Yannis Schumann
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 65b1ece |
| git_last_commit_date: 2024-02-28 02:41:28 -0400 (Wed, 28 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:38:50 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 155/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 0.99.16 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 0.99.16 |
| 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_0.99.16.tar.gz |
| StartedAt: 2024-03-27 19:40:00 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 19:41:25 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 84.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_0.99.16.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘0.99.16’
* 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 27.082 1.522 19.473
* 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-x86_64/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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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")
2024-03-27 19:41:03.951761 INFO::Formatting Data.
2024-03-27 19:41:03.955589 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:03.970746 INFO::Removing potential empty rows and columns
2024-03-27 19:41:04.299195 INFO::Found 0 missing values.
2024-03-27 19:41:04.304303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:04.304996 INFO::Done
2024-03-27 19:41:04.305773 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:04.323175 INFO::Starting hierarchical adjustment
2024-03-27 19:41:04.32443 INFO::Found 3 batches.
2024-03-27 19:41:04.325281 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:04.326839 INFO::Using default BPPARAM
2024-03-27 19:41:04.327573 INFO::Processing subtree level 1
2024-03-27 19:41:04.473613 INFO::Adjusting the last 1 batches sequentially
2024-03-27 19:41:04.478305 INFO::Done
2024-03-27 19:41:04.479524 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:04.483033 INFO::ASW Batch was -0.0750387452738414 prior to batch effect correction and is now -0.0750387452738414 .
2024-03-27 19:41:04.484685 INFO::Total function execution time is 0.53389310836792 s and adjustment time is 0.154153108596802 s ( 28.87 )
2024-03-27 19:41:04.506405 INFO::Formatting Data.
2024-03-27 19:41:04.507528 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:04.508816 INFO::Removing potential empty rows and columns
2024-03-27 19:41:04.510335 INFO::Found 0 missing values.
2024-03-27 19:41:04.511645 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.
2024-03-27 19:41:04.524981 INFO::Formatting Data.
2024-03-27 19:41:04.525938 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:04.527274 INFO::Removing potential empty rows and columns
2024-03-27 19:41:04.528977 INFO::Found 0 missing values.
2024-03-27 19:41:04.529921 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.
2024-03-27 19:41:04.552273 INFO::Formatting Data.
2024-03-27 19:41:04.553458 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:04.554711 INFO::Removing potential empty rows and columns
2024-03-27 19:41:04.556085 INFO::Found 0 missing values.
2024-03-27 19:41:04.557318 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.
2024-03-27 19:41:04.561637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:04.562205 INFO::Done
2024-03-27 19:41:04.563176 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:04.566459 INFO::Starting hierarchical adjustment
2024-03-27 19:41:04.5675 INFO::Found 2 batches.
2024-03-27 19:41:04.568254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:04.569208 INFO::Using default BPPARAM
2024-03-27 19:41:04.569699 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:04.570531 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:04.59613 INFO::Done
2024-03-27 19:41:04.597017 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:04.599701 INFO::ASW Batch was 0.0363297744627844 prior to batch effect correction and is now -0.0563714427581129 .
2024-03-27 19:41:04.60107 INFO::Total function execution time is 0.0488109588623047 s and adjustment time is 0.0287988185882568 s ( 59 )
2024-03-27 19:41:04.606062 INFO::Formatting Data.
2024-03-27 19:41:04.60695 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:04.619223 INFO::Formatting Data.
2024-03-27 19:41:04.620182 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:04.621026 INFO::Removing potential empty rows and columns
2024-03-27 19:41:04.621912 INFO::Found 0 missing values.
2024-03-27 19:41:04.624349 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:04.624809 INFO::Done
2024-03-27 19:41:04.625258 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:04.626996 INFO::Starting hierarchical adjustment
2024-03-27 19:41:04.627621 INFO::Found 2 batches.
2024-03-27 19:41:04.628077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:04.628611 INFO::Using default BPPARAM
2024-03-27 19:41:04.629065 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:04.629856 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:04.642792 INFO::Done
2024-03-27 19:41:04.643397 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:04.645208 INFO::ASW Batch was 0.003607776001682 prior to batch effect correction and is now -0.118388697844893 .
