Yannis Schumann
| Snapshot Date: 2026-02-12 13:45 -0500 (Thu, 12 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-16 11:57 -0500 (Mon, 16 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4889 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2026-02-12 21:53:45 -0500 (Thu, 12 Feb 2026) |
| EndedAt: 2026-02-12 21:55:14 -0500 (Thu, 12 Feb 2026) |
| EllapsedTime: 89.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.639 1.487 17.884
* 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 ‘1.6.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
2026-02-12 21:54:37.572023 INFO::Formatting Data.
2026-02-12 21:54:37.573592 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:37.585183 INFO::Removing potential empty rows and columns
2026-02-12 21:54:37.86359 INFO::Found 0 missing values.
2026-02-12 21:54:37.867686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:37.868368 INFO::Done
2026-02-12 21:54:37.868934 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:37.88155 INFO::Starting hierarchical adjustment
2026-02-12 21:54:37.882526 INFO::Found 3 batches.
2026-02-12 21:54:37.883147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:37.884408 INFO::Using default BPPARAM
2026-02-12 21:54:37.88499 INFO::Processing subtree level 1
2026-02-12 21:54:38.000713 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:54:38.002846 INFO::Done
2026-02-12 21:54:38.003662 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:38.006688 INFO::ASW Batch was -0.109740087484216 prior to batch effect correction and is now -0.109740087484216 .
2026-02-12 21:54:38.007915 INFO::Total function execution time is 0.436604022979736 s and adjustment time is 0.120518445968628 s ( 27.6 )
2026-02-12 21:54:38.026645 INFO::Formatting Data.
2026-02-12 21:54:38.027591 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:38.02865 INFO::Removing potential empty rows and columns
2026-02-12 21:54:38.029907 INFO::Found 0 missing values.
2026-02-12 21:54:38.030991 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-12 21:54:38.043501 INFO::Formatting Data.
2026-02-12 21:54:38.044415 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:38.045445 INFO::Removing potential empty rows and columns
2026-02-12 21:54:38.046627 INFO::Found 0 missing values.
2026-02-12 21:54:38.047628 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-12 21:54:38.065799 INFO::Formatting Data.
2026-02-12 21:54:38.066769 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:38.067801 INFO::Removing potential empty rows and columns
2026-02-12 21:54:38.068978 INFO::Found 0 missing values.
2026-02-12 21:54:38.070009 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-12 21:54:38.074832 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:38.075421 INFO::Done
2026-02-12 21:54:38.075972 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:38.078229 INFO::Starting hierarchical adjustment
2026-02-12 21:54:38.078952 INFO::Found 2 batches.
2026-02-12 21:54:38.079525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:38.080201 INFO::Using default BPPARAM
2026-02-12 21:54:38.080755 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:38.08174 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:54:38.107391 INFO::Done
2026-02-12 21:54:38.10825 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:38.110782 INFO::ASW Batch was 0.0265182000559375 prior to batch effect correction and is now -0.0925277763440272 .
2026-02-12 21:54:38.11173 INFO::Total function execution time is 0.0460610389709473 s and adjustment time is 0.0284984111785889 s ( 61.87 )
2026-02-12 21:54:38.115059 INFO::Formatting Data.
2026-02-12 21:54:38.115755 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:38.125446 INFO::Formatting Data.
2026-02-12 21:54:38.126348 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:38.127371 INFO::Removing potential empty rows and columns
2026-02-12 21:54:38.128495 INFO::Found 0 missing values.
2026-02-12 21:54:38.131752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:38.132337 INFO::Done
2026-02-12 21:54:38.132898 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:38.189677 INFO::Starting hierarchical adjustment
2026-02-12 21:54:38.193835 INFO::Found 2 batches.
2026-02-12 21:54:38.19461 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:38.195251 INFO::Using default BPPARAM
2026-02-12 21:54:38.195843 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:38.197016 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:38.214033 INFO::Done
2026-02-12 21:54:38.214884 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:38.217366 INFO::ASW Batch was -0.0255962928827667 prior to batch effect correction and is now -0.105120014230721 .
2026-02-12 21:54:38.218279 INFO::Total function execution time is 0.0929245948791504 s and adjustment time is 0.0204432010650635 s ( 22 )
2026-02-12 21:54:38.219477 INFO::Formatting Data.
2026-02-12 21:54:38.220139 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:38.221108 INFO::Removing potential empty rows and columns
2026-02-12 21:54:38.22218 INFO::Found 0 missing values.
2026-02-12 21:54:38.225208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:38.225796 INFO::Done
2026-02-12 21:54:38.226339 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:38.228743 INFO::Starting hierarchical adjustment
2026-02-12 21:54:38.229499 INFO::Found 2 batches.
2026-02-12 21:54:38.230035 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:38.230688 INFO::Using default BPPARAM
2026-02-12 21:54:38.231228 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:38.232241 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:38.249081 INFO::Done
2026-02-12 21:54:38.249922 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:38.252239 INFO::ASW Batch was -0.0255962928827667 prior to batch effect correction and is now -0.105120014230721 .
2026-02-12 21:54:38.253134 INFO::Total function execution time is 0.0336601734161377 s and adjustment time is 0.0196928977966309 s ( 58.51 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-12 21:54:41.727965 INFO::Formatting Data.
2026-02-12 21:54:41.728756 INFO::Recognized SummarizedExperiment
2026-02-12 21:54:41.72931 INFO::Typecasting input to dataframe.
2026-02-12 21:54:41.761932 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:41.763331 INFO::Removing potential empty rows and columns
2026-02-12 21:54:41.767321 INFO::Found 0 missing values.
2026-02-12 21:54:41.774866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:41.775606 INFO::Done
2026-02-12 21:54:41.776155 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:41.779866 INFO::Starting hierarchical adjustment
2026-02-12 21:54:41.780606 INFO::Found 2 batches.
2026-02-12 21:54:41.781137 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:41.782247 INFO::Using default BPPARAM
2026-02-12 21:54:41.782779 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:41.783756 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:54:41.841371 INFO::Done
2026-02-12 21:54:41.842152 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:41.845946 INFO::ASW Batch was -0.00355812252379879 prior to batch effect correction and is now -0.0894760964384092 .
2026-02-12 21:54:41.846887 INFO::Total function execution time is 0.119197368621826 s and adjustment time is 0.060884952545166 s ( 51.08 )
Warning: stack imbalance in '{', 73 then 75
2026-02-12 21:54:41.866565 INFO::Formatting Data.
2026-02-12 21:54:41.867359 INFO::Recognized SummarizedExperiment
2026-02-12 21:54:41.867919 INFO::Typecasting input to dataframe.
2026-02-12 21:54:41.877578 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:41.878791 INFO::Removing potential empty rows and columns
2026-02-12 21:54:41.88253 INFO::Found 0 missing values.
2026-02-12 21:54:41.890115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:41.890842 INFO::Done
2026-02-12 21:54:41.891409 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:41.895105 INFO::Starting hierarchical adjustment
2026-02-12 21:54:41.895866 INFO::Found 2 batches.
2026-02-12 21:54:41.896399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:41.897023 INFO::Using default BPPARAM
2026-02-12 21:54:41.897559 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:41.898547 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:54:41.924121 INFO::Done
2026-02-12 21:54:41.924875 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:41.92858 INFO::ASW Batch was -0.0103964219777776 prior to batch effect correction and is now -0.0103964219777776 .
2026-02-12 21:54:41.929469 INFO::Total function execution time is 0.0629355907440186 s and adjustment time is 0.0283606052398682 s ( 45.06 )
2026-02-12 21:54:41.9489 INFO::Formatting Data.
2026-02-12 21:54:41.94971 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:41.950613 INFO::Removing potential empty rows and columns
2026-02-12 21:54:41.951638 INFO::Found 0 missing values.
2026-02-12 21:54:41.954577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:41.955104 INFO::Done
2026-02-12 21:54:41.955625 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:41.957628 INFO::Starting hierarchical adjustment
2026-02-12 21:54:41.958304 INFO::Found 3 batches.
2026-02-12 21:54:41.958848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:41.959429 INFO::Using default BPPARAM
2026-02-12 21:54:41.959962 INFO::Processing subtree level 1
2026-02-12 21:54:42.095659 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:54:42.097391 INFO::Done
2026-02-12 21:54:42.098031 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:42.100448 INFO::ASW Batch was 0.0230298344142828 prior to batch effect correction and is now -0.157798834776871 .
2026-02-12 21:54:42.101381 INFO::Total function execution time is 0.152551889419556 s and adjustment time is 0.139216661453247 s ( 91.26 )
2026-02-12 21:54:42.115837 INFO::Skipping initial DF formatting
2026-02-12 21:54:42.11656 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:42.120718 INFO::Starting hierarchical adjustment
2026-02-12 21:54:42.121527 INFO::Found 5 batches.
2026-02-12 21:54:42.122094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:42.12273 INFO::Using default BPPARAM
2026-02-12 21:54:42.123253 INFO::Processing subtree level 1
2026-02-12 21:54:42.360154 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:42.361795 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:54:42.381595 INFO::Done
2026-02-12 21:54:42.382331 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:42.386646 INFO::ASW Batch was 0.52233860680649 prior to batch effect correction and is now 0.52233860680649 .
2026-02-12 21:54:42.38728 INFO::ASW Label was 0.354661602948257 prior to batch effect correction and is now 0.354661602948257 .
2026-02-12 21:54:42.388146 INFO::Total function execution time is 0.272388219833374 s and adjustment time is 0.260186433792114 s ( 95.52 )
2026-02-12 21:54:42.453691 INFO::Formatting Data.
2026-02-12 21:54:42.454464 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:42.455357 INFO::Removing potential empty rows and columns
2026-02-12 21:54:42.456354 INFO::Found 0 missing values.
2026-02-12 21:54:42.460373 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:42.460899 INFO::Done
2026-02-12 21:54:42.461381 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:42.464236 INFO::Starting hierarchical adjustment
2026-02-12 21:54:42.464925 INFO::Found 5 batches.
2026-02-12 21:54:42.465419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:42.466016 INFO::Using default BPPARAM
2026-02-12 21:54:42.466522 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:42.601584 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:42.603213 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:42.620192 INFO::Done
2026-02-12 21:54:42.620954 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:42.624387 INFO::ASW Batch was 0.424096064837739 prior to batch effect correction and is now -0.0804008625651461 .
2026-02-12 21:54:42.624995 INFO::ASW Label was 0.414598734601125 prior to batch effect correction and is now 0.725322251219574 .
2026-02-12 21:54:42.625803 INFO::Total function execution time is 0.172279596328735 s and adjustment time is 0.155376434326172 s ( 90.19 )
2026-02-12 21:54:42.626651 INFO::Formatting Data.
2026-02-12 21:54:42.62729 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:42.628251 INFO::Removing potential empty rows and columns
2026-02-12 21:54:42.629327 INFO::Found 0 missing values.
2026-02-12 21:54:42.633573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:42.634124 INFO::Done
2026-02-12 21:54:42.634664 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:42.637736 INFO::Starting hierarchical adjustment
2026-02-12 21:54:42.638461 INFO::Found 5 batches.
2026-02-12 21:54:42.638993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:42.639603 INFO::Using default BPPARAM
2026-02-12 21:54:42.640141 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:42.762536 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:42.764089 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:42.779968 INFO::Done
2026-02-12 21:54:42.780709 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:42.784195 INFO::ASW Batch was 0.424096064837739 prior to batch effect correction and is now -0.0804008625651461 .
2026-02-12 21:54:42.784796 INFO::ASW Label was 0.414598734601125 prior to batch effect correction and is now 0.725322251219574 .
2026-02-12 21:54:42.785588 INFO::Total function execution time is 0.158936977386475 s and adjustment time is 0.141615867614746 s ( 89.1 )
2026-02-12 21:54:42.798951 INFO::Formatting Data.
2026-02-12 21:54:42.799777 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:42.80069 INFO::Removing potential empty rows and columns
2026-02-12 21:54:42.801676 INFO::Found 0 missing values.
2026-02-12 21:54:42.805599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:42.806156 INFO::Done
2026-02-12 21:54:42.806669 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:42.809584 INFO::Starting hierarchical adjustment
2026-02-12 21:54:42.810276 INFO::Found 5 batches.
2026-02-12 21:54:42.810827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:42.811461 INFO::Using default BPPARAM
2026-02-12 21:54:42.812039 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:42.935874 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:42.937426 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:42.952894 INFO::Done
2026-02-12 21:54:42.953629 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:42.956794 INFO::ASW Batch was 0.303199442860791 prior to batch effect correction and is now -0.00964028475295894 .
2026-02-12 21:54:42.957391 INFO::ASW Label was 0.448213528257599 prior to batch effect correction and is now 0.832297622664205 .
2026-02-12 21:54:42.958192 INFO::Total function execution time is 0.159314393997192 s and adjustment time is 0.142720222473145 s ( 89.58 )
2026-02-12 21:54:42.958987 INFO::Formatting Data.
2026-02-12 21:54:42.959594 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:42.960449 INFO::Removing potential empty rows and columns
2026-02-12 21:54:42.961436 INFO::Found 0 missing values.
2026-02-12 21:54:42.965302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:42.965844 INFO::Done
2026-02-12 21:54:42.966336 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:42.969231 INFO::Starting hierarchical adjustment
2026-02-12 21:54:42.969948 INFO::Found 5 batches.
2026-02-12 21:54:42.970476 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:42.971102 INFO::Using default BPPARAM
2026-02-12 21:54:42.971632 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:43.1048 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:43.106685 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:43.126086 INFO::Done
2026-02-12 21:54:43.127112 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.131087 INFO::ASW Batch was 0.303199442860791 prior to batch effect correction and is now -0.00964028475295894 .
2026-02-12 21:54:43.131816 INFO::ASW Label was 0.448213528257599 prior to batch effect correction and is now 0.832297622664205 .
2026-02-12 21:54:43.132756 INFO::Total function execution time is 0.173735618591309 s and adjustment time is 0.156196594238281 s ( 89.9 )
2026-02-12 21:54:43.148041 INFO::Formatting Data.
2026-02-12 21:54:43.148918 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:43.149916 INFO::Removing potential empty rows and columns
2026-02-12 21:54:43.15102 INFO::Found 0 missing values.
2026-02-12 21:54:43.154416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:43.155186 INFO::Done
2026-02-12 21:54:43.155756 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:43.159057 INFO::Starting hierarchical adjustment
2026-02-12 21:54:43.159848 INFO::Found 2 batches.
2026-02-12 21:54:43.160398 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:43.161056 INFO::Using default BPPARAM
2026-02-12 21:54:43.161632 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:43.162626 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:43.17799 INFO::Done
2026-02-12 21:54:43.178664 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.181499 INFO::ASW Batch was 0.654646923813778 prior to batch effect correction and is now 0.0435013033672459 .
2026-02-12 21:54:43.182058 INFO::ASW Label was 0.412088172844894 prior to batch effect correction and is now 0.853876607142594 .
2026-02-12 21:54:43.182815 INFO::Total function execution time is 0.0348951816558838 s and adjustment time is 0.0182995796203613 s ( 52.44 )
2026-02-12 21:54:43.183586 INFO::Formatting Data.
2026-02-12 21:54:43.184176 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:43.185004 INFO::Removing potential empty rows and columns
2026-02-12 21:54:43.185941 INFO::Found 0 missing values.
2026-02-12 21:54:43.188446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:43.188966 INFO::Done
2026-02-12 21:54:43.189452 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:43.192151 INFO::Starting hierarchical adjustment
2026-02-12 21:54:43.192826 INFO::Found 2 batches.
2026-02-12 21:54:43.193332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:43.193913 INFO::Using default BPPARAM
2026-02-12 21:54:43.194401 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:43.19526 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:54:43.20909 INFO::Done
2026-02-12 21:54:43.209718 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.212458 INFO::ASW Batch was 0.654646923813778 prior to batch effect correction and is now 0.0435013033672459 .
2026-02-12 21:54:43.21303 INFO::ASW Label was 0.412088172844894 prior to batch effect correction and is now 0.853876607142594 .
2026-02-12 21:54:43.213781 INFO::Total function execution time is 0.0302131175994873 s and adjustment time is 0.0163872241973877 s ( 54.24 )
2026-02-12 21:54:43.224835 INFO::Formatting Data.
2026-02-12 21:54:43.225623 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:43.226464 INFO::Removing potential empty rows and columns
2026-02-12 21:54:43.227332 INFO::Found 0 missing values.
2026-02-12 21:54:43.229322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:43.229838 INFO::Done
2026-02-12 21:54:43.230317 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:43.232108 INFO::Starting hierarchical adjustment
2026-02-12 21:54:43.232769 INFO::Found 2 batches.
2026-02-12 21:54:43.233258 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:43.233831 INFO::Using default BPPARAM
2026-02-12 21:54:43.234322 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:43.235156 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:54:43.2643 INFO::Done
2026-02-12 21:54:43.264966 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.26679 INFO::ASW Batch was -0.0243741875406881 prior to batch effect correction and is now -0.0918240715175611 .
2026-02-12 21:54:43.267567 INFO::Total function execution time is 0.042809009552002 s and adjustment time is 0.0316309928894043 s ( 73.89 )
2026-02-12 21:54:43.278771 INFO::Formatting Data.
2026-02-12 21:54:43.2795 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:43.280345 INFO::Removing potential empty rows and columns
2026-02-12 21:54:43.281294 INFO::Found 0 missing values.
2026-02-12 21:54:43.282451 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-12 21:54:43.286876 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:43.287431 INFO::Done
2026-02-12 21:54:43.287949 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:43.290771 INFO::Starting hierarchical adjustment
2026-02-12 21:54:43.291433 INFO::Found 2 batches.
2026-02-12 21:54:43.291948 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:43.292527 INFO::Using default BPPARAM
2026-02-12 21:54:43.293019 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:43.2939 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:54:43.309395 INFO::Done
2026-02-12 21:54:43.310022 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.312765 INFO::ASW Batch was 0.810586098573527 prior to batch effect correction and is now 0.03076428908346 .
2026-02-12 21:54:43.313315 INFO::ASW Label was 0.197333814224984 prior to batch effect correction and is now 0.784188097448231 .
2026-02-12 21:54:43.314064 INFO::Total function execution time is 0.0353717803955078 s and adjustment time is 0.0180847644805908 s ( 51.13 )
2026-02-12 21:54:43.314798 INFO::Formatting Data.
2026-02-12 21:54:43.315371 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:43.316225 INFO::Removing potential empty rows and columns
2026-02-12 21:54:43.317139 INFO::Found 0 missing values.
2026-02-12 21:54:43.317983 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-12 21:54:43.322074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:43.322587 INFO::Done
2026-02-12 21:54:43.323075 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:43.325727 INFO::Starting hierarchical adjustment
2026-02-12 21:54:43.326379 INFO::Found 2 batches.
2026-02-12 21:54:43.326882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:43.32744 INFO::Using default BPPARAM
2026-02-12 21:54:43.32794 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:43.32881 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:54:43.343943 INFO::Done
2026-02-12 21:54:43.344562 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.347252 INFO::ASW Batch was 0.810586098573527 prior to batch effect correction and is now 0.03076428908346 .
2026-02-12 21:54:43.347793 INFO::ASW Label was 0.197333814224984 prior to batch effect correction and is now 0.784188097448231 .
2026-02-12 21:54:43.348528 INFO::Total function execution time is 0.0337297916412354 s and adjustment time is 0.0176811218261719 s ( 52.42 )
2026-02-12 21:54:43.549878 INFO::Formatting Data.
2026-02-12 21:54:43.550705 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:43.551594 INFO::Removing potential empty rows and columns
2026-02-12 21:54:43.552618 INFO::Found 0 missing values.
2026-02-12 21:54:43.555612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:43.556151 INFO::Done
2026-02-12 21:54:43.556669 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:43.558689 INFO::Starting hierarchical adjustment
2026-02-12 21:54:43.559381 INFO::Found 3 batches.
2026-02-12 21:54:43.559911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:43.560495 INFO::Using default BPPARAM
2026-02-12 21:54:43.561031 INFO::Processing subtree level 1
2026-02-12 21:54:43.648783 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:54:43.650473 INFO::Done
2026-02-12 21:54:43.651089 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.653482 INFO::ASW Batch was -0.063062753227186 prior to batch effect correction and is now -0.063062753227186 .
2026-02-12 21:54:43.654371 INFO::Total function execution time is 0.104583024978638 s and adjustment time is 0.0912289619445801 s ( 87.23 )
2026-02-12 21:54:43.65539 INFO::Formatting Data.
2026-02-12 21:54:43.656029 INFO::Typecasting input to dataframe.
2026-02-12 21:54:43.656777 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:43.657682 INFO::Removing potential empty rows and columns
2026-02-12 21:54:43.658732 INFO::Found 0 missing values.
2026-02-12 21:54:43.661745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:43.662304 INFO::Done
2026-02-12 21:54:43.662837 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:43.664836 INFO::Starting hierarchical adjustment
2026-02-12 21:54:43.665567 INFO::Found 3 batches.
2026-02-12 21:54:43.666091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:43.666709 INFO::Using default BPPARAM
2026-02-12 21:54:43.667227 INFO::Processing subtree level 1
2026-02-12 21:54:43.749916 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:54:43.751642 INFO::Done
2026-02-12 21:54:43.752251 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.754677 INFO::ASW Batch was -0.063062753227186 prior to batch effect correction and is now -0.063062753227186 .
2026-02-12 21:54:43.755599 INFO::Total function execution time is 0.100180387496948 s and adjustment time is 0.086237907409668 s ( 86.08 )
2026-02-12 21:54:43.768659 INFO::Formatting Data.
2026-02-12 21:54:43.769433 INFO::Typecasting input to dataframe.
2026-02-12 21:54:43.770287 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:43.771184 INFO::Removing potential empty rows and columns
2026-02-12 21:54:43.772247 INFO::Found 0 missing values.
2026-02-12 21:54:43.775416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:43.775973 INFO::Done
2026-02-12 21:54:43.776478 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:43.778466 INFO::Starting hierarchical adjustment
2026-02-12 21:54:43.779175 INFO::Found 3 batches.
2026-02-12 21:54:43.779715 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:43.780316 INFO::Using default BPPARAM
2026-02-12 21:54:43.780861 INFO::Processing subtree level 1
2026-02-12 21:54:43.862836 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:54:43.864635 INFO::Done
2026-02-12 21:54:43.865277 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:43.867792 INFO::ASW Batch was -0.126716336169872 prior to batch effect correction and is now -0.126716336169872 .
2026-02-12 21:54:43.868742 INFO::Total function execution time is 0.100162267684937 s and adjustment time is 0.0855729579925537 s ( 85.43 )
2026-02-12 21:54:44.000733 INFO::Formatting Data.
2026-02-12 21:54:44.001526 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:44.002603 INFO::Removing potential empty rows and columns
2026-02-12 21:54:44.005317 INFO::Found 1000 missing values.
2026-02-12 21:54:44.024012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:44.024738 INFO::Done
2026-02-12 21:54:44.025262 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:44.030661 INFO::Starting hierarchical adjustment
2026-02-12 21:54:44.03142 INFO::Found 10 batches.
2026-02-12 21:54:44.031959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:44.032573 INFO::Using default BPPARAM
2026-02-12 21:54:44.033096 INFO::Processing subtree level 1
2026-02-12 21:54:44.164684 INFO::Processing subtree level 2
2026-02-12 21:54:44.297698 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:54:44.299535 INFO::Done
2026-02-12 21:54:44.300191 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:44.305551 INFO::ASW Batch was 0.48956969911796 prior to batch effect correction and is now 0.48956969911796 .
2026-02-12 21:54:44.306157 INFO::ASW Label was 0.358493487961487 prior to batch effect correction and is now 0.358493487961487 .
2026-02-12 21:54:44.30714 INFO::Total function execution time is 0.306396484375 s and adjustment time is 0.268248558044434 s ( 87.55 )
2026-02-12 21:54:44.307968 INFO::Formatting Data.
2026-02-12 21:54:44.308595 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:44.309798 INFO::Removing potential empty rows and columns
2026-02-12 21:54:44.3125 INFO::Found 1000 missing values.
2026-02-12 21:54:44.331214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:44.331949 INFO::Done
2026-02-12 21:54:44.332488 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:44.33792 INFO::Starting hierarchical adjustment
2026-02-12 21:54:44.338717 INFO::Found 10 batches.
2026-02-12 21:54:45.275214 INFO::Set up parallel execution backend with 2 workers
2026-02-12 21:54:45.277049 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-12 21:54:46.875257 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:54:46.877875 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:54:46.896096 INFO::Done
2026-02-12 21:54:46.896818 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:46.901706 INFO::ASW Batch was 0.48956969911796 prior to batch effect correction and is now 0.48956969911796 .
2026-02-12 21:54:46.902327 INFO::ASW Label was 0.358493487961487 prior to batch effect correction and is now 0.358493487961487 .
2026-02-12 21:54:46.903121 INFO::Total function execution time is 2.59517860412598 s and adjustment time is 2.55749750137329 s ( 98.55 )
2026-02-12 21:54:47.063645 INFO::Formatting Data.
2026-02-12 21:54:47.064532 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.065485 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.066604 INFO::Found 0 missing values.
2026-02-12 21:54:47.070233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.070763 INFO::Done
2026-02-12 21:54:47.071263 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:54:47.074084 INFO::Starting hierarchical adjustment
2026-02-12 21:54:47.074791 INFO::Found 3 batches.
2026-02-12 21:54:47.075294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:54:47.075898 INFO::Using default BPPARAM
2026-02-12 21:54:47.076402 INFO::Processing subtree level 1
2026-02-12 21:54:47.186414 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:54:47.18826 INFO::Done
2026-02-12 21:54:47.188902 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:54:47.192132 INFO::ASW Batch was 0.223682730137125 prior to batch effect correction and is now -0.113861276638838 .
2026-02-12 21:54:47.192857 INFO::ASW Label was -0.234508596998252 prior to batch effect correction and is now -0.0740821674071018 .
2026-02-12 21:54:47.193759 INFO::Total function execution time is 0.130229949951172 s and adjustment time is 0.11359167098999 s ( 87.22 )
2026-02-12 21:54:47.314207 INFO::Formatting Data.
2026-02-12 21:54:47.315087 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.316 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.317048 INFO::Found 2 missing values.
2026-02-12 21:54:47.319884 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.320404 INFO::Done
2026-02-12 21:54:47.347457 INFO::Found NA in Reference column
2026-02-12 21:54:47.356858 INFO::Require at least two references per batch.
2026-02-12 21:54:47.376932 INFO::Formatting Data.
2026-02-12 21:54:47.3777 INFO::Recognized SummarizedExperiment
2026-02-12 21:54:47.378222 INFO::Typecasting input to dataframe.
2026-02-12 21:54:47.387903 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.389061 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.392348 INFO::Found 0 missing values.
2026-02-12 21:54:47.398809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.399387 INFO::Done
2026-02-12 21:54:47.41535 INFO::Formatting Data.
2026-02-12 21:54:47.416176 INFO::Recognized SummarizedExperiment
2026-02-12 21:54:47.416721 INFO::Typecasting input to dataframe.
2026-02-12 21:54:47.434574 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.435903 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.439428 INFO::Found 0 missing values.
2026-02-12 21:54:47.449982 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.450692 INFO::Done
2026-02-12 21:54:47.466853 INFO::Formatting Data.
2026-02-12 21:54:47.46765 INFO::Recognized SummarizedExperiment
2026-02-12 21:54:47.46817 INFO::Typecasting input to dataframe.
2026-02-12 21:54:47.48571 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.486866 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.487983 INFO::Found 0 missing values.
2026-02-12 21:54:47.488924 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-12 21:54:47.493309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.493877 INFO::Done
2026-02-12 21:54:47.505136 INFO::Formatting Data.
2026-02-12 21:54:47.505972 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.506908 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.518921 INFO::Found 0 missing values.
2026-02-12 21:54:47.522245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.522885 INFO::Done
2026-02-12 21:54:47.535322 INFO::Formatting Data.
2026-02-12 21:54:47.536316 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.537468 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.538573 INFO::Found 0 missing values.
2026-02-12 21:54:47.541711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.542303 INFO::Done
2026-02-12 21:54:47.576082 INFO::Formatting Data.
2026-02-12 21:54:47.577036 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.578257 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.579596 INFO::Found 1 missing values.
2026-02-12 21:54:47.582534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.583127 INFO::Done
2026-02-12 21:54:47.604869 INFO::Formatting Data.
2026-02-12 21:54:47.60582 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.606819 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.607858 INFO::Found 2 missing values.
2026-02-12 21:54:47.608877 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-12 21:54:47.611413 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.611995 INFO::Done
2026-02-12 21:54:47.623323 INFO::Formatting Data.
2026-02-12 21:54:47.624168 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.625083 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.626099 INFO::Found 2 missing values.
2026-02-12 21:54:47.627812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.62835 INFO::Done
2026-02-12 21:54:47.63944 INFO::Formatting Data.
2026-02-12 21:54:47.640292 INFO::Typecasting input to dataframe.
2026-02-12 21:54:47.641113 INFO::Replacing NaNs with NAs.
2026-02-12 21:54:47.641996 INFO::Removing potential empty rows and columns
2026-02-12 21:54:47.64301 INFO::Found 0 missing values.
2026-02-12 21:54:47.646058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:54:47.646617 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.865 4.046 21.703
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.639 | 1.487 | 17.884 | |
| compute_asw | 0.024 | 0.002 | 0.026 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.010 | 0.001 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |