Yannis Schumann
| Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 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 2024-07-24 11:38 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 157/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | | ||||||||
|
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: 1.1.2 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-07-23 21:19:18 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 21:20:48 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --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: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 26.682 1.642 19.489
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-07-23 21:20:12.101897 INFO::Formatting Data.
2024-07-23 21:20:12.103522 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:12.114968 INFO::Removing potential empty rows and columns
2024-07-23 21:20:12.407849 INFO::Found 0 missing values.
2024-07-23 21:20:12.411811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:12.412579 INFO::Done
2024-07-23 21:20:12.413286 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:12.428187 INFO::Starting hierarchical adjustment
2024-07-23 21:20:12.429178 INFO::Found 3 batches.
2024-07-23 21:20:12.429753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:12.430992 INFO::Using default BPPARAM
2024-07-23 21:20:12.43166 INFO::Processing subtree level 1
2024-07-23 21:20:12.526675 INFO::Adjusting the last 1 batches sequentially
2024-07-23 21:20:12.528494 INFO::Done
2024-07-23 21:20:12.529214 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:12.531795 INFO::ASW Batch was -0.0226270298456085 prior to batch effect correction and is now -0.0226270298456085 .
2024-07-23 21:20:12.53294 INFO::Total function execution time is 0.431955814361572 s and adjustment time is 0.099524974822998 s ( 23.04 )
2024-07-23 21:20:12.547051 INFO::Formatting Data.
2024-07-23 21:20:12.54781 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:12.548749 INFO::Removing potential empty rows and columns
2024-07-23 21:20:12.549855 INFO::Found 0 missing values.
2024-07-23 21:20:12.55079 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.
2024-07-23 21:20:12.562502 INFO::Formatting Data.
2024-07-23 21:20:12.563345 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:12.564366 INFO::Removing potential empty rows and columns
2024-07-23 21:20:12.565482 INFO::Found 0 missing values.
2024-07-23 21:20:12.566528 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.
2024-07-23 21:20:12.583387 INFO::Formatting Data.
2024-07-23 21:20:12.584205 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:12.585096 INFO::Removing potential empty rows and columns
2024-07-23 21:20:12.586091 INFO::Found 0 missing values.
2024-07-23 21:20:12.586986 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.
2024-07-23 21:20:12.591286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:12.59183 INFO::Done
2024-07-23 21:20:12.59234 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:12.59434 INFO::Starting hierarchical adjustment
2024-07-23 21:20:12.594994 INFO::Found 2 batches.
2024-07-23 21:20:12.595484 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:12.596071 INFO::Using default BPPARAM
2024-07-23 21:20:12.596575 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:12.597491 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:12.62029 INFO::Done
2024-07-23 21:20:12.621033 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:12.623083 INFO::ASW Batch was 0.0890742643344331 prior to batch effect correction and is now -0.118589703564359 .
2024-07-23 21:20:12.623971 INFO::Total function execution time is 0.0405809879302979 s and adjustment time is 0.0253822803497314 s ( 62.55 )
2024-07-23 21:20:12.626814 INFO::Formatting Data.
2024-07-23 21:20:12.627414 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:12.636349 INFO::Formatting Data.
2024-07-23 21:20:12.637137 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:12.63804 INFO::Removing potential empty rows and columns
2024-07-23 21:20:12.639045 INFO::Found 0 missing values.
2024-07-23 21:20:12.641862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:12.642373 INFO::Done
2024-07-23 21:20:12.642842 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:12.644865 INFO::Starting hierarchical adjustment
2024-07-23 21:20:12.645518 INFO::Found 2 batches.
2024-07-23 21:20:12.645999 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:12.646551 INFO::Using default BPPARAM
2024-07-23 21:20:12.647021 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:12.64791 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:12.662883 INFO::Done
2024-07-23 21:20:12.663601 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:12.665727 INFO::ASW Batch was 0.00475042296122136 prior to batch effect correction and is now -0.111559768826228 .
2024-07-23 21:20:12.666556 INFO::Total function execution time is 0.030315637588501 s and adjustment time is 0.0174498558044434 s ( 57.56 )
2024-07-23 21:20:12.667632 INFO::Formatting Data.
2024-07-23 21:20:12.668237 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:12.669089 INFO::Removing potential empty rows and columns
2024-07-23 21:20:12.670102 INFO::Found 0 missing values.
2024-07-23 21:20:12.67295 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:12.673442 INFO::Done
2024-07-23 21:20:12.673918 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:12.675915 INFO::Starting hierarchical adjustment
2024-07-23 21:20:12.67658 INFO::Found 2 batches.
2024-07-23 21:20:12.677052 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:12.677599 INFO::Using default BPPARAM
2024-07-23 21:20:12.678077 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:12.678933 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:12.693847 INFO::Done
2024-07-23 21:20:12.694534 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:12.696675 INFO::ASW Batch was 0.00475042296122136 prior to batch effect correction and is now -0.111559768826228 .
2024-07-23 21:20:12.697474 INFO::Total function execution time is 0.029836893081665 s and adjustment time is 0.0173771381378174 s ( 58.24 )
2024-07-23 21:20:14.919801 INFO::Formatting Data.
2024-07-23 21:20:14.920808 INFO::Recognized SummarizedExperiment
2024-07-23 21:20:14.921315 INFO::Typecasting input to dataframe.
2024-07-23 21:20:14.998138 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:14.999487 INFO::Removing potential empty rows and columns
2024-07-23 21:20:15.00298 INFO::Found 0 missing values.
2024-07-23 21:20:15.009351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:15.010005 INFO::Done
2024-07-23 21:20:15.010485 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:15.014076 INFO::Starting hierarchical adjustment
2024-07-23 21:20:15.014792 INFO::Found 2 batches.
2024-07-23 21:20:15.015263 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:15.016426 INFO::Using default BPPARAM
2024-07-23 21:20:15.016928 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:15.01794 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:15.069907 INFO::Done
2024-07-23 21:20:15.070531 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:15.073554 INFO::ASW Batch was 0.00638841882996073 prior to batch effect correction and is now -0.0994762049941725 .
2024-07-23 21:20:15.074317 INFO::Total function execution time is 0.155004024505615 s and adjustment time is 0.055239200592041 s ( 35.64 )
2024-07-23 21:20:15.089869 INFO::Formatting Data.
2024-07-23 21:20:15.09053 INFO::Recognized SummarizedExperiment
2024-07-23 21:20:15.090969 INFO::Typecasting input to dataframe.
2024-07-23 21:20:15.098542 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:15.099539 INFO::Removing potential empty rows and columns
2024-07-23 21:20:15.102312 INFO::Found 0 missing values.
2024-07-23 21:20:15.107756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:15.108249 INFO::Done
2024-07-23 21:20:15.108673 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:15.111519 INFO::Starting hierarchical adjustment
2024-07-23 21:20:15.11214 INFO::Found 2 batches.
2024-07-23 21:20:15.112571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:15.113051 INFO::Using default BPPARAM
2024-07-23 21:20:15.113468 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:15.114298 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:15.134108 INFO::Done
2024-07-23 21:20:15.134782 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:15.137722 INFO::ASW Batch was -0.0233428685111794 prior to batch effect correction and is now -0.0233428685111794 .
2024-07-23 21:20:15.138499 INFO::Total function execution time is 0.0486080646514893 s and adjustment time is 0.0220463275909424 s ( 45.36 )
2024-07-23 21:20:15.154026 INFO::Formatting Data.
2024-07-23 21:20:15.154785 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:15.155654 INFO::Removing potential empty rows and columns
2024-07-23 21:20:15.156569 INFO::Found 0 missing values.
2024-07-23 21:20:15.159212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:15.159691 INFO::Done
2024-07-23 21:20:15.160151 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:15.161917 INFO::Starting hierarchical adjustment
2024-07-23 21:20:15.16252 INFO::Found 3 batches.
2024-07-23 21:20:15.162971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:15.163484 INFO::Using default BPPARAM
2024-07-23 21:20:15.163955 INFO::Processing subtree level 1
2024-07-23 21:20:15.337387 INFO::Adjusting the last 1 batches sequentially
2024-07-23 21:20:15.339339 INFO::Done
2024-07-23 21:20:15.339999 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:15.342947 INFO::ASW Batch was -0.043151307084158 prior to batch effect correction and is now -0.142908715822887 .
2024-07-23 21:20:15.34393 INFO::Total function execution time is 0.189907073974609 s and adjustment time is 0.176911592483521 s ( 93.16 )
2024-07-23 21:20:15.359911 INFO::Skipping initial DF formatting
2024-07-23 21:20:15.360628 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:15.364987 INFO::Starting hierarchical adjustment
2024-07-23 21:20:15.365794 INFO::Found 5 batches.
2024-07-23 21:20:15.366343 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:15.367034 INFO::Using default BPPARAM
2024-07-23 21:20:15.367573 INFO::Processing subtree level 1
2024-07-23 21:20:15.497704 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:15.499347 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:15.519775 INFO::Done
2024-07-23 21:20:15.520499 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:15.525198 INFO::ASW Batch was 0.464137331821227 prior to batch effect correction and is now 0.464137331821227 .
2024-07-23 21:20:15.525786 INFO::ASW Label was 0.402681700445082 prior to batch effect correction and is now 0.402681700445082 .
2024-07-23 21:20:15.526617 INFO::Total function execution time is 0.166795015335083 s and adjustment time is 0.154131174087524 s ( 92.41 )
2024-07-23 21:20:15.544799 INFO::Formatting Data.
2024-07-23 21:20:15.545619 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:15.546522 INFO::Removing potential empty rows and columns
2024-07-23 21:20:15.547526 INFO::Found 0 missing values.
2024-07-23 21:20:15.551753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:15.552315 INFO::Done
2024-07-23 21:20:15.552818 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:15.555828 INFO::Starting hierarchical adjustment
2024-07-23 21:20:15.556509 INFO::Found 5 batches.
2024-07-23 21:20:15.557001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:15.557578 INFO::Using default BPPARAM
2024-07-23 21:20:15.558057 INFO::Processing subtree level 1
2024-07-23 21:20:15.667664 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:15.669231 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:15.684692 INFO::Done
2024-07-23 21:20:15.685353 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:15.688391 INFO::ASW Batch was 0.697122255746439 prior to batch effect correction and is now -0.104877168936048 .
2024-07-23 21:20:15.688969 INFO::ASW Label was 0.0785142657704853 prior to batch effect correction and is now 0.788292898393269 .
2024-07-23 21:20:15.689732 INFO::Total function execution time is 0.145029544830322 s and adjustment time is 0.128286600112915 s ( 88.46 )
2024-07-23 21:20:15.690511 INFO::Formatting Data.
2024-07-23 21:20:15.691096 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:15.691935 INFO::Removing potential empty rows and columns
2024-07-23 21:20:15.692858 INFO::Found 0 missing values.
2024-07-23 21:20:15.696733 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:15.697223 INFO::Done
2024-07-23 21:20:15.697695 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:15.700503 INFO::Starting hierarchical adjustment
2024-07-23 21:20:15.701148 INFO::Found 5 batches.
2024-07-23 21:20:15.701616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:15.702171 INFO::Using default BPPARAM
2024-07-23 21:20:15.702645 INFO::Processing subtree level 1
2024-07-23 21:20:15.812248 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:15.814046 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:15.830239 INFO::Done
2024-07-23 21:20:15.831038 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:15.834505 INFO::ASW Batch was 0.697122255746439 prior to batch effect correction and is now -0.104877168936048 .
2024-07-23 21:20:15.835122 INFO::ASW Label was 0.0785142657704853 prior to batch effect correction and is now 0.788292898393269 .
2024-07-23 21:20:15.835974 INFO::Total function execution time is 0.145418167114258 s and adjustment time is 0.129164457321167 s ( 88.82 )
2024-07-23 21:20:15.849863 INFO::Formatting Data.
2024-07-23 21:20:15.850703 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:15.851658 INFO::Removing potential empty rows and columns
2024-07-23 21:20:15.852697 INFO::Found 0 missing values.
2024-07-23 21:20:15.856813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:15.857353 INFO::Done
2024-07-23 21:20:15.857859 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:15.861105 INFO::Starting hierarchical adjustment
2024-07-23 21:20:15.861853 INFO::Found 5 batches.
2024-07-23 21:20:15.862406 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:15.863092 INFO::Using default BPPARAM
2024-07-23 21:20:15.863629 INFO::Processing subtree level 1
2024-07-23 21:20:15.981973 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:15.983692 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:16.000124 INFO::Done
2024-07-23 21:20:16.000906 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.004333 INFO::ASW Batch was 0.338189749353521 prior to batch effect correction and is now -0.0689735179787538 .
2024-07-23 21:20:16.004956 INFO::ASW Label was 0.408701578381351 prior to batch effect correction and is now 0.850139320316538 .
2024-07-23 21:20:16.005845 INFO::Total function execution time is 0.156092882156372 s and adjustment time is 0.138386011123657 s ( 88.66 )
2024-07-23 21:20:16.006692 INFO::Formatting Data.
2024-07-23 21:20:16.007294 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.00819 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.009168 INFO::Found 0 missing values.
2024-07-23 21:20:16.013053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.013566 INFO::Done
2024-07-23 21:20:16.014039 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.017129 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.017823 INFO::Found 5 batches.
2024-07-23 21:20:16.018317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.018935 INFO::Using default BPPARAM
2024-07-23 21:20:16.019419 INFO::Processing subtree level 1
2024-07-23 21:20:16.132108 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:16.133726 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:16.149234 INFO::Done
2024-07-23 21:20:16.149976 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.153285 INFO::ASW Batch was 0.338189749353521 prior to batch effect correction and is now -0.0689735179787538 .
2024-07-23 21:20:16.153841 INFO::ASW Label was 0.408701578381351 prior to batch effect correction and is now 0.850139320316538 .
2024-07-23 21:20:16.154628 INFO::Total function execution time is 0.147953510284424 s and adjustment time is 0.131511449813843 s ( 88.89 )
2024-07-23 21:20:16.167932 INFO::Formatting Data.
2024-07-23 21:20:16.168665 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.169579 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.170562 INFO::Found 0 missing values.
2024-07-23 21:20:16.173961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.174768 INFO::Done
2024-07-23 21:20:16.175294 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.17856 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.179322 INFO::Found 2 batches.
2024-07-23 21:20:16.179834 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.180477 INFO::Using default BPPARAM
2024-07-23 21:20:16.181024 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:16.181967 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:16.197523 INFO::Done
2024-07-23 21:20:16.198253 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.201231 INFO::ASW Batch was 0.570580889598609 prior to batch effect correction and is now 0.0293500516913698 .
2024-07-23 21:20:16.201795 INFO::ASW Label was 0.481640068260466 prior to batch effect correction and is now 0.893826732447521 .
2024-07-23 21:20:16.20259 INFO::Total function execution time is 0.0347692966461182 s and adjustment time is 0.018324613571167 s ( 52.7 )
2024-07-23 21:20:16.203366 INFO::Formatting Data.
2024-07-23 21:20:16.203964 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.204821 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.205759 INFO::Found 0 missing values.
2024-07-23 21:20:16.208443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.208937 INFO::Done
2024-07-23 21:20:16.209401 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.212233 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.212911 INFO::Found 2 batches.
2024-07-23 21:20:16.213397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.213972 INFO::Using default BPPARAM
2024-07-23 21:20:16.214469 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:16.215339 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:16.246701 INFO::Done
2024-07-23 21:20:16.247396 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.250408 INFO::ASW Batch was 0.570580889598609 prior to batch effect correction and is now 0.0293500516913698 .
2024-07-23 21:20:16.250968 INFO::ASW Label was 0.481640068260466 prior to batch effect correction and is now 0.893826732447521 .
2024-07-23 21:20:16.25172 INFO::Total function execution time is 0.0483646392822266 s and adjustment time is 0.0338823795318604 s ( 70.06 )
2024-07-23 21:20:16.26283 INFO::Formatting Data.
2024-07-23 21:20:16.263544 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.26441 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.265254 INFO::Found 0 missing values.
2024-07-23 21:20:16.267262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.267748 INFO::Done
2024-07-23 21:20:16.268223 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.270056 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.2707 INFO::Found 2 batches.
2024-07-23 21:20:16.27117 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.271739 INFO::Using default BPPARAM
2024-07-23 21:20:16.272224 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:16.273055 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:16.3043 INFO::Done
2024-07-23 21:20:16.304976 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.3069 INFO::ASW Batch was 0.12185240409804 prior to batch effect correction and is now -0.127010481805205 .
2024-07-23 21:20:16.307669 INFO::Total function execution time is 0.044935941696167 s and adjustment time is 0.0337142944335938 s ( 75.03 )
2024-07-23 21:20:16.319082 INFO::Formatting Data.
2024-07-23 21:20:16.319796 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.320671 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.321653 INFO::Found 0 missing values.
2024-07-23 21:20:16.322889 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.
2024-07-23 21:20:16.32743 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.327966 INFO::Done
2024-07-23 21:20:16.328427 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.33136 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.332042 INFO::Found 2 batches.
2024-07-23 21:20:16.332545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.333107 INFO::Using default BPPARAM
2024-07-23 21:20:16.333581 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:16.334461 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:16.351378 INFO::Done
2024-07-23 21:20:16.352015 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.354805 INFO::ASW Batch was 0.626095961223531 prior to batch effect correction and is now 0.0207434392753995 .
2024-07-23 21:20:16.355339 INFO::ASW Label was 0.411820918618969 prior to batch effect correction and is now 0.889329741453822 .
2024-07-23 21:20:16.356049 INFO::Total function execution time is 0.0370619297027588 s and adjustment time is 0.0194840431213379 s ( 52.57 )
2024-07-23 21:20:16.356778 INFO::Formatting Data.
2024-07-23 21:20:16.357335 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.35818 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.359131 INFO::Found 0 missing values.
2024-07-23 21:20:16.359992 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.
2024-07-23 21:20:16.364258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.364787 INFO::Done
2024-07-23 21:20:16.365273 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.368104 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.368765 INFO::Found 2 batches.
2024-07-23 21:20:16.369253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.3698 INFO::Using default BPPARAM
2024-07-23 21:20:16.370285 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:16.371175 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:16.388328 INFO::Done
2024-07-23 21:20:16.389022 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.392217 INFO::ASW Batch was 0.626095961223531 prior to batch effect correction and is now 0.0207434392753995 .
2024-07-23 21:20:16.392856 INFO::ASW Label was 0.411820918618969 prior to batch effect correction and is now 0.889329741453822 .
2024-07-23 21:20:16.393674 INFO::Total function execution time is 0.0368847846984863 s and adjustment time is 0.0196683406829834 s ( 53.32 )
2024-07-23 21:20:16.630832 INFO::Formatting Data.
2024-07-23 21:20:16.631828 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.632722 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.633724 INFO::Found 0 missing values.
2024-07-23 21:20:16.636511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.637025 INFO::Done
2024-07-23 21:20:16.637496 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.639577 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.640285 INFO::Found 3 batches.
2024-07-23 21:20:16.640764 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.641335 INFO::Using default BPPARAM
2024-07-23 21:20:16.641806 INFO::Processing subtree level 1
2024-07-23 21:20:16.734706 INFO::Adjusting the last 1 batches sequentially
2024-07-23 21:20:16.736785 INFO::Done
2024-07-23 21:20:16.737604 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.740544 INFO::ASW Batch was -0.0581450310493719 prior to batch effect correction and is now -0.0581450310493719 .
2024-07-23 21:20:16.74173 INFO::Total function execution time is 0.110924959182739 s and adjustment time is 0.0966215133666992 s ( 87.11 )
2024-07-23 21:20:16.742995 INFO::Formatting Data.
2024-07-23 21:20:16.743776 INFO::Typecasting input to dataframe.
2024-07-23 21:20:16.744658 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.745651 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.746757 INFO::Found 0 missing values.
2024-07-23 21:20:16.74983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.750383 INFO::Done
2024-07-23 21:20:16.750907 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.753128 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.753852 INFO::Found 3 batches.
2024-07-23 21:20:16.754407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.755025 INFO::Using default BPPARAM
2024-07-23 21:20:16.755544 INFO::Processing subtree level 1
2024-07-23 21:20:16.84571 INFO::Adjusting the last 1 batches sequentially
2024-07-23 21:20:16.847622 INFO::Done
2024-07-23 21:20:16.848341 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.850967 INFO::ASW Batch was -0.0581450310493719 prior to batch effect correction and is now -0.0581450310493719 .
2024-07-23 21:20:16.851968 INFO::Total function execution time is 0.108986377716064 s and adjustment time is 0.0938775539398193 s ( 86.14 )
2024-07-23 21:20:16.86546 INFO::Formatting Data.
2024-07-23 21:20:16.866246 INFO::Typecasting input to dataframe.
2024-07-23 21:20:16.867054 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:16.867973 INFO::Removing potential empty rows and columns
2024-07-23 21:20:16.869058 INFO::Found 0 missing values.
2024-07-23 21:20:16.871974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:16.87251 INFO::Done
2024-07-23 21:20:16.873025 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:16.875077 INFO::Starting hierarchical adjustment
2024-07-23 21:20:16.875744 INFO::Found 3 batches.
2024-07-23 21:20:16.876248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:16.876854 INFO::Using default BPPARAM
2024-07-23 21:20:16.877377 INFO::Processing subtree level 1
2024-07-23 21:20:16.981391 INFO::Adjusting the last 1 batches sequentially
2024-07-23 21:20:16.983449 INFO::Done
2024-07-23 21:20:16.984192 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:16.986903 INFO::ASW Batch was -0.0861111940358868 prior to batch effect correction and is now -0.0861111940358868 .
2024-07-23 21:20:16.987963 INFO::Total function execution time is 0.12252402305603 s and adjustment time is 0.107809066772461 s ( 87.99 )
2024-07-23 21:20:17.141878 INFO::Formatting Data.
2024-07-23 21:20:17.142664 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:17.143848 INFO::Removing potential empty rows and columns
2024-07-23 21:20:17.146826 INFO::Found 1000 missing values.
2024-07-23 21:20:17.166817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:17.167531 INFO::Done
2024-07-23 21:20:17.168086 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:17.173654 INFO::Starting hierarchical adjustment
2024-07-23 21:20:17.174394 INFO::Found 10 batches.
2024-07-23 21:20:17.174949 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:17.175543 INFO::Using default BPPARAM
2024-07-23 21:20:17.17609 INFO::Processing subtree level 1
2024-07-23 21:20:17.375278 INFO::Processing subtree level 2
2024-07-23 21:20:17.552685 INFO::Adjusting the last 1 batches sequentially
2024-07-23 21:20:17.554866 INFO::Done
2024-07-23 21:20:17.555635 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:17.562732 INFO::ASW Batch was 0.482140034944709 prior to batch effect correction and is now 0.482140034944709 .
2024-07-23 21:20:17.563526 INFO::ASW Label was 0.320002471156682 prior to batch effect correction and is now 0.320002471156682 .
2024-07-23 21:20:17.564646 INFO::Total function execution time is 0.422779083251953 s and adjustment time is 0.380584001541138 s ( 90.02 )
2024-07-23 21:20:17.565709 INFO::Formatting Data.
2024-07-23 21:20:17.56651 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:17.568219 INFO::Removing potential empty rows and columns
2024-07-23 21:20:17.572495 INFO::Found 1000 missing values.
2024-07-23 21:20:17.597694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:17.598497 INFO::Done
2024-07-23 21:20:17.599124 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:17.60557 INFO::Starting hierarchical adjustment
2024-07-23 21:20:17.606423 INFO::Found 10 batches.
2024-07-23 21:20:18.725522 INFO::Set up parallel execution backend with 2 workers
2024-07-23 21:20:18.726963 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-23 21:20:19.888829 INFO::Adjusting the last 2 batches sequentially
2024-07-23 21:20:19.890279 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 21:20:19.90564 INFO::Done
2024-07-23 21:20:19.906221 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:19.910714 INFO::ASW Batch was 0.482140034944709 prior to batch effect correction and is now 0.482140034944709 .
2024-07-23 21:20:19.91122 INFO::ASW Label was 0.320002471156682 prior to batch effect correction and is now 0.320002471156682 .
2024-07-23 21:20:19.915164 INFO::Total function execution time is 2.3462655544281 s and adjustment time is 2.29938244819641 s ( 98 )
2024-07-23 21:20:20.075792 INFO::Formatting Data.
2024-07-23 21:20:20.07661 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.077583 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.07862 INFO::Found 0 missing values.
2024-07-23 21:20:20.082277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.082797 INFO::Done
2024-07-23 21:20:20.083296 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 21:20:20.086088 INFO::Starting hierarchical adjustment
2024-07-23 21:20:20.086766 INFO::Found 3 batches.
2024-07-23 21:20:20.087279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 21:20:20.08788 INFO::Using default BPPARAM
2024-07-23 21:20:20.088419 INFO::Processing subtree level 1
2024-07-23 21:20:20.188098 INFO::Adjusting the last 1 batches sequentially
2024-07-23 21:20:20.189778 INFO::Done
2024-07-23 21:20:20.1904 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 21:20:20.193542 INFO::ASW Batch was 0.267443751762306 prior to batch effect correction and is now -0.125963722647055 .
2024-07-23 21:20:20.194139 INFO::ASW Label was -0.213130935687875 prior to batch effect correction and is now 0.022051581920788 .
2024-07-23 21:20:20.195013 INFO::Total function execution time is 0.119275331497192 s and adjustment time is 0.103131532669067 s ( 86.47 )
2024-07-23 21:20:20.306652 INFO::Formatting Data.
2024-07-23 21:20:20.307396 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.308259 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.309227 INFO::Found 2 missing values.
2024-07-23 21:20:20.311973 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.31247 INFO::Done
2024-07-23 21:20:20.337519 INFO::Found NA in Reference column
2024-07-23 21:20:20.346688 INFO::Require at least two references per batch.
2024-07-23 21:20:20.366577 INFO::Formatting Data.
2024-07-23 21:20:20.367307 INFO::Recognized SummarizedExperiment
2024-07-23 21:20:20.367851 INFO::Typecasting input to dataframe.
2024-07-23 21:20:20.377482 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.378607 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.382169 INFO::Found 0 missing values.
2024-07-23 21:20:20.389091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.38963 INFO::Done
2024-07-23 21:20:20.405139 INFO::Formatting Data.
2024-07-23 21:20:20.405863 INFO::Recognized SummarizedExperiment
2024-07-23 21:20:20.406362 INFO::Typecasting input to dataframe.
2024-07-23 21:20:20.423044 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.42425 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.427532 INFO::Found 0 missing values.
2024-07-23 21:20:20.437709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.438387 INFO::Done
2024-07-23 21:20:20.454011 INFO::Formatting Data.
2024-07-23 21:20:20.454745 INFO::Recognized SummarizedExperiment
2024-07-23 21:20:20.455243 INFO::Typecasting input to dataframe.
2024-07-23 21:20:20.472044 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.473051 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.474194 INFO::Found 0 missing values.
2024-07-23 21:20:20.475077 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.
2024-07-23 21:20:20.479277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.479773 INFO::Done
2024-07-23 21:20:20.489989 INFO::Formatting Data.
2024-07-23 21:20:20.490713 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.491532 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.492502 INFO::Found 0 missing values.
2024-07-23 21:20:20.495387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.495901 INFO::Done
2024-07-23 21:20:20.506275 INFO::Formatting Data.
2024-07-23 21:20:20.50693 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.507713 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.508689 INFO::Found 0 missing values.
2024-07-23 21:20:20.511389 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.512014 INFO::Done
2024-07-23 21:20:20.538686 INFO::Formatting Data.
2024-07-23 21:20:20.539413 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.540342 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.541356 INFO::Found 1 missing values.
2024-07-23 21:20:20.543674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.544165 INFO::Done
2024-07-23 21:20:20.560127 INFO::Formatting Data.
2024-07-23 21:20:20.560874 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.561726 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.562579 INFO::Found 2 missing values.
2024-07-23 21:20:20.563425 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.
2024-07-23 21:20:20.565571 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.566077 INFO::Done
2024-07-23 21:20:20.574961 INFO::Formatting Data.
2024-07-23 21:20:20.575651 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.576492 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.577342 INFO::Found 2 missing values.
2024-07-23 21:20:20.578934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.579468 INFO::Done
2024-07-23 21:20:20.588861 INFO::Formatting Data.
2024-07-23 21:20:20.589525 INFO::Typecasting input to dataframe.
2024-07-23 21:20:20.590266 INFO::Replacing NaNs with NAs.
2024-07-23 21:20:20.591059 INFO::Removing potential empty rows and columns
2024-07-23 21:20:20.59202 INFO::Found 0 missing values.
2024-07-23 21:20:20.594814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 21:20:20.595318 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.452 3.546 20.833
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.682 | 1.642 | 19.489 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.010 | 0.007 | 0.016 | |
| generate_data_covariables | 0.014 | 0.000 | 0.015 | |
| generate_dataset | 0.010 | 0.004 | 0.014 | |