Yannis Schumann
| Snapshot Date: 2024-06-30 14:00 -0400 (Sun, 30 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-03 10:19 -0400 (Wed, 03 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4480 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4511 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4469 |
| 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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.0.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-06-30 22:29:09 -0400 (Sun, 30 Jun 2024) |
| EndedAt: 2024-06-30 22:31:20 -0400 (Sun, 30 Jun 2024) |
| EllapsedTime: 130.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 8.61 0.53 17.67
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'BERT' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-06-30 22:30:09.72496 INFO::Formatting Data.
2024-06-30 22:30:09.727965 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:09.74273 INFO::Removing potential empty rows and columns
2024-06-30 22:30:09.965227 INFO::Found 0 missing values.
2024-06-30 22:30:09.968209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:09.969018 INFO::Done
2024-06-30 22:30:09.96975 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:09.983059 INFO::Starting hierarchical adjustment
2024-06-30 22:30:09.984096 INFO::Found 3 batches.
2024-06-30 22:30:09.984833 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:09.986085 INFO::Using default BPPARAM
2024-06-30 22:30:09.986829 INFO::Processing subtree level 1
2024-06-30 22:30:12.544962 INFO::Adjusting the last 1 batches sequentially
2024-06-30 22:30:12.547395 INFO::Done
2024-06-30 22:30:12.54886 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:12.552492 INFO::ASW Batch was -0.125077724461129 prior to batch effect correction and is now -0.125077724461129 .
2024-06-30 22:30:12.554389 INFO::Total function execution time is 2.83005309104919 s and adjustment time is 2.5634069442749 s ( 90.58 )
2024-06-30 22:30:12.578566 INFO::Formatting Data.
2024-06-30 22:30:12.580194 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:12.582038 INFO::Removing potential empty rows and columns
2024-06-30 22:30:12.584045 INFO::Found 0 missing values.
2024-06-30 22:30:12.585897 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.
2024-06-30 22:30:12.599657 INFO::Formatting Data.
2024-06-30 22:30:12.601282 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:12.603202 INFO::Removing potential empty rows and columns
2024-06-30 22:30:12.60527 INFO::Found 0 missing values.
2024-06-30 22:30:12.607035 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.
2024-06-30 22:30:12.633554 INFO::Formatting Data.
2024-06-30 22:30:12.635114 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:12.636877 INFO::Removing potential empty rows and columns
2024-06-30 22:30:12.638745 INFO::Found 0 missing values.
2024-06-30 22:30:12.64051 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.
2024-06-30 22:30:12.646636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:12.647889 INFO::Done
2024-06-30 22:30:12.649069 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:12.652276 INFO::Starting hierarchical adjustment
2024-06-30 22:30:12.653682 INFO::Found 2 batches.
2024-06-30 22:30:12.654881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:12.656253 INFO::Using default BPPARAM
2024-06-30 22:30:12.657513 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:12.659344 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:12.685114 INFO::Done
2024-06-30 22:30:12.686548 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:12.690006 INFO::ASW Batch was 0.0530335005614566 prior to batch effect correction and is now -0.127410955336729 .
2024-06-30 22:30:12.69164 INFO::Total function execution time is 0.0581769943237305 s and adjustment time is 0.031580924987793 s ( 54.28 )
2024-06-30 22:30:12.695992 INFO::Formatting Data.
2024-06-30 22:30:12.697333 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:12.709177 INFO::Formatting Data.
2024-06-30 22:30:12.710751 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:12.712586 INFO::Removing potential empty rows and columns
2024-06-30 22:30:12.714524 INFO::Found 0 missing values.
2024-06-30 22:30:12.719054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:12.720361 INFO::Done
2024-06-30 22:30:12.721611 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:12.725008 INFO::Starting hierarchical adjustment
2024-06-30 22:30:12.72647 INFO::Found 2 batches.
2024-06-30 22:30:12.727654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:12.728945 INFO::Using default BPPARAM
2024-06-30 22:30:12.730123 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:12.731913 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:12.752169 INFO::Done
2024-06-30 22:30:12.7536 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:12.757018 INFO::ASW Batch was 0.065452135071899 prior to batch effect correction and is now -0.105857314152551 .
2024-06-30 22:30:12.758557 INFO::Total function execution time is 0.0494589805603027 s and adjustment time is 0.0258650779724121 s ( 52.3 )
2024-06-30 22:30:12.760462 INFO::Formatting Data.
2024-06-30 22:30:12.761731 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:12.763384 INFO::Removing potential empty rows and columns
2024-06-30 22:30:12.765205 INFO::Found 0 missing values.
2024-06-30 22:30:12.769583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:12.770824 INFO::Done
2024-06-30 22:30:12.772033 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:12.775308 INFO::Starting hierarchical adjustment
2024-06-30 22:30:12.7767 INFO::Found 2 batches.
2024-06-30 22:30:12.777828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:12.77914 INFO::Using default BPPARAM
2024-06-30 22:30:12.780382 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:12.782184 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:12.802561 INFO::Done
2024-06-30 22:30:12.803768 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:12.806214 INFO::ASW Batch was 0.065452135071899 prior to batch effect correction and is now -0.105857314152551 .
2024-06-30 22:30:12.807761 INFO::Total function execution time is 0.0472590923309326 s and adjustment time is 0.0260140895843506 s ( 55.05 )
2024-06-30 22:30:15.168637 INFO::Formatting Data.
2024-06-30 22:30:15.169564 INFO::Recognized SummarizedExperiment
2024-06-30 22:30:15.170316 INFO::Typecasting input to dataframe.
2024-06-30 22:30:15.209526 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:15.211902 INFO::Removing potential empty rows and columns
2024-06-30 22:30:15.217388 INFO::Found 0 missing values.
2024-06-30 22:30:15.949354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:15.950375 INFO::Done
2024-06-30 22:30:15.951145 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:15.954795 INFO::Starting hierarchical adjustment
2024-06-30 22:30:15.95569 INFO::Found 2 batches.
2024-06-30 22:30:15.956385 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:15.957608 INFO::Using default BPPARAM
2024-06-30 22:30:15.958322 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:15.959522 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:16.012576 INFO::Done
2024-06-30 22:30:16.013516 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:16.017221 INFO::ASW Batch was -0.010526175263635 prior to batch effect correction and is now -0.0990214399660123 .
2024-06-30 22:30:16.018323 INFO::Total function execution time is 0.849948883056641 s and adjustment time is 0.0569911003112793 s ( 6.71 )
2024-06-30 22:30:16.036448 INFO::Formatting Data.
2024-06-30 22:30:16.03743 INFO::Recognized SummarizedExperiment
2024-06-30 22:30:16.03832 INFO::Typecasting input to dataframe.
2024-06-30 22:30:16.046208 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:16.047532 INFO::Removing potential empty rows and columns
2024-06-30 22:30:16.050401 INFO::Found 0 missing values.
2024-06-30 22:30:16.0558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:16.05661 INFO::Done
2024-06-30 22:30:16.057395 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:16.061226 INFO::Starting hierarchical adjustment
2024-06-30 22:30:16.062121 INFO::Found 2 batches.
2024-06-30 22:30:16.062836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:16.063599 INFO::Using default BPPARAM
2024-06-30 22:30:16.064308 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:16.065481 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:16.085286 INFO::Done
2024-06-30 22:30:16.086277 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:16.090105 INFO::ASW Batch was 0.00373509194942827 prior to batch effect correction and is now 0.00373509194942827 .
2024-06-30 22:30:16.091176 INFO::Total function execution time is 0.054671049118042 s and adjustment time is 0.0232138633728027 s ( 42.46 )
2024-06-30 22:30:16.112018 INFO::Formatting Data.
2024-06-30 22:30:16.11299 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:16.114116 INFO::Removing potential empty rows and columns
2024-06-30 22:30:16.115298 INFO::Found 0 missing values.
2024-06-30 22:30:16.118021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:16.118762 INFO::Done
2024-06-30 22:30:16.119467 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:16.12163 INFO::Starting hierarchical adjustment
2024-06-30 22:30:16.122492 INFO::Found 3 batches.
2024-06-30 22:30:16.1232 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:16.123994 INFO::Using default BPPARAM
2024-06-30 22:30:16.1247 INFO::Processing subtree level 1
2024-06-30 22:30:25.867735 INFO::Adjusting the last 1 batches sequentially
2024-06-30 22:30:25.870159 INFO::Done
2024-06-30 22:30:25.871478 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:25.87452 INFO::ASW Batch was 0.0293074310683697 prior to batch effect correction and is now -0.174870108858147 .
2024-06-30 22:30:25.875622 INFO::Total function execution time is 9.76366901397705 s and adjustment time is 9.74771285057068 s ( 99.84 )
2024-06-30 22:30:25.900489 INFO::Skipping initial DF formatting
2024-06-30 22:30:25.901932 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:25.908865 INFO::Starting hierarchical adjustment
2024-06-30 22:30:25.910582 INFO::Found 5 batches.
2024-06-30 22:30:25.911865 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:25.91319 INFO::Using default BPPARAM
2024-06-30 22:30:25.914411 INFO::Processing subtree level 1
2024-06-30 22:30:29.166746 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:29.169085 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:29.194325 INFO::Done
2024-06-30 22:30:29.195932 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:29.202973 INFO::ASW Batch was 0.537897429847896 prior to batch effect correction and is now 0.537897429847896 .
2024-06-30 22:30:29.203901 INFO::ASW Label was 0.353456499486244 prior to batch effect correction and is now 0.353456499486244 .
2024-06-30 22:30:29.205446 INFO::Total function execution time is 3.30502414703369 s and adjustment time is 3.28396105766296 s ( 99.36 )
2024-06-30 22:30:29.228837 INFO::Formatting Data.
2024-06-30 22:30:29.229837 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:29.230923 INFO::Removing potential empty rows and columns
2024-06-30 22:30:29.232108 INFO::Found 0 missing values.
2024-06-30 22:30:29.235671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:29.23646 INFO::Done
2024-06-30 22:30:29.237214 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:29.24037 INFO::Starting hierarchical adjustment
2024-06-30 22:30:29.241336 INFO::Found 5 batches.
2024-06-30 22:30:29.242054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:29.242851 INFO::Using default BPPARAM
2024-06-30 22:30:29.243556 INFO::Processing subtree level 1
2024-06-30 22:30:32.607861 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:32.609291 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:32.628256 INFO::Done
2024-06-30 22:30:32.629491 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:32.632583 INFO::ASW Batch was 0.363326469552049 prior to batch effect correction and is now -0.0364767269817931 .
2024-06-30 22:30:32.633422 INFO::ASW Label was 0.376767123515125 prior to batch effect correction and is now 0.792970554579719 .
2024-06-30 22:30:32.634393 INFO::Total function execution time is 3.4056510925293 s and adjustment time is 3.38698792457581 s ( 99.45 )
2024-06-30 22:30:32.635338 INFO::Formatting Data.
2024-06-30 22:30:32.636121 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:32.637143 INFO::Removing potential empty rows and columns
2024-06-30 22:30:32.638248 INFO::Found 0 missing values.
2024-06-30 22:30:32.641735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:32.642456 INFO::Done
2024-06-30 22:30:32.643152 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:32.646281 INFO::Starting hierarchical adjustment
2024-06-30 22:30:32.647158 INFO::Found 5 batches.
2024-06-30 22:30:32.647857 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:32.648645 INFO::Using default BPPARAM
2024-06-30 22:30:32.649337 INFO::Processing subtree level 1
2024-06-30 22:30:35.536076 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:35.537917 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:35.549806 INFO::Done
2024-06-30 22:30:35.550696 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:35.553757 INFO::ASW Batch was 0.363326469552049 prior to batch effect correction and is now -0.0364767269817931 .
2024-06-30 22:30:35.55462 INFO::ASW Label was 0.376767123515125 prior to batch effect correction and is now 0.792970554579719 .
2024-06-30 22:30:35.555562 INFO::Total function execution time is 2.92023301124573 s and adjustment time is 2.90275001525879 s ( 99.4 )
2024-06-30 22:30:35.573366 INFO::Formatting Data.
2024-06-30 22:30:35.574942 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:35.576676 INFO::Removing potential empty rows and columns
2024-06-30 22:30:35.578394 INFO::Found 0 missing values.
2024-06-30 22:30:35.583983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:35.585198 INFO::Done
2024-06-30 22:30:35.586365 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:35.590164 INFO::Starting hierarchical adjustment
2024-06-30 22:30:35.591088 INFO::Found 5 batches.
2024-06-30 22:30:35.591866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:35.59283 INFO::Using default BPPARAM
2024-06-30 22:30:35.593975 INFO::Processing subtree level 1
2024-06-30 22:30:38.456406 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:38.458305 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:38.477228 INFO::Done
2024-06-30 22:30:38.478672 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:38.483501 INFO::ASW Batch was 0.390398265300256 prior to batch effect correction and is now -0.0555122514496299 .
2024-06-30 22:30:38.484884 INFO::ASW Label was 0.482262760552983 prior to batch effect correction and is now 0.80378905588219 .
2024-06-30 22:30:38.486486 INFO::Total function execution time is 2.91319894790649 s and adjustment time is 2.8862099647522 s ( 99.07 )
2024-06-30 22:30:38.488077 INFO::Formatting Data.
2024-06-30 22:30:38.489441 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:38.491111 INFO::Removing potential empty rows and columns
2024-06-30 22:30:38.492935 INFO::Found 0 missing values.
2024-06-30 22:30:38.498859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:38.500181 INFO::Done
2024-06-30 22:30:38.501428 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:38.50611 INFO::Starting hierarchical adjustment
2024-06-30 22:30:38.507603 INFO::Found 5 batches.
2024-06-30 22:30:38.508823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:38.510143 INFO::Using default BPPARAM
2024-06-30 22:30:38.511362 INFO::Processing subtree level 1
2024-06-30 22:30:41.306117 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:41.308153 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:41.320812 INFO::Done
2024-06-30 22:30:41.321671 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:41.324621 INFO::ASW Batch was 0.390398265300256 prior to batch effect correction and is now -0.0555122514496299 .
2024-06-30 22:30:41.325396 INFO::ASW Label was 0.482262760552983 prior to batch effect correction and is now 0.80378905588219 .
2024-06-30 22:30:41.326323 INFO::Total function execution time is 2.83835697174072 s and adjustment time is 2.81344699859619 s ( 99.12 )
2024-06-30 22:30:41.341758 INFO::Formatting Data.
2024-06-30 22:30:41.342713 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:41.343767 INFO::Removing potential empty rows and columns
2024-06-30 22:30:41.344863 INFO::Found 0 missing values.
2024-06-30 22:30:41.347217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:41.347921 INFO::Done
2024-06-30 22:30:41.348608 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:41.352876 INFO::Starting hierarchical adjustment
2024-06-30 22:30:41.354163 INFO::Found 2 batches.
2024-06-30 22:30:41.355169 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:41.356292 INFO::Using default BPPARAM
2024-06-30 22:30:41.357306 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:41.358845 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:41.373753 INFO::Done
2024-06-30 22:30:41.374664 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:41.377623 INFO::ASW Batch was 0.67017633022085 prior to batch effect correction and is now 0.0226262758217046 .
2024-06-30 22:30:41.378414 INFO::ASW Label was 0.390977436746745 prior to batch effect correction and is now 0.879290471249368 .
2024-06-30 22:30:41.379368 INFO::Total function execution time is 0.0376949310302734 s and adjustment time is 0.0197868347167969 s ( 52.49 )
2024-06-30 22:30:41.380347 INFO::Formatting Data.
2024-06-30 22:30:41.381147 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:41.382168 INFO::Removing potential empty rows and columns
2024-06-30 22:30:41.383249 INFO::Found 0 missing values.
2024-06-30 22:30:41.385637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:41.386354 INFO::Done
2024-06-30 22:30:41.387047 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:41.389969 INFO::Starting hierarchical adjustment
2024-06-30 22:30:41.390858 INFO::Found 2 batches.
2024-06-30 22:30:41.391562 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:41.392331 INFO::Using default BPPARAM
2024-06-30 22:30:41.393029 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:41.394138 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:41.410802 INFO::Done
2024-06-30 22:30:41.411758 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:41.415881 INFO::ASW Batch was 0.67017633022085 prior to batch effect correction and is now 0.0226262758217046 .
2024-06-30 22:30:41.417212 INFO::ASW Label was 0.390977436746745 prior to batch effect correction and is now 0.879290471249368 .
2024-06-30 22:30:41.418836 INFO::Total function execution time is 0.0384008884429932 s and adjustment time is 0.020035982131958 s ( 52.18 )
2024-06-30 22:30:41.440986 INFO::Formatting Data.
2024-06-30 22:30:41.442481 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:41.444351 INFO::Removing potential empty rows and columns
2024-06-30 22:30:41.445582 INFO::Found 0 missing values.
2024-06-30 22:30:41.447596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:41.448317 INFO::Done
2024-06-30 22:30:41.44901 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:41.450988 INFO::Starting hierarchical adjustment
2024-06-30 22:30:41.451862 INFO::Found 2 batches.
2024-06-30 22:30:41.452565 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:41.453339 INFO::Using default BPPARAM
2024-06-30 22:30:41.454041 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:41.455114 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:41.479979 INFO::Done
2024-06-30 22:30:41.480852 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:41.482871 INFO::ASW Batch was 0.339340839033829 prior to batch effect correction and is now -0.0859755680975061 .
2024-06-30 22:30:41.483838 INFO::Total function execution time is 0.0430698394775391 s and adjustment time is 0.0282139778137207 s ( 65.51 )
2024-06-30 22:30:41.499026 INFO::Formatting Data.
2024-06-30 22:30:41.499987 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:41.501094 INFO::Removing potential empty rows and columns
2024-06-30 22:30:41.502222 INFO::Found 0 missing values.
2024-06-30 22:30:41.503476 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.
2024-06-30 22:30:41.50747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:41.508207 INFO::Done
2024-06-30 22:30:41.508908 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:41.511851 INFO::Starting hierarchical adjustment
2024-06-30 22:30:41.512751 INFO::Found 2 batches.
2024-06-30 22:30:41.513482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:41.514312 INFO::Using default BPPARAM
2024-06-30 22:30:41.515026 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:41.516113 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:41.529757 INFO::Done
2024-06-30 22:30:41.53063 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:41.533617 INFO::ASW Batch was 0.787485583677867 prior to batch effect correction and is now -0.0216639068802404 .
2024-06-30 22:30:41.53441 INFO::ASW Label was 0.174267967953751 prior to batch effect correction and is now 0.840723448893595 .
2024-06-30 22:30:41.535365 INFO::Total function execution time is 0.0364151000976562 s and adjustment time is 0.0171329975128174 s ( 47.05 )
2024-06-30 22:30:41.536352 INFO::Formatting Data.
2024-06-30 22:30:41.537184 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:41.538245 INFO::Removing potential empty rows and columns
2024-06-30 22:30:41.539367 INFO::Found 0 missing values.
2024-06-30 22:30:41.54108 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.
2024-06-30 22:30:41.546107 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:41.546883 INFO::Done
2024-06-30 22:30:41.547601 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:41.551037 INFO::Starting hierarchical adjustment
2024-06-30 22:30:41.552373 INFO::Found 2 batches.
2024-06-30 22:30:41.553511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:41.554831 INFO::Using default BPPARAM
2024-06-30 22:30:41.556026 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:30:41.55772 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:30:41.579935 INFO::Done
2024-06-30 22:30:41.58134 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:41.586079 INFO::ASW Batch was 0.787485583677867 prior to batch effect correction and is now -0.0216639068802404 .
2024-06-30 22:30:41.587416 INFO::ASW Label was 0.174267967953751 prior to batch effect correction and is now 0.840723448893595 .
2024-06-30 22:30:41.589002 INFO::Total function execution time is 0.0525789260864258 s and adjustment time is 0.0276980400085449 s ( 52.68 )
2024-06-30 22:30:41.901669 INFO::Formatting Data.
2024-06-30 22:30:41.903166 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:41.905045 INFO::Removing potential empty rows and columns
2024-06-30 22:30:41.907277 INFO::Found 0 missing values.
2024-06-30 22:30:41.91294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:41.914436 INFO::Done
2024-06-30 22:30:41.915814 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:41.919413 INFO::Starting hierarchical adjustment
2024-06-30 22:30:41.921049 INFO::Found 3 batches.
2024-06-30 22:30:41.922344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:41.923699 INFO::Using default BPPARAM
2024-06-30 22:30:41.924906 INFO::Processing subtree level 1
2024-06-30 22:30:44.675664 INFO::Adjusting the last 1 batches sequentially
2024-06-30 22:30:44.677942 INFO::Done
2024-06-30 22:30:44.679308 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:44.682658 INFO::ASW Batch was -0.0982976732230866 prior to batch effect correction and is now -0.0982976732230866 .
2024-06-30 22:30:44.684271 INFO::Total function execution time is 2.78267693519592 s and adjustment time is 2.75710391998291 s ( 99.08 )
2024-06-30 22:30:44.686131 INFO::Formatting Data.
2024-06-30 22:30:44.687492 INFO::Typecasting input to dataframe.
2024-06-30 22:30:44.689013 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:44.690679 INFO::Removing potential empty rows and columns
2024-06-30 22:30:44.692538 INFO::Found 0 missing values.
2024-06-30 22:30:44.696968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:44.698182 INFO::Done
2024-06-30 22:30:44.699351 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:44.702587 INFO::Starting hierarchical adjustment
2024-06-30 22:30:44.703968 INFO::Found 3 batches.
2024-06-30 22:30:44.705151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:44.706424 INFO::Using default BPPARAM
2024-06-30 22:30:44.707564 INFO::Processing subtree level 1
2024-06-30 22:30:47.52086 INFO::Adjusting the last 1 batches sequentially
2024-06-30 22:30:47.522947 INFO::Done
2024-06-30 22:30:47.524021 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:47.526132 INFO::ASW Batch was -0.0982976732230866 prior to batch effect correction and is now -0.0982976732230866 .
2024-06-30 22:30:47.527132 INFO::Total function execution time is 2.84110498428345 s and adjustment time is 2.81916403770447 s ( 99.23 )
2024-06-30 22:30:47.545813 INFO::Formatting Data.
2024-06-30 22:30:47.54733 INFO::Typecasting input to dataframe.
2024-06-30 22:30:47.548943 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:47.550576 INFO::Removing potential empty rows and columns
2024-06-30 22:30:47.55243 INFO::Found 0 missing values.
2024-06-30 22:30:47.556094 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:47.556954 INFO::Done
2024-06-30 22:30:47.557831 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:47.560359 INFO::Starting hierarchical adjustment
2024-06-30 22:30:47.561619 INFO::Found 3 batches.
2024-06-30 22:30:47.562685 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:47.563916 INFO::Using default BPPARAM
2024-06-30 22:30:47.565153 INFO::Processing subtree level 1
2024-06-30 22:30:50.447389 INFO::Adjusting the last 1 batches sequentially
2024-06-30 22:30:50.449471 INFO::Done
2024-06-30 22:30:50.450564 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:50.452694 INFO::ASW Batch was -0.091669702218259 prior to batch effect correction and is now -0.091669702218259 .
2024-06-30 22:30:50.453724 INFO::Total function execution time is 2.90808606147766 s and adjustment time is 2.88804507255554 s ( 99.31 )
2024-06-30 22:30:53.437553 INFO::Formatting Data.
2024-06-30 22:30:53.439081 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:53.441115 INFO::Removing potential empty rows and columns
2024-06-30 22:30:53.444905 INFO::Found 1000 missing values.
2024-06-30 22:30:53.468537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:53.47 INFO::Done
2024-06-30 22:30:53.471314 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:53.481148 INFO::Starting hierarchical adjustment
2024-06-30 22:30:53.482778 INFO::Found 10 batches.
2024-06-30 22:30:53.484069 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:30:53.485393 INFO::Using default BPPARAM
2024-06-30 22:30:53.486559 INFO::Processing subtree level 1
2024-06-30 22:30:56.379076 INFO::Processing subtree level 2
2024-06-30 22:30:59.227088 INFO::Adjusting the last 1 batches sequentially
2024-06-30 22:30:59.229462 INFO::Done
2024-06-30 22:30:59.230655 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:30:59.238949 INFO::ASW Batch was 0.514894819402017 prior to batch effect correction and is now 0.514894819402017 .
2024-06-30 22:30:59.240209 INFO::ASW Label was 0.318968242224673 prior to batch effect correction and is now 0.318968242224673 .
2024-06-30 22:30:59.241714 INFO::Total function execution time is 5.80429792404175 s and adjustment time is 5.74695014953613 s ( 99.01 )
2024-06-30 22:30:59.243057 INFO::Formatting Data.
2024-06-30 22:30:59.2442 INFO::Replacing NaNs with NAs.
2024-06-30 22:30:59.245941 INFO::Removing potential empty rows and columns
2024-06-30 22:30:59.24929 INFO::Found 1000 missing values.
2024-06-30 22:30:59.262136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:30:59.263146 INFO::Done
2024-06-30 22:30:59.263922 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:30:59.271237 INFO::Starting hierarchical adjustment
2024-06-30 22:30:59.272246 INFO::Found 10 batches.
2024-06-30 22:31:00.040155 INFO::Set up parallel execution backend with 2 workers
2024-06-30 22:31:00.041689 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-30 22:31:02.858599 INFO::Adjusting the last 2 batches sequentially
2024-06-30 22:31:02.860048 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-30 22:31:02.874201 INFO::Done
2024-06-30 22:31:02.875065 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:31:02.880737 INFO::ASW Batch was 0.514894819402017 prior to batch effect correction and is now 0.514894819402017 .
2024-06-30 22:31:02.881542 INFO::ASW Label was 0.318968242224673 prior to batch effect correction and is now 0.318968242224673 .
2024-06-30 22:31:02.882493 INFO::Total function execution time is 3.63950395584106 s and adjustment time is 3.60209393501282 s ( 98.97 )
2024-06-30 22:31:05.829278 INFO::Formatting Data.
2024-06-30 22:31:05.830879 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:05.832735 INFO::Removing potential empty rows and columns
2024-06-30 22:31:05.834505 INFO::Found 0 missing values.
2024-06-30 22:31:05.839592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:05.840827 INFO::Done
2024-06-30 22:31:05.842 INFO::Acquiring quality metrics before batch effect correction.
2024-06-30 22:31:05.846306 INFO::Starting hierarchical adjustment
2024-06-30 22:31:05.847711 INFO::Found 3 batches.
2024-06-30 22:31:05.84889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-30 22:31:05.85017 INFO::Using default BPPARAM
2024-06-30 22:31:05.851352 INFO::Processing subtree level 1
2024-06-30 22:31:08.940558 INFO::Adjusting the last 1 batches sequentially
2024-06-30 22:31:08.942705 INFO::Done
2024-06-30 22:31:08.943993 INFO::Acquiring quality metrics after batch effect correction.
2024-06-30 22:31:08.94822 INFO::ASW Batch was 0.240768618163622 prior to batch effect correction and is now -0.14003778341033 .
2024-06-30 22:31:08.949473 INFO::ASW Label was -0.210359150815171 prior to batch effect correction and is now -0.118520876130415 .
2024-06-30 22:31:08.950963 INFO::Total function execution time is 3.1217930316925 s and adjustment time is 3.09517288208008 s ( 99.15 )
2024-06-30 22:31:09.163954 INFO::Formatting Data.
2024-06-30 22:31:09.165487 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.16718 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.168971 INFO::Found 2 missing values.
2024-06-30 22:31:09.173181 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.174363 INFO::Done
2024-06-30 22:31:09.231025 INFO::Found NA in Reference column
2024-06-30 22:31:09.246708 INFO::Require at least two references per batch.
2024-06-30 22:31:09.27461 INFO::Formatting Data.
2024-06-30 22:31:09.276089 INFO::Recognized SummarizedExperiment
2024-06-30 22:31:09.277362 INFO::Typecasting input to dataframe.
2024-06-30 22:31:09.2857 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.287044 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.289734 INFO::Found 0 missing values.
2024-06-30 22:31:09.298385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.299764 INFO::Done
2024-06-30 22:31:09.316086 INFO::Formatting Data.
2024-06-30 22:31:09.317576 INFO::Recognized SummarizedExperiment
2024-06-30 22:31:09.318884 INFO::Typecasting input to dataframe.
2024-06-30 22:31:09.342642 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.344871 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.349871 INFO::Found 0 missing values.
2024-06-30 22:31:09.364142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.365573 INFO::Done
2024-06-30 22:31:09.389028 INFO::Formatting Data.
2024-06-30 22:31:09.390543 INFO::Recognized SummarizedExperiment
2024-06-30 22:31:09.391795 INFO::Typecasting input to dataframe.
2024-06-30 22:31:09.415294 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.417235 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.419252 INFO::Found 0 missing values.
2024-06-30 22:31:09.421025 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.
2024-06-30 22:31:09.427494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.42882 INFO::Done
2024-06-30 22:31:09.449852 INFO::Formatting Data.
2024-06-30 22:31:09.451386 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.453095 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.454902 INFO::Found 0 missing values.
2024-06-30 22:31:09.459484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.460733 INFO::Done
2024-06-30 22:31:09.483401 INFO::Formatting Data.
2024-06-30 22:31:09.484916 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.48664 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.488477 INFO::Found 0 missing values.
2024-06-30 22:31:09.493071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.494327 INFO::Done
2024-06-30 22:31:09.555497 INFO::Formatting Data.
2024-06-30 22:31:09.557139 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.559139 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.561223 INFO::Found 1 missing values.
2024-06-30 22:31:09.565118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.566402 INFO::Done
2024-06-30 22:31:09.603991 INFO::Formatting Data.
2024-06-30 22:31:09.605591 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.607357 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.609181 INFO::Found 2 missing values.
2024-06-30 22:31:09.610962 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.
2024-06-30 22:31:09.614509 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.615728 INFO::Done
2024-06-30 22:31:09.637157 INFO::Formatting Data.
2024-06-30 22:31:09.638755 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.64042 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.64155 INFO::Found 2 missing values.
2024-06-30 22:31:09.644275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.645462 INFO::Done
2024-06-30 22:31:09.666424 INFO::Formatting Data.
2024-06-30 22:31:09.668042 INFO::Typecasting input to dataframe.
2024-06-30 22:31:09.669744 INFO::Replacing NaNs with NAs.
2024-06-30 22:31:09.671617 INFO::Removing potential empty rows and columns
2024-06-30 22:31:09.672783 INFO::Found 0 missing values.
2024-06-30 22:31:09.675375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-30 22:31:09.676129 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
29.03 1.73 74.81
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.61 | 0.53 | 17.67 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0.01 | 0.00 | 0.02 | |