Yannis Schumann
| Snapshot Date: 2025-10-13 13:45 -0400 (Mon, 13 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 2025-10-14 12:03 -0400 (Tue, 14 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" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
| 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 164/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-10-13 21:28:06 -0400 (Mon, 13 Oct 2025) |
| EndedAt: 2025-10-13 21:30:12 -0400 (Mon, 13 Oct 2025) |
| EllapsedTime: 126.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 30.444 2.192 24.262
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-10-13 21:29:18.436965 INFO::Formatting Data.
2025-10-13 21:29:18.438355 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:18.450948 INFO::Removing potential empty rows and columns
2025-10-13 21:29:18.769366 INFO::Found 0 missing values.
2025-10-13 21:29:18.773101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:18.7738 INFO::Done
2025-10-13 21:29:18.774415 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:18.786788 INFO::Starting hierarchical adjustment
2025-10-13 21:29:18.787677 INFO::Found 3 batches.
2025-10-13 21:29:18.788285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:18.789541 INFO::Using default BPPARAM
2025-10-13 21:29:18.790166 INFO::Processing subtree level 1
2025-10-13 21:29:18.932547 INFO::Adjusting the last 1 batches sequentially
2025-10-13 21:29:18.936545 INFO::Done
2025-10-13 21:29:18.937427 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:18.944895 INFO::ASW Batch was -0.0123110258616286 prior to batch effect correction and is now -0.0123110258616286 .
2025-10-13 21:29:18.950402 INFO::Total function execution time is 0.514042615890503 s and adjustment time is 0.149016141891479 s ( 28.99 )
2025-10-13 21:29:18.965817 INFO::Formatting Data.
2025-10-13 21:29:18.966717 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:18.967737 INFO::Removing potential empty rows and columns
2025-10-13 21:29:18.968955 INFO::Found 0 missing values.
2025-10-13 21:29:18.969991 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.
2025-10-13 21:29:18.982069 INFO::Formatting Data.
2025-10-13 21:29:18.982853 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:18.983834 INFO::Removing potential empty rows and columns
2025-10-13 21:29:18.988915 INFO::Found 0 missing values.
2025-10-13 21:29:18.989996 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.
2025-10-13 21:29:19.011362 INFO::Formatting Data.
2025-10-13 21:29:19.012423 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:19.013423 INFO::Removing potential empty rows and columns
2025-10-13 21:29:19.014589 INFO::Found 0 missing values.
2025-10-13 21:29:19.015595 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.
2025-10-13 21:29:19.021482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:19.022106 INFO::Done
2025-10-13 21:29:19.022947 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:19.026113 INFO::Starting hierarchical adjustment
2025-10-13 21:29:19.026941 INFO::Found 2 batches.
2025-10-13 21:29:19.027582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:19.0283 INFO::Using default BPPARAM
2025-10-13 21:29:19.028945 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:19.030458 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 21:29:19.067277 INFO::Done
2025-10-13 21:29:19.069522 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:19.072642 INFO::ASW Batch was -0.00446065914950121 prior to batch effect correction and is now -0.111372277954478 .
2025-10-13 21:29:19.073956 INFO::Total function execution time is 0.0626342296600342 s and adjustment time is 0.040424108505249 s ( 64.54 )
2025-10-13 21:29:19.078152 INFO::Formatting Data.
2025-10-13 21:29:19.080167 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:19.098083 INFO::Formatting Data.
2025-10-13 21:29:19.099439 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:19.101269 INFO::Removing potential empty rows and columns
2025-10-13 21:29:19.103344 INFO::Found 0 missing values.
2025-10-13 21:29:19.108775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:19.109641 INFO::Done
2025-10-13 21:29:19.110528 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:19.11454 INFO::Starting hierarchical adjustment
2025-10-13 21:29:19.1159 INFO::Found 2 batches.
2025-10-13 21:29:19.116965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:19.118262 INFO::Using default BPPARAM
2025-10-13 21:29:19.11931 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:19.121188 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 21:29:19.165344 INFO::Done
2025-10-13 21:29:19.166101 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:19.168291 INFO::ASW Batch was -0.0231107361277175 prior to batch effect correction and is now -0.11515780186044 .
2025-10-13 21:29:19.169174 INFO::Total function execution time is 0.0724368095397949 s and adjustment time is 0.0497875213623047 s ( 68.73 )
2025-10-13 21:29:19.170311 INFO::Formatting Data.
2025-10-13 21:29:19.170961 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:19.171888 INFO::Removing potential empty rows and columns
2025-10-13 21:29:19.173001 INFO::Found 0 missing values.
2025-10-13 21:29:19.175989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:19.176576 INFO::Done
2025-10-13 21:29:19.177136 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:19.179267 INFO::Starting hierarchical adjustment
2025-10-13 21:29:19.180018 INFO::Found 2 batches.
2025-10-13 21:29:19.180598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:19.181241 INFO::Using default BPPARAM
2025-10-13 21:29:19.181795 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:19.182754 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 21:29:19.198697 INFO::Done
2025-10-13 21:29:19.199497 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:19.201605 INFO::ASW Batch was -0.0231107361277175 prior to batch effect correction and is now -0.11515780186044 .
2025-10-13 21:29:19.202437 INFO::Total function execution time is 0.03212571144104 s and adjustment time is 0.0188252925872803 s ( 58.6 )
2025-10-13 21:29:23.602198 INFO::Formatting Data.
2025-10-13 21:29:23.603015 INFO::Recognized SummarizedExperiment
2025-10-13 21:29:23.603567 INFO::Typecasting input to dataframe.
2025-10-13 21:29:23.649847 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:23.65141 INFO::Removing potential empty rows and columns
2025-10-13 21:29:23.656398 INFO::Found 0 missing values.
2025-10-13 21:29:23.66584 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:23.666692 INFO::Done
2025-10-13 21:29:23.667374 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:23.672211 INFO::Starting hierarchical adjustment
2025-10-13 21:29:23.673151 INFO::Found 2 batches.
2025-10-13 21:29:23.6738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:23.675162 INFO::Using default BPPARAM
2025-10-13 21:29:23.67583 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:23.677071 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 21:29:23.753356 INFO::Done
2025-10-13 21:29:23.754239 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:23.758974 INFO::ASW Batch was 0.00560178863309212 prior to batch effect correction and is now -0.0964473956113271 .
2025-10-13 21:29:23.760045 INFO::Total function execution time is 0.158204078674316 s and adjustment time is 0.080376148223877 s ( 50.81 )
2025-10-13 21:29:23.783186 INFO::Formatting Data.
2025-10-13 21:29:23.783996 INFO::Recognized SummarizedExperiment
2025-10-13 21:29:23.784629 INFO::Typecasting input to dataframe.
2025-10-13 21:29:23.796416 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:23.797644 INFO::Removing potential empty rows and columns
2025-10-13 21:29:23.802234 INFO::Found 0 missing values.
2025-10-13 21:29:23.817764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:23.81847 INFO::Done
2025-10-13 21:29:23.819092 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:23.82784 INFO::Starting hierarchical adjustment
2025-10-13 21:29:23.828724 INFO::Found 2 batches.
2025-10-13 21:29:23.829362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:23.830084 INFO::Using default BPPARAM
2025-10-13 21:29:23.830745 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:23.831953 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 21:29:23.86602 INFO::Done
2025-10-13 21:29:23.866873 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:23.871582 INFO::ASW Batch was 0.00798188703514227 prior to batch effect correction and is now 0.00798188703514227 .
2025-10-13 21:29:23.872651 INFO::Total function execution time is 0.0894243717193604 s and adjustment time is 0.0374312400817871 s ( 41.86 )
2025-10-13 21:29:23.894929 INFO::Formatting Data.
2025-10-13 21:29:23.8958 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:23.896806 INFO::Removing potential empty rows and columns
2025-10-13 21:29:23.897977 INFO::Found 0 missing values.
2025-10-13 21:29:23.901476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:23.902088 INFO::Done
2025-10-13 21:29:23.902688 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:23.90925 INFO::Starting hierarchical adjustment
2025-10-13 21:29:23.910101 INFO::Found 3 batches.
2025-10-13 21:29:23.910768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:23.911515 INFO::Using default BPPARAM
2025-10-13 21:29:23.912174 INFO::Processing subtree level 1
2025-10-13 21:29:24.130371 INFO::Adjusting the last 1 batches sequentially
2025-10-13 21:29:24.140181 INFO::Done
2025-10-13 21:29:24.141305 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:24.148222 INFO::ASW Batch was -0.00376587862976981 prior to batch effect correction and is now -0.18340982012611 .
2025-10-13 21:29:24.153737 INFO::Total function execution time is 0.258718252182007 s and adjustment time is 0.230188131332397 s ( 88.97 )
2025-10-13 21:29:24.1782 INFO::Skipping initial DF formatting
2025-10-13 21:29:24.17936 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:24.186294 INFO::Starting hierarchical adjustment
2025-10-13 21:29:24.187562 INFO::Found 5 batches.
2025-10-13 21:29:24.188488 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:24.189532 INFO::Using default BPPARAM
2025-10-13 21:29:24.190405 INFO::Processing subtree level 1
2025-10-13 21:29:24.553691 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:24.556108 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 21:29:24.607151 INFO::Done
2025-10-13 21:29:24.608369 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:24.679059 INFO::ASW Batch was 0.510347468647408 prior to batch effect correction and is now 0.510347468647408 .
2025-10-13 21:29:24.68009 INFO::ASW Label was 0.359990708259766 prior to batch effect correction and is now 0.359990708259766 .
2025-10-13 21:29:24.68135 INFO::Total function execution time is 0.503262996673584 s and adjustment time is 0.419803142547607 s ( 83.42 )
2025-10-13 21:29:24.707148 INFO::Formatting Data.
2025-10-13 21:29:24.708275 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:24.709656 INFO::Removing potential empty rows and columns
2025-10-13 21:29:24.711091 INFO::Found 0 missing values.
2025-10-13 21:29:24.717602 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:24.718508 INFO::Done
2025-10-13 21:29:24.719396 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:24.724152 INFO::Starting hierarchical adjustment
2025-10-13 21:29:24.72526 INFO::Found 5 batches.
2025-10-13 21:29:24.726058 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:24.727015 INFO::Using default BPPARAM
2025-10-13 21:29:24.727848 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.
2025-10-13 21:29:24.936987 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:24.942854 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 21:29:24.988279 INFO::Done
2025-10-13 21:29:24.989197 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:24.997452 INFO::ASW Batch was 0.465130672582511 prior to batch effect correction and is now -0.047498922585207 .
2025-10-13 21:29:24.998256 INFO::ASW Label was 0.328626938971551 prior to batch effect correction and is now 0.80442580760955 .
2025-10-13 21:29:24.999408 INFO::Total function execution time is 0.292370080947876 s and adjustment time is 0.263227701187134 s ( 90.03 )
2025-10-13 21:29:25.004524 INFO::Formatting Data.
2025-10-13 21:29:25.005427 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:25.006589 INFO::Removing potential empty rows and columns
2025-10-13 21:29:25.007944 INFO::Found 0 missing values.
2025-10-13 21:29:25.020331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:25.021011 INFO::Done
2025-10-13 21:29:25.025695 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:25.03364 INFO::Starting hierarchical adjustment
2025-10-13 21:29:25.034586 INFO::Found 5 batches.
2025-10-13 21:29:25.035239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:25.036017 INFO::Using default BPPARAM
2025-10-13 21:29:25.039698 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.
2025-10-13 21:29:25.241018 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:25.249276 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 21:29:25.284327 INFO::Done
2025-10-13 21:29:25.289193 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:25.292981 INFO::ASW Batch was 0.465130672582511 prior to batch effect correction and is now -0.047498922585207 .
2025-10-13 21:29:25.296679 INFO::ASW Label was 0.328626938971551 prior to batch effect correction and is now 0.80442580760955 .
2025-10-13 21:29:25.297593 INFO::Total function execution time is 0.293109893798828 s and adjustment time is 0.249939203262329 s ( 85.27 )
2025-10-13 21:29:25.327653 INFO::Formatting Data.
2025-10-13 21:29:25.328535 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:25.33256 INFO::Removing potential empty rows and columns
2025-10-13 21:29:25.333715 INFO::Found 0 missing values.
2025-10-13 21:29:25.340612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:25.345253 INFO::Done
2025-10-13 21:29:25.345847 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:25.353328 INFO::Starting hierarchical adjustment
2025-10-13 21:29:25.354173 INFO::Found 5 batches.
2025-10-13 21:29:25.354768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:25.355483 INFO::Using default BPPARAM
2025-10-13 21:29:25.356085 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.
2025-10-13 21:29:25.58519 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:25.590525 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 21:29:25.626672 INFO::Done
2025-10-13 21:29:25.628191 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:25.640986 INFO::ASW Batch was 0.439843919893675 prior to batch effect correction and is now -0.0946624398633665 .
2025-10-13 21:29:25.642017 INFO::ASW Label was 0.246801203271739 prior to batch effect correction and is now 0.880510791569864 .
2025-10-13 21:29:25.643451 INFO::Total function execution time is 0.315780878067017 s and adjustment time is 0.272557497024536 s ( 86.31 )
2025-10-13 21:29:25.644875 INFO::Formatting Data.
2025-10-13 21:29:25.645958 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:25.651542 INFO::Removing potential empty rows and columns
2025-10-13 21:29:25.65332 INFO::Found 0 missing values.
2025-10-13 21:29:25.669163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:25.669975 INFO::Done
2025-10-13 21:29:25.670679 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:25.677924 INFO::Starting hierarchical adjustment
2025-10-13 21:29:25.683041 INFO::Found 5 batches.
2025-10-13 21:29:25.683814 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:25.684659 INFO::Using default BPPARAM
2025-10-13 21:29:25.687205 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.
2025-10-13 21:29:25.898279 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:25.905097 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 21:29:25.93065 INFO::Done
2025-10-13 21:29:25.931636 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:25.935807 INFO::ASW Batch was 0.439843919893675 prior to batch effect correction and is now -0.0946624398633665 .
2025-10-13 21:29:25.936566 INFO::ASW Label was 0.246801203271739 prior to batch effect correction and is now 0.880510791569864 .
2025-10-13 21:29:25.937615 INFO::Total function execution time is 0.292775392532349 s and adjustment time is 0.24779748916626 s ( 84.64 )
2025-10-13 21:29:25.953345 INFO::Formatting Data.
2025-10-13 21:29:25.954215 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:25.955288 INFO::Removing potential empty rows and columns
2025-10-13 21:29:25.956507 INFO::Found 0 missing values.
2025-10-13 21:29:25.959766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:25.96042 INFO::Done
2025-10-13 21:29:25.961022 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:25.964516 INFO::Starting hierarchical adjustment
2025-10-13 21:29:25.965346 INFO::Found 2 batches.
2025-10-13 21:29:25.965966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:25.966722 INFO::Using default BPPARAM
2025-10-13 21:29:25.967372 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:25.968444 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 21:29:25.986065 INFO::Done
2025-10-13 21:29:25.986761 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:25.990194 INFO::ASW Batch was 0.750597493086782 prior to batch effect correction and is now 0.00195768553133417 .
2025-10-13 21:29:25.990872 INFO::ASW Label was 0.289485430690013 prior to batch effect correction and is now 0.834537635720471 .
2025-10-13 21:29:25.991779 INFO::Total function execution time is 0.0385293960571289 s and adjustment time is 0.0208935737609863 s ( 54.23 )
2025-10-13 21:29:25.992702 INFO::Formatting Data.
2025-10-13 21:29:25.993414 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:25.994414 INFO::Removing potential empty rows and columns
2025-10-13 21:29:25.995589 INFO::Found 0 missing values.
2025-10-13 21:29:25.998755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:25.999422 INFO::Done
2025-10-13 21:29:26.00004 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:26.003391 INFO::Starting hierarchical adjustment
2025-10-13 21:29:26.004213 INFO::Found 2 batches.
2025-10-13 21:29:26.00482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:26.005518 INFO::Using default BPPARAM
2025-10-13 21:29:26.006107 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:26.007113 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-13 21:29:26.023811 INFO::Done
2025-10-13 21:29:26.024475 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:26.027678 INFO::ASW Batch was 0.750597493086782 prior to batch effect correction and is now 0.00195768553133417 .
2025-10-13 21:29:26.028327 INFO::ASW Label was 0.289485430690013 prior to batch effect correction and is now 0.834537635720471 .
2025-10-13 21:29:26.029166 INFO::Total function execution time is 0.0364654064178467 s and adjustment time is 0.0197756290435791 s ( 54.23 )
2025-10-13 21:29:26.041161 INFO::Formatting Data.
2025-10-13 21:29:26.04188 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:26.042918 INFO::Removing potential empty rows and columns
2025-10-13 21:29:26.043986 INFO::Found 0 missing values.
2025-10-13 21:29:26.04644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:26.047082 INFO::Done
2025-10-13 21:29:26.047705 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:26.049864 INFO::Starting hierarchical adjustment
2025-10-13 21:29:26.050696 INFO::Found 2 batches.
2025-10-13 21:29:26.051335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:26.05205 INFO::Using default BPPARAM
2025-10-13 21:29:26.05269 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:26.053732 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 21:29:26.090469 INFO::Done
2025-10-13 21:29:26.091213 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:26.093438 INFO::ASW Batch was -0.0127006767504914 prior to batch effect correction and is now -0.0957300214343044 .
2025-10-13 21:29:26.094378 INFO::Total function execution time is 0.0532562732696533 s and adjustment time is 0.0399386882781982 s ( 74.99 )
2025-10-13 21:29:26.107254 INFO::Formatting Data.
2025-10-13 21:29:26.108007 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:26.108973 INFO::Removing potential empty rows and columns
2025-10-13 21:29:26.110073 INFO::Found 0 missing values.
2025-10-13 21:29:26.111373 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.
2025-10-13 21:29:26.116763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:26.117425 INFO::Done
2025-10-13 21:29:26.11805 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:26.121504 INFO::Starting hierarchical adjustment
2025-10-13 21:29:26.122371 INFO::Found 2 batches.
2025-10-13 21:29:26.123019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:26.123753 INFO::Using default BPPARAM
2025-10-13 21:29:26.124398 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:26.12929 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 21:29:26.152534 INFO::Done
2025-10-13 21:29:26.153274 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:26.156637 INFO::ASW Batch was 0.709475068209285 prior to batch effect correction and is now -0.0100626182148715 .
2025-10-13 21:29:26.157326 INFO::ASW Label was 0.327215399417982 prior to batch effect correction and is now 0.847158704265088 .
2025-10-13 21:29:26.158223 INFO::Total function execution time is 0.0510082244873047 s and adjustment time is 0.0303518772125244 s ( 59.5 )
2025-10-13 21:29:26.159162 INFO::Formatting Data.
2025-10-13 21:29:26.159885 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:26.160961 INFO::Removing potential empty rows and columns
2025-10-13 21:29:26.162098 INFO::Found 0 missing values.
2025-10-13 21:29:26.163172 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.
2025-10-13 21:29:26.168421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:26.169063 INFO::Done
2025-10-13 21:29:26.169683 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:26.17293 INFO::Starting hierarchical adjustment
2025-10-13 21:29:26.173761 INFO::Found 2 batches.
2025-10-13 21:29:26.174394 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:26.175105 INFO::Using default BPPARAM
2025-10-13 21:29:26.175733 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:26.176793 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 21:29:26.1957 INFO::Done
2025-10-13 21:29:26.196364 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:26.199537 INFO::ASW Batch was 0.709475068209285 prior to batch effect correction and is now -0.0100626182148715 .
2025-10-13 21:29:26.200181 INFO::ASW Label was 0.327215399417982 prior to batch effect correction and is now 0.847158704265088 .
2025-10-13 21:29:26.201043 INFO::Total function execution time is 0.0419104099273682 s and adjustment time is 0.0221149921417236 s ( 52.77 )
2025-10-13 21:29:26.449356 INFO::Formatting Data.
2025-10-13 21:29:26.450486 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:26.451612 INFO::Removing potential empty rows and columns
2025-10-13 21:29:26.45296 INFO::Found 0 missing values.
2025-10-13 21:29:26.456726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:26.457378 INFO::Done
2025-10-13 21:29:26.458001 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:26.46077 INFO::Starting hierarchical adjustment
2025-10-13 21:29:26.461632 INFO::Found 3 batches.
2025-10-13 21:29:26.462281 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:26.463051 INFO::Using default BPPARAM
2025-10-13 21:29:26.463704 INFO::Processing subtree level 1
2025-10-13 21:29:26.670913 INFO::Adjusting the last 1 batches sequentially
2025-10-13 21:29:26.677213 INFO::Done
2025-10-13 21:29:26.678028 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:26.685019 INFO::ASW Batch was -0.0150897928384336 prior to batch effect correction and is now -0.0150897928384336 .
2025-10-13 21:29:26.686162 INFO::Total function execution time is 0.237235307693481 s and adjustment time is 0.211608648300171 s ( 89.2 )
2025-10-13 21:29:26.689986 INFO::Formatting Data.
2025-10-13 21:29:26.690997 INFO::Typecasting input to dataframe.
2025-10-13 21:29:26.69216 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:26.69759 INFO::Removing potential empty rows and columns
2025-10-13 21:29:26.699209 INFO::Found 0 missing values.
2025-10-13 21:29:26.707977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:26.708789 INFO::Done
2025-10-13 21:29:26.7096 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:26.720577 INFO::Starting hierarchical adjustment
2025-10-13 21:29:26.721628 INFO::Found 3 batches.
2025-10-13 21:29:26.72247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:26.730479 INFO::Using default BPPARAM
2025-10-13 21:29:26.731293 INFO::Processing subtree level 1
2025-10-13 21:29:26.918059 INFO::Adjusting the last 1 batches sequentially
2025-10-13 21:29:26.926645 INFO::Done
2025-10-13 21:29:26.927652 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:26.935278 INFO::ASW Batch was -0.0150897928384336 prior to batch effect correction and is now -0.0150897928384336 .
2025-10-13 21:29:26.936659 INFO::Total function execution time is 0.24662971496582 s and adjustment time is 0.205214977264404 s ( 83.21 )
2025-10-13 21:29:26.956071 INFO::Formatting Data.
2025-10-13 21:29:26.95727 INFO::Typecasting input to dataframe.
2025-10-13 21:29:26.95855 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:26.959904 INFO::Removing potential empty rows and columns
2025-10-13 21:29:26.961601 INFO::Found 0 missing values.
2025-10-13 21:29:26.966357 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:26.967188 INFO::Done
2025-10-13 21:29:26.968038 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:26.971039 INFO::Starting hierarchical adjustment
2025-10-13 21:29:26.972124 INFO::Found 3 batches.
2025-10-13 21:29:26.972933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:26.973933 INFO::Using default BPPARAM
2025-10-13 21:29:26.974789 INFO::Processing subtree level 1
2025-10-13 21:29:27.110791 INFO::Adjusting the last 1 batches sequentially
2025-10-13 21:29:27.117347 INFO::Done
2025-10-13 21:29:27.118337 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:27.125974 INFO::ASW Batch was -0.0928577110594932 prior to batch effect correction and is now -0.0928577110594932 .
