Yannis Schumann
| Snapshot Date: 2024-10-04 13:40 -0400 (Fri, 04 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-05 11:44 -0400 (Sat, 05 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| 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 158/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-10-05 03:07:04 -0000 (Sat, 05 Oct 2024) |
| EndedAt: 2024-10-05 03:08:24 -0000 (Sat, 05 Oct 2024) |
| EllapsedTime: 79.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 31.437 1.806 22.692
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-10-05 03:08:09.459281 INFO::Formatting Data.
2024-10-05 03:08:09.461328 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:09.480493 INFO::Removing potential empty rows and columns
2024-10-05 03:08:09.871764 INFO::Found 0 missing values.
2024-10-05 03:08:09.87687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:09.877738 INFO::Done
2024-10-05 03:08:09.878488 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:09.894588 INFO::Starting hierarchical adjustment
2024-10-05 03:08:09.895755 INFO::Found 3 batches.
2024-10-05 03:08:09.896501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:09.898121 INFO::Using default BPPARAM
2024-10-05 03:08:09.898911 INFO::Processing subtree level 1
2024-10-05 03:08:10.026165 INFO::Adjusting the last 1 batches sequentially
2024-10-05 03:08:10.028622 INFO::Done
2024-10-05 03:08:10.029505 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:10.033234 INFO::ASW Batch was 0.0129782855245352 prior to batch effect correction and is now 0.0129782855245352 .
2024-10-05 03:08:10.034841 INFO::Total function execution time is 0.576653718948364 s and adjustment time is 0.133121252059937 s ( 23.09 )
2024-10-05 03:08:10.055248 INFO::Formatting Data.
2024-10-05 03:08:10.056212 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:10.057457 INFO::Removing potential empty rows and columns
2024-10-05 03:08:10.05898 INFO::Found 0 missing values.
2024-10-05 03:08:10.06038 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.
2024-10-05 03:08:10.075785 INFO::Formatting Data.
2024-10-05 03:08:10.076754 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:10.077927 INFO::Removing potential empty rows and columns
2024-10-05 03:08:10.079333 INFO::Found 0 missing values.
2024-10-05 03:08:10.080535 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.
2024-10-05 03:08:10.101809 INFO::Formatting Data.
2024-10-05 03:08:10.102742 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:10.10389 INFO::Removing potential empty rows and columns
2024-10-05 03:08:10.105227 INFO::Found 0 missing values.
2024-10-05 03:08:10.106472 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.
2024-10-05 03:08:10.11283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:10.113684 INFO::Done
2024-10-05 03:08:10.114417 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:10.117067 INFO::Starting hierarchical adjustment
2024-10-05 03:08:10.118055 INFO::Found 2 batches.
2024-10-05 03:08:10.118778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:10.119662 INFO::Using default BPPARAM
2024-10-05 03:08:10.1204 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:10.121701 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:10.153475 INFO::Done
2024-10-05 03:08:10.154406 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:10.157258 INFO::ASW Batch was -0.00112833062474746 prior to batch effect correction and is now -0.124025420221206 .
2024-10-05 03:08:10.158432 INFO::Total function execution time is 0.0566918849945068 s and adjustment time is 0.0355808734893799 s ( 62.76 )
2024-10-05 03:08:10.168678 INFO::Formatting Data.
2024-10-05 03:08:10.169815 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:10.185347 INFO::Formatting Data.
2024-10-05 03:08:10.186411 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:10.187696 INFO::Removing potential empty rows and columns
2024-10-05 03:08:10.189258 INFO::Found 0 missing values.
2024-10-05 03:08:10.193618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:10.194454 INFO::Done
2024-10-05 03:08:10.195315 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:10.198641 INFO::Starting hierarchical adjustment
2024-10-05 03:08:10.19978 INFO::Found 2 batches.
2024-10-05 03:08:10.200552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:10.201556 INFO::Using default BPPARAM
2024-10-05 03:08:10.202468 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:10.203984 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:10.226924 INFO::Done
2024-10-05 03:08:10.227811 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:10.230551 INFO::ASW Batch was 0.0577738840219001 prior to batch effect correction and is now -0.0916457452181953 .
2024-10-05 03:08:10.231722 INFO::Total function execution time is 0.0463724136352539 s and adjustment time is 0.0273811817169189 s ( 59.05 )
2024-10-05 03:08:10.233173 INFO::Formatting Data.
2024-10-05 03:08:10.233992 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:10.235185 INFO::Removing potential empty rows and columns
2024-10-05 03:08:10.236613 INFO::Found 0 missing values.
2024-10-05 03:08:10.240693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:10.241532 INFO::Done
2024-10-05 03:08:10.24253 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:10.245435 INFO::Starting hierarchical adjustment
2024-10-05 03:08:10.246439 INFO::Found 2 batches.
2024-10-05 03:08:10.247195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:10.248015 INFO::Using default BPPARAM
2024-10-05 03:08:10.248751 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:10.250203 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:10.271556 INFO::Done
2024-10-05 03:08:10.272449 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:10.275302 INFO::ASW Batch was 0.0577738840219001 prior to batch effect correction and is now -0.0916457452181953 .
2024-10-05 03:08:10.276402 INFO::Total function execution time is 0.0432019233703613 s and adjustment time is 0.0253045558929443 s ( 58.57 )
2024-10-05 03:08:13.381686 INFO::Formatting Data.
2024-10-05 03:08:13.382657 INFO::Recognized SummarizedExperiment
2024-10-05 03:08:13.383413 INFO::Typecasting input to dataframe.
2024-10-05 03:08:13.426746 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:13.428245 INFO::Removing potential empty rows and columns
2024-10-05 03:08:13.43323 INFO::Found 0 missing values.
2024-10-05 03:08:13.442841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:13.443679 INFO::Done
2024-10-05 03:08:13.444338 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:13.449093 INFO::Starting hierarchical adjustment
2024-10-05 03:08:13.450134 INFO::Found 2 batches.
2024-10-05 03:08:13.450834 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:13.452209 INFO::Using default BPPARAM
2024-10-05 03:08:13.452975 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:13.45434 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:13.531277 INFO::Done
2024-10-05 03:08:13.532136 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:13.536964 INFO::ASW Batch was -0.00697258892587492 prior to batch effect correction and is now -0.0953053939956833 .
2024-10-05 03:08:13.538237 INFO::Total function execution time is 0.157030582427979 s and adjustment time is 0.0813262462615967 s ( 51.79 )
2024-10-05 03:08:13.561959 INFO::Formatting Data.
2024-10-05 03:08:13.562865 INFO::Recognized SummarizedExperiment
2024-10-05 03:08:13.563572 INFO::Typecasting input to dataframe.
2024-10-05 03:08:13.575994 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:13.577489 INFO::Removing potential empty rows and columns
2024-10-05 03:08:13.582549 INFO::Found 0 missing values.
2024-10-05 03:08:13.592712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:13.593566 INFO::Done
2024-10-05 03:08:13.594292 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:13.59907 INFO::Starting hierarchical adjustment
2024-10-05 03:08:13.600176 INFO::Found 2 batches.
2024-10-05 03:08:13.600891 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:13.601686 INFO::Using default BPPARAM
2024-10-05 03:08:13.602369 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:13.603685 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:13.637626 INFO::Done
2024-10-05 03:08:13.638473 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:13.643195 INFO::ASW Batch was -0.00107284927156936 prior to batch effect correction and is now -0.00107284927156936 .
2024-10-05 03:08:13.644322 INFO::Total function execution time is 0.0823376178741455 s and adjustment time is 0.0376501083374023 s ( 45.73 )
2024-10-05 03:08:13.666435 INFO::Formatting Data.
2024-10-05 03:08:13.667366 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:13.668438 INFO::Removing potential empty rows and columns
2024-10-05 03:08:13.669711 INFO::Found 0 missing values.
2024-10-05 03:08:13.673455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:13.674299 INFO::Done
2024-10-05 03:08:13.674969 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:13.67743 INFO::Starting hierarchical adjustment
2024-10-05 03:08:13.678335 INFO::Found 3 batches.
2024-10-05 03:08:13.679016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:13.679784 INFO::Using default BPPARAM
2024-10-05 03:08:13.68045 INFO::Processing subtree level 1
2024-10-05 03:08:13.88129 INFO::Adjusting the last 1 batches sequentially
2024-10-05 03:08:13.883824 INFO::Done
2024-10-05 03:08:13.884763 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:13.888381 INFO::ASW Batch was -0.0324600792738384 prior to batch effect correction and is now -0.157517633708363 .
2024-10-05 03:08:13.889859 INFO::Total function execution time is 0.223361968994141 s and adjustment time is 0.20564341545105 s ( 92.07 )
2024-10-05 03:08:13.912096 INFO::Skipping initial DF formatting
2024-10-05 03:08:13.913063 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:13.918914 INFO::Starting hierarchical adjustment
2024-10-05 03:08:13.920089 INFO::Found 5 batches.
2024-10-05 03:08:13.920843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:13.921747 INFO::Using default BPPARAM
2024-10-05 03:08:13.922464 INFO::Processing subtree level 1
2024-10-05 03:08:14.110059 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:14.112324 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:14.144357 INFO::Done
2024-10-05 03:08:14.145313 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:14.151733 INFO::ASW Batch was 0.508292850680841 prior to batch effect correction and is now 0.508292850680841 .
2024-10-05 03:08:14.152685 INFO::ASW Label was 0.384029799759588 prior to batch effect correction and is now 0.384029799759588 .
2024-10-05 03:08:14.153957 INFO::Total function execution time is 0.241932392120361 s and adjustment time is 0.224451303482056 s ( 92.77 )
2024-10-05 03:08:14.181154 INFO::Formatting Data.
2024-10-05 03:08:14.182221 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:14.183577 INFO::Removing potential empty rows and columns
2024-10-05 03:08:14.185027 INFO::Found 0 missing values.
2024-10-05 03:08:14.191383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:14.192313 INFO::Done
2024-10-05 03:08:14.193089 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:14.197458 INFO::Starting hierarchical adjustment
2024-10-05 03:08:14.198745 INFO::Found 5 batches.
2024-10-05 03:08:14.199607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:14.200584 INFO::Using default BPPARAM
2024-10-05 03:08:14.201378 INFO::Processing subtree level 1
2024-10-05 03:08:14.359823 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:14.361881 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:14.384678 INFO::Done
2024-10-05 03:08:14.385642 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:14.394753 INFO::ASW Batch was 0.285267340180966 prior to batch effect correction and is now -0.0814774560315689 .
2024-10-05 03:08:14.395966 INFO::ASW Label was 0.491606549173249 prior to batch effect correction and is now 0.84877301930587 .
2024-10-05 03:08:14.397266 INFO::Total function execution time is 0.216170787811279 s and adjustment time is 0.186186075210571 s ( 86.13 )
2024-10-05 03:08:14.398598 INFO::Formatting Data.
2024-10-05 03:08:14.399509 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:14.400802 INFO::Removing potential empty rows and columns
2024-10-05 03:08:14.402311 INFO::Found 0 missing values.
2024-10-05 03:08:14.408653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:14.409529 INFO::Done
2024-10-05 03:08:14.410325 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:14.414456 INFO::Starting hierarchical adjustment
2024-10-05 03:08:14.415593 INFO::Found 5 batches.
2024-10-05 03:08:14.416357 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:14.417359 INFO::Using default BPPARAM
2024-10-05 03:08:14.418142 INFO::Processing subtree level 1
2024-10-05 03:08:14.570232 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:14.572308 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:14.595858 INFO::Done
2024-10-05 03:08:14.599458 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:14.604138 INFO::ASW Batch was 0.285267340180966 prior to batch effect correction and is now -0.0814774560315689 .
2024-10-05 03:08:14.605044 INFO::ASW Label was 0.491606549173249 prior to batch effect correction and is now 0.84877301930587 .
2024-10-05 03:08:14.606233 INFO::Total function execution time is 0.207618236541748 s and adjustment time is 0.180450201034546 s ( 86.91 )
2024-10-05 03:08:14.626372 INFO::Formatting Data.
2024-10-05 03:08:14.627428 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:14.62872 INFO::Removing potential empty rows and columns
2024-10-05 03:08:14.630152 INFO::Found 0 missing values.
2024-10-05 03:08:14.636356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:14.637223 INFO::Done
2024-10-05 03:08:14.638046 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:14.642193 INFO::Starting hierarchical adjustment
2024-10-05 03:08:14.643322 INFO::Found 5 batches.
2024-10-05 03:08:14.644152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:14.645048 INFO::Using default BPPARAM
2024-10-05 03:08:14.645838 INFO::Processing subtree level 1
2024-10-05 03:08:14.84572 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:14.847729 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:14.869993 INFO::Done
2024-10-05 03:08:14.870916 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:14.875641 INFO::ASW Batch was 0.485617021644463 prior to batch effect correction and is now -0.0318920708843744 .
2024-10-05 03:08:14.876555 INFO::ASW Label was 0.338586319250513 prior to batch effect correction and is now 0.740731365977837 .
2024-10-05 03:08:14.877707 INFO::Total function execution time is 0.251370668411255 s and adjustment time is 0.226906299591064 s ( 90.27 )
2024-10-05 03:08:14.878833 INFO::Formatting Data.
2024-10-05 03:08:14.879702 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:14.880902 INFO::Removing potential empty rows and columns
2024-10-05 03:08:14.882324 INFO::Found 0 missing values.
2024-10-05 03:08:14.888546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:14.889409 INFO::Done
2024-10-05 03:08:14.890198 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:14.894347 INFO::Starting hierarchical adjustment
2024-10-05 03:08:14.895465 INFO::Found 5 batches.
2024-10-05 03:08:14.896249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:14.897118 INFO::Using default BPPARAM
2024-10-05 03:08:14.897909 INFO::Processing subtree level 1
2024-10-05 03:08:15.099531 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:15.101848 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:15.127409 INFO::Done
2024-10-05 03:08:15.128428 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:15.133422 INFO::ASW Batch was 0.485617021644463 prior to batch effect correction and is now -0.0318920708843744 .
2024-10-05 03:08:15.1344 INFO::ASW Label was 0.338586319250513 prior to batch effect correction and is now 0.740731365977837 .
2024-10-05 03:08:15.135783 INFO::Total function execution time is 0.256917238235474 s and adjustment time is 0.232139110565186 s ( 90.36 )
2024-10-05 03:08:15.157736 INFO::Formatting Data.
2024-10-05 03:08:15.158871 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:15.160271 INFO::Removing potential empty rows and columns
2024-10-05 03:08:15.161974 INFO::Found 0 missing values.
2024-10-05 03:08:15.166461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:15.16751 INFO::Done
2024-10-05 03:08:15.168325 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:15.173126 INFO::Starting hierarchical adjustment
2024-10-05 03:08:15.174338 INFO::Found 2 batches.
2024-10-05 03:08:15.175189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:15.176198 INFO::Using default BPPARAM
2024-10-05 03:08:15.177012 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:15.178345 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:15.200864 INFO::Done
2024-10-05 03:08:15.201894 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:15.206712 INFO::ASW Batch was 0.402320842604394 prior to batch effect correction and is now -0.0321352624781333 .
2024-10-05 03:08:15.207689 INFO::ASW Label was 0.545920892486391 prior to batch effect correction and is now 0.891199934656691 .
2024-10-05 03:08:15.20886 INFO::Total function execution time is 0.051236629486084 s and adjustment time is 0.0267689228057861 s ( 52.25 )
2024-10-05 03:08:15.210027 INFO::Formatting Data.
2024-10-05 03:08:15.210885 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:15.212184 INFO::Removing potential empty rows and columns
2024-10-05 03:08:15.213718 INFO::Found 0 missing values.
2024-10-05 03:08:15.217992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:15.218856 INFO::Done
2024-10-05 03:08:15.219672 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:15.22418 INFO::Starting hierarchical adjustment
2024-10-05 03:08:15.225302 INFO::Found 2 batches.
2024-10-05 03:08:15.226149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:15.227052 INFO::Using default BPPARAM
2024-10-05 03:08:15.227828 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:15.229191 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:15.25161 INFO::Done
2024-10-05 03:08:15.252472 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:15.256583 INFO::ASW Batch was 0.402320842604394 prior to batch effect correction and is now -0.0321352624781333 .
2024-10-05 03:08:15.25744 INFO::ASW Label was 0.545920892486391 prior to batch effect correction and is now 0.891199934656691 .
2024-10-05 03:08:15.258552 INFO::Total function execution time is 0.048588752746582 s and adjustment time is 0.0265090465545654 s ( 54.56 )
2024-10-05 03:08:15.274523 INFO::Formatting Data.
2024-10-05 03:08:15.275588 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:15.276876 INFO::Removing potential empty rows and columns
2024-10-05 03:08:15.278345 INFO::Found 0 missing values.
2024-10-05 03:08:15.281885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:15.282698 INFO::Done
2024-10-05 03:08:15.283474 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:15.286165 INFO::Starting hierarchical adjustment
2024-10-05 03:08:15.287246 INFO::Found 2 batches.
2024-10-05 03:08:15.288021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:15.288902 INFO::Using default BPPARAM
2024-10-05 03:08:15.289741 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:15.29112 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:15.338948 INFO::Done
2024-10-05 03:08:15.339844 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:15.34249 INFO::ASW Batch was -0.0294576693015664 prior to batch effect correction and is now -0.148143440248052 .
2024-10-05 03:08:15.343669 INFO::Total function execution time is 0.0692360401153564 s and adjustment time is 0.0519299507141113 s ( 75 )
2024-10-05 03:08:15.361279 INFO::Formatting Data.
2024-10-05 03:08:15.362473 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:15.363729 INFO::Removing potential empty rows and columns
2024-10-05 03:08:15.365216 INFO::Found 0 missing values.
2024-10-05 03:08:15.367135 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.
2024-10-05 03:08:15.37446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:15.375422 INFO::Done
2024-10-05 03:08:15.37625 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:15.380631 INFO::Starting hierarchical adjustment
2024-10-05 03:08:15.381763 INFO::Found 2 batches.
2024-10-05 03:08:15.382571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:15.383485 INFO::Using default BPPARAM
2024-10-05 03:08:15.384272 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:15.385698 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:15.411371 INFO::Done
2024-10-05 03:08:15.412318 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:15.416516 INFO::ASW Batch was 0.361261119996319 prior to batch effect correction and is now 0.0795944799614144 .
2024-10-05 03:08:15.417411 INFO::ASW Label was 0.564729629215892 prior to batch effect correction and is now 0.891476508252984 .
2024-10-05 03:08:15.418546 INFO::Total function execution time is 0.0574586391448975 s and adjustment time is 0.0298280715942383 s ( 51.91 )
2024-10-05 03:08:15.419715 INFO::Formatting Data.
2024-10-05 03:08:15.420781 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:15.422179 INFO::Removing potential empty rows and columns
2024-10-05 03:08:15.423708 INFO::Found 0 missing values.
2024-10-05 03:08:15.425143 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.
2024-10-05 03:08:15.432992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:15.433893 INFO::Done
2024-10-05 03:08:15.434644 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:15.442492 INFO::Starting hierarchical adjustment
2024-10-05 03:08:15.443693 INFO::Found 2 batches.
2024-10-05 03:08:15.444438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:15.445263 INFO::Using default BPPARAM
2024-10-05 03:08:15.445992 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:15.44734 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:15.472485 INFO::Done
2024-10-05 03:08:15.473424 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:15.477742 INFO::ASW Batch was 0.361261119996319 prior to batch effect correction and is now 0.0795944799614144 .
2024-10-05 03:08:15.478666 INFO::ASW Label was 0.564729629215892 prior to batch effect correction and is now 0.891476508252984 .
2024-10-05 03:08:15.479865 INFO::Total function execution time is 0.0601592063903809 s and adjustment time is 0.0290000438690186 s ( 48.21 )
2024-10-05 03:08:15.817225 INFO::Formatting Data.
2024-10-05 03:08:15.818335 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:15.819582 INFO::Removing potential empty rows and columns
2024-10-05 03:08:15.821065 INFO::Found 0 missing values.
2024-10-05 03:08:15.825683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:15.826556 INFO::Done
2024-10-05 03:08:15.82736 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:15.830237 INFO::Starting hierarchical adjustment
2024-10-05 03:08:15.831357 INFO::Found 3 batches.
2024-10-05 03:08:15.832201 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:15.833111 INFO::Using default BPPARAM
2024-10-05 03:08:15.833917 INFO::Processing subtree level 1
2024-10-05 03:08:15.957003 INFO::Adjusting the last 1 batches sequentially
2024-10-05 03:08:15.959289 INFO::Done
2024-10-05 03:08:15.96016 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:15.963485 INFO::ASW Batch was 0.139670869670613 prior to batch effect correction and is now 0.139670869670613 .
2024-10-05 03:08:15.964844 INFO::Total function execution time is 0.147651672363281 s and adjustment time is 0.128201961517334 s ( 86.83 )
2024-10-05 03:08:15.966393 INFO::Formatting Data.
2024-10-05 03:08:15.967298 INFO::Typecasting input to dataframe.
2024-10-05 03:08:15.96832 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:15.969575 INFO::Removing potential empty rows and columns
2024-10-05 03:08:15.971145 INFO::Found 0 missing values.
2024-10-05 03:08:15.975745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:15.976633 INFO::Done
2024-10-05 03:08:15.977431 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:15.980263 INFO::Starting hierarchical adjustment
2024-10-05 03:08:15.981323 INFO::Found 3 batches.
2024-10-05 03:08:15.982151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:15.983048 INFO::Using default BPPARAM
2024-10-05 03:08:15.983821 INFO::Processing subtree level 1
2024-10-05 03:08:16.150265 INFO::Adjusting the last 1 batches sequentially
2024-10-05 03:08:16.152472 INFO::Done
2024-10-05 03:08:16.153326 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:16.15661 INFO::ASW Batch was 0.139670869670613 prior to batch effect correction and is now 0.139670869670613 .
2024-10-05 03:08:16.157957 INFO::Total function execution time is 0.191537618637085 s and adjustment time is 0.171378135681152 s ( 89.47 )
2024-10-05 03:08:16.17604 INFO::Formatting Data.
2024-10-05 03:08:16.17709 INFO::Typecasting input to dataframe.
2024-10-05 03:08:16.178271 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:16.179564 INFO::Removing potential empty rows and columns
2024-10-05 03:08:16.181121 INFO::Found 0 missing values.
2024-10-05 03:08:16.185627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:16.186514 INFO::Done
2024-10-05 03:08:16.187275 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:16.190121 INFO::Starting hierarchical adjustment
2024-10-05 03:08:16.191146 INFO::Found 3 batches.
2024-10-05 03:08:16.191895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:16.192749 INFO::Using default BPPARAM
2024-10-05 03:08:16.193495 INFO::Processing subtree level 1
2024-10-05 03:08:16.363804 INFO::Adjusting the last 1 batches sequentially
2024-10-05 03:08:16.390485 INFO::Done
2024-10-05 03:08:16.392307 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:16.396092 INFO::ASW Batch was -0.0512500415424132 prior to batch effect correction and is now -0.0512500415424132 .
2024-10-05 03:08:16.397463 INFO::Total function execution time is 0.221467733383179 s and adjustment time is 0.199483633041382 s ( 90.07 )
2024-10-05 03:08:16.61636 INFO::Formatting Data.
2024-10-05 03:08:16.617578 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:16.619312 INFO::Removing potential empty rows and columns
2024-10-05 03:08:16.624072 INFO::Found 1000 missing values.
2024-10-05 03:08:16.655352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:16.656276 INFO::Done
2024-10-05 03:08:16.657037 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:16.665244 INFO::Starting hierarchical adjustment
2024-10-05 03:08:16.666511 INFO::Found 10 batches.
2024-10-05 03:08:16.66743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:16.668331 INFO::Using default BPPARAM
2024-10-05 03:08:16.669082 INFO::Processing subtree level 1
2024-10-05 03:08:16.874712 INFO::Processing subtree level 2
2024-10-05 03:08:17.110017 INFO::Adjusting the last 1 batches sequentially
2024-10-05 03:08:17.112421 INFO::Done
2024-10-05 03:08:17.113268 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:17.121437 INFO::ASW Batch was 0.487786673069796 prior to batch effect correction and is now 0.487786673069796 .
2024-10-05 03:08:17.122404 INFO::ASW Label was 0.329561306891622 prior to batch effect correction and is now 0.329561306891622 .
2024-10-05 03:08:17.123704 INFO::Total function execution time is 0.507621288299561 s and adjustment time is 0.446196556091309 s ( 87.9 )
2024-10-05 03:08:17.124917 INFO::Formatting Data.
2024-10-05 03:08:17.125821 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:17.127756 INFO::Removing potential empty rows and columns
2024-10-05 03:08:17.132473 INFO::Found 1000 missing values.
2024-10-05 03:08:17.164282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:17.165205 INFO::Done
2024-10-05 03:08:17.165998 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:17.174333 INFO::Starting hierarchical adjustment
2024-10-05 03:08:17.175593 INFO::Found 10 batches.
2024-10-05 03:08:18.495188 INFO::Set up parallel execution backend with 2 workers
2024-10-05 03:08:18.496339 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-05 03:08:19.891285 INFO::Adjusting the last 2 batches sequentially
2024-10-05 03:08:19.892972 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-05 03:08:19.917585 INFO::Done
2024-10-05 03:08:19.918423 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:19.925001 INFO::ASW Batch was 0.487786673069796 prior to batch effect correction and is now 0.487786673069796 .
2024-10-05 03:08:19.92583 INFO::ASW Label was 0.329561306891622 prior to batch effect correction and is now 0.329561306891622 .
2024-10-05 03:08:19.926816 INFO::Total function execution time is 2.80194473266602 s and adjustment time is 2.7422206401825 s ( 97.87 )
2024-10-05 03:08:20.113059 INFO::Formatting Data.
2024-10-05 03:08:20.114149 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.115401 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.116934 INFO::Found 0 missing values.
2024-10-05 03:08:20.122519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.123415 INFO::Done
2024-10-05 03:08:20.124145 INFO::Acquiring quality metrics before batch effect correction.
2024-10-05 03:08:20.128006 INFO::Starting hierarchical adjustment
2024-10-05 03:08:20.128994 INFO::Found 3 batches.
2024-10-05 03:08:20.129818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-05 03:08:20.130682 INFO::Using default BPPARAM
2024-10-05 03:08:20.131442 INFO::Processing subtree level 1
2024-10-05 03:08:20.266068 INFO::Adjusting the last 1 batches sequentially
2024-10-05 03:08:20.268377 INFO::Done
2024-10-05 03:08:20.269178 INFO::Acquiring quality metrics after batch effect correction.
2024-10-05 03:08:20.273619 INFO::ASW Batch was 0.160351155800154 prior to batch effect correction and is now -0.125949099382605 .
2024-10-05 03:08:20.274579 INFO::ASW Label was -0.15847535634178 prior to batch effect correction and is now -0.0481331595350305 .
2024-10-05 03:08:20.275856 INFO::Total function execution time is 0.162828207015991 s and adjustment time is 0.139587640762329 s ( 85.73 )
2024-10-05 03:08:20.445609 INFO::Formatting Data.
2024-10-05 03:08:20.446782 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.44805 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.449478 INFO::Found 2 missing values.
2024-10-05 03:08:20.45384 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.454643 INFO::Done
2024-10-05 03:08:20.494737 INFO::Found NA in Reference column
2024-10-05 03:08:20.508378 INFO::Require at least two references per batch.
2024-10-05 03:08:20.538721 INFO::Formatting Data.
2024-10-05 03:08:20.539723 INFO::Recognized SummarizedExperiment
2024-10-05 03:08:20.540433 INFO::Typecasting input to dataframe.
2024-10-05 03:08:20.555352 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.55695 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.562811 INFO::Found 0 missing values.
2024-10-05 03:08:20.574121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.575008 INFO::Done
2024-10-05 03:08:20.602346 INFO::Formatting Data.
2024-10-05 03:08:20.603384 INFO::Recognized SummarizedExperiment
2024-10-05 03:08:20.604086 INFO::Typecasting input to dataframe.
2024-10-05 03:08:20.629839 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.631467 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.637009 INFO::Found 0 missing values.
2024-10-05 03:08:20.655475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.656423 INFO::Done
2024-10-05 03:08:20.679104 INFO::Formatting Data.
2024-10-05 03:08:20.680033 INFO::Recognized SummarizedExperiment
2024-10-05 03:08:20.680851 INFO::Typecasting input to dataframe.
2024-10-05 03:08:20.705845 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.707163 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.708683 INFO::Found 0 missing values.
2024-10-05 03:08:20.709909 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.
2024-10-05 03:08:20.716402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.717262 INFO::Done
2024-10-05 03:08:20.731797 INFO::Formatting Data.
2024-10-05 03:08:20.732863 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.734077 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.73565 INFO::Found 0 missing values.
2024-10-05 03:08:20.740766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.741668 INFO::Done
2024-10-05 03:08:20.75787 INFO::Formatting Data.
2024-10-05 03:08:20.758864 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.760209 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.761851 INFO::Found 0 missing values.
2024-10-05 03:08:20.766322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.767193 INFO::Done
2024-10-05 03:08:20.808114 INFO::Formatting Data.
2024-10-05 03:08:20.809097 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.810556 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.812356 INFO::Found 1 missing values.
2024-10-05 03:08:20.816547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.81738 INFO::Done
2024-10-05 03:08:20.844141 INFO::Formatting Data.
2024-10-05 03:08:20.845184 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.846359 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.847703 INFO::Found 2 missing values.
2024-10-05 03:08:20.848981 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.
2024-10-05 03:08:20.852164 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.852935 INFO::Done
2024-10-05 03:08:20.867702 INFO::Formatting Data.
2024-10-05 03:08:20.868733 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.869953 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.871374 INFO::Found 2 missing values.
2024-10-05 03:08:20.873614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.874433 INFO::Done
2024-10-05 03:08:20.890129 INFO::Formatting Data.
2024-10-05 03:08:20.89116 INFO::Typecasting input to dataframe.
2024-10-05 03:08:20.892293 INFO::Replacing NaNs with NAs.
2024-10-05 03:08:20.893577 INFO::Removing potential empty rows and columns
2024-10-05 03:08:20.895082 INFO::Found 0 missing values.
2024-10-05 03:08:20.899896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-05 03:08:20.900683 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.019 4.669 26.178
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.437 | 1.806 | 22.692 | |
| compute_asw | 0.035 | 0.000 | 0.035 | |
| count_existing | 0.016 | 0.003 | 0.020 | |
| generate_data_covariables | 0.017 | 0.000 | 0.017 | |
| generate_dataset | 0.015 | 0.000 | 0.015 | |