Yannis Schumann
| Snapshot Date: 2026-05-14 13:45 -0400 (Thu, 14 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-15 11:33 -0400 (Fri, 15 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4894 |
| 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 174/2375 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 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: 1.9.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz |
| StartedAt: 2026-05-14 21:38:29 -0400 (Thu, 14 May 2026) |
| EndedAt: 2026-05-14 21:39:59 -0400 (Thu, 14 May 2026) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-15 01:38:29 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 24.468 1.368 17.446
* 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-3.24-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.9.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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")
2026-05-14 21:39:22.270911 INFO::Formatting Data.
2026-05-14 21:39:22.27243 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:22.284246 INFO::Removing potential empty rows and columns
2026-05-14 21:39:22.539735 INFO::Found 0 missing values.
2026-05-14 21:39:22.543048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:22.543756 INFO::Done
2026-05-14 21:39:22.544332 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:22.557113 INFO::Starting hierarchical adjustment
2026-05-14 21:39:22.55811 INFO::Found 3 batches.
2026-05-14 21:39:22.558781 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:22.559964 INFO::Using default BPPARAM
2026-05-14 21:39:22.560599 INFO::Processing subtree level 1
2026-05-14 21:39:22.665962 INFO::Adjusting the last 1 batches sequentially
2026-05-14 21:39:22.66782 INFO::Done
2026-05-14 21:39:22.668537 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:22.671186 INFO::ASW Batch was -0.0920832911654986 prior to batch effect correction and is now -0.0920832911654986 .
2026-05-14 21:39:22.67234 INFO::Total function execution time is 0.402139186859131 s and adjustment time is 0.109907388687134 s ( 27.33 )
2026-05-14 21:39:22.686928 INFO::Formatting Data.
2026-05-14 21:39:22.687787 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:22.688784 INFO::Removing potential empty rows and columns
2026-05-14 21:39:22.689921 INFO::Found 0 missing values.
2026-05-14 21:39:22.690953 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.
2026-05-14 21:39:22.702363 INFO::Formatting Data.
2026-05-14 21:39:22.70324 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:22.704218 INFO::Removing potential empty rows and columns
2026-05-14 21:39:22.705473 INFO::Found 0 missing values.
2026-05-14 21:39:22.706589 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.
2026-05-14 21:39:22.72518 INFO::Formatting Data.
2026-05-14 21:39:22.726223 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:22.727308 INFO::Removing potential empty rows and columns
2026-05-14 21:39:22.728529 INFO::Found 0 missing values.
2026-05-14 21:39:22.729589 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.
2026-05-14 21:39:22.734117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:22.734746 INFO::Done
2026-05-14 21:39:22.735313 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:22.73746 INFO::Starting hierarchical adjustment
2026-05-14 21:39:22.738208 INFO::Found 2 batches.
2026-05-14 21:39:22.738796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:22.73947 INFO::Using default BPPARAM
2026-05-14 21:39:22.740057 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:22.741086 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-14 21:39:22.763171 INFO::Done
2026-05-14 21:39:22.763981 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:22.766163 INFO::ASW Batch was -0.0240640925220336 prior to batch effect correction and is now -0.12875937724202 .
2026-05-14 21:39:22.767002 INFO::Total function execution time is 0.0419955253601074 s and adjustment time is 0.0250763893127441 s ( 59.71 )
2026-05-14 21:39:22.769893 INFO::Formatting Data.
2026-05-14 21:39:22.770585 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:22.779678 INFO::Formatting Data.
2026-05-14 21:39:22.780523 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:22.781515 INFO::Removing potential empty rows and columns
2026-05-14 21:39:22.78266 INFO::Found 0 missing values.
2026-05-14 21:39:22.785693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:22.786279 INFO::Done
2026-05-14 21:39:22.786873 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:22.789133 INFO::Starting hierarchical adjustment
2026-05-14 21:39:22.789886 INFO::Found 2 batches.
