
2025-08-01 04:27:58.287468 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-01 04:27:59.605184 INFO::Adjusting the last 2 batches sequentially
2025-08-01 04:27:59.607797 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 04:27:59.633146 INFO::Done
2025-08-01 04:27:59.634191 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:27:59.641301 INFO::ASW Batch was 0.516599045236436 prior to batch effect correction and is now 0.516599045236436 .
2025-08-01 04:27:59.64223 INFO::ASW Label was 0.312377557755943 prior to batch effect correction and is now 0.312377557755943 .
2025-08-01 04:27:59.643399 INFO::Total function execution time is 2.73911690711975 s and adjustment time is 2.68386936187744 s ( 97.98 )
2025-08-01 04:27:59.840434 INFO::Formatting Data.
2025-08-01 04:27:59.841631 INFO::Replacing NaNs with NAs.
2025-08-01 04:27:59.843297 INFO::Removing potential empty rows and columns
2025-08-01 04:27:59.845098 INFO::Found 0 missing values.
2025-08-01 04:27:59.851374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:27:59.852337 INFO::Done
2025-08-01 04:27:59.853234 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 04:27:59.857651 INFO::Starting hierarchical adjustment
2025-08-01 04:27:59.858934 INFO::Found 3 batches.
2025-08-01 04:27:59.859816 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 04:27:59.860831 INFO::Using default BPPARAM
2025-08-01 04:27:59.86171 INFO::Processing subtree level 1
2025-08-01 04:28:00.000339 INFO::Adjusting the last 1 batches sequentially
2025-08-01 04:28:00.003017 INFO::Done
2025-08-01 04:28:00.004038 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 04:28:00.009241 INFO::ASW Batch was 0.135559728163607 prior to batch effect correction and is now -0.109125688951744 .
2025-08-01 04:28:00.01035 INFO::ASW Label was -0.212775822998987 prior to batch effect correction and is now -0.0583733729261358 .
2025-08-01 04:28:00.011866 INFO::Total function execution time is 0.171471118927002 s and adjustment time is 0.144321918487549 s ( 84.17 )
2025-08-01 04:28:00.207504 INFO::Formatting Data.
2025-08-01 04:28:00.20861 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.209921 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.211503 INFO::Found 2 missing values.
2025-08-01 04:28:00.215935 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.216892 INFO::Done
2025-08-01 04:28:00.258949 INFO::Found NA in Reference column
2025-08-01 04:28:00.27373 INFO::Require at least two references per batch.
2025-08-01 04:28:00.305154 INFO::Formatting Data.
2025-08-01 04:28:00.306161 INFO::Recognized SummarizedExperiment
2025-08-01 04:28:00.306997 INFO::Typecasting input to dataframe.
2025-08-01 04:28:00.321674 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.323369 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.328829 INFO::Found 0 missing values.
2025-08-01 04:28:00.339397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.340308 INFO::Done
2025-08-01 04:28:00.363101 INFO::Formatting Data.
2025-08-01 04:28:00.364067 INFO::Recognized SummarizedExperiment
2025-08-01 04:28:00.364836 INFO::Typecasting input to dataframe.
2025-08-01 04:28:00.391282 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.392896 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.398156 INFO::Found 0 missing values.
2025-08-01 04:28:00.415071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.415989 INFO::Done
2025-08-01 04:28:00.438529 INFO::Formatting Data.
2025-08-01 04:28:00.439514 INFO::Recognized SummarizedExperiment
2025-08-01 04:28:00.440278 INFO::Typecasting input to dataframe.
2025-08-01 04:28:00.465091 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.466494 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.468004 INFO::Found 0 missing values.
2025-08-01 04:28:00.469321 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-01 04:28:00.475854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.476766 INFO::Done
2025-08-01 04:28:00.491127 INFO::Formatting Data.
2025-08-01 04:28:00.492176 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.493418 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.494894 INFO::Found 0 missing values.
2025-08-01 04:28:00.499237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.500148 INFO::Done
2025-08-01 04:28:00.51643 INFO::Formatting Data.
2025-08-01 04:28:00.51749 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.518745 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.520215 INFO::Found 0 missing values.
2025-08-01 04:28:00.524686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.525623 INFO::Done
2025-08-01 04:28:00.570293 INFO::Formatting Data.
2025-08-01 04:28:00.571415 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.572893 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.574698 INFO::Found 1 missing values.
2025-08-01 04:28:00.579162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.580189 INFO::Done
2025-08-01 04:28:00.611247 INFO::Formatting Data.
2025-08-01 04:28:00.61236 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.61373 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.615279 INFO::Found 2 missing values.
2025-08-01 04:28:00.616701 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-01 04:28:00.620416 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.621416 INFO::Done
2025-08-01 04:28:00.63729 INFO::Formatting Data.
2025-08-01 04:28:00.63853 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.639905 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.641424 INFO::Found 2 missing values.
2025-08-01 04:28:00.644044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.645014 INFO::Done
2025-08-01 04:28:00.662107 INFO::Formatting Data.
2025-08-01 04:28:00.663337 INFO::Typecasting input to dataframe.
2025-08-01 04:28:00.664652 INFO::Replacing NaNs with NAs.
2025-08-01 04:28:00.666061 INFO::Removing potential empty rows and columns
2025-08-01 04:28:00.667734 INFO::Found 0 missing values.
2025-08-01 04:28:00.67246 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 04:28:00.673446 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.536 5.634 26.485
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.128 | 1.257 | 20.409 | |
| compute_asw | 0.034 | 0.000 | 0.034 | |
| count_existing | 0.013 | 0.004 | 0.017 | |
| generate_data_covariables | 0.015 | 0.000 | 0.015 | |
| generate_dataset | 0.014 | 0.000 | 0.014 | |