Yannis Schumann
| Snapshot Date: 2025-11-04 13:40 -0500 (Tue, 04 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-05 11:32 -0500 (Wed, 05 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 166/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-11-04 21:14:57 -0500 (Tue, 04 Nov 2025) |
| EndedAt: 2025-11-04 21:16:27 -0500 (Tue, 04 Nov 2025) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.7.0’
* 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 24.294 1.269 17.515
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-11-04 21:15:48.051071 INFO::Formatting Data.
2025-11-04 21:15:48.052367 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:48.063286 INFO::Removing potential empty rows and columns
2025-11-04 21:15:48.29838 INFO::Found 0 missing values.
2025-11-04 21:15:48.301706 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:48.302361 INFO::Done
2025-11-04 21:15:48.302908 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:48.314132 INFO::Starting hierarchical adjustment
2025-11-04 21:15:48.315038 INFO::Found 3 batches.
2025-11-04 21:15:48.315589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:48.316713 INFO::Using default BPPARAM
2025-11-04 21:15:48.317266 INFO::Processing subtree level 1
2025-11-04 21:15:48.420432 INFO::Adjusting the last 1 batches sequentially
2025-11-04 21:15:48.422446 INFO::Done
2025-11-04 21:15:48.423216 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:48.426249 INFO::ASW Batch was -0.0894999120773221 prior to batch effect correction and is now -0.0894999120773221 .
2025-11-04 21:15:48.42748 INFO::Total function execution time is 0.376945018768311 s and adjustment time is 0.107582092285156 s ( 28.54 )
2025-11-04 21:15:48.442035 INFO::Formatting Data.
2025-11-04 21:15:48.442917 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:48.443909 INFO::Removing potential empty rows and columns
2025-11-04 21:15:48.445061 INFO::Found 0 missing values.
2025-11-04 21:15:48.446052 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-04 21:15:48.457051 INFO::Formatting Data.
2025-11-04 21:15:48.457768 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:48.45866 INFO::Removing potential empty rows and columns
2025-11-04 21:15:48.459722 INFO::Found 0 missing values.
2025-11-04 21:15:48.460674 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-04 21:15:48.476642 INFO::Formatting Data.
2025-11-04 21:15:48.477451 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:48.478409 INFO::Removing potential empty rows and columns
2025-11-04 21:15:48.479485 INFO::Found 0 missing values.
2025-11-04 21:15:48.480436 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-04 21:15:48.484971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:48.485527 INFO::Done
2025-11-04 21:15:48.486058 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:48.488212 INFO::Starting hierarchical adjustment
2025-11-04 21:15:48.488905 INFO::Found 2 batches.
2025-11-04 21:15:48.489437 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:48.490072 INFO::Using default BPPARAM
2025-11-04 21:15:48.49059 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:48.491553 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-04 21:15:48.513593 INFO::Done
2025-11-04 21:15:48.514339 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:48.516454 INFO::ASW Batch was 0.0186299217780948 prior to batch effect correction and is now -0.118612741505062 .
2025-11-04 21:15:48.517334 INFO::Total function execution time is 0.0407586097717285 s and adjustment time is 0.0248038768768311 s ( 60.86 )
2025-11-04 21:15:48.52009 INFO::Formatting Data.
2025-11-04 21:15:48.520727 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:48.52945 INFO::Formatting Data.
2025-11-04 21:15:48.538562 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:48.539934 INFO::Removing potential empty rows and columns
2025-11-04 21:15:48.541137 INFO::Found 0 missing values.
2025-11-04 21:15:48.544209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:48.544777 INFO::Done
2025-11-04 21:15:48.545368 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:48.548253 INFO::Starting hierarchical adjustment
2025-11-04 21:15:48.549017 INFO::Found 2 batches.
2025-11-04 21:15:48.549616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:48.550368 INFO::Using default BPPARAM
2025-11-04 21:15:48.550956 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:48.552026 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:48.604645 INFO::Done
2025-11-04 21:15:48.605371 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:48.60739 INFO::ASW Batch was 0.0293165857324683 prior to batch effect correction and is now -0.0680759777697846 .
2025-11-04 21:15:48.608195 INFO::Total function execution time is 0.0787737369537354 s and adjustment time is 0.0557973384857178 s ( 70.83 )
2025-11-04 21:15:48.609252 INFO::Formatting Data.
2025-11-04 21:15:48.609856 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:48.610661 INFO::Removing potential empty rows and columns
2025-11-04 21:15:48.611657 INFO::Found 0 missing values.
2025-11-04 21:15:48.614356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:48.614917 INFO::Done
2025-11-04 21:15:48.615433 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:48.617382 INFO::Starting hierarchical adjustment
2025-11-04 21:15:48.618081 INFO::Found 2 batches.
2025-11-04 21:15:48.618583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:48.619164 INFO::Using default BPPARAM
2025-11-04 21:15:48.619669 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:48.620576 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:48.635566 INFO::Done
2025-11-04 21:15:48.636266 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:48.63829 INFO::ASW Batch was 0.0293165857324683 prior to batch effect correction and is now -0.0680759777697846 .
2025-11-04 21:15:48.639074 INFO::Total function execution time is 0.0298285484313965 s and adjustment time is 0.0175983905792236 s ( 59 )
2025-11-04 21:15:51.791309 INFO::Formatting Data.
2025-11-04 21:15:51.792011 INFO::Recognized SummarizedExperiment
2025-11-04 21:15:51.79251 INFO::Typecasting input to dataframe.
2025-11-04 21:15:51.82196 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:51.823084 INFO::Removing potential empty rows and columns
2025-11-04 21:15:51.82612 INFO::Found 0 missing values.
2025-11-04 21:15:51.83194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:51.832514 INFO::Done
2025-11-04 21:15:51.833014 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:51.83612 INFO::Starting hierarchical adjustment
2025-11-04 21:15:51.836793 INFO::Found 2 batches.
2025-11-04 21:15:51.837291 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:51.838331 INFO::Using default BPPARAM
2025-11-04 21:15:51.838824 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:51.83974 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-04 21:15:51.888254 INFO::Done
2025-11-04 21:15:51.888951 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:51.892321 INFO::ASW Batch was 0.036118978992865 prior to batch effect correction and is now -0.0944561485115635 .
2025-11-04 21:15:51.893168 INFO::Total function execution time is 0.102141141891479 s and adjustment time is 0.0515799522399902 s ( 50.5 )
2025-11-04 21:15:51.910474 INFO::Formatting Data.
2025-11-04 21:15:51.911187 INFO::Recognized SummarizedExperiment
2025-11-04 21:15:51.911706 INFO::Typecasting input to dataframe.
2025-11-04 21:15:51.920449 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:51.921535 INFO::Removing potential empty rows and columns
2025-11-04 21:15:51.924932 INFO::Found 0 missing values.
2025-11-04 21:15:51.931474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:51.932073 INFO::Done
2025-11-04 21:15:51.93259 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:51.935909 INFO::Starting hierarchical adjustment
2025-11-04 21:15:51.936584 INFO::Found 2 batches.
2025-11-04 21:15:51.937103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:51.937665 INFO::Using default BPPARAM
2025-11-04 21:15:51.938178 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:51.939121 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-04 21:15:51.964226 INFO::Done
2025-11-04 21:15:51.965057 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:51.968945 INFO::ASW Batch was -0.0083026875324478 prior to batch effect correction and is now -0.0083026875324478 .
2025-11-04 21:15:51.969806 INFO::Total function execution time is 0.0593149662017822 s and adjustment time is 0.0276975631713867 s ( 46.7 )
2025-11-04 21:15:51.987545 INFO::Formatting Data.
2025-11-04 21:15:51.988373 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:51.989287 INFO::Removing potential empty rows and columns
2025-11-04 21:15:51.990313 INFO::Found 0 missing values.
2025-11-04 21:15:51.993217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:51.993756 INFO::Done
2025-11-04 21:15:51.994277 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:51.996271 INFO::Starting hierarchical adjustment
2025-11-04 21:15:51.99699 INFO::Found 3 batches.
2025-11-04 21:15:51.997517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:51.998124 INFO::Using default BPPARAM
2025-11-04 21:15:51.998643 INFO::Processing subtree level 1
2025-11-04 21:15:52.133991 INFO::Adjusting the last 1 batches sequentially
2025-11-04 21:15:52.135715 INFO::Done
2025-11-04 21:15:52.136364 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:52.138857 INFO::ASW Batch was -0.121591428381355 prior to batch effect correction and is now -0.177124581007721 .
2025-11-04 21:15:52.139757 INFO::Total function execution time is 0.152244091033936 s and adjustment time is 0.138868093490601 s ( 91.21 )
2025-11-04 21:15:52.153613 INFO::Skipping initial DF formatting
2025-11-04 21:15:52.154338 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:52.158306 INFO::Starting hierarchical adjustment
2025-11-04 21:15:52.159085 INFO::Found 5 batches.
2025-11-04 21:15:52.159649 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:52.160306 INFO::Using default BPPARAM
2025-11-04 21:15:52.160881 INFO::Processing subtree level 1
2025-11-04 21:15:52.284939 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:52.286777 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-04 21:15:52.307128 INFO::Done
2025-11-04 21:15:52.307987 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:52.312658 INFO::ASW Batch was 0.518360459316735 prior to batch effect correction and is now 0.518360459316735 .
2025-11-04 21:15:52.313369 INFO::ASW Label was 0.394386283019097 prior to batch effect correction and is now 0.394386283019097 .
2025-11-04 21:15:52.314386 INFO::Total function execution time is 0.160758972167969 s and adjustment time is 0.148154258728027 s ( 92.16 )
2025-11-04 21:15:52.334366 INFO::Formatting Data.
2025-11-04 21:15:52.335302 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:52.336272 INFO::Removing potential empty rows and columns
2025-11-04 21:15:52.337319 INFO::Found 0 missing values.
2025-11-04 21:15:52.341395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:52.341952 INFO::Done
2025-11-04 21:15:52.342484 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:52.345612 INFO::Starting hierarchical adjustment
2025-11-04 21:15:52.346341 INFO::Found 5 batches.
2025-11-04 21:15:52.346927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:52.347567 INFO::Using default BPPARAM
2025-11-04 21:15:52.34813 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:52.461264 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:52.463093 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:52.480562 INFO::Done
2025-11-04 21:15:52.48144 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:52.485071 INFO::ASW Batch was 0.485215033459992 prior to batch effect correction and is now -0.0620319259205167 .
2025-11-04 21:15:52.485763 INFO::ASW Label was 0.32395819632079 prior to batch effect correction and is now 0.695390273245296 .
2025-11-04 21:15:52.486706 INFO::Total function execution time is 0.152453660964966 s and adjustment time is 0.134297609329224 s ( 88.09 )
2025-11-04 21:15:52.487617 INFO::Formatting Data.
2025-11-04 21:15:52.488268 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:52.489221 INFO::Removing potential empty rows and columns
2025-11-04 21:15:52.490277 INFO::Found 0 missing values.
2025-11-04 21:15:52.494554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:52.495191 INFO::Done
2025-11-04 21:15:52.495727 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:52.499477 INFO::Starting hierarchical adjustment
2025-11-04 21:15:52.500525 INFO::Found 5 batches.
2025-11-04 21:15:52.501115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:52.501758 INFO::Using default BPPARAM
2025-11-04 21:15:52.502356 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:52.619667 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:52.621459 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:52.63851 INFO::Done
2025-11-04 21:15:52.639356 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:52.642929 INFO::ASW Batch was 0.485215033459992 prior to batch effect correction and is now -0.0620319259205167 .
2025-11-04 21:15:52.643603 INFO::ASW Label was 0.32395819632079 prior to batch effect correction and is now 0.695390273245296 .
2025-11-04 21:15:52.644987 INFO::Total function execution time is 0.157248020172119 s and adjustment time is 0.138114213943481 s ( 87.83 )
2025-11-04 21:15:52.658919 INFO::Formatting Data.
2025-11-04 21:15:52.659756 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:52.660734 INFO::Removing potential empty rows and columns
2025-11-04 21:15:52.661762 INFO::Found 0 missing values.
2025-11-04 21:15:52.665888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:52.666447 INFO::Done
2025-11-04 21:15:52.667 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:52.670146 INFO::Starting hierarchical adjustment
2025-11-04 21:15:52.670887 INFO::Found 5 batches.
2025-11-04 21:15:52.671431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:52.672073 INFO::Using default BPPARAM
2025-11-04 21:15:52.672612 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:52.782422 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:52.784068 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:52.799986 INFO::Done
2025-11-04 21:15:52.800721 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:52.804126 INFO::ASW Batch was 0.180473607331273 prior to batch effect correction and is now -0.0273886379144964 .
2025-11-04 21:15:52.804769 INFO::ASW Label was 0.619912985728084 prior to batch effect correction and is now 0.801069521023236 .
2025-11-04 21:15:52.805656 INFO::Total function execution time is 0.14683985710144 s and adjustment time is 0.129236936569214 s ( 88.01 )
2025-11-04 21:15:52.806527 INFO::Formatting Data.
2025-11-04 21:15:52.8072 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:52.808121 INFO::Removing potential empty rows and columns
2025-11-04 21:15:52.809164 INFO::Found 0 missing values.
2025-11-04 21:15:52.813424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:52.813989 INFO::Done
2025-11-04 21:15:52.814521 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:52.81751 INFO::Starting hierarchical adjustment
2025-11-04 21:15:52.818232 INFO::Found 5 batches.
2025-11-04 21:15:52.818774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:52.819446 INFO::Using default BPPARAM
2025-11-04 21:15:52.820006 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:52.944639 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:52.94651 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:52.963775 INFO::Done
2025-11-04 21:15:52.964652 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:52.96827 INFO::ASW Batch was 0.180473607331273 prior to batch effect correction and is now -0.0273886379144964 .
2025-11-04 21:15:52.968969 INFO::ASW Label was 0.619912985728084 prior to batch effect correction and is now 0.801069521023236 .
2025-11-04 21:15:52.969887 INFO::Total function execution time is 0.163333892822266 s and adjustment time is 0.145636558532715 s ( 89.16 )
2025-11-04 21:15:52.984259 INFO::Formatting Data.
2025-11-04 21:15:52.985161 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:52.986189 INFO::Removing potential empty rows and columns
2025-11-04 21:15:52.987607 INFO::Found 0 missing values.
2025-11-04 21:15:52.991446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:52.9921 INFO::Done
2025-11-04 21:15:52.992663 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:52.996268 INFO::Starting hierarchical adjustment
2025-11-04 21:15:52.997066 INFO::Found 2 batches.
2025-11-04 21:15:52.997651 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:52.999325 INFO::Using default BPPARAM
2025-11-04 21:15:52.999984 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:53.00114 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:53.01848 INFO::Done
2025-11-04 21:15:53.019333 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:53.023034 INFO::ASW Batch was 0.548413077917242 prior to batch effect correction and is now 0.228366756914673 .
2025-11-04 21:15:53.023758 INFO::ASW Label was 0.67467024579454 prior to batch effect correction and is now 0.77744946973935 .
2025-11-04 21:15:53.024765 INFO::Total function execution time is 0.0405642986297607 s and adjustment time is 0.0215613842010498 s ( 53.15 )
2025-11-04 21:15:53.025802 INFO::Formatting Data.
2025-11-04 21:15:53.026462 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:53.027414 INFO::Removing potential empty rows and columns
2025-11-04 21:15:53.028461 INFO::Found 0 missing values.
2025-11-04 21:15:53.031308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:53.031873 INFO::Done
2025-11-04 21:15:53.032448 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:53.035756 INFO::Starting hierarchical adjustment
2025-11-04 21:15:53.036518 INFO::Found 2 batches.
2025-11-04 21:15:53.037088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:53.037713 INFO::Using default BPPARAM
2025-11-04 21:15:53.038271 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:53.039289 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-04 21:15:53.054685 INFO::Done
2025-11-04 21:15:53.055507 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:53.058882 INFO::ASW Batch was 0.548413077917242 prior to batch effect correction and is now 0.228366756914673 .
2025-11-04 21:15:53.059554 INFO::ASW Label was 0.67467024579454 prior to batch effect correction and is now 0.77744946973935 .
2025-11-04 21:15:53.060419 INFO::Total function execution time is 0.0346331596374512 s and adjustment time is 0.018291711807251 s ( 52.82 )
2025-11-04 21:15:53.073154 INFO::Formatting Data.
2025-11-04 21:15:53.074047 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:53.075019 INFO::Removing potential empty rows and columns
2025-11-04 21:15:53.075974 INFO::Found 0 missing values.
2025-11-04 21:15:53.078207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:53.078769 INFO::Done
2025-11-04 21:15:53.079358 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:53.081422 INFO::Starting hierarchical adjustment
2025-11-04 21:15:53.082173 INFO::Found 2 batches.
2025-11-04 21:15:53.082736 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:53.083377 INFO::Using default BPPARAM
2025-11-04 21:15:53.08394 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:53.084892 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-04 21:15:53.118837 INFO::Done
2025-11-04 21:15:53.119709 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:53.121889 INFO::ASW Batch was 0.0581732795195371 prior to batch effect correction and is now -0.074123135849996 .
2025-11-04 21:15:53.122764 INFO::Total function execution time is 0.0497303009033203 s and adjustment time is 0.0367667675018311 s ( 73.93 )
2025-11-04 21:15:53.135822 INFO::Formatting Data.
2025-11-04 21:15:53.136755 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:53.137754 INFO::Removing potential empty rows and columns
2025-11-04 21:15:53.138786 INFO::Found 0 missing values.
2025-11-04 21:15:53.140005 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-04 21:15:53.144864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:53.145477 INFO::Done
2025-11-04 21:15:53.146035 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:53.149354 INFO::Starting hierarchical adjustment
2025-11-04 21:15:53.150096 INFO::Found 2 batches.
2025-11-04 21:15:53.150644 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:53.151276 INFO::Using default BPPARAM
2025-11-04 21:15:53.151819 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:53.152823 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-04 21:15:53.170405 INFO::Done
2025-11-04 21:15:53.171197 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:53.174334 INFO::ASW Batch was 0.607485894169476 prior to batch effect correction and is now 0.0136873495092254 .
2025-11-04 21:15:53.174989 INFO::ASW Label was 0.485530321908978 prior to batch effect correction and is now 0.914900274363776 .
2025-11-04 21:15:53.175825 INFO::Total function execution time is 0.0400996208190918 s and adjustment time is 0.0204470157623291 s ( 50.99 )
2025-11-04 21:15:53.176703 INFO::Formatting Data.
2025-11-04 21:15:53.177365 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:53.178381 INFO::Removing potential empty rows and columns
2025-11-04 21:15:53.179423 INFO::Found 0 missing values.
2025-11-04 21:15:53.180387 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-04 21:15:53.185158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:53.185723 INFO::Done
2025-11-04 21:15:53.18629 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:53.189439 INFO::Starting hierarchical adjustment
2025-11-04 21:15:53.19019 INFO::Found 2 batches.
2025-11-04 21:15:53.190741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:53.191461 INFO::Using default BPPARAM
2025-11-04 21:15:53.192029 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:53.193015 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-04 21:15:53.211002 INFO::Done
2025-11-04 21:15:53.211815 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:53.215054 INFO::ASW Batch was 0.607485894169476 prior to batch effect correction and is now 0.0136873495092254 .
2025-11-04 21:15:53.215682 INFO::ASW Label was 0.485530321908978 prior to batch effect correction and is now 0.914900274363776 .
2025-11-04 21:15:53.216564 INFO::Total function execution time is 0.0398726463317871 s and adjustment time is 0.0209379196166992 s ( 52.51 )
2025-11-04 21:15:53.456939 INFO::Formatting Data.
2025-11-04 21:15:53.458102 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:53.459185 INFO::Removing potential empty rows and columns
2025-11-04 21:15:53.46042 INFO::Found 0 missing values.
2025-11-04 21:15:53.463817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:53.464454 INFO::Done
2025-11-04 21:15:53.465041 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:53.46762 INFO::Starting hierarchical adjustment
2025-11-04 21:15:53.468398 INFO::Found 3 batches.
2025-11-04 21:15:53.468975 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:53.469689 INFO::Using default BPPARAM
2025-11-04 21:15:53.470296 INFO::Processing subtree level 1
2025-11-04 21:15:53.582671 INFO::Adjusting the last 1 batches sequentially
2025-11-04 21:15:53.584854 INFO::Done
2025-11-04 21:15:53.585597 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:53.588496 INFO::ASW Batch was -0.117571699863527 prior to batch effect correction and is now -0.117571699863527 .
2025-11-04 21:15:53.589661 INFO::Total function execution time is 0.13303804397583 s and adjustment time is 0.116593360900879 s ( 87.64 )
2025-11-04 21:15:53.590948 INFO::Formatting Data.
2025-11-04 21:15:53.59168 INFO::Typecasting input to dataframe.
2025-11-04 21:15:53.592544 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:53.593597 INFO::Removing potential empty rows and columns
2025-11-04 21:15:53.59483 INFO::Found 0 missing values.
2025-11-04 21:15:53.598221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:53.598821 INFO::Done
2025-11-04 21:15:53.599399 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:53.601758 INFO::Starting hierarchical adjustment
2025-11-04 21:15:53.602536 INFO::Found 3 batches.
2025-11-04 21:15:53.603149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:53.6038 INFO::Using default BPPARAM
2025-11-04 21:15:53.604383 INFO::Processing subtree level 1
2025-11-04 21:15:53.707574 INFO::Adjusting the last 1 batches sequentially
2025-11-04 21:15:53.709735 INFO::Done
2025-11-04 21:15:53.710498 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:53.713295 INFO::ASW Batch was -0.117571699863527 prior to batch effect correction and is now -0.117571699863527 .
2025-11-04 21:15:53.714347 INFO::Total function execution time is 0.123402833938599 s and adjustment time is 0.107331991195679 s ( 86.98 )
2025-11-04 21:15:53.728478 INFO::Formatting Data.
2025-11-04 21:15:53.729397 INFO::Typecasting input to dataframe.
2025-11-04 21:15:53.730362 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:53.731361 INFO::Removing potential empty rows and columns
2025-11-04 21:15:53.732519 INFO::Found 0 missing values.
2025-11-04 21:15:53.736026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:53.73658 INFO::Done
2025-11-04 21:15:53.73714 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:53.739348 INFO::Starting hierarchical adjustment
2025-11-04 21:15:53.740103 INFO::Found 3 batches.
2025-11-04 21:15:53.740676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:53.741343 INFO::Using default BPPARAM
2025-11-04 21:15:53.741911 INFO::Processing subtree level 1
2025-11-04 21:15:53.841705 INFO::Adjusting the last 1 batches sequentially
2025-11-04 21:15:53.84391 INFO::Done
2025-11-04 21:15:53.844661 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:53.847501 INFO::ASW Batch was -0.149278462665791 prior to batch effect correction and is now -0.149278462665791 .
2025-11-04 21:15:53.848577 INFO::Total function execution time is 0.12015700340271 s and adjustment time is 0.10393762588501 s ( 86.5 )
2025-11-04 21:15:54.008165 INFO::Formatting Data.
2025-11-04 21:15:54.009095 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:54.010317 INFO::Removing potential empty rows and columns
2025-11-04 21:15:54.013209 INFO::Found 1000 missing values.
2025-11-04 21:15:54.032544 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:54.03337 INFO::Done
2025-11-04 21:15:54.033996 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:54.039708 INFO::Starting hierarchical adjustment
2025-11-04 21:15:54.040499 INFO::Found 10 batches.
2025-11-04 21:15:54.041066 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:54.04172 INFO::Using default BPPARAM
2025-11-04 21:15:54.042307 INFO::Processing subtree level 1
2025-11-04 21:15:54.200946 INFO::Processing subtree level 2
2025-11-04 21:15:55.792373 INFO::Adjusting the last 1 batches sequentially
2025-11-04 21:15:55.79482 INFO::Done
2025-11-04 21:15:55.795719 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:55.803558 INFO::ASW Batch was 0.487754080466535 prior to batch effect correction and is now 0.487754080466535 .
2025-11-04 21:15:55.804396 INFO::ASW Label was 0.323916810604646 prior to batch effect correction and is now 0.323916810604646 .
2025-11-04 21:15:55.805587 INFO::Total function execution time is 1.79756331443787 s and adjustment time is 1.75442910194397 s ( 97.6 )
2025-11-04 21:15:55.806785 INFO::Formatting Data.
2025-11-04 21:15:55.807688 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:55.809212 INFO::Removing potential empty rows and columns
2025-11-04 21:15:55.813247 INFO::Found 1000 missing values.
2025-11-04 21:15:55.914935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:55.91572 INFO::Done
2025-11-04 21:15:55.91633 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:55.921928 INFO::Starting hierarchical adjustment
2025-11-04 21:15:55.922729 INFO::Found 10 batches.
2025-11-04 21:15:57.253513 INFO::Set up parallel execution backend with 2 workers
2025-11-04 21:15:57.255387 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-04 21:15:58.753103 INFO::Adjusting the last 2 batches sequentially
2025-11-04 21:15:58.756969 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-04 21:15:58.774297 INFO::Done
2025-11-04 21:15:58.775055 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:58.779792 INFO::ASW Batch was 0.487754080466535 prior to batch effect correction and is now 0.487754080466535 .
2025-11-04 21:15:58.780419 INFO::ASW Label was 0.323916810604646 prior to batch effect correction and is now 0.323916810604646 .
2025-11-04 21:15:58.781225 INFO::Total function execution time is 2.97453689575195 s and adjustment time is 2.85167908668518 s ( 95.87 )
2025-11-04 21:15:58.942179 INFO::Formatting Data.
2025-11-04 21:15:58.943212 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:58.944328 INFO::Removing potential empty rows and columns
2025-11-04 21:15:58.945518 INFO::Found 0 missing values.
2025-11-04 21:15:58.949458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:58.950066 INFO::Done
2025-11-04 21:15:58.950659 INFO::Acquiring quality metrics before batch effect correction.
2025-11-04 21:15:58.953803 INFO::Starting hierarchical adjustment
2025-11-04 21:15:58.954576 INFO::Found 3 batches.
2025-11-04 21:15:58.955149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-04 21:15:58.955773 INFO::Using default BPPARAM
2025-11-04 21:15:58.956327 INFO::Processing subtree level 1
2025-11-04 21:15:59.073263 INFO::Adjusting the last 1 batches sequentially
2025-11-04 21:15:59.075162 INFO::Done
2025-11-04 21:15:59.075797 INFO::Acquiring quality metrics after batch effect correction.
2025-11-04 21:15:59.079121 INFO::ASW Batch was 0.178072759608196 prior to batch effect correction and is now -0.159271611814392 .
2025-11-04 21:15:59.079745 INFO::ASW Label was -0.222128145803995 prior to batch effect correction and is now -0.20163782168219 .
2025-11-04 21:15:59.080654 INFO::Total function execution time is 0.138580560684204 s and adjustment time is 0.120735645294189 s ( 87.12 )
2025-11-04 21:15:59.197262 INFO::Formatting Data.
2025-11-04 21:15:59.198196 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.199159 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.200203 INFO::Found 2 missing values.
2025-11-04 21:15:59.202942 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.203467 INFO::Done
2025-11-04 21:15:59.229017 INFO::Found NA in Reference column
2025-11-04 21:15:59.238132 INFO::Require at least two references per batch.
2025-11-04 21:15:59.258612 INFO::Formatting Data.
2025-11-04 21:15:59.25952 INFO::Recognized SummarizedExperiment
2025-11-04 21:15:59.260121 INFO::Typecasting input to dataframe.
2025-11-04 21:15:59.276426 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.277905 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.281488 INFO::Found 0 missing values.
2025-11-04 21:15:59.288206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.288813 INFO::Done
2025-11-04 21:15:59.304464 INFO::Formatting Data.
2025-11-04 21:15:59.305216 INFO::Recognized SummarizedExperiment
2025-11-04 21:15:59.305767 INFO::Typecasting input to dataframe.
2025-11-04 21:15:59.323257 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.324487 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.328031 INFO::Found 0 missing values.
2025-11-04 21:15:59.338435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.339153 INFO::Done
2025-11-04 21:15:59.354953 INFO::Formatting Data.
2025-11-04 21:15:59.355716 INFO::Recognized SummarizedExperiment
2025-11-04 21:15:59.356279 INFO::Typecasting input to dataframe.
2025-11-04 21:15:59.372567 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.373721 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.374811 INFO::Found 0 missing values.
2025-11-04 21:15:59.375756 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-04 21:15:59.380099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.380652 INFO::Done
2025-11-04 21:15:59.390547 INFO::Formatting Data.
2025-11-04 21:15:59.391339 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.392215 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.393208 INFO::Found 0 missing values.
2025-11-04 21:15:59.396077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.396619 INFO::Done
2025-11-04 21:15:59.407329 INFO::Formatting Data.
2025-11-04 21:15:59.408042 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.40887 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.409812 INFO::Found 0 missing values.
2025-11-04 21:15:59.412645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.413207 INFO::Done
2025-11-04 21:15:59.441263 INFO::Formatting Data.
2025-11-04 21:15:59.442193 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.443295 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.444464 INFO::Found 1 missing values.
2025-11-04 21:15:59.447104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.447641 INFO::Done
2025-11-04 21:15:59.466535 INFO::Formatting Data.
2025-11-04 21:15:59.467488 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.468438 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.469456 INFO::Found 2 missing values.
2025-11-04 21:15:59.470452 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-11-04 21:15:59.472777 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.473362 INFO::Done
2025-11-04 21:15:59.483068 INFO::Formatting Data.
2025-11-04 21:15:59.48388 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.484731 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.485698 INFO::Found 2 missing values.
2025-11-04 21:15:59.487382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.487946 INFO::Done
2025-11-04 21:15:59.499299 INFO::Formatting Data.
2025-11-04 21:15:59.500127 INFO::Typecasting input to dataframe.
2025-11-04 21:15:59.501037 INFO::Replacing NaNs with NAs.
2025-11-04 21:15:59.501952 INFO::Removing potential empty rows and columns
2025-11-04 21:15:59.503003 INFO::Found 0 missing values.
2025-11-04 21:15:59.505826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-04 21:15:59.506364 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.464 4.609 22.601
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.294 | 1.269 | 17.515 | |
| compute_asw | 0.022 | 0.002 | 0.024 | |
| count_existing | 0.012 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |