Yannis Schumann
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 Dec 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 2025-12-11 12:07 -0500 (Thu, 11 Dec 2025).
| 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-12-09 08:06:44 -0000 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 08:08:10 -0000 (Tue, 09 Dec 2025) |
| EllapsedTime: 86.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* 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 28.154 1.277 20.323
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-12-09 08:07:54.970757 INFO::Formatting Data.
2025-12-09 08:07:54.973133 INFO::Replacing NaNs with NAs.
2025-12-09 08:07:54.997645 INFO::Removing potential empty rows and columns
2025-12-09 08:07:55.645256 INFO::Found 0 missing values.
2025-12-09 08:07:55.650187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:07:55.651129 INFO::Done
2025-12-09 08:07:55.651885 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:07:55.667422 INFO::Starting hierarchical adjustment
2025-12-09 08:07:55.668619 INFO::Found 3 batches.
2025-12-09 08:07:55.669452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:07:55.671037 INFO::Using default BPPARAM
2025-12-09 08:07:55.671856 INFO::Processing subtree level 1
2025-12-09 08:07:55.798358 INFO::Adjusting the last 1 batches sequentially
2025-12-09 08:07:55.800954 INFO::Done
2025-12-09 08:07:55.801891 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:07:55.805772 INFO::ASW Batch was -0.0380982704670044 prior to batch effect correction and is now -0.0380982704670044 .
2025-12-09 08:07:55.807472 INFO::Total function execution time is 0.837951898574829 s and adjustment time is 0.132582187652588 s ( 15.82 )
2025-12-09 08:07:55.827667 INFO::Formatting Data.
2025-12-09 08:07:55.828665 INFO::Replacing NaNs with NAs.
2025-12-09 08:07:55.829956 INFO::Removing potential empty rows and columns
2025-12-09 08:07:55.831587 INFO::Found 0 missing values.
2025-12-09 08:07:55.832961 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.
2025-12-09 08:07:55.849282 INFO::Formatting Data.
2025-12-09 08:07:55.850349 INFO::Replacing NaNs with NAs.
2025-12-09 08:07:55.851726 INFO::Removing potential empty rows and columns
2025-12-09 08:07:55.853303 INFO::Found 0 missing values.
2025-12-09 08:07:55.854729 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.
2025-12-09 08:07:55.877951 INFO::Formatting Data.
2025-12-09 08:07:55.879026 INFO::Replacing NaNs with NAs.
2025-12-09 08:07:55.880245 INFO::Removing potential empty rows and columns
2025-12-09 08:07:55.881785 INFO::Found 0 missing values.
2025-12-09 08:07:55.883073 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.
2025-12-09 08:07:55.889537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:07:55.890447 INFO::Done
2025-12-09 08:07:55.891242 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:07:55.894065 INFO::Starting hierarchical adjustment
2025-12-09 08:07:55.895174 INFO::Found 2 batches.
2025-12-09 08:07:55.895931 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:07:55.896866 INFO::Using default BPPARAM
2025-12-09 08:07:55.897634 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:07:55.899046 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 08:07:55.930314 INFO::Done
2025-12-09 08:07:55.931264 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:07:55.934149 INFO::ASW Batch was 0.022331433360676 prior to batch effect correction and is now -0.0974198435396142 .
2025-12-09 08:07:55.935318 INFO::Total function execution time is 0.0574309825897217 s and adjustment time is 0.0353341102600098 s ( 61.52 )
2025-12-09 08:07:55.939116 INFO::Formatting Data.
2025-12-09 08:07:55.940098 INFO::Replacing NaNs with NAs.
2025-12-09 08:07:55.952592 INFO::Formatting Data.
2025-12-09 08:07:55.953629 INFO::Replacing NaNs with NAs.
2025-12-09 08:07:55.955141 INFO::Removing potential empty rows and columns
2025-12-09 08:07:55.956584 INFO::Found 0 missing values.
2025-12-09 08:07:55.960827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:07:55.961712 INFO::Done
2025-12-09 08:07:55.962487 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:07:55.965387 INFO::Starting hierarchical adjustment
2025-12-09 08:07:55.966465 INFO::Found 2 batches.
2025-12-09 08:07:55.967248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:07:55.96824 INFO::Using default BPPARAM
2025-12-09 08:07:55.969162 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:07:55.970795 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 08:07:56.030571 INFO::Done
2025-12-09 08:07:56.031489 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:07:56.034307 INFO::ASW Batch was 0.079469824662038 prior to batch effect correction and is now -0.113781141104397 .
2025-12-09 08:07:56.03547 INFO::Total function execution time is 0.0829367637634277 s and adjustment time is 0.0642929077148438 s ( 77.52 )
2025-12-09 08:07:56.037031 INFO::Formatting Data.
2025-12-09 08:07:56.037883 INFO::Replacing NaNs with NAs.
2025-12-09 08:07:56.039186 INFO::Removing potential empty rows and columns
2025-12-09 08:07:56.040645 INFO::Found 0 missing values.
2025-12-09 08:07:56.044948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:07:56.045819 INFO::Done
2025-12-09 08:07:56.046578 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:07:56.049482 INFO::Starting hierarchical adjustment
2025-12-09 08:07:56.050554 INFO::Found 2 batches.
2025-12-09 08:07:56.051369 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:07:56.052229 INFO::Using default BPPARAM
2025-12-09 08:07:56.053 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:07:56.054294 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 08:07:56.076138 INFO::Done
2025-12-09 08:07:56.077081 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:07:56.079881 INFO::ASW Batch was 0.079469824662038 prior to batch effect correction and is now -0.113781141104397 .
2025-12-09 08:07:56.080967 INFO::Total function execution time is 0.0439059734344482 s and adjustment time is 0.0257577896118164 s ( 58.67 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-09 08:07:59.927456 INFO::Formatting Data.
2025-12-09 08:07:59.928344 INFO::Recognized SummarizedExperiment
2025-12-09 08:07:59.929017 INFO::Typecasting input to dataframe.
2025-12-09 08:07:59.970207 INFO::Replacing NaNs with NAs.
2025-12-09 08:07:59.97185 INFO::Removing potential empty rows and columns
2025-12-09 08:07:59.977173 INFO::Found 0 missing values.
2025-12-09 08:07:59.987282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:07:59.988183 INFO::Done
2025-12-09 08:07:59.988968 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:07:59.993811 INFO::Starting hierarchical adjustment
2025-12-09 08:07:59.994952 INFO::Found 2 batches.
2025-12-09 08:07:59.995703 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:07:59.997112 INFO::Using default BPPARAM
2025-12-09 08:07:59.997896 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:07:59.999298 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 08:08:00.076539 INFO::Done
2025-12-09 08:08:00.077452 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:00.082237 INFO::ASW Batch was -0.00387649932697734 prior to batch effect correction and is now -0.0939485620315407 .
2025-12-09 08:08:00.083491 INFO::Total function execution time is 0.156426906585693 s and adjustment time is 0.0818250179290771 s ( 52.31 )
Warning: stack imbalance in '{', 73 then 75
2025-12-09 08:08:00.108526 INFO::Formatting Data.
2025-12-09 08:08:00.109486 INFO::Recognized SummarizedExperiment
2025-12-09 08:08:00.110211 INFO::Typecasting input to dataframe.
2025-12-09 08:08:00.12316 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:00.124688 INFO::Removing potential empty rows and columns
2025-12-09 08:08:00.129745 INFO::Found 0 missing values.
2025-12-09 08:08:00.139949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:00.140885 INFO::Done
2025-12-09 08:08:00.141639 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:00.146492 INFO::Starting hierarchical adjustment
2025-12-09 08:08:00.147608 INFO::Found 2 batches.
2025-12-09 08:08:00.148347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:00.14936 INFO::Using default BPPARAM
2025-12-09 08:08:00.150083 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:00.151465 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 08:08:00.186106 INFO::Done
2025-12-09 08:08:00.187044 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:00.19183 INFO::ASW Batch was 0.00688614348194875 prior to batch effect correction and is now 0.00688614348194875 .
2025-12-09 08:08:00.193068 INFO::Total function execution time is 0.0845098495483398 s and adjustment time is 0.0386848449707031 s ( 45.78 )
2025-12-09 08:08:00.217763 INFO::Formatting Data.
2025-12-09 08:08:00.218801 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:00.219958 INFO::Removing potential empty rows and columns
2025-12-09 08:08:00.221544 INFO::Found 0 missing values.
2025-12-09 08:08:00.225782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:00.226719 INFO::Done
2025-12-09 08:08:00.227463 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:00.230291 INFO::Starting hierarchical adjustment
2025-12-09 08:08:00.231398 INFO::Found 3 batches.
2025-12-09 08:08:00.232144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:00.232998 INFO::Using default BPPARAM
2025-12-09 08:08:00.233719 INFO::Processing subtree level 1
2025-12-09 08:08:00.413031 INFO::Adjusting the last 1 batches sequentially
2025-12-09 08:08:00.415817 INFO::Done
2025-12-09 08:08:00.416646 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:00.420268 INFO::ASW Batch was -0.11621199965618 prior to batch effect correction and is now -0.168565661784004 .
2025-12-09 08:08:00.421678 INFO::Total function execution time is 0.203933000564575 s and adjustment time is 0.184641361236572 s ( 90.54 )
2025-12-09 08:08:00.4421 INFO::Skipping initial DF formatting
2025-12-09 08:08:00.44303 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:00.448504 INFO::Starting hierarchical adjustment
2025-12-09 08:08:00.449664 INFO::Found 5 batches.
2025-12-09 08:08:00.450436 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:00.451368 INFO::Using default BPPARAM
2025-12-09 08:08:00.452143 INFO::Processing subtree level 1
2025-12-09 08:08:00.715618 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:00.71781 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 08:08:00.74578 INFO::Done
2025-12-09 08:08:00.746723 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:00.752473 INFO::ASW Batch was 0.499546558611611 prior to batch effect correction and is now 0.499546558611611 .
2025-12-09 08:08:00.753397 INFO::ASW Label was 0.349841850619042 prior to batch effect correction and is now 0.349841850619042 .
2025-12-09 08:08:00.754577 INFO::Total function execution time is 0.312517404556274 s and adjustment time is 0.296334743499756 s ( 94.82 )
2025-12-09 08:08:00.849386 INFO::Formatting Data.
2025-12-09 08:08:00.850471 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:00.851902 INFO::Removing potential empty rows and columns
2025-12-09 08:08:00.853578 INFO::Found 0 missing values.
2025-12-09 08:08:00.860139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:00.861121 INFO::Done
2025-12-09 08:08:00.861989 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:00.8666 INFO::Starting hierarchical adjustment
2025-12-09 08:08:00.867864 INFO::Found 5 batches.
2025-12-09 08:08:00.868818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:00.869841 INFO::Using default BPPARAM
2025-12-09 08:08:00.870767 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.
2025-12-09 08:08:01.031391 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:01.033853 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 08:08:01.061544 INFO::Done
2025-12-09 08:08:01.062599 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:01.06794 INFO::ASW Batch was 0.333085045905416 prior to batch effect correction and is now -0.0347966226956047 .
2025-12-09 08:08:01.069005 INFO::ASW Label was 0.489751083290743 prior to batch effect correction and is now 0.803677222128485 .
2025-12-09 08:08:01.0703 INFO::Total function execution time is 0.22093939781189 s and adjustment time is 0.193907737731934 s ( 87.77 )
2025-12-09 08:08:01.071686 INFO::Formatting Data.
2025-12-09 08:08:01.072668 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:01.07416 INFO::Removing potential empty rows and columns
2025-12-09 08:08:01.075939 INFO::Found 0 missing values.
2025-12-09 08:08:01.083495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:01.084492 INFO::Done
2025-12-09 08:08:01.085419 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:01.090193 INFO::Starting hierarchical adjustment
2025-12-09 08:08:01.091529 INFO::Found 5 batches.
2025-12-09 08:08:01.0924 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:01.09346 INFO::Using default BPPARAM
2025-12-09 08:08:01.094337 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.
2025-12-09 08:08:01.247814 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:01.250279 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 08:08:01.276063 INFO::Done
2025-12-09 08:08:01.27711 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:01.282127 INFO::ASW Batch was 0.333085045905416 prior to batch effect correction and is now -0.0347966226956047 .
2025-12-09 08:08:01.283138 INFO::ASW Label was 0.489751083290743 prior to batch effect correction and is now 0.803677222128485 .
2025-12-09 08:08:01.28443 INFO::Total function execution time is 0.21270227432251 s and adjustment time is 0.184780120849609 s ( 86.87 )
2025-12-09 08:08:01.306047 INFO::Formatting Data.
2025-12-09 08:08:01.307209 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:01.308557 INFO::Removing potential empty rows and columns
2025-12-09 08:08:01.310124 INFO::Found 0 missing values.
2025-12-09 08:08:01.316791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:01.317766 INFO::Done
2025-12-09 08:08:01.318682 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:01.323351 INFO::Starting hierarchical adjustment
2025-12-09 08:08:01.324558 INFO::Found 5 batches.
2025-12-09 08:08:01.325398 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:01.326338 INFO::Using default BPPARAM
2025-12-09 08:08:01.327199 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.
2025-12-09 08:08:01.484493 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:01.486955 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 08:08:01.511737 INFO::Done
2025-12-09 08:08:01.512736 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:01.517674 INFO::ASW Batch was 0.368651987778513 prior to batch effect correction and is now -0.03074305759833 .
2025-12-09 08:08:01.518703 INFO::ASW Label was 0.339255087257947 prior to batch effect correction and is now 0.773074012244277 .
2025-12-09 08:08:01.519941 INFO::Total function execution time is 0.213966846466064 s and adjustment time is 0.187344551086426 s ( 87.56 )
2025-12-09 08:08:01.521196 INFO::Formatting Data.
2025-12-09 08:08:01.522131 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:01.523533 INFO::Removing potential empty rows and columns
2025-12-09 08:08:01.525155 INFO::Found 0 missing values.
2025-12-09 08:08:01.531782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:01.532722 INFO::Done
2025-12-09 08:08:01.53355 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:01.538047 INFO::Starting hierarchical adjustment
2025-12-09 08:08:01.539256 INFO::Found 5 batches.
2025-12-09 08:08:01.540084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:01.541029 INFO::Using default BPPARAM
2025-12-09 08:08:01.541857 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.
2025-12-09 08:08:01.703887 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:01.706291 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 08:08:01.731447 INFO::Done
2025-12-09 08:08:01.732486 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:01.737505 INFO::ASW Batch was 0.368651987778513 prior to batch effect correction and is now -0.03074305759833 .
2025-12-09 08:08:01.738544 INFO::ASW Label was 0.339255087257947 prior to batch effect correction and is now 0.773074012244277 .
2025-12-09 08:08:01.739907 INFO::Total function execution time is 0.218670845031738 s and adjustment time is 0.192395925521851 s ( 87.98 )
2025-12-09 08:08:01.761687 INFO::Formatting Data.
2025-12-09 08:08:01.762839 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:01.764211 INFO::Removing potential empty rows and columns
2025-12-09 08:08:01.765819 INFO::Found 0 missing values.
2025-12-09 08:08:01.77069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:01.771678 INFO::Done
2025-12-09 08:08:01.772511 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:01.777104 INFO::Starting hierarchical adjustment
2025-12-09 08:08:01.778322 INFO::Found 2 batches.
2025-12-09 08:08:01.779198 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:01.780165 INFO::Using default BPPARAM
2025-12-09 08:08:01.781031 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:01.782437 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 08:08:01.804353 INFO::Done
2025-12-09 08:08:01.805332 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:01.80964 INFO::ASW Batch was 0.384751312742835 prior to batch effect correction and is now 0.0681318243298336 .
2025-12-09 08:08:01.810572 INFO::ASW Label was 0.698992182818062 prior to batch effect correction and is now 0.886890417614122 .
2025-12-09 08:08:01.811725 INFO::Total function execution time is 0.0501227378845215 s and adjustment time is 0.0262451171875 s ( 52.36 )
2025-12-09 08:08:01.812883 INFO::Formatting Data.
2025-12-09 08:08:01.81378 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:01.815118 INFO::Removing potential empty rows and columns
2025-12-09 08:08:01.816614 INFO::Found 0 missing values.
2025-12-09 08:08:01.820797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:01.821689 INFO::Done
2025-12-09 08:08:01.82247 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:01.826822 INFO::Starting hierarchical adjustment
2025-12-09 08:08:01.827975 INFO::Found 2 batches.
2025-12-09 08:08:01.828782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:01.829658 INFO::Using default BPPARAM
2025-12-09 08:08:01.830406 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:01.831805 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 08:08:01.853092 INFO::Done
2025-12-09 08:08:01.854012 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:01.858194 INFO::ASW Batch was 0.384751312742835 prior to batch effect correction and is now 0.0681318243298336 .
2025-12-09 08:08:01.859179 INFO::ASW Label was 0.698992182818062 prior to batch effect correction and is now 0.886890417614122 .
2025-12-09 08:08:01.860264 INFO::Total function execution time is 0.0474169254302979 s and adjustment time is 0.0253129005432129 s ( 53.38 )
2025-12-09 08:08:01.876993 INFO::Formatting Data.
2025-12-09 08:08:01.87805 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:01.879367 INFO::Removing potential empty rows and columns
2025-12-09 08:08:01.880694 INFO::Found 0 missing values.
2025-12-09 08:08:01.884021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:01.884961 INFO::Done
2025-12-09 08:08:01.885765 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:01.888554 INFO::Starting hierarchical adjustment
2025-12-09 08:08:01.88969 INFO::Found 2 batches.
2025-12-09 08:08:01.890461 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:01.891374 INFO::Using default BPPARAM
2025-12-09 08:08:01.892159 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:01.893538 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 08:08:01.93986 INFO::Done
2025-12-09 08:08:01.940768 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:01.943432 INFO::ASW Batch was -0.0232990742136437 prior to batch effect correction and is now -0.11113625710109 .
2025-12-09 08:08:01.944528 INFO::Total function execution time is 0.0676698684692383 s and adjustment time is 0.0503764152526855 s ( 74.44 )
2025-12-09 08:08:01.962151 INFO::Formatting Data.
2025-12-09 08:08:01.963218 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:01.964457 INFO::Removing potential empty rows and columns
2025-12-09 08:08:01.96594 INFO::Found 0 missing values.
2025-12-09 08:08:01.967612 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.
2025-12-09 08:08:01.974577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:01.97553 INFO::Done
2025-12-09 08:08:01.976292 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:01.980519 INFO::Starting hierarchical adjustment
2025-12-09 08:08:01.981673 INFO::Found 2 batches.
2025-12-09 08:08:01.982459 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:01.98336 INFO::Using default BPPARAM
2025-12-09 08:08:01.984119 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:01.985502 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 08:08:02.009421 INFO::Done
2025-12-09 08:08:02.010336 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:02.014489 INFO::ASW Batch was 0.522855805375645 prior to batch effect correction and is now 0.0138612851202343 .
2025-12-09 08:08:02.015424 INFO::ASW Label was 0.56695268209997 prior to batch effect correction and is now 0.91405583538209 .
2025-12-09 08:08:02.016504 INFO::Total function execution time is 0.0544281005859375 s and adjustment time is 0.0279467105865479 s ( 51.35 )
2025-12-09 08:08:02.017634 INFO::Formatting Data.
2025-12-09 08:08:02.018496 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:02.019841 INFO::Removing potential empty rows and columns
2025-12-09 08:08:02.021292 INFO::Found 0 missing values.
2025-12-09 08:08:02.022608 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.
2025-12-09 08:08:02.029376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:02.030257 INFO::Done
2025-12-09 08:08:02.031031 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:02.035236 INFO::Starting hierarchical adjustment
2025-12-09 08:08:02.036458 INFO::Found 2 batches.
2025-12-09 08:08:02.037373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:02.038325 INFO::Using default BPPARAM
2025-12-09 08:08:02.039177 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:02.040704 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 08:08:02.065881 INFO::Done
2025-12-09 08:08:02.066932 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:02.071479 INFO::ASW Batch was 0.522855805375645 prior to batch effect correction and is now 0.0138612851202343 .
2025-12-09 08:08:02.072448 INFO::ASW Label was 0.56695268209997 prior to batch effect correction and is now 0.91405583538209 .
2025-12-09 08:08:02.07367 INFO::Total function execution time is 0.056018590927124 s and adjustment time is 0.0296502113342285 s ( 52.93 )
2025-12-09 08:08:02.384096 INFO::Formatting Data.
2025-12-09 08:08:02.386506 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:02.387973 INFO::Removing potential empty rows and columns
2025-12-09 08:08:02.38963 INFO::Found 0 missing values.
2025-12-09 08:08:02.394245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:02.395183 INFO::Done
2025-12-09 08:08:02.395914 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:02.399225 INFO::Starting hierarchical adjustment
2025-12-09 08:08:02.400347 INFO::Found 3 batches.
2025-12-09 08:08:02.401143 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:02.402043 INFO::Using default BPPARAM
2025-12-09 08:08:02.402841 INFO::Processing subtree level 1
2025-12-09 08:08:02.515108 INFO::Adjusting the last 1 batches sequentially
2025-12-09 08:08:02.517732 INFO::Done
2025-12-09 08:08:02.518792 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:02.522502 INFO::ASW Batch was -0.0807765834929238 prior to batch effect correction and is now -0.0807765834929238 .
2025-12-09 08:08:02.523988 INFO::Total function execution time is 0.14021110534668 s and adjustment time is 0.117577314376831 s ( 83.86 )
2025-12-09 08:08:02.525518 INFO::Formatting Data.
2025-12-09 08:08:02.526431 INFO::Typecasting input to dataframe.
2025-12-09 08:08:02.527603 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:02.528986 INFO::Removing potential empty rows and columns
2025-12-09 08:08:02.53061 INFO::Found 0 missing values.
2025-12-09 08:08:02.535335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:02.53631 INFO::Done
2025-12-09 08:08:02.537149 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:02.540121 INFO::Starting hierarchical adjustment
2025-12-09 08:08:02.541263 INFO::Found 3 batches.
2025-12-09 08:08:02.542037 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:02.542974 INFO::Using default BPPARAM
2025-12-09 08:08:02.543747 INFO::Processing subtree level 1
2025-12-09 08:08:02.653852 INFO::Adjusting the last 1 batches sequentially
2025-12-09 08:08:02.656363 INFO::Done
2025-12-09 08:08:02.657377 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:02.660928 INFO::ASW Batch was -0.0807765834929238 prior to batch effect correction and is now -0.0807765834929238 .
2025-12-09 08:08:02.662355 INFO::Total function execution time is 0.136788129806519 s and adjustment time is 0.115297079086304 s ( 84.29 )
2025-12-09 08:08:02.680234 INFO::Formatting Data.
2025-12-09 08:08:02.681275 INFO::Typecasting input to dataframe.
2025-12-09 08:08:02.682424 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:02.683709 INFO::Removing potential empty rows and columns
2025-12-09 08:08:02.685263 INFO::Found 0 missing values.
2025-12-09 08:08:02.689622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:02.690477 INFO::Done
2025-12-09 08:08:02.691303 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:02.694074 INFO::Starting hierarchical adjustment
2025-12-09 08:08:02.69513 INFO::Found 3 batches.
2025-12-09 08:08:02.695919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:02.696824 INFO::Using default BPPARAM
2025-12-09 08:08:02.697617 INFO::Processing subtree level 1
2025-12-09 08:08:02.803155 INFO::Adjusting the last 1 batches sequentially
2025-12-09 08:08:02.806042 INFO::Done
2025-12-09 08:08:02.806973 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:02.810856 INFO::ASW Batch was -0.052621459317654 prior to batch effect correction and is now -0.052621459317654 .
2025-12-09 08:08:02.812195 INFO::Total function execution time is 0.131990194320679 s and adjustment time is 0.111101627349854 s ( 84.17 )
2025-12-09 08:08:02.994711 INFO::Formatting Data.
2025-12-09 08:08:02.995789 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:02.997384 INFO::Removing potential empty rows and columns
2025-12-09 08:08:03.001624 INFO::Found 1000 missing values.
2025-12-09 08:08:03.030278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:03.03122 INFO::Done
2025-12-09 08:08:03.031993 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:03.039591 INFO::Starting hierarchical adjustment
2025-12-09 08:08:03.04081 INFO::Found 10 batches.
2025-12-09 08:08:03.041645 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:03.042536 INFO::Using default BPPARAM
2025-12-09 08:08:03.043612 INFO::Processing subtree level 1
2025-12-09 08:08:03.201073 INFO::Processing subtree level 2
2025-12-09 08:08:03.385691 INFO::Adjusting the last 1 batches sequentially
2025-12-09 08:08:03.388479 INFO::Done
2025-12-09 08:08:03.389565 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:03.397614 INFO::ASW Batch was 0.481134283171965 prior to batch effect correction and is now 0.481134283171965 .
2025-12-09 08:08:03.398585 INFO::ASW Label was 0.325122312880012 prior to batch effect correction and is now 0.325122312880012 .
2025-12-09 08:08:03.399918 INFO::Total function execution time is 0.405286073684692 s and adjustment time is 0.347913503646851 s ( 85.84 )
2025-12-09 08:08:03.401309 INFO::Formatting Data.
2025-12-09 08:08:03.402218 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:03.403954 INFO::Removing potential empty rows and columns
2025-12-09 08:08:03.408078 INFO::Found 1000 missing values.
2025-12-09 08:08:03.436047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:03.437005 INFO::Done
2025-12-09 08:08:03.437807 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:03.445399 INFO::Starting hierarchical adjustment
2025-12-09 08:08:03.446579 INFO::Found 10 batches.
2025-12-09 08:08:04.547822 INFO::Set up parallel execution backend with 2 workers
2025-12-09 08:08:04.550694 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-09 08:08:05.780919 INFO::Adjusting the last 2 batches sequentially
2025-12-09 08:08:05.783376 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 08:08:05.80905 INFO::Done
2025-12-09 08:08:05.809965 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:05.816886 INFO::ASW Batch was 0.481134283171965 prior to batch effect correction and is now 0.481134283171965 .
2025-12-09 08:08:05.817809 INFO::ASW Label was 0.325122312880012 prior to batch effect correction and is now 0.325122312880012 .
2025-12-09 08:08:05.819023 INFO::Total function execution time is 2.41769361495972 s and adjustment time is 2.36269068717957 s ( 97.72 )
2025-12-09 08:08:06.013653 INFO::Formatting Data.
2025-12-09 08:08:06.014735 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.015981 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.017501 INFO::Found 0 missing values.
2025-12-09 08:08:06.023043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.023913 INFO::Done
2025-12-09 08:08:06.02463 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 08:08:06.028399 INFO::Starting hierarchical adjustment
2025-12-09 08:08:06.029439 INFO::Found 3 batches.
2025-12-09 08:08:06.030185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 08:08:06.031095 INFO::Using default BPPARAM
2025-12-09 08:08:06.031857 INFO::Processing subtree level 1
2025-12-09 08:08:06.171741 INFO::Adjusting the last 1 batches sequentially
2025-12-09 08:08:06.174158 INFO::Done
2025-12-09 08:08:06.17502 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 08:08:06.179518 INFO::ASW Batch was 0.257380514041165 prior to batch effect correction and is now -0.125979964858225 .
2025-12-09 08:08:06.180493 INFO::ASW Label was -0.21618461491351 prior to batch effect correction and is now 0.0577843233038195 .
2025-12-09 08:08:06.181759 INFO::Total function execution time is 0.168154954910278 s and adjustment time is 0.144920110702515 s ( 86.18 )
2025-12-09 08:08:06.354412 INFO::Formatting Data.
2025-12-09 08:08:06.355579 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.365185 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.367179 INFO::Found 2 missing values.
2025-12-09 08:08:06.372121 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.373141 INFO::Done
2025-12-09 08:08:06.41933 INFO::Found NA in Reference column
2025-12-09 08:08:06.43612 INFO::Require at least two references per batch.
2025-12-09 08:08:06.470779 INFO::Formatting Data.
2025-12-09 08:08:06.471852 INFO::Recognized SummarizedExperiment
2025-12-09 08:08:06.472711 INFO::Typecasting input to dataframe.
2025-12-09 08:08:06.488585 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.490367 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.496096 INFO::Found 0 missing values.
2025-12-09 08:08:06.507236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.508184 INFO::Done
2025-12-09 08:08:06.532598 INFO::Formatting Data.
2025-12-09 08:08:06.533644 INFO::Recognized SummarizedExperiment
2025-12-09 08:08:06.534484 INFO::Typecasting input to dataframe.
2025-12-09 08:08:06.562904 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.56464 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.570448 INFO::Found 0 missing values.
2025-12-09 08:08:06.589291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.590285 INFO::Done
2025-12-09 08:08:06.615629 INFO::Formatting Data.
2025-12-09 08:08:06.616654 INFO::Recognized SummarizedExperiment
2025-12-09 08:08:06.617527 INFO::Typecasting input to dataframe.
2025-12-09 08:08:06.645786 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.647329 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.649062 INFO::Found 0 missing values.
2025-12-09 08:08:06.650529 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.
2025-12-09 08:08:06.658029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.65909 INFO::Done
2025-12-09 08:08:06.675579 INFO::Formatting Data.
2025-12-09 08:08:06.676769 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.67817 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.67983 INFO::Found 0 missing values.
2025-12-09 08:08:06.684649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.68571 INFO::Done
2025-12-09 08:08:06.704557 INFO::Formatting Data.
2025-12-09 08:08:06.705731 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.707188 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.70902 INFO::Found 0 missing values.
2025-12-09 08:08:06.714737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.715805 INFO::Done
2025-12-09 08:08:06.767905 INFO::Formatting Data.
2025-12-09 08:08:06.769331 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.77132 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.77349 INFO::Found 1 missing values.
2025-12-09 08:08:06.778444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.779616 INFO::Done
2025-12-09 08:08:06.811454 INFO::Formatting Data.
2025-12-09 08:08:06.812545 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.814074 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.815495 INFO::Found 2 missing values.
2025-12-09 08:08:06.816782 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.
2025-12-09 08:08:06.820151 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.821103 INFO::Done
2025-12-09 08:08:06.836058 INFO::Formatting Data.
2025-12-09 08:08:06.837115 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.83827 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.839594 INFO::Found 2 missing values.
2025-12-09 08:08:06.84191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.842784 INFO::Done
2025-12-09 08:08:06.857792 INFO::Formatting Data.
2025-12-09 08:08:06.858838 INFO::Typecasting input to dataframe.
2025-12-09 08:08:06.85992 INFO::Replacing NaNs with NAs.
2025-12-09 08:08:06.861104 INFO::Removing potential empty rows and columns
2025-12-09 08:08:06.862544 INFO::Found 0 missing values.
2025-12-09 08:08:06.866816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 08:08:06.867697 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.313 4.672 25.919
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.154 | 1.277 | 20.323 | |
| compute_asw | 0.037 | 0.004 | 0.042 | |
| count_existing | 0.013 | 0.004 | 0.018 | |
| generate_data_covariables | 0.015 | 0.000 | 0.015 | |
| generate_dataset | 0.015 | 0.000 | 0.015 | |