2024-03-27 19:41:04.645894 INFO::Total function execution time is 0.026824951171875 s and adjustment time is 0.0152440071105957 s ( 56.83 )
2024-03-27 19:41:04.646857 INFO::Formatting Data.
2024-03-27 19:41:04.647368 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:04.648132 INFO::Removing potential empty rows and columns
2024-03-27 19:41:04.649214 INFO::Found 0 missing values.
2024-03-27 19:41:04.653088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:04.653821 INFO::Done
2024-03-27 19:41:04.654522 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:04.657215 INFO::Starting hierarchical adjustment
2024-03-27 19:41:04.658081 INFO::Found 2 batches.
2024-03-27 19:41:04.658716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:04.659258 INFO::Using default BPPARAM
2024-03-27 19:41:04.659715 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:04.660821 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:04.676827 INFO::Done
2024-03-27 19:41:04.677875 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:04.680852 INFO::ASW Batch was 0.003607776001682 prior to batch effect correction and is now -0.118388697844893 .
2024-03-27 19:41:04.68197 INFO::Total function execution time is 0.0350630283355713 s and adjustment time is 0.0188770294189453 s ( 53.84 )
2024-03-27 19:41:07.285067 INFO::Formatting Data.
2024-03-27 19:41:07.285734 INFO::Recognized SummarizedExperiment
2024-03-27 19:41:07.286411 INFO::Typecasting input to dataframe.
2024-03-27 19:41:07.321956 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:07.323353 INFO::Removing potential empty rows and columns
2024-03-27 19:41:07.327229 INFO::Found 0 missing values.
2024-03-27 19:41:07.332503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:07.333047 INFO::Done
2024-03-27 19:41:07.333569 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:07.337494 INFO::Starting hierarchical adjustment
2024-03-27 19:41:07.338092 INFO::Found 2 batches.
2024-03-27 19:41:07.338559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:07.339803 INFO::Using default BPPARAM
2024-03-27 19:41:07.340308 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:07.341123 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:08.176426 INFO::Done
2024-03-27 19:41:08.176975 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:08.179778 INFO::ASW Batch was -0.0138476218716606 prior to batch effect correction and is now -0.0970994486822935 .
2024-03-27 19:41:08.180488 INFO::Total function execution time is 0.895695209503174 s and adjustment time is 0.838406085968018 s ( 93.6 )
2024-03-27 19:41:08.201336 INFO::Formatting Data.
2024-03-27 19:41:08.201957 INFO::Recognized SummarizedExperiment
2024-03-27 19:41:08.202388 INFO::Typecasting input to dataframe.
2024-03-27 19:41:08.210345 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:08.21133 INFO::Removing potential empty rows and columns
2024-03-27 19:41:08.214128 INFO::Found 0 missing values.
2024-03-27 19:41:08.221158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:08.221829 INFO::Done
2024-03-27 19:41:08.222273 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:08.225858 INFO::Starting hierarchical adjustment
2024-03-27 19:41:08.226705 INFO::Found 2 batches.
2024-03-27 19:41:08.227309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:08.227979 INFO::Using default BPPARAM
2024-03-27 19:41:08.228562 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:08.229854 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:08.255484 INFO::Done
2024-03-27 19:41:08.256364 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:08.260617 INFO::ASW Batch was -0.01472026907123 prior to batch effect correction and is now -0.01472026907123 .
2024-03-27 19:41:08.2617 INFO::Total function execution time is 0.0602889060974121 s and adjustment time is 0.0288910865783691 s ( 47.92 )
2024-03-27 19:41:08.28775 INFO::Formatting Data.
2024-03-27 19:41:08.288565 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:08.289746 INFO::Removing potential empty rows and columns
2024-03-27 19:41:08.291001 INFO::Found 0 missing values.
2024-03-27 19:41:08.294611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:08.295287 INFO::Done
2024-03-27 19:41:08.295997 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:08.29805 INFO::Starting hierarchical adjustment
2024-03-27 19:41:08.298611 INFO::Found 3 batches.
2024-03-27 19:41:08.299015 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:08.299471 INFO::Using default BPPARAM
2024-03-27 19:41:08.299865 INFO::Processing subtree level 1
2024-03-27 19:41:08.547831 INFO::Adjusting the last 1 batches sequentially
2024-03-27 19:41:08.571973 INFO::Done
2024-03-27 19:41:08.5732 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:08.582214 INFO::ASW Batch was -0.067029759586822 prior to batch effect correction and is now -0.150635859537529 .
2024-03-27 19:41:08.586994 INFO::Total function execution time is 0.298998117446899 s and adjustment time is 0.273356199264526 s ( 91.42 )
2024-03-27 19:41:08.613721 INFO::Skipping initial DF formatting
2024-03-27 19:41:08.614746 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:08.621084 INFO::Starting hierarchical adjustment
2024-03-27 19:41:08.623265 INFO::Found 5 batches.
2024-03-27 19:41:08.624087 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:08.624976 INFO::Using default BPPARAM
2024-03-27 19:41:08.626051 INFO::Processing subtree level 1
2024-03-27 19:41:08.850638 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:08.859154 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:08.901897 INFO::Done
2024-03-27 19:41:08.902555 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:08.90958 INFO::ASW Batch was 0.506841546614801 prior to batch effect correction and is now 0.506841546614801 .
2024-03-27 19:41:08.910484 INFO::ASW Label was 0.354356168412361 prior to batch effect correction and is now 0.354356168412361 .
2024-03-27 19:41:08.913402 INFO::Total function execution time is 0.29988694190979 s and adjustment time is 0.279345989227295 s ( 93.15 )
2024-03-27 19:41:08.939168 INFO::Formatting Data.
2024-03-27 19:41:08.940062 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:08.940981 INFO::Removing potential empty rows and columns
2024-03-27 19:41:08.942074 INFO::Found 0 missing values.
2024-03-27 19:41:08.946056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:08.946584 INFO::Done
2024-03-27 19:41:08.947073 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:08.949959 INFO::Starting hierarchical adjustment
2024-03-27 19:41:08.950647 INFO::Found 5 batches.
2024-03-27 19:41:08.951176 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:08.95185 INFO::Using default BPPARAM
2024-03-27 19:41:08.952465 INFO::Processing subtree level 1
2024-03-27 19:41:09.142016 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:09.172188 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:09.216284 INFO::Done
2024-03-27 19:41:09.217252 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:09.22241 INFO::ASW Batch was 0.438316168261467 prior to batch effect correction and is now -0.0797932638290788 .
2024-03-27 19:41:09.223122 INFO::ASW Label was 0.327411660857538 prior to batch effect correction and is now 0.776856373751307 .
2024-03-27 19:41:09.225538 INFO::Total function execution time is 0.286261081695557 s and adjustment time is 0.265689134597778 s ( 92.81 )
2024-03-27 19:41:09.227071 INFO::Formatting Data.
2024-03-27 19:41:09.228438 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:09.230111 INFO::Removing potential empty rows and columns
2024-03-27 19:41:09.231638 INFO::Found 0 missing values.
2024-03-27 19:41:09.238386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:09.239429 INFO::Done
2024-03-27 19:41:09.240397 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:09.244924 INFO::Starting hierarchical adjustment
2024-03-27 19:41:09.246602 INFO::Found 5 batches.
2024-03-27 19:41:09.247444 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:09.248266 INFO::Using default BPPARAM
2024-03-27 19:41:09.248888 INFO::Processing subtree level 1
2024-03-27 19:41:09.418311 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:09.424985 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:09.456315 INFO::Done
2024-03-27 19:41:09.457517 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:09.461803 INFO::ASW Batch was 0.438316168261467 prior to batch effect correction and is now -0.0797932638290788 .
2024-03-27 19:41:09.462852 INFO::ASW Label was 0.327411660857538 prior to batch effect correction and is now 0.776856373751307 .
2024-03-27 19:41:09.464702 INFO::Total function execution time is 0.237874031066895 s and adjustment time is 0.209843158721924 s ( 88.22 )
2024-03-27 19:41:09.485661 INFO::Formatting Data.
2024-03-27 19:41:09.486495 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:09.487421 INFO::Removing potential empty rows and columns
2024-03-27 19:41:09.488379 INFO::Found 0 missing values.
2024-03-27 19:41:09.492255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:09.493132 INFO::Done
2024-03-27 19:41:09.493967 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:09.497398 INFO::Starting hierarchical adjustment
2024-03-27 19:41:09.498436 INFO::Found 5 batches.
2024-03-27 19:41:09.499357 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:09.500203 INFO::Using default BPPARAM
2024-03-27 19:41:09.500901 INFO::Processing subtree level 1
2024-03-27 19:41:09.631247 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:09.63446 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:09.656447 INFO::Done
2024-03-27 19:41:09.657231 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:09.661629 INFO::ASW Batch was 0.371368014646737 prior to batch effect correction and is now -0.105228360659655 .
2024-03-27 19:41:09.662403 INFO::ASW Label was 0.440493583718709 prior to batch effect correction and is now 0.8224015032534 .
2024-03-27 19:41:09.663388 INFO::Total function execution time is 0.177703142166138 s and adjustment time is 0.158250093460083 s ( 89.05 )
2024-03-27 19:41:09.664559 INFO::Formatting Data.
2024-03-27 19:41:09.66516 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:09.666172 INFO::Removing potential empty rows and columns
2024-03-27 19:41:09.667562 INFO::Found 0 missing values.
2024-03-27 19:41:09.672122 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:09.672857 INFO::Done
2024-03-27 19:41:09.673792 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:09.678055 INFO::Starting hierarchical adjustment
2024-03-27 19:41:09.678901 INFO::Found 5 batches.
2024-03-27 19:41:09.679915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:09.680841 INFO::Using default BPPARAM
2024-03-27 19:41:09.681436 INFO::Processing subtree level 1
2024-03-27 19:41:09.808674 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:09.813008 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:09.846196 INFO::Done
2024-03-27 19:41:09.847391 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:09.853314 INFO::ASW Batch was 0.371368014646737 prior to batch effect correction and is now -0.105228360659655 .
2024-03-27 19:41:09.854101 INFO::ASW Label was 0.440493583718709 prior to batch effect correction and is now 0.8224015032534 .
2024-03-27 19:41:09.85557 INFO::Total function execution time is 0.190858125686646 s and adjustment time is 0.167349100112915 s ( 87.68 )
2024-03-27 19:41:09.885951 INFO::Formatting Data.
2024-03-27 19:41:09.887214 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:09.888394 INFO::Removing potential empty rows and columns
2024-03-27 19:41:09.890041 INFO::Found 0 missing values.
2024-03-27 19:41:09.893231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:09.894067 INFO::Done
2024-03-27 19:41:09.89514 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:09.900936 INFO::Starting hierarchical adjustment
2024-03-27 19:41:09.902153 INFO::Found 2 batches.
2024-03-27 19:41:09.902981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:09.903866 INFO::Using default BPPARAM
2024-03-27 19:41:09.904592 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:09.905907 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:09.926693 INFO::Done
2024-03-27 19:41:09.927441 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:09.932032 INFO::ASW Batch was 0.670039808622412 prior to batch effect correction and is now 0.0307615235295075 .
2024-03-27 19:41:09.933161 INFO::ASW Label was 0.429519063372797 prior to batch effect correction and is now 0.897800511979328 .
2024-03-27 19:41:09.934591 INFO::Total function execution time is 0.0487060546875 s and adjustment time is 0.0247910022735596 s ( 50.9 )
2024-03-27 19:41:09.935926 INFO::Formatting Data.
2024-03-27 19:41:09.936903 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:09.93821 INFO::Removing potential empty rows and columns
2024-03-27 19:41:09.93985 INFO::Found 0 missing values.
2024-03-27 19:41:09.943817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:09.944678 INFO::Done
2024-03-27 19:41:09.945197 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:09.949764 INFO::Starting hierarchical adjustment
2024-03-27 19:41:09.951105 INFO::Found 2 batches.
2024-03-27 19:41:09.951746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:09.952323 INFO::Using default BPPARAM
2024-03-27 19:41:09.953099 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:09.954232 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:09.973832 INFO::Done
2024-03-27 19:41:09.974853 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:09.979098 INFO::ASW Batch was 0.670039808622412 prior to batch effect correction and is now 0.0307615235295075 .
2024-03-27 19:41:09.980013 INFO::ASW Label was 0.429519063372797 prior to batch effect correction and is now 0.897800511979328 .
2024-03-27 19:41:09.981352 INFO::Total function execution time is 0.0454690456390381 s and adjustment time is 0.0229620933532715 s ( 50.5 )
2024-03-27 19:41:10.001218 INFO::Formatting Data.
2024-03-27 19:41:10.002038 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:10.002868 INFO::Removing potential empty rows and columns
2024-03-27 19:41:10.003713 INFO::Found 0 missing values.
2024-03-27 19:41:10.006944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:10.007763 INFO::Done
2024-03-27 19:41:10.008543 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:10.011101 INFO::Starting hierarchical adjustment
2024-03-27 19:41:10.012585 INFO::Found 2 batches.
2024-03-27 19:41:10.01325 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:10.01406 INFO::Using default BPPARAM
2024-03-27 19:41:10.014642 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:10.015952 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:10.062402 INFO::Done
2024-03-27 19:41:10.06338 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:10.065996 INFO::ASW Batch was -0.141000633873691 prior to batch effect correction and is now -0.152044784066143 .
2024-03-27 19:41:10.066794 INFO::Total function execution time is 0.0656969547271729 s and adjustment time is 0.0502278804779053 s ( 76.45 )
2024-03-27 19:41:10.086294 INFO::Formatting Data.
2024-03-27 19:41:10.087223 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:10.088261 INFO::Removing potential empty rows and columns
2024-03-27 19:41:10.090182 INFO::Found 0 missing values.
2024-03-27 19:41:10.091854 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.
2024-03-27 19:41:10.097454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:10.09833 INFO::Done
2024-03-27 19:41:10.099104 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:10.103075 INFO::Starting hierarchical adjustment
2024-03-27 19:41:10.103821 INFO::Found 2 batches.
2024-03-27 19:41:10.104513 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:10.105311 INFO::Using default BPPARAM
2024-03-27 19:41:10.105991 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:10.107372 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:10.128235 INFO::Done
2024-03-27 19:41:10.129175 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:10.133077 INFO::ASW Batch was 0.540397721667714 prior to batch effect correction and is now 0.032076003631671 .
2024-03-27 19:41:10.134072 INFO::ASW Label was 0.551243559633779 prior to batch effect correction and is now 0.906168506344044 .
2024-03-27 19:41:10.135243 INFO::Total function execution time is 0.049232006072998 s and adjustment time is 0.0244958400726318 s ( 49.76 )
2024-03-27 19:41:10.13656 INFO::Formatting Data.
2024-03-27 19:41:10.13741 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:10.138721 INFO::Removing potential empty rows and columns
2024-03-27 19:41:10.140062 INFO::Found 0 missing values.
2024-03-27 19:41:10.14134 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.
2024-03-27 19:41:10.147736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:10.14868 INFO::Done
2024-03-27 19:41:10.149807 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:10.154269 INFO::Starting hierarchical adjustment
2024-03-27 19:41:10.155323 INFO::Found 2 batches.
2024-03-27 19:41:10.156306 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:10.157263 INFO::Using default BPPARAM
2024-03-27 19:41:10.158161 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:10.159248 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:10.179659 INFO::Done
2024-03-27 19:41:10.18039 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:10.184539 INFO::ASW Batch was 0.540397721667714 prior to batch effect correction and is now 0.032076003631671 .
2024-03-27 19:41:10.185479 INFO::ASW Label was 0.551243559633779 prior to batch effect correction and is now 0.906168506344044 .
