Yannis Schumann
| Snapshot Date: 2026-02-25 13:45 -0500 (Wed, 25 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-26 11:57 -0500 (Thu, 26 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-02-25 21:58:17 -0500 (Wed, 25 Feb 2026) |
| EndedAt: 2026-02-25 21:59:46 -0500 (Wed, 25 Feb 2026) |
| EllapsedTime: 89.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.542 1.402 17.712
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-25 21:59:09.066858 INFO::Formatting Data.
2026-02-25 21:59:09.068091 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:09.078755 INFO::Removing potential empty rows and columns
2026-02-25 21:59:09.31449 INFO::Found 0 missing values.
2026-02-25 21:59:09.317798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:09.318444 INFO::Done
2026-02-25 21:59:09.318984 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:09.329762 INFO::Starting hierarchical adjustment
2026-02-25 21:59:09.330631 INFO::Found 3 batches.
2026-02-25 21:59:09.331181 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:09.332336 INFO::Using default BPPARAM
2026-02-25 21:59:09.332895 INFO::Processing subtree level 1
2026-02-25 21:59:09.428213 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:59:09.430181 INFO::Done
2026-02-25 21:59:09.430894 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:09.433383 INFO::ASW Batch was -0.0820756699777361 prior to batch effect correction and is now -0.0820756699777361 .
2026-02-25 21:59:09.434416 INFO::Total function execution time is 0.368172407150269 s and adjustment time is 0.0997231006622314 s ( 27.09 )
2026-02-25 21:59:09.448448 INFO::Formatting Data.
2026-02-25 21:59:09.449217 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:09.450185 INFO::Removing potential empty rows and columns
2026-02-25 21:59:09.451465 INFO::Found 0 missing values.
2026-02-25 21:59:09.452442 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-25 21:59:09.463554 INFO::Formatting Data.
2026-02-25 21:59:09.464291 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:09.465246 INFO::Removing potential empty rows and columns
2026-02-25 21:59:09.466368 INFO::Found 0 missing values.
2026-02-25 21:59:09.467324 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-25 21:59:09.48379 INFO::Formatting Data.
2026-02-25 21:59:09.484536 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:09.485418 INFO::Removing potential empty rows and columns
2026-02-25 21:59:09.486453 INFO::Found 0 missing values.
2026-02-25 21:59:09.487379 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-25 21:59:09.491807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:09.492362 INFO::Done
2026-02-25 21:59:09.492887 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:09.494897 INFO::Starting hierarchical adjustment
2026-02-25 21:59:09.495599 INFO::Found 2 batches.
2026-02-25 21:59:09.496124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:09.496763 INFO::Using default BPPARAM
2026-02-25 21:59:09.497293 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:09.498209 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:59:09.519862 INFO::Done
2026-02-25 21:59:09.520587 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:09.522908 INFO::ASW Batch was 0.0441313857645121 prior to batch effect correction and is now -0.0843607388696665 .
2026-02-25 21:59:09.52374 INFO::Total function execution time is 0.040003776550293 s and adjustment time is 0.0243830680847168 s ( 60.95 )
2026-02-25 21:59:09.526869 INFO::Formatting Data.
2026-02-25 21:59:09.527526 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:09.536667 INFO::Formatting Data.
2026-02-25 21:59:09.537405 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:09.53831 INFO::Removing potential empty rows and columns
2026-02-25 21:59:09.53936 INFO::Found 0 missing values.
2026-02-25 21:59:09.542371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:09.542926 INFO::Done
2026-02-25 21:59:09.543543 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:09.569655 INFO::Starting hierarchical adjustment
2026-02-25 21:59:09.570939 INFO::Found 2 batches.
2026-02-25 21:59:09.571457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:09.572022 INFO::Using default BPPARAM
2026-02-25 21:59:09.572516 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:09.573368 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:09.58714 INFO::Done
2026-02-25 21:59:09.587739 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:09.58956 INFO::ASW Batch was -0.00869903190188279 prior to batch effect correction and is now -0.107531636634597 .
2026-02-25 21:59:09.590261 INFO::Total function execution time is 0.0536653995513916 s and adjustment time is 0.0163779258728027 s ( 30.52 )
2026-02-25 21:59:09.591196 INFO::Formatting Data.
2026-02-25 21:59:09.59176 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:09.592553 INFO::Removing potential empty rows and columns
2026-02-25 21:59:09.593465 INFO::Found 0 missing values.
2026-02-25 21:59:09.596027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:09.596541 INFO::Done
2026-02-25 21:59:09.597018 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:09.598818 INFO::Starting hierarchical adjustment
2026-02-25 21:59:09.599468 INFO::Found 2 batches.
2026-02-25 21:59:09.59995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:09.600522 INFO::Using default BPPARAM
2026-02-25 21:59:09.60101 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:09.601838 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:09.615308 INFO::Done
2026-02-25 21:59:09.615892 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:09.6177 INFO::ASW Batch was -0.00869903190188279 prior to batch effect correction and is now -0.107531636634597 .
2026-02-25 21:59:09.618408 INFO::Total function execution time is 0.0272009372711182 s and adjustment time is 0.0159690380096436 s ( 58.71 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-25 21:59:12.303001 INFO::Formatting Data.
2026-02-25 21:59:12.303637 INFO::Recognized SummarizedExperiment
2026-02-25 21:59:12.304108 INFO::Typecasting input to dataframe.
2026-02-25 21:59:12.332236 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:12.333441 INFO::Removing potential empty rows and columns
2026-02-25 21:59:12.337198 INFO::Found 0 missing values.
2026-02-25 21:59:12.344467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:12.34506 INFO::Done
2026-02-25 21:59:12.345591 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:12.349125 INFO::Starting hierarchical adjustment
2026-02-25 21:59:12.349843 INFO::Found 2 batches.
2026-02-25 21:59:12.350354 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:12.351423 INFO::Using default BPPARAM
2026-02-25 21:59:12.351961 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:12.352914 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:59:12.407999 INFO::Done
2026-02-25 21:59:12.408701 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:12.412223 INFO::ASW Batch was 0.00904281958870019 prior to batch effect correction and is now -0.0935637820780957 .
2026-02-25 21:59:12.413065 INFO::Total function execution time is 0.110315322875977 s and adjustment time is 0.0582795143127441 s ( 52.83 )
Warning: stack imbalance in '{', 73 then 75
2026-02-25 21:59:12.431645 INFO::Formatting Data.
2026-02-25 21:59:12.432387 INFO::Recognized SummarizedExperiment
2026-02-25 21:59:12.432957 INFO::Typecasting input to dataframe.
2026-02-25 21:59:12.441981 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:12.443088 INFO::Removing potential empty rows and columns
2026-02-25 21:59:12.446977 INFO::Found 0 missing values.
2026-02-25 21:59:12.454058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:12.454673 INFO::Done
2026-02-25 21:59:12.455187 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:12.458709 INFO::Starting hierarchical adjustment
2026-02-25 21:59:12.459422 INFO::Found 2 batches.
2026-02-25 21:59:12.459951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:12.460544 INFO::Using default BPPARAM
2026-02-25 21:59:12.461058 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:12.462001 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:59:12.486926 INFO::Done
2026-02-25 21:59:12.487633 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:12.491386 INFO::ASW Batch was -0.0157042620439854 prior to batch effect correction and is now -0.0157042620439854 .
2026-02-25 21:59:12.492252 INFO::Total function execution time is 0.0606024265289307 s and adjustment time is 0.027623176574707 s ( 45.58 )
2026-02-25 21:59:12.510491 INFO::Formatting Data.
2026-02-25 21:59:12.511349 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:12.512297 INFO::Removing potential empty rows and columns
2026-02-25 21:59:12.513335 INFO::Found 0 missing values.
2026-02-25 21:59:12.516355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:12.516899 INFO::Done
2026-02-25 21:59:12.517406 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:12.519373 INFO::Starting hierarchical adjustment
2026-02-25 21:59:12.520095 INFO::Found 3 batches.
2026-02-25 21:59:12.520621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:12.521207 INFO::Using default BPPARAM
2026-02-25 21:59:12.52173 INFO::Processing subtree level 1
2026-02-25 21:59:12.650759 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:59:12.652499 INFO::Done
2026-02-25 21:59:12.653131 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:12.655535 INFO::ASW Batch was -0.0932415915589971 prior to batch effect correction and is now -0.151182449729112 .
2026-02-25 21:59:12.656404 INFO::Total function execution time is 0.145965337753296 s and adjustment time is 0.132544994354248 s ( 90.81 )
2026-02-25 21:59:12.670534 INFO::Skipping initial DF formatting
2026-02-25 21:59:12.671237 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:12.675184 INFO::Starting hierarchical adjustment
2026-02-25 21:59:12.675946 INFO::Found 5 batches.
2026-02-25 21:59:12.676482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:12.677108 INFO::Using default BPPARAM
2026-02-25 21:59:12.677649 INFO::Processing subtree level 1
2026-02-25 21:59:12.9024 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:12.904293 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:59:12.925458 INFO::Done
2026-02-25 21:59:12.926288 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:12.931012 INFO::ASW Batch was 0.572502221105377 prior to batch effect correction and is now 0.572502221105377 .
2026-02-25 21:59:12.931758 INFO::ASW Label was 0.359337941106772 prior to batch effect correction and is now 0.359337941106772 .
2026-02-25 21:59:12.932708 INFO::Total function execution time is 0.262192964553833 s and adjustment time is 0.249591112136841 s ( 95.19 )
2026-02-25 21:59:13.005984 INFO::Formatting Data.
2026-02-25 21:59:13.006989 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.008018 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.009111 INFO::Found 0 missing values.
2026-02-25 21:59:13.013325 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.013986 INFO::Done
2026-02-25 21:59:13.014533 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.017787 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.018589 INFO::Found 5 batches.
2026-02-25 21:59:13.019164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.01983 INFO::Using default BPPARAM
2026-02-25 21:59:13.020368 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.153426 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.155245 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.172795 INFO::Done
2026-02-25 21:59:13.173516 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.17718 INFO::ASW Batch was 0.366953099140428 prior to batch effect correction and is now -0.0803848890083424 .
2026-02-25 21:59:13.177831 INFO::ASW Label was 0.445173780050257 prior to batch effect correction and is now 0.783333786247993 .
2026-02-25 21:59:13.178697 INFO::Total function execution time is 0.172810077667236 s and adjustment time is 0.154340267181396 s ( 89.31 )
2026-02-25 21:59:13.179605 INFO::Formatting Data.
2026-02-25 21:59:13.180235 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.181206 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.182287 INFO::Found 0 missing values.
2026-02-25 21:59:13.186884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.187474 INFO::Done
2026-02-25 21:59:13.188044 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.191191 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.191933 INFO::Found 5 batches.
2026-02-25 21:59:13.192452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.193088 INFO::Using default BPPARAM
2026-02-25 21:59:13.193672 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.318445 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.320348 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.339321 INFO::Done
2026-02-25 21:59:13.340194 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.344105 INFO::ASW Batch was 0.366953099140428 prior to batch effect correction and is now -0.0803848890083424 .
2026-02-25 21:59:13.344866 INFO::ASW Label was 0.445173780050257 prior to batch effect correction and is now 0.783333786247993 .
2026-02-25 21:59:13.345809 INFO::Total function execution time is 0.16619086265564 s and adjustment time is 0.147480487823486 s ( 88.74 )
2026-02-25 21:59:13.361477 INFO::Formatting Data.
2026-02-25 21:59:13.362582 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.363705 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.364969 INFO::Found 0 missing values.
2026-02-25 21:59:13.369524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.370211 INFO::Done
2026-02-25 21:59:13.370784 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.374293 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.375124 INFO::Found 5 batches.
2026-02-25 21:59:13.375708 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.376378 INFO::Using default BPPARAM
2026-02-25 21:59:13.376952 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.516385 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.518359 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.537173 INFO::Done
2026-02-25 21:59:13.538131 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.542082 INFO::ASW Batch was 0.312784802384954 prior to batch effect correction and is now -0.0213283418941743 .
2026-02-25 21:59:13.542887 INFO::ASW Label was 0.524290621957018 prior to batch effect correction and is now 0.779518727165344 .
2026-02-25 21:59:13.543833 INFO::Total function execution time is 0.18247127532959 s and adjustment time is 0.162146091461182 s ( 88.86 )
2026-02-25 21:59:13.544777 INFO::Formatting Data.
2026-02-25 21:59:13.545471 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.555421 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.556913 INFO::Found 0 missing values.
2026-02-25 21:59:13.5619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.562558 INFO::Done
2026-02-25 21:59:13.563205 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.567218 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.568073 INFO::Found 5 batches.
2026-02-25 21:59:13.568657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.569422 INFO::Using default BPPARAM
2026-02-25 21:59:13.570048 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.699862 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.701607 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.718256 INFO::Done
2026-02-25 21:59:13.718922 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.722458 INFO::ASW Batch was 0.312784802384954 prior to batch effect correction and is now -0.0213283418941743 .
2026-02-25 21:59:13.723174 INFO::ASW Label was 0.524290621957018 prior to batch effect correction and is now 0.779518727165344 .
2026-02-25 21:59:13.724321 INFO::Total function execution time is 0.179521083831787 s and adjustment time is 0.150401830673218 s ( 83.78 )
2026-02-25 21:59:13.738182 INFO::Formatting Data.
2026-02-25 21:59:13.738926 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.739831 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.740812 INFO::Found 0 missing values.
2026-02-25 21:59:13.743446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.743998 INFO::Done
2026-02-25 21:59:13.744498 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.747371 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.748085 INFO::Found 2 batches.
2026-02-25 21:59:13.748605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.749203 INFO::Using default BPPARAM
2026-02-25 21:59:13.749739 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.750608 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.764819 INFO::Done
2026-02-25 21:59:13.76542 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.768258 INFO::ASW Batch was 0.71142794932666 prior to batch effect correction and is now 0.0880134231613635 .
2026-02-25 21:59:13.768826 INFO::ASW Label was 0.344017359232786 prior to batch effect correction and is now 0.802007048315302 .
2026-02-25 21:59:13.769568 INFO::Total function execution time is 0.0314505100250244 s and adjustment time is 0.0168788433074951 s ( 53.67 )
2026-02-25 21:59:13.770298 INFO::Formatting Data.
2026-02-25 21:59:13.770904 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.771725 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.772679 INFO::Found 0 missing values.
2026-02-25 21:59:13.775215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.775744 INFO::Done
2026-02-25 21:59:13.776233 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.779014 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.779737 INFO::Found 2 batches.
2026-02-25 21:59:13.780247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.780839 INFO::Using default BPPARAM
2026-02-25 21:59:13.781336 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.782213 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:59:13.796453 INFO::Done
2026-02-25 21:59:13.79707 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.799956 INFO::ASW Batch was 0.71142794932666 prior to batch effect correction and is now 0.0880134231613635 .
2026-02-25 21:59:13.800559 INFO::ASW Label was 0.344017359232786 prior to batch effect correction and is now 0.802007048315302 .
2026-02-25 21:59:13.801326 INFO::Total function execution time is 0.0310192108154297 s and adjustment time is 0.0168695449829102 s ( 54.38 )
2026-02-25 21:59:13.812375 INFO::Formatting Data.
2026-02-25 21:59:13.813175 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.814035 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.814912 INFO::Found 0 missing values.
2026-02-25 21:59:13.816944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.817462 INFO::Done
2026-02-25 21:59:13.817976 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.819907 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.820595 INFO::Found 2 batches.
2026-02-25 21:59:13.821118 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.821705 INFO::Using default BPPARAM
2026-02-25 21:59:13.822227 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.823092 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:59:13.853857 INFO::Done
2026-02-25 21:59:13.854528 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.856415 INFO::ASW Batch was 0.168925025685905 prior to batch effect correction and is now -0.077497221395498 .
2026-02-25 21:59:13.857221 INFO::Total function execution time is 0.0449068546295166 s and adjustment time is 0.0333878993988037 s ( 74.35 )
2026-02-25 21:59:13.868498 INFO::Formatting Data.
2026-02-25 21:59:13.869206 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.87006 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.871012 INFO::Found 0 missing values.
2026-02-25 21:59:13.872105 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-25 21:59:13.876455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.87699 INFO::Done
2026-02-25 21:59:13.877481 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.880257 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.880925 INFO::Found 2 batches.
2026-02-25 21:59:13.88142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.882002 INFO::Using default BPPARAM
2026-02-25 21:59:13.882489 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.883369 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:59:13.898967 INFO::Done
2026-02-25 21:59:13.8996 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.902363 INFO::ASW Batch was 0.810440580431267 prior to batch effect correction and is now 0.0357492712134397 .
2026-02-25 21:59:13.90294 INFO::ASW Label was 0.200715139482491 prior to batch effect correction and is now 0.80667842107642 .
2026-02-25 21:59:13.903654 INFO::Total function execution time is 0.0352108478546143 s and adjustment time is 0.0181639194488525 s ( 51.59 )
2026-02-25 21:59:13.904403 INFO::Formatting Data.
2026-02-25 21:59:13.905013 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:13.90589 INFO::Removing potential empty rows and columns
2026-02-25 21:59:13.906835 INFO::Found 0 missing values.
2026-02-25 21:59:13.907686 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-25 21:59:13.911906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:13.912433 INFO::Done
2026-02-25 21:59:13.912937 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:13.915674 INFO::Starting hierarchical adjustment
2026-02-25 21:59:13.916355 INFO::Found 2 batches.
2026-02-25 21:59:13.916863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:13.917423 INFO::Using default BPPARAM
2026-02-25 21:59:13.917929 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:13.918804 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:59:13.934441 INFO::Done
2026-02-25 21:59:13.93507 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:13.937834 INFO::ASW Batch was 0.810440580431267 prior to batch effect correction and is now 0.0357492712134397 .
2026-02-25 21:59:13.938393 INFO::ASW Label was 0.200715139482491 prior to batch effect correction and is now 0.80667842107642 .
2026-02-25 21:59:13.939142 INFO::Total function execution time is 0.0347530841827393 s and adjustment time is 0.0182178020477295 s ( 52.42 )
2026-02-25 21:59:14.138155 INFO::Formatting Data.
2026-02-25 21:59:14.138982 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:14.139883 INFO::Removing potential empty rows and columns
2026-02-25 21:59:14.140922 INFO::Found 0 missing values.
2026-02-25 21:59:14.143904 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:14.144437 INFO::Done
2026-02-25 21:59:14.144961 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:14.146939 INFO::Starting hierarchical adjustment
2026-02-25 21:59:14.147641 INFO::Found 3 batches.
2026-02-25 21:59:14.148165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:14.148757 INFO::Using default BPPARAM
2026-02-25 21:59:14.149265 INFO::Processing subtree level 1
2026-02-25 21:59:14.231773 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:59:14.233449 INFO::Done
2026-02-25 21:59:14.234068 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:14.236439 INFO::ASW Batch was 0.132666344864495 prior to batch effect correction and is now 0.132666344864495 .
2026-02-25 21:59:14.237396 INFO::Total function execution time is 0.0992839336395264 s and adjustment time is 0.085921049118042 s ( 86.54 )
2026-02-25 21:59:14.238399 INFO::Formatting Data.
2026-02-25 21:59:14.239057 INFO::Typecasting input to dataframe.
2026-02-25 21:59:14.24444 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:14.245529 INFO::Removing potential empty rows and columns
2026-02-25 21:59:14.246614 INFO::Found 0 missing values.
2026-02-25 21:59:14.249809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:14.25035 INFO::Done
2026-02-25 21:59:14.250907 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:14.25293 INFO::Starting hierarchical adjustment
2026-02-25 21:59:14.253649 INFO::Found 3 batches.
2026-02-25 21:59:14.254187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:14.254814 INFO::Using default BPPARAM
2026-02-25 21:59:14.255346 INFO::Processing subtree level 1
2026-02-25 21:59:14.335451 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:59:14.337274 INFO::Done
2026-02-25 21:59:14.337962 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:14.340478 INFO::ASW Batch was 0.132666344864495 prior to batch effect correction and is now 0.132666344864495 .
2026-02-25 21:59:14.341417 INFO::Total function execution time is 0.102986097335815 s and adjustment time is 0.08376145362854 s ( 81.33 )
2026-02-25 21:59:14.354822 INFO::Formatting Data.
2026-02-25 21:59:14.355636 INFO::Typecasting input to dataframe.
2026-02-25 21:59:14.356499 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:14.357415 INFO::Removing potential empty rows and columns
2026-02-25 21:59:14.358481 INFO::Found 0 missing values.
2026-02-25 21:59:14.361567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:14.362099 INFO::Done
2026-02-25 21:59:14.362638 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:14.364642 INFO::Starting hierarchical adjustment
2026-02-25 21:59:14.365349 INFO::Found 3 batches.
2026-02-25 21:59:14.365896 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:14.366523 INFO::Using default BPPARAM
2026-02-25 21:59:14.367067 INFO::Processing subtree level 1
2026-02-25 21:59:14.4504 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:59:14.452372 INFO::Done
2026-02-25 21:59:14.4531 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:14.455927 INFO::ASW Batch was -0.0325734176264895 prior to batch effect correction and is now -0.0325734176264895 .
2026-02-25 21:59:14.456896 INFO::Total function execution time is 0.102103471755981 s and adjustment time is 0.087130069732666 s ( 85.34 )
2026-02-25 21:59:14.588304 INFO::Formatting Data.
2026-02-25 21:59:14.589101 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:14.590194 INFO::Removing potential empty rows and columns
2026-02-25 21:59:14.592977 INFO::Found 1000 missing values.
2026-02-25 21:59:14.611748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:14.612492 INFO::Done
2026-02-25 21:59:14.61306 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:14.618494 INFO::Starting hierarchical adjustment
2026-02-25 21:59:14.619272 INFO::Found 10 batches.
2026-02-25 21:59:14.619817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:14.620425 INFO::Using default BPPARAM
2026-02-25 21:59:14.620966 INFO::Processing subtree level 1
2026-02-25 21:59:14.750726 INFO::Processing subtree level 2
2026-02-25 21:59:14.88652 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:59:14.888877 INFO::Done
2026-02-25 21:59:14.889701 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:14.896772 INFO::ASW Batch was 0.491312620390469 prior to batch effect correction and is now 0.491312620390469 .
2026-02-25 21:59:14.897602 INFO::ASW Label was 0.325721143954209 prior to batch effect correction and is now 0.325721143954209 .
2026-02-25 21:59:14.898755 INFO::Total function execution time is 0.310455560684204 s and adjustment time is 0.269726037979126 s ( 86.88 )
2026-02-25 21:59:14.89987 INFO::Formatting Data.
2026-02-25 21:59:14.900751 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:14.902258 INFO::Removing potential empty rows and columns
2026-02-25 21:59:14.905956 INFO::Found 1000 missing values.
2026-02-25 21:59:14.931253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:14.932095 INFO::Done
2026-02-25 21:59:14.932769 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:14.939143 INFO::Starting hierarchical adjustment
2026-02-25 21:59:14.939948 INFO::Found 10 batches.
2026-02-25 21:59:16.056144 INFO::Set up parallel execution backend with 2 workers
2026-02-25 21:59:16.057985 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-25 21:59:17.05908 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:59:17.06073 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:59:17.076046 INFO::Done
2026-02-25 21:59:17.076656 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:17.080922 INFO::ASW Batch was 0.491312620390469 prior to batch effect correction and is now 0.491312620390469 .
2026-02-25 21:59:17.081447 INFO::ASW Label was 0.325721143954209 prior to batch effect correction and is now 0.325721143954209 .
2026-02-25 21:59:17.082139 INFO::Total function execution time is 2.18236923217773 s and adjustment time is 2.13625526428223 s ( 97.89 )
2026-02-25 21:59:17.237111 INFO::Formatting Data.
2026-02-25 21:59:17.237977 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.238959 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.240091 INFO::Found 0 missing values.
2026-02-25 21:59:17.24392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.244463 INFO::Done
2026-02-25 21:59:17.244997 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:59:17.247882 INFO::Starting hierarchical adjustment
2026-02-25 21:59:17.248626 INFO::Found 3 batches.
2026-02-25 21:59:17.249163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:59:17.249812 INFO::Using default BPPARAM
2026-02-25 21:59:17.250351 INFO::Processing subtree level 1
2026-02-25 21:59:17.358187 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:59:17.360477 INFO::Done
2026-02-25 21:59:17.361288 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:59:17.364616 INFO::ASW Batch was 0.198134422946743 prior to batch effect correction and is now -0.156749972310464 .
2026-02-25 21:59:17.365247 INFO::ASW Label was -0.153958286838326 prior to batch effect correction and is now 0.0585975731117818 .
2026-02-25 21:59:17.36618 INFO::Total function execution time is 0.129128456115723 s and adjustment time is 0.111923694610596 s ( 86.68 )
2026-02-25 21:59:17.483306 INFO::Formatting Data.
2026-02-25 21:59:17.484174 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.485059 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.486069 INFO::Found 2 missing values.
2026-02-25 21:59:17.488832 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.489341 INFO::Done
2026-02-25 21:59:17.514971 INFO::Found NA in Reference column
2026-02-25 21:59:17.523866 INFO::Require at least two references per batch.
2026-02-25 21:59:17.544119 INFO::Formatting Data.
2026-02-25 21:59:17.544929 INFO::Recognized SummarizedExperiment
2026-02-25 21:59:17.545442 INFO::Typecasting input to dataframe.
2026-02-25 21:59:17.555377 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.556462 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.55973 INFO::Found 0 missing values.
2026-02-25 21:59:17.566092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.566632 INFO::Done
2026-02-25 21:59:17.58149 INFO::Formatting Data.
2026-02-25 21:59:17.582162 INFO::Recognized SummarizedExperiment
2026-02-25 21:59:17.58267 INFO::Typecasting input to dataframe.
2026-02-25 21:59:17.599211 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.600423 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.603773 INFO::Found 0 missing values.
2026-02-25 21:59:17.613961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.614494 INFO::Done
2026-02-25 21:59:17.62938 INFO::Formatting Data.
2026-02-25 21:59:17.63007 INFO::Recognized SummarizedExperiment
2026-02-25 21:59:17.630587 INFO::Typecasting input to dataframe.
2026-02-25 21:59:17.653249 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.654547 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.655666 INFO::Found 0 missing values.
2026-02-25 21:59:17.656612 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-25 21:59:17.661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.661524 INFO::Done
2026-02-25 21:59:17.67131 INFO::Formatting Data.
2026-02-25 21:59:17.672086 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.67291 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.673851 INFO::Found 0 missing values.
2026-02-25 21:59:17.676592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.677093 INFO::Done
2026-02-25 21:59:17.688293 INFO::Formatting Data.
2026-02-25 21:59:17.689237 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.690393 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.691566 INFO::Found 0 missing values.
2026-02-25 21:59:17.694625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.695179 INFO::Done
2026-02-25 21:59:17.726338 INFO::Formatting Data.
2026-02-25 21:59:17.727251 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.728344 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.729681 INFO::Found 1 missing values.
2026-02-25 21:59:17.732539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.733066 INFO::Done
2026-02-25 21:59:17.753425 INFO::Formatting Data.
2026-02-25 21:59:17.754331 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.755233 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.756258 INFO::Found 2 missing values.
2026-02-25 21:59:17.757221 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-25 21:59:17.759625 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.760188 INFO::Done
2026-02-25 21:59:17.770442 INFO::Formatting Data.
2026-02-25 21:59:17.771243 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.772122 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.773063 INFO::Found 2 missing values.
2026-02-25 21:59:17.774756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.775327 INFO::Done
2026-02-25 21:59:17.785688 INFO::Formatting Data.
2026-02-25 21:59:17.786386 INFO::Typecasting input to dataframe.
2026-02-25 21:59:17.787181 INFO::Replacing NaNs with NAs.
2026-02-25 21:59:17.788008 INFO::Removing potential empty rows and columns
2026-02-25 21:59:17.788989 INFO::Found 0 missing values.
2026-02-25 21:59:17.791927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:59:17.792465 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.820 3.262 19.842
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.542 | 1.402 | 17.712 | |
| compute_asw | 0.023 | 0.001 | 0.025 | |
| count_existing | 0.014 | 0.000 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.011 | |
| generate_dataset | 0.010 | 0.001 | 0.011 | |