Yannis Schumann
| Snapshot Date: 2025-02-09 13:40 -0500 (Sun, 09 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0500 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-10 11:39 -0500 (Mon, 10 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| 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 159/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.3.6 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-02-09 20:18:10 -0500 (Sun, 09 Feb 2025) |
| EndedAt: 2025-02-09 20:19:44 -0500 (Sun, 09 Feb 2025) |
| EllapsedTime: 94.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 25.165 1.342 18.4
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.3.6’ ** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-02-09 20:19:04.004282 INFO::Formatting Data.
2025-02-09 20:19:04.005689 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:04.017057 INFO::Removing potential empty rows and columns
2025-02-09 20:19:04.268968 INFO::Found 0 missing values.
2025-02-09 20:19:04.272853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:04.27362 INFO::Done
2025-02-09 20:19:04.274229 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:04.287299 INFO::Starting hierarchical adjustment
2025-02-09 20:19:04.288366 INFO::Found 3 batches.
2025-02-09 20:19:04.289007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:04.290281 INFO::Using default BPPARAM
2025-02-09 20:19:04.290866 INFO::Processing subtree level 1
2025-02-09 20:19:04.398863 INFO::Adjusting the last 1 batches sequentially
2025-02-09 20:19:04.401111 INFO::Done
2025-02-09 20:19:04.401938 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:04.404952 INFO::ASW Batch was -0.0324099611911687 prior to batch effect correction and is now -0.0324099611911687 .
2025-02-09 20:19:04.406217 INFO::Total function execution time is 0.402507305145264 s and adjustment time is 0.112964630126953 s ( 28.07 )
2025-02-09 20:19:04.421033 INFO::Formatting Data.
2025-02-09 20:19:04.421922 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:04.422947 INFO::Removing potential empty rows and columns
2025-02-09 20:19:04.42418 INFO::Found 0 missing values.
2025-02-09 20:19:04.425279 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.
2025-02-09 20:19:04.437383 INFO::Formatting Data.
2025-02-09 20:19:04.438265 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:04.439334 INFO::Removing potential empty rows and columns
2025-02-09 20:19:04.440513 INFO::Found 0 missing values.
2025-02-09 20:19:04.441579 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.
2025-02-09 20:19:04.459018 INFO::Formatting Data.
2025-02-09 20:19:04.459893 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:04.460955 INFO::Removing potential empty rows and columns
2025-02-09 20:19:04.462128 INFO::Found 0 missing values.
2025-02-09 20:19:04.463224 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.
2025-02-09 20:19:04.468296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:04.46896 INFO::Done
2025-02-09 20:19:04.469569 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:04.471931 INFO::Starting hierarchical adjustment
2025-02-09 20:19:04.472749 INFO::Found 2 batches.
2025-02-09 20:19:04.473355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:04.474045 INFO::Using default BPPARAM
2025-02-09 20:19:04.474628 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:04.475714 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:04.500171 INFO::Done
2025-02-09 20:19:04.501106 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:04.503606 INFO::ASW Batch was -0.0467533060453572 prior to batch effect correction and is now -0.115658504436824 .
2025-02-09 20:19:04.504596 INFO::Total function execution time is 0.0456373691558838 s and adjustment time is 0.0275301933288574 s ( 60.32 )
2025-02-09 20:19:04.508084 INFO::Formatting Data.
2025-02-09 20:19:04.508835 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:04.518756 INFO::Formatting Data.
2025-02-09 20:19:04.519622 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:04.520663 INFO::Removing potential empty rows and columns
2025-02-09 20:19:04.521806 INFO::Found 0 missing values.
2025-02-09 20:19:04.555704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:04.557101 INFO::Done
2025-02-09 20:19:04.557734 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:04.56003 INFO::Starting hierarchical adjustment
2025-02-09 20:19:04.560868 INFO::Found 2 batches.
