Yannis Schumann
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_21 |
| git_last_commit: dedce04 |
| git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:38 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.4.0.tar.gz |
| StartedAt: 2025-09-24 21:36:15 -0400 (Wed, 24 Sep 2025) |
| EndedAt: 2025-09-24 21:37:46 -0400 (Wed, 24 Sep 2025) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.4.0’
* 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 25.446 1.503 18.797
* 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-3.21-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.4.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-09-24 21:37:09.251195 INFO::Formatting Data.
2025-09-24 21:37:09.252665 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:09.264819 INFO::Removing potential empty rows and columns
2025-09-24 21:37:09.529684 INFO::Found 0 missing values.
2025-09-24 21:37:09.533527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:09.534283 INFO::Done
2025-09-24 21:37:09.534908 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:09.547485 INFO::Starting hierarchical adjustment
2025-09-24 21:37:09.548516 INFO::Found 3 batches.
2025-09-24 21:37:09.549148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:09.550467 INFO::Using default BPPARAM
2025-09-24 21:37:09.551071 INFO::Processing subtree level 1
2025-09-24 21:37:09.684407 INFO::Adjusting the last 1 batches sequentially
2025-09-24 21:37:09.686735 INFO::Done
2025-09-24 21:37:09.687531 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:09.690806 INFO::ASW Batch was -0.10817072530747 prior to batch effect correction and is now -0.10817072530747 .
2025-09-24 21:37:09.692162 INFO::Total function execution time is 0.441553831100464 s and adjustment time is 0.138390302658081 s ( 31.34 )
2025-09-24 21:37:09.707757 INFO::Formatting Data.
2025-09-24 21:37:09.708729 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:09.709731 INFO::Removing potential empty rows and columns
2025-09-24 21:37:09.710951 INFO::Found 0 missing values.
2025-09-24 21:37:09.712021 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.
2025-09-24 21:37:09.723431 INFO::Formatting Data.
2025-09-24 21:37:09.72423 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:09.725227 INFO::Removing potential empty rows and columns
2025-09-24 21:37:09.726326 INFO::Found 0 missing values.
2025-09-24 21:37:09.727285 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.
2025-09-24 21:37:09.743887 INFO::Formatting Data.
2025-09-24 21:37:09.744753 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:09.745686 INFO::Removing potential empty rows and columns
2025-09-24 21:37:09.746953 INFO::Found 0 missing values.
2025-09-24 21:37:09.748116 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.
2025-09-24 21:37:09.754062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:09.754791 INFO::Done
2025-09-24 21:37:09.755796 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:09.758452 INFO::Starting hierarchical adjustment
2025-09-24 21:37:09.759346 INFO::Found 2 batches.
2025-09-24 21:37:09.759947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:09.760718 INFO::Using default BPPARAM
2025-09-24 21:37:09.761303 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:09.762367 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-24 21:37:09.787889 INFO::Done
2025-09-24 21:37:09.78876 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:09.791182 INFO::ASW Batch was 0.0691385831106906 prior to batch effect correction and is now -0.106707174444381 .
2025-09-24 21:37:09.792119 INFO::Total function execution time is 0.0483496189117432 s and adjustment time is 0.0287017822265625 s ( 59.36 )
2025-09-24 21:37:09.795474 INFO::Formatting Data.
2025-09-24 21:37:09.796215 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:09.805969 INFO::Formatting Data.
2025-09-24 21:37:09.807079 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:09.80811 INFO::Removing potential empty rows and columns
2025-09-24 21:37:09.844083 INFO::Found 0 missing values.
2025-09-24 21:37:09.847394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:09.848119 INFO::Done
2025-09-24 21:37:09.84868 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:09.850888 INFO::Starting hierarchical adjustment
2025-09-24 21:37:09.851644 INFO::Found 2 batches.
2025-09-24 21:37:09.85219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:09.852832 INFO::Using default BPPARAM
2025-09-24 21:37:09.853347 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:09.854319 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-24 21:37:09.869303 INFO::Done
2025-09-24 21:37:09.870041 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:09.872124 INFO::ASW Batch was -0.0430311393997026 prior to batch effect correction and is now -0.109946483580084 .
2025-09-24 21:37:09.872962 INFO::Total function execution time is 0.0670630931854248 s and adjustment time is 0.0178296566009521 s ( 26.59 )
2025-09-24 21:37:09.873976 INFO::Formatting Data.
2025-09-24 21:37:09.874543 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:09.875388 INFO::Removing potential empty rows and columns
2025-09-24 21:37:09.876371 INFO::Found 0 missing values.
2025-09-24 21:37:09.879081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:09.879613 INFO::Done
2025-09-24 21:37:09.880116 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:09.882088 INFO::Starting hierarchical adjustment
2025-09-24 21:37:09.882798 INFO::Found 2 batches.
2025-09-24 21:37:09.883304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:09.883918 INFO::Using default BPPARAM
2025-09-24 21:37:09.884423 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:09.885324 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-24 21:37:09.902271 INFO::Done
2025-09-24 21:37:09.903344 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:09.905797 INFO::ASW Batch was -0.0430311393997026 prior to batch effect correction and is now -0.109946483580084 .
2025-09-24 21:37:09.906699 INFO::Total function execution time is 0.0326802730560303 s and adjustment time is 0.019507884979248 s ( 59.69 )
2025-09-24 21:37:13.444323 INFO::Formatting Data.
2025-09-24 21:37:13.445102 INFO::Recognized SummarizedExperiment
2025-09-24 21:37:13.445594 INFO::Typecasting input to dataframe.
2025-09-24 21:37:13.476449 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:13.477782 INFO::Removing potential empty rows and columns
2025-09-24 21:37:13.481276 INFO::Found 0 missing values.
2025-09-24 21:37:13.488598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:13.489395 INFO::Done
2025-09-24 21:37:13.489985 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:13.493864 INFO::Starting hierarchical adjustment
2025-09-24 21:37:13.494644 INFO::Found 2 batches.
2025-09-24 21:37:13.495242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:13.496368 INFO::Using default BPPARAM
2025-09-24 21:37:13.496927 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:13.497937 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-24 21:37:13.556108 INFO::Done
2025-09-24 21:37:13.55685 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:13.560473 INFO::ASW Batch was 0.0128085413097618 prior to batch effect correction and is now -0.106227987944366 .
2025-09-24 21:37:13.561355 INFO::Total function execution time is 0.117300271987915 s and adjustment time is 0.0616190433502197 s ( 52.53 )
2025-09-24 21:37:13.580163 INFO::Formatting Data.
2025-09-24 21:37:13.580908 INFO::Recognized SummarizedExperiment
2025-09-24 21:37:13.581451 INFO::Typecasting input to dataframe.
2025-09-24 21:37:13.590508 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:13.591668 INFO::Removing potential empty rows and columns
2025-09-24 21:37:13.595468 INFO::Found 0 missing values.
2025-09-24 21:37:13.602565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:13.603214 INFO::Done
2025-09-24 21:37:13.60378 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:13.607329 INFO::Starting hierarchical adjustment
2025-09-24 21:37:13.608066 INFO::Found 2 batches.
2025-09-24 21:37:13.60859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:13.609205 INFO::Using default BPPARAM
2025-09-24 21:37:13.60974 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:13.610723 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-24 21:37:13.635395 INFO::Done
2025-09-24 21:37:13.636119 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:13.639656 INFO::ASW Batch was 0.00982374647067996 prior to batch effect correction and is now 0.00982374647067996 .
2025-09-24 21:37:13.640612 INFO::Total function execution time is 0.0604298114776611 s and adjustment time is 0.0274560451507568 s ( 45.43 )
2025-09-24 21:37:13.658447 INFO::Formatting Data.
2025-09-24 21:37:13.659281 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:13.66018 INFO::Removing potential empty rows and columns
2025-09-24 21:37:13.661202 INFO::Found 0 missing values.
2025-09-24 21:37:13.664106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:13.664666 INFO::Done
2025-09-24 21:37:13.665179 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:13.667202 INFO::Starting hierarchical adjustment
2025-09-24 21:37:13.667905 INFO::Found 3 batches.
2025-09-24 21:37:13.668455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:13.669074 INFO::Using default BPPARAM
2025-09-24 21:37:13.669599 INFO::Processing subtree level 1
2025-09-24 21:37:13.922059 INFO::Adjusting the last 1 batches sequentially
2025-09-24 21:37:13.923953 INFO::Done
2025-09-24 21:37:13.924647 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:13.927225 INFO::ASW Batch was 0.00579491193285102 prior to batch effect correction and is now -0.147001404514218 .
2025-09-24 21:37:13.928186 INFO::Total function execution time is 0.26975154876709 s and adjustment time is 0.25616717338562 s ( 94.96 )
2025-09-24 21:37:14.039927 INFO::Skipping initial DF formatting
2025-09-24 21:37:14.040817 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:14.044939 INFO::Starting hierarchical adjustment
2025-09-24 21:37:14.045694 INFO::Found 5 batches.
2025-09-24 21:37:14.04623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:14.046881 INFO::Using default BPPARAM
2025-09-24 21:37:14.047395 INFO::Processing subtree level 1
2025-09-24 21:37:14.243948 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:14.24615 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-24 21:37:14.271095 INFO::Done
2025-09-24 21:37:14.272069 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:14.277372 INFO::ASW Batch was 0.497609356129676 prior to batch effect correction and is now 0.497609356129676 .
2025-09-24 21:37:14.278187 INFO::ASW Label was 0.402882582396909 prior to batch effect correction and is now 0.402882582396909 .
2025-09-24 21:37:14.279296 INFO::Total function execution time is 0.23943829536438 s and adjustment time is 0.225448131561279 s ( 94.16 )
2025-09-24 21:37:14.300302 INFO::Formatting Data.
2025-09-24 21:37:14.301368 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:14.302561 INFO::Removing potential empty rows and columns
2025-09-24 21:37:14.303916 INFO::Found 0 missing values.
2025-09-24 21:37:14.308882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:14.309532 INFO::Done
2025-09-24 21:37:14.310241 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:14.31433 INFO::Starting hierarchical adjustment
2025-09-24 21:37:14.315292 INFO::Found 5 batches.
2025-09-24 21:37:14.315982 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:14.316739 INFO::Using default BPPARAM
2025-09-24 21:37:14.317402 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.
2025-09-24 21:37:14.491616 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:14.493608 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-24 21:37:14.510821 INFO::Done
2025-09-24 21:37:14.511577 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:14.515131 INFO::ASW Batch was 0.183319805595699 prior to batch effect correction and is now -0.074464226289071 .
2025-09-24 21:37:14.5158 INFO::ASW Label was 0.491678248066279 prior to batch effect correction and is now 0.909375498884889 .
2025-09-24 21:37:14.51671 INFO::Total function execution time is 0.216524600982666 s and adjustment time is 0.195733547210693 s ( 90.4 )
2025-09-24 21:37:14.517678 INFO::Formatting Data.
2025-09-24 21:37:14.518341 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:14.519292 INFO::Removing potential empty rows and columns
2025-09-24 21:37:14.520348 INFO::Found 0 missing values.
2025-09-24 21:37:14.524495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:14.525082 INFO::Done
2025-09-24 21:37:14.525653 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:14.528678 INFO::Starting hierarchical adjustment
2025-09-24 21:37:14.529443 INFO::Found 5 batches.
2025-09-24 21:37:14.530004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:14.530672 INFO::Using default BPPARAM
2025-09-24 21:37:14.531228 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.
2025-09-24 21:37:14.666104 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:14.667981 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-24 21:37:14.68475 INFO::Done
2025-09-24 21:37:14.685596 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:14.689125 INFO::ASW Batch was 0.183319805595699 prior to batch effect correction and is now -0.074464226289071 .
2025-09-24 21:37:14.689778 INFO::ASW Label was 0.491678248066279 prior to batch effect correction and is now 0.909375498884889 .
2025-09-24 21:37:14.690657 INFO::Total function execution time is 0.173004865646362 s and adjustment time is 0.155401706695557 s ( 89.83 )
2025-09-24 21:37:14.705032 INFO::Formatting Data.
2025-09-24 21:37:14.705902 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:14.706912 INFO::Removing potential empty rows and columns
2025-09-24 21:37:14.708003 INFO::Found 0 missing values.
2025-09-24 21:37:14.712392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:14.713003 INFO::Done
2025-09-24 21:37:14.713552 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:14.716924 INFO::Starting hierarchical adjustment
2025-09-24 21:37:14.717754 INFO::Found 5 batches.
2025-09-24 21:37:14.718317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:14.719094 INFO::Using default BPPARAM
2025-09-24 21:37:14.71969 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.
2025-09-24 21:37:14.857536 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:14.859498 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-24 21:37:14.877452 INFO::Done
2025-09-24 21:37:14.878343 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:14.882264 INFO::ASW Batch was 0.494621337254552 prior to batch effect correction and is now 0.0362819154487781 .
2025-09-24 21:37:14.88309 INFO::ASW Label was 0.368362750163057 prior to batch effect correction and is now 0.706279060266151 .
2025-09-24 21:37:14.884054 INFO::Total function execution time is 0.179120779037476 s and adjustment time is 0.159800052642822 s ( 89.21 )
2025-09-24 21:37:14.885026 INFO::Formatting Data.
2025-09-24 21:37:14.885748 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:14.886774 INFO::Removing potential empty rows and columns
2025-09-24 21:37:14.887875 INFO::Found 0 missing values.
2025-09-24 21:37:14.892352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:14.892998 INFO::Done
2025-09-24 21:37:14.893575 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:14.897141 INFO::Starting hierarchical adjustment
2025-09-24 21:37:14.897943 INFO::Found 5 batches.
2025-09-24 21:37:14.898508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:14.899212 INFO::Using default BPPARAM
2025-09-24 21:37:14.899796 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.
2025-09-24 21:37:15.035518 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:15.037147 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-24 21:37:15.051993 INFO::Done
2025-09-24 21:37:15.052655 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.05579 INFO::ASW Batch was 0.494621337254552 prior to batch effect correction and is now 0.0362819154487781 .
2025-09-24 21:37:15.056383 INFO::ASW Label was 0.368362750163057 prior to batch effect correction and is now 0.706279060266151 .
2025-09-24 21:37:15.057189 INFO::Total function execution time is 0.172202110290527 s and adjustment time is 0.154218196868896 s ( 89.56 )
2025-09-24 21:37:15.070139 INFO::Formatting Data.
2025-09-24 21:37:15.070922 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:15.071873 INFO::Removing potential empty rows and columns
2025-09-24 21:37:15.072906 INFO::Found 0 missing values.
2025-09-24 21:37:15.07551 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:15.076055 INFO::Done
2025-09-24 21:37:15.076587 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:15.079442 INFO::Starting hierarchical adjustment
2025-09-24 21:37:15.080148 INFO::Found 2 batches.
2025-09-24 21:37:15.080679 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:15.081287 INFO::Using default BPPARAM
2025-09-24 21:37:15.081812 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:15.082717 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-24 21:37:15.096827 INFO::Done
2025-09-24 21:37:15.097439 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.100242 INFO::ASW Batch was 0.207536716880885 prior to batch effect correction and is now 0.0698525550681941 .
2025-09-24 21:37:15.100819 INFO::ASW Label was 0.814763384571451 prior to batch effect correction and is now 0.877220050960276 .
2025-09-24 21:37:15.101567 INFO::Total function execution time is 0.0315024852752686 s and adjustment time is 0.016810417175293 s ( 53.36 )
2025-09-24 21:37:15.102368 INFO::Formatting Data.
2025-09-24 21:37:15.102987 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:15.103837 INFO::Removing potential empty rows and columns
2025-09-24 21:37:15.10486 INFO::Found 0 missing values.
2025-09-24 21:37:15.107449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:15.107988 INFO::Done
2025-09-24 21:37:15.108494 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:15.111351 INFO::Starting hierarchical adjustment
2025-09-24 21:37:15.112054 INFO::Found 2 batches.
2025-09-24 21:37:15.112576 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:15.113181 INFO::Using default BPPARAM
2025-09-24 21:37:15.113699 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:15.114576 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-24 21:37:15.129015 INFO::Done
2025-09-24 21:37:15.12966 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.132489 INFO::ASW Batch was 0.207536716880885 prior to batch effect correction and is now 0.0698525550681941 .
2025-09-24 21:37:15.133069 INFO::ASW Label was 0.814763384571451 prior to batch effect correction and is now 0.877220050960276 .
2025-09-24 21:37:15.133834 INFO::Total function execution time is 0.0314826965332031 s and adjustment time is 0.0170915126800537 s ( 54.29 )
2025-09-24 21:37:15.144504 INFO::Formatting Data.
2025-09-24 21:37:15.145257 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:15.146117 INFO::Removing potential empty rows and columns
2025-09-24 21:37:15.14701 INFO::Found 0 missing values.
2025-09-24 21:37:15.149038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:15.149568 INFO::Done
2025-09-24 21:37:15.150091 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:15.151982 INFO::Starting hierarchical adjustment
2025-09-24 21:37:15.152685 INFO::Found 2 batches.
2025-09-24 21:37:15.153208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:15.153821 INFO::Using default BPPARAM
2025-09-24 21:37:15.154352 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:15.155218 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-24 21:37:15.187589 INFO::Done
2025-09-24 21:37:15.188359 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.190327 INFO::ASW Batch was -0.0691616643636134 prior to batch effect correction and is now -0.113306878807016 .
2025-09-24 21:37:15.191141 INFO::Total function execution time is 0.0466878414154053 s and adjustment time is 0.0350127220153809 s ( 74.99 )
2025-09-24 21:37:15.202487 INFO::Formatting Data.
2025-09-24 21:37:15.203238 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:15.204144 INFO::Removing potential empty rows and columns
2025-09-24 21:37:15.205102 INFO::Found 0 missing values.
2025-09-24 21:37:15.206184 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.
2025-09-24 21:37:15.210535 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:15.211116 INFO::Done
2025-09-24 21:37:15.211693 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:15.214592 INFO::Starting hierarchical adjustment
2025-09-24 21:37:15.215277 INFO::Found 2 batches.
2025-09-24 21:37:15.215799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:15.216384 INFO::Using default BPPARAM
2025-09-24 21:37:15.216912 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:15.217837 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-24 21:37:15.233407 INFO::Done
2025-09-24 21:37:15.234096 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.236984 INFO::ASW Batch was 0.602546082924184 prior to batch effect correction and is now -0.0291222567142457 .
2025-09-24 21:37:15.237576 INFO::ASW Label was 0.465791851946127 prior to batch effect correction and is now 0.933882786769822 .
2025-09-24 21:37:15.238348 INFO::Total function execution time is 0.0359396934509277 s and adjustment time is 0.0182509422302246 s ( 50.78 )
2025-09-24 21:37:15.239181 INFO::Formatting Data.
2025-09-24 21:37:15.239851 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:15.240757 INFO::Removing potential empty rows and columns
2025-09-24 21:37:15.241705 INFO::Found 0 missing values.
2025-09-24 21:37:15.242608 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.
2025-09-24 21:37:15.246963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:15.247508 INFO::Done
2025-09-24 21:37:15.248052 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:15.250855 INFO::Starting hierarchical adjustment
2025-09-24 21:37:15.251547 INFO::Found 2 batches.
2025-09-24 21:37:15.252098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:15.252711 INFO::Using default BPPARAM
2025-09-24 21:37:15.253235 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:15.254146 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-24 21:37:15.270274 INFO::Done
2025-09-24 21:37:15.270965 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.273875 INFO::ASW Batch was 0.602546082924184 prior to batch effect correction and is now -0.0291222567142457 .
2025-09-24 21:37:15.274455 INFO::ASW Label was 0.465791851946127 prior to batch effect correction and is now 0.933882786769822 .
2025-09-24 21:37:15.275291 INFO::Total function execution time is 0.0361223220825195 s and adjustment time is 0.0188503265380859 s ( 52.18 )
2025-09-24 21:37:15.477608 INFO::Formatting Data.
2025-09-24 21:37:15.478427 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:15.47936 INFO::Removing potential empty rows and columns
2025-09-24 21:37:15.480404 INFO::Found 0 missing values.
2025-09-24 21:37:15.483434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:15.484012 INFO::Done
2025-09-24 21:37:15.484537 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:15.486666 INFO::Starting hierarchical adjustment
2025-09-24 21:37:15.487363 INFO::Found 3 batches.
2025-09-24 21:37:15.487905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:15.488508 INFO::Using default BPPARAM
2025-09-24 21:37:15.48907 INFO::Processing subtree level 1
2025-09-24 21:37:15.587997 INFO::Adjusting the last 1 batches sequentially
2025-09-24 21:37:15.591151 INFO::Done
2025-09-24 21:37:15.59213 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.594764 INFO::ASW Batch was -0.00439157027732084 prior to batch effect correction and is now -0.00439157027732084 .
2025-09-24 21:37:15.595798 INFO::Total function execution time is 0.118192911148071 s and adjustment time is 0.103821516036987 s ( 87.84 )
2025-09-24 21:37:15.596952 INFO::Formatting Data.
2025-09-24 21:37:15.597655 INFO::Typecasting input to dataframe.
2025-09-24 21:37:15.598449 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:15.599436 INFO::Removing potential empty rows and columns
2025-09-24 21:37:15.600595 INFO::Found 0 missing values.
2025-09-24 21:37:15.603771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:15.604338 INFO::Done
2025-09-24 21:37:15.604911 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:15.607052 INFO::Starting hierarchical adjustment
2025-09-24 21:37:15.607813 INFO::Found 3 batches.
2025-09-24 21:37:15.608371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:15.609123 INFO::Using default BPPARAM
2025-09-24 21:37:15.609718 INFO::Processing subtree level 1
2025-09-24 21:37:15.70335 INFO::Adjusting the last 1 batches sequentially
2025-09-24 21:37:15.705425 INFO::Done
2025-09-24 21:37:15.706287 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.709233 INFO::ASW Batch was -0.00439157027732084 prior to batch effect correction and is now -0.00439157027732084 .
2025-09-24 21:37:15.71036 INFO::Total function execution time is 0.113337278366089 s and adjustment time is 0.0977349281311035 s ( 86.23 )
2025-09-24 21:37:15.725057 INFO::Formatting Data.
2025-09-24 21:37:15.726107 INFO::Typecasting input to dataframe.
2025-09-24 21:37:15.727109 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:15.728149 INFO::Removing potential empty rows and columns
2025-09-24 21:37:15.729326 INFO::Found 0 missing values.
2025-09-24 21:37:15.732593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:15.733179 INFO::Done
2025-09-24 21:37:15.733717 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:15.736086 INFO::Starting hierarchical adjustment
2025-09-24 21:37:15.736827 INFO::Found 3 batches.
2025-09-24 21:37:15.737399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:15.738059 INFO::Using default BPPARAM
2025-09-24 21:37:15.738597 INFO::Processing subtree level 1
2025-09-24 21:37:15.836512 INFO::Adjusting the last 1 batches sequentially
2025-09-24 21:37:15.838535 INFO::Done
2025-09-24 21:37:15.839225 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:15.841832 INFO::ASW Batch was -0.0248293210831657 prior to batch effect correction and is now -0.0248293210831657 .
2025-09-24 21:37:15.842864 INFO::Total function execution time is 0.117968082427979 s and adjustment time is 0.101861953735352 s ( 86.35 )
2025-09-24 21:37:16.007296 INFO::Formatting Data.
2025-09-24 21:37:16.008279 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:16.009552 INFO::Removing potential empty rows and columns
2025-09-24 21:37:16.012514 INFO::Found 1000 missing values.
2025-09-24 21:37:16.031947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:16.032763 INFO::Done
2025-09-24 21:37:16.033361 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:16.038958 INFO::Starting hierarchical adjustment
2025-09-24 21:37:16.039797 INFO::Found 10 batches.
2025-09-24 21:37:16.040362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:16.04102 INFO::Using default BPPARAM
2025-09-24 21:37:16.041596 INFO::Processing subtree level 1
2025-09-24 21:37:16.214689 INFO::Processing subtree level 2
2025-09-24 21:37:16.361011 INFO::Adjusting the last 1 batches sequentially
2025-09-24 21:37:16.363425 INFO::Done
2025-09-24 21:37:16.364267 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:16.371172 INFO::ASW Batch was 0.52604122758944 prior to batch effect correction and is now 0.52604122758944 .
2025-09-24 21:37:16.37204 INFO::ASW Label was 0.299177197261522 prior to batch effect correction and is now 0.299177197261522 .
2025-09-24 21:37:16.373235 INFO::Total function execution time is 0.36601448059082 s and adjustment time is 0.323759317398071 s ( 88.46 )
2025-09-24 21:37:16.374343 INFO::Formatting Data.
2025-09-24 21:37:16.375202 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:16.376684 INFO::Removing potential empty rows and columns
2025-09-24 21:37:16.380268 INFO::Found 1000 missing values.
2025-09-24 21:37:16.404406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:16.405349 INFO::Done
2025-09-24 21:37:16.40606 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:16.412141 INFO::Starting hierarchical adjustment
2025-09-24 21:37:16.413016 INFO::Found 10 batches.
2025-09-24 21:37:17.568804 INFO::Set up parallel execution backend with 2 workers
2025-09-24 21:37:17.572906 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-24 21:37:18.671987 INFO::Adjusting the last 2 batches sequentially
2025-09-24 21:37:18.67386 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-24 21:37:18.689703 INFO::Done
2025-09-24 21:37:18.69036 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:18.69471 INFO::ASW Batch was 0.52604122758944 prior to batch effect correction and is now 0.52604122758944 .
2025-09-24 21:37:18.695236 INFO::ASW Label was 0.299177197261522 prior to batch effect correction and is now 0.299177197261522 .
2025-09-24 21:37:18.695976 INFO::Total function execution time is 2.32172131538391 s and adjustment time is 2.27683544158936 s ( 98.07 )
2025-09-24 21:37:18.848202 INFO::Formatting Data.
2025-09-24 21:37:18.849016 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:18.849976 INFO::Removing potential empty rows and columns
2025-09-24 21:37:18.851091 INFO::Found 0 missing values.
2025-09-24 21:37:18.854671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:18.855217 INFO::Done
2025-09-24 21:37:18.855803 INFO::Acquiring quality metrics before batch effect correction.
2025-09-24 21:37:18.858555 INFO::Starting hierarchical adjustment
2025-09-24 21:37:18.859281 INFO::Found 3 batches.
2025-09-24 21:37:18.859823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-24 21:37:18.86044 INFO::Using default BPPARAM
2025-09-24 21:37:18.860993 INFO::Processing subtree level 1
2025-09-24 21:37:18.969226 INFO::Adjusting the last 1 batches sequentially
2025-09-24 21:37:18.971316 INFO::Done
2025-09-24 21:37:18.972076 INFO::Acquiring quality metrics after batch effect correction.
2025-09-24 21:37:18.975605 INFO::ASW Batch was 0.206165255027044 prior to batch effect correction and is now -0.159615537238201 .
2025-09-24 21:37:18.976301 INFO::ASW Label was -0.143448467127604 prior to batch effect correction and is now 0.101262191306379 .
2025-09-24 21:37:18.977312 INFO::Total function execution time is 0.129131317138672 s and adjustment time is 0.112130880355835 s ( 86.83 )
2025-09-24 21:37:19.090353 INFO::Formatting Data.
2025-09-24 21:37:19.09125 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.092149 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.093179 INFO::Found 2 missing values.
2025-09-24 21:37:19.095939 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.096462 INFO::Done
2025-09-24 21:37:19.130416 INFO::Found NA in Reference column
2025-09-24 21:37:19.14011 INFO::Require at least two references per batch.
2025-09-24 21:37:19.161215 INFO::Formatting Data.
2025-09-24 21:37:19.162 INFO::Recognized SummarizedExperiment
2025-09-24 21:37:19.162562 INFO::Typecasting input to dataframe.
2025-09-24 21:37:19.172581 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.173798 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.17755 INFO::Found 0 missing values.
2025-09-24 21:37:19.18467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.1853 INFO::Done
2025-09-24 21:37:19.201363 INFO::Formatting Data.
2025-09-24 21:37:19.202124 INFO::Recognized SummarizedExperiment
2025-09-24 21:37:19.202688 INFO::Typecasting input to dataframe.
2025-09-24 21:37:19.220715 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.221984 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.225686 INFO::Found 0 missing values.
2025-09-24 21:37:19.237025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.237756 INFO::Done
2025-09-24 21:37:19.253706 INFO::Formatting Data.
2025-09-24 21:37:19.254469 INFO::Recognized SummarizedExperiment
2025-09-24 21:37:19.255044 INFO::Typecasting input to dataframe.
2025-09-24 21:37:19.271838 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.272889 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.273996 INFO::Found 0 missing values.
2025-09-24 21:37:19.274951 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.
2025-09-24 21:37:19.279525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.280118 INFO::Done
2025-09-24 21:37:19.290088 INFO::Formatting Data.
2025-09-24 21:37:19.290954 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.291865 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.292896 INFO::Found 0 missing values.
2025-09-24 21:37:19.295855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.296402 INFO::Done
2025-09-24 21:37:19.307536 INFO::Formatting Data.
2025-09-24 21:37:19.308336 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.309233 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.310269 INFO::Found 0 missing values.
2025-09-24 21:37:19.313273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.313874 INFO::Done
2025-09-24 21:37:19.342827 INFO::Formatting Data.
2025-09-24 21:37:19.343655 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.344732 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.34601 INFO::Found 1 missing values.
2025-09-24 21:37:19.34865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.349177 INFO::Done
2025-09-24 21:37:19.367583 INFO::Formatting Data.
2025-09-24 21:37:19.368441 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.369379 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.370401 INFO::Found 2 missing values.
2025-09-24 21:37:19.371306 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.
2025-09-24 21:37:19.373557 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.374133 INFO::Done
2025-09-24 21:37:19.383505 INFO::Formatting Data.
2025-09-24 21:37:19.384229 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.385089 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.386012 INFO::Found 2 missing values.
2025-09-24 21:37:19.387585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.388107 INFO::Done
2025-09-24 21:37:19.398089 INFO::Formatting Data.
2025-09-24 21:37:19.398849 INFO::Typecasting input to dataframe.
2025-09-24 21:37:19.399685 INFO::Replacing NaNs with NAs.
2025-09-24 21:37:19.400533 INFO::Removing potential empty rows and columns
2025-09-24 21:37:19.401492 INFO::Found 0 missing values.
2025-09-24 21:37:19.40427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-24 21:37:19.404785 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.363 4.475 22.262
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.446 | 1.503 | 18.797 | |
| compute_asw | 0.028 | 0.000 | 0.028 | |
| count_existing | 0.015 | 0.001 | 0.016 | |
| generate_data_covariables | 0.012 | 0.002 | 0.014 | |
| generate_dataset | 0.012 | 0.001 | 0.013 | |