Yannis Schumann
| Snapshot Date: 2024-07-22 14:00 -0400 (Mon, 22 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-23 11:41 -0400 (Tue, 23 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4280 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 157/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /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_1.1.2.tar.gz |
| StartedAt: 2024-07-22 20:03:25 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 20:03:54 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 29.3 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_1.1.2.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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 9.629 0.322 6.778
* 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")
2024-07-22 20:03:47.703118 INFO::Formatting Data.
2024-07-22 20:03:47.704566 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:47.70841 INFO::Removing potential empty rows and columns
2024-07-22 20:03:47.807272 INFO::Found 0 missing values.
2024-07-22 20:03:47.808398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:47.808601 INFO::Done
2024-07-22 20:03:47.808795 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:47.814155 INFO::Starting hierarchical adjustment
2024-07-22 20:03:47.814472 INFO::Found 3 batches.
2024-07-22 20:03:47.814645 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:47.815018 INFO::Using default BPPARAM
2024-07-22 20:03:47.81518 INFO::Processing subtree level 1
2024-07-22 20:03:47.86063 INFO::Adjusting the last 1 batches sequentially
2024-07-22 20:03:47.862166 INFO::Done
2024-07-22 20:03:47.862395 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:47.863776 INFO::ASW Batch was -0.0220334732149096 prior to batch effect correction and is now -0.0220334732149096 .
2024-07-22 20:03:47.864291 INFO::Total function execution time is 0.161484956741333 s and adjustment time is 0.047760009765625 s ( 29.58 )
2024-07-22 20:03:47.871865 INFO::Formatting Data.
2024-07-22 20:03:47.872156 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:47.872562 INFO::Removing potential empty rows and columns
2024-07-22 20:03:47.873141 INFO::Found 0 missing values.
2024-07-22 20:03:47.873445 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.
2024-07-22 20:03:47.877623 INFO::Formatting Data.
2024-07-22 20:03:47.877842 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:47.878154 INFO::Removing potential empty rows and columns
2024-07-22 20:03:47.878466 INFO::Found 0 missing values.
2024-07-22 20:03:47.878746 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.
2024-07-22 20:03:47.884921 INFO::Formatting Data.
2024-07-22 20:03:47.885148 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:47.885407 INFO::Removing potential empty rows and columns
2024-07-22 20:03:47.885716 INFO::Found 0 missing values.
2024-07-22 20:03:47.885974 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.
2024-07-22 20:03:47.887234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:47.887407 INFO::Done
2024-07-22 20:03:47.887557 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:47.888201 INFO::Starting hierarchical adjustment
2024-07-22 20:03:47.888394 INFO::Found 2 batches.
2024-07-22 20:03:47.888552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:47.888788 INFO::Using default BPPARAM
2024-07-22 20:03:47.888931 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:47.889212 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:47.898842 INFO::Done
2024-07-22 20:03:47.899103 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:47.899811 INFO::ASW Batch was 0.0157502243077264 prior to batch effect correction and is now -0.118134375274276 .
2024-07-22 20:03:47.90006 INFO::Total function execution time is 0.0151679515838623 s and adjustment time is 0.0104610919952393 s ( 68.97 )
2024-07-22 20:03:47.901096 INFO::Formatting Data.
2024-07-22 20:03:47.90129 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:47.904189 INFO::Formatting Data.
2024-07-22 20:03:47.904402 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:47.904656 INFO::Removing potential empty rows and columns
2024-07-22 20:03:47.904971 INFO::Found 0 missing values.
2024-07-22 20:03:47.905866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:47.906035 INFO::Done
2024-07-22 20:03:47.906182 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:47.906783 INFO::Starting hierarchical adjustment
2024-07-22 20:03:47.906978 INFO::Found 2 batches.
2024-07-22 20:03:47.907147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:47.907317 INFO::Using default BPPARAM
2024-07-22 20:03:47.907459 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:47.907696 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:47.91254 INFO::Done
2024-07-22 20:03:47.912749 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:47.91336 INFO::ASW Batch was 0.0733893105914486 prior to batch effect correction and is now -0.120487826421334 .
2024-07-22 20:03:47.913601 INFO::Total function execution time is 0.0094149112701416 s and adjustment time is 0.00559496879577637 s ( 59.43 )
2024-07-22 20:03:47.913927 INFO::Formatting Data.
2024-07-22 20:03:47.914091 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:47.914338 INFO::Removing potential empty rows and columns
2024-07-22 20:03:47.914641 INFO::Found 0 missing values.
2024-07-22 20:03:47.915452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:47.915592 INFO::Done
2024-07-22 20:03:47.915735 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:47.916271 INFO::Starting hierarchical adjustment
2024-07-22 20:03:47.916486 INFO::Found 2 batches.
2024-07-22 20:03:47.916627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:47.916804 INFO::Using default BPPARAM
2024-07-22 20:03:47.916948 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:47.917206 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:47.921991 INFO::Done
2024-07-22 20:03:47.922199 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:47.922783 INFO::ASW Batch was 0.0733893105914486 prior to batch effect correction and is now -0.120487826421334 .
2024-07-22 20:03:47.923012 INFO::Total function execution time is 0.00907588005065918 s and adjustment time is 0.00553607940673828 s ( 61 )
2024-07-22 20:03:49.061783 INFO::Formatting Data.
2024-07-22 20:03:49.062045 INFO::Recognized SummarizedExperiment
2024-07-22 20:03:49.062187 INFO::Typecasting input to dataframe.
2024-07-22 20:03:49.072368 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.07277 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.073833 INFO::Found 0 missing values.
2024-07-22 20:03:49.075748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.075913 INFO::Done
2024-07-22 20:03:49.076054 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.077205 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.077408 INFO::Found 2 batches.
2024-07-22 20:03:49.077539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.077837 INFO::Using default BPPARAM
2024-07-22 20:03:49.077971 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.078229 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.094092 INFO::Done
2024-07-22 20:03:49.094322 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.095431 INFO::ASW Batch was 0.0132676052503069 prior to batch effect correction and is now -0.101416117353886 .
2024-07-22 20:03:49.095671 INFO::Total function execution time is 0.033991813659668 s and adjustment time is 0.0167069435119629 s ( 49.15 )
2024-07-22 20:03:49.101233 INFO::Formatting Data.
2024-07-22 20:03:49.101437 INFO::Recognized SummarizedExperiment
2024-07-22 20:03:49.101581 INFO::Typecasting input to dataframe.
2024-07-22 20:03:49.104449 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.104808 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.105905 INFO::Found 0 missing values.
2024-07-22 20:03:49.107968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.108128 INFO::Done
2024-07-22 20:03:49.108268 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.109438 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.10964 INFO::Found 2 batches.
2024-07-22 20:03:49.109781 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.109951 INFO::Using default BPPARAM
2024-07-22 20:03:49.11009 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.110365 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.118111 INFO::Done
2024-07-22 20:03:49.118318 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.119475 INFO::ASW Batch was 0.0071628291032224 prior to batch effect correction and is now 0.0071628291032224 .
2024-07-22 20:03:49.119726 INFO::Total function execution time is 0.0184872150421143 s and adjustment time is 0.00850105285644531 s ( 45.98 )
2024-07-22 20:03:49.125906 INFO::Formatting Data.
2024-07-22 20:03:49.126118 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.126372 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.126684 INFO::Found 0 missing values.
2024-07-22 20:03:49.127514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.127675 INFO::Done
2024-07-22 20:03:49.127821 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.128418 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.128602 INFO::Found 3 batches.
2024-07-22 20:03:49.128737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.128912 INFO::Using default BPPARAM
2024-07-22 20:03:49.129045 INFO::Processing subtree level 1
2024-07-22 20:03:49.183986 INFO::Adjusting the last 1 batches sequentially
2024-07-22 20:03:49.185527 INFO::Done
2024-07-22 20:03:49.185717 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.187265 INFO::ASW Batch was -0.0447867081203669 prior to batch effect correction and is now -0.175610608111986 .
2024-07-22 20:03:49.188042 INFO::Total function execution time is 0.0619759559631348 s and adjustment time is 0.056952953338623 s ( 91.9 )
2024-07-22 20:03:49.194645 INFO::Skipping initial DF formatting
2024-07-22 20:03:49.194866 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.196174 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.196441 INFO::Found 5 batches.
2024-07-22 20:03:49.196605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.196834 INFO::Using default BPPARAM
2024-07-22 20:03:49.196989 INFO::Processing subtree level 1
2024-07-22 20:03:49.246634 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.247654 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.256613 INFO::Done
2024-07-22 20:03:49.256879 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.25872 INFO::ASW Batch was 0.505591748006876 prior to batch effect correction and is now 0.505591748006876 .
2024-07-22 20:03:49.258917 INFO::ASW Label was 0.342804371932665 prior to batch effect correction and is now 0.342804371932665 .
2024-07-22 20:03:49.259598 INFO::Total function execution time is 0.0649569034576416 s and adjustment time is 0.0602350234985352 s ( 92.73 )
2024-07-22 20:03:49.267403 INFO::Formatting Data.
2024-07-22 20:03:49.267666 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.268097 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.268615 INFO::Found 0 missing values.
2024-07-22 20:03:49.269872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.270037 INFO::Done
2024-07-22 20:03:49.270192 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.271161 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.271388 INFO::Found 5 batches.
2024-07-22 20:03:49.27154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.271744 INFO::Using default BPPARAM
2024-07-22 20:03:49.271895 INFO::Processing subtree level 1
2024-07-22 20:03:49.313487 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.315579 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.324154 INFO::Done
2024-07-22 20:03:49.324385 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.325574 INFO::ASW Batch was 0.350406103855146 prior to batch effect correction and is now -0.0864125199387614 .
2024-07-22 20:03:49.325768 INFO::ASW Label was 0.311176701150192 prior to batch effect correction and is now 0.833243859925577 .
2024-07-22 20:03:49.326258 INFO::Total function execution time is 0.058772087097168 s and adjustment time is 0.0528149604797363 s ( 89.86 )
2024-07-22 20:03:49.326564 INFO::Formatting Data.
2024-07-22 20:03:49.326753 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.327021 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.327322 INFO::Found 0 missing values.
2024-07-22 20:03:49.328426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.32859 INFO::Done
2024-07-22 20:03:49.328733 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.329634 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.32988 INFO::Found 5 batches.
2024-07-22 20:03:49.330036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.330249 INFO::Using default BPPARAM
2024-07-22 20:03:49.330405 INFO::Processing subtree level 1
2024-07-22 20:03:49.370847 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.372433 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.380912 INFO::Done
2024-07-22 20:03:49.381157 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.382552 INFO::ASW Batch was 0.350406103855146 prior to batch effect correction and is now -0.0864125199387614 .
2024-07-22 20:03:49.382747 INFO::ASW Label was 0.311176701150192 prior to batch effect correction and is now 0.833243859925577 .
2024-07-22 20:03:49.383139 INFO::Total function execution time is 0.0565311908721924 s and adjustment time is 0.0510721206665039 s ( 90.34 )
2024-07-22 20:03:49.39048 INFO::Formatting Data.
2024-07-22 20:03:49.390725 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.391021 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.391385 INFO::Found 0 missing values.
2024-07-22 20:03:49.392563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.392725 INFO::Done
2024-07-22 20:03:49.392881 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.393763 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.393996 INFO::Found 5 batches.
2024-07-22 20:03:49.394154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.394369 INFO::Using default BPPARAM
2024-07-22 20:03:49.394521 INFO::Processing subtree level 1
2024-07-22 20:03:49.436414 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.438378 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.447251 INFO::Done
2024-07-22 20:03:49.447516 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.448904 INFO::ASW Batch was 0.550569366373383 prior to batch effect correction and is now -0.104621853547772 .
2024-07-22 20:03:49.44911 INFO::ASW Label was 0.114660788884961 prior to batch effect correction and is now 0.831255919367102 .
2024-07-22 20:03:49.449554 INFO::Total function execution time is 0.0590739250183105 s and adjustment time is 0.0532910823822021 s ( 90.21 )
2024-07-22 20:03:49.44984 INFO::Formatting Data.
2024-07-22 20:03:49.45002 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.450296 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.450614 INFO::Found 0 missing values.
2024-07-22 20:03:49.451768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.451928 INFO::Done
2024-07-22 20:03:49.452088 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.452965 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.4534 INFO::Found 5 batches.
2024-07-22 20:03:49.45355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.453757 INFO::Using default BPPARAM
2024-07-22 20:03:49.453904 INFO::Processing subtree level 1
2024-07-22 20:03:49.496351 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.497793 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.506073 INFO::Done
2024-07-22 20:03:49.506309 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.507586 INFO::ASW Batch was 0.550569366373383 prior to batch effect correction and is now -0.104621853547772 .
2024-07-22 20:03:49.507767 INFO::ASW Label was 0.114660788884961 prior to batch effect correction and is now 0.831255919367102 .
2024-07-22 20:03:49.508142 INFO::Total function execution time is 0.0582609176635742 s and adjustment time is 0.0529241561889648 s ( 90.84 )
2024-07-22 20:03:49.514115 INFO::Formatting Data.
2024-07-22 20:03:49.514348 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.514624 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.514953 INFO::Found 0 missing values.
2024-07-22 20:03:49.515737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.515887 INFO::Done
2024-07-22 20:03:49.51603 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.516882 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.517084 INFO::Found 2 batches.
2024-07-22 20:03:49.517233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.51743 INFO::Using default BPPARAM
2024-07-22 20:03:49.51757 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.517802 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.522149 INFO::Done
2024-07-22 20:03:49.522336 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.523164 INFO::ASW Batch was 0.516758651001887 prior to batch effect correction and is now 0.25942390839244 .
2024-07-22 20:03:49.523332 INFO::ASW Label was 0.625945235518999 prior to batch effect correction and is now 0.730620752799723 .
2024-07-22 20:03:49.523564 INFO::Total function execution time is 0.00947093963623047 s and adjustment time is 0.00510382652282715 s ( 53.89 )
2024-07-22 20:03:49.523776 INFO::Formatting Data.
2024-07-22 20:03:49.523928 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.524156 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.52443 INFO::Found 0 missing values.
2024-07-22 20:03:49.525172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.525326 INFO::Done
2024-07-22 20:03:49.525461 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.526304 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.526508 INFO::Found 2 batches.
2024-07-22 20:03:49.526653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.526829 INFO::Using default BPPARAM
2024-07-22 20:03:49.526961 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.527195 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.531626 INFO::Done
2024-07-22 20:03:49.531822 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.532645 INFO::ASW Batch was 0.516758651001887 prior to batch effect correction and is now 0.25942390839244 .
2024-07-22 20:03:49.532813 INFO::ASW Label was 0.625945235518999 prior to batch effect correction and is now 0.730620752799723 .
2024-07-22 20:03:49.533034 INFO::Total function execution time is 0.00925517082214355 s and adjustment time is 0.00515484809875488 s ( 55.7 )
2024-07-22 20:03:49.536994 INFO::Formatting Data.
2024-07-22 20:03:49.537207 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.537452 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.537719 INFO::Found 0 missing values.
2024-07-22 20:03:49.538313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.538458 INFO::Done
2024-07-22 20:03:49.538723 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.539236 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.539429 INFO::Found 2 batches.
2024-07-22 20:03:49.539574 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.539736 INFO::Using default BPPARAM
2024-07-22 20:03:49.539867 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.540102 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.550224 INFO::Done
2024-07-22 20:03:49.550423 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.550981 INFO::ASW Batch was -0.112147389279424 prior to batch effect correction and is now -0.124830305058702 .
2024-07-22 20:03:49.551224 INFO::Total function execution time is 0.0142450332641602 s and adjustment time is 0.0108270645141602 s ( 76.01 )
2024-07-22 20:03:49.555227 INFO::Formatting Data.
2024-07-22 20:03:49.555419 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.555665 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.555952 INFO::Found 0 missing values.
2024-07-22 20:03:49.556347 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.
2024-07-22 20:03:49.557759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.557922 INFO::Done
2024-07-22 20:03:49.558066 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.558861 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.55907 INFO::Found 2 batches.
2024-07-22 20:03:49.55921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.559374 INFO::Using default BPPARAM
2024-07-22 20:03:49.559512 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.559765 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.564611 INFO::Done
2024-07-22 20:03:49.5648 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.56562 INFO::ASW Batch was 0.463714303266226 prior to batch effect correction and is now 0.0389642060301491 .
2024-07-22 20:03:49.565793 INFO::ASW Label was 0.572148533112159 prior to batch effect correction and is now 0.882925973833181 .
2024-07-22 20:03:49.56601 INFO::Total function execution time is 0.0107829570770264 s and adjustment time is 0.00557398796081543 s ( 51.69 )
2024-07-22 20:03:49.566223 INFO::Formatting Data.
2024-07-22 20:03:49.566377 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.566618 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.566882 INFO::Found 0 missing values.
2024-07-22 20:03:49.567118 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.
2024-07-22 20:03:49.568334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.568494 INFO::Done
2024-07-22 20:03:49.568637 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.569418 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.569615 INFO::Found 2 batches.
2024-07-22 20:03:49.569757 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.569919 INFO::Using default BPPARAM
2024-07-22 20:03:49.570066 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:49.570301 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:49.574993 INFO::Done
2024-07-22 20:03:49.575172 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.575985 INFO::ASW Batch was 0.463714303266226 prior to batch effect correction and is now 0.0389642060301491 .
2024-07-22 20:03:49.576155 INFO::ASW Label was 0.572148533112159 prior to batch effect correction and is now 0.882925973833181 .
2024-07-22 20:03:49.576381 INFO::Total function execution time is 0.0101461410522461 s and adjustment time is 0.00541305541992188 s ( 53.35 )
2024-07-22 20:03:49.683243 INFO::Formatting Data.
2024-07-22 20:03:49.683496 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.683758 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.684073 INFO::Found 0 missing values.
2024-07-22 20:03:49.684973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.68513 INFO::Done
2024-07-22 20:03:49.685275 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.685891 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.686082 INFO::Found 3 batches.
2024-07-22 20:03:49.686215 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.686379 INFO::Using default BPPARAM
2024-07-22 20:03:49.686511 INFO::Processing subtree level 1
2024-07-22 20:03:49.731214 INFO::Adjusting the last 1 batches sequentially
2024-07-22 20:03:49.73265 INFO::Done
2024-07-22 20:03:49.733003 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.734612 INFO::ASW Batch was -0.104822327355935 prior to batch effect correction and is now -0.104822327355935 .
2024-07-22 20:03:49.735258 INFO::Total function execution time is 0.0520248413085938 s and adjustment time is 0.0465948581695557 s ( 89.56 )
2024-07-22 20:03:49.735746 INFO::Formatting Data.
2024-07-22 20:03:49.735973 INFO::Typecasting input to dataframe.
2024-07-22 20:03:49.736212 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.736535 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.737078 INFO::Found 0 missing values.
2024-07-22 20:03:49.738099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.738351 INFO::Done
2024-07-22 20:03:49.738542 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.739396 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.739707 INFO::Found 3 batches.
2024-07-22 20:03:49.739871 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.740091 INFO::Using default BPPARAM
2024-07-22 20:03:49.740247 INFO::Processing subtree level 1
2024-07-22 20:03:49.788129 INFO::Adjusting the last 1 batches sequentially
2024-07-22 20:03:49.790209 INFO::Done
2024-07-22 20:03:49.790603 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.792164 INFO::ASW Batch was -0.104822327355935 prior to batch effect correction and is now -0.104822327355935 .
2024-07-22 20:03:49.792853 INFO::Total function execution time is 0.057197093963623 s and adjustment time is 0.0505690574645996 s ( 88.41 )
2024-07-22 20:03:49.801193 INFO::Formatting Data.
2024-07-22 20:03:49.801471 INFO::Typecasting input to dataframe.
2024-07-22 20:03:49.801773 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.80214 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.802798 INFO::Found 0 missing values.
2024-07-22 20:03:49.804773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.805082 INFO::Done
2024-07-22 20:03:49.805404 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.806243 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.806485 INFO::Found 3 batches.
2024-07-22 20:03:49.806639 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.806857 INFO::Using default BPPARAM
2024-07-22 20:03:49.807015 INFO::Processing subtree level 1
2024-07-22 20:03:49.852044 INFO::Adjusting the last 1 batches sequentially
2024-07-22 20:03:49.853636 INFO::Done
2024-07-22 20:03:49.853885 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:49.855765 INFO::ASW Batch was -0.100025459321465 prior to batch effect correction and is now -0.100025459321465 .
2024-07-22 20:03:49.85648 INFO::Total function execution time is 0.0555150508880615 s and adjustment time is 0.0472040176391602 s ( 85.03 )
2024-07-22 20:03:49.930809 INFO::Formatting Data.
2024-07-22 20:03:49.931078 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:49.931444 INFO::Removing potential empty rows and columns
2024-07-22 20:03:49.93256 INFO::Found 1000 missing values.
2024-07-22 20:03:49.939223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:49.939488 INFO::Done
2024-07-22 20:03:49.939678 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:49.941786 INFO::Starting hierarchical adjustment
2024-07-22 20:03:49.942096 INFO::Found 10 batches.
2024-07-22 20:03:49.942269 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:49.942487 INFO::Using default BPPARAM
2024-07-22 20:03:49.942654 INFO::Processing subtree level 1
2024-07-22 20:03:49.99896 INFO::Processing subtree level 2
2024-07-22 20:03:50.067697 INFO::Adjusting the last 1 batches sequentially
2024-07-22 20:03:50.069653 INFO::Done
2024-07-22 20:03:50.069925 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:50.073335 INFO::ASW Batch was 0.486249292110715 prior to batch effect correction and is now 0.486249292110715 .
2024-07-22 20:03:50.073582 INFO::ASW Label was 0.36157849991241 prior to batch effect correction and is now 0.36157849991241 .
2024-07-22 20:03:50.074308 INFO::Total function execution time is 0.14351487159729 s and adjustment time is 0.127618074417114 s ( 88.92 )
2024-07-22 20:03:50.074608 INFO::Formatting Data.
2024-07-22 20:03:50.074799 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:50.075265 INFO::Removing potential empty rows and columns
2024-07-22 20:03:50.076675 INFO::Found 1000 missing values.
2024-07-22 20:03:50.08386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:50.084125 INFO::Done
2024-07-22 20:03:50.084299 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:50.086396 INFO::Starting hierarchical adjustment
2024-07-22 20:03:50.086685 INFO::Found 10 batches.
2024-07-22 20:03:50.524945 INFO::Set up parallel execution backend with 2 workers
2024-07-22 20:03:50.525244 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-22 20:03:51.004274 INFO::Adjusting the last 2 batches sequentially
2024-07-22 20:03:51.00479 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 20:03:51.010305 INFO::Done
2024-07-22 20:03:51.010515 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:51.012295 INFO::ASW Batch was 0.486249292110715 prior to batch effect correction and is now 0.486249292110715 .
2024-07-22 20:03:51.01246 INFO::ASW Label was 0.36157849991241 prior to batch effect correction and is now 0.36157849991241 .
2024-07-22 20:03:51.012685 INFO::Total function execution time is 0.938077926635742 s and adjustment time is 0.9236741065979 s ( 98.46 )
2024-07-22 20:03:51.07701 INFO::Formatting Data.
2024-07-22 20:03:51.077272 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.077621 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.078088 INFO::Found 0 missing values.
2024-07-22 20:03:51.079478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.079661 INFO::Done
2024-07-22 20:03:51.079829 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 20:03:51.080804 INFO::Starting hierarchical adjustment
2024-07-22 20:03:51.081063 INFO::Found 3 batches.
2024-07-22 20:03:51.081228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 20:03:51.081464 INFO::Using default BPPARAM
2024-07-22 20:03:51.081638 INFO::Processing subtree level 1
2024-07-22 20:03:51.131526 INFO::Adjusting the last 1 batches sequentially
2024-07-22 20:03:51.132775 INFO::Done
2024-07-22 20:03:51.132985 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 20:03:51.134713 INFO::ASW Batch was 0.151737325449169 prior to batch effect correction and is now -0.135904215853603 .
2024-07-22 20:03:51.13503 INFO::ASW Label was -0.243108959548783 prior to batch effect correction and is now -0.0835824906738621 .
2024-07-22 20:03:51.135762 INFO::Total function execution time is 0.0587561130523682 s and adjustment time is 0.0517680644989014 s ( 88.11 )
2024-07-22 20:03:51.180389 INFO::Formatting Data.
2024-07-22 20:03:51.180721 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.18107 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.181632 INFO::Found 2 missing values.
2024-07-22 20:03:51.182686 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.18288 INFO::Done
2024-07-22 20:03:51.192175 INFO::Found NA in Reference column
2024-07-22 20:03:51.195484 INFO::Require at least two references per batch.
2024-07-22 20:03:51.203119 INFO::Formatting Data.
2024-07-22 20:03:51.20334 INFO::Recognized SummarizedExperiment
2024-07-22 20:03:51.203518 INFO::Typecasting input to dataframe.
2024-07-22 20:03:51.207367 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.207705 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.208884 INFO::Found 0 missing values.
2024-07-22 20:03:51.211051 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.211214 INFO::Done
2024-07-22 20:03:51.215905 INFO::Formatting Data.
2024-07-22 20:03:51.216107 INFO::Recognized SummarizedExperiment
2024-07-22 20:03:51.216261 INFO::Typecasting input to dataframe.
2024-07-22 20:03:51.221585 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.221938 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.223098 INFO::Found 0 missing values.
2024-07-22 20:03:51.226709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.226876 INFO::Done
2024-07-22 20:03:51.231772 INFO::Formatting Data.
2024-07-22 20:03:51.231964 INFO::Recognized SummarizedExperiment
2024-07-22 20:03:51.232115 INFO::Typecasting input to dataframe.
2024-07-22 20:03:51.237127 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.2374 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.23771 INFO::Found 0 missing values.
2024-07-22 20:03:51.237982 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.
2024-07-22 20:03:51.23936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.23953 INFO::Done
2024-07-22 20:03:51.24291 INFO::Formatting Data.
2024-07-22 20:03:51.243111 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.243357 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.243669 INFO::Found 0 missing values.
2024-07-22 20:03:51.244478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.244626 INFO::Done
2024-07-22 20:03:51.248422 INFO::Formatting Data.
2024-07-22 20:03:51.248622 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.248843 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.249106 INFO::Found 0 missing values.
2024-07-22 20:03:51.249896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.250047 INFO::Done
2024-07-22 20:03:51.259822 INFO::Formatting Data.
2024-07-22 20:03:51.260026 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.260293 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.260606 INFO::Found 1 missing values.
2024-07-22 20:03:51.261284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.261437 INFO::Done
2024-07-22 20:03:51.267204 INFO::Formatting Data.
2024-07-22 20:03:51.267412 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.267645 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.267907 INFO::Found 2 missing values.
2024-07-22 20:03:51.268153 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.
2024-07-22 20:03:51.26879 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.26893 INFO::Done
2024-07-22 20:03:51.272293 INFO::Formatting Data.
2024-07-22 20:03:51.272497 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.272752 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.273144 INFO::Found 2 missing values.
2024-07-22 20:03:51.273559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.273705 INFO::Done
2024-07-22 20:03:51.277437 INFO::Formatting Data.
2024-07-22 20:03:51.277644 INFO::Typecasting input to dataframe.
2024-07-22 20:03:51.277868 INFO::Replacing NaNs with NAs.
2024-07-22 20:03:51.278101 INFO::Removing potential empty rows and columns
2024-07-22 20:03:51.27838 INFO::Found 0 missing values.
2024-07-22 20:03:51.279295 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 20:03:51.279487 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.578 1.356 8.087
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.629 | 0.322 | 6.778 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.006 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |