Yannis Schumann
| Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 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 2025-08-18 11:41 -0400 (Mon, 18 Aug 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" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.4.0.tar.gz |
| StartedAt: 2025-08-14 23:44:09 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-14 23:46:26 -0400 (Thu, 14 Aug 2025) |
| EllapsedTime: 136.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 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 9.19 0.62 19.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2025-08-14 23:45:14.945938 INFO::Formatting Data.
2025-08-14 23:45:14.948705 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:14.962474 INFO::Removing potential empty rows and columns
2025-08-14 23:45:15.213463 INFO::Found 0 missing values.
2025-08-14 23:45:15.21679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:15.217724 INFO::Done
2025-08-14 23:45:15.21891 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:15.23447 INFO::Starting hierarchical adjustment
2025-08-14 23:45:15.235665 INFO::Found 3 batches.
2025-08-14 23:45:15.236447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:15.237774 INFO::Using default BPPARAM
2025-08-14 23:45:15.238534 INFO::Processing subtree level 1
2025-08-14 23:45:17.828253 INFO::Adjusting the last 1 batches sequentially
2025-08-14 23:45:17.830514 INFO::Done
2025-08-14 23:45:17.831859 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:17.83524 INFO::ASW Batch was 0.00545127765602478 prior to batch effect correction and is now 0.00545127765602478 .
2025-08-14 23:45:17.83705 INFO::Total function execution time is 2.89169979095459 s and adjustment time is 2.59502100944519 s ( 89.74 )
2025-08-14 23:45:17.856408 INFO::Formatting Data.
2025-08-14 23:45:17.857496 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:17.858654 INFO::Removing potential empty rows and columns
2025-08-14 23:45:17.859866 INFO::Found 0 missing values.
2025-08-14 23:45:17.860955 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.
2025-08-14 23:45:17.869631 INFO::Formatting Data.
2025-08-14 23:45:17.870622 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:17.871924 INFO::Removing potential empty rows and columns
2025-08-14 23:45:17.87336 INFO::Found 0 missing values.
2025-08-14 23:45:17.874968 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.
2025-08-14 23:45:17.899975 INFO::Formatting Data.
2025-08-14 23:45:17.901679 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:17.903643 INFO::Removing potential empty rows and columns
2025-08-14 23:45:17.905756 INFO::Found 0 missing values.
2025-08-14 23:45:17.907761 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.
2025-08-14 23:45:17.914671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:17.915624 INFO::Done
2025-08-14 23:45:17.916396 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:17.918651 INFO::Starting hierarchical adjustment
2025-08-14 23:45:17.919741 INFO::Found 2 batches.
2025-08-14 23:45:17.920654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:17.921535 INFO::Using default BPPARAM
2025-08-14 23:45:17.922276 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:17.923937 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-14 23:45:17.946043 INFO::Done
2025-08-14 23:45:17.947477 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:17.950863 INFO::ASW Batch was -0.0390444973832397 prior to batch effect correction and is now -0.110320512603537 .
2025-08-14 23:45:17.952417 INFO::Total function execution time is 0.0525758266448975 s and adjustment time is 0.026439905166626 s ( 50.29 )
2025-08-14 23:45:17.9561 INFO::Formatting Data.
2025-08-14 23:45:17.957263 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:17.965253 INFO::Formatting Data.
2025-08-14 23:45:17.966208 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:17.967281 INFO::Removing potential empty rows and columns
2025-08-14 23:45:17.968433 INFO::Found 0 missing values.
2025-08-14 23:45:17.971027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:17.971763 INFO::Done
2025-08-14 23:45:17.972449 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:17.974536 INFO::Starting hierarchical adjustment
2025-08-14 23:45:17.975414 INFO::Found 2 batches.
2025-08-14 23:45:17.976109 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:17.976984 INFO::Using default BPPARAM
2025-08-14 23:45:17.977975 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:17.979088 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-14 23:45:17.996729 INFO::Done
2025-08-14 23:45:17.998133 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:18.001508 INFO::ASW Batch was 0.0384660873514397 prior to batch effect correction and is now -0.116161880115257 .
2025-08-14 23:45:18.003106 INFO::Total function execution time is 0.0378189086914062 s and adjustment time is 0.0213608741760254 s ( 56.48 )
2025-08-14 23:45:18.005197 INFO::Formatting Data.
2025-08-14 23:45:18.006554 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:18.008303 INFO::Removing potential empty rows and columns
2025-08-14 23:45:18.010168 INFO::Found 0 missing values.
2025-08-14 23:45:18.014472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:18.015766 INFO::Done
2025-08-14 23:45:18.01697 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:18.020212 INFO::Starting hierarchical adjustment
2025-08-14 23:45:18.02164 INFO::Found 2 batches.
2025-08-14 23:45:18.022794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:18.024037 INFO::Using default BPPARAM
2025-08-14 23:45:18.025158 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:18.026866 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-14 23:45:18.045453 INFO::Done
2025-08-14 23:45:18.046332 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:18.048638 INFO::ASW Batch was 0.0384660873514397 prior to batch effect correction and is now -0.116161880115257 .
2025-08-14 23:45:18.049613 INFO::Total function execution time is 0.0445270538330078 s and adjustment time is 0.0240468978881836 s ( 54.01 )
2025-08-14 23:45:20.813624 INFO::Formatting Data.
2025-08-14 23:45:20.814575 INFO::Recognized SummarizedExperiment
2025-08-14 23:45:20.815302 INFO::Typecasting input to dataframe.
2025-08-14 23:45:20.851312 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:20.853625 INFO::Removing potential empty rows and columns
2025-08-14 23:45:20.859089 INFO::Found 0 missing values.
2025-08-14 23:45:20.869593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:20.871129 INFO::Done
2025-08-14 23:45:20.872564 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:20.879243 INFO::Starting hierarchical adjustment
2025-08-14 23:45:20.880911 INFO::Found 2 batches.
2025-08-14 23:45:20.882253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:20.884365 INFO::Using default BPPARAM
2025-08-14 23:45:20.885645 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:20.887681 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-14 23:45:21.775774 INFO::Done
2025-08-14 23:45:21.777156 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:21.782381 INFO::ASW Batch was 0.0065344854472133 prior to batch effect correction and is now -0.0935424158813416 .
2025-08-14 23:45:21.784105 INFO::Total function execution time is 0.970672845840454 s and adjustment time is 0.895114898681641 s ( 92.22 )
2025-08-14 23:45:21.813974 INFO::Formatting Data.
2025-08-14 23:45:21.815512 INFO::Recognized SummarizedExperiment
2025-08-14 23:45:21.816862 INFO::Typecasting input to dataframe.
2025-08-14 23:45:21.830321 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:21.832638 INFO::Removing potential empty rows and columns
2025-08-14 23:45:21.83761 INFO::Found 0 missing values.
2025-08-14 23:45:21.845224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:21.84621 INFO::Done
2025-08-14 23:45:21.847035 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:21.851096 INFO::Starting hierarchical adjustment
2025-08-14 23:45:21.852231 INFO::Found 2 batches.
2025-08-14 23:45:21.853113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:21.854094 INFO::Using default BPPARAM
2025-08-14 23:45:21.854973 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:21.857032 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-14 23:45:21.882181 INFO::Done
2025-08-14 23:45:21.883565 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:21.887568 INFO::ASW Batch was 0.0235272294053069 prior to batch effect correction and is now 0.0235272294053069 .
2025-08-14 23:45:21.888773 INFO::Total function execution time is 0.0748310089111328 s and adjustment time is 0.0301151275634766 s ( 40.24 )
2025-08-14 23:45:21.921604 INFO::Formatting Data.
2025-08-14 23:45:21.923301 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:21.925084 INFO::Removing potential empty rows and columns
2025-08-14 23:45:21.927014 INFO::Found 0 missing values.
2025-08-14 23:45:21.931327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:21.932606 INFO::Done
2025-08-14 23:45:21.93384 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:21.93714 INFO::Starting hierarchical adjustment
2025-08-14 23:45:21.938589 INFO::Found 3 batches.
2025-08-14 23:45:21.939922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:21.941276 INFO::Using default BPPARAM
2025-08-14 23:45:21.942412 INFO::Processing subtree level 1
2025-08-14 23:45:31.907682 INFO::Adjusting the last 1 batches sequentially
2025-08-14 23:45:31.909631 INFO::Done
2025-08-14 23:45:31.910451 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:31.912731 INFO::ASW Batch was -0.0284394400188852 prior to batch effect correction and is now -0.174906855999859 .
2025-08-14 23:45:31.913705 INFO::Total function execution time is 9.99228501319885 s and adjustment time is 9.97127509117126 s ( 99.79 )
2025-08-14 23:45:31.930526 INFO::Skipping initial DF formatting
2025-08-14 23:45:31.931423 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:31.935539 INFO::Starting hierarchical adjustment
2025-08-14 23:45:31.936806 INFO::Found 5 batches.
2025-08-14 23:45:31.937581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:31.938366 INFO::Using default BPPARAM
2025-08-14 23:45:31.93907 INFO::Processing subtree level 1
2025-08-14 23:45:34.96452 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:34.966619 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-14 23:45:34.987469 INFO::Done
2025-08-14 23:45:34.988825 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:34.995304 INFO::ASW Batch was 0.459586749825381 prior to batch effect correction and is now 0.459586749825381 .
2025-08-14 23:45:34.996603 INFO::ASW Label was 0.403970552151107 prior to batch effect correction and is now 0.403970552151107 .
2025-08-14 23:45:34.998097 INFO::Total function execution time is 3.06758999824524 s and adjustment time is 3.05081295967102 s ( 99.45 )
2025-08-14 23:45:35.026322 INFO::Formatting Data.
2025-08-14 23:45:35.027741 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:35.029461 INFO::Removing potential empty rows and columns
2025-08-14 23:45:35.031004 INFO::Found 0 missing values.
2025-08-14 23:45:35.034612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:35.035368 INFO::Done
2025-08-14 23:45:35.036151 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:35.039472 INFO::Starting hierarchical adjustment
2025-08-14 23:45:35.040559 INFO::Found 5 batches.
2025-08-14 23:45:35.04138 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:35.042285 INFO::Using default BPPARAM
2025-08-14 23:45:35.04301 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.
2025-08-14 23:45:38.184576 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:38.186656 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-14 23:45:38.206036 INFO::Done
2025-08-14 23:45:38.207473 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:38.212539 INFO::ASW Batch was 0.300560977637789 prior to batch effect correction and is now -0.0601322588235797 .
2025-08-14 23:45:38.213828 INFO::ASW Label was 0.436613092843985 prior to batch effect correction and is now 0.867012943996516 .
2025-08-14 23:45:38.215369 INFO::Total function execution time is 3.18918609619141 s and adjustment time is 3.16558408737183 s ( 99.26 )
2025-08-14 23:45:38.216866 INFO::Formatting Data.
2025-08-14 23:45:38.21813 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:38.219731 INFO::Removing potential empty rows and columns
2025-08-14 23:45:38.221436 INFO::Found 0 missing values.
2025-08-14 23:45:38.227114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:38.22866 INFO::Done
2025-08-14 23:45:38.230058 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:38.235023 INFO::Starting hierarchical adjustment
2025-08-14 23:45:38.236549 INFO::Found 5 batches.
2025-08-14 23:45:38.237869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:38.2393 INFO::Using default BPPARAM
2025-08-14 23:45:38.24062 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.
2025-08-14 23:45:41.489583 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:41.491485 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-14 23:45:41.503168 INFO::Done
2025-08-14 23:45:41.50403 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:41.506968 INFO::ASW Batch was 0.300560977637789 prior to batch effect correction and is now -0.0601322588235797 .
2025-08-14 23:45:41.507787 INFO::ASW Label was 0.436613092843985 prior to batch effect correction and is now 0.867012943996516 .
2025-08-14 23:45:41.508739 INFO::Total function execution time is 3.29196715354919 s and adjustment time is 3.26689887046814 s ( 99.24 )
2025-08-14 23:45:41.532646 INFO::Formatting Data.
2025-08-14 23:45:41.533628 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:41.534685 INFO::Removing potential empty rows and columns
2025-08-14 23:45:41.535763 INFO::Found 0 missing values.
2025-08-14 23:45:41.539191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:41.539975 INFO::Done
2025-08-14 23:45:41.540688 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:41.543945 INFO::Starting hierarchical adjustment
2025-08-14 23:45:41.544906 INFO::Found 5 batches.
2025-08-14 23:45:41.545616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:41.546378 INFO::Using default BPPARAM
2025-08-14 23:45:41.547079 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.
2025-08-14 23:45:44.641218 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:44.643536 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-14 23:45:44.662586 INFO::Done
2025-08-14 23:45:44.663933 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:44.668473 INFO::ASW Batch was 0.531960270895427 prior to batch effect correction and is now -0.0520886729856047 .
2025-08-14 23:45:44.669747 INFO::ASW Label was 0.214318994691962 prior to batch effect correction and is now 0.757154863817451 .
2025-08-14 23:45:44.671427 INFO::Total function execution time is 3.13882994651794 s and adjustment time is 3.11774301528931 s ( 99.33 )
2025-08-14 23:45:44.673074 INFO::Formatting Data.
2025-08-14 23:45:44.674476 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:44.67604 INFO::Removing potential empty rows and columns
2025-08-14 23:45:44.677657 INFO::Found 0 missing values.
2025-08-14 23:45:44.680971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:44.681694 INFO::Done
2025-08-14 23:45:44.682377 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:44.685382 INFO::Starting hierarchical adjustment
2025-08-14 23:45:44.686285 INFO::Found 5 batches.
2025-08-14 23:45:44.686979 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:44.687727 INFO::Using default BPPARAM
2025-08-14 23:45:44.688411 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.
2025-08-14 23:45:47.707583 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:47.709499 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-14 23:45:47.727983 INFO::Done
2025-08-14 23:45:47.729302 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:47.733948 INFO::ASW Batch was 0.531960270895427 prior to batch effect correction and is now -0.0520886729856047 .
2025-08-14 23:45:47.735366 INFO::ASW Label was 0.214318994691962 prior to batch effect correction and is now 0.757154863817451 .
2025-08-14 23:45:47.737027 INFO::Total function execution time is 3.06397199630737 s and adjustment time is 3.04176497459412 s ( 99.28 )
2025-08-14 23:45:47.755825 INFO::Formatting Data.
2025-08-14 23:45:47.75691 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:47.758171 INFO::Removing potential empty rows and columns
2025-08-14 23:45:47.759394 INFO::Found 0 missing values.
2025-08-14 23:45:47.762043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:47.762826 INFO::Done
2025-08-14 23:45:47.763662 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:47.766754 INFO::Starting hierarchical adjustment
2025-08-14 23:45:47.767707 INFO::Found 2 batches.
2025-08-14 23:45:47.768514 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:47.769404 INFO::Using default BPPARAM
2025-08-14 23:45:47.770135 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:47.771279 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-14 23:45:47.78906 INFO::Done
2025-08-14 23:45:47.789938 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:47.792853 INFO::ASW Batch was 0.656426430511048 prior to batch effect correction and is now -0.00887506500121481 .
2025-08-14 23:45:47.793628 INFO::ASW Label was 0.376823668082219 prior to batch effect correction and is now 0.891917962112794 .
2025-08-14 23:45:47.794548 INFO::Total function execution time is 0.0388281345367432 s and adjustment time is 0.02146315574646 s ( 55.28 )
2025-08-14 23:45:47.795475 INFO::Formatting Data.
2025-08-14 23:45:47.796256 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:47.797254 INFO::Removing potential empty rows and columns
2025-08-14 23:45:47.798318 INFO::Found 0 missing values.
2025-08-14 23:45:47.800783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:47.801518 INFO::Done
2025-08-14 23:45:47.802228 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:47.805196 INFO::Starting hierarchical adjustment
2025-08-14 23:45:47.806105 INFO::Found 2 batches.