2025-10-13 21:29:27.130401 INFO::Total function execution time is 0.171300888061523 s and adjustment time is 0.145435094833374 s ( 84.9 )
2025-10-13 21:29:27.360804 INFO::Formatting Data.
2025-10-13 21:29:27.361996 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:27.363682 INFO::Removing potential empty rows and columns
2025-10-13 21:29:27.368123 INFO::Found 1000 missing values.
2025-10-13 21:29:27.399931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:27.401019 INFO::Done
2025-10-13 21:29:27.401923 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:27.410393 INFO::Starting hierarchical adjustment
2025-10-13 21:29:27.411487 INFO::Found 10 batches.
2025-10-13 21:29:27.412316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:27.413261 INFO::Using default BPPARAM
2025-10-13 21:29:27.414087 INFO::Processing subtree level 1
2025-10-13 21:29:27.69901 INFO::Processing subtree level 2
2025-10-13 21:29:27.905645 INFO::Adjusting the last 1 batches sequentially
2025-10-13 21:29:27.910866 INFO::Done
2025-10-13 21:29:27.911911 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:27.928098 INFO::ASW Batch was 0.407499652607793 prior to batch effect correction and is now 0.407499652607793 .
2025-10-13 21:29:27.92907 INFO::ASW Label was 0.393986278034546 prior to batch effect correction and is now 0.393986278034546 .
2025-10-13 21:29:27.934386 INFO::Total function execution time is 0.569586038589478 s and adjustment time is 0.499534845352173 s ( 87.7 )
2025-10-13 21:29:27.935688 INFO::Formatting Data.
2025-10-13 21:29:27.936685 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:27.942484 INFO::Removing potential empty rows and columns
2025-10-13 21:29:27.950601 INFO::Found 1000 missing values.
2025-10-13 21:29:27.984093 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:27.985032 INFO::Done
2025-10-13 21:29:27.985793 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:27.993871 INFO::Starting hierarchical adjustment
2025-10-13 21:29:27.994865 INFO::Found 10 batches.
2025-10-13 21:29:29.327217 INFO::Set up parallel execution backend with 2 workers
2025-10-13 21:29:29.329447 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-13 21:29:30.731348 INFO::Adjusting the last 2 batches sequentially
2025-10-13 21:29:30.733486 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-13 21:29:30.756101 INFO::Done
2025-10-13 21:29:30.758416 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:30.764853 INFO::ASW Batch was 0.407499652607793 prior to batch effect correction and is now 0.407499652607793 .
2025-10-13 21:29:30.76559 INFO::ASW Label was 0.393986278034546 prior to batch effect correction and is now 0.393986278034546 .
2025-10-13 21:29:30.766437 INFO::Total function execution time is 2.83086037635803 s and adjustment time is 2.76122570037842 s ( 97.54 )
2025-10-13 21:29:30.973926 INFO::Formatting Data.
2025-10-13 21:29:30.97488 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:30.975968 INFO::Removing potential empty rows and columns
2025-10-13 21:29:30.977421 INFO::Found 0 missing values.
2025-10-13 21:29:30.983167 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:30.983825 INFO::Done
2025-10-13 21:29:30.984437 INFO::Acquiring quality metrics before batch effect correction.
2025-10-13 21:29:30.990669 INFO::Starting hierarchical adjustment
2025-10-13 21:29:30.991496 INFO::Found 3 batches.
2025-10-13 21:29:30.99209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-13 21:29:30.993778 INFO::Using default BPPARAM
2025-10-13 21:29:30.994501 INFO::Processing subtree level 1
2025-10-13 21:29:31.187553 INFO::Adjusting the last 1 batches sequentially
2025-10-13 21:29:31.190125 INFO::Done
2025-10-13 21:29:31.191062 INFO::Acquiring quality metrics after batch effect correction.
2025-10-13 21:29:31.195796 INFO::ASW Batch was 0.301249879289364 prior to batch effect correction and is now -0.187590643545938 .
