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 11:37:22 -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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_0.99.16.tar.gz |
| StartedAt: 2024-03-27 23:35:17 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 23:37:33 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 135.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_0.99.16.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '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 whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.2 0.54 18.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'BERT' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-03-27 23:36:20.78402 INFO::Formatting Data.
2024-03-27 23:36:20.787145 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:20.802696 INFO::Removing potential empty rows and columns
2024-03-27 23:36:21.130016 INFO::Found 0 missing values.
2024-03-27 23:36:21.135373 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:21.136806 INFO::Done
2024-03-27 23:36:21.138117 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:21.158821 INFO::Starting hierarchical adjustment
2024-03-27 23:36:21.160475 INFO::Found 3 batches.
2024-03-27 23:36:21.16171 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:21.163677 INFO::Using default BPPARAM
2024-03-27 23:36:21.164916 INFO::Processing subtree level 1
2024-03-27 23:36:23.626402 INFO::Adjusting the last 1 batches sequentially
2024-03-27 23:36:23.628679 INFO::Done
2024-03-27 23:36:23.629944 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:23.632964 INFO::ASW Batch was -0.0711521796827205 prior to batch effect correction and is now -0.0711521796827205 .
2024-03-27 23:36:23.634555 INFO::Total function execution time is 2.85131812095642 s and adjustment time is 2.46846699714661 s ( 86.57 )
2024-03-27 23:36:23.656473 INFO::Formatting Data.
2024-03-27 23:36:23.657486 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:23.658634 INFO::Removing potential empty rows and columns
2024-03-27 23:36:23.659801 INFO::Found 0 missing values.
2024-03-27 23:36:23.660924 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 23:36:23.669917 INFO::Formatting Data.
2024-03-27 23:36:23.670855 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:23.671916 INFO::Removing potential empty rows and columns
2024-03-27 23:36:23.673056 INFO::Found 0 missing values.
2024-03-27 23:36:23.674157 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 23:36:23.690735 INFO::Formatting Data.
2024-03-27 23:36:23.691708 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:23.692766 INFO::Removing potential empty rows and columns
2024-03-27 23:36:23.69389 INFO::Found 0 missing values.
2024-03-27 23:36:23.694952 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 23:36:23.698579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:23.699312 INFO::Done
2024-03-27 23:36:23.700028 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:23.70211 INFO::Starting hierarchical adjustment
2024-03-27 23:36:23.702974 INFO::Found 2 batches.
2024-03-27 23:36:23.703769 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:23.70457 INFO::Using default BPPARAM
2024-03-27 23:36:23.705309 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:23.706393 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:23.722615 INFO::Done
2024-03-27 23:36:23.723512 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:23.725664 INFO::ASW Batch was 0.0233624557429257 prior to batch effect correction and is now -0.0970365891652807 .
2024-03-27 23:36:23.726665 INFO::Total function execution time is 0.0360209941864014 s and adjustment time is 0.0197288990020752 s ( 54.77 )
2024-03-27 23:36:23.729575 INFO::Formatting Data.
2024-03-27 23:36:23.730428 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:23.737863 INFO::Formatting Data.
2024-03-27 23:36:23.739001 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:23.740122 INFO::Removing potential empty rows and columns
2024-03-27 23:36:23.741254 INFO::Found 0 missing values.
2024-03-27 23:36:23.743747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:23.744475 INFO::Done
2024-03-27 23:36:23.745176 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:23.747289 INFO::Starting hierarchical adjustment
2024-03-27 23:36:23.748172 INFO::Found 2 batches.
2024-03-27 23:36:23.748885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:23.749665 INFO::Using default BPPARAM
2024-03-27 23:36:23.750384 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:23.751462 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:23.763711 INFO::Done
2024-03-27 23:36:23.764592 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:23.766699 INFO::ASW Batch was 0.0740029182320381 prior to batch effect correction and is now -0.127294159975376 .
2024-03-27 23:36:23.767691 INFO::Total function execution time is 0.0299079418182373 s and adjustment time is 0.0156509876251221 s ( 52.33 )
2024-03-27 23:36:23.768901 INFO::Formatting Data.
2024-03-27 23:36:23.769708 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:23.770769 INFO::Removing potential empty rows and columns
2024-03-27 23:36:23.771891 INFO::Found 0 missing values.
2024-03-27 23:36:23.774407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:23.775123 INFO::Done
2024-03-27 23:36:23.775822 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:23.777932 INFO::Starting hierarchical adjustment
2024-03-27 23:36:23.778811 INFO::Found 2 batches.
2024-03-27 23:36:23.779526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:23.780323 INFO::Using default BPPARAM
2024-03-27 23:36:23.781033 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:23.782095 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:23.794492 INFO::Done
2024-03-27 23:36:23.795544 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:23.797781 INFO::ASW Batch was 0.0740029182320381 prior to batch effect correction and is now -0.127294159975376 .
2024-03-27 23:36:23.798813 INFO::Total function execution time is 0.0298850536346436 s and adjustment time is 0.0157818794250488 s ( 52.81 )
2024-03-27 23:36:26.514396 INFO::Formatting Data.
2024-03-27 23:36:26.515398 INFO::Recognized SummarizedExperiment
2024-03-27 23:36:26.516177 INFO::Typecasting input to dataframe.
2024-03-27 23:36:26.546424 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:26.547935 INFO::Removing potential empty rows and columns
2024-03-27 23:36:26.551095 INFO::Found 0 missing values.
2024-03-27 23:36:26.556802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:26.557766 INFO::Done
2024-03-27 23:36:26.558582 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:26.562578 INFO::Starting hierarchical adjustment
2024-03-27 23:36:26.563518 INFO::Found 2 batches.
2024-03-27 23:36:26.56429 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:26.565658 INFO::Using default BPPARAM
2024-03-27 23:36:26.566396 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:26.567653 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:26.61457 INFO::Done
2024-03-27 23:36:26.615516 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:26.619909 INFO::ASW Batch was -0.00470640815822598 prior to batch effect correction and is now -0.0906436125435891 .
2024-03-27 23:36:26.62107 INFO::Total function execution time is 0.106985092163086 s and adjustment time is 0.0511429309844971 s ( 47.8 )
2024-03-27 23:36:26.656913 INFO::Formatting Data.
2024-03-27 23:36:26.658446 INFO::Recognized SummarizedExperiment
2024-03-27 23:36:26.659687 INFO::Typecasting input to dataframe.
2024-03-27 23:36:26.673166 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:26.675425 INFO::Removing potential empty rows and columns
2024-03-27 23:36:26.680744 INFO::Found 0 missing values.
2024-03-27 23:36:26.690113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:26.69152 INFO::Done
2024-03-27 23:36:26.692886 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:26.699234 INFO::Starting hierarchical adjustment
2024-03-27 23:36:26.700772 INFO::Found 2 batches.
2024-03-27 23:36:26.702045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:26.703369 INFO::Using default BPPARAM
2024-03-27 23:36:26.704594 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:26.706616 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:26.744343 INFO::Done
2024-03-27 23:36:26.745885 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:26.752951 INFO::ASW Batch was -0.0159707374542882 prior to batch effect correction and is now -0.0159707374542882 .
2024-03-27 23:36:26.754854 INFO::Total function execution time is 0.0978670120239258 s and adjustment time is 0.0437350273132324 s ( 44.69 )
2024-03-27 23:36:26.802218 INFO::Formatting Data.
2024-03-27 23:36:26.803893 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:26.805805 INFO::Removing potential empty rows and columns
2024-03-27 23:36:26.807931 INFO::Found 0 missing values.
2024-03-27 23:36:26.813164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:26.814521 INFO::Done
2024-03-27 23:36:26.815878 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:26.819552 INFO::Starting hierarchical adjustment
2024-03-27 23:36:26.821155 INFO::Found 3 batches.
