Yannis Schumann
| Snapshot Date: 2024-11-07 13:40 -0500 (Thu, 07 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-08 12:07 -0500 (Fri, 08 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4765 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | 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 | | ||||||||
| 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: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2024-11-08 05:44:23 -0000 (Fri, 08 Nov 2024) |
| EndedAt: 2024-11-08 05:45:42 -0000 (Fri, 08 Nov 2024) |
| EllapsedTime: 79.1 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_1.2.0.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 ‘1.2.0’
* 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 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 31.277 1.676 22.864
* 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")
2024-11-08 05:45:27.147229 INFO::Formatting Data.
2024-11-08 05:45:27.148918 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:27.165648 INFO::Removing potential empty rows and columns
2024-11-08 05:45:27.517373 INFO::Found 0 missing values.
2024-11-08 05:45:27.521856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:27.522704 INFO::Done
2024-11-08 05:45:27.523456 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:27.538234 INFO::Starting hierarchical adjustment
2024-11-08 05:45:27.539359 INFO::Found 3 batches.
2024-11-08 05:45:27.54008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:27.541553 INFO::Using default BPPARAM
2024-11-08 05:45:27.542331 INFO::Processing subtree level 1
2024-11-08 05:45:27.666881 INFO::Adjusting the last 1 batches sequentially
2024-11-08 05:45:27.66922 INFO::Done
2024-11-08 05:45:27.670121 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:27.673695 INFO::ASW Batch was -0.0450117472856582 prior to batch effect correction and is now -0.0450117472856582 .
2024-11-08 05:45:27.675364 INFO::Total function execution time is 0.528881311416626 s and adjustment time is 0.130093812942505 s ( 24.6 )
2024-11-08 05:45:27.701939 INFO::Formatting Data.
2024-11-08 05:45:27.703031 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:27.704332 INFO::Removing potential empty rows and columns
2024-11-08 05:45:27.70584 INFO::Found 0 missing values.
2024-11-08 05:45:27.707114 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.
2024-11-08 05:45:27.722425 INFO::Formatting Data.
2024-11-08 05:45:27.723489 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:27.724704 INFO::Removing potential empty rows and columns
2024-11-08 05:45:27.726146 INFO::Found 0 missing values.
2024-11-08 05:45:27.72744 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.
2024-11-08 05:45:27.749786 INFO::Formatting Data.
2024-11-08 05:45:27.750766 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:27.751945 INFO::Removing potential empty rows and columns
2024-11-08 05:45:27.753301 INFO::Found 0 missing values.
2024-11-08 05:45:27.754518 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.
2024-11-08 05:45:27.760789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:27.76165 INFO::Done
2024-11-08 05:45:27.762403 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:27.765519 INFO::Starting hierarchical adjustment
2024-11-08 05:45:27.766602 INFO::Found 2 batches.
2024-11-08 05:45:27.767371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:27.768265 INFO::Using default BPPARAM
2024-11-08 05:45:27.76903 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:27.770381 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:27.802331 INFO::Done
2024-11-08 05:45:27.803232 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:27.805972 INFO::ASW Batch was -0.0326035781684869 prior to batch effect correction and is now -0.118961010869161 .
2024-11-08 05:45:27.807015 INFO::Total function execution time is 0.0573203563690186 s and adjustment time is 0.0359277725219727 s ( 62.68 )
2024-11-08 05:45:27.8106 INFO::Formatting Data.
2024-11-08 05:45:27.811502 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:27.823565 INFO::Formatting Data.
2024-11-08 05:45:27.824533 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:27.825684 INFO::Removing potential empty rows and columns
2024-11-08 05:45:27.827132 INFO::Found 0 missing values.
2024-11-08 05:45:27.831221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:27.832047 INFO::Done
2024-11-08 05:45:27.832764 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:27.835703 INFO::Starting hierarchical adjustment
2024-11-08 05:45:27.836711 INFO::Found 2 batches.
2024-11-08 05:45:27.837492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:27.838336 INFO::Using default BPPARAM
2024-11-08 05:45:27.839118 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:27.840472 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:27.860431 INFO::Done
2024-11-08 05:45:27.861254 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:27.863852 INFO::ASW Batch was -0.0124385530749569 prior to batch effect correction and is now -0.121001343810986 .
2024-11-08 05:45:27.864884 INFO::Total function execution time is 0.0413956642150879 s and adjustment time is 0.0239095687866211 s ( 57.76 )
2024-11-08 05:45:27.866285 INFO::Formatting Data.
2024-11-08 05:45:27.867085 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:27.868219 INFO::Removing potential empty rows and columns
2024-11-08 05:45:27.869548 INFO::Found 0 missing values.
2024-11-08 05:45:27.87353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:27.874336 INFO::Done
2024-11-08 05:45:27.875062 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:27.877717 INFO::Starting hierarchical adjustment
2024-11-08 05:45:27.878695 INFO::Found 2 batches.
2024-11-08 05:45:27.879433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:27.880233 INFO::Using default BPPARAM
2024-11-08 05:45:27.880936 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:27.882199 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:27.901919 INFO::Done
2024-11-08 05:45:27.902773 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:27.905404 INFO::ASW Batch was -0.0124385530749569 prior to batch effect correction and is now -0.121001343810986 .
2024-11-08 05:45:27.906481 INFO::Total function execution time is 0.0401849746704102 s and adjustment time is 0.0234034061431885 s ( 58.24 )
2024-11-08 05:45:30.768872 INFO::Formatting Data.
2024-11-08 05:45:30.769711 INFO::Recognized SummarizedExperiment
2024-11-08 05:45:30.770352 INFO::Typecasting input to dataframe.
2024-11-08 05:45:30.812141 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:30.813578 INFO::Removing potential empty rows and columns
2024-11-08 05:45:30.818528 INFO::Found 0 missing values.
2024-11-08 05:45:30.82789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:30.828691 INFO::Done
2024-11-08 05:45:30.829336 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:30.833941 INFO::Starting hierarchical adjustment
2024-11-08 05:45:30.83493 INFO::Found 2 batches.
2024-11-08 05:45:30.835631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:30.836995 INFO::Using default BPPARAM
2024-11-08 05:45:30.837698 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:30.839 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:30.915678 INFO::Done
2024-11-08 05:45:30.916472 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:30.920965 INFO::ASW Batch was 0.00247295272067142 prior to batch effect correction and is now -0.0900992359362437 .
2024-11-08 05:45:30.922099 INFO::Total function execution time is 0.153631687164307 s and adjustment time is 0.0809221267700195 s ( 52.67 )
2024-11-08 05:45:30.944788 INFO::Formatting Data.
2024-11-08 05:45:30.945664 INFO::Recognized SummarizedExperiment
2024-11-08 05:45:30.946363 INFO::Typecasting input to dataframe.
2024-11-08 05:45:30.958704 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:30.960224 INFO::Removing potential empty rows and columns
2024-11-08 05:45:30.965313 INFO::Found 0 missing values.
2024-11-08 05:45:30.97521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:30.976056 INFO::Done
2024-11-08 05:45:30.976743 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:30.981377 INFO::Starting hierarchical adjustment
2024-11-08 05:45:30.982409 INFO::Found 2 batches.
2024-11-08 05:45:30.983105 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:30.983872 INFO::Using default BPPARAM
2024-11-08 05:45:30.984532 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:30.985794 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:31.018172 INFO::Done
2024-11-08 05:45:31.01897 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:31.023432 INFO::ASW Batch was 0.0087369837313458 prior to batch effect correction and is now 0.0087369837313458 .
2024-11-08 05:45:31.024526 INFO::Total function execution time is 0.0796899795532227 s and adjustment time is 0.0359418392181396 s ( 45.1 )
2024-11-08 05:45:31.046646 INFO::Formatting Data.
2024-11-08 05:45:31.047562 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:31.04863 INFO::Removing potential empty rows and columns
2024-11-08 05:45:31.049895 INFO::Found 0 missing values.
2024-11-08 05:45:31.053597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:31.054383 INFO::Done
2024-11-08 05:45:31.055053 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:31.057465 INFO::Starting hierarchical adjustment
2024-11-08 05:45:31.058364 INFO::Found 3 batches.
2024-11-08 05:45:31.059025 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:31.059808 INFO::Using default BPPARAM
2024-11-08 05:45:31.06047 INFO::Processing subtree level 1
2024-11-08 05:45:31.2609 INFO::Adjusting the last 1 batches sequentially
2024-11-08 05:45:31.263338 INFO::Done
2024-11-08 05:45:31.264253 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:31.267697 INFO::ASW Batch was -0.0377004455757581 prior to batch effect correction and is now -0.164994912518911 .
2024-11-08 05:45:31.26909 INFO::Total function execution time is 0.222419500350952 s and adjustment time is 0.205124616622925 s ( 92.22 )
2024-11-08 05:45:31.290383 INFO::Skipping initial DF formatting
2024-11-08 05:45:31.291389 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:31.297295 INFO::Starting hierarchical adjustment
2024-11-08 05:45:31.298536 INFO::Found 5 batches.
2024-11-08 05:45:31.299437 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:31.300364 INFO::Using default BPPARAM
2024-11-08 05:45:31.30116 INFO::Processing subtree level 1
2024-11-08 05:45:31.474184 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:31.476362 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:31.507949 INFO::Done
2024-11-08 05:45:31.508848 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:31.515021 INFO::ASW Batch was 0.472915137056485 prior to batch effect correction and is now 0.472915137056485 .
2024-11-08 05:45:31.515953 INFO::ASW Label was 0.39416199863824 prior to batch effect correction and is now 0.39416199863824 .
2024-11-08 05:45:31.517119 INFO::Total function execution time is 0.226797342300415 s and adjustment time is 0.209640979766846 s ( 92.44 )
2024-11-08 05:45:31.548063 INFO::Formatting Data.
2024-11-08 05:45:31.549084 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:31.55034 INFO::Removing potential empty rows and columns
2024-11-08 05:45:31.551714 INFO::Found 0 missing values.
2024-11-08 05:45:31.557684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:31.55857 INFO::Done
2024-11-08 05:45:31.559632 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:31.564221 INFO::Starting hierarchical adjustment
2024-11-08 05:45:31.565329 INFO::Found 5 batches.
2024-11-08 05:45:31.566108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:31.566984 INFO::Using default BPPARAM
2024-11-08 05:45:31.567758 INFO::Processing subtree level 1
2024-11-08 05:45:31.714352 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:31.716997 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:31.741611 INFO::Done
2024-11-08 05:45:31.742647 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:31.747741 INFO::ASW Batch was 0.25205708612164 prior to batch effect correction and is now -0.0851962660090406 .
2024-11-08 05:45:31.748851 INFO::ASW Label was 0.356058859210827 prior to batch effect correction and is now 0.847230226737525 .
2024-11-08 05:45:31.750303 INFO::Total function execution time is 0.202228546142578 s and adjustment time is 0.176465272903442 s ( 87.26 )
2024-11-08 05:45:31.751757 INFO::Formatting Data.
2024-11-08 05:45:31.752987 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:31.754467 INFO::Removing potential empty rows and columns
2024-11-08 05:45:31.756174 INFO::Found 0 missing values.
2024-11-08 05:45:31.763087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:31.764077 INFO::Done
2024-11-08 05:45:31.764963 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:31.769628 INFO::Starting hierarchical adjustment
2024-11-08 05:45:31.771016 INFO::Found 5 batches.
2024-11-08 05:45:31.772016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:31.773045 INFO::Using default BPPARAM
2024-11-08 05:45:31.77395 INFO::Processing subtree level 1
2024-11-08 05:45:31.918607 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:31.920929 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:31.943386 INFO::Done
2024-11-08 05:45:31.944343 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:31.948988 INFO::ASW Batch was 0.25205708612164 prior to batch effect correction and is now -0.0851962660090406 .
2024-11-08 05:45:31.94994 INFO::ASW Label was 0.356058859210827 prior to batch effect correction and is now 0.847230226737525 .
2024-11-08 05:45:31.951143 INFO::Total function execution time is 0.199402332305908 s and adjustment time is 0.172706842422485 s ( 86.61 )
2024-11-08 05:45:31.970694 INFO::Formatting Data.
2024-11-08 05:45:31.971789 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:31.973081 INFO::Removing potential empty rows and columns
2024-11-08 05:45:31.974525 INFO::Found 0 missing values.
2024-11-08 05:45:31.981006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:31.98198 INFO::Done
2024-11-08 05:45:31.982757 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:31.987151 INFO::Starting hierarchical adjustment
2024-11-08 05:45:31.988388 INFO::Found 5 batches.
2024-11-08 05:45:31.989195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:31.990093 INFO::Using default BPPARAM
2024-11-08 05:45:31.99089 INFO::Processing subtree level 1
2024-11-08 05:45:32.191198 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:32.193403 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:32.216396 INFO::Done
2024-11-08 05:45:32.217303 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:32.221725 INFO::ASW Batch was 0.329501775678227 prior to batch effect correction and is now -0.0639407536144155 .
2024-11-08 05:45:32.222697 INFO::ASW Label was 0.37891362103406 prior to batch effect correction and is now 0.848028910659138 .
2024-11-08 05:45:32.223952 INFO::Total function execution time is 0.25326681137085 s and adjustment time is 0.228257179260254 s ( 90.13 )
2024-11-08 05:45:32.22517 INFO::Formatting Data.
2024-11-08 05:45:32.226061 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:32.227314 INFO::Removing potential empty rows and columns
2024-11-08 05:45:32.228718 INFO::Found 0 missing values.
2024-11-08 05:45:32.234789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:32.235733 INFO::Done
2024-11-08 05:45:32.236493 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:32.270937 INFO::Starting hierarchical adjustment
2024-11-08 05:45:32.272125 INFO::Found 5 batches.
2024-11-08 05:45:32.272884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:32.273721 INFO::Using default BPPARAM
2024-11-08 05:45:32.27445 INFO::Processing subtree level 1
2024-11-08 05:45:32.437444 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:32.439635 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:32.464428 INFO::Done
2024-11-08 05:45:32.465412 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:32.470525 INFO::ASW Batch was 0.329501775678227 prior to batch effect correction and is now -0.0639407536144155 .
2024-11-08 05:45:32.471471 INFO::ASW Label was 0.37891362103406 prior to batch effect correction and is now 0.848028910659138 .
2024-11-08 05:45:32.472684 INFO::Total function execution time is 0.247496604919434 s and adjustment time is 0.192532300949097 s ( 77.79 )
2024-11-08 05:45:32.494061 INFO::Formatting Data.
2024-11-08 05:45:32.495134 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:32.496443 INFO::Removing potential empty rows and columns
2024-11-08 05:45:32.498089 INFO::Found 0 missing values.
2024-11-08 05:45:32.502716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:32.503604 INFO::Done
2024-11-08 05:45:32.504413 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:32.508837 INFO::Starting hierarchical adjustment
2024-11-08 05:45:32.509983 INFO::Found 2 batches.
2024-11-08 05:45:32.510789 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:32.511738 INFO::Using default BPPARAM
2024-11-08 05:45:32.512514 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:32.513964 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:32.536695 INFO::Done
2024-11-08 05:45:32.537657 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:32.542215 INFO::ASW Batch was 0.688242666321273 prior to batch effect correction and is now 0.000244763974717885 .
2024-11-08 05:45:32.543164 INFO::ASW Label was 0.263409609652542 prior to batch effect correction and is now 0.822869113435008 .
2024-11-08 05:45:32.54438 INFO::Total function execution time is 0.0504100322723389 s and adjustment time is 0.0269417762756348 s ( 53.45 )
2024-11-08 05:45:32.545518 INFO::Formatting Data.
2024-11-08 05:45:32.546474 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:32.552037 INFO::Removing potential empty rows and columns
2024-11-08 05:45:32.553938 INFO::Found 0 missing values.
2024-11-08 05:45:32.558501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:32.559458 INFO::Done
2024-11-08 05:45:32.56029 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:32.564943 INFO::Starting hierarchical adjustment
2024-11-08 05:45:32.566103 INFO::Found 2 batches.
2024-11-08 05:45:32.56691 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:32.567893 INFO::Using default BPPARAM
2024-11-08 05:45:32.568729 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:32.570197 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:32.592827 INFO::Done
2024-11-08 05:45:32.593769 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:32.598268 INFO::ASW Batch was 0.688242666321273 prior to batch effect correction and is now 0.000244763974717885 .
2024-11-08 05:45:32.599269 INFO::ASW Label was 0.263409609652542 prior to batch effect correction and is now 0.822869113435008 .
2024-11-08 05:45:32.600413 INFO::Total function execution time is 0.0548996925354004 s and adjustment time is 0.0269701480865479 s ( 49.13 )
2024-11-08 05:45:32.617886 INFO::Formatting Data.
2024-11-08 05:45:32.618945 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:32.62028 INFO::Removing potential empty rows and columns
2024-11-08 05:45:32.621706 INFO::Found 0 missing values.
2024-11-08 05:45:32.625253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:32.626156 INFO::Done
2024-11-08 05:45:32.627058 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:32.629971 INFO::Starting hierarchical adjustment
2024-11-08 05:45:32.631127 INFO::Found 2 batches.
2024-11-08 05:45:32.632005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:32.632935 INFO::Using default BPPARAM
2024-11-08 05:45:32.633786 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:32.63522 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:32.683782 INFO::Done
2024-11-08 05:45:32.684712 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:32.687613 INFO::ASW Batch was -0.130847423854796 prior to batch effect correction and is now -0.165820504583122 .
2024-11-08 05:45:32.688934 INFO::Total function execution time is 0.0711243152618408 s and adjustment time is 0.0528790950775146 s ( 74.35 )
2024-11-08 05:45:32.70816 INFO::Formatting Data.
2024-11-08 05:45:32.709434 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:32.710799 INFO::Removing potential empty rows and columns
2024-11-08 05:45:32.712416 INFO::Found 0 missing values.
2024-11-08 05:45:32.714268 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.
2024-11-08 05:45:32.721877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:32.722855 INFO::Done
2024-11-08 05:45:32.723728 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:32.728468 INFO::Starting hierarchical adjustment
2024-11-08 05:45:32.729774 INFO::Found 2 batches.
2024-11-08 05:45:32.730654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:32.731756 INFO::Using default BPPARAM
2024-11-08 05:45:32.732592 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:32.734192 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:32.761479 INFO::Done
2024-11-08 05:45:32.762697 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:32.767901 INFO::ASW Batch was 0.762773950201197 prior to batch effect correction and is now 0.163619018257529 .
2024-11-08 05:45:32.76897 INFO::ASW Label was 0.344150380930971 prior to batch effect correction and is now 0.803464122892946 .
2024-11-08 05:45:32.770268 INFO::Total function execution time is 0.0621542930603027 s and adjustment time is 0.0319654941558838 s ( 51.43 )
2024-11-08 05:45:32.771571 INFO::Formatting Data.
2024-11-08 05:45:32.772639 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:32.774306 INFO::Removing potential empty rows and columns
2024-11-08 05:45:32.776223 INFO::Found 0 missing values.
2024-11-08 05:45:32.777864 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.
2024-11-08 05:45:32.785244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:32.786202 INFO::Done
2024-11-08 05:45:32.786971 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:32.791244 INFO::Starting hierarchical adjustment
2024-11-08 05:45:32.792354 INFO::Found 2 batches.
2024-11-08 05:45:32.793123 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:32.79399 INFO::Using default BPPARAM
2024-11-08 05:45:32.794739 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:32.796123 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:32.820138 INFO::Done
2024-11-08 05:45:32.82105 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:32.825342 INFO::ASW Batch was 0.762773950201197 prior to batch effect correction and is now 0.163619018257529 .
2024-11-08 05:45:32.826306 INFO::ASW Label was 0.344150380930971 prior to batch effect correction and is now 0.803464122892946 .
2024-11-08 05:45:32.827451 INFO::Total function execution time is 0.055922269821167 s and adjustment time is 0.0279967784881592 s ( 50.06 )
2024-11-08 05:45:33.154783 INFO::Formatting Data.
2024-11-08 05:45:33.156163 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:33.157531 INFO::Removing potential empty rows and columns
2024-11-08 05:45:33.15916 INFO::Found 0 missing values.
2024-11-08 05:45:33.164059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:33.164975 INFO::Done
2024-11-08 05:45:33.165813 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:33.168995 INFO::Starting hierarchical adjustment
2024-11-08 05:45:33.170176 INFO::Found 3 batches.
2024-11-08 05:45:33.170993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:33.171937 INFO::Using default BPPARAM
2024-11-08 05:45:33.172737 INFO::Processing subtree level 1
2024-11-08 05:45:33.339545 INFO::Adjusting the last 1 batches sequentially
2024-11-08 05:45:33.342547 INFO::Done
2024-11-08 05:45:33.343619 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:33.347519 INFO::ASW Batch was -0.0611658734319106 prior to batch effect correction and is now -0.0611658734319106 .
2024-11-08 05:45:33.349229 INFO::Total function execution time is 0.194709062576294 s and adjustment time is 0.172617435455322 s ( 88.65 )
2024-11-08 05:45:33.351155 INFO::Formatting Data.
2024-11-08 05:45:33.352303 INFO::Typecasting input to dataframe.
2024-11-08 05:45:33.353538 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:33.354984 INFO::Removing potential empty rows and columns
2024-11-08 05:45:33.356964 INFO::Found 0 missing values.
2024-11-08 05:45:33.362396 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:33.363681 INFO::Done
2024-11-08 05:45:33.364704 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:33.368123 INFO::Starting hierarchical adjustment
2024-11-08 05:45:33.369499 INFO::Found 3 batches.
2024-11-08 05:45:33.370559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:33.371648 INFO::Using default BPPARAM
2024-11-08 05:45:33.372558 INFO::Processing subtree level 1
2024-11-08 05:45:33.546465 INFO::Adjusting the last 1 batches sequentially
2024-11-08 05:45:33.549053 INFO::Done
2024-11-08 05:45:33.550125 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:33.554141 INFO::ASW Batch was -0.0611658734319106 prior to batch effect correction and is now -0.0611658734319106 .
2024-11-08 05:45:33.555697 INFO::Total function execution time is 0.204682588577271 s and adjustment time is 0.179913520812988 s ( 87.9 )
2024-11-08 05:45:33.575398 INFO::Formatting Data.
2024-11-08 05:45:33.576555 INFO::Typecasting input to dataframe.
2024-11-08 05:45:33.577862 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:33.579257 INFO::Removing potential empty rows and columns
2024-11-08 05:45:33.580878 INFO::Found 0 missing values.
2024-11-08 05:45:33.585585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:33.586535 INFO::Done
2024-11-08 05:45:33.587352 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:33.590237 INFO::Starting hierarchical adjustment
2024-11-08 05:45:33.591352 INFO::Found 3 batches.
2024-11-08 05:45:33.592154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:33.593077 INFO::Using default BPPARAM
2024-11-08 05:45:33.593892 INFO::Processing subtree level 1
2024-11-08 05:45:33.772327 INFO::Adjusting the last 1 batches sequentially
2024-11-08 05:45:33.774872 INFO::Done
2024-11-08 05:45:33.77587 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:33.779884 INFO::ASW Batch was 0.0213313149781981 prior to batch effect correction and is now 0.0213313149781981 .
2024-11-08 05:45:33.781336 INFO::Total function execution time is 0.205952405929565 s and adjustment time is 0.183740854263306 s ( 89.22 )
2024-11-08 05:45:34.003373 INFO::Formatting Data.
2024-11-08 05:45:34.004557 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:34.006246 INFO::Removing potential empty rows and columns
2024-11-08 05:45:34.011197 INFO::Found 1000 missing values.
2024-11-08 05:45:34.043329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:34.044289 INFO::Done
2024-11-08 05:45:34.045055 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:34.05311 INFO::Starting hierarchical adjustment
2024-11-08 05:45:34.054345 INFO::Found 10 batches.
2024-11-08 05:45:34.05517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:34.05612 INFO::Using default BPPARAM
2024-11-08 05:45:34.056994 INFO::Processing subtree level 1
2024-11-08 05:45:34.262529 INFO::Processing subtree level 2
2024-11-08 05:45:34.501841 INFO::Adjusting the last 1 batches sequentially
2024-11-08 05:45:34.504857 INFO::Done
2024-11-08 05:45:34.506017 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:34.517838 INFO::ASW Batch was 0.550210220142614 prior to batch effect correction and is now 0.550210220142614 .
2024-11-08 05:45:34.518932 INFO::ASW Label was 0.290058776869003 prior to batch effect correction and is now 0.290058776869002 .
2024-11-08 05:45:34.520555 INFO::Total function execution time is 0.517197847366333 s and adjustment time is 0.450704574584961 s ( 87.14 )
2024-11-08 05:45:34.521987 INFO::Formatting Data.
2024-11-08 05:45:34.523113 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:34.525436 INFO::Removing potential empty rows and columns
2024-11-08 05:45:34.530874 INFO::Found 1000 missing values.
2024-11-08 05:45:34.566293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:34.567539 INFO::Done
2024-11-08 05:45:34.568536 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:34.577156 INFO::Starting hierarchical adjustment
2024-11-08 05:45:34.578592 INFO::Found 10 batches.
2024-11-08 05:45:35.930258 INFO::Set up parallel execution backend with 2 workers
2024-11-08 05:45:35.931859 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-08 05:45:37.373127 INFO::Adjusting the last 2 batches sequentially
2024-11-08 05:45:37.375096 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 05:45:37.40073 INFO::Done
2024-11-08 05:45:37.401548 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:37.408333 INFO::ASW Batch was 0.550210220142614 prior to batch effect correction and is now 0.550210220142614 .
2024-11-08 05:45:37.409197 INFO::ASW Label was 0.290058776869003 prior to batch effect correction and is now 0.290058776869002 .
2024-11-08 05:45:37.41023 INFO::Total function execution time is 2.88837242126465 s and adjustment time is 2.8225109577179 s ( 97.72 )
2024-11-08 05:45:37.598515 INFO::Formatting Data.
2024-11-08 05:45:37.599703 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:37.601145 INFO::Removing potential empty rows and columns
2024-11-08 05:45:37.602773 INFO::Found 0 missing values.
2024-11-08 05:45:37.608948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:37.609877 INFO::Done
2024-11-08 05:45:37.610706 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 05:45:37.614931 INFO::Starting hierarchical adjustment
2024-11-08 05:45:37.616091 INFO::Found 3 batches.
2024-11-08 05:45:37.616955 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 05:45:37.617846 INFO::Using default BPPARAM
2024-11-08 05:45:37.618698 INFO::Processing subtree level 1
2024-11-08 05:45:37.754233 INFO::Adjusting the last 1 batches sequentially
2024-11-08 05:45:37.756628 INFO::Done
2024-11-08 05:45:37.757422 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 05:45:37.761965 INFO::ASW Batch was 0.311475607472019 prior to batch effect correction and is now -0.140999928762673 .
2024-11-08 05:45:37.762896 INFO::ASW Label was -0.208880833161643 prior to batch effect correction and is now -0.0868889291126388 .
2024-11-08 05:45:37.764189 INFO::Total function execution time is 0.165719032287598 s and adjustment time is 0.140766620635986 s ( 84.94 )
2024-11-08 05:45:37.953923 INFO::Formatting Data.
2024-11-08 05:45:37.955165 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:37.956471 INFO::Removing potential empty rows and columns
2024-11-08 05:45:37.958118 INFO::Found 2 missing values.
2024-11-08 05:45:37.962714 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:37.963655 INFO::Done
2024-11-08 05:45:38.007303 INFO::Found NA in Reference column
2024-11-08 05:45:38.022519 INFO::Require at least two references per batch.
2024-11-08 05:45:38.055762 INFO::Formatting Data.
2024-11-08 05:45:38.056811 INFO::Recognized SummarizedExperiment
2024-11-08 05:45:38.057583 INFO::Typecasting input to dataframe.
2024-11-08 05:45:38.073669 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.075551 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.081716 INFO::Found 0 missing values.
2024-11-08 05:45:38.093562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.094491 INFO::Done
2024-11-08 05:45:38.118767 INFO::Formatting Data.
2024-11-08 05:45:38.119799 INFO::Recognized SummarizedExperiment
2024-11-08 05:45:38.12073 INFO::Typecasting input to dataframe.
2024-11-08 05:45:38.149539 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.151341 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.157351 INFO::Found 0 missing values.
2024-11-08 05:45:38.176567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.177495 INFO::Done
2024-11-08 05:45:38.202365 INFO::Formatting Data.
2024-11-08 05:45:38.203544 INFO::Recognized SummarizedExperiment
2024-11-08 05:45:38.204473 INFO::Typecasting input to dataframe.
2024-11-08 05:45:38.233304 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.234845 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.236672 INFO::Found 0 missing values.
2024-11-08 05:45:38.238115 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.
2024-11-08 05:45:38.245573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.246634 INFO::Done
2024-11-08 05:45:38.270161 INFO::Formatting Data.
2024-11-08 05:45:38.271528 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.272994 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.274718 INFO::Found 0 missing values.
2024-11-08 05:45:38.280334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.28133 INFO::Done
2024-11-08 05:45:38.299217 INFO::Formatting Data.
2024-11-08 05:45:38.300452 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.301808 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.303488 INFO::Found 0 missing values.
2024-11-08 05:45:38.308374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.309329 INFO::Done
2024-11-08 05:45:38.355019 INFO::Formatting Data.
2024-11-08 05:45:38.356198 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.358141 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.36007 INFO::Found 1 missing values.
2024-11-08 05:45:38.364771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.365731 INFO::Done
2024-11-08 05:45:38.395512 INFO::Formatting Data.
2024-11-08 05:45:38.39667 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.39806 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.39964 INFO::Found 2 missing values.
2024-11-08 05:45:38.401097 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.
2024-11-08 05:45:38.404726 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.405662 INFO::Done
2024-11-08 05:45:38.421566 INFO::Formatting Data.
2024-11-08 05:45:38.422746 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.424296 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.425966 INFO::Found 2 missing values.
2024-11-08 05:45:38.428812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.429827 INFO::Done
2024-11-08 05:45:38.447966 INFO::Formatting Data.
2024-11-08 05:45:38.449268 INFO::Typecasting input to dataframe.
2024-11-08 05:45:38.450958 INFO::Replacing NaNs with NAs.
2024-11-08 05:45:38.452431 INFO::Removing potential empty rows and columns
2024-11-08 05:45:38.454336 INFO::Found 0 missing values.
2024-11-08 05:45:38.459898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 05:45:38.460903 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.694 4.892 25.946
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.277 | 1.676 | 22.864 | |
| compute_asw | 0.037 | 0.004 | 0.041 | |
| count_existing | 0.019 | 0.004 | 0.023 | |
| generate_data_covariables | 0.020 | 0.000 | 0.019 | |
| generate_dataset | 0.018 | 0.000 | 0.018 | |