Yannis Schumann
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:43 -0400 (Tue, 16 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" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 154/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | 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 | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | 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: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-07-15 19:23:50 -0400 (Mon, 15 Jul 2024) |
| EndedAt: 2024-07-15 19:24:17 -0400 (Mon, 15 Jul 2024) |
| EllapsedTime: 27.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.0’
* 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 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 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 8.949 0.302 6.401
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")
2024-07-15 19:24:11.023033 INFO::Formatting Data.
2024-07-15 19:24:11.024667 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:11.028886 INFO::Removing potential empty rows and columns
2024-07-15 19:24:11.138633 INFO::Found 0 missing values.
2024-07-15 19:24:11.139888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:11.140112 INFO::Done
2024-07-15 19:24:11.140334 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:11.146213 INFO::Starting hierarchical adjustment
2024-07-15 19:24:11.146552 INFO::Found 3 batches.
2024-07-15 19:24:11.146729 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:11.147171 INFO::Using default BPPARAM
2024-07-15 19:24:11.147341 INFO::Processing subtree level 1
2024-07-15 19:24:11.198855 INFO::Adjusting the last 1 batches sequentially
2024-07-15 19:24:11.200054 INFO::Done
2024-07-15 19:24:11.200246 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:11.201546 INFO::ASW Batch was -0.0633787792256997 prior to batch effect correction and is now -0.0633787792256997 .
2024-07-15 19:24:11.202067 INFO::Total function execution time is 0.179326057434082 s and adjustment time is 0.0535871982574463 s ( 29.88 )
2024-07-15 19:24:11.208188 INFO::Formatting Data.
2024-07-15 19:24:11.208438 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:11.208761 INFO::Removing potential empty rows and columns
2024-07-15 19:24:11.209155 INFO::Found 0 missing values.
2024-07-15 19:24:11.209442 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.
2024-07-15 19:24:11.213206 INFO::Formatting Data.
2024-07-15 19:24:11.213401 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:11.213691 INFO::Removing potential empty rows and columns
2024-07-15 19:24:11.214009 INFO::Found 0 missing values.
2024-07-15 19:24:11.214261 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.
2024-07-15 19:24:11.219456 INFO::Formatting Data.
2024-07-15 19:24:11.219643 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:11.219879 INFO::Removing potential empty rows and columns
2024-07-15 19:24:11.220149 INFO::Found 0 missing values.
2024-07-15 19:24:11.220383 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.
2024-07-15 19:24:11.221555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:11.221712 INFO::Done
2024-07-15 19:24:11.221863 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:11.222464 INFO::Starting hierarchical adjustment
2024-07-15 19:24:11.222642 INFO::Found 2 batches.
2024-07-15 19:24:11.222783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:11.222987 INFO::Using default BPPARAM
2024-07-15 19:24:11.223115 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:11.223359 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:11.231712 INFO::Done
2024-07-15 19:24:11.231935 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:11.232582 INFO::ASW Batch was -0.0251904519618812 prior to batch effect correction and is now -0.108434703387911 .
2024-07-15 19:24:11.232808 INFO::Total function execution time is 0.013355016708374 s and adjustment time is 0.00908803939819336 s ( 68.05 )
2024-07-15 19:24:11.233753 INFO::Formatting Data.
2024-07-15 19:24:11.233929 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:11.236553 INFO::Formatting Data.
2024-07-15 19:24:11.236754 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:11.237009 INFO::Removing potential empty rows and columns
2024-07-15 19:24:11.237308 INFO::Found 0 missing values.
2024-07-15 19:24:11.238142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:11.238285 INFO::Done
2024-07-15 19:24:11.238417 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:11.238974 INFO::Starting hierarchical adjustment
2024-07-15 19:24:11.239163 INFO::Found 2 batches.
2024-07-15 19:24:11.239305 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:11.239468 INFO::Using default BPPARAM
2024-07-15 19:24:11.239614 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:11.23984 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:11.244919 INFO::Done
2024-07-15 19:24:11.245129 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:11.245741 INFO::ASW Batch was -0.0310691789454822 prior to batch effect correction and is now -0.135814873671117 .
2024-07-15 19:24:11.245963 INFO::Total function execution time is 0.00940513610839844 s and adjustment time is 0.00578713417053223 s ( 61.53 )
2024-07-15 19:24:11.246293 INFO::Formatting Data.
2024-07-15 19:24:11.246468 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:11.246714 INFO::Removing potential empty rows and columns
2024-07-15 19:24:11.247026 INFO::Found 0 missing values.
2024-07-15 19:24:11.247856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:11.248014 INFO::Done
2024-07-15 19:24:11.248155 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:11.248708 INFO::Starting hierarchical adjustment
2024-07-15 19:24:11.248907 INFO::Found 2 batches.
2024-07-15 19:24:11.24905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:11.249224 INFO::Using default BPPARAM
2024-07-15 19:24:11.249368 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:11.249611 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:11.253969 INFO::Done
2024-07-15 19:24:11.254123 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:11.254609 INFO::ASW Batch was -0.0310691789454822 prior to batch effect correction and is now -0.135814873671117 .
2024-07-15 19:24:11.25482 INFO::Total function execution time is 0.00852489471435547 s and adjustment time is 0.00510001182556152 s ( 59.82 )
2024-07-15 19:24:12.316517 INFO::Formatting Data.
2024-07-15 19:24:12.316764 INFO::Recognized SummarizedExperiment
2024-07-15 19:24:12.31691 INFO::Typecasting input to dataframe.
2024-07-15 19:24:12.326508 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.326869 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.327987 INFO::Found 0 missing values.
2024-07-15 19:24:12.329875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.330033 INFO::Done
2024-07-15 19:24:12.330165 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.331186 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.331354 INFO::Found 2 batches.
2024-07-15 19:24:12.331471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.33177 INFO::Using default BPPARAM
2024-07-15 19:24:12.331886 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.332117 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.346193 INFO::Done
2024-07-15 19:24:12.346363 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.347348 INFO::ASW Batch was 0.022269365794817 prior to batch effect correction and is now -0.0914811748495123 .
2024-07-15 19:24:12.347559 INFO::Total function execution time is 0.0311388969421387 s and adjustment time is 0.0148680210113525 s ( 47.75 )
2024-07-15 19:24:12.352536 INFO::Formatting Data.
2024-07-15 19:24:12.352699 INFO::Recognized SummarizedExperiment
2024-07-15 19:24:12.352826 INFO::Typecasting input to dataframe.
2024-07-15 19:24:12.355297 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.355598 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.356624 INFO::Found 0 missing values.
2024-07-15 19:24:12.358559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.358709 INFO::Done
2024-07-15 19:24:12.358844 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.359876 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.360051 INFO::Found 2 batches.
2024-07-15 19:24:12.36018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.36033 INFO::Using default BPPARAM
2024-07-15 19:24:12.360453 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.360706 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.367832 INFO::Done
2024-07-15 19:24:12.367994 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.369009 INFO::ASW Batch was 0.00185881461394151 prior to batch effect correction and is now 0.00185881461394151 .
2024-07-15 19:24:12.369221 INFO::Total function execution time is 0.0166709423065186 s and adjustment time is 0.00782108306884766 s ( 46.91 )
2024-07-15 19:24:12.374755 INFO::Formatting Data.
2024-07-15 19:24:12.37495 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.375183 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.37545 INFO::Found 0 missing values.
2024-07-15 19:24:12.376222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.376362 INFO::Done
2024-07-15 19:24:12.376494 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.37701 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.377183 INFO::Found 3 batches.
2024-07-15 19:24:12.377309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.377459 INFO::Using default BPPARAM
2024-07-15 19:24:12.377587 INFO::Processing subtree level 1
2024-07-15 19:24:12.431204 INFO::Adjusting the last 1 batches sequentially
2024-07-15 19:24:12.432364 INFO::Done
2024-07-15 19:24:12.432817 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.434445 INFO::ASW Batch was -0.129473173495777 prior to batch effect correction and is now -0.191977290105264 .
2024-07-15 19:24:12.43494 INFO::Total function execution time is 0.0601558685302734 s and adjustment time is 0.0552089214324951 s ( 91.78 )
2024-07-15 19:24:12.442863 INFO::Skipping initial DF formatting
2024-07-15 19:24:12.443138 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.444496 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.444745 INFO::Found 5 batches.
2024-07-15 19:24:12.444918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.44515 INFO::Using default BPPARAM
2024-07-15 19:24:12.445313 INFO::Processing subtree level 1
2024-07-15 19:24:12.488945 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.490904 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.499847 INFO::Done
2024-07-15 19:24:12.500107 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.502273 INFO::ASW Batch was 0.49085878066462 prior to batch effect correction and is now 0.49085878066462 .
2024-07-15 19:24:12.502592 INFO::ASW Label was 0.383356367020997 prior to batch effect correction and is now 0.383356367020998 .
2024-07-15 19:24:12.503316 INFO::Total function execution time is 0.0604598522186279 s and adjustment time is 0.0551459789276123 s ( 91.21 )
2024-07-15 19:24:12.511645 INFO::Formatting Data.
2024-07-15 19:24:12.511916 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.512222 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.512671 INFO::Found 0 missing values.
2024-07-15 19:24:12.513852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.514014 INFO::Done
2024-07-15 19:24:12.514173 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.515181 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.515413 INFO::Found 5 batches.
2024-07-15 19:24:12.515568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.515786 INFO::Using default BPPARAM
2024-07-15 19:24:12.516008 INFO::Processing subtree level 1
2024-07-15 19:24:12.554742 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.556489 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.564441 INFO::Done
2024-07-15 19:24:12.564651 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.565808 INFO::ASW Batch was 0.347871353506548 prior to batch effect correction and is now -0.0725723490707788 .
2024-07-15 19:24:12.566073 INFO::ASW Label was 0.442088002443901 prior to batch effect correction and is now 0.860835964173035 .
2024-07-15 19:24:12.566427 INFO::Total function execution time is 0.0547151565551758 s and adjustment time is 0.0490820407867432 s ( 89.7 )
2024-07-15 19:24:12.566675 INFO::Formatting Data.
2024-07-15 19:24:12.56684 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.567094 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.567392 INFO::Found 0 missing values.
2024-07-15 19:24:12.568443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.568592 INFO::Done
2024-07-15 19:24:12.568729 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.569476 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.569674 INFO::Found 5 batches.
2024-07-15 19:24:12.569812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.570014 INFO::Using default BPPARAM
2024-07-15 19:24:12.570204 INFO::Processing subtree level 1
2024-07-15 19:24:12.608302 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.61014 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.61806 INFO::Done
2024-07-15 19:24:12.618293 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.619529 INFO::ASW Batch was 0.347871353506548 prior to batch effect correction and is now -0.0725723490707788 .
2024-07-15 19:24:12.619704 INFO::ASW Label was 0.442088002443901 prior to batch effect correction and is now 0.860835964173035 .
2024-07-15 19:24:12.61998 INFO::Total function execution time is 0.0532729625701904 s and adjustment time is 0.0484130382537842 s ( 90.88 )
2024-07-15 19:24:12.625435 INFO::Formatting Data.
2024-07-15 19:24:12.625645 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.625916 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.626231 INFO::Found 0 missing values.
2024-07-15 19:24:12.627386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.627543 INFO::Done
2024-07-15 19:24:12.627692 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.628545 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.628752 INFO::Found 5 batches.
2024-07-15 19:24:12.628903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.629091 INFO::Using default BPPARAM
2024-07-15 19:24:12.629301 INFO::Processing subtree level 1
2024-07-15 19:24:12.663533 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.66463 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.671535 INFO::Done
2024-07-15 19:24:12.67186 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.673038 INFO::ASW Batch was 0.386892364113082 prior to batch effect correction and is now -0.0953496790181036 .
2024-07-15 19:24:12.673227 INFO::ASW Label was 0.336553729181736 prior to batch effect correction and is now 0.914201453185611 .
2024-07-15 19:24:12.673511 INFO::Total function execution time is 0.0480668544769287 s and adjustment time is 0.0428211688995361 s ( 89.09 )
2024-07-15 19:24:12.673777 INFO::Formatting Data.
2024-07-15 19:24:12.673945 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.674195 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.674482 INFO::Found 0 missing values.
2024-07-15 19:24:12.675605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.675759 INFO::Done
2024-07-15 19:24:12.675905 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.676742 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.67695 INFO::Found 5 batches.
2024-07-15 19:24:12.677099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.677286 INFO::Using default BPPARAM
2024-07-15 19:24:12.677473 INFO::Processing subtree level 1
2024-07-15 19:24:12.711566 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.712861 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.721003 INFO::Done
2024-07-15 19:24:12.721232 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.722539 INFO::ASW Batch was 0.386892364113082 prior to batch effect correction and is now -0.0953496790181036 .
2024-07-15 19:24:12.722925 INFO::ASW Label was 0.336553729181736 prior to batch effect correction and is now 0.914201453185611 .
2024-07-15 19:24:12.723406 INFO::Total function execution time is 0.0495979785919189 s and adjustment time is 0.0440878868103027 s ( 88.89 )
2024-07-15 19:24:12.728972 INFO::Formatting Data.
2024-07-15 19:24:12.729195 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.729471 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.72978 INFO::Found 0 missing values.
2024-07-15 19:24:12.730586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.730741 INFO::Done
2024-07-15 19:24:12.730892 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.731729 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.731922 INFO::Found 2 batches.
2024-07-15 19:24:12.732072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.732261 INFO::Using default BPPARAM
2024-07-15 19:24:12.732401 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.732638 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.736977 INFO::Done
2024-07-15 19:24:12.737158 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.737979 INFO::ASW Batch was 0.598490543139901 prior to batch effect correction and is now 0.0915464933673737 .
2024-07-15 19:24:12.738137 INFO::ASW Label was 0.386311579454997 prior to batch effect correction and is now 0.809264241667298 .
2024-07-15 19:24:12.738365 INFO::Total function execution time is 0.00940799713134766 s and adjustment time is 0.0050959587097168 s ( 54.17 )
2024-07-15 19:24:12.738576 INFO::Formatting Data.
2024-07-15 19:24:12.738733 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.738973 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.739237 INFO::Found 0 missing values.
2024-07-15 19:24:12.739963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.740113 INFO::Done
2024-07-15 19:24:12.740254 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.741062 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.741276 INFO::Found 2 batches.
2024-07-15 19:24:12.741416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.741589 INFO::Using default BPPARAM
2024-07-15 19:24:12.74173 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.741977 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.746418 INFO::Done
2024-07-15 19:24:12.746618 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.747481 INFO::ASW Batch was 0.598490543139901 prior to batch effect correction and is now 0.0915464933673737 .
2024-07-15 19:24:12.747645 INFO::ASW Label was 0.386311579454997 prior to batch effect correction and is now 0.809264241667298 .
2024-07-15 19:24:12.747885 INFO::Total function execution time is 0.00930404663085938 s and adjustment time is 0.00518012046813965 s ( 55.68 )
2024-07-15 19:24:12.751947 INFO::Formatting Data.
2024-07-15 19:24:12.752174 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.752437 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.752829 INFO::Found 0 missing values.
2024-07-15 19:24:12.753455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.7536 INFO::Done
2024-07-15 19:24:12.753747 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.754278 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.754459 INFO::Found 2 batches.
2024-07-15 19:24:12.754602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.754771 INFO::Using default BPPARAM
2024-07-15 19:24:12.754905 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.755135 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.76525 INFO::Done
2024-07-15 19:24:12.765436 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.765967 INFO::ASW Batch was -0.1609698643048 prior to batch effect correction and is now -0.20540688590393 .
2024-07-15 19:24:12.766199 INFO::Total function execution time is 0.0142860412597656 s and adjustment time is 0.0108199119567871 s ( 75.74 )
2024-07-15 19:24:12.770201 INFO::Formatting Data.
2024-07-15 19:24:12.770396 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.770635 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.771025 INFO::Found 0 missing values.
2024-07-15 19:24:12.771417 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.
2024-07-15 19:24:12.772718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.772872 INFO::Done
2024-07-15 19:24:12.773018 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.773831 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.774019 INFO::Found 2 batches.
2024-07-15 19:24:12.77416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.774323 INFO::Using default BPPARAM
2024-07-15 19:24:12.774452 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.774706 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.779511 INFO::Done
2024-07-15 19:24:12.779696 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.780512 INFO::ASW Batch was 0.618911672015784 prior to batch effect correction and is now -0.0287683184460998 .
2024-07-15 19:24:12.780671 INFO::ASW Label was 0.484560877697906 prior to batch effect correction and is now 0.9293760994508 .
2024-07-15 19:24:12.780903 INFO::Total function execution time is 0.0107131004333496 s and adjustment time is 0.0055229663848877 s ( 51.55 )
2024-07-15 19:24:12.781112 INFO::Formatting Data.
2024-07-15 19:24:12.781266 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.781498 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.781765 INFO::Found 0 missing values.
2024-07-15 19:24:12.782001 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.
2024-07-15 19:24:12.78323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.783382 INFO::Done
2024-07-15 19:24:12.783524 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.784308 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.784513 INFO::Found 2 batches.
2024-07-15 19:24:12.784659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.784825 INFO::Using default BPPARAM
2024-07-15 19:24:12.78497 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:12.785221 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:12.790019 INFO::Done
2024-07-15 19:24:12.790208 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.791006 INFO::ASW Batch was 0.618911672015784 prior to batch effect correction and is now -0.0287683184460998 .
2024-07-15 19:24:12.791164 INFO::ASW Label was 0.484560877697906 prior to batch effect correction and is now 0.9293760994508 .
2024-07-15 19:24:12.79139 INFO::Total function execution time is 0.0102720260620117 s and adjustment time is 0.00554180145263672 s ( 53.95 )
2024-07-15 19:24:12.884677 INFO::Formatting Data.
2024-07-15 19:24:12.88497 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.885283 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.885653 INFO::Found 0 missing values.
2024-07-15 19:24:12.886765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.886966 INFO::Done
2024-07-15 19:24:12.887128 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.887876 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.888093 INFO::Found 3 batches.
2024-07-15 19:24:12.888403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.888671 INFO::Using default BPPARAM
2024-07-15 19:24:12.888871 INFO::Processing subtree level 1
2024-07-15 19:24:12.937741 INFO::Adjusting the last 1 batches sequentially
2024-07-15 19:24:12.939057 INFO::Done
2024-07-15 19:24:12.939295 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.9409 INFO::ASW Batch was -0.0360547215489911 prior to batch effect correction and is now -0.0360547215489911 .
2024-07-15 19:24:12.941361 INFO::Total function execution time is 0.0567078590393066 s and adjustment time is 0.0510120391845703 s ( 89.96 )
2024-07-15 19:24:12.941886 INFO::Formatting Data.
2024-07-15 19:24:12.942103 INFO::Typecasting input to dataframe.
2024-07-15 19:24:12.942514 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:12.943027 INFO::Removing potential empty rows and columns
2024-07-15 19:24:12.943561 INFO::Found 0 missing values.
2024-07-15 19:24:12.945046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:12.94529 INFO::Done
2024-07-15 19:24:12.945534 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:12.946424 INFO::Starting hierarchical adjustment
2024-07-15 19:24:12.946705 INFO::Found 3 batches.
2024-07-15 19:24:12.946886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:12.947169 INFO::Using default BPPARAM
2024-07-15 19:24:12.947366 INFO::Processing subtree level 1
2024-07-15 19:24:12.99018 INFO::Adjusting the last 1 batches sequentially
2024-07-15 19:24:12.991421 INFO::Done
2024-07-15 19:24:12.991749 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:12.993182 INFO::ASW Batch was -0.0360547215489911 prior to batch effect correction and is now -0.0360547215489911 .
2024-07-15 19:24:12.993669 INFO::Total function execution time is 0.0518569946289062 s and adjustment time is 0.0447719097137451 s ( 86.34 )
2024-07-15 19:24:12.999697 INFO::Formatting Data.
2024-07-15 19:24:12.999927 INFO::Typecasting input to dataframe.
2024-07-15 19:24:13.000191 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:13.000597 INFO::Removing potential empty rows and columns
2024-07-15 19:24:13.000981 INFO::Found 0 missing values.
2024-07-15 19:24:13.001914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:13.002071 INFO::Done
2024-07-15 19:24:13.002218 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:13.002831 INFO::Starting hierarchical adjustment
2024-07-15 19:24:13.003031 INFO::Found 3 batches.
2024-07-15 19:24:13.003182 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:13.003375 INFO::Using default BPPARAM
2024-07-15 19:24:13.003522 INFO::Processing subtree level 1
2024-07-15 19:24:13.045882 INFO::Adjusting the last 1 batches sequentially
2024-07-15 19:24:13.046875 INFO::Done
2024-07-15 19:24:13.04717 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:13.048411 INFO::ASW Batch was -0.132618313548826 prior to batch effect correction and is now -0.132618313548826 .
2024-07-15 19:24:13.048947 INFO::Total function execution time is 0.0493559837341309 s and adjustment time is 0.0438790321350098 s ( 88.9 )
2024-07-15 19:24:13.110489 INFO::Formatting Data.
2024-07-15 19:24:13.110757 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:13.111144 INFO::Removing potential empty rows and columns
2024-07-15 19:24:13.112137 INFO::Found 1000 missing values.
2024-07-15 19:24:13.119235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:13.11943 INFO::Done
2024-07-15 19:24:13.119589 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:13.121459 INFO::Starting hierarchical adjustment
2024-07-15 19:24:13.121694 INFO::Found 10 batches.
2024-07-15 19:24:13.121853 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:13.122047 INFO::Using default BPPARAM
2024-07-15 19:24:13.122196 INFO::Processing subtree level 1
2024-07-15 19:24:13.17056 INFO::Processing subtree level 2
2024-07-15 19:24:13.236623 INFO::Adjusting the last 1 batches sequentially
2024-07-15 19:24:13.238122 INFO::Done
2024-07-15 19:24:13.238434 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:13.241264 INFO::ASW Batch was 0.519295714098038 prior to batch effect correction and is now 0.519295714098038 .
2024-07-15 19:24:13.241509 INFO::ASW Label was 0.301713150325016 prior to batch effect correction and is now 0.301713150325017 .
2024-07-15 19:24:13.24238 INFO::Total function execution time is 0.131847858428955 s and adjustment time is 0.116472959518433 s ( 88.34 )
2024-07-15 19:24:13.242693 INFO::Formatting Data.
2024-07-15 19:24:13.2429 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:13.24345 INFO::Removing potential empty rows and columns
2024-07-15 19:24:13.244702 INFO::Found 1000 missing values.
2024-07-15 19:24:13.252311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:13.252545 INFO::Done
2024-07-15 19:24:13.25277 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:13.25486 INFO::Starting hierarchical adjustment
2024-07-15 19:24:13.255097 INFO::Found 10 batches.
2024-07-15 19:24:13.638978 INFO::Set up parallel execution backend with 2 workers
2024-07-15 19:24:13.63923 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-15 19:24:14.090184 INFO::Adjusting the last 2 batches sequentially
2024-07-15 19:24:14.090764 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 19:24:14.096128 INFO::Done
2024-07-15 19:24:14.096319 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:14.098045 INFO::ASW Batch was 0.519295714098038 prior to batch effect correction and is now 0.519295714098038 .
2024-07-15 19:24:14.098212 INFO::ASW Label was 0.301713150325016 prior to batch effect correction and is now 0.301713150325017 .
2024-07-15 19:24:14.098433 INFO::Total function execution time is 0.855746030807495 s and adjustment time is 0.841087818145752 s ( 98.29 )
2024-07-15 19:24:14.157733 INFO::Formatting Data.
2024-07-15 19:24:14.158018 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.1584 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.158899 INFO::Found 0 missing values.
2024-07-15 19:24:14.160427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.160621 INFO::Done
2024-07-15 19:24:14.160795 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 19:24:14.161891 INFO::Starting hierarchical adjustment
2024-07-15 19:24:14.162192 INFO::Found 3 batches.
2024-07-15 19:24:14.162383 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 19:24:14.162676 INFO::Using default BPPARAM
2024-07-15 19:24:14.16288 INFO::Processing subtree level 1
2024-07-15 19:24:14.209217 INFO::Adjusting the last 1 batches sequentially
2024-07-15 19:24:14.210385 INFO::Done
2024-07-15 19:24:14.21063 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 19:24:14.212279 INFO::ASW Batch was 0.315938950444806 prior to batch effect correction and is now -0.189377967145393 .
2024-07-15 19:24:14.21252 INFO::ASW Label was -0.191726036755229 prior to batch effect correction and is now 0.124920820527806 .
2024-07-15 19:24:14.212958 INFO::Total function execution time is 0.0552132129669189 s and adjustment time is 0.0482511520385742 s ( 87.39 )
2024-07-15 19:24:14.264509 INFO::Formatting Data.
2024-07-15 19:24:14.264885 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.265238 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.26574 INFO::Found 2 missing values.
2024-07-15 19:24:14.266856 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.267058 INFO::Done
2024-07-15 19:24:14.277966 INFO::Found NA in Reference column
2024-07-15 19:24:14.282027 INFO::Require at least two references per batch.
2024-07-15 19:24:14.292127 INFO::Formatting Data.
2024-07-15 19:24:14.292425 INFO::Recognized SummarizedExperiment
2024-07-15 19:24:14.292627 INFO::Typecasting input to dataframe.
2024-07-15 19:24:14.298036 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.298537 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.300243 INFO::Found 0 missing values.
2024-07-15 19:24:14.303286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.303497 INFO::Done
2024-07-15 19:24:14.309845 INFO::Formatting Data.
2024-07-15 19:24:14.310113 INFO::Recognized SummarizedExperiment
2024-07-15 19:24:14.310293 INFO::Typecasting input to dataframe.
2024-07-15 19:24:14.317868 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.318509 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.320164 INFO::Found 0 missing values.
2024-07-15 19:24:14.325275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.32547 INFO::Done
2024-07-15 19:24:14.332108 INFO::Formatting Data.
2024-07-15 19:24:14.332365 INFO::Recognized SummarizedExperiment
2024-07-15 19:24:14.332569 INFO::Typecasting input to dataframe.
2024-07-15 19:24:14.339517 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.339887 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.34032 INFO::Found 0 missing values.
2024-07-15 19:24:14.340647 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.
2024-07-15 19:24:14.342552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.342736 INFO::Done
2024-07-15 19:24:14.346909 INFO::Formatting Data.
2024-07-15 19:24:14.347173 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.347456 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.347756 INFO::Found 0 missing values.
2024-07-15 19:24:14.348708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.348882 INFO::Done
2024-07-15 19:24:14.35372 INFO::Formatting Data.
2024-07-15 19:24:14.353952 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.354233 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.354552 INFO::Found 0 missing values.
2024-07-15 19:24:14.355524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.355722 INFO::Done
2024-07-15 19:24:14.367727 INFO::Formatting Data.
2024-07-15 19:24:14.367969 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.3683 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.368733 INFO::Found 1 missing values.
2024-07-15 19:24:14.369617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.369781 INFO::Done
2024-07-15 19:24:14.376393 INFO::Formatting Data.
2024-07-15 19:24:14.376649 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.376965 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.377299 INFO::Found 2 missing values.
2024-07-15 19:24:14.377597 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.
2024-07-15 19:24:14.37838 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.378566 INFO::Done
2024-07-15 19:24:14.383191 INFO::Formatting Data.
2024-07-15 19:24:14.38351 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.384038 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.38436 INFO::Found 2 missing values.
2024-07-15 19:24:14.384978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.385151 INFO::Done
2024-07-15 19:24:14.389161 INFO::Formatting Data.
2024-07-15 19:24:14.389417 INFO::Typecasting input to dataframe.
2024-07-15 19:24:14.389665 INFO::Replacing NaNs with NAs.
2024-07-15 19:24:14.389991 INFO::Removing potential empty rows and columns
2024-07-15 19:24:14.390341 INFO::Found 0 missing values.
2024-07-15 19:24:14.391313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 19:24:14.391481 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.022 1.212 7.460
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.949 | 0.302 | 6.401 | |
| compute_asw | 0.009 | 0.000 | 0.010 | |
| count_existing | 0.004 | 0.000 | 0.005 | |
| generate_data_covariables | 0.004 | 0.001 | 0.004 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |