Yannis Schumann
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:29 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the BERT package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-05-06 19:51:07 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 19:51:36 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 29.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 8.846 0.352 6.29
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-05-06 19:51:29.498474 INFO::Formatting Data.
2024-05-06 19:51:29.499817 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:29.50336 INFO::Removing potential empty rows and columns
2024-05-06 19:51:29.595941 INFO::Found 0 missing values.
2024-05-06 19:51:29.597104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:29.597285 INFO::Done
2024-05-06 19:51:29.597446 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:29.60239 INFO::Starting hierarchical adjustment
2024-05-06 19:51:29.602653 INFO::Found 3 batches.
2024-05-06 19:51:29.602817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:29.603159 INFO::Using default BPPARAM
2024-05-06 19:51:29.603316 INFO::Processing subtree level 1
2024-05-06 19:51:29.646958 INFO::Adjusting the last 1 batches sequentially
2024-05-06 19:51:29.64796 INFO::Done
2024-05-06 19:51:29.648161 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:29.649281 INFO::ASW Batch was -0.0880636496953542 prior to batch effect correction and is now -0.0880636496953542 .
2024-05-06 19:51:29.649696 INFO::Total function execution time is 0.151543140411377 s and adjustment time is 0.0453641414642334 s ( 29.93 )
2024-05-06 19:51:29.65551 INFO::Formatting Data.
2024-05-06 19:51:29.655737 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:29.656037 INFO::Removing potential empty rows and columns
2024-05-06 19:51:29.656436 INFO::Found 0 missing values.
2024-05-06 19:51:29.656728 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.
2024-05-06 19:51:29.660601 INFO::Formatting Data.
2024-05-06 19:51:29.660906 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:29.661191 INFO::Removing potential empty rows and columns
2024-05-06 19:51:29.66154 INFO::Found 0 missing values.
2024-05-06 19:51:29.661826 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.
2024-05-06 19:51:29.667797 INFO::Formatting Data.
2024-05-06 19:51:29.668171 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:29.668559 INFO::Removing potential empty rows and columns
2024-05-06 19:51:29.66899 INFO::Found 0 missing values.
2024-05-06 19:51:29.669279 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.
2024-05-06 19:51:29.670758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:29.670946 INFO::Done
2024-05-06 19:51:29.671103 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:29.671761 INFO::Starting hierarchical adjustment
2024-05-06 19:51:29.671956 INFO::Found 2 batches.
2024-05-06 19:51:29.672108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:29.672328 INFO::Using default BPPARAM
2024-05-06 19:51:29.672468 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:29.672767 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:29.681833 INFO::Done
2024-05-06 19:51:29.682061 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:29.682708 INFO::ASW Batch was -0.0591880105255168 prior to batch effect correction and is now -0.131190117167012 .
2024-05-06 19:51:29.682955 INFO::Total function execution time is 0.0152080059051514 s and adjustment time is 0.00989484786987305 s ( 65.06 )
2024-05-06 19:51:29.683971 INFO::Formatting Data.
2024-05-06 19:51:29.684149 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:29.686948 INFO::Formatting Data.
2024-05-06 19:51:29.687151 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:29.687406 INFO::Removing potential empty rows and columns
2024-05-06 19:51:29.6877 INFO::Found 0 missing values.
2024-05-06 19:51:29.688498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:29.688651 INFO::Done
2024-05-06 19:51:29.688794 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:29.689363 INFO::Starting hierarchical adjustment
2024-05-06 19:51:29.689552 INFO::Found 2 batches.
2024-05-06 19:51:29.689688 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:29.689858 INFO::Using default BPPARAM
2024-05-06 19:51:29.689995 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:29.690234 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:29.694981 INFO::Done
2024-05-06 19:51:29.695207 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:29.695823 INFO::ASW Batch was 0.057511945624419 prior to batch effect correction and is now -0.121982249263062 .
2024-05-06 19:51:29.696061 INFO::Total function execution time is 0.00911307334899902 s and adjustment time is 0.00545811653137207 s ( 59.89 )
2024-05-06 19:51:29.696375 INFO::Formatting Data.
2024-05-06 19:51:29.696546 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:29.696793 INFO::Removing potential empty rows and columns
2024-05-06 19:51:29.697085 INFO::Found 0 missing values.
2024-05-06 19:51:29.697888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:29.698041 INFO::Done
2024-05-06 19:51:29.698178 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:29.69872 INFO::Starting hierarchical adjustment
2024-05-06 19:51:29.698914 INFO::Found 2 batches.
2024-05-06 19:51:29.699054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:29.69922 INFO::Using default BPPARAM
2024-05-06 19:51:29.699351 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:29.699599 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:29.704118 INFO::Done
2024-05-06 19:51:29.704307 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:29.704932 INFO::ASW Batch was 0.057511945624419 prior to batch effect correction and is now -0.121982249263062 .
2024-05-06 19:51:29.70517 INFO::Total function execution time is 0.00878310203552246 s and adjustment time is 0.00524115562438965 s ( 59.67 )
2024-05-06 19:51:30.56474 INFO::Formatting Data.
2024-05-06 19:51:30.565 INFO::Recognized SummarizedExperiment
2024-05-06 19:51:30.565152 INFO::Typecasting input to dataframe.
2024-05-06 19:51:30.576012 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:30.576401 INFO::Removing potential empty rows and columns
2024-05-06 19:51:30.886124 INFO::Found 0 missing values.
2024-05-06 19:51:30.88821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:30.888392 INFO::Done
2024-05-06 19:51:30.888529 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:30.889617 INFO::Starting hierarchical adjustment
2024-05-06 19:51:30.889804 INFO::Found 2 batches.
2024-05-06 19:51:30.889933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:30.890228 INFO::Using default BPPARAM
2024-05-06 19:51:30.890355 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:30.890604 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:30.90562 INFO::Done
2024-05-06 19:51:30.905808 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:30.906848 INFO::ASW Batch was -0.00876192731449014 prior to batch effect correction and is now -0.092663200137993 .
2024-05-06 19:51:30.907071 INFO::Total function execution time is 0.342449903488159 s and adjustment time is 0.0158448219299316 s ( 4.63 )
2024-05-06 19:51:30.912403 INFO::Formatting Data.
2024-05-06 19:51:30.912583 INFO::Recognized SummarizedExperiment
2024-05-06 19:51:30.912727 INFO::Typecasting input to dataframe.
2024-05-06 19:51:30.915251 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:30.915547 INFO::Removing potential empty rows and columns
2024-05-06 19:51:30.916528 INFO::Found 0 missing values.
2024-05-06 19:51:30.918378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:30.918516 INFO::Done
2024-05-06 19:51:30.918643 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:30.919665 INFO::Starting hierarchical adjustment
2024-05-06 19:51:30.919847 INFO::Found 2 batches.
2024-05-06 19:51:30.919978 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:30.920127 INFO::Using default BPPARAM
2024-05-06 19:51:30.920251 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:30.9205 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:30.927498 INFO::Done
2024-05-06 19:51:30.927681 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:30.928721 INFO::ASW Batch was 0.00911837988561466 prior to batch effect correction and is now 0.00911837988561466 .
2024-05-06 19:51:30.928943 INFO::Total function execution time is 0.0165309906005859 s and adjustment time is 0.00768184661865234 s ( 46.47 )
2024-05-06 19:51:30.934872 INFO::Formatting Data.
2024-05-06 19:51:30.935075 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:30.935317 INFO::Removing potential empty rows and columns
2024-05-06 19:51:30.93559 INFO::Found 0 missing values.
2024-05-06 19:51:30.936342 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:30.93648 INFO::Done
2024-05-06 19:51:30.93661 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:30.937148 INFO::Starting hierarchical adjustment
2024-05-06 19:51:30.937321 INFO::Found 3 batches.
2024-05-06 19:51:30.937447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:30.937599 INFO::Using default BPPARAM
2024-05-06 19:51:30.937723 INFO::Processing subtree level 1
2024-05-06 19:51:31.019612 INFO::Adjusting the last 1 batches sequentially
2024-05-06 19:51:31.020837 INFO::Done
2024-05-06 19:51:31.021041 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.02273 INFO::ASW Batch was 0.00888542827458036 prior to batch effect correction and is now -0.19072574345813 .
2024-05-06 19:51:31.023355 INFO::Total function execution time is 0.0884718894958496 s and adjustment time is 0.0835480690002441 s ( 94.43 )
2024-05-06 19:51:31.030193 INFO::Skipping initial DF formatting
2024-05-06 19:51:31.030424 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.031892 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.032178 INFO::Found 5 batches.
2024-05-06 19:51:31.03236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.032588 INFO::Using default BPPARAM
2024-05-06 19:51:31.032768 INFO::Processing subtree level 1
2024-05-06 19:51:31.090833 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.092743 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.104693 INFO::Done
2024-05-06 19:51:31.104965 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.107486 INFO::ASW Batch was 0.503188915409949 prior to batch effect correction and is now 0.503188915409949 .
2024-05-06 19:51:31.107809 INFO::ASW Label was 0.375847315926821 prior to batch effect correction and is now 0.375847315926821 .
2024-05-06 19:51:31.108447 INFO::Total function execution time is 0.078233003616333 s and adjustment time is 0.0725700855255127 s ( 92.76 )
2024-05-06 19:51:31.118079 INFO::Formatting Data.
2024-05-06 19:51:31.118334 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.118691 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.119088 INFO::Found 0 missing values.
2024-05-06 19:51:31.120578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.120744 INFO::Done
2024-05-06 19:51:31.120908 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.121985 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.122252 INFO::Found 5 batches.
2024-05-06 19:51:31.122443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.122669 INFO::Using default BPPARAM
2024-05-06 19:51:31.122815 INFO::Processing subtree level 1
2024-05-06 19:51:31.167398 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.169475 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.177596 INFO::Done
2024-05-06 19:51:31.177823 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.179193 INFO::ASW Batch was 0.234347628101678 prior to batch effect correction and is now -0.0909658342635782 .
2024-05-06 19:51:31.179376 INFO::ASW Label was 0.49479843571106 prior to batch effect correction and is now 0.887164870851564 .
2024-05-06 19:51:31.179864 INFO::Total function execution time is 0.0617811679840088 s and adjustment time is 0.0553929805755615 s ( 89.66 )
2024-05-06 19:51:31.180124 INFO::Formatting Data.
2024-05-06 19:51:31.180299 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.180548 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.180861 INFO::Found 0 missing values.
2024-05-06 19:51:31.182024 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.18219 INFO::Done
2024-05-06 19:51:31.182347 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.183168 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.183369 INFO::Found 5 batches.
2024-05-06 19:51:31.183523 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.183724 INFO::Using default BPPARAM
2024-05-06 19:51:31.183885 INFO::Processing subtree level 1
2024-05-06 19:51:31.227811 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.22971 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.238636 INFO::Done
2024-05-06 19:51:31.238856 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.240053 INFO::ASW Batch was 0.234347628101678 prior to batch effect correction and is now -0.0909658342635782 .
2024-05-06 19:51:31.240236 INFO::ASW Label was 0.49479843571106 prior to batch effect correction and is now 0.887164870851564 .
2024-05-06 19:51:31.24066 INFO::Total function execution time is 0.0605020523071289 s and adjustment time is 0.0553021430969238 s ( 91.41 )
2024-05-06 19:51:31.247274 INFO::Formatting Data.
2024-05-06 19:51:31.247519 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.247808 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.248167 INFO::Found 0 missing values.
2024-05-06 19:51:31.249348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.249508 INFO::Done
2024-05-06 19:51:31.24967 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.250551 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.25077 INFO::Found 5 batches.
2024-05-06 19:51:31.250919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.25114 INFO::Using default BPPARAM
2024-05-06 19:51:31.251289 INFO::Processing subtree level 1
2024-05-06 19:51:31.295925 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.297847 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.305066 INFO::Done
2024-05-06 19:51:31.305293 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.306673 INFO::ASW Batch was 0.542179970197044 prior to batch effect correction and is now -0.0473079038991312 .
2024-05-06 19:51:31.306864 INFO::ASW Label was 0.240307752381804 prior to batch effect correction and is now 0.748814784226522 .
2024-05-06 19:51:31.307518 INFO::Total function execution time is 0.060236930847168 s and adjustment time is 0.0543360710144043 s ( 90.2 )
2024-05-06 19:51:31.307793 INFO::Formatting Data.
2024-05-06 19:51:31.307979 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.30824 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.308579 INFO::Found 0 missing values.
2024-05-06 19:51:31.30976 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.309921 INFO::Done
2024-05-06 19:51:31.310095 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.310925 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.31113 INFO::Found 5 batches.
2024-05-06 19:51:31.311282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.311485 INFO::Using default BPPARAM
2024-05-06 19:51:31.31163 INFO::Processing subtree level 1
2024-05-06 19:51:31.353491 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.355295 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.362357 INFO::Done
2024-05-06 19:51:31.362603 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.363763 INFO::ASW Batch was 0.542179970197044 prior to batch effect correction and is now -0.0473079038991312 .
2024-05-06 19:51:31.363971 INFO::ASW Label was 0.240307752381804 prior to batch effect correction and is now 0.748814784226522 .
2024-05-06 19:51:31.364658 INFO::Total function execution time is 0.0568230152130127 s and adjustment time is 0.051267147064209 s ( 90.22 )
2024-05-06 19:51:31.371324 INFO::Formatting Data.
2024-05-06 19:51:31.371578 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.371871 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.372246 INFO::Found 0 missing values.
2024-05-06 19:51:31.373057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.373219 INFO::Done
2024-05-06 19:51:31.373374 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.374246 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.374469 INFO::Found 2 batches.
2024-05-06 19:51:31.374623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.374841 INFO::Using default BPPARAM
2024-05-06 19:51:31.37499 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.375234 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.379831 INFO::Done
2024-05-06 19:51:31.380021 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.380897 INFO::ASW Batch was 0.583107639358084 prior to batch effect correction and is now 0.189302681450503 .
2024-05-06 19:51:31.381067 INFO::ASW Label was 0.514484784313907 prior to batch effect correction and is now 0.80361510250989 .
2024-05-06 19:51:31.381321 INFO::Total function execution time is 0.0100300312042236 s and adjustment time is 0.00540685653686523 s ( 53.91 )
2024-05-06 19:51:31.38154 INFO::Formatting Data.
2024-05-06 19:51:31.381709 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.381943 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.38222 INFO::Found 0 missing values.
2024-05-06 19:51:31.382971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.383122 INFO::Done
2024-05-06 19:51:31.383622 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.384421 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.384619 INFO::Found 2 batches.
2024-05-06 19:51:31.384768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.384942 INFO::Using default BPPARAM
2024-05-06 19:51:31.385102 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.385343 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.389698 INFO::Done
2024-05-06 19:51:31.389877 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.390697 INFO::ASW Batch was 0.583107639358084 prior to batch effect correction and is now 0.189302681450503 .
2024-05-06 19:51:31.39086 INFO::ASW Label was 0.514484784313907 prior to batch effect correction and is now 0.80361510250989 .
2024-05-06 19:51:31.391085 INFO::Total function execution time is 0.00953888893127441 s and adjustment time is 0.00511503219604492 s ( 53.62 )
2024-05-06 19:51:31.395285 INFO::Formatting Data.
2024-05-06 19:51:31.395489 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.395732 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.39598 INFO::Found 0 missing values.
2024-05-06 19:51:31.39657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.396721 INFO::Done
2024-05-06 19:51:31.396868 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.397403 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.397594 INFO::Found 2 batches.
2024-05-06 19:51:31.39774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.39791 INFO::Using default BPPARAM
2024-05-06 19:51:31.398058 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.398294 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.408821 INFO::Done
2024-05-06 19:51:31.409032 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.409635 INFO::ASW Batch was -0.0346884941421752 prior to batch effect correction and is now -0.156912929032415 .
2024-05-06 19:51:31.409882 INFO::Total function execution time is 0.0145969390869141 s and adjustment time is 0.0112559795379639 s ( 77.11 )
2024-05-06 19:51:31.41447 INFO::Formatting Data.
2024-05-06 19:51:31.414702 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.414963 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.415251 INFO::Found 0 missing values.
2024-05-06 19:51:31.415658 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.
2024-05-06 19:51:31.416979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.417148 INFO::Done
2024-05-06 19:51:31.417297 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.418155 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.418346 INFO::Found 2 batches.
2024-05-06 19:51:31.41849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.418657 INFO::Using default BPPARAM
2024-05-06 19:51:31.418795 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.419064 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.424038 INFO::Done
2024-05-06 19:51:31.424229 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.425066 INFO::ASW Batch was 0.140124559030359 prior to batch effect correction and is now -0.0254213385463519 .
2024-05-06 19:51:31.425235 INFO::ASW Label was 0.843499633765292 prior to batch effect correction and is now 0.932244517279303 .
2024-05-06 19:51:31.42545 INFO::Total function execution time is 0.010998010635376 s and adjustment time is 0.00573205947875977 s ( 52.12 )
2024-05-06 19:51:31.42566 INFO::Formatting Data.
2024-05-06 19:51:31.425826 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.426081 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.426367 INFO::Found 0 missing values.
2024-05-06 19:51:31.426609 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.
2024-05-06 19:51:31.427861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.428013 INFO::Done
2024-05-06 19:51:31.428163 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.428954 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.429148 INFO::Found 2 batches.
2024-05-06 19:51:31.42929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.429461 INFO::Using default BPPARAM
2024-05-06 19:51:31.429597 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:31.429842 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:31.434697 INFO::Done
2024-05-06 19:51:31.434883 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.435707 INFO::ASW Batch was 0.140124559030359 prior to batch effect correction and is now -0.0254213385463519 .
2024-05-06 19:51:31.435876 INFO::ASW Label was 0.843499633765292 prior to batch effect correction and is now 0.932244517279303 .
2024-05-06 19:51:31.436119 INFO::Total function execution time is 0.0104460716247559 s and adjustment time is 0.00558710098266602 s ( 53.49 )
2024-05-06 19:51:31.500171 INFO::Formatting Data.
2024-05-06 19:51:31.500464 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.500754 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.501084 INFO::Found 0 missing values.
2024-05-06 19:51:31.501994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.502163 INFO::Done
2024-05-06 19:51:31.50231 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.502991 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.503195 INFO::Found 3 batches.
2024-05-06 19:51:31.503344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.503517 INFO::Using default BPPARAM
2024-05-06 19:51:31.503655 INFO::Processing subtree level 1
2024-05-06 19:51:31.543882 INFO::Adjusting the last 1 batches sequentially
2024-05-06 19:51:31.544869 INFO::Done
2024-05-06 19:51:31.545073 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.546395 INFO::ASW Batch was 0.0524185140966447 prior to batch effect correction and is now 0.0524185140966447 .
2024-05-06 19:51:31.546779 INFO::Total function execution time is 0.0466480255126953 s and adjustment time is 0.0417139530181885 s ( 89.42 )
2024-05-06 19:51:31.547131 INFO::Formatting Data.
2024-05-06 19:51:31.547339 INFO::Typecasting input to dataframe.
2024-05-06 19:51:31.547565 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.547881 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.548244 INFO::Found 0 missing values.
2024-05-06 19:51:31.549187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.549358 INFO::Done
2024-05-06 19:51:31.549629 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.550483 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.550716 INFO::Found 3 batches.
2024-05-06 19:51:31.550904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.55111 INFO::Using default BPPARAM
2024-05-06 19:51:31.551264 INFO::Processing subtree level 1
2024-05-06 19:51:31.586389 INFO::Adjusting the last 1 batches sequentially
2024-05-06 19:51:31.587488 INFO::Done
2024-05-06 19:51:31.58767 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.589005 INFO::ASW Batch was 0.0524185140966447 prior to batch effect correction and is now 0.0524185140966447 .
2024-05-06 19:51:31.589344 INFO::Total function execution time is 0.0422029495239258 s and adjustment time is 0.0368239879608154 s ( 87.25 )
2024-05-06 19:51:31.595194 INFO::Formatting Data.
2024-05-06 19:51:31.595424 INFO::Typecasting input to dataframe.
2024-05-06 19:51:31.595664 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.595941 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.596298 INFO::Found 0 missing values.
2024-05-06 19:51:31.597148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.597297 INFO::Done
2024-05-06 19:51:31.597445 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.598015 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.598213 INFO::Found 3 batches.
2024-05-06 19:51:31.598363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.598554 INFO::Using default BPPARAM
2024-05-06 19:51:31.5987 INFO::Processing subtree level 1
2024-05-06 19:51:31.635425 INFO::Adjusting the last 1 batches sequentially
2024-05-06 19:51:31.63663 INFO::Done
2024-05-06 19:51:31.636815 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.638311 INFO::ASW Batch was 0.06410649429178 prior to batch effect correction and is now 0.06410649429178 .
2024-05-06 19:51:31.638702 INFO::Total function execution time is 0.0434958934783936 s and adjustment time is 0.0384571552276611 s ( 88.42 )
2024-05-06 19:51:31.698277 INFO::Formatting Data.
2024-05-06 19:51:31.698538 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.698895 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.699767 INFO::Found 1000 missing values.
2024-05-06 19:51:31.705419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.705639 INFO::Done
2024-05-06 19:51:31.7058 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.707639 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.707866 INFO::Found 10 batches.
2024-05-06 19:51:31.708028 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:31.708231 INFO::Using default BPPARAM
2024-05-06 19:51:31.708376 INFO::Processing subtree level 1
2024-05-06 19:51:31.752379 INFO::Processing subtree level 2
2024-05-06 19:51:31.810952 INFO::Adjusting the last 1 batches sequentially
2024-05-06 19:51:31.812187 INFO::Done
2024-05-06 19:51:31.812408 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:31.815268 INFO::ASW Batch was 0.547448127953015 prior to batch effect correction and is now 0.547448127953015 .
2024-05-06 19:51:31.815527 INFO::ASW Label was 0.306410824602459 prior to batch effect correction and is now 0.306410824602459 .
2024-05-06 19:51:31.816048 INFO::Total function execution time is 0.117729902267456 s and adjustment time is 0.104367971420288 s ( 88.65 )
2024-05-06 19:51:31.816371 INFO::Formatting Data.
2024-05-06 19:51:31.816568 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:31.817413 INFO::Removing potential empty rows and columns
2024-05-06 19:51:31.818395 INFO::Found 1000 missing values.
2024-05-06 19:51:31.825116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:31.825367 INFO::Done
2024-05-06 19:51:31.825541 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:31.827504 INFO::Starting hierarchical adjustment
2024-05-06 19:51:31.827797 INFO::Found 10 batches.
2024-05-06 19:51:32.368317 INFO::Set up parallel execution backend with 2 workers
2024-05-06 19:51:32.368683 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-06 19:51:32.891622 INFO::Adjusting the last 2 batches sequentially
2024-05-06 19:51:32.892394 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-06 19:51:32.898829 INFO::Done
2024-05-06 19:51:32.899047 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:32.901014 INFO::ASW Batch was 0.547448127953015 prior to batch effect correction and is now 0.547448127953015 .
2024-05-06 19:51:32.90118 INFO::ASW Label was 0.306410824602459 prior to batch effect correction and is now 0.306410824602459 .
2024-05-06 19:51:32.901408 INFO::Total function execution time is 1.08504796028137 s and adjustment time is 1.07108283042908 s ( 98.71 )
2024-05-06 19:51:32.972575 INFO::Formatting Data.
2024-05-06 19:51:32.97281 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:32.9731 INFO::Removing potential empty rows and columns
2024-05-06 19:51:32.973453 INFO::Found 0 missing values.
2024-05-06 19:51:32.974575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:32.974735 INFO::Done
2024-05-06 19:51:32.974886 INFO::Acquiring quality metrics before batch effect correction.
2024-05-06 19:51:32.975719 INFO::Starting hierarchical adjustment
2024-05-06 19:51:32.97593 INFO::Found 3 batches.
2024-05-06 19:51:32.976074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-06 19:51:32.976269 INFO::Using default BPPARAM
2024-05-06 19:51:32.976422 INFO::Processing subtree level 1
2024-05-06 19:51:33.022284 INFO::Adjusting the last 1 batches sequentially
2024-05-06 19:51:33.023358 INFO::Done
2024-05-06 19:51:33.023548 INFO::Acquiring quality metrics after batch effect correction.
2024-05-06 19:51:33.025137 INFO::ASW Batch was 0.109765450659143 prior to batch effect correction and is now -0.152221354316494 .
2024-05-06 19:51:33.02533 INFO::ASW Label was -0.192430970154408 prior to batch effect correction and is now 0.023620903442925 .
2024-05-06 19:51:33.026039 INFO::Total function execution time is 0.0534610748291016 s and adjustment time is 0.0474741458892822 s ( 88.8 )
2024-05-06 19:51:33.07081 INFO::Formatting Data.
2024-05-06 19:51:33.071125 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.071431 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.071803 INFO::Found 2 missing values.
2024-05-06 19:51:33.072726 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.072888 INFO::Done
2024-05-06 19:51:33.083245 INFO::Found NA in Reference column
2024-05-06 19:51:33.086734 INFO::Require at least two references per batch.
2024-05-06 19:51:33.094096 INFO::Formatting Data.
2024-05-06 19:51:33.094302 INFO::Recognized SummarizedExperiment
2024-05-06 19:51:33.094457 INFO::Typecasting input to dataframe.
2024-05-06 19:51:33.097925 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.098281 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.09949 INFO::Found 0 missing values.
2024-05-06 19:51:33.101757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.101921 INFO::Done
2024-05-06 19:51:33.106763 INFO::Formatting Data.
2024-05-06 19:51:33.106956 INFO::Recognized SummarizedExperiment
2024-05-06 19:51:33.107116 INFO::Typecasting input to dataframe.
2024-05-06 19:51:33.112436 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.112819 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.114089 INFO::Found 0 missing values.
2024-05-06 19:51:33.117827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.118024 INFO::Done
2024-05-06 19:51:33.122981 INFO::Formatting Data.
2024-05-06 19:51:33.12317 INFO::Recognized SummarizedExperiment
2024-05-06 19:51:33.123322 INFO::Typecasting input to dataframe.
2024-05-06 19:51:33.128367 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.128654 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.128974 INFO::Found 0 missing values.
2024-05-06 19:51:33.129247 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.
2024-05-06 19:51:33.130644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.130831 INFO::Done
2024-05-06 19:51:33.134968 INFO::Formatting Data.
2024-05-06 19:51:33.135238 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.13555 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.135868 INFO::Found 0 missing values.
2024-05-06 19:51:33.136851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.137023 INFO::Done
2024-05-06 19:51:33.14142 INFO::Formatting Data.
2024-05-06 19:51:33.141622 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.14186 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.14214 INFO::Found 0 missing values.
2024-05-06 19:51:33.142952 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.143094 INFO::Done
2024-05-06 19:51:33.153424 INFO::Formatting Data.
2024-05-06 19:51:33.153691 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.154007 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.154381 INFO::Found 1 missing values.
2024-05-06 19:51:33.155134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.155309 INFO::Done
2024-05-06 19:51:33.162465 INFO::Formatting Data.
2024-05-06 19:51:33.162708 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.16298 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.163265 INFO::Found 2 missing values.
2024-05-06 19:51:33.163577 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.
2024-05-06 19:51:33.164299 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.164456 INFO::Done
2024-05-06 19:51:33.168369 INFO::Formatting Data.
2024-05-06 19:51:33.16864 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.168889 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.16919 INFO::Found 2 missing values.
2024-05-06 19:51:33.169686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.169836 INFO::Done
2024-05-06 19:51:33.174656 INFO::Formatting Data.
2024-05-06 19:51:33.17493 INFO::Typecasting input to dataframe.
2024-05-06 19:51:33.175212 INFO::Replacing NaNs with NAs.
2024-05-06 19:51:33.175681 INFO::Removing potential empty rows and columns
2024-05-06 19:51:33.176094 INFO::Found 0 missing values.
2024-05-06 19:51:33.177191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-06 19:51:33.177356 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.489 1.427 8.062
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.846 | 0.352 | 6.290 | |
| compute_asw | 0.009 | 0.000 | 0.009 | |
| count_existing | 0.005 | 0.001 | 0.006 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.005 | 0.000 | 0.005 | |