2025-02-09 20:19:04.561439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:04.562091 INFO::Using default BPPARAM
2025-02-09 20:19:04.562655 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:04.563712 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:04.579441 INFO::Done
2025-02-09 20:19:04.580188 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:04.582337 INFO::ASW Batch was 0.0458807806350935 prior to batch effect correction and is now -0.0973762124067795 .
2025-02-09 20:19:04.583188 INFO::Total function execution time is 0.0645296573638916 s and adjustment time is 0.0187301635742188 s ( 29.03 )
2025-02-09 20:19:04.584301 INFO::Formatting Data.
2025-02-09 20:19:04.584886 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:04.585768 INFO::Removing potential empty rows and columns
2025-02-09 20:19:04.586802 INFO::Found 0 missing values.
2025-02-09 20:19:04.58959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:04.590112 INFO::Done
2025-02-09 20:19:04.590656 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:04.592724 INFO::Starting hierarchical adjustment
2025-02-09 20:19:04.593439 INFO::Found 2 batches.
2025-02-09 20:19:04.59395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:04.594561 INFO::Using default BPPARAM
2025-02-09 20:19:04.595079 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:04.595993 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:04.611414 INFO::Done
2025-02-09 20:19:04.612222 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:04.61449 INFO::ASW Batch was 0.0458807806350935 prior to batch effect correction and is now -0.0973762124067795 .
2025-02-09 20:19:04.61536 INFO::Total function execution time is 0.0310511589050293 s and adjustment time is 0.0181081295013428 s ( 58.32 )
2025-02-09 20:19:07.75794 INFO::Formatting Data.
2025-02-09 20:19:07.758824 INFO::Recognized SummarizedExperiment
2025-02-09 20:19:07.759386 INFO::Typecasting input to dataframe.
2025-02-09 20:19:07.791044 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:07.792359 INFO::Removing potential empty rows and columns
2025-02-09 20:19:07.795862 INFO::Found 0 missing values.
2025-02-09 20:19:07.803471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:07.804243 INFO::Done
2025-02-09 20:19:07.804804 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:07.808602 INFO::Starting hierarchical adjustment
2025-02-09 20:19:07.809401 INFO::Found 2 batches.
2025-02-09 20:19:07.809935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:07.811163 INFO::Using default BPPARAM
2025-02-09 20:19:07.811723 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:07.812779 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:07.873204 INFO::Done
2025-02-09 20:19:07.874125 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:07.878241 INFO::ASW Batch was 0.0119539481529756 prior to batch effect correction and is now -0.0905874396191954 .
2025-02-09 20:19:07.879242 INFO::Total function execution time is 0.121590375900269 s and adjustment time is 0.0638964176177979 s ( 52.55 )
2025-02-09 20:19:07.898401 INFO::Formatting Data.
2025-02-09 20:19:07.899333 INFO::Recognized SummarizedExperiment
2025-02-09 20:19:07.899957 INFO::Typecasting input to dataframe.
2025-02-09 20:19:07.909984 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:07.911329 INFO::Removing potential empty rows and columns
2025-02-09 20:19:07.915179 INFO::Found 0 missing values.
2025-02-09 20:19:07.922763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:07.923488 INFO::Done
2025-02-09 20:19:07.924047 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:07.927964 INFO::Starting hierarchical adjustment
2025-02-09 20:19:07.928795 INFO::Found 2 batches.
2025-02-09 20:19:07.929347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:07.929965 INFO::Using default BPPARAM
2025-02-09 20:19:07.930504 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:07.931579 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:07.957757 INFO::Done
2025-02-09 20:19:07.958533 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:07.962333 INFO::ASW Batch was 0.0135753005073581 prior to batch effect correction and is now 0.0135753005073581 .
2025-02-09 20:19:07.963302 INFO::Total function execution time is 0.0648989677429199 s and adjustment time is 0.0290772914886475 s ( 44.8 )
2025-02-09 20:19:07.982347 INFO::Formatting Data.
2025-02-09 20:19:07.983159 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:07.984073 INFO::Removing potential empty rows and columns
2025-02-09 20:19:07.985132 INFO::Found 0 missing values.
2025-02-09 20:19:07.988095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:07.988642 INFO::Done
2025-02-09 20:19:07.989155 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:07.991215 INFO::Starting hierarchical adjustment
2025-02-09 20:19:07.99193 INFO::Found 3 batches.
2025-02-09 20:19:07.992473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:07.993093 INFO::Using default BPPARAM
2025-02-09 20:19:07.993627 INFO::Processing subtree level 1
2025-02-09 20:19:08.277404 INFO::Adjusting the last 1 batches sequentially
2025-02-09 20:19:08.27978 INFO::Done
2025-02-09 20:19:08.280589 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:08.283719 INFO::ASW Batch was -0.0837472669415237 prior to batch effect correction and is now -0.169507004787158 .
2025-02-09 20:19:08.284841 INFO::Total function execution time is 0.302505493164062 s and adjustment time is 0.287927389144897 s ( 95.18 )
2025-02-09 20:19:08.368697 INFO::Skipping initial DF formatting
2025-02-09 20:19:08.370795 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:08.375419 INFO::Starting hierarchical adjustment
2025-02-09 20:19:08.376313 INFO::Found 5 batches.
2025-02-09 20:19:08.376881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:08.377559 INFO::Using default BPPARAM
2025-02-09 20:19:08.378112 INFO::Processing subtree level 1
2025-02-09 20:19:08.57798 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:08.580254 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:08.606774 INFO::Done
2025-02-09 20:19:08.607692 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:08.612912 INFO::ASW Batch was 0.552496224510232 prior to batch effect correction and is now 0.552496224510232 .
2025-02-09 20:19:08.613725 INFO::ASW Label was 0.383679046291605 prior to batch effect correction and is now 0.383679046291605 .
2025-02-09 20:19:08.614877 INFO::Total function execution time is 0.246321439743042 s and adjustment time is 0.230608701705933 s ( 93.62 )
2025-02-09 20:19:08.637113 INFO::Formatting Data.
2025-02-09 20:19:08.638208 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:08.639379 INFO::Removing potential empty rows and columns
2025-02-09 20:19:08.640626 INFO::Found 0 missing values.
2025-02-09 20:19:08.645469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:08.646141 INFO::Done
2025-02-09 20:19:08.646758 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:08.650683 INFO::Starting hierarchical adjustment
2025-02-09 20:19:08.651575 INFO::Found 5 batches.
2025-02-09 20:19:08.652246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:08.653022 INFO::Using default BPPARAM
2025-02-09 20:19:08.653676 INFO::Processing subtree level 1
2025-02-09 20:19:08.809255 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:08.811475 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:08.832582 INFO::Done
2025-02-09 20:19:08.833656 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:08.837744 INFO::ASW Batch was 0.4299025067789 prior to batch effect correction and is now -0.0621406528482335 .
2025-02-09 20:19:08.838618 INFO::ASW Label was 0.440829961967542 prior to batch effect correction and is now 0.73512793429014 .
2025-02-09 20:19:08.839622 INFO::Total function execution time is 0.202699661254883 s and adjustment time is 0.18113374710083 s ( 89.36 )
2025-02-09 20:19:08.840634 INFO::Formatting Data.
2025-02-09 20:19:08.841372 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:08.842468 INFO::Removing potential empty rows and columns
2025-02-09 20:19:08.8436 INFO::Found 0 missing values.
2025-02-09 20:19:08.848463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:08.849097 INFO::Done
2025-02-09 20:19:08.849681 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:08.853166 INFO::Starting hierarchical adjustment
2025-02-09 20:19:08.853989 INFO::Found 5 batches.
2025-02-09 20:19:08.854613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:08.855361 INFO::Using default BPPARAM
2025-02-09 20:19:08.855965 INFO::Processing subtree level 1
2025-02-09 20:19:09.003339 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:09.005288 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:09.021654 INFO::Done
2025-02-09 20:19:09.022451 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:09.02586 INFO::ASW Batch was 0.4299025067789 prior to batch effect correction and is now -0.0621406528482335 .
2025-02-09 20:19:09.026539 INFO::ASW Label was 0.440829961967542 prior to batch effect correction and is now 0.73512793429014 .
2025-02-09 20:19:09.036502 INFO::Total function execution time is 0.186771631240845 s and adjustment time is 0.16780948638916 s ( 89.85 )
2025-02-09 20:19:09.054404 INFO::Formatting Data.
2025-02-09 20:19:09.055386 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:09.056547 INFO::Removing potential empty rows and columns
2025-02-09 20:19:09.057811 INFO::Found 0 missing values.
2025-02-09 20:19:09.062214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:09.062812 INFO::Done
2025-02-09 20:19:09.063376 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:09.066921 INFO::Starting hierarchical adjustment
2025-02-09 20:19:09.067724 INFO::Found 5 batches.
2025-02-09 20:19:09.068345 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:09.069173 INFO::Using default BPPARAM
2025-02-09 20:19:09.069755 INFO::Processing subtree level 1
2025-02-09 20:19:09.224987 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:09.227319 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:09.249152 INFO::Done
2025-02-09 20:19:09.250285 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:09.254764 INFO::ASW Batch was 0.338903017675484 prior to batch effect correction and is now -0.0328644822759782 .
2025-02-09 20:19:09.25568 INFO::ASW Label was 0.485921989084785 prior to batch effect correction and is now 0.828325136892875 .
2025-02-09 20:19:09.256823 INFO::Total function execution time is 0.202678918838501 s and adjustment time is 0.181483507156372 s ( 89.54 )
2025-02-09 20:19:09.257947 INFO::Formatting Data.
2025-02-09 20:19:09.258778 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:09.259922 INFO::Removing potential empty rows and columns
2025-02-09 20:19:09.261197 INFO::Found 0 missing values.
2025-02-09 20:19:09.266328 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:09.267059 INFO::Done
2025-02-09 20:19:09.267761 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:09.271358 INFO::Starting hierarchical adjustment
2025-02-09 20:19:09.272196 INFO::Found 5 batches.
2025-02-09 20:19:09.27285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:09.273588 INFO::Using default BPPARAM
2025-02-09 20:19:09.274193 INFO::Processing subtree level 1
2025-02-09 20:19:09.412414 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:09.414651 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:09.434306 INFO::Done
2025-02-09 20:19:09.435373 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:09.439453 INFO::ASW Batch was 0.338903017675484 prior to batch effect correction and is now -0.0328644822759782 .
2025-02-09 20:19:09.440292 INFO::ASW Label was 0.485921989084785 prior to batch effect correction and is now 0.828325136892875 .
2025-02-09 20:19:09.441348 INFO::Total function execution time is 0.183416128158569 s and adjustment time is 0.162176370620728 s ( 88.42 )
2025-02-09 20:19:09.456372 INFO::Formatting Data.
2025-02-09 20:19:09.457269 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:09.458332 INFO::Removing potential empty rows and columns
2025-02-09 20:19:09.459496 INFO::Found 0 missing values.
2025-02-09 20:19:09.462581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:09.463225 INFO::Done
2025-02-09 20:19:09.463822 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:09.467338 INFO::Starting hierarchical adjustment
2025-02-09 20:19:09.468225 INFO::Found 2 batches.
2025-02-09 20:19:09.468845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:09.469602 INFO::Using default BPPARAM
2025-02-09 20:19:09.470242 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:09.471332 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:09.487528 INFO::Done
2025-02-09 20:19:09.488283 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:09.491303 INFO::ASW Batch was 0.591566447170576 prior to batch effect correction and is now 0.170302023491816 .
2025-02-09 20:19:09.491948 INFO::ASW Label was 0.572950893272438 prior to batch effect correction and is now 0.78754089170444 .
2025-02-09 20:19:09.492796 INFO::Total function execution time is 0.0365293025970459 s and adjustment time is 0.0194740295410156 s ( 53.31 )
2025-02-09 20:19:09.493661 INFO::Formatting Data.
2025-02-09 20:19:09.494317 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:09.495235 INFO::Removing potential empty rows and columns
2025-02-09 20:19:09.496257 INFO::Found 0 missing values.
2025-02-09 20:19:09.498935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:09.49953 INFO::Done
2025-02-09 20:19:09.500046 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:09.50296 INFO::Starting hierarchical adjustment
2025-02-09 20:19:09.503692 INFO::Found 2 batches.
2025-02-09 20:19:09.504237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:09.504831 INFO::Using default BPPARAM
2025-02-09 20:19:09.505383 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:09.506307 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:09.521457 INFO::Done
2025-02-09 20:19:09.522257 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:09.525394 INFO::ASW Batch was 0.591566447170576 prior to batch effect correction and is now 0.170302023491816 .
2025-02-09 20:19:09.526029 INFO::ASW Label was 0.572950893272438 prior to batch effect correction and is now 0.78754089170444 .
2025-02-09 20:19:09.526868 INFO::Total function execution time is 0.0332369804382324 s and adjustment time is 0.0178680419921875 s ( 53.76 )
2025-02-09 20:19:09.538073 INFO::Formatting Data.
2025-02-09 20:19:09.538877 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:09.539786 INFO::Removing potential empty rows and columns
2025-02-09 20:19:09.5407 INFO::Found 0 missing values.
2025-02-09 20:19:09.542783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:09.543377 INFO::Done
2025-02-09 20:19:09.543904 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:09.545897 INFO::Starting hierarchical adjustment
2025-02-09 20:19:09.546667 INFO::Found 2 batches.
2025-02-09 20:19:09.547239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:09.5479 INFO::Using default BPPARAM
2025-02-09 20:19:09.548464 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:09.549467 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:09.583726 INFO::Done
2025-02-09 20:19:09.584612 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:09.58682 INFO::ASW Batch was -0.0211662807905865 prior to batch effect correction and is now -0.111229591902907 .
2025-02-09 20:19:09.587731 INFO::Total function execution time is 0.049729585647583 s and adjustment time is 0.0371689796447754 s ( 74.74 )
2025-02-09 20:19:09.600686 INFO::Formatting Data.
2025-02-09 20:19:09.601703 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:09.602831 INFO::Removing potential empty rows and columns
2025-02-09 20:19:09.603999 INFO::Found 0 missing values.
2025-02-09 20:19:09.605369 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.
2025-02-09 20:19:09.610379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:09.611032 INFO::Done
2025-02-09 20:19:09.61159 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:09.614676 INFO::Starting hierarchical adjustment
2025-02-09 20:19:09.615481 INFO::Found 2 batches.
2025-02-09 20:19:09.616049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:09.61667 INFO::Using default BPPARAM
2025-02-09 20:19:09.617228 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:09.618265 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:09.636016 INFO::Done
2025-02-09 20:19:09.6368 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:09.639885 INFO::ASW Batch was 0.337311006529265 prior to batch effect correction and is now 0.172318632352659 .
2025-02-09 20:19:09.640537 INFO::ASW Label was 0.77514381694858 prior to batch effect correction and is now 0.863612559981916 .
2025-02-09 20:19:09.641404 INFO::Total function execution time is 0.0408675670623779 s and adjustment time is 0.0206680297851562 s ( 50.57 )
2025-02-09 20:19:09.642272 INFO::Formatting Data.
2025-02-09 20:19:09.642927 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:09.64389 INFO::Removing potential empty rows and columns
2025-02-09 20:19:09.644932 INFO::Found 0 missing values.
2025-02-09 20:19:09.645951 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.
2025-02-09 20:19:09.650995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:09.651685 INFO::Done
2025-02-09 20:19:09.652276 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:09.655565 INFO::Starting hierarchical adjustment
2025-02-09 20:19:09.656357 INFO::Found 2 batches.
2025-02-09 20:19:09.656935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:09.657678 INFO::Using default BPPARAM
2025-02-09 20:19:09.658292 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:09.659366 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:09.677924 INFO::Done
2025-02-09 20:19:09.678723 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:09.681834 INFO::ASW Batch was 0.337311006529265 prior to batch effect correction and is now 0.172318632352659 .
2025-02-09 20:19:09.68251 INFO::ASW Label was 0.77514381694858 prior to batch effect correction and is now 0.863612559981916 .
2025-02-09 20:19:09.683369 INFO::Total function execution time is 0.0411109924316406 s and adjustment time is 0.0216903686523438 s ( 52.76 )
2025-02-09 20:19:09.911967 INFO::Formatting Data.
2025-02-09 20:19:09.913041 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:09.914042 INFO::Removing potential empty rows and columns
2025-02-09 20:19:09.91518 INFO::Found 0 missing values.
2025-02-09 20:19:09.918374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:09.918948 INFO::Done
2025-02-09 20:19:09.919493 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:09.921994 INFO::Starting hierarchical adjustment
2025-02-09 20:19:09.922794 INFO::Found 3 batches.
2025-02-09 20:19:09.923345 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:09.924025 INFO::Using default BPPARAM
2025-02-09 20:19:09.924596 INFO::Processing subtree level 1
2025-02-09 20:19:10.01604 INFO::Adjusting the last 1 batches sequentially
2025-02-09 20:19:10.017962 INFO::Done
2025-02-09 20:19:10.018721 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:10.021313 INFO::ASW Batch was -0.0816155390016502 prior to batch effect correction and is now -0.0816155390016502 .
2025-02-09 20:19:10.022359 INFO::Total function execution time is 0.110572099685669 s and adjustment time is 0.0953531265258789 s ( 86.24 )
2025-02-09 20:19:10.02354 INFO::Formatting Data.
2025-02-09 20:19:10.024265 INFO::Typecasting input to dataframe.
2025-02-09 20:19:10.025089 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:10.026083 INFO::Removing potential empty rows and columns
2025-02-09 20:19:10.027233 INFO::Found 0 missing values.
2025-02-09 20:19:10.030424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:10.031009 INFO::Done
2025-02-09 20:19:10.031592 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:10.033787 INFO::Starting hierarchical adjustment
2025-02-09 20:19:10.034544 INFO::Found 3 batches.
2025-02-09 20:19:10.035097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:10.035778 INFO::Using default BPPARAM
2025-02-09 20:19:10.036336 INFO::Processing subtree level 1
2025-02-09 20:19:10.168828 INFO::Adjusting the last 1 batches sequentially
2025-02-09 20:19:10.171187 INFO::Done
2025-02-09 20:19:10.172134 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:10.175122 INFO::ASW Batch was -0.0816155390016502 prior to batch effect correction and is now -0.0816155390016502 .
2025-02-09 20:19:10.176297 INFO::Total function execution time is 0.152692079544067 s and adjustment time is 0.136734247207642 s ( 89.55 )
2025-02-09 20:19:10.193093 INFO::Formatting Data.
2025-02-09 20:19:10.194196 INFO::Typecasting input to dataframe.
2025-02-09 20:19:10.195445 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:10.196635 INFO::Removing potential empty rows and columns
2025-02-09 20:19:10.197968 INFO::Found 0 missing values.
2025-02-09 20:19:10.201427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:10.202046 INFO::Done
2025-02-09 20:19:10.202611 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:10.204983 INFO::Starting hierarchical adjustment
2025-02-09 20:19:10.205815 INFO::Found 3 batches.
2025-02-09 20:19:10.206399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:10.207084 INFO::Using default BPPARAM
2025-02-09 20:19:10.207689 INFO::Processing subtree level 1
2025-02-09 20:19:10.316769 INFO::Adjusting the last 1 batches sequentially
2025-02-09 20:19:10.319295 INFO::Done
2025-02-09 20:19:10.320319 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:10.32411 INFO::ASW Batch was -0.0819574033741888 prior to batch effect correction and is now -0.0819574033741888 .
2025-02-09 20:19:10.325546 INFO::Total function execution time is 0.132569551467896 s and adjustment time is 0.113583326339722 s ( 85.68 )
2025-02-09 20:19:10.501017 INFO::Formatting Data.
2025-02-09 20:19:10.502599 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:10.504297 INFO::Removing potential empty rows and columns
2025-02-09 20:19:10.507738 INFO::Found 1000 missing values.
2025-02-09 20:19:10.528927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:10.530182 INFO::Done
2025-02-09 20:19:10.530923 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:10.537852 INFO::Starting hierarchical adjustment
2025-02-09 20:19:10.539097 INFO::Found 10 batches.
2025-02-09 20:19:10.539832 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:10.540596 INFO::Using default BPPARAM
2025-02-09 20:19:10.541191 INFO::Processing subtree level 1
2025-02-09 20:19:10.729803 INFO::Processing subtree level 2
2025-02-09 20:19:10.897523 INFO::Adjusting the last 1 batches sequentially
2025-02-09 20:19:10.900219 INFO::Done
2025-02-09 20:19:10.901101 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:10.907557 INFO::ASW Batch was 0.48452628134402 prior to batch effect correction and is now 0.48452628134402 .
2025-02-09 20:19:10.908461 INFO::ASW Label was 0.336412854912221 prior to batch effect correction and is now 0.336412854912221 .
2025-02-09 20:19:10.909616 INFO::Total function execution time is 0.408932685852051 s and adjustment time is 0.361335515975952 s ( 88.36 )
2025-02-09 20:19:10.910652 INFO::Formatting Data.
2025-02-09 20:19:10.911439 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:10.912878 INFO::Removing potential empty rows and columns
2025-02-09 20:19:10.915907 INFO::Found 1000 missing values.
2025-02-09 20:19:10.936393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:10.937451 INFO::Done
2025-02-09 20:19:10.938185 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:10.944815 INFO::Starting hierarchical adjustment
2025-02-09 20:19:10.946136 INFO::Found 10 batches.
2025-02-09 20:19:12.728601 INFO::Set up parallel execution backend with 2 workers
2025-02-09 20:19:12.731483 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-09 20:19:14.2241 INFO::Adjusting the last 2 batches sequentially
2025-02-09 20:19:14.22642 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 20:19:14.243888 INFO::Done
2025-02-09 20:19:14.24467 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:14.249481 INFO::ASW Batch was 0.48452628134402 prior to batch effect correction and is now 0.48452628134402 .
2025-02-09 20:19:14.250092 INFO::ASW Label was 0.336412854912221 prior to batch effect correction and is now 0.336412854912221 .
2025-02-09 20:19:14.250918 INFO::Total function execution time is 3.3403525352478 s and adjustment time is 3.29798865318298 s ( 98.73 )
2025-02-09 20:19:14.413874 INFO::Formatting Data.
2025-02-09 20:19:14.414932 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.416069 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.417314 INFO::Found 0 missing values.
2025-02-09 20:19:14.421237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.421901 INFO::Done
2025-02-09 20:19:14.422449 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 20:19:14.425526 INFO::Starting hierarchical adjustment
2025-02-09 20:19:14.426325 INFO::Found 3 batches.
2025-02-09 20:19:14.42688 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 20:19:14.427562 INFO::Using default BPPARAM
2025-02-09 20:19:14.428116 INFO::Processing subtree level 1
2025-02-09 20:19:14.54766 INFO::Adjusting the last 1 batches sequentially
2025-02-09 20:19:14.550068 INFO::Done
2025-02-09 20:19:14.550992 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 20:19:14.555105 INFO::ASW Batch was 0.109733213382234 prior to batch effect correction and is now -0.150906893552483 .
2025-02-09 20:19:14.555896 INFO::ASW Label was -0.192391824906613 prior to batch effect correction and is now -0.0766871399889704 .
2025-02-09 20:19:14.557032 INFO::Total function execution time is 0.143228769302368 s and adjustment time is 0.123855352401733 s ( 86.47 )
2025-02-09 20:19:14.707363 INFO::Formatting Data.
2025-02-09 20:19:14.708645 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.709732 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.710973 INFO::Found 2 missing values.
2025-02-09 20:19:14.714049 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.714645 INFO::Done
2025-02-09 20:19:14.744664 INFO::Found NA in Reference column
2025-02-09 20:19:14.754735 INFO::Require at least two references per batch.
2025-02-09 20:19:14.777677 INFO::Formatting Data.
2025-02-09 20:19:14.778587 INFO::Recognized SummarizedExperiment
2025-02-09 20:19:14.779168 INFO::Typecasting input to dataframe.
2025-02-09 20:19:14.790012 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.791298 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.794761 INFO::Found 0 missing values.
2025-02-09 20:19:14.801555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.802184 INFO::Done
2025-02-09 20:19:14.817472 INFO::Formatting Data.
2025-02-09 20:19:14.818267 INFO::Recognized SummarizedExperiment
2025-02-09 20:19:14.818815 INFO::Typecasting input to dataframe.
2025-02-09 20:19:14.836508 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.837884 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.84146 INFO::Found 0 missing values.
2025-02-09 20:19:14.852091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.852892 INFO::Done
2025-02-09 20:19:14.868218 INFO::Formatting Data.
2025-02-09 20:19:14.86902 INFO::Recognized SummarizedExperiment
2025-02-09 20:19:14.869566 INFO::Typecasting input to dataframe.
2025-02-09 20:19:14.886976 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.888134 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.889255 INFO::Found 0 missing values.
2025-02-09 20:19:14.890254 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.
2025-02-09 20:19:14.894598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.895141 INFO::Done
2025-02-09 20:19:14.905531 INFO::Formatting Data.
2025-02-09 20:19:14.906405 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.907412 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.908566 INFO::Found 0 missing values.
2025-02-09 20:19:14.911467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.912025 INFO::Done
2025-02-09 20:19:14.923716 INFO::Formatting Data.
2025-02-09 20:19:14.924582 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.925496 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.926524 INFO::Found 0 missing values.
2025-02-09 20:19:14.929424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.92999 INFO::Done
2025-02-09 20:19:14.960594 INFO::Formatting Data.
2025-02-09 20:19:14.961499 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.962686 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.963987 INFO::Found 1 missing values.
2025-02-09 20:19:14.966826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.967409 INFO::Done
2025-02-09 20:19:14.987858 INFO::Formatting Data.
2025-02-09 20:19:14.988844 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:14.989852 INFO::Removing potential empty rows and columns
2025-02-09 20:19:14.991 INFO::Found 2 missing values.
2025-02-09 20:19:14.992033 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.
2025-02-09 20:19:14.994616 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:14.995228 INFO::Done
2025-02-09 20:19:15.006548 INFO::Formatting Data.
2025-02-09 20:19:15.007544 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:15.00858 INFO::Removing potential empty rows and columns
2025-02-09 20:19:15.009653 INFO::Found 2 missing values.
2025-02-09 20:19:15.011561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:15.012122 INFO::Done
2025-02-09 20:19:15.02388 INFO::Formatting Data.
2025-02-09 20:19:15.02487 INFO::Typecasting input to dataframe.
2025-02-09 20:19:15.025802 INFO::Replacing NaNs with NAs.
2025-02-09 20:19:15.02679 INFO::Removing potential empty rows and columns
2025-02-09 20:19:15.027902 INFO::Found 0 missing values.
2025-02-09 20:19:15.030953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 20:19:15.031588 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.232 4.594 23.371
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.165 | 1.342 | 18.400 | |
| compute_asw | 0.022 | 0.003 | 0.026 | |
| count_existing | 0.012 | 0.003 | 0.015 | |
| generate_data_covariables | 0.012 | 0.002 | 0.014 | |
| generate_dataset | 0.008 | 0.005 | 0.013 | |