2024-03-27 19:41:10.18686 INFO::Total function execution time is 0.0503470897674561 s and adjustment time is 0.0245771408081055 s ( 48.82 )
2024-03-27 19:41:10.488263 INFO::Formatting Data.
2024-03-27 19:41:10.489174 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:10.490218 INFO::Removing potential empty rows and columns
2024-03-27 19:41:10.491713 INFO::Found 0 missing values.
2024-03-27 19:41:10.496383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:10.497256 INFO::Done
2024-03-27 19:41:10.497982 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:10.501113 INFO::Starting hierarchical adjustment
2024-03-27 19:41:10.502107 INFO::Found 3 batches.
2024-03-27 19:41:10.502873 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:10.503672 INFO::Using default BPPARAM
2024-03-27 19:41:10.504359 INFO::Processing subtree level 1
2024-03-27 19:41:10.640502 INFO::Adjusting the last 1 batches sequentially
2024-03-27 19:41:10.642965 INFO::Done
2024-03-27 19:41:10.643645 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:10.647117 INFO::ASW Batch was -0.108623112683632 prior to batch effect correction and is now -0.108623112683632 .
2024-03-27 19:41:10.648518 INFO::Total function execution time is 0.160206079483032 s and adjustment time is 0.141046047210693 s ( 88.04 )
2024-03-27 19:41:10.650051 INFO::Formatting Data.
2024-03-27 19:41:10.650998 INFO::Typecasting input to dataframe.
2024-03-27 19:41:10.651794 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:10.652921 INFO::Removing potential empty rows and columns
2024-03-27 19:41:10.654909 INFO::Found 0 missing values.
2024-03-27 19:41:10.659313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:10.660112 INFO::Done
2024-03-27 19:41:10.660839 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:10.663465 INFO::Starting hierarchical adjustment
2024-03-27 19:41:10.664324 INFO::Found 3 batches.
2024-03-27 19:41:10.66522 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:10.665911 INFO::Using default BPPARAM
2024-03-27 19:41:10.666725 INFO::Processing subtree level 1
2024-03-27 19:41:10.862009 INFO::Adjusting the last 1 batches sequentially
2024-03-27 19:41:10.875579 INFO::Done
2024-03-27 19:41:10.876215 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:10.885786 INFO::ASW Batch was -0.108623112683632 prior to batch effect correction and is now -0.108623112683632 .
2024-03-27 19:41:10.88946 INFO::Total function execution time is 0.239033937454224 s and adjustment time is 0.211426019668579 s ( 88.45 )
2024-03-27 19:41:10.916076 INFO::Formatting Data.
2024-03-27 19:41:10.917631 INFO::Typecasting input to dataframe.
2024-03-27 19:41:10.918678 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:10.919973 INFO::Removing potential empty rows and columns
2024-03-27 19:41:10.922511 INFO::Found 0 missing values.
2024-03-27 19:41:10.92638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:10.927087 INFO::Done
2024-03-27 19:41:10.927762 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:10.930205 INFO::Starting hierarchical adjustment
2024-03-27 19:41:10.931086 INFO::Found 3 batches.
2024-03-27 19:41:10.931755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:10.932537 INFO::Using default BPPARAM
2024-03-27 19:41:10.933224 INFO::Processing subtree level 1
2024-03-27 19:41:11.070157 INFO::Adjusting the last 1 batches sequentially
2024-03-27 19:41:11.078044 INFO::Done
2024-03-27 19:41:11.081031 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:11.091144 INFO::ASW Batch was -0.0365236767863297 prior to batch effect correction and is now -0.0365236767863297 .
2024-03-27 19:41:11.09368 INFO::Total function execution time is 0.177335023880005 s and adjustment time is 0.147088050842285 s ( 82.94 )
2024-03-27 19:41:11.341993 INFO::Formatting Data.
2024-03-27 19:41:11.343023 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:11.345174 INFO::Removing potential empty rows and columns
2024-03-27 19:41:11.350368 INFO::Found 1000 missing values.
2024-03-27 19:41:11.373357 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:11.374014 INFO::Done
2024-03-27 19:41:11.374862 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:11.380948 INFO::Starting hierarchical adjustment
2024-03-27 19:41:11.381682 INFO::Found 10 batches.
2024-03-27 19:41:11.382165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:11.382709 INFO::Using default BPPARAM
2024-03-27 19:41:11.383166 INFO::Processing subtree level 1
2024-03-27 19:41:11.549876 INFO::Processing subtree level 2
2024-03-27 19:41:11.768287 INFO::Adjusting the last 1 batches sequentially
2024-03-27 19:41:11.780103 INFO::Done
2024-03-27 19:41:11.781792 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:11.793609 INFO::ASW Batch was 0.486862145159734 prior to batch effect correction and is now 0.486862145159734 .
2024-03-27 19:41:11.794271 INFO::ASW Label was 0.36131075764847 prior to batch effect correction and is now 0.36131075764847 .
2024-03-27 19:41:11.796165 INFO::Total function execution time is 0.454262018203735 s and adjustment time is 0.398470163345337 s ( 87.72 )
2024-03-27 19:41:11.797341 INFO::Formatting Data.
2024-03-27 19:41:11.798142 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:11.800199 INFO::Removing potential empty rows and columns
2024-03-27 19:41:11.804937 INFO::Found 1000 missing values.
2024-03-27 19:41:11.828692 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:11.829616 INFO::Done
2024-03-27 19:41:11.830353 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:11.836752 INFO::Starting hierarchical adjustment
2024-03-27 19:41:11.837545 INFO::Found 10 batches.
2024-03-27 19:41:12.845489 INFO::Set up parallel execution backend with 2 workers
2024-03-27 19:41:12.846386 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-03-27 19:41:14.156177 INFO::Adjusting the last 2 batches sequentially
2024-03-27 19:41:14.157287 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 19:41:14.177001 INFO::Done
2024-03-27 19:41:14.177853 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:14.183767 INFO::ASW Batch was 0.486862145159734 prior to batch effect correction and is now 0.486862145159734 .
2024-03-27 19:41:14.184289 INFO::ASW Label was 0.36131075764847 prior to batch effect correction and is now 0.36131075764847 .
2024-03-27 19:41:14.184922 INFO::Total function execution time is 2.38769888877869 s and adjustment time is 2.33955717086792 s ( 97.98 )
2024-03-27 19:41:14.417106 INFO::Formatting Data.
2024-03-27 19:41:14.418343 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:14.419845 INFO::Removing potential empty rows and columns
2024-03-27 19:41:14.422493 INFO::Found 0 missing values.
2024-03-27 19:41:14.426666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:14.427259 INFO::Done
2024-03-27 19:41:14.428094 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 19:41:14.431711 INFO::Starting hierarchical adjustment
2024-03-27 19:41:14.432704 INFO::Found 3 batches.
2024-03-27 19:41:14.433473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 19:41:14.434136 INFO::Using default BPPARAM
2024-03-27 19:41:14.435338 INFO::Processing subtree level 1
2024-03-27 19:41:14.61238 INFO::Adjusting the last 1 batches sequentially
2024-03-27 19:41:14.637811 INFO::Done
2024-03-27 19:41:14.642511 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 19:41:14.661602 INFO::ASW Batch was 0.189749586721897 prior to batch effect correction and is now -0.137703091303643 .
2024-03-27 19:41:14.662388 INFO::ASW Label was -0.174062623609806 prior to batch effect correction and is now 0.156516559141807 .
2024-03-27 19:41:14.665719 INFO::Total function execution time is 0.24754810333252 s and adjustment time is 0.204152822494507 s ( 82.47 )
2024-03-27 19:41:14.856968 INFO::Formatting Data.
2024-03-27 19:41:14.858133 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:14.859522 INFO::Removing potential empty rows and columns
2024-03-27 19:41:14.861062 INFO::Found 2 missing values.
2024-03-27 19:41:14.864828 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:14.865348 INFO::Done
2024-03-27 19:41:14.91218 INFO::Found NA in Reference column
2024-03-27 19:41:14.928329 INFO::Require at least two references per batch.
2024-03-27 19:41:14.957406 INFO::Formatting Data.
2024-03-27 19:41:14.958503 INFO::Recognized SummarizedExperiment
2024-03-27 19:41:14.959172 INFO::Typecasting input to dataframe.
2024-03-27 19:41:14.972212 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:14.973374 INFO::Removing potential empty rows and columns
2024-03-27 19:41:14.97646 INFO::Found 0 missing values.
2024-03-27 19:41:14.982398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:14.98299 INFO::Done
2024-03-27 19:41:15.004588 INFO::Formatting Data.
2024-03-27 19:41:15.005629 INFO::Recognized SummarizedExperiment
2024-03-27 19:41:15.006432 INFO::Typecasting input to dataframe.
2024-03-27 19:41:15.030554 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:15.031966 INFO::Removing potential empty rows and columns
2024-03-27 19:41:15.036666 INFO::Found 0 missing values.
2024-03-27 19:41:15.049018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:15.050003 INFO::Done
2024-03-27 19:41:15.072189 INFO::Formatting Data.
2024-03-27 19:41:15.073273 INFO::Recognized SummarizedExperiment
2024-03-27 19:41:15.074084 INFO::Typecasting input to dataframe.
2024-03-27 19:41:15.094274 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:15.096186 INFO::Removing potential empty rows and columns
2024-03-27 19:41:15.098372 INFO::Found 0 missing values.
2024-03-27 19:41:15.100034 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.
2024-03-27 19:41:15.106785 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:15.10766 INFO::Done
2024-03-27 19:41:15.124791 INFO::Formatting Data.
2024-03-27 19:41:15.125549 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:15.126349 INFO::Removing potential empty rows and columns
2024-03-27 19:41:15.12723 INFO::Found 0 missing values.
2024-03-27 19:41:15.129755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:15.130227 INFO::Done
2024-03-27 19:41:15.148162 INFO::Formatting Data.
2024-03-27 19:41:15.149345 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:15.150758 INFO::Removing potential empty rows and columns
2024-03-27 19:41:15.151985 INFO::Found 0 missing values.
2024-03-27 19:41:15.156461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:15.157846 INFO::Done
2024-03-27 19:41:15.205966 INFO::Formatting Data.
2024-03-27 19:41:15.207073 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:15.208591 INFO::Removing potential empty rows and columns
2024-03-27 19:41:15.210173 INFO::Found 1 missing values.
2024-03-27 19:41:15.214088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:15.215023 INFO::Done
2024-03-27 19:41:15.246432 INFO::Formatting Data.
2024-03-27 19:41:15.247168 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:15.248134 INFO::Removing potential empty rows and columns
2024-03-27 19:41:15.248976 INFO::Found 2 missing values.
2024-03-27 19:41:15.249828 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.
2024-03-27 19:41:15.253067 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:15.25389 INFO::Done
2024-03-27 19:41:15.27237 INFO::Formatting Data.
2024-03-27 19:41:15.27349 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:15.274715 INFO::Removing potential empty rows and columns
2024-03-27 19:41:15.276001 INFO::Found 2 missing values.
2024-03-27 19:41:15.278268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:15.278931 INFO::Done
2024-03-27 19:41:15.295325 INFO::Formatting Data.
2024-03-27 19:41:15.296313 INFO::Typecasting input to dataframe.
2024-03-27 19:41:15.297335 INFO::Replacing NaNs with NAs.
2024-03-27 19:41:15.29848 INFO::Removing potential empty rows and columns
2024-03-27 19:41:15.300091 INFO::Found 0 missing values.
2024-03-27 19:41:15.302959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 19:41:15.303453 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.960 4.034 25.473
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.082 | 1.522 | 19.473 | |
| compute_asw | 0.027 | 0.001 | 0.028 | |
| count_existing | 0.017 | 0.001 | 0.018 | |
| generate_data_covariables | 0.016 | 0.002 | 0.017 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |