Yannis Schumann
| Snapshot Date: 2025-11-14 13:45 -0500 (Fri, 14 Nov 2025) |
| 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 Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-15 11:58 -0500 (Sat, 15 Nov 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" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | | ||||||||
| 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: 1.6.0 |
| 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: 2025-11-14 21:32:34 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 21:34:09 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 95.1 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 4.5.1 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 ‘1.6.0’
* 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 24.63 2.199 18.028
* 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 4.5.1 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")
2025-11-14 21:33:30.05849 INFO::Formatting Data.
2025-11-14 21:33:30.06015 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:30.072337 INFO::Removing potential empty rows and columns
2025-11-14 21:33:30.347072 INFO::Found 0 missing values.
2025-11-14 21:33:30.351095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:30.351919 INFO::Done
2025-11-14 21:33:30.352585 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:30.367445 INFO::Starting hierarchical adjustment
2025-11-14 21:33:30.368581 INFO::Found 3 batches.
2025-11-14 21:33:30.369236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:30.37067 INFO::Using default BPPARAM
2025-11-14 21:33:30.371306 INFO::Processing subtree level 1
2025-11-14 21:33:30.516055 INFO::Adjusting the last 1 batches sequentially
2025-11-14 21:33:30.518365 INFO::Done
2025-11-14 21:33:30.519169 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:30.522226 INFO::ASW Batch was -0.0486561295911338 prior to batch effect correction and is now -0.0486561295911338 .
2025-11-14 21:33:30.523454 INFO::Total function execution time is 0.465723752975464 s and adjustment time is 0.150002241134644 s ( 32.21 )
2025-11-14 21:33:30.540306 INFO::Formatting Data.
2025-11-14 21:33:30.541204 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:30.542213 INFO::Removing potential empty rows and columns
2025-11-14 21:33:30.543443 INFO::Found 0 missing values.
2025-11-14 21:33:30.544538 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.
2025-11-14 21:33:30.55711 INFO::Formatting Data.
2025-11-14 21:33:30.558169 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:30.55929 INFO::Removing potential empty rows and columns
2025-11-14 21:33:30.560592 INFO::Found 0 missing values.
2025-11-14 21:33:30.561738 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.
2025-11-14 21:33:30.582947 INFO::Formatting Data.
2025-11-14 21:33:30.58407 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:30.585256 INFO::Removing potential empty rows and columns
2025-11-14 21:33:30.586527 INFO::Found 0 missing values.
2025-11-14 21:33:30.587688 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.
2025-11-14 21:33:30.593161 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:30.593813 INFO::Done
2025-11-14 21:33:30.594407 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:30.596833 INFO::Starting hierarchical adjustment
2025-11-14 21:33:30.597649 INFO::Found 2 batches.
2025-11-14 21:33:30.598236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:30.598975 INFO::Using default BPPARAM
2025-11-14 21:33:30.599603 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:30.600675 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 21:33:30.628935 INFO::Done
2025-11-14 21:33:30.630141 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:30.63335 INFO::ASW Batch was 0.00194730600193527 prior to batch effect correction and is now -0.113755014811375 .
2025-11-14 21:33:30.634548 INFO::Total function execution time is 0.0517292022705078 s and adjustment time is 0.0313606262207031 s ( 60.62 )
2025-11-14 21:33:30.638175 INFO::Formatting Data.
2025-11-14 21:33:30.638957 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:30.650764 INFO::Formatting Data.
2025-11-14 21:33:30.651945 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:30.653218 INFO::Removing potential empty rows and columns
2025-11-14 21:33:30.654609 INFO::Found 0 missing values.
2025-11-14 21:33:30.658475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:30.659145 INFO::Done
2025-11-14 21:33:30.659757 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:30.662587 INFO::Starting hierarchical adjustment
2025-11-14 21:33:30.663476 INFO::Found 2 batches.
2025-11-14 21:33:30.664076 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:30.665059 INFO::Using default BPPARAM
2025-11-14 21:33:30.702361 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:30.724083 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 21:33:30.744394 INFO::Done
2025-11-14 21:33:30.745323 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:30.747815 INFO::ASW Batch was 0.0220660484900445 prior to batch effect correction and is now -0.124994550974392 .
2025-11-14 21:33:30.748737 INFO::Total function execution time is 0.0981817245483398 s and adjustment time is 0.081057071685791 s ( 82.56 )
2025-11-14 21:33:30.749928 INFO::Formatting Data.
2025-11-14 21:33:30.750578 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:30.751528 INFO::Removing potential empty rows and columns
2025-11-14 21:33:30.752606 INFO::Found 0 missing values.
2025-11-14 21:33:30.755513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:30.756054 INFO::Done
2025-11-14 21:33:30.756605 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:30.758849 INFO::Starting hierarchical adjustment
2025-11-14 21:33:30.759596 INFO::Found 2 batches.
2025-11-14 21:33:30.760138 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:30.760805 INFO::Using default BPPARAM
2025-11-14 21:33:30.761345 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:30.762398 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 21:33:30.778944 INFO::Done
2025-11-14 21:33:30.779668 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:30.781842 INFO::ASW Batch was 0.0220660484900445 prior to batch effect correction and is now -0.124994550974392 .
2025-11-14 21:33:30.782724 INFO::Total function execution time is 0.0327823162078857 s and adjustment time is 0.0194816589355469 s ( 59.43 )
2025-11-14 21:33:34.054982 INFO::Formatting Data.
2025-11-14 21:33:34.055912 INFO::Recognized SummarizedExperiment
2025-11-14 21:33:34.056457 INFO::Typecasting input to dataframe.
2025-11-14 21:33:34.088176 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:34.089595 INFO::Removing potential empty rows and columns
2025-11-14 21:33:34.093598 INFO::Found 0 missing values.
2025-11-14 21:33:34.101108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:34.101836 INFO::Done
2025-11-14 21:33:34.102407 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:34.106497 INFO::Starting hierarchical adjustment
2025-11-14 21:33:34.107248 INFO::Found 2 batches.
2025-11-14 21:33:34.107781 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:34.108948 INFO::Using default BPPARAM
2025-11-14 21:33:34.109516 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:34.110528 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 21:33:34.168874 INFO::Done
2025-11-14 21:33:34.169694 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:34.173541 INFO::ASW Batch was 0.0125128898688308 prior to batch effect correction and is now -0.0941755752252716 .
2025-11-14 21:33:34.174543 INFO::Total function execution time is 0.119906663894653 s and adjustment time is 0.0617387294769287 s ( 51.49 )
2025-11-14 21:33:34.194205 INFO::Formatting Data.
2025-11-14 21:33:34.195005 INFO::Recognized SummarizedExperiment
2025-11-14 21:33:34.195568 INFO::Typecasting input to dataframe.
2025-11-14 21:33:34.205007 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:34.206226 INFO::Removing potential empty rows and columns
2025-11-14 21:33:34.20996 INFO::Found 0 missing values.
2025-11-14 21:33:34.217479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:34.218152 INFO::Done
2025-11-14 21:33:34.218677 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:34.222393 INFO::Starting hierarchical adjustment
2025-11-14 21:33:34.223155 INFO::Found 2 batches.
2025-11-14 21:33:34.223675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:34.224291 INFO::Using default BPPARAM
2025-11-14 21:33:34.224815 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:34.225821 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 21:33:34.251798 INFO::Done
2025-11-14 21:33:34.252645 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:34.256492 INFO::ASW Batch was -0.0126449111701447 prior to batch effect correction and is now -0.0126449111701447 .
2025-11-14 21:33:34.257446 INFO::Total function execution time is 0.0632429122924805 s and adjustment time is 0.0287389755249023 s ( 45.44 )
2025-11-14 21:33:34.277704 INFO::Formatting Data.
2025-11-14 21:33:34.278616 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:34.279569 INFO::Removing potential empty rows and columns
2025-11-14 21:33:34.280634 INFO::Found 0 missing values.
2025-11-14 21:33:34.283702 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:34.284261 INFO::Done
2025-11-14 21:33:34.284773 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:34.286928 INFO::Starting hierarchical adjustment
2025-11-14 21:33:34.287666 INFO::Found 3 batches.
2025-11-14 21:33:34.288197 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:34.288807 INFO::Using default BPPARAM
2025-11-14 21:33:34.289351 INFO::Processing subtree level 1
2025-11-14 21:33:34.443404 INFO::Adjusting the last 1 batches sequentially
2025-11-14 21:33:34.445346 INFO::Done
2025-11-14 21:33:34.446049 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:34.448677 INFO::ASW Batch was -0.0942898115569669 prior to batch effect correction and is now -0.156385745311709 .
2025-11-14 21:33:34.449681 INFO::Total function execution time is 0.172057390213013 s and adjustment time is 0.1578049659729 s ( 91.72 )
2025-11-14 21:33:34.465 INFO::Skipping initial DF formatting
2025-11-14 21:33:34.465753 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:34.46997 INFO::Starting hierarchical adjustment
2025-11-14 21:33:34.470804 INFO::Found 5 batches.
2025-11-14 21:33:34.471379 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:34.472007 INFO::Using default BPPARAM
2025-11-14 21:33:34.472558 INFO::Processing subtree level 1
2025-11-14 21:33:34.721023 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:34.722954 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 21:33:34.744089 INFO::Done
2025-11-14 21:33:34.744983 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:34.749556 INFO::ASW Batch was 0.48545131483729 prior to batch effect correction and is now 0.48545131483729 .
2025-11-14 21:33:34.75025 INFO::ASW Label was 0.40188673637982 prior to batch effect correction and is now 0.40188673637982 .
2025-11-14 21:33:34.751193 INFO::Total function execution time is 0.286243438720703 s and adjustment time is 0.273405790328979 s ( 95.52 )
2025-11-14 21:33:34.832558 INFO::Formatting Data.
2025-11-14 21:33:34.833475 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:34.834491 INFO::Removing potential empty rows and columns
2025-11-14 21:33:34.835625 INFO::Found 0 missing values.
2025-11-14 21:33:34.839834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:34.84042 INFO::Done
2025-11-14 21:33:34.840945 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:34.844166 INFO::Starting hierarchical adjustment
2025-11-14 21:33:34.844897 INFO::Found 5 batches.
2025-11-14 21:33:34.845453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:34.846071 INFO::Using default BPPARAM
2025-11-14 21:33:34.846636 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.
2025-11-14 21:33:35.036513 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.039126 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 21:33:35.063175 INFO::Done
2025-11-14 21:33:35.064276 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.068797 INFO::ASW Batch was 0.539572718754951 prior to batch effect correction and is now -0.0224863218351377 .
2025-11-14 21:33:35.069577 INFO::ASW Label was 0.142374469496322 prior to batch effect correction and is now 0.688373559613386 .
2025-11-14 21:33:35.070607 INFO::Total function execution time is 0.238145589828491 s and adjustment time is 0.218306303024292 s ( 91.67 )
2025-11-14 21:33:35.071619 INFO::Formatting Data.
2025-11-14 21:33:35.072381 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:35.073504 INFO::Removing potential empty rows and columns
2025-11-14 21:33:35.074808 INFO::Found 0 missing values.
2025-11-14 21:33:35.080308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:35.080971 INFO::Done
2025-11-14 21:33:35.081583 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:35.085057 INFO::Starting hierarchical adjustment
2025-11-14 21:33:35.085862 INFO::Found 5 batches.
2025-11-14 21:33:35.086463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:35.08717 INFO::Using default BPPARAM
2025-11-14 21:33:35.087768 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.
2025-11-14 21:33:35.262333 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.264389 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 21:33:35.28523 INFO::Done
2025-11-14 21:33:35.286139 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.28977 INFO::ASW Batch was 0.539572718754951 prior to batch effect correction and is now -0.0224863218351377 .
2025-11-14 21:33:35.290469 INFO::ASW Label was 0.142374469496322 prior to batch effect correction and is now 0.688373559613386 .
2025-11-14 21:33:35.291365 INFO::Total function execution time is 0.219734191894531 s and adjustment time is 0.199427843093872 s ( 90.76 )
2025-11-14 21:33:35.306812 INFO::Formatting Data.
2025-11-14 21:33:35.307768 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:35.30878 INFO::Removing potential empty rows and columns
2025-11-14 21:33:35.309884 INFO::Found 0 missing values.
2025-11-14 21:33:35.314438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:35.315038 INFO::Done
2025-11-14 21:33:35.315666 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:35.319142 INFO::Starting hierarchical adjustment
2025-11-14 21:33:35.319887 INFO::Found 5 batches.
2025-11-14 21:33:35.320442 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:35.32106 INFO::Using default BPPARAM
2025-11-14 21:33:35.32161 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.
2025-11-14 21:33:35.472672 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.47469 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 21:33:35.493906 INFO::Done
2025-11-14 21:33:35.494977 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.499285 INFO::ASW Batch was 0.342358639379975 prior to batch effect correction and is now -0.0593951728055644 .
2025-11-14 21:33:35.500031 INFO::ASW Label was 0.404802064927925 prior to batch effect correction and is now 0.871764656062473 .
2025-11-14 21:33:35.501037 INFO::Total function execution time is 0.194295883178711 s and adjustment time is 0.174073457717896 s ( 89.59 )
2025-11-14 21:33:35.502026 INFO::Formatting Data.
2025-11-14 21:33:35.502742 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:35.503768 INFO::Removing potential empty rows and columns
2025-11-14 21:33:35.50493 INFO::Found 0 missing values.
2025-11-14 21:33:35.509551 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:35.510178 INFO::Done
2025-11-14 21:33:35.510746 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:35.514245 INFO::Starting hierarchical adjustment
2025-11-14 21:33:35.515019 INFO::Found 5 batches.
2025-11-14 21:33:35.515607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:35.516306 INFO::Using default BPPARAM
2025-11-14 21:33:35.516903 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.
2025-11-14 21:33:35.695527 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.697906 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 21:33:35.718095 INFO::Done
2025-11-14 21:33:35.719129 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.723374 INFO::ASW Batch was 0.342358639379975 prior to batch effect correction and is now -0.0593951728055644 .
2025-11-14 21:33:35.724206 INFO::ASW Label was 0.404802064927925 prior to batch effect correction and is now 0.871764656062473 .
2025-11-14 21:33:35.725325 INFO::Total function execution time is 0.223253011703491 s and adjustment time is 0.203148126602173 s ( 90.99 )
2025-11-14 21:33:35.744005 INFO::Formatting Data.
2025-11-14 21:33:35.745214 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:35.746431 INFO::Removing potential empty rows and columns
2025-11-14 21:33:35.747779 INFO::Found 0 missing values.
2025-11-14 21:33:35.75129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:35.751947 INFO::Done
2025-11-14 21:33:35.75257 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:35.756372 INFO::Starting hierarchical adjustment
2025-11-14 21:33:35.757257 INFO::Found 2 batches.
2025-11-14 21:33:35.757861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:35.75859 INFO::Using default BPPARAM
2025-11-14 21:33:35.759224 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.760351 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 21:33:35.778617 INFO::Done
2025-11-14 21:33:35.779471 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.78309 INFO::ASW Batch was 0.498558280796715 prior to batch effect correction and is now 0.0708674569815016 .
2025-11-14 21:33:35.783851 INFO::ASW Label was 0.511069558746061 prior to batch effect correction and is now 0.885689099108757 .
2025-11-14 21:33:35.784836 INFO::Total function execution time is 0.041062593460083 s and adjustment time is 0.0215103626251221 s ( 52.38 )
2025-11-14 21:33:35.785783 INFO::Formatting Data.
2025-11-14 21:33:35.786478 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:35.787459 INFO::Removing potential empty rows and columns
2025-11-14 21:33:35.788567 INFO::Found 0 missing values.
2025-11-14 21:33:35.791497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:35.792066 INFO::Done
2025-11-14 21:33:35.792621 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:35.795898 INFO::Starting hierarchical adjustment
2025-11-14 21:33:35.796709 INFO::Found 2 batches.
2025-11-14 21:33:35.797291 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:35.797945 INFO::Using default BPPARAM
2025-11-14 21:33:35.798547 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.799571 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-14 21:33:35.815401 INFO::Done
2025-11-14 21:33:35.81618 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.81936 INFO::ASW Batch was 0.498558280796715 prior to batch effect correction and is now 0.0708674569815016 .
2025-11-14 21:33:35.819983 INFO::ASW Label was 0.511069558746061 prior to batch effect correction and is now 0.885689099108757 .
2025-11-14 21:33:35.820794 INFO::Total function execution time is 0.0350539684295654 s and adjustment time is 0.018822193145752 s ( 53.69 )
2025-11-14 21:33:35.833597 INFO::Formatting Data.
2025-11-14 21:33:35.834378 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:35.835302 INFO::Removing potential empty rows and columns
2025-11-14 21:33:35.8363 INFO::Found 0 missing values.
2025-11-14 21:33:35.838666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:35.83926 INFO::Done
2025-11-14 21:33:35.83978 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:35.841897 INFO::Starting hierarchical adjustment
2025-11-14 21:33:35.842666 INFO::Found 2 batches.
2025-11-14 21:33:35.84322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:35.843843 INFO::Using default BPPARAM
2025-11-14 21:33:35.844387 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.845355 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 21:33:35.878325 INFO::Done
2025-11-14 21:33:35.879097 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.881173 INFO::ASW Batch was 0.308583181722863 prior to batch effect correction and is now -0.15981326577767 .
2025-11-14 21:33:35.882017 INFO::Total function execution time is 0.0485086441040039 s and adjustment time is 0.0357840061187744 s ( 73.77 )
2025-11-14 21:33:35.894816 INFO::Formatting Data.
2025-11-14 21:33:35.895658 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:35.89656 INFO::Removing potential empty rows and columns
2025-11-14 21:33:35.897596 INFO::Found 0 missing values.
2025-11-14 21:33:35.898833 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.
2025-11-14 21:33:35.903753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:35.904364 INFO::Done
2025-11-14 21:33:35.904901 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:35.907916 INFO::Starting hierarchical adjustment
2025-11-14 21:33:35.908668 INFO::Found 2 batches.
2025-11-14 21:33:35.909207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:35.909803 INFO::Using default BPPARAM
2025-11-14 21:33:35.910349 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.91132 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 21:33:35.928224 INFO::Done
2025-11-14 21:33:35.928943 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.932014 INFO::ASW Batch was 0.694216730491554 prior to batch effect correction and is now 0.056648391329926 .
2025-11-14 21:33:35.932637 INFO::ASW Label was 0.393636057219574 prior to batch effect correction and is now 0.889206958107982 .
2025-11-14 21:33:35.933396 INFO::Total function execution time is 0.0387203693389893 s and adjustment time is 0.0196528434753418 s ( 50.76 )
2025-11-14 21:33:35.934176 INFO::Formatting Data.
2025-11-14 21:33:35.934777 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:35.9357 INFO::Removing potential empty rows and columns
2025-11-14 21:33:35.936684 INFO::Found 0 missing values.
2025-11-14 21:33:35.937607 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.
2025-11-14 21:33:35.942134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:35.942727 INFO::Done
2025-11-14 21:33:35.943249 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:35.946302 INFO::Starting hierarchical adjustment
2025-11-14 21:33:35.947056 INFO::Found 2 batches.
2025-11-14 21:33:35.947594 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:35.948215 INFO::Using default BPPARAM
2025-11-14 21:33:35.948731 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:35.9497 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 21:33:35.967213 INFO::Done
2025-11-14 21:33:35.967983 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:35.971224 INFO::ASW Batch was 0.694216730491554 prior to batch effect correction and is now 0.056648391329926 .
2025-11-14 21:33:35.971876 INFO::ASW Label was 0.393636057219574 prior to batch effect correction and is now 0.889206958107982 .
2025-11-14 21:33:35.972786 INFO::Total function execution time is 0.0386121273040771 s and adjustment time is 0.0202310085296631 s ( 52.4 )
2025-11-14 21:33:36.188258 INFO::Formatting Data.
2025-11-14 21:33:36.189076 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:36.18999 INFO::Removing potential empty rows and columns
2025-11-14 21:33:36.19121 INFO::Found 0 missing values.
2025-11-14 21:33:36.194326 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:36.194879 INFO::Done
2025-11-14 21:33:36.195401 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:36.197465 INFO::Starting hierarchical adjustment
2025-11-14 21:33:36.198187 INFO::Found 3 batches.
2025-11-14 21:33:36.198706 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:36.199316 INFO::Using default BPPARAM
2025-11-14 21:33:36.199834 INFO::Processing subtree level 1
2025-11-14 21:33:36.295418 INFO::Adjusting the last 1 batches sequentially
2025-11-14 21:33:36.297462 INFO::Done
2025-11-14 21:33:36.298177 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:36.300959 INFO::ASW Batch was -0.148905330007666 prior to batch effect correction and is now -0.148905330007666 .
2025-11-14 21:33:36.302025 INFO::Total function execution time is 0.113870143890381 s and adjustment time is 0.0993866920471191 s ( 87.28 )
2025-11-14 21:33:36.30322 INFO::Formatting Data.
2025-11-14 21:33:36.303899 INFO::Typecasting input to dataframe.
2025-11-14 21:33:36.304724 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:36.305757 INFO::Removing potential empty rows and columns
2025-11-14 21:33:36.306963 INFO::Found 0 missing values.
2025-11-14 21:33:36.310275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:36.310848 INFO::Done
2025-11-14 21:33:36.311404 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:36.313634 INFO::Starting hierarchical adjustment
2025-11-14 21:33:36.314395 INFO::Found 3 batches.
2025-11-14 21:33:36.314991 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:36.315662 INFO::Using default BPPARAM
2025-11-14 21:33:36.316206 INFO::Processing subtree level 1
2025-11-14 21:33:36.418154 INFO::Adjusting the last 1 batches sequentially
2025-11-14 21:33:36.420212 INFO::Done
2025-11-14 21:33:36.420878 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:36.423779 INFO::ASW Batch was -0.148905330007666 prior to batch effect correction and is now -0.148905330007666 .
2025-11-14 21:33:36.424829 INFO::Total function execution time is 0.121588945388794 s and adjustment time is 0.10595965385437 s ( 87.15 )
2025-11-14 21:33:36.43984 INFO::Formatting Data.
2025-11-14 21:33:36.440841 INFO::Typecasting input to dataframe.
2025-11-14 21:33:36.441788 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:36.442791 INFO::Removing potential empty rows and columns
2025-11-14 21:33:36.443943 INFO::Found 0 missing values.
2025-11-14 21:33:36.447193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:36.447753 INFO::Done
2025-11-14 21:33:36.448304 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:36.450695 INFO::Starting hierarchical adjustment
2025-11-14 21:33:36.451487 INFO::Found 3 batches.
2025-11-14 21:33:36.452031 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:36.452695 INFO::Using default BPPARAM
2025-11-14 21:33:36.453266 INFO::Processing subtree level 1
2025-11-14 21:33:36.561595 INFO::Adjusting the last 1 batches sequentially
2025-11-14 21:33:36.563804 INFO::Done
2025-11-14 21:33:36.564575 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:36.567571 INFO::ASW Batch was -0.0389347180644112 prior to batch effect correction and is now -0.0389347180644112 .
2025-11-14 21:33:36.568602 INFO::Total function execution time is 0.128896236419678 s and adjustment time is 0.112448692321777 s ( 87.24 )
2025-11-14 21:33:36.725728 INFO::Formatting Data.
2025-11-14 21:33:36.726677 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:36.72795 INFO::Removing potential empty rows and columns
2025-11-14 21:33:36.73082 INFO::Found 1000 missing values.
2025-11-14 21:33:36.749969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:36.750812 INFO::Done
2025-11-14 21:33:36.751375 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:36.756977 INFO::Starting hierarchical adjustment
2025-11-14 21:33:36.757814 INFO::Found 10 batches.
2025-11-14 21:33:36.758379 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:36.759002 INFO::Using default BPPARAM
2025-11-14 21:33:36.759545 INFO::Processing subtree level 1
2025-11-14 21:33:36.905709 INFO::Processing subtree level 2
2025-11-14 21:33:37.048415 INFO::Adjusting the last 1 batches sequentially
2025-11-14 21:33:37.050494 INFO::Done
2025-11-14 21:33:37.05124 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:37.05726 INFO::ASW Batch was 0.472229969988705 prior to batch effect correction and is now 0.472229969988705 .
2025-11-14 21:33:37.057977 INFO::ASW Label was 0.334355828317678 prior to batch effect correction and is now 0.334355828317678 .
2025-11-14 21:33:37.058948 INFO::Total function execution time is 0.333351135253906 s and adjustment time is 0.292819023132324 s ( 87.84 )
2025-11-14 21:33:37.059818 INFO::Formatting Data.
2025-11-14 21:33:37.060479 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:37.061788 INFO::Removing potential empty rows and columns
2025-11-14 21:33:37.064807 INFO::Found 1000 missing values.
2025-11-14 21:33:37.084613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:37.085405 INFO::Done
2025-11-14 21:33:37.085978 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:37.091784 INFO::Starting hierarchical adjustment
2025-11-14 21:33:37.092641 INFO::Found 10 batches.
2025-11-14 21:33:38.11062 INFO::Set up parallel execution backend with 2 workers
2025-11-14 21:33:38.113614 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-14 21:33:39.610734 INFO::Adjusting the last 2 batches sequentially
2025-11-14 21:33:39.612714 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-14 21:33:39.629897 INFO::Done
2025-11-14 21:33:39.630652 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:39.635319 INFO::ASW Batch was 0.472229969988705 prior to batch effect correction and is now 0.472229969988705 .
2025-11-14 21:33:39.635898 INFO::ASW Label was 0.334355828317678 prior to batch effect correction and is now 0.334355828317678 .
2025-11-14 21:33:39.636673 INFO::Total function execution time is 2.57688999176025 s and adjustment time is 2.53738522529602 s ( 98.47 )
2025-11-14 21:33:39.795642 INFO::Formatting Data.
2025-11-14 21:33:39.796606 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:39.797586 INFO::Removing potential empty rows and columns
2025-11-14 21:33:39.798657 INFO::Found 0 missing values.
2025-11-14 21:33:39.802186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:39.802687 INFO::Done
2025-11-14 21:33:39.803184 INFO::Acquiring quality metrics before batch effect correction.
2025-11-14 21:33:39.805793 INFO::Starting hierarchical adjustment
2025-11-14 21:33:39.80648 INFO::Found 3 batches.
2025-11-14 21:33:39.806984 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-14 21:33:39.807587 INFO::Using default BPPARAM
2025-11-14 21:33:39.80809 INFO::Processing subtree level 1
2025-11-14 21:33:39.916637 INFO::Adjusting the last 1 batches sequentially
2025-11-14 21:33:39.918575 INFO::Done
2025-11-14 21:33:39.919326 INFO::Acquiring quality metrics after batch effect correction.
2025-11-14 21:33:39.922718 INFO::ASW Batch was 0.185754391174767 prior to batch effect correction and is now -0.122316648075565 .
2025-11-14 21:33:39.923414 INFO::ASW Label was -0.184786668702531 prior to batch effect correction and is now -0.0915055282626295 .
2025-11-14 21:33:39.924388 INFO::Total function execution time is 0.128831624984741 s and adjustment time is 0.112194061279297 s ( 87.09 )
2025-11-14 21:33:40.05111 INFO::Formatting Data.
2025-11-14 21:33:40.052028 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.052964 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.054012 INFO::Found 2 missing values.
2025-11-14 21:33:40.056796 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.057353 INFO::Done
2025-11-14 21:33:40.085557 INFO::Found NA in Reference column
2025-11-14 21:33:40.095237 INFO::Require at least two references per batch.
2025-11-14 21:33:40.115686 INFO::Formatting Data.
2025-11-14 21:33:40.11644 INFO::Recognized SummarizedExperiment
2025-11-14 21:33:40.116969 INFO::Typecasting input to dataframe.
2025-11-14 21:33:40.127754 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.129256 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.132941 INFO::Found 0 missing values.
2025-11-14 21:33:40.140229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.140948 INFO::Done
2025-11-14 21:33:40.157864 INFO::Formatting Data.
2025-11-14 21:33:40.158634 INFO::Recognized SummarizedExperiment
2025-11-14 21:33:40.159149 INFO::Typecasting input to dataframe.
2025-11-14 21:33:40.176065 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.177355 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.180702 INFO::Found 0 missing values.
2025-11-14 21:33:40.200725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.201503 INFO::Done
2025-11-14 21:33:40.21854 INFO::Formatting Data.
2025-11-14 21:33:40.219331 INFO::Recognized SummarizedExperiment
2025-11-14 21:33:40.219869 INFO::Typecasting input to dataframe.
2025-11-14 21:33:40.237617 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.238764 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.239968 INFO::Found 0 missing values.
2025-11-14 21:33:40.240908 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.
2025-11-14 21:33:40.245497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.246048 INFO::Done
2025-11-14 21:33:40.256938 INFO::Formatting Data.
2025-11-14 21:33:40.257745 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.258623 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.259636 INFO::Found 0 missing values.
2025-11-14 21:33:40.262605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.26317 INFO::Done
2025-11-14 21:33:40.275257 INFO::Formatting Data.
2025-11-14 21:33:40.276213 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.277232 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.27824 INFO::Found 0 missing values.
2025-11-14 21:33:40.281169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.281698 INFO::Done
2025-11-14 21:33:40.313104 INFO::Formatting Data.
2025-11-14 21:33:40.31413 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.315252 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.316519 INFO::Found 1 missing values.
2025-11-14 21:33:40.319431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.320085 INFO::Done
2025-11-14 21:33:40.339914 INFO::Formatting Data.
2025-11-14 21:33:40.340771 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.341689 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.342643 INFO::Found 2 missing values.
2025-11-14 21:33:40.343529 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.
2025-11-14 21:33:40.345792 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.346356 INFO::Done
2025-11-14 21:33:40.35687 INFO::Formatting Data.
2025-11-14 21:33:40.357653 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.358546 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.35948 INFO::Found 2 missing values.
2025-11-14 21:33:40.361111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.361655 INFO::Done
2025-11-14 21:33:40.372005 INFO::Formatting Data.
2025-11-14 21:33:40.372871 INFO::Typecasting input to dataframe.
2025-11-14 21:33:40.373697 INFO::Replacing NaNs with NAs.
2025-11-14 21:33:40.374571 INFO::Removing potential empty rows and columns
2025-11-14 21:33:40.375551 INFO::Found 0 missing values.
2025-11-14 21:33:40.378356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-14 21:33:40.378896 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.759 4.380 23.685
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.630 | 2.199 | 18.028 | |
| compute_asw | 0.026 | 0.003 | 0.027 | |
| count_existing | 0.014 | 0.003 | 0.018 | |
| generate_data_covariables | 0.013 | 0.004 | 0.016 | |
| generate_dataset | 0.011 | 0.003 | 0.015 | |