Yannis Schumann
| Snapshot Date: 2024-09-11 14:00 -0400 (Wed, 11 Sep 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-12 11:49 -0400 (Thu, 12 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4713 |
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
| 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 158/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-09-12 02:54:10 -0000 (Thu, 12 Sep 2024) |
| EndedAt: 2024-09-12 02:55:30 -0000 (Thu, 12 Sep 2024) |
| EllapsedTime: 80.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 31.703 1.759 22.817
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-09-12 02:55:15.294029 INFO::Formatting Data.
2024-09-12 02:55:15.295952 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:15.314142 INFO::Removing potential empty rows and columns
2024-09-12 02:55:15.680885 INFO::Found 0 missing values.
2024-09-12 02:55:15.686383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:15.687284 INFO::Done
2024-09-12 02:55:15.688022 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:15.704885 INFO::Starting hierarchical adjustment
2024-09-12 02:55:15.706042 INFO::Found 3 batches.
2024-09-12 02:55:15.706793 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:15.708462 INFO::Using default BPPARAM
2024-09-12 02:55:15.709253 INFO::Processing subtree level 1
2024-09-12 02:55:15.839036 INFO::Adjusting the last 1 batches sequentially
2024-09-12 02:55:15.841251 INFO::Done
2024-09-12 02:55:15.842085 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:15.845518 INFO::ASW Batch was -0.118081132639126 prior to batch effect correction and is now -0.118081132639126 .
2024-09-12 02:55:15.847081 INFO::Total function execution time is 0.553955793380737 s and adjustment time is 0.135489225387573 s ( 24.46 )
2024-09-12 02:55:15.866174 INFO::Formatting Data.
2024-09-12 02:55:15.86716 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:15.868345 INFO::Removing potential empty rows and columns
2024-09-12 02:55:15.869824 INFO::Found 0 missing values.
2024-09-12 02:55:15.871063 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.
2024-09-12 02:55:15.887043 INFO::Formatting Data.
2024-09-12 02:55:15.88803 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:15.889205 INFO::Removing potential empty rows and columns
2024-09-12 02:55:15.890635 INFO::Found 0 missing values.
2024-09-12 02:55:15.891864 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.
2024-09-12 02:55:15.913736 INFO::Formatting Data.
2024-09-12 02:55:15.914677 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:15.915823 INFO::Removing potential empty rows and columns
2024-09-12 02:55:15.917175 INFO::Found 0 missing values.
2024-09-12 02:55:15.918408 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.
2024-09-12 02:55:15.92485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:15.925734 INFO::Done
2024-09-12 02:55:15.926472 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:15.929239 INFO::Starting hierarchical adjustment
2024-09-12 02:55:15.930323 INFO::Found 2 batches.
2024-09-12 02:55:15.931147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:15.932102 INFO::Using default BPPARAM
2024-09-12 02:55:15.932888 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:15.934283 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:15.965341 INFO::Done
2024-09-12 02:55:15.966235 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:15.968978 INFO::ASW Batch was 0.140830961447126 prior to batch effect correction and is now -0.103202922675325 .
2024-09-12 02:55:15.970166 INFO::Total function execution time is 0.0564932823181152 s and adjustment time is 0.0352325439453125 s ( 62.37 )
2024-09-12 02:55:15.974022 INFO::Formatting Data.
2024-09-12 02:55:15.974965 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:15.987252 INFO::Formatting Data.
2024-09-12 02:55:15.988203 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:15.989463 INFO::Removing potential empty rows and columns
2024-09-12 02:55:15.990946 INFO::Found 0 missing values.
2024-09-12 02:55:15.995421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:15.99627 INFO::Done
2024-09-12 02:55:15.997045 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:15.999872 INFO::Starting hierarchical adjustment
2024-09-12 02:55:16.000916 INFO::Found 2 batches.
2024-09-12 02:55:16.001709 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:16.002539 INFO::Using default BPPARAM
2024-09-12 02:55:16.003352 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:16.004687 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:16.024962 INFO::Done
2024-09-12 02:55:16.025816 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:16.028506 INFO::ASW Batch was -0.0340226137776428 prior to batch effect correction and is now -0.0946350588813948 .
2024-09-12 02:55:16.029556 INFO::Total function execution time is 0.0423929691314697 s and adjustment time is 0.0242533683776855 s ( 57.21 )
2024-09-12 02:55:16.030954 INFO::Formatting Data.
2024-09-12 02:55:16.03177 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:16.032898 INFO::Removing potential empty rows and columns
2024-09-12 02:55:16.034274 INFO::Found 0 missing values.
2024-09-12 02:55:16.038231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:16.039041 INFO::Done
2024-09-12 02:55:16.039762 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:16.042445 INFO::Starting hierarchical adjustment
2024-09-12 02:55:16.043464 INFO::Found 2 batches.
2024-09-12 02:55:16.044185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:16.045009 INFO::Using default BPPARAM
2024-09-12 02:55:16.045732 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:16.046982 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:16.067098 INFO::Done
2024-09-12 02:55:16.067933 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:16.070636 INFO::ASW Batch was -0.0340226137776428 prior to batch effect correction and is now -0.0946350588813948 .
2024-09-12 02:55:16.071736 INFO::Total function execution time is 0.0407705307006836 s and adjustment time is 0.0238144397735596 s ( 58.41 )
2024-09-12 02:55:19.116717 INFO::Formatting Data.
2024-09-12 02:55:19.117802 INFO::Recognized SummarizedExperiment
2024-09-12 02:55:19.118562 INFO::Typecasting input to dataframe.
2024-09-12 02:55:19.166862 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:19.168744 INFO::Removing potential empty rows and columns
2024-09-12 02:55:19.17457 INFO::Found 0 missing values.
2024-09-12 02:55:19.185717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:19.186602 INFO::Done
2024-09-12 02:55:19.1874 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:19.192844 INFO::Starting hierarchical adjustment
2024-09-12 02:55:19.194022 INFO::Found 2 batches.
2024-09-12 02:55:19.194818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:19.196421 INFO::Using default BPPARAM
2024-09-12 02:55:19.197251 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:19.198725 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:19.33593 INFO::Done
2024-09-12 02:55:19.336894 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:19.342318 INFO::ASW Batch was -0.00707054234785442 prior to batch effect correction and is now -0.0908896647838994 .
2024-09-12 02:55:19.343722 INFO::Total function execution time is 0.227519989013672 s and adjustment time is 0.142172336578369 s ( 62.49 )
2024-09-12 02:55:19.371071 INFO::Formatting Data.
2024-09-12 02:55:19.372156 INFO::Recognized SummarizedExperiment
2024-09-12 02:55:19.373062 INFO::Typecasting input to dataframe.
2024-09-12 02:55:19.387576 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:19.389283 INFO::Removing potential empty rows and columns
2024-09-12 02:55:19.394969 INFO::Found 0 missing values.
2024-09-12 02:55:19.406822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:19.407791 INFO::Done
2024-09-12 02:55:19.408653 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:19.414156 INFO::Starting hierarchical adjustment
2024-09-12 02:55:19.41542 INFO::Found 2 batches.
2024-09-12 02:55:19.416324 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:19.417279 INFO::Using default BPPARAM
2024-09-12 02:55:19.418126 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:19.419676 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:19.457859 INFO::Done
2024-09-12 02:55:19.45872 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:19.463668 INFO::ASW Batch was -0.039559289254486 prior to batch effect correction and is now -0.039559289254486 .
2024-09-12 02:55:19.464892 INFO::Total function execution time is 0.0938076972961426 s and adjustment time is 0.0427176952362061 s ( 45.54 )
2024-09-12 02:55:19.490494 INFO::Formatting Data.
2024-09-12 02:55:19.491561 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:19.492777 INFO::Removing potential empty rows and columns
2024-09-12 02:55:19.494208 INFO::Found 0 missing values.
2024-09-12 02:55:19.498554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:19.499449 INFO::Done
2024-09-12 02:55:19.500213 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:19.502908 INFO::Starting hierarchical adjustment
2024-09-12 02:55:19.503962 INFO::Found 3 batches.
2024-09-12 02:55:19.504695 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:19.505492 INFO::Using default BPPARAM
2024-09-12 02:55:19.50621 INFO::Processing subtree level 1
2024-09-12 02:55:19.726623 INFO::Adjusting the last 1 batches sequentially
2024-09-12 02:55:19.729294 INFO::Done
2024-09-12 02:55:19.730926 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:19.734689 INFO::ASW Batch was -0.0476080094050611 prior to batch effect correction and is now -0.173493243367247 .
2024-09-12 02:55:19.736209 INFO::Total function execution time is 0.24570107460022 s and adjustment time is 0.225522756576538 s ( 91.79 )
2024-09-12 02:55:19.759185 INFO::Skipping initial DF formatting
2024-09-12 02:55:19.760156 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:19.766491 INFO::Starting hierarchical adjustment
2024-09-12 02:55:19.767719 INFO::Found 5 batches.
2024-09-12 02:55:19.768528 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:19.769551 INFO::Using default BPPARAM
2024-09-12 02:55:19.770403 INFO::Processing subtree level 1
2024-09-12 02:55:19.959301 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:19.96168 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:19.996763 INFO::Done
2024-09-12 02:55:19.997877 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:20.004797 INFO::ASW Batch was 0.471818801939521 prior to batch effect correction and is now 0.471818801939521 .
2024-09-12 02:55:20.005791 INFO::ASW Label was 0.437976534332062 prior to batch effect correction and is now 0.437976534332062 .
2024-09-12 02:55:20.007165 INFO::Total function execution time is 0.248000144958496 s and adjustment time is 0.229276895523071 s ( 92.45 )
2024-09-12 02:55:20.034762 INFO::Formatting Data.
2024-09-12 02:55:20.035891 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:20.037277 INFO::Removing potential empty rows and columns
2024-09-12 02:55:20.038821 INFO::Found 0 missing values.
2024-09-12 02:55:20.045618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:20.046803 INFO::Done
2024-09-12 02:55:20.047685 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:20.052841 INFO::Starting hierarchical adjustment
2024-09-12 02:55:20.054073 INFO::Found 5 batches.
2024-09-12 02:55:20.054907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:20.055885 INFO::Using default BPPARAM
2024-09-12 02:55:20.056686 INFO::Processing subtree level 1
2024-09-12 02:55:20.211432 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:20.213659 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:20.237963 INFO::Done
2024-09-12 02:55:20.239106 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:20.244558 INFO::ASW Batch was 0.223798006275828 prior to batch effect correction and is now 0.000185690222914305 .
2024-09-12 02:55:20.245578 INFO::ASW Label was 0.445909355232344 prior to batch effect correction and is now 0.810793040593855 .
2024-09-12 02:55:20.246924 INFO::Total function execution time is 0.212180852890015 s and adjustment time is 0.184134721755981 s ( 86.78 )
2024-09-12 02:55:20.248342 INFO::Formatting Data.
2024-09-12 02:55:20.249378 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:20.250844 INFO::Removing potential empty rows and columns
2024-09-12 02:55:20.252553 INFO::Found 0 missing values.
2024-09-12 02:55:20.259588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:20.260579 INFO::Done
2024-09-12 02:55:20.261473 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:20.266213 INFO::Starting hierarchical adjustment
2024-09-12 02:55:20.267455 INFO::Found 5 batches.
2024-09-12 02:55:20.268362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:20.269372 INFO::Using default BPPARAM
2024-09-12 02:55:20.270275 INFO::Processing subtree level 1
2024-09-12 02:55:20.423206 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:20.425302 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:20.448334 INFO::Done
2024-09-12 02:55:20.449356 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:20.454359 INFO::ASW Batch was 0.223798006275828 prior to batch effect correction and is now 0.000185690222914305 .
2024-09-12 02:55:20.455413 INFO::ASW Label was 0.445909355232344 prior to batch effect correction and is now 0.810793040593855 .
2024-09-12 02:55:20.456722 INFO::Total function execution time is 0.208389043807983 s and adjustment time is 0.181114912033081 s ( 86.91 )
2024-09-12 02:55:20.477109 INFO::Formatting Data.
2024-09-12 02:55:20.478191 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:20.479582 INFO::Removing potential empty rows and columns
2024-09-12 02:55:20.481056 INFO::Found 0 missing values.
2024-09-12 02:55:20.487467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:20.488524 INFO::Done
2024-09-12 02:55:20.489325 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:20.49366 INFO::Starting hierarchical adjustment
2024-09-12 02:55:20.494848 INFO::Found 5 batches.
2024-09-12 02:55:20.495699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:20.496647 INFO::Using default BPPARAM
2024-09-12 02:55:20.497451 INFO::Processing subtree level 1
2024-09-12 02:55:20.6458 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:20.647935 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:20.670553 INFO::Done
2024-09-12 02:55:20.671516 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:20.676226 INFO::ASW Batch was 0.405512550939168 prior to batch effect correction and is now 0.0171646524797474 .
2024-09-12 02:55:20.677205 INFO::ASW Label was 0.447150106797434 prior to batch effect correction and is now 0.689357087886657 .
2024-09-12 02:55:20.678405 INFO::Total function execution time is 0.201343774795532 s and adjustment time is 0.175912618637085 s ( 87.37 )
2024-09-12 02:55:20.679657 INFO::Formatting Data.
2024-09-12 02:55:20.680524 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:20.681832 INFO::Removing potential empty rows and columns
2024-09-12 02:55:20.683302 INFO::Found 0 missing values.
2024-09-12 02:55:20.689761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:20.690668 INFO::Done
2024-09-12 02:55:20.691481 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:20.695815 INFO::Starting hierarchical adjustment
2024-09-12 02:55:20.697056 INFO::Found 5 batches.
2024-09-12 02:55:20.697938 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:20.698833 INFO::Using default BPPARAM
2024-09-12 02:55:20.699648 INFO::Processing subtree level 1
2024-09-12 02:55:20.842885 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:20.845309 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:20.867959 INFO::Done
2024-09-12 02:55:20.868888 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:20.873331 INFO::ASW Batch was 0.405512550939168 prior to batch effect correction and is now 0.0171646524797474 .
2024-09-12 02:55:20.874253 INFO::ASW Label was 0.447150106797434 prior to batch effect correction and is now 0.689357087886657 .
2024-09-12 02:55:20.875416 INFO::Total function execution time is 0.19575834274292 s and adjustment time is 0.171161651611328 s ( 87.44 )
2024-09-12 02:55:20.894331 INFO::Formatting Data.
2024-09-12 02:55:20.895375 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:20.896663 INFO::Removing potential empty rows and columns
2024-09-12 02:55:20.898096 INFO::Found 0 missing values.
2024-09-12 02:55:20.902411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:20.903348 INFO::Done
2024-09-12 02:55:20.904102 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:20.908261 INFO::Starting hierarchical adjustment
2024-09-12 02:55:20.909358 INFO::Found 2 batches.
2024-09-12 02:55:20.910159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:20.911071 INFO::Using default BPPARAM
2024-09-12 02:55:20.911846 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:20.91318 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:20.934767 INFO::Done
2024-09-12 02:55:20.935677 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:20.93983 INFO::ASW Batch was 0.656782477740682 prior to batch effect correction and is now 0.0447675588876622 .
2024-09-12 02:55:20.94074 INFO::ASW Label was 0.469015658746168 prior to batch effect correction and is now 0.891402256739405 .
2024-09-12 02:55:20.941903 INFO::Total function execution time is 0.047605037689209 s and adjustment time is 0.0256273746490479 s ( 53.83 )
2024-09-12 02:55:20.943288 INFO::Formatting Data.
2024-09-12 02:55:20.944352 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:20.945628 INFO::Removing potential empty rows and columns
2024-09-12 02:55:20.947114 INFO::Found 0 missing values.
2024-09-12 02:55:20.951172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:20.952036 INFO::Done
2024-09-12 02:55:20.952908 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:20.957079 INFO::Starting hierarchical adjustment
2024-09-12 02:55:20.958194 INFO::Found 2 batches.
2024-09-12 02:55:20.958955 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:20.959835 INFO::Using default BPPARAM
2024-09-12 02:55:20.960555 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:20.961852 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:20.982805 INFO::Done
2024-09-12 02:55:20.983694 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:20.987637 INFO::ASW Batch was 0.656782477740682 prior to batch effect correction and is now 0.0447675588876622 .
2024-09-12 02:55:20.988501 INFO::ASW Label was 0.469015658746168 prior to batch effect correction and is now 0.891402256739405 .
2024-09-12 02:55:20.989613 INFO::Total function execution time is 0.0465402603149414 s and adjustment time is 0.02482008934021 s ( 53.33 )
2024-09-12 02:55:21.005461 INFO::Formatting Data.
2024-09-12 02:55:21.006565 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:21.00782 INFO::Removing potential empty rows and columns
2024-09-12 02:55:21.009108 INFO::Found 0 missing values.
2024-09-12 02:55:21.012771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:21.013594 INFO::Done
2024-09-12 02:55:21.014364 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:21.016953 INFO::Starting hierarchical adjustment
2024-09-12 02:55:21.018 INFO::Found 2 batches.
2024-09-12 02:55:21.018746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:21.019699 INFO::Using default BPPARAM
2024-09-12 02:55:21.020429 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:21.021727 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:21.066166 INFO::Done
2024-09-12 02:55:21.067075 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:21.069725 INFO::ASW Batch was -0.0243358442878736 prior to batch effect correction and is now -0.137447804539331 .
2024-09-12 02:55:21.070893 INFO::Total function execution time is 0.0655126571655273 s and adjustment time is 0.0483822822570801 s ( 73.85 )
2024-09-12 02:55:21.087359 INFO::Formatting Data.
2024-09-12 02:55:21.088366 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:21.089577 INFO::Removing potential empty rows and columns
2024-09-12 02:55:21.090974 INFO::Found 0 missing values.
2024-09-12 02:55:21.09256 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.
2024-09-12 02:55:21.099527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:21.100383 INFO::Done
2024-09-12 02:55:21.101125 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:21.105203 INFO::Starting hierarchical adjustment
2024-09-12 02:55:21.106346 INFO::Found 2 batches.
2024-09-12 02:55:21.107147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:21.107996 INFO::Using default BPPARAM
2024-09-12 02:55:21.108816 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:21.110179 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:21.156115 INFO::Done
2024-09-12 02:55:21.157034 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:21.161281 INFO::ASW Batch was 0.314151924459034 prior to batch effect correction and is now -0.00555823133317448 .
2024-09-12 02:55:21.162227 INFO::ASW Label was 0.661473609711873 prior to batch effect correction and is now 0.898821346170536 .
2024-09-12 02:55:21.163353 INFO::Total function execution time is 0.0760581493377686 s and adjustment time is 0.0499680042266846 s ( 65.7 )
2024-09-12 02:55:21.164476 INFO::Formatting Data.
2024-09-12 02:55:21.165359 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:21.166709 INFO::Removing potential empty rows and columns
2024-09-12 02:55:21.1682 INFO::Found 0 missing values.
2024-09-12 02:55:21.169575 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.
2024-09-12 02:55:21.176846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:21.177742 INFO::Done
2024-09-12 02:55:21.178512 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:21.182909 INFO::Starting hierarchical adjustment
2024-09-12 02:55:21.184146 INFO::Found 2 batches.
2024-09-12 02:55:21.184945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:21.185851 INFO::Using default BPPARAM
2024-09-12 02:55:21.186641 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:21.188122 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:21.214243 INFO::Done
2024-09-12 02:55:21.215165 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:21.219459 INFO::ASW Batch was 0.314151924459034 prior to batch effect correction and is now -0.00555823133317448 .
2024-09-12 02:55:21.22034 INFO::ASW Label was 0.661473609711873 prior to batch effect correction and is now 0.898821346170536 .
2024-09-12 02:55:21.221479 INFO::Total function execution time is 0.057011604309082 s and adjustment time is 0.0303399562835693 s ( 53.22 )
2024-09-12 02:55:21.549126 INFO::Formatting Data.
2024-09-12 02:55:21.5502 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:21.551478 INFO::Removing potential empty rows and columns
2024-09-12 02:55:21.553061 INFO::Found 0 missing values.
2024-09-12 02:55:21.557941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:21.558809 INFO::Done
2024-09-12 02:55:21.559592 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:21.562446 INFO::Starting hierarchical adjustment
2024-09-12 02:55:21.563565 INFO::Found 3 batches.
2024-09-12 02:55:21.564348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:21.565232 INFO::Using default BPPARAM
2024-09-12 02:55:21.566011 INFO::Processing subtree level 1
2024-09-12 02:55:21.691575 INFO::Adjusting the last 1 batches sequentially
2024-09-12 02:55:21.693943 INFO::Done
2024-09-12 02:55:21.694802 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:21.69824 INFO::ASW Batch was -0.0881612186996515 prior to batch effect correction and is now -0.0881612186996515 .
2024-09-12 02:55:21.699614 INFO::Total function execution time is 0.150475978851318 s and adjustment time is 0.130597591400146 s ( 86.79 )
2024-09-12 02:55:21.701138 INFO::Formatting Data.
2024-09-12 02:55:21.702105 INFO::Typecasting input to dataframe.
2024-09-12 02:55:21.70321 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:21.70452 INFO::Removing potential empty rows and columns
2024-09-12 02:55:21.70611 INFO::Found 0 missing values.
2024-09-12 02:55:21.710754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:21.711647 INFO::Done
2024-09-12 02:55:21.712438 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:21.715382 INFO::Starting hierarchical adjustment
2024-09-12 02:55:21.716488 INFO::Found 3 batches.
2024-09-12 02:55:21.717283 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:21.71821 INFO::Using default BPPARAM
2024-09-12 02:55:21.719022 INFO::Processing subtree level 1
2024-09-12 02:55:21.84231 INFO::Adjusting the last 1 batches sequentially
2024-09-12 02:55:21.844673 INFO::Done
2024-09-12 02:55:21.84558 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:21.84915 INFO::ASW Batch was -0.0881612186996515 prior to batch effect correction and is now -0.0881612186996515 .
2024-09-12 02:55:21.850583 INFO::Total function execution time is 0.149383068084717 s and adjustment time is 0.128376722335815 s ( 85.94 )
2024-09-12 02:55:21.869558 INFO::Formatting Data.
2024-09-12 02:55:21.870655 INFO::Typecasting input to dataframe.
2024-09-12 02:55:21.871948 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:21.873306 INFO::Removing potential empty rows and columns
2024-09-12 02:55:21.875022 INFO::Found 0 missing values.
2024-09-12 02:55:21.879803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:21.880726 INFO::Done
2024-09-12 02:55:21.881544 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:21.884555 INFO::Starting hierarchical adjustment
2024-09-12 02:55:21.885722 INFO::Found 3 batches.
2024-09-12 02:55:21.886621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:21.887711 INFO::Using default BPPARAM
2024-09-12 02:55:21.888527 INFO::Processing subtree level 1
2024-09-12 02:55:22.010326 INFO::Adjusting the last 1 batches sequentially
2024-09-12 02:55:22.012966 INFO::Done
2024-09-12 02:55:22.014006 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:22.017884 INFO::ASW Batch was -0.0710879633572997 prior to batch effect correction and is now -0.0710879633572997 .
2024-09-12 02:55:22.019418 INFO::Total function execution time is 0.149824142456055 s and adjustment time is 0.127478122711182 s ( 85.09 )
2024-09-12 02:55:22.220737 INFO::Formatting Data.
2024-09-12 02:55:22.221987 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:22.223865 INFO::Removing potential empty rows and columns
2024-09-12 02:55:22.22883 INFO::Found 1000 missing values.
2024-09-12 02:55:22.262519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:22.263553 INFO::Done
2024-09-12 02:55:22.264476 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:22.272998 INFO::Starting hierarchical adjustment
2024-09-12 02:55:22.274338 INFO::Found 10 batches.
2024-09-12 02:55:22.275352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:22.276407 INFO::Using default BPPARAM
2024-09-12 02:55:22.277315 INFO::Processing subtree level 1
2024-09-12 02:55:22.465453 INFO::Processing subtree level 2
2024-09-12 02:55:22.732087 INFO::Adjusting the last 1 batches sequentially
2024-09-12 02:55:22.73484 INFO::Done
2024-09-12 02:55:22.735823 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:22.744228 INFO::ASW Batch was 0.508289328974073 prior to batch effect correction and is now 0.508289328974073 .
2024-09-12 02:55:22.745259 INFO::ASW Label was 0.295321519642337 prior to batch effect correction and is now 0.295321519642337 .
2024-09-12 02:55:22.746647 INFO::Total function execution time is 0.525963068008423 s and adjustment time is 0.460809469223022 s ( 87.61 )
2024-09-12 02:55:22.747945 INFO::Formatting Data.
2024-09-12 02:55:22.748905 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:22.750734 INFO::Removing potential empty rows and columns
2024-09-12 02:55:22.755655 INFO::Found 1000 missing values.
2024-09-12 02:55:22.788209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:22.789202 INFO::Done
2024-09-12 02:55:22.790064 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:22.798259 INFO::Starting hierarchical adjustment
2024-09-12 02:55:22.799665 INFO::Found 10 batches.
2024-09-12 02:55:24.52206 INFO::Set up parallel execution backend with 2 workers
2024-09-12 02:55:24.524051 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-09-12 02:55:26.043247 INFO::Adjusting the last 2 batches sequentially
2024-09-12 02:55:26.045335 INFO::Adjusting sequential tree level 1 with 2 batches
2024-09-12 02:55:26.072549 INFO::Done
2024-09-12 02:55:26.073396 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:26.080433 INFO::ASW Batch was 0.508289328974073 prior to batch effect correction and is now 0.508289328974073 .
2024-09-12 02:55:26.081295 INFO::ASW Label was 0.295321519642337 prior to batch effect correction and is now 0.295321519642337 .
2024-09-12 02:55:26.082382 INFO::Total function execution time is 3.33447051048279 s and adjustment time is 3.27319407463074 s ( 98.16 )
2024-09-12 02:55:26.278356 INFO::Formatting Data.
2024-09-12 02:55:26.279519 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:26.280924 INFO::Removing potential empty rows and columns
2024-09-12 02:55:26.282577 INFO::Found 0 missing values.
2024-09-12 02:55:26.288669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:26.28958 INFO::Done
2024-09-12 02:55:26.290378 INFO::Acquiring quality metrics before batch effect correction.
2024-09-12 02:55:26.294499 INFO::Starting hierarchical adjustment
2024-09-12 02:55:26.295678 INFO::Found 3 batches.
2024-09-12 02:55:26.296476 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-09-12 02:55:26.297381 INFO::Using default BPPARAM
2024-09-12 02:55:26.298199 INFO::Processing subtree level 1
2024-09-12 02:55:26.445645 INFO::Adjusting the last 1 batches sequentially
2024-09-12 02:55:26.448114 INFO::Done
2024-09-12 02:55:26.449047 INFO::Acquiring quality metrics after batch effect correction.
2024-09-12 02:55:26.453856 INFO::ASW Batch was 0.114578778691812 prior to batch effect correction and is now -0.1317465510992 .
2024-09-12 02:55:26.454837 INFO::ASW Label was -0.202311631967733 prior to batch effect correction and is now -0.180584283330656 .
2024-09-12 02:55:26.456194 INFO::Total function execution time is 0.177852630615234 s and adjustment time is 0.152649164199829 s ( 85.83 )
2024-09-12 02:55:26.635428 INFO::Formatting Data.
2024-09-12 02:55:26.636543 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:26.637849 INFO::Removing potential empty rows and columns
2024-09-12 02:55:26.639428 INFO::Found 2 missing values.
2024-09-12 02:55:26.643907 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:26.644781 INFO::Done
2024-09-12 02:55:26.685864 INFO::Found NA in Reference column
2024-09-12 02:55:26.700396 INFO::Require at least two references per batch.
2024-09-12 02:55:26.731384 INFO::Formatting Data.
2024-09-12 02:55:26.732348 INFO::Recognized SummarizedExperiment
2024-09-12 02:55:26.733088 INFO::Typecasting input to dataframe.
2024-09-12 02:55:26.748128 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:26.749798 INFO::Removing potential empty rows and columns
2024-09-12 02:55:26.755748 INFO::Found 0 missing values.
2024-09-12 02:55:26.767224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:26.768113 INFO::Done
2024-09-12 02:55:26.790057 INFO::Formatting Data.
2024-09-12 02:55:26.791045 INFO::Recognized SummarizedExperiment
2024-09-12 02:55:26.791754 INFO::Typecasting input to dataframe.
2024-09-12 02:55:26.818924 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:26.820584 INFO::Removing potential empty rows and columns
2024-09-12 02:55:26.826455 INFO::Found 0 missing values.
2024-09-12 02:55:26.844534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:26.845424 INFO::Done
2024-09-12 02:55:26.867592 INFO::Formatting Data.
2024-09-12 02:55:26.868586 INFO::Recognized SummarizedExperiment
2024-09-12 02:55:26.869368 INFO::Typecasting input to dataframe.
2024-09-12 02:55:26.895323 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:26.89672 INFO::Removing potential empty rows and columns
2024-09-12 02:55:26.898352 INFO::Found 0 missing values.
2024-09-12 02:55:26.89975 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.
2024-09-12 02:55:26.906763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:26.907679 INFO::Done
2024-09-12 02:55:26.922096 INFO::Formatting Data.
2024-09-12 02:55:26.923181 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:26.92441 INFO::Removing potential empty rows and columns
2024-09-12 02:55:26.925852 INFO::Found 0 missing values.
2024-09-12 02:55:26.930173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:26.931071 INFO::Done
2024-09-12 02:55:26.947404 INFO::Formatting Data.
2024-09-12 02:55:26.948428 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:26.949636 INFO::Removing potential empty rows and columns
2024-09-12 02:55:26.951122 INFO::Found 0 missing values.
2024-09-12 02:55:26.955547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:26.956442 INFO::Done
2024-09-12 02:55:27.000753 INFO::Formatting Data.
2024-09-12 02:55:27.001801 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:27.003233 INFO::Removing potential empty rows and columns
2024-09-12 02:55:27.004861 INFO::Found 1 missing values.
2024-09-12 02:55:27.008698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:27.009539 INFO::Done
2024-09-12 02:55:27.036711 INFO::Formatting Data.
2024-09-12 02:55:27.037812 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:27.039129 INFO::Removing potential empty rows and columns
2024-09-12 02:55:27.040526 INFO::Found 2 missing values.
2024-09-12 02:55:27.041899 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.
2024-09-12 02:55:27.0454 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:27.046274 INFO::Done
2024-09-12 02:55:27.060888 INFO::Formatting Data.
2024-09-12 02:55:27.061933 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:27.063146 INFO::Removing potential empty rows and columns
2024-09-12 02:55:27.064516 INFO::Found 2 missing values.
2024-09-12 02:55:27.066944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:27.067784 INFO::Done
2024-09-12 02:55:27.083309 INFO::Formatting Data.
2024-09-12 02:55:27.084391 INFO::Typecasting input to dataframe.
2024-09-12 02:55:27.085576 INFO::Replacing NaNs with NAs.
2024-09-12 02:55:27.086852 INFO::Removing potential empty rows and columns
2024-09-12 02:55:27.088395 INFO::Found 0 missing values.
2024-09-12 02:55:27.09293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-09-12 02:55:27.093833 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.986 4.808 26.345
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.703 | 1.759 | 22.817 | |
| compute_asw | 0.027 | 0.032 | 0.059 | |
| count_existing | 0.025 | 0.008 | 0.033 | |
| generate_data_covariables | 0.014 | 0.012 | 0.026 | |
| generate_dataset | 0.017 | 0.008 | 0.025 | |