2025-10-13 21:29:31.196703 INFO::ASW Label was -0.206745872553635 prior to batch effect correction and is now 0.0870882449008789 .
2025-10-13 21:29:31.198082 INFO::Total function execution time is 0.224153518676758 s and adjustment time is 0.198734521865845 s ( 88.66 )
2025-10-13 21:29:31.374068 INFO::Formatting Data.
2025-10-13 21:29:31.375265 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.376556 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.378052 INFO::Found 2 missing values.
2025-10-13 21:29:31.382323 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.383087 INFO::Done
2025-10-13 21:29:31.420488 INFO::Found NA in Reference column
2025-10-13 21:29:31.433422 INFO::Require at least two references per batch.
2025-10-13 21:29:31.462916 INFO::Formatting Data.
2025-10-13 21:29:31.46394 INFO::Recognized SummarizedExperiment
2025-10-13 21:29:31.46471 INFO::Typecasting input to dataframe.
2025-10-13 21:29:31.478689 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.480287 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.485654 INFO::Found 0 missing values.
2025-10-13 21:29:31.505068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.505969 INFO::Done
2025-10-13 21:29:31.531295 INFO::Formatting Data.
2025-10-13 21:29:31.532274 INFO::Recognized SummarizedExperiment
2025-10-13 21:29:31.533122 INFO::Typecasting input to dataframe.
2025-10-13 21:29:31.561124 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.562892 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.569068 INFO::Found 0 missing values.
2025-10-13 21:29:31.58832 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.58922 INFO::Done
2025-10-13 21:29:31.614229 INFO::Formatting Data.
2025-10-13 21:29:31.615216 INFO::Recognized SummarizedExperiment
2025-10-13 21:29:31.616046 INFO::Typecasting input to dataframe.
2025-10-13 21:29:31.642484 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.644034 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.64573 INFO::Found 0 missing values.
2025-10-13 21:29:31.647131 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.
2025-10-13 21:29:31.654129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.654965 INFO::Done
2025-10-13 21:29:31.670311 INFO::Formatting Data.
2025-10-13 21:29:31.671408 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.672704 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.674223 INFO::Found 0 missing values.
2025-10-13 21:29:31.678807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.679665 INFO::Done
2025-10-13 21:29:31.69638 INFO::Formatting Data.
2025-10-13 21:29:31.697464 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.698758 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.700324 INFO::Found 0 missing values.
2025-10-13 21:29:31.705189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.705946 INFO::Done
2025-10-13 21:29:31.747648 INFO::Formatting Data.
2025-10-13 21:29:31.7488 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.750212 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.751788 INFO::Found 1 missing values.
2025-10-13 21:29:31.755605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.75637 INFO::Done
2025-10-13 21:29:31.780514 INFO::Formatting Data.
2025-10-13 21:29:31.781452 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.782448 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.783694 INFO::Found 2 missing values.
2025-10-13 21:29:31.784776 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.
2025-10-13 21:29:31.787932 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.788574 INFO::Done
2025-10-13 21:29:31.799562 INFO::Formatting Data.
2025-10-13 21:29:31.800371 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.801332 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.802373 INFO::Found 2 missing values.
2025-10-13 21:29:31.804184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.804798 INFO::Done
2025-10-13 21:29:31.818223 INFO::Formatting Data.
2025-10-13 21:29:31.819278 INFO::Typecasting input to dataframe.
2025-10-13 21:29:31.82048 INFO::Replacing NaNs with NAs.
2025-10-13 21:29:31.821714 INFO::Removing potential empty rows and columns
2025-10-13 21:29:31.823304 INFO::Found 0 missing values.
2025-10-13 21:29:31.827783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-13 21:29:31.828578 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.288 5.255 28.518
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 30.444 | 2.192 | 24.262 | |
| compute_asw | 0.032 | 0.000 | 0.032 | |
| count_existing | 0.016 | 0.002 | 0.018 | |
| generate_data_covariables | 0.015 | 0.002 | 0.017 | |
| generate_dataset | 0.015 | 0.001 | 0.016 | |