2025-08-14 23:45:47.806842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:47.80762 INFO::Using default BPPARAM
2025-08-14 23:45:47.808366 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:47.80949 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-14 23:45:47.82145 INFO::Done
2025-08-14 23:45:47.822289 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:47.825322 INFO::ASW Batch was 0.656426430511048 prior to batch effect correction and is now -0.00887506500121481 .
2025-08-14 23:45:47.826134 INFO::ASW Label was 0.376823668082219 prior to batch effect correction and is now 0.891917962112794 .
2025-08-14 23:45:47.827069 INFO::Total function execution time is 0.0315971374511719 s and adjustment time is 0.0154850482940674 s ( 49.01 )
2025-08-14 23:45:47.841711 INFO::Formatting Data.
2025-08-14 23:45:47.842687 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:47.84376 INFO::Removing potential empty rows and columns
2025-08-14 23:45:47.844846 INFO::Found 0 missing values.
2025-08-14 23:45:47.846858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:47.847629 INFO::Done
2025-08-14 23:45:47.848345 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:47.850346 INFO::Starting hierarchical adjustment
2025-08-14 23:45:47.851228 INFO::Found 2 batches.
2025-08-14 23:45:47.851954 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:47.852774 INFO::Using default BPPARAM
2025-08-14 23:45:47.853519 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:47.854571 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-14 23:45:47.880216 INFO::Done
2025-08-14 23:45:47.881123 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:47.883186 INFO::ASW Batch was 0.0687255343596329 prior to batch effect correction and is now -0.173422887322519 .
2025-08-14 23:45:47.884192 INFO::Total function execution time is 0.0425651073455811 s and adjustment time is 0.0290839672088623 s ( 68.33 )
2025-08-14 23:45:47.900401 INFO::Formatting Data.
2025-08-14 23:45:47.901396 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:47.90247 INFO::Removing potential empty rows and columns
2025-08-14 23:45:47.90359 INFO::Found 0 missing values.
2025-08-14 23:45:47.904857 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.
2025-08-14 23:45:47.909043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:47.909906 INFO::Done
2025-08-14 23:45:47.910638 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:47.914432 INFO::Starting hierarchical adjustment
2025-08-14 23:45:47.915878 INFO::Found 2 batches.
2025-08-14 23:45:47.916682 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:47.917478 INFO::Using default BPPARAM
2025-08-14 23:45:47.918209 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:47.919339 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-14 23:45:47.933146 INFO::Done
2025-08-14 23:45:47.934047 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:47.9371 INFO::ASW Batch was 0.611012473386497 prior to batch effect correction and is now 0.035020194263349 .
2025-08-14 23:45:47.937925 INFO::ASW Label was 0.502349798883624 prior to batch effect correction and is now 0.900780432411447 .
2025-08-14 23:45:47.938912 INFO::Total function execution time is 0.038599967956543 s and adjustment time is 0.0175180435180664 s ( 45.38 )
2025-08-14 23:45:47.939874 INFO::Formatting Data.
2025-08-14 23:45:47.940671 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:47.941869 INFO::Removing potential empty rows and columns
2025-08-14 23:45:47.943011 INFO::Found 0 missing values.
2025-08-14 23:45:47.944102 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.
2025-08-14 23:45:47.948351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:47.949126 INFO::Done
2025-08-14 23:45:47.94985 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:47.953066 INFO::Starting hierarchical adjustment
2025-08-14 23:45:47.954013 INFO::Found 2 batches.
2025-08-14 23:45:47.954739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:47.955521 INFO::Using default BPPARAM
2025-08-14 23:45:47.956234 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:45:47.958033 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-14 23:45:47.97987 INFO::Done
2025-08-14 23:45:47.980805 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:47.983999 INFO::ASW Batch was 0.611012473386497 prior to batch effect correction and is now 0.035020194263349 .
2025-08-14 23:45:47.984871 INFO::ASW Label was 0.502349798883624 prior to batch effect correction and is now 0.900780432411447 .
2025-08-14 23:45:47.985929 INFO::Total function execution time is 0.0460338592529297 s and adjustment time is 0.0259499549865723 s ( 56.37 )
2025-08-14 23:45:48.202376 INFO::Formatting Data.
2025-08-14 23:45:48.203463 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:48.204681 INFO::Removing potential empty rows and columns
2025-08-14 23:45:48.20599 INFO::Found 0 missing values.
2025-08-14 23:45:48.209145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:48.209972 INFO::Done
2025-08-14 23:45:48.210746 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:48.213077 INFO::Starting hierarchical adjustment
2025-08-14 23:45:48.214047 INFO::Found 3 batches.
2025-08-14 23:45:48.21484 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:48.215709 INFO::Using default BPPARAM
2025-08-14 23:45:48.216562 INFO::Processing subtree level 1
2025-08-14 23:45:51.135924 INFO::Adjusting the last 1 batches sequentially
2025-08-14 23:45:51.138095 INFO::Done
2025-08-14 23:45:51.139371 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:51.142507 INFO::ASW Batch was -0.0360629527992322 prior to batch effect correction and is now -0.0360629527992322 .
2025-08-14 23:45:51.144014 INFO::Total function execution time is 2.94164800643921 s and adjustment time is 2.92412400245667 s ( 99.4 )
2025-08-14 23:45:51.14569 INFO::Formatting Data.
2025-08-14 23:45:51.146935 INFO::Typecasting input to dataframe.
2025-08-14 23:45:51.148356 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:51.149954 INFO::Removing potential empty rows and columns
2025-08-14 23:45:51.151645 INFO::Found 0 missing values.
2025-08-14 23:45:51.156036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:51.157219 INFO::Done
2025-08-14 23:45:51.158318 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:51.161499 INFO::Starting hierarchical adjustment
2025-08-14 23:45:51.162872 INFO::Found 3 batches.
2025-08-14 23:45:51.163947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:51.165129 INFO::Using default BPPARAM
2025-08-14 23:45:51.166176 INFO::Processing subtree level 1
2025-08-14 23:45:54.268806 INFO::Adjusting the last 1 batches sequentially
2025-08-14 23:45:54.271018 INFO::Done
2025-08-14 23:45:54.272289 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:54.275619 INFO::ASW Batch was -0.0360629527992322 prior to batch effect correction and is now -0.0360629527992322 .
2025-08-14 23:45:54.277199 INFO::Total function execution time is 3.13155293464661 s and adjustment time is 3.10836100578308 s ( 99.26 )
2025-08-14 23:45:54.298223 INFO::Formatting Data.
2025-08-14 23:45:54.299379 INFO::Typecasting input to dataframe.
2025-08-14 23:45:54.300431 INFO::Replacing NaNs with NAs.
2025-08-14 23:45:54.301473 INFO::Removing potential empty rows and columns
2025-08-14 23:45:54.302585 INFO::Found 0 missing values.
2025-08-14 23:45:54.305245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:45:54.305993 INFO::Done
2025-08-14 23:45:54.306789 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:45:54.308859 INFO::Starting hierarchical adjustment
2025-08-14 23:45:54.309768 INFO::Found 3 batches.
2025-08-14 23:45:54.310555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:45:54.311346 INFO::Using default BPPARAM
2025-08-14 23:45:54.312056 INFO::Processing subtree level 1
2025-08-14 23:45:57.238899 INFO::Adjusting the last 1 batches sequentially
2025-08-14 23:45:57.241123 INFO::Done
2025-08-14 23:45:57.242431 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:45:57.245737 INFO::ASW Batch was -0.130437180179544 prior to batch effect correction and is now -0.130437180179544 .
2025-08-14 23:45:57.247369 INFO::Total function execution time is 2.94917607307434 s and adjustment time is 2.93143510818481 s ( 99.4 )
2025-08-14 23:46:00.381857 INFO::Formatting Data.
2025-08-14 23:46:00.38369 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:00.386186 INFO::Removing potential empty rows and columns
2025-08-14 23:46:00.390884 INFO::Found 1000 missing values.
2025-08-14 23:46:00.418715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:00.420399 INFO::Done
2025-08-14 23:46:00.422052 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:46:00.432406 INFO::Starting hierarchical adjustment
2025-08-14 23:46:00.43415 INFO::Found 10 batches.
2025-08-14 23:46:00.435486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:46:00.436885 INFO::Using default BPPARAM
2025-08-14 23:46:00.438011 INFO::Processing subtree level 1
2025-08-14 23:46:03.489061 INFO::Processing subtree level 2
2025-08-14 23:46:06.36457 INFO::Adjusting the last 1 batches sequentially
2025-08-14 23:46:06.366972 INFO::Done
2025-08-14 23:46:06.368257 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:46:06.378003 INFO::ASW Batch was 0.429341914360601 prior to batch effect correction and is now 0.429341914360601 .
2025-08-14 23:46:06.379402 INFO::ASW Label was 0.386422055947313 prior to batch effect correction and is now 0.386422055947313 .
2025-08-14 23:46:06.380934 INFO::Total function execution time is 5.99927806854248 s and adjustment time is 5.93311619758606 s ( 98.9 )
2025-08-14 23:46:06.382392 INFO::Formatting Data.
2025-08-14 23:46:06.383629 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:06.385527 INFO::Removing potential empty rows and columns
2025-08-14 23:46:06.389125 INFO::Found 1000 missing values.
2025-08-14 23:46:06.407227 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:06.40816 INFO::Done
2025-08-14 23:46:06.408909 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:46:06.415394 INFO::Starting hierarchical adjustment
2025-08-14 23:46:06.41699 INFO::Found 10 batches.
2025-08-14 23:46:07.19793 INFO::Set up parallel execution backend with 2 workers
2025-08-14 23:46:07.19945 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-14 23:46:10.308856 INFO::Adjusting the last 2 batches sequentially
2025-08-14 23:46:10.311045 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-14 23:46:10.333851 INFO::Done
2025-08-14 23:46:10.335215 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:46:10.344544 INFO::ASW Batch was 0.429341914360601 prior to batch effect correction and is now 0.429341914360601 .
2025-08-14 23:46:10.345872 INFO::ASW Label was 0.386422055947313 prior to batch effect correction and is now 0.386422055947313 .
2025-08-14 23:46:10.347387 INFO::Total function execution time is 3.96500492095947 s and adjustment time is 3.91708898544312 s ( 98.79 )
2025-08-14 23:46:13.417239 INFO::Formatting Data.
2025-08-14 23:46:13.418633 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:13.420254 INFO::Removing potential empty rows and columns
2025-08-14 23:46:13.421982 INFO::Found 0 missing values.
2025-08-14 23:46:13.427014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:13.428101 INFO::Done
2025-08-14 23:46:13.429139 INFO::Acquiring quality metrics before batch effect correction.
2025-08-14 23:46:13.433159 INFO::Starting hierarchical adjustment
2025-08-14 23:46:13.434471 INFO::Found 3 batches.
2025-08-14 23:46:13.435677 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-14 23:46:13.43679 INFO::Using default BPPARAM
2025-08-14 23:46:13.437789 INFO::Processing subtree level 1
2025-08-14 23:46:16.525059 INFO::Adjusting the last 1 batches sequentially
2025-08-14 23:46:16.527309 INFO::Done
2025-08-14 23:46:16.528708 INFO::Acquiring quality metrics after batch effect correction.
2025-08-14 23:46:16.533054 INFO::ASW Batch was 0.210340405327998 prior to batch effect correction and is now -0.152123416304747 .
2025-08-14 23:46:16.53435 INFO::ASW Label was -0.188495092240865 prior to batch effect correction and is now -0.110797761023331 .
2025-08-14 23:46:16.535942 INFO::Total function execution time is 3.11877799034119 s and adjustment time is 3.0930449962616 s ( 99.17 )
2025-08-14 23:46:16.719439 INFO::Formatting Data.
2025-08-14 23:46:16.72047 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:16.72153 INFO::Removing potential empty rows and columns
2025-08-14 23:46:16.722641 INFO::Found 2 missing values.
2025-08-14 23:46:16.725249 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:16.72598 INFO::Done
2025-08-14 23:46:16.771059 INFO::Found NA in Reference column
2025-08-14 23:46:16.791075 INFO::Require at least two references per batch.
2025-08-14 23:46:16.824518 INFO::Formatting Data.
2025-08-14 23:46:16.826038 INFO::Recognized SummarizedExperiment
2025-08-14 23:46:16.827316 INFO::Typecasting input to dataframe.
2025-08-14 23:46:16.840183 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:16.842322 INFO::Removing potential empty rows and columns
2025-08-14 23:46:16.847043 INFO::Found 0 missing values.
2025-08-14 23:46:16.855896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:16.857287 INFO::Done
2025-08-14 23:46:16.874609 INFO::Formatting Data.
2025-08-14 23:46:16.875574 INFO::Recognized SummarizedExperiment
2025-08-14 23:46:16.876301 INFO::Typecasting input to dataframe.
2025-08-14 23:46:16.891165 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:16.892557 INFO::Removing potential empty rows and columns
2025-08-14 23:46:16.895411 INFO::Found 0 missing values.
2025-08-14 23:46:16.903958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:16.904871 INFO::Done
2025-08-14 23:46:16.929051 INFO::Formatting Data.
2025-08-14 23:46:16.930565 INFO::Recognized SummarizedExperiment
2025-08-14 23:46:16.931902 INFO::Typecasting input to dataframe.
2025-08-14 23:46:16.95627 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:16.958203 INFO::Removing potential empty rows and columns
2025-08-14 23:46:16.96009 INFO::Found 0 missing values.
2025-08-14 23:46:16.961841 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.
2025-08-14 23:46:16.968282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:16.969569 INFO::Done
2025-08-14 23:46:16.990521 INFO::Formatting Data.
2025-08-14 23:46:16.992128 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:16.993861 INFO::Removing potential empty rows and columns
2025-08-14 23:46:16.995661 INFO::Found 0 missing values.
2025-08-14 23:46:17.000421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:17.001704 INFO::Done
2025-08-14 23:46:17.025877 INFO::Formatting Data.
2025-08-14 23:46:17.027634 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:17.029611 INFO::Removing potential empty rows and columns
2025-08-14 23:46:17.031694 INFO::Found 0 missing values.
2025-08-14 23:46:17.036756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:17.038162 INFO::Done
2025-08-14 23:46:17.09897 INFO::Formatting Data.
2025-08-14 23:46:17.100518 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:17.102388 INFO::Removing potential empty rows and columns
2025-08-14 23:46:17.104285 INFO::Found 1 missing values.
2025-08-14 23:46:17.108257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:17.109608 INFO::Done
2025-08-14 23:46:17.148976 INFO::Formatting Data.
2025-08-14 23:46:17.150497 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:17.15217 INFO::Removing potential empty rows and columns
2025-08-14 23:46:17.154102 INFO::Found 2 missing values.
2025-08-14 23:46:17.155775 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.
2025-08-14 23:46:17.159037 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:17.160216 INFO::Done
2025-08-14 23:46:17.180615 INFO::Formatting Data.
2025-08-14 23:46:17.182133 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:17.183834 INFO::Removing potential empty rows and columns
2025-08-14 23:46:17.185522 INFO::Found 2 missing values.
2025-08-14 23:46:17.188103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:17.189293 INFO::Done
2025-08-14 23:46:17.210056 INFO::Formatting Data.
2025-08-14 23:46:17.211748 INFO::Typecasting input to dataframe.
2025-08-14 23:46:17.213598 INFO::Replacing NaNs with NAs.
2025-08-14 23:46:17.215439 INFO::Removing potential empty rows and columns
2025-08-14 23:46:17.217401 INFO::Found 0 missing values.
2025-08-14 23:46:17.222145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-14 23:46:17.223542 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
31.65 1.43 78.20
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.19 | 0.62 | 19.09 | |
| compute_asw | 0.05 | 0.00 | 0.04 | |
| count_existing | 0.01 | 0.00 | 0.02 | |
| generate_data_covariables | 0.03 | 0.00 | 0.03 | |
| generate_dataset | 0.02 | 0.00 | 0.01 | |