2026-05-14 21:39:22.79048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:22.791129 INFO::Using default BPPARAM
2026-05-14 21:39:22.791698 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:22.792704 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-14 21:39:22.809445 INFO::Done
2026-05-14 21:39:22.810328 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:22.812531 INFO::ASW Batch was -0.0552062190812436 prior to batch effect correction and is now -0.111650259934701 .
2026-05-14 21:39:22.813415 INFO::Total function execution time is 0.0337905883789062 s and adjustment time is 0.0196514129638672 s ( 58.16 )
2026-05-14 21:39:22.814619 INFO::Formatting Data.
2026-05-14 21:39:22.815307 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:22.816301 INFO::Removing potential empty rows and columns
2026-05-14 21:39:22.817424 INFO::Found 0 missing values.
2026-05-14 21:39:22.820534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:22.821129 INFO::Done
2026-05-14 21:39:22.821717 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:22.824003 INFO::Starting hierarchical adjustment
2026-05-14 21:39:22.824835 INFO::Found 2 batches.
2026-05-14 21:39:22.82544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:22.826117 INFO::Using default BPPARAM
2026-05-14 21:39:22.826743 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:22.827809 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-14 21:39:22.843465 INFO::Done
2026-05-14 21:39:22.844228 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:22.846395 INFO::ASW Batch was -0.0552062190812436 prior to batch effect correction and is now -0.111650259934701 .
2026-05-14 21:39:22.847222 INFO::Total function execution time is 0.0326168537139893 s and adjustment time is 0.0187504291534424 s ( 57.49 )
2026-05-14 21:39:25.964492 INFO::Formatting Data.
2026-05-14 21:39:25.965247 INFO::Recognized SummarizedExperiment
2026-05-14 21:39:25.965796 INFO::Typecasting input to dataframe.
2026-05-14 21:39:25.995608 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:25.996819 INFO::Removing potential empty rows and columns
2026-05-14 21:39:26.00005 INFO::Found 0 missing values.
2026-05-14 21:39:26.006122 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:26.006733 INFO::Done
2026-05-14 21:39:26.007245 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:26.010404 INFO::Starting hierarchical adjustment
2026-05-14 21:39:26.011081 INFO::Found 2 batches.
2026-05-14 21:39:26.011602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:26.012624 INFO::Using default BPPARAM
2026-05-14 21:39:26.013138 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:26.01406 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-14 21:39:26.064425 INFO::Done
2026-05-14 21:39:26.065218 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:26.068582 INFO::ASW Batch was -0.00368606716406475 prior to batch effect correction and is now -0.0954404865268892 .
2026-05-14 21:39:26.069481 INFO::Total function execution time is 0.105233669281006 s and adjustment time is 0.0534169673919678 s ( 50.76 )
2026-05-14 21:39:26.086508 INFO::Formatting Data.
2026-05-14 21:39:26.087278 INFO::Recognized SummarizedExperiment
2026-05-14 21:39:26.087827 INFO::Typecasting input to dataframe.
2026-05-14 21:39:26.096133 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:26.097294 INFO::Removing potential empty rows and columns
2026-05-14 21:39:26.100528 INFO::Found 0 missing values.
2026-05-14 21:39:26.106742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:26.107389 INFO::Done
2026-05-14 21:39:26.107924 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:26.111195 INFO::Starting hierarchical adjustment
2026-05-14 21:39:26.111955 INFO::Found 2 batches.
2026-05-14 21:39:26.112494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:26.113068 INFO::Using default BPPARAM
2026-05-14 21:39:26.113581 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:26.114498 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-14 21:39:26.138842 INFO::Done
2026-05-14 21:39:26.139653 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:26.143332 INFO::ASW Batch was 0.00521716894834192 prior to batch effect correction and is now 0.00521716894834192 .
2026-05-14 21:39:26.144477 INFO::Total function execution time is 0.0579400062561035 s and adjustment time is 0.0269834995269775 s ( 46.57 )
2026-05-14 21:39:26.163092 INFO::Formatting Data.
2026-05-14 21:39:26.163975 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:26.164934 INFO::Removing potential empty rows and columns
2026-05-14 21:39:26.166015 INFO::Found 0 missing values.
2026-05-14 21:39:26.169042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:26.169642 INFO::Done
2026-05-14 21:39:26.170192 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:26.172256 INFO::Starting hierarchical adjustment
2026-05-14 21:39:26.173002 INFO::Found 3 batches.
2026-05-14 21:39:26.173573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:26.174213 INFO::Using default BPPARAM
2026-05-14 21:39:26.174777 INFO::Processing subtree level 1
2026-05-14 21:39:26.310337 INFO::Adjusting the last 1 batches sequentially
2026-05-14 21:39:26.312303 INFO::Done
2026-05-14 21:39:26.313074 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:26.315754 INFO::ASW Batch was -0.0518810110053108 prior to batch effect correction and is now -0.148531102393769 .
2026-05-14 21:39:26.316806 INFO::Total function execution time is 0.153723478317261 s and adjustment time is 0.139414548873901 s ( 90.69 )
2026-05-14 21:39:26.332242 INFO::Skipping initial DF formatting
2026-05-14 21:39:26.333082 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:26.33742 INFO::Starting hierarchical adjustment
2026-05-14 21:39:26.3383 INFO::Found 5 batches.
2026-05-14 21:39:26.338935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:26.339621 INFO::Using default BPPARAM
2026-05-14 21:39:26.340206 INFO::Processing subtree level 1
2026-05-14 21:39:26.46423 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:26.466034 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-14 21:39:26.48706 INFO::Done
2026-05-14 21:39:26.487939 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:26.492446 INFO::ASW Batch was 0.505751265606774 prior to batch effect correction and is now 0.505751265606774 .
2026-05-14 21:39:26.493139 INFO::ASW Label was 0.429847244971237 prior to batch effect correction and is now 0.429847244971237 .
2026-05-14 21:39:26.494092 INFO::Total function execution time is 0.161935567855835 s and adjustment time is 0.148894309997559 s ( 91.95 )
2026-05-14 21:39:26.51325 INFO::Formatting Data.
2026-05-14 21:39:26.514164 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:26.515179 INFO::Removing potential empty rows and columns
2026-05-14 21:39:26.516274 INFO::Found 0 missing values.
2026-05-14 21:39:26.52078 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:26.521566 INFO::Done
2026-05-14 21:39:26.522182 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:26.525451 INFO::Starting hierarchical adjustment
2026-05-14 21:39:26.526249 INFO::Found 5 batches.
2026-05-14 21:39:26.526851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:26.527538 INFO::Using default BPPARAM
2026-05-14 21:39:26.528116 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.
2026-05-14 21:39:26.637111 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:26.638812 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-14 21:39:26.655202 INFO::Done
2026-05-14 21:39:26.656065 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:26.65941 INFO::ASW Batch was 0.330997767093559 prior to batch effect correction and is now -0.023685599373798 .
2026-05-14 21:39:26.66008 INFO::ASW Label was 0.444255061246312 prior to batch effect correction and is now 0.819164927928764 .
2026-05-14 21:39:26.660967 INFO::Total function execution time is 0.147804737091064 s and adjustment time is 0.129084587097168 s ( 87.33 )
2026-05-14 21:39:26.66187 INFO::Formatting Data.
2026-05-14 21:39:26.662559 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:26.663532 INFO::Removing potential empty rows and columns
2026-05-14 21:39:26.664597 INFO::Found 0 missing values.
2026-05-14 21:39:26.668842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:26.669496 INFO::Done
2026-05-14 21:39:26.67007 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:26.67311 INFO::Starting hierarchical adjustment
2026-05-14 21:39:26.673883 INFO::Found 5 batches.
2026-05-14 21:39:26.674463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:26.675126 INFO::Using default BPPARAM
2026-05-14 21:39:26.675718 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.
2026-05-14 21:39:26.786518 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:26.788511 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-14 21:39:26.806434 INFO::Done
2026-05-14 21:39:26.807329 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:26.811007 INFO::ASW Batch was 0.330997767093559 prior to batch effect correction and is now -0.023685599373798 .
2026-05-14 21:39:26.811719 INFO::ASW Label was 0.444255061246312 prior to batch effect correction and is now 0.819164927928764 .
2026-05-14 21:39:26.812646 INFO::Total function execution time is 0.15078067779541 s and adjustment time is 0.132619619369507 s ( 87.96 )
2026-05-14 21:39:26.827983 INFO::Formatting Data.
2026-05-14 21:39:26.828986 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:26.830049 INFO::Removing potential empty rows and columns
2026-05-14 21:39:26.831156 INFO::Found 0 missing values.
2026-05-14 21:39:26.835552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:26.836189 INFO::Done
2026-05-14 21:39:26.836787 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:26.840121 INFO::Starting hierarchical adjustment
2026-05-14 21:39:26.840906 INFO::Found 5 batches.
2026-05-14 21:39:26.841508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:26.842175 INFO::Using default BPPARAM
2026-05-14 21:39:26.842752 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.
2026-05-14 21:39:26.958024 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:26.959893 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-14 21:39:26.976145 INFO::Done
2026-05-14 21:39:26.976941 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:26.980479 INFO::ASW Batch was 0.322163872520396 prior to batch effect correction and is now -0.0353055408256287 .
2026-05-14 21:39:26.981226 INFO::ASW Label was 0.517542164246618 prior to batch effect correction and is now 0.8242484330578 .
2026-05-14 21:39:26.982131 INFO::Total function execution time is 0.154278755187988 s and adjustment time is 0.135352373123169 s ( 87.73 )
2026-05-14 21:39:26.983055 INFO::Formatting Data.
2026-05-14 21:39:26.983781 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:26.984771 INFO::Removing potential empty rows and columns
2026-05-14 21:39:26.985842 INFO::Found 0 missing values.
2026-05-14 21:39:26.990101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:26.990799 INFO::Done
2026-05-14 21:39:26.991465 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:26.994651 INFO::Starting hierarchical adjustment
2026-05-14 21:39:26.995529 INFO::Found 5 batches.
2026-05-14 21:39:26.996144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:26.996817 INFO::Using default BPPARAM
2026-05-14 21:39:26.997406 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.
2026-05-14 21:39:27.108237 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:27.110091 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-14 21:39:27.128345 INFO::Done
2026-05-14 21:39:27.129256 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:27.132821 INFO::ASW Batch was 0.322163872520396 prior to batch effect correction and is now -0.0353055408256287 .
2026-05-14 21:39:27.133526 INFO::ASW Label was 0.517542164246618 prior to batch effect correction and is now 0.8242484330578 .
2026-05-14 21:39:27.134441 INFO::Total function execution time is 0.151370525360107 s and adjustment time is 0.132939100265503 s ( 87.82 )
2026-05-14 21:39:27.149323 INFO::Formatting Data.
2026-05-14 21:39:27.150281 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:27.151351 INFO::Removing potential empty rows and columns
2026-05-14 21:39:27.152483 INFO::Found 0 missing values.
2026-05-14 21:39:27.155436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:27.156034 INFO::Done
2026-05-14 21:39:27.156621 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:27.159974 INFO::Starting hierarchical adjustment
2026-05-14 21:39:27.160793 INFO::Found 2 batches.
2026-05-14 21:39:27.16136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:27.162045 INFO::Using default BPPARAM
2026-05-14 21:39:27.162631 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:27.163655 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-14 21:39:27.179754 INFO::Done
2026-05-14 21:39:27.180635 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:27.183902 INFO::ASW Batch was 0.540249999635868 prior to batch effect correction and is now -0.00399377823706733 .
2026-05-14 21:39:27.184623 INFO::ASW Label was 0.506290097660686 prior to batch effect correction and is now 0.888864771016524 .
2026-05-14 21:39:27.185498 INFO::Total function execution time is 0.0363028049468994 s and adjustment time is 0.0190722942352295 s ( 52.54 )
2026-05-14 21:39:27.186356 INFO::Formatting Data.
2026-05-14 21:39:27.187061 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:27.188016 INFO::Removing potential empty rows and columns
2026-05-14 21:39:27.18908 INFO::Found 0 missing values.
2026-05-14 21:39:27.191974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:27.192553 INFO::Done
2026-05-14 21:39:27.1931 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:27.196257 INFO::Starting hierarchical adjustment
2026-05-14 21:39:27.197031 INFO::Found 2 batches.
2026-05-14 21:39:27.197621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:27.198267 INFO::Using default BPPARAM
2026-05-14 21:39:27.19884 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:27.199831 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-14 21:39:27.216076 INFO::Done
2026-05-14 21:39:27.216955 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:27.220327 INFO::ASW Batch was 0.540249999635868 prior to batch effect correction and is now -0.00399377823706733 .
2026-05-14 21:39:27.221014 INFO::ASW Label was 0.506290097660686 prior to batch effect correction and is now 0.888864771016524 .
2026-05-14 21:39:27.221883 INFO::Total function execution time is 0.0355491638183594 s and adjustment time is 0.019136905670166 s ( 53.83 )
2026-05-14 21:39:27.23437 INFO::Formatting Data.
2026-05-14 21:39:27.235268 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:27.23636 INFO::Removing potential empty rows and columns
2026-05-14 21:39:27.23735 INFO::Found 0 missing values.
2026-05-14 21:39:27.239677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:27.240245 INFO::Done
2026-05-14 21:39:27.240817 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:27.242999 INFO::Starting hierarchical adjustment
2026-05-14 21:39:27.243764 INFO::Found 2 batches.
2026-05-14 21:39:27.244336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:27.245068 INFO::Using default BPPARAM
2026-05-14 21:39:27.245647 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:27.246627 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-14 21:39:27.280452 INFO::Done
2026-05-14 21:39:27.281342 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:27.283709 INFO::ASW Batch was -0.149095799223113 prior to batch effect correction and is now -0.163627288664325 .
2026-05-14 21:39:27.284634 INFO::Total function execution time is 0.0503666400909424 s and adjustment time is 0.0367743968963623 s ( 73.01 )
2026-05-14 21:39:27.298021 INFO::Formatting Data.
2026-05-14 21:39:27.29893 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:27.299934 INFO::Removing potential empty rows and columns
2026-05-14 21:39:27.301085 INFO::Found 0 missing values.
2026-05-14 21:39:27.302351 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.
2026-05-14 21:39:27.307252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:27.307853 INFO::Done
2026-05-14 21:39:27.308417 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:27.311678 INFO::Starting hierarchical adjustment
2026-05-14 21:39:27.312443 INFO::Found 2 batches.
2026-05-14 21:39:27.313006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:27.313668 INFO::Using default BPPARAM
2026-05-14 21:39:27.314226 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:27.315212 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-14 21:39:27.332897 INFO::Done
2026-05-14 21:39:27.333755 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:27.337019 INFO::ASW Batch was 0.37026979525582 prior to batch effect correction and is now -0.00856279393773122 .
2026-05-14 21:39:27.337693 INFO::ASW Label was 0.456122394795568 prior to batch effect correction and is now 0.895575620601076 .
2026-05-14 21:39:27.338539 INFO::Total function execution time is 0.0406274795532227 s and adjustment time is 0.0205752849578857 s ( 50.64 )
2026-05-14 21:39:27.339405 INFO::Formatting Data.
2026-05-14 21:39:27.34009 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:27.341078 INFO::Removing potential empty rows and columns
2026-05-14 21:39:27.342136 INFO::Found 0 missing values.
2026-05-14 21:39:27.343104 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.
2026-05-14 21:39:27.347932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:27.348554 INFO::Done
2026-05-14 21:39:27.349121 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:27.352283 INFO::Starting hierarchical adjustment
2026-05-14 21:39:27.35306 INFO::Found 2 batches.
2026-05-14 21:39:27.353637 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:27.354292 INFO::Using default BPPARAM
2026-05-14 21:39:27.354872 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:27.355862 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-14 21:39:27.373481 INFO::Done
2026-05-14 21:39:27.374293 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:27.377578 INFO::ASW Batch was 0.37026979525582 prior to batch effect correction and is now -0.00856279393773122 .
2026-05-14 21:39:27.37824 INFO::ASW Label was 0.456122394795568 prior to batch effect correction and is now 0.895575620601076 .
2026-05-14 21:39:27.379121 INFO::Total function execution time is 0.0397365093231201 s and adjustment time is 0.0205211639404297 s ( 51.64 )
2026-05-14 21:39:27.608935 INFO::Formatting Data.
2026-05-14 21:39:27.609959 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:27.61109 INFO::Removing potential empty rows and columns
2026-05-14 21:39:27.612314 INFO::Found 0 missing values.
2026-05-14 21:39:27.615865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:27.616499 INFO::Done
2026-05-14 21:39:27.617108 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:27.619627 INFO::Starting hierarchical adjustment
2026-05-14 21:39:27.620457 INFO::Found 3 batches.
2026-05-14 21:39:27.621057 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:27.62176 INFO::Using default BPPARAM
2026-05-14 21:39:27.622356 INFO::Processing subtree level 1
2026-05-14 21:39:27.730105 INFO::Adjusting the last 1 batches sequentially
2026-05-14 21:39:27.732149 INFO::Done
2026-05-14 21:39:27.732929 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:27.735862 INFO::ASW Batch was -0.101747259847698 prior to batch effect correction and is now -0.101747259847698 .
2026-05-14 21:39:27.737166 INFO::Total function execution time is 0.128343343734741 s and adjustment time is 0.111846685409546 s ( 87.15 )
2026-05-14 21:39:27.738467 INFO::Formatting Data.
2026-05-14 21:39:27.739243 INFO::Typecasting input to dataframe.
2026-05-14 21:39:27.74015 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:27.741262 INFO::Removing potential empty rows and columns
2026-05-14 21:39:27.742583 INFO::Found 0 missing values.
2026-05-14 21:39:27.746212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:27.746871 INFO::Done
2026-05-14 21:39:27.74753 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:27.750016 INFO::Starting hierarchical adjustment
2026-05-14 21:39:27.750887 INFO::Found 3 batches.
2026-05-14 21:39:27.751515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:27.752248 INFO::Using default BPPARAM
2026-05-14 21:39:27.752865 INFO::Processing subtree level 1
2026-05-14 21:39:27.85823 INFO::Adjusting the last 1 batches sequentially
2026-05-14 21:39:27.860784 INFO::Done
2026-05-14 21:39:27.861681 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:27.86475 INFO::ASW Batch was -0.101747259847698 prior to batch effect correction and is now -0.101747259847698 .
2026-05-14 21:39:27.865908 INFO::Total function execution time is 0.127442121505737 s and adjustment time is 0.110039710998535 s ( 86.34 )
2026-05-14 21:39:27.882658 INFO::Formatting Data.
2026-05-14 21:39:27.883748 INFO::Typecasting input to dataframe.
2026-05-14 21:39:27.884786 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:27.885875 INFO::Removing potential empty rows and columns
2026-05-14 21:39:27.887116 INFO::Found 0 missing values.
2026-05-14 21:39:27.89048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:27.891069 INFO::Done
2026-05-14 21:39:27.891654 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:27.893951 INFO::Starting hierarchical adjustment
2026-05-14 21:39:27.894742 INFO::Found 3 batches.
2026-05-14 21:39:27.895309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:27.896013 INFO::Using default BPPARAM
2026-05-14 21:39:27.89663 INFO::Processing subtree level 1
2026-05-14 21:39:27.998237 INFO::Adjusting the last 1 batches sequentially
2026-05-14 21:39:28.000507 INFO::Done
2026-05-14 21:39:28.001308 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:28.004478 INFO::ASW Batch was -0.0516248337947809 prior to batch effect correction and is now -0.0516248337947809 .
2026-05-14 21:39:28.005689 INFO::Total function execution time is 0.123175144195557 s and adjustment time is 0.105878353118896 s ( 85.96 )
2026-05-14 21:39:28.16397 INFO::Formatting Data.
2026-05-14 21:39:28.164919 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:28.166166 INFO::Removing potential empty rows and columns
2026-05-14 21:39:28.169181 INFO::Found 1000 missing values.
2026-05-14 21:39:28.189763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:28.19065 INFO::Done
2026-05-14 21:39:28.191308 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:28.197225 INFO::Starting hierarchical adjustment
2026-05-14 21:39:28.198251 INFO::Found 10 batches.
2026-05-14 21:39:28.198922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:28.199631 INFO::Using default BPPARAM
2026-05-14 21:39:28.200233 INFO::Processing subtree level 1
2026-05-14 21:39:28.352103 INFO::Processing subtree level 2
2026-05-14 21:39:28.501304 INFO::Adjusting the last 1 batches sequentially
2026-05-14 21:39:28.50391 INFO::Done
2026-05-14 21:39:28.504853 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:28.511915 INFO::ASW Batch was 0.47593738628345 prior to batch effect correction and is now 0.47593738628345 .
2026-05-14 21:39:28.512898 INFO::ASW Label was 0.363036175354834 prior to batch effect correction and is now 0.363036175354834 .
2026-05-14 21:39:28.514122 INFO::Total function execution time is 0.350169658660889 s and adjustment time is 0.305807113647461 s ( 87.33 )
2026-05-14 21:39:28.515242 INFO::Formatting Data.
2026-05-14 21:39:28.516116 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:28.517778 INFO::Removing potential empty rows and columns
2026-05-14 21:39:28.52142 INFO::Found 1000 missing values.
2026-05-14 21:39:28.546075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:28.547056 INFO::Done
2026-05-14 21:39:28.547775 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:28.55411 INFO::Starting hierarchical adjustment
2026-05-14 21:39:28.555126 INFO::Found 10 batches.
2026-05-14 21:39:29.596742 INFO::Set up parallel execution backend with 2 workers
2026-05-14 21:39:29.599662 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-14 21:39:30.77427 INFO::Adjusting the last 2 batches sequentially
2026-05-14 21:39:30.777458 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-14 21:39:30.793873 INFO::Done
2026-05-14 21:39:30.794621 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:30.79927 INFO::ASW Batch was 0.47593738628345 prior to batch effect correction and is now 0.47593738628345 .
2026-05-14 21:39:30.799908 INFO::ASW Label was 0.363036175354834 prior to batch effect correction and is now 0.363036175354834 .
2026-05-14 21:39:30.800682 INFO::Total function execution time is 2.28553104400635 s and adjustment time is 2.23892188072205 s ( 97.96 )
2026-05-14 21:39:30.949705 INFO::Formatting Data.
2026-05-14 21:39:30.950615 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:30.951625 INFO::Removing potential empty rows and columns
2026-05-14 21:39:30.952765 INFO::Found 0 missing values.
2026-05-14 21:39:30.956507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:30.957095 INFO::Done
2026-05-14 21:39:30.957673 INFO::Acquiring quality metrics before batch effect correction.
2026-05-14 21:39:30.960469 INFO::Starting hierarchical adjustment
2026-05-14 21:39:30.961207 INFO::Found 3 batches.
2026-05-14 21:39:30.96178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-14 21:39:30.962435 INFO::Using default BPPARAM
2026-05-14 21:39:30.963004 INFO::Processing subtree level 1
2026-05-14 21:39:31.069162 INFO::Adjusting the last 1 batches sequentially
2026-05-14 21:39:31.071061 INFO::Done
2026-05-14 21:39:31.071761 INFO::Acquiring quality metrics after batch effect correction.
2026-05-14 21:39:31.075097 INFO::ASW Batch was 0.146930294564026 prior to batch effect correction and is now -0.149101901100672 .
2026-05-14 21:39:31.075786 INFO::ASW Label was -0.180048140282382 prior to batch effect correction and is now -0.0102802221027367 .
2026-05-14 21:39:31.076749 INFO::Total function execution time is 0.127103567123413 s and adjustment time is 0.109974145889282 s ( 86.52 )
2026-05-14 21:39:31.199609 INFO::Formatting Data.
2026-05-14 21:39:31.200541 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.201521 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.202585 INFO::Found 2 missing values.
2026-05-14 21:39:31.205444 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.206019 INFO::Done
2026-05-14 21:39:31.246148 INFO::Found NA in Reference column
2026-05-14 21:39:31.257326 INFO::Require at least two references per batch.
2026-05-14 21:39:31.278419 INFO::Formatting Data.
2026-05-14 21:39:31.279217 INFO::Recognized SummarizedExperiment
2026-05-14 21:39:31.279824 INFO::Typecasting input to dataframe.
2026-05-14 21:39:31.289603 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.290833 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.294463 INFO::Found 0 missing values.
2026-05-14 21:39:31.301324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.30199 INFO::Done
2026-05-14 21:39:31.317886 INFO::Formatting Data.
2026-05-14 21:39:31.318726 INFO::Recognized SummarizedExperiment
2026-05-14 21:39:31.319301 INFO::Typecasting input to dataframe.
2026-05-14 21:39:31.337729 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.339028 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.342771 INFO::Found 0 missing values.
2026-05-14 21:39:31.353859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.354628 INFO::Done
2026-05-14 21:39:31.370247 INFO::Formatting Data.
2026-05-14 21:39:31.371076 INFO::Recognized SummarizedExperiment
2026-05-14 21:39:31.371649 INFO::Typecasting input to dataframe.
2026-05-14 21:39:31.387758 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.388909 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.390095 INFO::Found 0 missing values.
2026-05-14 21:39:31.391081 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.
2026-05-14 21:39:31.395655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.39627 INFO::Done
2026-05-14 21:39:31.406983 INFO::Formatting Data.
2026-05-14 21:39:31.407859 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.4088 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.409875 INFO::Found 0 missing values.
2026-05-14 21:39:31.412838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.413432 INFO::Done
2026-05-14 21:39:31.425343 INFO::Formatting Data.
2026-05-14 21:39:31.426186 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.427238 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.428312 INFO::Found 0 missing values.
2026-05-14 21:39:31.431357 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.43196 INFO::Done
2026-05-14 21:39:31.463165 INFO::Formatting Data.
2026-05-14 21:39:31.46409 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.465242 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.466571 INFO::Found 1 missing values.
2026-05-14 21:39:31.469455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.470057 INFO::Done
2026-05-14 21:39:31.490836 INFO::Formatting Data.
2026-05-14 21:39:31.491728 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.492728 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.493837 INFO::Found 2 missing values.
2026-05-14 21:39:31.494881 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.
2026-05-14 21:39:31.497433 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.498099 INFO::Done
2026-05-14 21:39:31.509709 INFO::Formatting Data.
2026-05-14 21:39:31.510696 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.511747 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.512823 INFO::Found 2 missing values.
2026-05-14 21:39:31.514678 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.515287 INFO::Done
2026-05-14 21:39:31.527952 INFO::Formatting Data.
2026-05-14 21:39:31.52892 INFO::Typecasting input to dataframe.
2026-05-14 21:39:31.529863 INFO::Replacing NaNs with NAs.
2026-05-14 21:39:31.530832 INFO::Removing potential empty rows and columns
2026-05-14 21:39:31.532003 INFO::Found 0 missing values.
2026-05-14 21:39:31.535169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-14 21:39:31.535777 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.380 3.327 21.430
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.468 | 1.368 | 17.446 | |
| compute_asw | 0.024 | 0.000 | 0.023 | |
| count_existing | 0.014 | 0.000 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.010 | 0.001 | 0.011 | |