Yannis Schumann
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:06 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| taishan | 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: 1.2.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-03-17 23:04:25 -0400 (Mon, 17 Mar 2025) |
| EndedAt: 2025-03-17 23:06:44 -0400 (Mon, 17 Mar 2025) |
| EllapsedTime: 139.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '1.2.0'
* 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 8.93 0.5 18.4
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BERT' ... ** 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 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
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")
2025-03-17 23:05:29.1001 INFO::Formatting Data.
2025-03-17 23:05:29.102099 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:29.110881 INFO::Removing potential empty rows and columns
2025-03-17 23:05:29.326968 INFO::Found 0 missing values.
2025-03-17 23:05:29.331662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:29.333037 INFO::Done
2025-03-17 23:05:29.334288 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:29.350769 INFO::Starting hierarchical adjustment
2025-03-17 23:05:29.351817 INFO::Found 3 batches.
2025-03-17 23:05:29.352539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:29.35378 INFO::Using default BPPARAM
2025-03-17 23:05:29.354485 INFO::Processing subtree level 1
2025-03-17 23:05:31.92257 INFO::Adjusting the last 1 batches sequentially
2025-03-17 23:05:31.924715 INFO::Done
2025-03-17 23:05:31.92598 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:31.929254 INFO::ASW Batch was 0.0448993804253098 prior to batch effect correction and is now 0.0448993804253098 .
2025-03-17 23:05:31.930954 INFO::Total function execution time is 2.83115601539612 s and adjustment time is 2.57304215431213 s ( 90.88 )
2025-03-17 23:05:31.952849 INFO::Formatting Data.
2025-03-17 23:05:31.954314 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:31.955966 INFO::Removing potential empty rows and columns
2025-03-17 23:05:31.957781 INFO::Found 0 missing values.
2025-03-17 23:05:31.959476 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.
2025-03-17 23:05:31.97305 INFO::Formatting Data.
2025-03-17 23:05:31.974512 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:31.976192 INFO::Removing potential empty rows and columns
2025-03-17 23:05:31.977974 INFO::Found 0 missing values.
2025-03-17 23:05:31.979614 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.
2025-03-17 23:05:32.00387 INFO::Formatting Data.
2025-03-17 23:05:32.005353 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:32.006951 INFO::Removing potential empty rows and columns
2025-03-17 23:05:32.008342 INFO::Found 0 missing values.
2025-03-17 23:05:32.009754 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.
2025-03-17 23:05:32.013656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:32.014433 INFO::Done
2025-03-17 23:05:32.015168 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:32.017221 INFO::Starting hierarchical adjustment
2025-03-17 23:05:32.018065 INFO::Found 2 batches.
2025-03-17 23:05:32.01883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:32.019599 INFO::Using default BPPARAM
2025-03-17 23:05:32.02028 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:32.021334 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:32.040094 INFO::Done
2025-03-17 23:05:32.040947 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:32.042987 INFO::ASW Batch was 0.0149224378162035 prior to batch effect correction and is now -0.129302660243054 .
2025-03-17 23:05:32.043931 INFO::Total function execution time is 0.0402231216430664 s and adjustment time is 0.0221240520477295 s ( 55 )
2025-03-17 23:05:32.046632 INFO::Formatting Data.
2025-03-17 23:05:32.047445 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:32.054307 INFO::Formatting Data.
2025-03-17 23:05:32.055164 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:32.056147 INFO::Removing potential empty rows and columns
2025-03-17 23:05:32.057207 INFO::Found 0 missing values.
2025-03-17 23:05:32.059635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:32.060307 INFO::Done
2025-03-17 23:05:32.060962 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:32.062927 INFO::Starting hierarchical adjustment
2025-03-17 23:05:32.063748 INFO::Found 2 batches.
2025-03-17 23:05:32.064422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:32.065148 INFO::Using default BPPARAM
2025-03-17 23:05:32.065805 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:32.066803 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:32.078498 INFO::Done
2025-03-17 23:05:32.079299 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:32.081252 INFO::ASW Batch was 0.041917095189968 prior to batch effect correction and is now -0.127826880942933 .
2025-03-17 23:05:32.082159 INFO::Total function execution time is 0.0279109477996826 s and adjustment time is 0.0148630142211914 s ( 53.25 )
2025-03-17 23:05:32.083278 INFO::Formatting Data.
2025-03-17 23:05:32.084014 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:32.084996 INFO::Removing potential empty rows and columns
2025-03-17 23:05:32.08605 INFO::Found 0 missing values.
2025-03-17 23:05:32.088412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:32.089077 INFO::Done
2025-03-17 23:05:32.089724 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:32.091648 INFO::Starting hierarchical adjustment
2025-03-17 23:05:32.09246 INFO::Found 2 batches.
2025-03-17 23:05:32.093117 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:32.093841 INFO::Using default BPPARAM
2025-03-17 23:05:32.094509 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:32.095495 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:32.107137 INFO::Done
2025-03-17 23:05:32.107945 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:32.109916 INFO::ASW Batch was 0.041917095189968 prior to batch effect correction and is now -0.127826880942933 .
2025-03-17 23:05:32.110812 INFO::Total function execution time is 0.0275299549102783 s and adjustment time is 0.0147819519042969 s ( 53.69 )
2025-03-17 23:05:34.490175 INFO::Formatting Data.
2025-03-17 23:05:34.491068 INFO::Recognized SummarizedExperiment
2025-03-17 23:05:34.491783 INFO::Typecasting input to dataframe.
2025-03-17 23:05:34.519941 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:34.521363 INFO::Removing potential empty rows and columns
2025-03-17 23:05:34.524386 INFO::Found 0 missing values.
2025-03-17 23:05:34.529827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:34.531075 INFO::Done
2025-03-17 23:05:34.532275 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:34.538596 INFO::Starting hierarchical adjustment
2025-03-17 23:05:34.540094 INFO::Found 2 batches.
2025-03-17 23:05:34.541313 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:34.543293 INFO::Using default BPPARAM
2025-03-17 23:05:34.544485 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:34.546476 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:34.597023 INFO::Done
2025-03-17 23:05:34.597911 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:34.601846 INFO::ASW Batch was -0.0070018197881481 prior to batch effect correction and is now -0.0939940031832146 .
2025-03-17 23:05:34.60287 INFO::Total function execution time is 0.112952947616577 s and adjustment time is 0.0571799278259277 s ( 50.62 )
2025-03-17 23:05:35.375765 INFO::Formatting Data.
2025-03-17 23:05:35.377177 INFO::Recognized SummarizedExperiment
2025-03-17 23:05:35.378372 INFO::Typecasting input to dataframe.
2025-03-17 23:05:35.39038 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:35.392425 INFO::Removing potential empty rows and columns
2025-03-17 23:05:35.396842 INFO::Found 0 missing values.
2025-03-17 23:05:35.405507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:35.40682 INFO::Done
2025-03-17 23:05:35.408001 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:35.413703 INFO::Starting hierarchical adjustment
2025-03-17 23:05:35.415183 INFO::Found 2 batches.
2025-03-17 23:05:35.416407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:35.417671 INFO::Using default BPPARAM
2025-03-17 23:05:35.418812 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:35.420679 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:35.450685 INFO::Done
2025-03-17 23:05:35.452021 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:35.457917 INFO::ASW Batch was -0.00982434039057549 prior to batch effect correction and is now -0.00982434039057549 .
2025-03-17 23:05:35.459545 INFO::Total function execution time is 0.0837459564208984 s and adjustment time is 0.0357019901275635 s ( 42.63 )
2025-03-17 23:05:35.488267 INFO::Formatting Data.
2025-03-17 23:05:35.489806 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:35.491498 INFO::Removing potential empty rows and columns
2025-03-17 23:05:35.493249 INFO::Found 0 missing values.
2025-03-17 23:05:35.497421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:35.498609 INFO::Done
2025-03-17 23:05:35.499793 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:35.50293 INFO::Starting hierarchical adjustment
2025-03-17 23:05:35.504342 INFO::Found 3 batches.
2025-03-17 23:05:35.505522 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:35.506674 INFO::Using default BPPARAM
2025-03-17 23:05:35.507737 INFO::Processing subtree level 1
2025-03-17 23:05:45.012257 INFO::Adjusting the last 1 batches sequentially
2025-03-17 23:05:45.014482 INFO::Done
2025-03-17 23:05:45.015839 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:45.019154 INFO::ASW Batch was -0.120731837037905 prior to batch effect correction and is now -0.182198141329727 .
2025-03-17 23:05:45.020759 INFO::Total function execution time is 9.53257894515991 s and adjustment time is 9.51031017303467 s ( 99.77 )
2025-03-17 23:05:45.043595 INFO::Skipping initial DF formatting
2025-03-17 23:05:45.044999 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:45.051784 INFO::Starting hierarchical adjustment
2025-03-17 23:05:45.053366 INFO::Found 5 batches.
2025-03-17 23:05:45.054592 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:45.055882 INFO::Using default BPPARAM
2025-03-17 23:05:45.057017 INFO::Processing subtree level 1
2025-03-17 23:05:48.036625 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:48.038626 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:48.061426 INFO::Done
2025-03-17 23:05:48.062724 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:48.06758 INFO::ASW Batch was 0.471381165495594 prior to batch effect correction and is now 0.471381165495594 .
2025-03-17 23:05:48.068374 INFO::ASW Label was 0.389855815448015 prior to batch effect correction and is now 0.389855815448015 .
2025-03-17 23:05:48.069285 INFO::Total function execution time is 3.02586197853088 s and adjustment time is 3.00827407836914 s ( 99.42 )
2025-03-17 23:05:48.086041 INFO::Formatting Data.
2025-03-17 23:05:48.087048 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:48.088087 INFO::Removing potential empty rows and columns
2025-03-17 23:05:48.089143 INFO::Found 0 missing values.
2025-03-17 23:05:48.092572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:48.093278 INFO::Done
2025-03-17 23:05:48.093955 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:48.09686 INFO::Starting hierarchical adjustment
2025-03-17 23:05:48.097748 INFO::Found 5 batches.
2025-03-17 23:05:48.098447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:48.099198 INFO::Using default BPPARAM
2025-03-17 23:05:48.099887 INFO::Processing subtree level 1
2025-03-17 23:05:51.151301 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:51.153269 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:51.171305 INFO::Done
2025-03-17 23:05:51.172579 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:51.176969 INFO::ASW Batch was 0.280785362768586 prior to batch effect correction and is now -0.0802752754046349 .
2025-03-17 23:05:51.178205 INFO::ASW Label was 0.380609310288005 prior to batch effect correction and is now 0.833394167710546 .
2025-03-17 23:05:51.17967 INFO::Total function execution time is 3.09363198280334 s and adjustment time is 3.07364106178284 s ( 99.35 )
2025-03-17 23:05:51.181129 INFO::Formatting Data.
2025-03-17 23:05:51.18234 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:51.183894 INFO::Removing potential empty rows and columns
2025-03-17 23:05:51.185181 INFO::Found 0 missing values.
2025-03-17 23:05:51.188562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:51.189242 INFO::Done
2025-03-17 23:05:51.189893 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:51.192974 INFO::Starting hierarchical adjustment
2025-03-17 23:05:51.193906 INFO::Found 5 batches.
2025-03-17 23:05:51.194578 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:51.195368 INFO::Using default BPPARAM
2025-03-17 23:05:51.196042 INFO::Processing subtree level 1
2025-03-17 23:05:54.219091 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:54.220583 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:54.238101 INFO::Done
2025-03-17 23:05:54.239399 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:54.243792 INFO::ASW Batch was 0.280785362768586 prior to batch effect correction and is now -0.0802752754046349 .
2025-03-17 23:05:54.244995 INFO::ASW Label was 0.380609310288005 prior to batch effect correction and is now 0.833394167710546 .
2025-03-17 23:05:54.246438 INFO::Total function execution time is 3.06530904769897 s and adjustment time is 3.04426789283752 s ( 99.31 )
2025-03-17 23:05:54.26756 INFO::Formatting Data.
2025-03-17 23:05:54.269128 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:54.27078 INFO::Removing potential empty rows and columns
2025-03-17 23:05:54.272443 INFO::Found 0 missing values.
2025-03-17 23:05:54.277881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:54.279072 INFO::Done
2025-03-17 23:05:54.280217 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:54.284718 INFO::Starting hierarchical adjustment
2025-03-17 23:05:54.286126 INFO::Found 5 batches.
2025-03-17 23:05:54.287272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:54.288487 INFO::Using default BPPARAM
2025-03-17 23:05:54.289603 INFO::Processing subtree level 1
2025-03-17 23:05:57.2944 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:05:57.296374 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:05:57.315628 INFO::Done
2025-03-17 23:05:57.316908 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:05:57.321431 INFO::ASW Batch was 0.224203996909771 prior to batch effect correction and is now -0.0747181643924105 .
2025-03-17 23:05:57.322639 INFO::ASW Label was 0.496295140143247 prior to batch effect correction and is now 0.912362440086438 .
2025-03-17 23:05:57.324074 INFO::Total function execution time is 3.05661296844482 s and adjustment time is 3.02966785430908 s ( 99.12 )
2025-03-17 23:05:57.325464 INFO::Formatting Data.
2025-03-17 23:05:57.326612 INFO::Replacing NaNs with NAs.
2025-03-17 23:05:57.328118 INFO::Removing potential empty rows and columns
2025-03-17 23:05:57.329741 INFO::Found 0 missing values.
2025-03-17 23:05:57.335569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:05:57.336739 INFO::Done
2025-03-17 23:05:57.337847 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:05:57.342328 INFO::Starting hierarchical adjustment
2025-03-17 23:05:57.343644 INFO::Found 5 batches.
2025-03-17 23:05:57.344708 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:05:57.345846 INFO::Using default BPPARAM
2025-03-17 23:05:57.346865 INFO::Processing subtree level 1
2025-03-17 23:06:00.595923 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:06:00.597859 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:06:00.614362 INFO::Done
2025-03-17 23:06:00.615524 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:00.619602 INFO::ASW Batch was 0.224203996909771 prior to batch effect correction and is now -0.0747181643924105 .
2025-03-17 23:06:00.620686 INFO::ASW Label was 0.496295140143247 prior to batch effect correction and is now 0.912362440086438 .
2025-03-17 23:06:00.621981 INFO::Total function execution time is 3.29655599594116 s and adjustment time is 3.27088117599487 s ( 99.22 )
2025-03-17 23:06:00.638238 INFO::Formatting Data.
2025-03-17 23:06:00.639215 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:00.640278 INFO::Removing potential empty rows and columns
2025-03-17 23:06:00.64136 INFO::Found 0 missing values.
2025-03-17 23:06:00.644039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:00.644889 INFO::Done
2025-03-17 23:06:00.645597 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:00.648955 INFO::Starting hierarchical adjustment
2025-03-17 23:06:00.649846 INFO::Found 2 batches.
2025-03-17 23:06:00.650534 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:00.651283 INFO::Using default BPPARAM
2025-03-17 23:06:00.651959 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:06:00.653004 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:06:00.665027 INFO::Done
2025-03-17 23:06:00.665898 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:00.668834 INFO::ASW Batch was 0.301229926541693 prior to batch effect correction and is now 0.0362718467127057 .
2025-03-17 23:06:00.669691 INFO::ASW Label was 0.757143740128893 prior to batch effect correction and is now 0.907793246033796 .
2025-03-17 23:06:00.670624 INFO::Total function execution time is 0.0324950218200684 s and adjustment time is 0.0152921676635742 s ( 47.06 )
2025-03-17 23:06:00.67153 INFO::Formatting Data.
2025-03-17 23:06:00.672296 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:00.673309 INFO::Removing potential empty rows and columns
2025-03-17 23:06:00.674362 INFO::Found 0 missing values.
2025-03-17 23:06:00.676712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:00.677398 INFO::Done
2025-03-17 23:06:00.678086 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:00.680925 INFO::Starting hierarchical adjustment
2025-03-17 23:06:00.68178 INFO::Found 2 batches.
2025-03-17 23:06:00.682457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:00.683213 INFO::Using default BPPARAM
2025-03-17 23:06:00.683885 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:06:00.685049 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:06:00.704564 INFO::Done
2025-03-17 23:06:00.705945 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:00.710662 INFO::ASW Batch was 0.301229926541693 prior to batch effect correction and is now 0.0362718467127057 .
2025-03-17 23:06:00.712001 INFO::ASW Label was 0.757143740128893 prior to batch effect correction and is now 0.907793246033796 .
2025-03-17 23:06:00.71356 INFO::Total function execution time is 0.0419399738311768 s and adjustment time is 0.0228309631347656 s ( 54.44 )
2025-03-17 23:06:00.734602 INFO::Formatting Data.
2025-03-17 23:06:00.736141 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:00.737846 INFO::Removing potential empty rows and columns
2025-03-17 23:06:00.739523 INFO::Found 0 missing values.
2025-03-17 23:06:00.742961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:00.744194 INFO::Done
2025-03-17 23:06:00.745432 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:00.748751 INFO::Starting hierarchical adjustment
2025-03-17 23:06:00.750211 INFO::Found 2 batches.
2025-03-17 23:06:00.751403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:00.752708 INFO::Using default BPPARAM
2025-03-17 23:06:00.753884 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:06:00.75567 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:06:00.798196 INFO::Done
2025-03-17 23:06:00.799605 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:00.80299 INFO::ASW Batch was -0.00642724934684292 prior to batch effect correction and is now -0.162637430761529 .
2025-03-17 23:06:00.804635 INFO::Total function execution time is 0.070112943649292 s and adjustment time is 0.0481600761413574 s ( 68.69 )
2025-03-17 23:06:00.827226 INFO::Formatting Data.
2025-03-17 23:06:00.828841 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:00.830625 INFO::Removing potential empty rows and columns
2025-03-17 23:06:00.832527 INFO::Found 0 missing values.
2025-03-17 23:06:00.83457 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.
2025-03-17 23:06:00.841463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:00.842854 INFO::Done
2025-03-17 23:06:00.844149 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:00.848977 INFO::Starting hierarchical adjustment
2025-03-17 23:06:00.850535 INFO::Found 2 batches.
2025-03-17 23:06:00.851788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:00.853118 INFO::Using default BPPARAM
2025-03-17 23:06:00.854354 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:06:00.85619 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:06:00.879309 INFO::Done
2025-03-17 23:06:00.880754 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:00.885803 INFO::ASW Batch was 0.559361087758207 prior to batch effect correction and is now -0.0055452069499857 .
2025-03-17 23:06:00.887243 INFO::ASW Label was 0.447562016783913 prior to batch effect correction and is now 0.901744110132529 .
2025-03-17 23:06:00.888903 INFO::Total function execution time is 0.0617601871490479 s and adjustment time is 0.0289812088012695 s ( 46.93 )
2025-03-17 23:06:00.890513 INFO::Formatting Data.
2025-03-17 23:06:00.891872 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:00.893647 INFO::Removing potential empty rows and columns
2025-03-17 23:06:00.895535 INFO::Found 0 missing values.
2025-03-17 23:06:00.897326 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.
2025-03-17 23:06:00.904131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:00.905531 INFO::Done
2025-03-17 23:06:00.906824 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:00.911706 INFO::Starting hierarchical adjustment
2025-03-17 23:06:00.913253 INFO::Found 2 batches.
2025-03-17 23:06:00.914506 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:00.915839 INFO::Using default BPPARAM
2025-03-17 23:06:00.917069 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:06:00.918935 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:06:00.943421 INFO::Done
2025-03-17 23:06:00.944977 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:00.95052 INFO::ASW Batch was 0.559361087758207 prior to batch effect correction and is now -0.0055452069499857 .
2025-03-17 23:06:00.952036 INFO::ASW Label was 0.447562016783913 prior to batch effect correction and is now 0.901744110132529 .
2025-03-17 23:06:00.953875 INFO::Total function execution time is 0.0633330345153809 s and adjustment time is 0.030332088470459 s ( 47.89 )
2025-03-17 23:06:01.264875 INFO::Formatting Data.
2025-03-17 23:06:01.266483 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:01.268376 INFO::Removing potential empty rows and columns
2025-03-17 23:06:01.270362 INFO::Found 0 missing values.
2025-03-17 23:06:01.275352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:01.276646 INFO::Done
2025-03-17 23:06:01.277808 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:01.281194 INFO::Starting hierarchical adjustment
2025-03-17 23:06:01.28272 INFO::Found 3 batches.
2025-03-17 23:06:01.283884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:01.285171 INFO::Using default BPPARAM
2025-03-17 23:06:01.286425 INFO::Processing subtree level 1
2025-03-17 23:06:04.1863 INFO::Adjusting the last 1 batches sequentially
2025-03-17 23:06:04.1878 INFO::Done
2025-03-17 23:06:04.188588 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:04.191455 INFO::ASW Batch was -0.0455080809174676 prior to batch effect correction and is now -0.0455080809174676 .
2025-03-17 23:06:04.193003 INFO::Total function execution time is 2.92828106880188 s and adjustment time is 2.90535402297974 s ( 99.22 )
2025-03-17 23:06:04.194657 INFO::Formatting Data.
2025-03-17 23:06:04.195889 INFO::Typecasting input to dataframe.
2025-03-17 23:06:04.197227 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:04.198718 INFO::Removing potential empty rows and columns
2025-03-17 23:06:04.200326 INFO::Found 0 missing values.
2025-03-17 23:06:04.204418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:04.205537 INFO::Done
2025-03-17 23:06:04.206573 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:04.209529 INFO::Starting hierarchical adjustment
2025-03-17 23:06:04.210807 INFO::Found 3 batches.
2025-03-17 23:06:04.21184 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:04.212969 INFO::Using default BPPARAM
2025-03-17 23:06:04.21402 INFO::Processing subtree level 1
2025-03-17 23:06:07.110048 INFO::Adjusting the last 1 batches sequentially
2025-03-17 23:06:07.1121 INFO::Done
2025-03-17 23:06:07.113301 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:07.116279 INFO::ASW Batch was -0.0455080809174676 prior to batch effect correction and is now -0.0455080809174676 .
2025-03-17 23:06:07.117726 INFO::Total function execution time is 2.92310285568237 s and adjustment time is 2.90148615837097 s ( 99.26 )
2025-03-17 23:06:07.137606 INFO::Formatting Data.
2025-03-17 23:06:07.139034 INFO::Typecasting input to dataframe.
2025-03-17 23:06:07.140595 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:07.141654 INFO::Removing potential empty rows and columns
2025-03-17 23:06:07.142811 INFO::Found 0 missing values.
2025-03-17 23:06:07.145294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:07.145987 INFO::Done
2025-03-17 23:06:07.146656 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:07.148635 INFO::Starting hierarchical adjustment
2025-03-17 23:06:07.149468 INFO::Found 3 batches.
2025-03-17 23:06:07.150203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:07.150947 INFO::Using default BPPARAM
2025-03-17 23:06:07.151729 INFO::Processing subtree level 1
2025-03-17 23:06:10.296463 INFO::Adjusting the last 1 batches sequentially
2025-03-17 23:06:10.298711 INFO::Done
2025-03-17 23:06:10.299986 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:10.302293 INFO::ASW Batch was -0.00534572739407489 prior to batch effect correction and is now -0.00534572739407489 .
2025-03-17 23:06:10.303344 INFO::Total function execution time is 3.16581392288208 s and adjustment time is 3.14929795265198 s ( 99.48 )
2025-03-17 23:06:13.154924 INFO::Formatting Data.
2025-03-17 23:06:13.155868 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:13.157061 INFO::Removing potential empty rows and columns
2025-03-17 23:06:13.159333 INFO::Found 1000 missing values.
2025-03-17 23:06:13.172795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:13.173699 INFO::Done
2025-03-17 23:06:13.174416 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:13.18114 INFO::Starting hierarchical adjustment
2025-03-17 23:06:13.182404 INFO::Found 10 batches.
2025-03-17 23:06:13.183499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:13.184769 INFO::Using default BPPARAM
2025-03-17 23:06:13.185813 INFO::Processing subtree level 1
2025-03-17 23:06:16.372344 INFO::Processing subtree level 2
2025-03-17 23:06:19.215239 INFO::Adjusting the last 1 batches sequentially
2025-03-17 23:06:19.217862 INFO::Done
2025-03-17 23:06:19.219039 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:19.228362 INFO::ASW Batch was 0.50845712628569 prior to batch effect correction and is now 0.50845712628569 .
2025-03-17 23:06:19.22973 INFO::ASW Label was 0.353019365882549 prior to batch effect correction and is now 0.353019365882549 .
2025-03-17 23:06:19.231453 INFO::Total function execution time is 6.07652688026428 s and adjustment time is 6.03561496734619 s ( 99.33 )
2025-03-17 23:06:19.232914 INFO::Formatting Data.
2025-03-17 23:06:19.234183 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:19.236004 INFO::Removing potential empty rows and columns
2025-03-17 23:06:19.239592 INFO::Found 1000 missing values.
2025-03-17 23:06:19.262601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:19.263993 INFO::Done
2025-03-17 23:06:19.265194 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:19.275067 INFO::Starting hierarchical adjustment
2025-03-17 23:06:19.27669 INFO::Found 10 batches.
2025-03-17 23:06:20.073706 INFO::Set up parallel execution backend with 2 workers
2025-03-17 23:06:20.074682 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-17 23:06:23.131308 INFO::Adjusting the last 2 batches sequentially
2025-03-17 23:06:23.133457 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 23:06:23.158491 INFO::Done
2025-03-17 23:06:23.159779 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:23.16884 INFO::ASW Batch was 0.50845712628569 prior to batch effect correction and is now 0.50845712628569 .
2025-03-17 23:06:23.170188 INFO::ASW Label was 0.353019365882549 prior to batch effect correction and is now 0.353019365882549 .
2025-03-17 23:06:23.171765 INFO::Total function execution time is 3.93885087966919 s and adjustment time is 3.8820219039917 s ( 98.56 )
2025-03-17 23:06:26.216464 INFO::Formatting Data.
2025-03-17 23:06:26.218033 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:26.21969 INFO::Removing potential empty rows and columns
2025-03-17 23:06:26.221591 INFO::Found 0 missing values.
2025-03-17 23:06:26.227133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:26.228393 INFO::Done
2025-03-17 23:06:26.229546 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 23:06:26.233836 INFO::Starting hierarchical adjustment
2025-03-17 23:06:26.235326 INFO::Found 3 batches.
2025-03-17 23:06:26.23654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 23:06:26.237641 INFO::Using default BPPARAM
2025-03-17 23:06:26.238502 INFO::Processing subtree level 1
2025-03-17 23:06:29.2479 INFO::Adjusting the last 1 batches sequentially
2025-03-17 23:06:29.250072 INFO::Done
2025-03-17 23:06:29.251426 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 23:06:29.255845 INFO::ASW Batch was 0.213492558963172 prior to batch effect correction and is now -0.134997752161874 .
2025-03-17 23:06:29.257117 INFO::ASW Label was -0.226143877284428 prior to batch effect correction and is now -0.0422031249473628 .
2025-03-17 23:06:29.258175 INFO::Total function execution time is 3.04188585281372 s and adjustment time is 3.01496005058289 s ( 99.11 )
2025-03-17 23:06:29.461044 INFO::Formatting Data.
2025-03-17 23:06:29.462709 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.464546 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.466485 INFO::Found 2 missing values.
2025-03-17 23:06:29.471326 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.472687 INFO::Done
2025-03-17 23:06:29.527349 INFO::Found NA in Reference column
2025-03-17 23:06:29.54646 INFO::Require at least two references per batch.
2025-03-17 23:06:29.579001 INFO::Formatting Data.
2025-03-17 23:06:29.580485 INFO::Recognized SummarizedExperiment
2025-03-17 23:06:29.581842 INFO::Typecasting input to dataframe.
2025-03-17 23:06:29.590307 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.591638 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.594473 INFO::Found 0 missing values.
2025-03-17 23:06:29.599736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.600563 INFO::Done
2025-03-17 23:06:29.614065 INFO::Formatting Data.
2025-03-17 23:06:29.614959 INFO::Recognized SummarizedExperiment
2025-03-17 23:06:29.615644 INFO::Typecasting input to dataframe.
2025-03-17 23:06:29.633076 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.634462 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.637509 INFO::Found 0 missing values.
2025-03-17 23:06:29.64948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.650908 INFO::Done
2025-03-17 23:06:29.674127 INFO::Formatting Data.
2025-03-17 23:06:29.675616 INFO::Recognized SummarizedExperiment
2025-03-17 23:06:29.67684 INFO::Typecasting input to dataframe.
2025-03-17 23:06:29.699675 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.701462 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.703336 INFO::Found 0 missing values.
2025-03-17 23:06:29.705044 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.
2025-03-17 23:06:29.711548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.712818 INFO::Done
2025-03-17 23:06:29.732264 INFO::Formatting Data.
2025-03-17 23:06:29.733782 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.735498 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.737299 INFO::Found 0 missing values.
2025-03-17 23:06:29.741801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.74303 INFO::Done
2025-03-17 23:06:29.764321 INFO::Formatting Data.
2025-03-17 23:06:29.765831 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.767587 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.769467 INFO::Found 0 missing values.
2025-03-17 23:06:29.773992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.775238 INFO::Done
2025-03-17 23:06:29.830896 INFO::Formatting Data.
2025-03-17 23:06:29.832436 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.834323 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.836374 INFO::Found 1 missing values.
2025-03-17 23:06:29.840287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.841505 INFO::Done
2025-03-17 23:06:29.877918 INFO::Formatting Data.
2025-03-17 23:06:29.879511 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.881314 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.883197 INFO::Found 2 missing values.
2025-03-17 23:06:29.885001 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.
2025-03-17 23:06:29.8888 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.890098 INFO::Done
2025-03-17 23:06:29.910086 INFO::Formatting Data.
2025-03-17 23:06:29.911567 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.913342 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.915118 INFO::Found 2 missing values.
2025-03-17 23:06:29.917857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.919092 INFO::Done
2025-03-17 23:06:29.941055 INFO::Formatting Data.
2025-03-17 23:06:29.942657 INFO::Typecasting input to dataframe.
2025-03-17 23:06:29.944413 INFO::Replacing NaNs with NAs.
2025-03-17 23:06:29.946189 INFO::Removing potential empty rows and columns
2025-03-17 23:06:29.948087 INFO::Found 0 missing values.
2025-03-17 23:06:29.952841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 23:06:29.95412 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.42 1.56 76.64
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.93 | 0.50 | 18.40 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.02 | 0.00 | 0.02 | |
| generate_data_covariables | 0.01 | 0.00 | 0.01 | |
| generate_dataset | 0.02 | 0.00 | 0.02 | |