Yannis Schumann
| Snapshot Date: 2024-10-02 13:40 -0400 (Wed, 02 Oct 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 2024-10-03 11:41 -0400 (Thu, 03 Oct 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" | 4461 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| 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 158/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 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. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-10-02 20:13:57 -0400 (Wed, 02 Oct 2024) |
| EndedAt: 2024-10-02 20:15:27 -0400 (Wed, 02 Oct 2024) |
| EllapsedTime: 89.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --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: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 25.172 1.262 18.662
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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: x86_64-pc-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")
2024-10-02 20:14:49.214918 INFO::Formatting Data.
2024-10-02 20:14:49.216451 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:49.228459 INFO::Removing potential empty rows and columns
2024-10-02 20:14:49.489455 INFO::Found 0 missing values.
2024-10-02 20:14:49.492858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:49.493506 INFO::Done
2024-10-02 20:14:49.494043 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:49.505997 INFO::Starting hierarchical adjustment
2024-10-02 20:14:49.506844 INFO::Found 3 batches.
2024-10-02 20:14:49.507397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:49.508612 INFO::Using default BPPARAM
2024-10-02 20:14:49.509182 INFO::Processing subtree level 1
2024-10-02 20:14:49.609576 INFO::Adjusting the last 1 batches sequentially
2024-10-02 20:14:49.611344 INFO::Done
2024-10-02 20:14:49.611996 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:49.614606 INFO::ASW Batch was -0.0132874351530301 prior to batch effect correction and is now -0.0132874351530301 .
2024-10-02 20:14:49.615653 INFO::Total function execution time is 0.401490449905396 s and adjustment time is 0.104672908782959 s ( 26.07 )
2024-10-02 20:14:49.628881 INFO::Formatting Data.
2024-10-02 20:14:49.629591 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:49.630501 INFO::Removing potential empty rows and columns
2024-10-02 20:14:49.631551 INFO::Found 0 missing values.
2024-10-02 20:14:49.632457 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.
2024-10-02 20:14:49.643374 INFO::Formatting Data.
2024-10-02 20:14:49.64405 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:49.644912 INFO::Removing potential empty rows and columns
2024-10-02 20:14:49.645939 INFO::Found 0 missing values.
2024-10-02 20:14:49.646843 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.
2024-10-02 20:14:49.662747 INFO::Formatting Data.
2024-10-02 20:14:49.663472 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:49.664313 INFO::Removing potential empty rows and columns
2024-10-02 20:14:49.665335 INFO::Found 0 missing values.
2024-10-02 20:14:49.666238 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.
2024-10-02 20:14:49.671095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:49.671644 INFO::Done
2024-10-02 20:14:49.672136 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:49.674171 INFO::Starting hierarchical adjustment
2024-10-02 20:14:49.674864 INFO::Found 2 batches.
2024-10-02 20:14:49.675364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:49.675983 INFO::Using default BPPARAM
2024-10-02 20:14:49.676499 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:49.677401 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:49.699777 INFO::Done
2024-10-02 20:14:49.700427 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:49.702491 INFO::ASW Batch was -0.0446134330670989 prior to batch effect correction and is now -0.121976352211291 .
2024-10-02 20:14:49.703282 INFO::Total function execution time is 0.0405895709991455 s and adjustment time is 0.0250232219696045 s ( 61.65 )
2024-10-02 20:14:49.706188 INFO::Formatting Data.
2024-10-02 20:14:49.706828 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:49.716447 INFO::Formatting Data.
2024-10-02 20:14:49.717186 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:49.718104 INFO::Removing potential empty rows and columns
2024-10-02 20:14:49.719137 INFO::Found 0 missing values.
2024-10-02 20:14:49.72219 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:49.722748 INFO::Done
2024-10-02 20:14:49.723254 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:49.725275 INFO::Starting hierarchical adjustment
2024-10-02 20:14:49.726014 INFO::Found 2 batches.
2024-10-02 20:14:49.726526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:49.727146 INFO::Using default BPPARAM
2024-10-02 20:14:49.727663 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:49.7286 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:49.743497 INFO::Done
2024-10-02 20:14:49.744076 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:49.746072 INFO::ASW Batch was 0.0617715160008347 prior to batch effect correction and is now -0.126204809701052 .
2024-10-02 20:14:49.746826 INFO::Total function execution time is 0.0304474830627441 s and adjustment time is 0.017646312713623 s ( 57.96 )
2024-10-02 20:14:49.747825 INFO::Formatting Data.
2024-10-02 20:14:49.748394 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:49.749211 INFO::Removing potential empty rows and columns
2024-10-02 20:14:49.750191 INFO::Found 0 missing values.
2024-10-02 20:14:49.752992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:49.75349 INFO::Done
2024-10-02 20:14:49.753962 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:49.755886 INFO::Starting hierarchical adjustment
2024-10-02 20:14:49.756549 INFO::Found 2 batches.
2024-10-02 20:14:49.757033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:49.757601 INFO::Using default BPPARAM
2024-10-02 20:14:49.758092 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:49.758946 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:49.773661 INFO::Done
2024-10-02 20:14:49.77426 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:49.776312 INFO::ASW Batch was 0.0617715160008347 prior to batch effect correction and is now -0.126204809701052 .
2024-10-02 20:14:49.777095 INFO::Total function execution time is 0.0292541980743408 s and adjustment time is 0.0172505378723145 s ( 58.97 )
2024-10-02 20:14:51.97114 INFO::Formatting Data.
2024-10-02 20:14:51.971979 INFO::Recognized SummarizedExperiment
2024-10-02 20:14:51.97244 INFO::Typecasting input to dataframe.
2024-10-02 20:14:52.003582 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:52.004867 INFO::Removing potential empty rows and columns
2024-10-02 20:14:52.0082 INFO::Found 0 missing values.
2024-10-02 20:14:52.014259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:52.014833 INFO::Done
2024-10-02 20:14:52.015264 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:52.018402 INFO::Starting hierarchical adjustment
2024-10-02 20:14:52.019046 INFO::Found 2 batches.
2024-10-02 20:14:52.019493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:52.02054 INFO::Using default BPPARAM
2024-10-02 20:14:52.021014 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:52.021918 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:52.072152 INFO::Done
2024-10-02 20:14:52.072793 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:52.075796 INFO::ASW Batch was 0.0414420763884412 prior to batch effect correction and is now -0.103672888317623 .
2024-10-02 20:14:52.076571 INFO::Total function execution time is 0.105778455734253 s and adjustment time is 0.0532205104827881 s ( 50.31 )
2024-10-02 20:14:52.092538 INFO::Formatting Data.
2024-10-02 20:14:52.093205 INFO::Recognized SummarizedExperiment
2024-10-02 20:14:52.093682 INFO::Typecasting input to dataframe.
2024-10-02 20:14:52.10193 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:52.102975 INFO::Removing potential empty rows and columns
2024-10-02 20:14:52.106129 INFO::Found 0 missing values.
2024-10-02 20:14:52.112211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:52.112727 INFO::Done
2024-10-02 20:14:52.113175 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:52.116337 INFO::Starting hierarchical adjustment
2024-10-02 20:14:52.11698 INFO::Found 2 batches.
2024-10-02 20:14:52.117427 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:52.117964 INFO::Using default BPPARAM
2024-10-02 20:14:52.118397 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:52.119285 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:52.140656 INFO::Done
2024-10-02 20:14:52.141297 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:52.144302 INFO::ASW Batch was -0.0104314139049131 prior to batch effect correction and is now -0.0104314139049131 .
2024-10-02 20:14:52.145054 INFO::Total function execution time is 0.0525379180908203 s and adjustment time is 0.0237867832183838 s ( 45.28 )
2024-10-02 20:14:52.161343 INFO::Formatting Data.
2024-10-02 20:14:52.16204 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:52.162863 INFO::Removing potential empty rows and columns
2024-10-02 20:14:52.163822 INFO::Found 0 missing values.
2024-10-02 20:14:52.166382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:52.166852 INFO::Done
2024-10-02 20:14:52.167284 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:52.169097 INFO::Starting hierarchical adjustment
2024-10-02 20:14:52.169705 INFO::Found 3 batches.
2024-10-02 20:14:52.170149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:52.170656 INFO::Using default BPPARAM
2024-10-02 20:14:52.171095 INFO::Processing subtree level 1
2024-10-02 20:14:52.323365 INFO::Adjusting the last 1 batches sequentially
2024-10-02 20:14:52.325209 INFO::Done
2024-10-02 20:14:52.325886 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:52.328418 INFO::ASW Batch was -0.0261580567809639 prior to batch effect correction and is now -0.149648623265482 .
2024-10-02 20:14:52.329381 INFO::Total function execution time is 0.16804313659668 s and adjustment time is 0.155593156814575 s ( 92.59 )
2024-10-02 20:14:52.344737 INFO::Skipping initial DF formatting
2024-10-02 20:14:52.345451 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:52.349555 INFO::Starting hierarchical adjustment
2024-10-02 20:14:52.350343 INFO::Found 5 batches.
2024-10-02 20:14:52.350872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:52.35146 INFO::Using default BPPARAM
2024-10-02 20:14:52.351973 INFO::Processing subtree level 1
2024-10-02 20:14:52.513455 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:52.51546 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:52.538016 INFO::Done
2024-10-02 20:14:52.538815 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:52.543251 INFO::ASW Batch was 0.47507886445438 prior to batch effect correction and is now 0.47507886445438 .
2024-10-02 20:14:52.54399 INFO::ASW Label was 0.39235762270228 prior to batch effect correction and is now 0.39235762270228 .
2024-10-02 20:14:52.544886 INFO::Total function execution time is 0.200249195098877 s and adjustment time is 0.187766313552856 s ( 93.77 )
2024-10-02 20:14:52.564707 INFO::Formatting Data.
2024-10-02 20:14:52.565612 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:52.566559 INFO::Removing potential empty rows and columns
2024-10-02 20:14:52.567583 INFO::Found 0 missing values.
2024-10-02 20:14:52.57165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:52.572187 INFO::Done
2024-10-02 20:14:52.572697 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:52.57582 INFO::Starting hierarchical adjustment
2024-10-02 20:14:52.576548 INFO::Found 5 batches.
2024-10-02 20:14:52.577081 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:52.577681 INFO::Using default BPPARAM
2024-10-02 20:14:52.578197 INFO::Processing subtree level 1
2024-10-02 20:14:52.720086 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:52.722013 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:52.739681 INFO::Done
2024-10-02 20:14:52.740611 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:52.744238 INFO::ASW Batch was 0.203943718813765 prior to batch effect correction and is now -0.0523389272620866 .
2024-10-02 20:14:52.744875 INFO::ASW Label was 0.624731466077016 prior to batch effect correction and is now 0.822683957908105 .
2024-10-02 20:14:52.745707 INFO::Total function execution time is 0.181166648864746 s and adjustment time is 0.163220167160034 s ( 90.09 )
2024-10-02 20:14:52.74655 INFO::Formatting Data.
2024-10-02 20:14:52.74714 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:52.748022 INFO::Removing potential empty rows and columns
2024-10-02 20:14:52.749014 INFO::Found 0 missing values.
2024-10-02 20:14:52.753078 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:52.753622 INFO::Done
2024-10-02 20:14:52.75411 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:52.757124 INFO::Starting hierarchical adjustment
2024-10-02 20:14:52.757827 INFO::Found 5 batches.
2024-10-02 20:14:52.7583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:52.758894 INFO::Using default BPPARAM
2024-10-02 20:14:52.759361 INFO::Processing subtree level 1
2024-10-02 20:14:52.8901 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:52.891837 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:52.907943 INFO::Done
2024-10-02 20:14:52.908682 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:52.911934 INFO::ASW Batch was 0.203943718813765 prior to batch effect correction and is now -0.0523389272620866 .
2024-10-02 20:14:52.912505 INFO::ASW Label was 0.624731466077016 prior to batch effect correction and is now 0.822683957908105 .
2024-10-02 20:14:52.913292 INFO::Total function execution time is 0.166744947433472 s and adjustment time is 0.150221347808838 s ( 90.09 )
2024-10-02 20:14:52.927291 INFO::Formatting Data.
2024-10-02 20:14:52.928153 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:52.929143 INFO::Removing potential empty rows and columns
2024-10-02 20:14:52.930201 INFO::Found 0 missing values.
2024-10-02 20:14:52.934558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:52.935107 INFO::Done
2024-10-02 20:14:52.935636 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:52.938768 INFO::Starting hierarchical adjustment
2024-10-02 20:14:52.939486 INFO::Found 5 batches.
2024-10-02 20:14:52.940014 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:52.940652 INFO::Using default BPPARAM
2024-10-02 20:14:52.94119 INFO::Processing subtree level 1
2024-10-02 20:14:53.147835 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:53.149551 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:53.174316 INFO::Done
2024-10-02 20:14:53.176763 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:53.182849 INFO::ASW Batch was 0.417930727610283 prior to batch effect correction and is now -0.0699144337615319 .
2024-10-02 20:14:53.183575 INFO::ASW Label was 0.249077468559149 prior to batch effect correction and is now 0.84987995628975 .
2024-10-02 20:14:53.185158 INFO::Total function execution time is 0.257879495620728 s and adjustment time is 0.233953475952148 s ( 90.72 )
2024-10-02 20:14:53.186193 INFO::Formatting Data.
2024-10-02 20:14:53.186829 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:53.187878 INFO::Removing potential empty rows and columns
2024-10-02 20:14:53.189259 INFO::Found 0 missing values.
2024-10-02 20:14:53.1939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:53.194502 INFO::Done
2024-10-02 20:14:53.19505 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:53.198396 INFO::Starting hierarchical adjustment
2024-10-02 20:14:53.199147 INFO::Found 5 batches.
2024-10-02 20:14:53.199703 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:53.200546 INFO::Using default BPPARAM
2024-10-02 20:14:53.201098 INFO::Processing subtree level 1
2024-10-02 20:14:53.469691 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:53.472662 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:53.489934 INFO::Done
2024-10-02 20:14:53.490714 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:53.494227 INFO::ASW Batch was 0.417930727610283 prior to batch effect correction and is now -0.0699144337615319 .
2024-10-02 20:14:53.494859 INFO::ASW Label was 0.249077468559149 prior to batch effect correction and is now 0.84987995628975 .
2024-10-02 20:14:53.495677 INFO::Total function execution time is 0.309484004974365 s and adjustment time is 0.290914535522461 s ( 94 )
2024-10-02 20:14:53.510867 INFO::Formatting Data.
2024-10-02 20:14:53.511649 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:53.512654 INFO::Removing potential empty rows and columns
2024-10-02 20:14:53.51381 INFO::Found 0 missing values.
2024-10-02 20:14:53.516689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:53.517208 INFO::Done
2024-10-02 20:14:53.517739 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:53.521019 INFO::Starting hierarchical adjustment
2024-10-02 20:14:53.521731 INFO::Found 2 batches.
2024-10-02 20:14:53.522254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:53.522901 INFO::Using default BPPARAM
2024-10-02 20:14:53.523442 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:53.524416 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:53.53973 INFO::Done
2024-10-02 20:14:53.540386 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:53.543485 INFO::ASW Batch was 0.478446181511403 prior to batch effect correction and is now 0.00278761376726539 .
2024-10-02 20:14:53.544075 INFO::ASW Label was 0.536740823666135 prior to batch effect correction and is now 0.920708481962185 .
2024-10-02 20:14:53.544882 INFO::Total function execution time is 0.0341587066650391 s and adjustment time is 0.0181760787963867 s ( 53.21 )
2024-10-02 20:14:53.545669 INFO::Formatting Data.
2024-10-02 20:14:53.546265 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:53.547175 INFO::Removing potential empty rows and columns
2024-10-02 20:14:53.548165 INFO::Found 0 missing values.
2024-10-02 20:14:53.550923 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:53.551436 INFO::Done
2024-10-02 20:14:53.551946 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:53.555 INFO::Starting hierarchical adjustment
2024-10-02 20:14:53.555714 INFO::Found 2 batches.
2024-10-02 20:14:53.556243 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:53.556855 INFO::Using default BPPARAM
2024-10-02 20:14:53.557336 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:53.558258 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:53.574158 INFO::Done
2024-10-02 20:14:53.574821 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:53.577862 INFO::ASW Batch was 0.478446181511403 prior to batch effect correction and is now 0.00278761376726539 .
2024-10-02 20:14:53.578415 INFO::ASW Label was 0.536740823666135 prior to batch effect correction and is now 0.920708481962185 .
2024-10-02 20:14:53.57917 INFO::Total function execution time is 0.0335209369659424 s and adjustment time is 0.0185942649841309 s ( 55.47 )
2024-10-02 20:14:53.590643 INFO::Formatting Data.
2024-10-02 20:14:53.591388 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:53.592298 INFO::Removing potential empty rows and columns
2024-10-02 20:14:53.593235 INFO::Found 0 missing values.
2024-10-02 20:14:53.595882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:53.596405 INFO::Done
2024-10-02 20:14:53.596888 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:53.598864 INFO::Starting hierarchical adjustment
2024-10-02 20:14:53.599568 INFO::Found 2 batches.
2024-10-02 20:14:53.600098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:53.600697 INFO::Using default BPPARAM
2024-10-02 20:14:53.601202 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:53.602185 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:53.63652 INFO::Done
2024-10-02 20:14:53.637278 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:53.639481 INFO::ASW Batch was -0.0280767257262332 prior to batch effect correction and is now -0.141203066866704 .
2024-10-02 20:14:53.640342 INFO::Total function execution time is 0.0498034954071045 s and adjustment time is 0.0370440483093262 s ( 74.38 )
2024-10-02 20:14:53.653173 INFO::Formatting Data.
2024-10-02 20:14:53.653953 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:53.654823 INFO::Removing potential empty rows and columns
2024-10-02 20:14:53.655843 INFO::Found 0 missing values.
2024-10-02 20:14:53.657095 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.
2024-10-02 20:14:53.662142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:53.662688 INFO::Done
2024-10-02 20:14:53.663166 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:53.666296 INFO::Starting hierarchical adjustment
2024-10-02 20:14:53.666971 INFO::Found 2 batches.
2024-10-02 20:14:53.667492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:53.66805 INFO::Using default BPPARAM
2024-10-02 20:14:53.668549 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:53.669535 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:53.688244 INFO::Done
2024-10-02 20:14:53.68901 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:53.692229 INFO::ASW Batch was 0.538046152941679 prior to batch effect correction and is now -0.017346300579422 .
2024-10-02 20:14:53.69291 INFO::ASW Label was 0.544533766627629 prior to batch effect correction and is now 0.897813044705632 .
2024-10-02 20:14:53.693755 INFO::Total function execution time is 0.0406746864318848 s and adjustment time is 0.0213768482208252 s ( 52.56 )
2024-10-02 20:14:53.694599 INFO::Formatting Data.
2024-10-02 20:14:53.695261 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:53.69627 INFO::Removing potential empty rows and columns
2024-10-02 20:14:53.697331 INFO::Found 0 missing values.
2024-10-02 20:14:53.698361 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.
2024-10-02 20:14:53.703915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:53.704449 INFO::Done
2024-10-02 20:14:53.704945 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:53.707916 INFO::Starting hierarchical adjustment
2024-10-02 20:14:53.708607 INFO::Found 2 batches.
2024-10-02 20:14:53.709108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:53.709688 INFO::Using default BPPARAM
2024-10-02 20:14:53.710176 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:53.711087 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:53.7281 INFO::Done
2024-10-02 20:14:53.728848 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:53.73192 INFO::ASW Batch was 0.538046152941679 prior to batch effect correction and is now -0.017346300579422 .
2024-10-02 20:14:53.732518 INFO::ASW Label was 0.544533766627629 prior to batch effect correction and is now 0.897813044705632 .
2024-10-02 20:14:53.733355 INFO::Total function execution time is 0.0388062000274658 s and adjustment time is 0.0196077823638916 s ( 50.53 )
2024-10-02 20:14:53.951875 INFO::Formatting Data.
2024-10-02 20:14:53.952954 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:53.95399 INFO::Removing potential empty rows and columns
2024-10-02 20:14:53.955185 INFO::Found 0 missing values.
2024-10-02 20:14:53.958292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:53.958832 INFO::Done
2024-10-02 20:14:53.959328 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:53.961713 INFO::Starting hierarchical adjustment
2024-10-02 20:14:53.962423 INFO::Found 3 batches.
2024-10-02 20:14:53.962924 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:53.963535 INFO::Using default BPPARAM
2024-10-02 20:14:53.964038 INFO::Processing subtree level 1
2024-10-02 20:14:54.070538 INFO::Adjusting the last 1 batches sequentially
2024-10-02 20:14:54.072441 INFO::Done
2024-10-02 20:14:54.073143 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:54.075763 INFO::ASW Batch was 0.0127705662930267 prior to batch effect correction and is now 0.0127705662930267 .
2024-10-02 20:14:54.076796 INFO::Total function execution time is 0.125144720077515 s and adjustment time is 0.110137701034546 s ( 88.01 )
2024-10-02 20:14:54.077884 INFO::Formatting Data.
2024-10-02 20:14:54.078583 INFO::Typecasting input to dataframe.
2024-10-02 20:14:54.07932 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:54.080254 INFO::Removing potential empty rows and columns
2024-10-02 20:14:54.081356 INFO::Found 0 missing values.
2024-10-02 20:14:54.084448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:54.08502 INFO::Done
2024-10-02 20:14:54.085599 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:54.087754 INFO::Starting hierarchical adjustment
2024-10-02 20:14:54.088497 INFO::Found 3 batches.
2024-10-02 20:14:54.089054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:54.089697 INFO::Using default BPPARAM
2024-10-02 20:14:54.09021 INFO::Processing subtree level 1
2024-10-02 20:14:54.241324 INFO::Adjusting the last 1 batches sequentially
2024-10-02 20:14:54.243427 INFO::Done
2024-10-02 20:14:54.244158 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:54.246846 INFO::ASW Batch was 0.0127705662930267 prior to batch effect correction and is now 0.0127705662930267 .
2024-10-02 20:14:54.247874 INFO::Total function execution time is 0.169994354248047 s and adjustment time is 0.155049562454224 s ( 91.21 )
2024-10-02 20:14:54.262511 INFO::Formatting Data.
2024-10-02 20:14:54.263495 INFO::Typecasting input to dataframe.
2024-10-02 20:14:54.264588 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:54.265749 INFO::Removing potential empty rows and columns
2024-10-02 20:14:54.267044 INFO::Found 0 missing values.
2024-10-02 20:14:54.270772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:54.271374 INFO::Done
2024-10-02 20:14:54.271945 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:54.274342 INFO::Starting hierarchical adjustment
2024-10-02 20:14:54.275103 INFO::Found 3 batches.
2024-10-02 20:14:54.275629 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:54.276258 INFO::Using default BPPARAM
2024-10-02 20:14:54.276811 INFO::Processing subtree level 1
2024-10-02 20:14:54.51169 INFO::Adjusting the last 1 batches sequentially
2024-10-02 20:14:54.513757 INFO::Done
2024-10-02 20:14:54.514449 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:54.541274 INFO::ASW Batch was -0.064459887290281 prior to batch effect correction and is now -0.064459887290281 .
2024-10-02 20:14:54.5427 INFO::Total function execution time is 0.28029990196228 s and adjustment time is 0.238790035247803 s ( 85.19 )
2024-10-02 20:14:54.721139 INFO::Formatting Data.
2024-10-02 20:14:54.722007 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:54.723332 INFO::Removing potential empty rows and columns
2024-10-02 20:14:54.726404 INFO::Found 1000 missing values.
2024-10-02 20:14:54.747715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:54.74845 INFO::Done
2024-10-02 20:14:54.749064 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:54.755099 INFO::Starting hierarchical adjustment
2024-10-02 20:14:54.755886 INFO::Found 10 batches.
2024-10-02 20:14:54.756443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:54.757139 INFO::Using default BPPARAM
2024-10-02 20:14:54.75786 INFO::Processing subtree level 1
2024-10-02 20:14:54.956627 INFO::Processing subtree level 2
2024-10-02 20:14:55.137065 INFO::Adjusting the last 1 batches sequentially
2024-10-02 20:14:55.139199 INFO::Done
2024-10-02 20:14:55.139908 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:55.146047 INFO::ASW Batch was 0.47542320166545 prior to batch effect correction and is now 0.47542320166545 .
2024-10-02 20:14:55.146763 INFO::ASW Label was 0.351912941292527 prior to batch effect correction and is now 0.351912941292527 .
2024-10-02 20:14:55.147747 INFO::Total function execution time is 0.426709651947021 s and adjustment time is 0.383450746536255 s ( 89.86 )
2024-10-02 20:14:55.148741 INFO::Formatting Data.
2024-10-02 20:14:55.149461 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:55.151085 INFO::Removing potential empty rows and columns
2024-10-02 20:14:55.154209 INFO::Found 1000 missing values.
2024-10-02 20:14:55.175392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:55.176207 INFO::Done
2024-10-02 20:14:55.176853 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:55.183309 INFO::Starting hierarchical adjustment
2024-10-02 20:14:55.184127 INFO::Found 10 batches.
2024-10-02 20:14:56.519092 INFO::Set up parallel execution backend with 2 workers
2024-10-02 20:14:56.520635 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-02 20:14:57.800541 INFO::Adjusting the last 2 batches sequentially
2024-10-02 20:14:57.802203 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-02 20:14:57.818635 INFO::Done
2024-10-02 20:14:57.819277 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:57.823843 INFO::ASW Batch was 0.47542320166545 prior to batch effect correction and is now 0.47542320166545 .
2024-10-02 20:14:57.824399 INFO::ASW Label was 0.351912941292527 prior to batch effect correction and is now 0.351912941292527 .
2024-10-02 20:14:57.825121 INFO::Total function execution time is 2.67644882202148 s and adjustment time is 2.63464903831482 s ( 98.44 )
2024-10-02 20:14:57.989642 INFO::Formatting Data.
2024-10-02 20:14:57.990453 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:57.991326 INFO::Removing potential empty rows and columns
2024-10-02 20:14:57.992363 INFO::Found 0 missing values.
2024-10-02 20:14:57.99593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:57.996494 INFO::Done
2024-10-02 20:14:57.99698 INFO::Acquiring quality metrics before batch effect correction.
2024-10-02 20:14:57.999674 INFO::Starting hierarchical adjustment
2024-10-02 20:14:58.000354 INFO::Found 3 batches.
2024-10-02 20:14:58.00084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-02 20:14:58.0014 INFO::Using default BPPARAM
2024-10-02 20:14:58.001889 INFO::Processing subtree level 1
2024-10-02 20:14:58.106143 INFO::Adjusting the last 1 batches sequentially
2024-10-02 20:14:58.107915 INFO::Done
2024-10-02 20:14:58.108554 INFO::Acquiring quality metrics after batch effect correction.
2024-10-02 20:14:58.111747 INFO::ASW Batch was 0.220865822082363 prior to batch effect correction and is now -0.149441108382706 .
2024-10-02 20:14:58.11234 INFO::ASW Label was -0.18450410551356 prior to batch effect correction and is now -0.0318315823410997 .
2024-10-02 20:14:58.113218 INFO::Total function execution time is 0.123640775680542 s and adjustment time is 0.107666969299316 s ( 87.08 )
2024-10-02 20:14:58.222934 INFO::Formatting Data.
2024-10-02 20:14:58.223717 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.224566 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.225548 INFO::Found 2 missing values.
2024-10-02 20:14:58.228216 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.228706 INFO::Done
2024-10-02 20:14:58.253614 INFO::Found NA in Reference column
2024-10-02 20:14:58.262697 INFO::Require at least two references per batch.
2024-10-02 20:14:58.281843 INFO::Formatting Data.
2024-10-02 20:14:58.282587 INFO::Recognized SummarizedExperiment
2024-10-02 20:14:58.283109 INFO::Typecasting input to dataframe.
2024-10-02 20:14:58.292393 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.293565 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.297056 INFO::Found 0 missing values.
2024-10-02 20:14:58.30363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.304161 INFO::Done
2024-10-02 20:14:58.319026 INFO::Formatting Data.
2024-10-02 20:14:58.319731 INFO::Recognized SummarizedExperiment
2024-10-02 20:14:58.320209 INFO::Typecasting input to dataframe.
2024-10-02 20:14:58.337202 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.338405 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.341819 INFO::Found 0 missing values.
2024-10-02 20:14:58.352345 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.352919 INFO::Done
2024-10-02 20:14:58.367872 INFO::Formatting Data.
2024-10-02 20:14:58.368555 INFO::Recognized SummarizedExperiment
2024-10-02 20:14:58.369047 INFO::Typecasting input to dataframe.
2024-10-02 20:14:58.386051 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.387135 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.38821 INFO::Found 0 missing values.
2024-10-02 20:14:58.389123 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.
2024-10-02 20:14:58.393387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.393879 INFO::Done
2024-10-02 20:14:58.403442 INFO::Formatting Data.
2024-10-02 20:14:58.404168 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.40501 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.406171 INFO::Found 0 missing values.
2024-10-02 20:14:58.409263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.409818 INFO::Done
2024-10-02 20:14:58.420881 INFO::Formatting Data.
2024-10-02 20:14:58.421684 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.422585 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.423704 INFO::Found 0 missing values.
2024-10-02 20:14:58.426637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.427133 INFO::Done
2024-10-02 20:14:58.456259 INFO::Formatting Data.
2024-10-02 20:14:58.457176 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.458298 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.459538 INFO::Found 1 missing values.
2024-10-02 20:14:58.462382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.462963 INFO::Done
2024-10-02 20:14:58.481111 INFO::Formatting Data.
2024-10-02 20:14:58.481952 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.482817 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.483795 INFO::Found 2 missing values.
2024-10-02 20:14:58.49468 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.
2024-10-02 20:14:58.4981 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.498717 INFO::Done
2024-10-02 20:14:58.510846 INFO::Formatting Data.
2024-10-02 20:14:58.511842 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.512825 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.513836 INFO::Found 2 missing values.
2024-10-02 20:14:58.515594 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.516123 INFO::Done
2024-10-02 20:14:58.527029 INFO::Formatting Data.
2024-10-02 20:14:58.52777 INFO::Typecasting input to dataframe.
2024-10-02 20:14:58.528611 INFO::Replacing NaNs with NAs.
2024-10-02 20:14:58.529538 INFO::Removing potential empty rows and columns
2024-10-02 20:14:58.530583 INFO::Found 0 missing values.
2024-10-02 20:14:58.533835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-02 20:14:58.534396 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.187 4.359 21.009
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.172 | 1.262 | 18.662 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.014 | 0.000 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.000 | 0.012 | |