2024-03-27 23:36:26.82253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:26.823963 INFO::Using default BPPARAM
2024-03-27 23:36:26.825295 INFO::Processing subtree level 1
2024-03-27 23:36:37.705173 INFO::Adjusting the last 1 batches sequentially
2024-03-27 23:36:37.707521 INFO::Done
2024-03-27 23:36:37.708815 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:37.712162 INFO::ASW Batch was -0.137224720345258 prior to batch effect correction and is now -0.182735631768425 .
2024-03-27 23:36:37.713706 INFO::Total function execution time is 10.9116439819336 s and adjustment time is 10.886607170105 s ( 99.77 )
2024-03-27 23:36:38.020931 INFO::Skipping initial DF formatting
2024-03-27 23:36:38.022218 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:38.028362 INFO::Starting hierarchical adjustment
2024-03-27 23:36:38.029601 INFO::Found 5 batches.
2024-03-27 23:36:38.030384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:38.031198 INFO::Using default BPPARAM
2024-03-27 23:36:38.032151 INFO::Processing subtree level 1
2024-03-27 23:36:41.178537 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:41.181038 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:41.209804 INFO::Done
2024-03-27 23:36:41.21149 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:41.220084 INFO::ASW Batch was 0.527344026154861 prior to batch effect correction and is now 0.527344026154861 .
2024-03-27 23:36:41.221722 INFO::ASW Label was 0.369561350907071 prior to batch effect correction and is now 0.369561350907071 .
2024-03-27 23:36:41.223695 INFO::Total function execution time is 3.20274209976196 s and adjustment time is 3.1803150177002 s ( 99.3 )
2024-03-27 23:36:41.260358 INFO::Formatting Data.
2024-03-27 23:36:41.262066 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:41.263794 INFO::Removing potential empty rows and columns
2024-03-27 23:36:41.265583 INFO::Found 0 missing values.
2024-03-27 23:36:41.271537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:41.272784 INFO::Done
2024-03-27 23:36:41.273994 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:41.278655 INFO::Starting hierarchical adjustment
2024-03-27 23:36:41.280095 INFO::Found 5 batches.
2024-03-27 23:36:41.281389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:41.282693 INFO::Using default BPPARAM
2024-03-27 23:36:41.28389 INFO::Processing subtree level 1
2024-03-27 23:36:44.490631 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:44.492709 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:44.512755 INFO::Done
2024-03-27 23:36:44.514205 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:44.519048 INFO::ASW Batch was 0.544186567477924 prior to batch effect correction and is now -0.108004323929065 .
2024-03-27 23:36:44.520389 INFO::ASW Label was 0.183132910015503 prior to batch effect correction and is now 0.827197975940544 .
2024-03-27 23:36:44.521995 INFO::Total function execution time is 3.26173901557922 s and adjustment time is 3.23279500007629 s ( 99.11 )
2024-03-27 23:36:44.523568 INFO::Formatting Data.
2024-03-27 23:36:44.524902 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:44.526638 INFO::Removing potential empty rows and columns
2024-03-27 23:36:44.52847 INFO::Found 0 missing values.
2024-03-27 23:36:44.534757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:44.536042 INFO::Done
2024-03-27 23:36:44.537273 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:44.542206 INFO::Starting hierarchical adjustment
2024-03-27 23:36:44.543695 INFO::Found 5 batches.
2024-03-27 23:36:44.544921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:44.546228 INFO::Using default BPPARAM
2024-03-27 23:36:44.547425 INFO::Processing subtree level 1
2024-03-27 23:36:47.80201 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:47.803503 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:47.821506 INFO::Done
2024-03-27 23:36:47.823009 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:47.827907 INFO::ASW Batch was 0.544186567477924 prior to batch effect correction and is now -0.108004323929065 .
2024-03-27 23:36:47.829159 INFO::ASW Label was 0.183132910015503 prior to batch effect correction and is now 0.827197975940544 .
2024-03-27 23:36:47.830641 INFO::Total function execution time is 3.30707693099976 s and adjustment time is 3.27796983718872 s ( 99.12 )
2024-03-27 23:36:47.855861 INFO::Formatting Data.
2024-03-27 23:36:47.857416 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:47.859214 INFO::Removing potential empty rows and columns
2024-03-27 23:36:47.861072 INFO::Found 0 missing values.
2024-03-27 23:36:47.867354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:47.868685 INFO::Done
2024-03-27 23:36:47.869936 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:47.874964 INFO::Starting hierarchical adjustment
2024-03-27 23:36:47.876474 INFO::Found 5 batches.
2024-03-27 23:36:47.877689 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:47.879013 INFO::Using default BPPARAM
2024-03-27 23:36:47.88022 INFO::Processing subtree level 1
2024-03-27 23:36:51.001961 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:51.003999 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:51.023891 INFO::Done
2024-03-27 23:36:51.025282 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:51.0297 INFO::ASW Batch was 0.167048465889047 prior to batch effect correction and is now -0.0713042633878957 .
2024-03-27 23:36:51.030525 INFO::ASW Label was 0.525447295192222 prior to batch effect correction and is now 0.792847410195787 .
2024-03-27 23:36:51.031591 INFO::Total function execution time is 3.17593002319336 s and adjustment time is 3.14759016036987 s ( 99.11 )
2024-03-27 23:36:51.032608 INFO::Formatting Data.
2024-03-27 23:36:51.033401 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:51.03443 INFO::Removing potential empty rows and columns
2024-03-27 23:36:51.035592 INFO::Found 0 missing values.
2024-03-27 23:36:51.039005 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:51.039737 INFO::Done
2024-03-27 23:36:51.040433 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:51.043475 INFO::Starting hierarchical adjustment
2024-03-27 23:36:51.044881 INFO::Found 5 batches.
2024-03-27 23:36:51.046033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:51.04728 INFO::Using default BPPARAM
2024-03-27 23:36:51.048448 INFO::Processing subtree level 1
2024-03-27 23:36:54.096261 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:54.098374 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:54.116723 INFO::Done
2024-03-27 23:36:54.118127 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:54.122893 INFO::ASW Batch was 0.167048465889047 prior to batch effect correction and is now -0.0713042633878957 .
2024-03-27 23:36:54.124187 INFO::ASW Label was 0.525447295192222 prior to batch effect correction and is now 0.792847410195787 .
2024-03-27 23:36:54.12576 INFO::Total function execution time is 3.09309387207031 s and adjustment time is 3.07199907302856 s ( 99.32 )
2024-03-27 23:36:54.148687 INFO::Formatting Data.
2024-03-27 23:36:54.149649 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:54.150704 INFO::Removing potential empty rows and columns
2024-03-27 23:36:54.15181 INFO::Found 0 missing values.
2024-03-27 23:36:54.154363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:54.15562 INFO::Done
2024-03-27 23:36:54.15638 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:54.159509 INFO::Starting hierarchical adjustment
2024-03-27 23:36:54.160924 INFO::Found 2 batches.
2024-03-27 23:36:54.161849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:54.162663 INFO::Using default BPPARAM
2024-03-27 23:36:54.163378 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:54.164462 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:54.176559 INFO::Done
2024-03-27 23:36:54.177397 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:54.180271 INFO::ASW Batch was 0.449372045362107 prior to batch effect correction and is now 0.0224566740629417 .
2024-03-27 23:36:54.18102 INFO::ASW Label was 0.575907431578234 prior to batch effect correction and is now 0.861412956284663 .
2024-03-27 23:36:54.181947 INFO::Total function execution time is 0.0333809852600098 s and adjustment time is 0.0158829689025879 s ( 47.58 )
2024-03-27 23:36:54.182865 INFO::Formatting Data.
2024-03-27 23:36:54.183656 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:54.184663 INFO::Removing potential empty rows and columns
2024-03-27 23:36:54.185767 INFO::Found 0 missing values.
2024-03-27 23:36:54.188136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:54.188853 INFO::Done
2024-03-27 23:36:54.189544 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:54.192435 INFO::Starting hierarchical adjustment
2024-03-27 23:36:54.193484 INFO::Found 2 batches.
2024-03-27 23:36:54.194272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:54.19529 INFO::Using default BPPARAM
2024-03-27 23:36:54.196038 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:54.197603 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:54.217582 INFO::Done
2024-03-27 23:36:54.218692 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:54.223544 INFO::ASW Batch was 0.449372045362107 prior to batch effect correction and is now 0.0224566740629417 .
2024-03-27 23:36:54.224904 INFO::ASW Label was 0.575907431578234 prior to batch effect correction and is now 0.861412956284663 .
2024-03-27 23:36:54.226525 INFO::Total function execution time is 0.0435671806335449 s and adjustment time is 0.0242340564727783 s ( 55.62 )
2024-03-27 23:36:54.247873 INFO::Formatting Data.
2024-03-27 23:36:54.249401 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:54.250915 INFO::Removing potential empty rows and columns
2024-03-27 23:36:54.25255 INFO::Found 0 missing values.
2024-03-27 23:36:54.255316 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:54.256192 INFO::Done
2024-03-27 23:36:54.256904 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:54.25917 INFO::Starting hierarchical adjustment
2024-03-27 23:36:54.260456 INFO::Found 2 batches.
2024-03-27 23:36:54.261493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:54.262806 INFO::Using default BPPARAM
2024-03-27 23:36:54.264018 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:54.265817 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:54.307633 INFO::Done
2024-03-27 23:36:54.309094 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:54.312563 INFO::ASW Batch was -0.0818279718375439 prior to batch effect correction and is now -0.174583608179688 .
2024-03-27 23:36:54.314218 INFO::Total function execution time is 0.0664129257202148 s and adjustment time is 0.0473430156707764 s ( 71.29 )
2024-03-27 23:36:54.338054 INFO::Formatting Data.
2024-03-27 23:36:54.339664 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:54.341436 INFO::Removing potential empty rows and columns
2024-03-27 23:36:54.343333 INFO::Found 0 missing values.
2024-03-27 23:36:54.345316 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 23:36:54.352125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:54.353464 INFO::Done
2024-03-27 23:36:54.354805 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:54.359511 INFO::Starting hierarchical adjustment
2024-03-27 23:36:54.361039 INFO::Found 2 batches.
2024-03-27 23:36:54.36224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:54.363538 INFO::Using default BPPARAM
2024-03-27 23:36:54.364735 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:54.366585 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:54.390663 INFO::Done
2024-03-27 23:36:54.39215 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:54.397142 INFO::ASW Batch was 0.556416630776782 prior to batch effect correction and is now 0.0156892526509625 .
2024-03-27 23:36:54.398566 INFO::ASW Label was 0.525572080544506 prior to batch effect correction and is now 0.896969575334593 .
2024-03-27 23:36:54.400178 INFO::Total function execution time is 0.0622611045837402 s and adjustment time is 0.0298030376434326 s ( 47.87 )
2024-03-27 23:36:54.401715 INFO::Formatting Data.
2024-03-27 23:36:54.403033 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:54.404769 INFO::Removing potential empty rows and columns
2024-03-27 23:36:54.406538 INFO::Found 0 missing values.
2024-03-27 23:36:54.408276 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 23:36:54.41455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:54.415823 INFO::Done
2024-03-27 23:36:54.417043 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:54.421859 INFO::Starting hierarchical adjustment
2024-03-27 23:36:54.423351 INFO::Found 2 batches.
2024-03-27 23:36:54.424522 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:54.425727 INFO::Using default BPPARAM
2024-03-27 23:36:54.426856 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:36:54.428569 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:36:54.451003 INFO::Done
2024-03-27 23:36:54.452398 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:54.457201 INFO::ASW Batch was 0.556416630776782 prior to batch effect correction and is now 0.0156892526509625 .
2024-03-27 23:36:54.458568 INFO::ASW Label was 0.525572080544506 prior to batch effect correction and is now 0.896969575334593 .
2024-03-27 23:36:54.460137 INFO::Total function execution time is 0.0584208965301514 s and adjustment time is 0.0277929306030273 s ( 47.57 )
2024-03-27 23:36:54.725588 INFO::Formatting Data.
2024-03-27 23:36:54.726776 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:54.728114 INFO::Removing potential empty rows and columns
2024-03-27 23:36:54.729495 INFO::Found 0 missing values.
2024-03-27 23:36:54.733636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:54.734519 INFO::Done
2024-03-27 23:36:54.735334 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:54.737834 INFO::Starting hierarchical adjustment
2024-03-27 23:36:54.738863 INFO::Found 3 batches.
2024-03-27 23:36:54.73965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:54.740658 INFO::Using default BPPARAM
2024-03-27 23:36:54.74146 INFO::Processing subtree level 1
2024-03-27 23:36:57.839781 INFO::Adjusting the last 1 batches sequentially
2024-03-27 23:36:57.842071 INFO::Done
2024-03-27 23:36:57.843436 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:36:57.846797 INFO::ASW Batch was -0.0212688105088026 prior to batch effect correction and is now -0.0212688105088026 .
2024-03-27 23:36:57.848435 INFO::Total function execution time is 3.1228940486908 s and adjustment time is 3.10330891609192 s ( 99.37 )
2024-03-27 23:36:57.850256 INFO::Formatting Data.
2024-03-27 23:36:57.851597 INFO::Typecasting input to dataframe.
2024-03-27 23:36:57.852976 INFO::Replacing NaNs with NAs.
2024-03-27 23:36:57.854583 INFO::Removing potential empty rows and columns
2024-03-27 23:36:57.856371 INFO::Found 0 missing values.
2024-03-27 23:36:57.860653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:36:57.861752 INFO::Done
2024-03-27 23:36:57.862935 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:36:57.866086 INFO::Starting hierarchical adjustment
2024-03-27 23:36:57.867423 INFO::Found 3 batches.
2024-03-27 23:36:57.868587 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:36:57.869846 INFO::Using default BPPARAM
2024-03-27 23:36:57.871006 INFO::Processing subtree level 1
2024-03-27 23:37:00.702273 INFO::Adjusting the last 1 batches sequentially
2024-03-27 23:37:00.704567 INFO::Done
2024-03-27 23:37:00.705968 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:37:00.709283 INFO::ASW Batch was -0.0212688105088026 prior to batch effect correction and is now -0.0212688105088026 .
2024-03-27 23:37:00.710889 INFO::Total function execution time is 2.86065196990967 s and adjustment time is 2.83729720115662 s ( 99.18 )
2024-03-27 23:37:00.730715 INFO::Formatting Data.
2024-03-27 23:37:00.731945 INFO::Typecasting input to dataframe.
2024-03-27 23:37:00.733473 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:00.734848 INFO::Removing potential empty rows and columns
2024-03-27 23:37:00.736571 INFO::Found 0 missing values.
2024-03-27 23:37:00.740857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:00.74207 INFO::Done
2024-03-27 23:37:00.743281 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:37:00.746427 INFO::Starting hierarchical adjustment
2024-03-27 23:37:00.74778 INFO::Found 3 batches.
2024-03-27 23:37:00.748871 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:37:00.750038 INFO::Using default BPPARAM
2024-03-27 23:37:00.750895 INFO::Processing subtree level 1
2024-03-27 23:37:03.590079 INFO::Adjusting the last 1 batches sequentially
2024-03-27 23:37:03.592365 INFO::Done
2024-03-27 23:37:03.593669 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:37:03.596794 INFO::ASW Batch was 0.0944390350116518 prior to batch effect correction and is now 0.0944390350116518 .
2024-03-27 23:37:03.598287 INFO::Total function execution time is 2.86772513389587 s and adjustment time is 2.84476590156555 s ( 99.2 )
2024-03-27 23:37:06.396731 INFO::Formatting Data.
2024-03-27 23:37:06.398381 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:06.400478 INFO::Removing potential empty rows and columns
2024-03-27 23:37:06.404324 INFO::Found 1000 missing values.
2024-03-27 23:37:06.428027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:06.429538 INFO::Done
2024-03-27 23:37:06.43083 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:37:06.440834 INFO::Starting hierarchical adjustment
2024-03-27 23:37:06.442479 INFO::Found 10 batches.
2024-03-27 23:37:06.443782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:37:06.445071 INFO::Using default BPPARAM
2024-03-27 23:37:06.446233 INFO::Processing subtree level 1
2024-03-27 23:37:09.620766 INFO::Processing subtree level 2
2024-03-27 23:37:12.944358 INFO::Adjusting the last 1 batches sequentially
2024-03-27 23:37:12.946719 INFO::Done
2024-03-27 23:37:12.947956 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:37:12.956691 INFO::ASW Batch was 0.497663365240321 prior to batch effect correction and is now 0.497663365240321 .
2024-03-27 23:37:12.958079 INFO::ASW Label was 0.357295483822363 prior to batch effect correction and is now 0.357295483822363 .
2024-03-27 23:37:12.959676 INFO::Total function execution time is 6.56310391426086 s and adjustment time is 6.50449204444885 s ( 99.11 )
2024-03-27 23:37:12.961079 INFO::Formatting Data.
2024-03-27 23:37:12.962288 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:12.964114 INFO::Removing potential empty rows and columns
2024-03-27 23:37:12.967464 INFO::Found 1000 missing values.
2024-03-27 23:37:12.984284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:12.985804 INFO::Done
2024-03-27 23:37:12.987142 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:37:12.997063 INFO::Starting hierarchical adjustment
2024-03-27 23:37:12.998677 INFO::Found 10 batches.
2024-03-27 23:37:13.829152 INFO::Set up parallel execution backend with 2 workers
2024-03-27 23:37:13.830679 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-03-27 23:37:16.692544 INFO::Adjusting the last 2 batches sequentially
2024-03-27 23:37:16.694103 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 23:37:16.708892 INFO::Done
2024-03-27 23:37:16.709873 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:37:16.715759 INFO::ASW Batch was 0.497663365240321 prior to batch effect correction and is now 0.497663365240321 .
2024-03-27 23:37:16.716622 INFO::ASW Label was 0.357295483822363 prior to batch effect correction and is now 0.357295483822363 .
2024-03-27 23:37:16.717612 INFO::Total function execution time is 3.75659894943237 s and adjustment time is 3.71047306060791 s ( 98.77 )
2024-03-27 23:37:19.520767 INFO::Formatting Data.
2024-03-27 23:37:19.522294 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:19.524045 INFO::Removing potential empty rows and columns
2024-03-27 23:37:19.525886 INFO::Found 0 missing values.
2024-03-27 23:37:19.531345 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:19.532602 INFO::Done
2024-03-27 23:37:19.533805 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 23:37:19.53806 INFO::Starting hierarchical adjustment
2024-03-27 23:37:19.539459 INFO::Found 3 batches.
2024-03-27 23:37:19.540584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 23:37:19.541832 INFO::Using default BPPARAM
2024-03-27 23:37:19.543014 INFO::Processing subtree level 1
2024-03-27 23:37:22.671432 INFO::Adjusting the last 1 batches sequentially
2024-03-27 23:37:22.673711 INFO::Done
2024-03-27 23:37:22.675027 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 23:37:22.679092 INFO::ASW Batch was 0.171297720285161 prior to batch effect correction and is now -0.153831773188023 .
2024-03-27 23:37:22.680287 INFO::ASW Label was -0.137782118366647 prior to batch effect correction and is now 0.149014503098516 .
2024-03-27 23:37:22.681733 INFO::Total function execution time is 3.16109204292297 s and adjustment time is 3.13441896438599 s ( 99.16 )
2024-03-27 23:37:22.844441 INFO::Formatting Data.
2024-03-27 23:37:22.845472 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:22.846558 INFO::Removing potential empty rows and columns
2024-03-27 23:37:22.847674 INFO::Found 2 missing values.
2024-03-27 23:37:22.850237 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:22.850966 INFO::Done
2024-03-27 23:37:22.895555 INFO::Found NA in Reference column
2024-03-27 23:37:22.91188 INFO::Require at least two references per batch.
2024-03-27 23:37:22.941273 INFO::Formatting Data.
2024-03-27 23:37:22.942744 INFO::Recognized SummarizedExperiment
2024-03-27 23:37:22.943522 INFO::Typecasting input to dataframe.
2024-03-27 23:37:22.951624 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:22.952981 INFO::Removing potential empty rows and columns
2024-03-27 23:37:22.955783 INFO::Found 0 missing values.
2024-03-27 23:37:22.961304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:22.962139 INFO::Done
2024-03-27 23:37:22.98238 INFO::Formatting Data.
2024-03-27 23:37:22.98338 INFO::Recognized SummarizedExperiment
2024-03-27 23:37:22.984143 INFO::Typecasting input to dataframe.
2024-03-27 23:37:22.999697 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:23.001118 INFO::Removing potential empty rows and columns
2024-03-27 23:37:23.005067 INFO::Found 0 missing values.
2024-03-27 23:37:23.018299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:23.019256 INFO::Done
2024-03-27 23:37:23.034198 INFO::Formatting Data.
2024-03-27 23:37:23.035178 INFO::Recognized SummarizedExperiment
2024-03-27 23:37:23.035928 INFO::Typecasting input to dataframe.
2024-03-27 23:37:23.055134 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:23.056451 INFO::Removing potential empty rows and columns
2024-03-27 23:37:23.05769 INFO::Found 0 missing values.
2024-03-27 23:37:23.058813 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 23:37:23.062582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:23.063338 INFO::Done
2024-03-27 23:37:23.080185 INFO::Formatting Data.
2024-03-27 23:37:23.081833 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:23.083586 INFO::Removing potential empty rows and columns
2024-03-27 23:37:23.085515 INFO::Found 0 missing values.
2024-03-27 23:37:23.089704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:23.090673 INFO::Done
2024-03-27 23:37:23.113819 INFO::Formatting Data.
2024-03-27 23:37:23.115472 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:23.117431 INFO::Removing potential empty rows and columns
2024-03-27 23:37:23.119387 INFO::Found 0 missing values.
2024-03-27 23:37:23.124183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:23.125461 INFO::Done
2024-03-27 23:37:23.171203 INFO::Formatting Data.
2024-03-27 23:37:23.172267 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:23.173498 INFO::Removing potential empty rows and columns
2024-03-27 23:37:23.174857 INFO::Found 1 missing values.
2024-03-27 23:37:23.177603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:23.178361 INFO::Done
2024-03-27 23:37:23.216105 INFO::Formatting Data.
2024-03-27 23:37:23.217687 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:23.219408 INFO::Removing potential empty rows and columns
2024-03-27 23:37:23.221131 INFO::Found 2 missing values.
2024-03-27 23:37:23.222855 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 23:37:23.226269 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:23.227495 INFO::Done
2024-03-27 23:37:23.248608 INFO::Formatting Data.
2024-03-27 23:37:23.250151 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:23.251881 INFO::Removing potential empty rows and columns
2024-03-27 23:37:23.253642 INFO::Found 2 missing values.
2024-03-27 23:37:23.256296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:23.257519 INFO::Done
2024-03-27 23:37:23.279756 INFO::Formatting Data.
2024-03-27 23:37:23.281403 INFO::Typecasting input to dataframe.
2024-03-27 23:37:23.283096 INFO::Replacing NaNs with NAs.
2024-03-27 23:37:23.284735 INFO::Removing potential empty rows and columns
2024-03-27 23:37:23.286579 INFO::Found 0 missing values.
2024-03-27 23:37:23.290978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 23:37:23.292199 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.68 1.48 78.18
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.20 | 0.54 | 18.55 | |
| compute_asw | 0.01 | 0.02 | 0.03 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0.01 | 0.00 | 0.01 | |