Yannis Schumann
| Snapshot Date: 2025-02-14 13:40 -0500 (Fri, 14 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0500 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-15 11:39 -0500 (Sat, 15 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| 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 159/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | 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: 1.3.6 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-02-14 20:03:37 -0500 (Fri, 14 Feb 2025) |
| EndedAt: 2025-02-14 20:05:07 -0500 (Fri, 14 Feb 2025) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.6’
* 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 24.627 1.387 17.975
* 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-3.21-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.3.6’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
2025-02-14 20:04:29.416266 INFO::Formatting Data.
2025-02-14 20:04:29.417931 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:29.430032 INFO::Removing potential empty rows and columns
2025-02-14 20:04:29.684608 INFO::Found 0 missing values.
2025-02-14 20:04:29.68838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:29.689192 INFO::Done
2025-02-14 20:04:29.689798 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:29.704068 INFO::Starting hierarchical adjustment
2025-02-14 20:04:29.705258 INFO::Found 3 batches.
2025-02-14 20:04:29.705919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:29.707299 INFO::Using default BPPARAM
2025-02-14 20:04:29.707925 INFO::Processing subtree level 1
2025-02-14 20:04:29.811304 INFO::Adjusting the last 1 batches sequentially
2025-02-14 20:04:29.813301 INFO::Done
2025-02-14 20:04:29.814065 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:29.816908 INFO::ASW Batch was -0.0595232632700433 prior to batch effect correction and is now -0.0595232632700433 .
2025-02-14 20:04:29.81806 INFO::Total function execution time is 0.40254282951355 s and adjustment time is 0.10828709602356 s ( 26.9 )
2025-02-14 20:04:29.832935 INFO::Formatting Data.
2025-02-14 20:04:29.833825 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:29.834816 INFO::Removing potential empty rows and columns
2025-02-14 20:04:29.835964 INFO::Found 0 missing values.
2025-02-14 20:04:29.836972 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.
2025-02-14 20:04:29.848152 INFO::Formatting Data.
2025-02-14 20:04:29.849 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:29.849941 INFO::Removing potential empty rows and columns
2025-02-14 20:04:29.850997 INFO::Found 0 missing values.
2025-02-14 20:04:29.851957 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.
2025-02-14 20:04:29.868059 INFO::Formatting Data.
2025-02-14 20:04:29.868869 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:29.86977 INFO::Removing potential empty rows and columns
2025-02-14 20:04:29.87084 INFO::Found 0 missing values.
2025-02-14 20:04:29.871788 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.
2025-02-14 20:04:29.876388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:29.876984 INFO::Done
2025-02-14 20:04:29.877541 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:29.879607 INFO::Starting hierarchical adjustment
2025-02-14 20:04:29.880342 INFO::Found 2 batches.
2025-02-14 20:04:29.880883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:29.881546 INFO::Using default BPPARAM
2025-02-14 20:04:29.882084 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:29.883081 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:29.906251 INFO::Done
2025-02-14 20:04:29.907085 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:29.909304 INFO::ASW Batch was 0.0210524603465136 prior to batch effect correction and is now -0.115123167837448 .
2025-02-14 20:04:29.910193 INFO::Total function execution time is 0.0422017574310303 s and adjustment time is 0.0260229110717773 s ( 61.66 )
2025-02-14 20:04:29.913279 INFO::Formatting Data.
2025-02-14 20:04:29.913962 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:29.923227 INFO::Formatting Data.
2025-02-14 20:04:29.924141 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:29.925083 INFO::Removing potential empty rows and columns
2025-02-14 20:04:29.926205 INFO::Found 0 missing values.
2025-02-14 20:04:29.929242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:29.929811 INFO::Done
2025-02-14 20:04:29.930355 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:29.932475 INFO::Starting hierarchical adjustment
2025-02-14 20:04:29.933238 INFO::Found 2 batches.
2025-02-14 20:04:29.933831 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:29.934657 INFO::Using default BPPARAM
2025-02-14 20:04:29.935286 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:29.936321 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:29.952302 INFO::Done
2025-02-14 20:04:29.953089 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:29.955265 INFO::ASW Batch was 0.0464365823634253 prior to batch effect correction and is now -0.126116299435931 .
2025-02-14 20:04:29.956152 INFO::Total function execution time is 0.0329916477203369 s and adjustment time is 0.0192031860351562 s ( 58.21 )
2025-02-14 20:04:29.957312 INFO::Formatting Data.
2025-02-14 20:04:29.957933 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:29.95886 INFO::Removing potential empty rows and columns
2025-02-14 20:04:29.959956 INFO::Found 0 missing values.
2025-02-14 20:04:29.963001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:29.96357 INFO::Done
2025-02-14 20:04:29.96414 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:29.966348 INFO::Starting hierarchical adjustment
2025-02-14 20:04:29.967098 INFO::Found 2 batches.
2025-02-14 20:04:29.967641 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:29.968262 INFO::Using default BPPARAM
2025-02-14 20:04:29.968808 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:29.969794 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:29.985855 INFO::Done
2025-02-14 20:04:29.986647 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:29.988772 INFO::ASW Batch was 0.0464365823634253 prior to batch effect correction and is now -0.126116299435931 .
2025-02-14 20:04:29.989608 INFO::Total function execution time is 0.0323035717010498 s and adjustment time is 0.0188827514648438 s ( 58.45 )
2025-02-14 20:04:33.217106 INFO::Formatting Data.
2025-02-14 20:04:33.217907 INFO::Recognized SummarizedExperiment
2025-02-14 20:04:33.218463 INFO::Typecasting input to dataframe.
2025-02-14 20:04:33.248281 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:33.249503 INFO::Removing potential empty rows and columns
2025-02-14 20:04:33.252772 INFO::Found 0 missing values.
2025-02-14 20:04:33.258904 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:33.259581 INFO::Done
2025-02-14 20:04:33.260103 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:33.263289 INFO::Starting hierarchical adjustment
2025-02-14 20:04:33.264024 INFO::Found 2 batches.
2025-02-14 20:04:33.264518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:33.265516 INFO::Using default BPPARAM
2025-02-14 20:04:33.266021 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:33.26693 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:33.316221 INFO::Done
2025-02-14 20:04:33.317032 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:33.320406 INFO::ASW Batch was 0.0114455871172429 prior to batch effect correction and is now -0.0903935349762679 .
2025-02-14 20:04:33.321304 INFO::Total function execution time is 0.104493379592896 s and adjustment time is 0.0523056983947754 s ( 50.06 )
2025-02-14 20:04:33.339556 INFO::Formatting Data.
2025-02-14 20:04:33.340454 INFO::Recognized SummarizedExperiment
2025-02-14 20:04:33.341076 INFO::Typecasting input to dataframe.
2025-02-14 20:04:33.350935 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:33.352248 INFO::Removing potential empty rows and columns
2025-02-14 20:04:33.356203 INFO::Found 0 missing values.
2025-02-14 20:04:33.363791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:33.364593 INFO::Done
2025-02-14 20:04:33.365165 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:33.368875 INFO::Starting hierarchical adjustment
2025-02-14 20:04:33.369748 INFO::Found 2 batches.
2025-02-14 20:04:33.3703 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:33.370934 INFO::Using default BPPARAM
2025-02-14 20:04:33.37148 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:33.372527 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:33.398735 INFO::Done
2025-02-14 20:04:33.399705 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:33.403956 INFO::ASW Batch was 0.00692165749323206 prior to batch effect correction and is now 0.00692165749323206 .
2025-02-14 20:04:33.405034 INFO::Total function execution time is 0.0654385089874268 s and adjustment time is 0.0290851593017578 s ( 44.45 )
2025-02-14 20:04:33.425069 INFO::Formatting Data.
2025-02-14 20:04:33.426007 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:33.426989 INFO::Removing potential empty rows and columns
2025-02-14 20:04:33.428157 INFO::Found 0 missing values.
2025-02-14 20:04:33.431281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:33.431859 INFO::Done
2025-02-14 20:04:33.432396 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:33.434533 INFO::Starting hierarchical adjustment
2025-02-14 20:04:33.435249 INFO::Found 3 batches.
2025-02-14 20:04:33.435793 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:33.436465 INFO::Using default BPPARAM
2025-02-14 20:04:33.436999 INFO::Processing subtree level 1
2025-02-14 20:04:33.577563 INFO::Adjusting the last 1 batches sequentially
2025-02-14 20:04:33.57946 INFO::Done
2025-02-14 20:04:33.580136 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:33.582811 INFO::ASW Batch was -0.0838664581486523 prior to batch effect correction and is now -0.158650250486649 .
2025-02-14 20:04:33.583814 INFO::Total function execution time is 0.15878963470459 s and adjustment time is 0.144320011138916 s ( 90.89 )
2025-02-14 20:04:33.598476 INFO::Skipping initial DF formatting
2025-02-14 20:04:33.599248 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:33.603467 INFO::Starting hierarchical adjustment
2025-02-14 20:04:33.604304 INFO::Found 5 batches.
2025-02-14 20:04:33.604896 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:33.605794 INFO::Using default BPPARAM
2025-02-14 20:04:33.60636 INFO::Processing subtree level 1
2025-02-14 20:04:33.736463 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:33.738384 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:33.759256 INFO::Done
2025-02-14 20:04:33.760111 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:33.764458 INFO::ASW Batch was 0.517339778244751 prior to batch effect correction and is now 0.517339778244751 .
2025-02-14 20:04:33.765153 INFO::ASW Label was 0.346686102316553 prior to batch effect correction and is now 0.346686102316553 .
2025-02-14 20:04:33.766039 INFO::Total function execution time is 0.167665481567383 s and adjustment time is 0.155096054077148 s ( 92.5 )
2025-02-14 20:04:33.784277 INFO::Formatting Data.
2025-02-14 20:04:33.785176 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:33.786144 INFO::Removing potential empty rows and columns
2025-02-14 20:04:33.78718 INFO::Found 0 missing values.
2025-02-14 20:04:33.791376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:33.791932 INFO::Done
2025-02-14 20:04:33.792489 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:33.795542 INFO::Starting hierarchical adjustment
2025-02-14 20:04:33.79628 INFO::Found 5 batches.
2025-02-14 20:04:33.796836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:33.797519 INFO::Using default BPPARAM
2025-02-14 20:04:33.798064 INFO::Processing subtree level 1
2025-02-14 20:04:33.915672 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:33.917636 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:33.934554 INFO::Done
2025-02-14 20:04:33.93538 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:33.938561 INFO::ASW Batch was 0.311151315154478 prior to batch effect correction and is now -0.0951145951958449 .
2025-02-14 20:04:33.939244 INFO::ASW Label was 0.281640992597333 prior to batch effect correction and is now 0.769865457964876 .
2025-02-14 20:04:33.940094 INFO::Total function execution time is 0.15589714050293 s and adjustment time is 0.138399362564087 s ( 88.78 )
2025-02-14 20:04:33.940969 INFO::Formatting Data.
2025-02-14 20:04:33.941622 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:33.942523 INFO::Removing potential empty rows and columns
2025-02-14 20:04:33.943508 INFO::Found 0 missing values.
2025-02-14 20:04:33.947596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:33.948149 INFO::Done
2025-02-14 20:04:33.948704 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:33.95162 INFO::Starting hierarchical adjustment
2025-02-14 20:04:33.952376 INFO::Found 5 batches.
2025-02-14 20:04:33.952919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:33.953567 INFO::Using default BPPARAM
2025-02-14 20:04:33.95411 INFO::Processing subtree level 1
2025-02-14 20:04:34.077491 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:34.079702 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:34.097944 INFO::Done
2025-02-14 20:04:34.098953 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:34.102728 INFO::ASW Batch was 0.311151315154478 prior to batch effect correction and is now -0.0951145951958449 .
2025-02-14 20:04:34.103523 INFO::ASW Label was 0.281640992597333 prior to batch effect correction and is now 0.769865457964876 .
2025-02-14 20:04:34.10449 INFO::Total function execution time is 0.163467884063721 s and adjustment time is 0.145602941513062 s ( 89.07 )
2025-02-14 20:04:34.119322 INFO::Formatting Data.
2025-02-14 20:04:34.1203 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:34.121384 INFO::Removing potential empty rows and columns
2025-02-14 20:04:34.122465 INFO::Found 0 missing values.
2025-02-14 20:04:34.126797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:34.127414 INFO::Done
2025-02-14 20:04:34.127958 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:34.131234 INFO::Starting hierarchical adjustment
2025-02-14 20:04:34.132054 INFO::Found 5 batches.
2025-02-14 20:04:34.132607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:34.133271 INFO::Using default BPPARAM
2025-02-14 20:04:34.133826 INFO::Processing subtree level 1
2025-02-14 20:04:34.256975 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:34.259521 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:34.283751 INFO::Done
2025-02-14 20:04:34.284905 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:34.289784 INFO::ASW Batch was 0.511074145489133 prior to batch effect correction and is now 0.0444276732837776 .
2025-02-14 20:04:34.290793 INFO::ASW Label was 0.363422663552866 prior to batch effect correction and is now 0.664692638389344 .
2025-02-14 20:04:34.292018 INFO::Total function execution time is 0.172794103622437 s and adjustment time is 0.151801109313965 s ( 87.85 )
2025-02-14 20:04:34.293364 INFO::Formatting Data.
2025-02-14 20:04:34.29428 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:34.295643 INFO::Removing potential empty rows and columns
2025-02-14 20:04:34.297117 INFO::Found 0 missing values.
2025-02-14 20:04:34.303547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:34.304441 INFO::Done
2025-02-14 20:04:34.305224 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:34.309741 INFO::Starting hierarchical adjustment
2025-02-14 20:04:34.310858 INFO::Found 5 batches.
2025-02-14 20:04:34.311727 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:34.312751 INFO::Using default BPPARAM
2025-02-14 20:04:34.313541 INFO::Processing subtree level 1
2025-02-14 20:04:34.443681 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:34.445624 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:34.462946 INFO::Done
2025-02-14 20:04:34.463861 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:34.467561 INFO::ASW Batch was 0.511074145489133 prior to batch effect correction and is now 0.0444276732837776 .
2025-02-14 20:04:34.468311 INFO::ASW Label was 0.363422663552866 prior to batch effect correction and is now 0.664692638389344 .
2025-02-14 20:04:34.46923 INFO::Total function execution time is 0.175941228866577 s and adjustment time is 0.152270317077637 s ( 86.55 )
2025-02-14 20:04:34.484231 INFO::Formatting Data.
2025-02-14 20:04:34.485154 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:34.486166 INFO::Removing potential empty rows and columns
2025-02-14 20:04:34.487267 INFO::Found 0 missing values.
2025-02-14 20:04:34.49022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:34.49078 INFO::Done
2025-02-14 20:04:34.491298 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:34.49456 INFO::Starting hierarchical adjustment
2025-02-14 20:04:34.495286 INFO::Found 2 batches.
2025-02-14 20:04:34.495879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:34.496558 INFO::Using default BPPARAM
2025-02-14 20:04:34.497099 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:34.498047 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:34.513929 INFO::Done
2025-02-14 20:04:34.514729 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:34.517998 INFO::ASW Batch was 0.654545245431225 prior to batch effect correction and is now 0.0293747998333771 .
2025-02-14 20:04:34.518636 INFO::ASW Label was 0.442588792070403 prior to batch effect correction and is now 0.896452939366372 .
2025-02-14 20:04:34.519508 INFO::Total function execution time is 0.0354223251342773 s and adjustment time is 0.018770694732666 s ( 52.99 )
2025-02-14 20:04:34.520352 INFO::Formatting Data.
2025-02-14 20:04:34.52099 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:34.521902 INFO::Removing potential empty rows and columns
2025-02-14 20:04:34.522915 INFO::Found 0 missing values.
2025-02-14 20:04:34.525726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:34.526285 INFO::Done
2025-02-14 20:04:34.526817 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:34.529888 INFO::Starting hierarchical adjustment
2025-02-14 20:04:34.530618 INFO::Found 2 batches.
2025-02-14 20:04:34.531151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:34.531776 INFO::Using default BPPARAM
2025-02-14 20:04:34.532343 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:34.533282 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:34.549286 INFO::Done
2025-02-14 20:04:34.550131 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:34.553474 INFO::ASW Batch was 0.654545245431225 prior to batch effect correction and is now 0.0293747998333771 .
2025-02-14 20:04:34.554094 INFO::ASW Label was 0.442588792070403 prior to batch effect correction and is now 0.896452939366372 .
2025-02-14 20:04:34.554975 INFO::Total function execution time is 0.0346410274505615 s and adjustment time is 0.018768310546875 s ( 54.18 )
2025-02-14 20:04:34.567279 INFO::Formatting Data.
2025-02-14 20:04:34.568197 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:34.569188 INFO::Removing potential empty rows and columns
2025-02-14 20:04:34.570168 INFO::Found 0 missing values.
2025-02-14 20:04:34.57244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:34.573013 INFO::Done
2025-02-14 20:04:34.57355 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:34.575725 INFO::Starting hierarchical adjustment
2025-02-14 20:04:34.576461 INFO::Found 2 batches.
2025-02-14 20:04:34.576986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:34.577609 INFO::Using default BPPARAM
2025-02-14 20:04:34.578133 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:34.579111 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:34.623589 INFO::Done
2025-02-14 20:04:34.624623 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:34.62694 INFO::ASW Batch was 0.0226861512671614 prior to batch effect correction and is now -0.0470412595818049 .
2025-02-14 20:04:34.627836 INFO::Total function execution time is 0.0607025623321533 s and adjustment time is 0.0471920967102051 s ( 77.74 )
2025-02-14 20:04:34.640666 INFO::Formatting Data.
2025-02-14 20:04:34.641513 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:34.642488 INFO::Removing potential empty rows and columns
2025-02-14 20:04:34.643625 INFO::Found 0 missing values.
2025-02-14 20:04:34.644841 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.
2025-02-14 20:04:34.64956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:34.650174 INFO::Done
2025-02-14 20:04:34.650723 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:34.653703 INFO::Starting hierarchical adjustment
2025-02-14 20:04:34.654434 INFO::Found 2 batches.
2025-02-14 20:04:34.654976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:34.655612 INFO::Using default BPPARAM
2025-02-14 20:04:34.656146 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:34.65717 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:34.674215 INFO::Done
2025-02-14 20:04:34.67497 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:34.67791 INFO::ASW Batch was 0.389665723650339 prior to batch effect correction and is now -0.0108933043508611 .
2025-02-14 20:04:34.678539 INFO::ASW Label was 0.631000049754882 prior to batch effect correction and is now 0.911940287904749 .
2025-02-14 20:04:34.679377 INFO::Total function execution time is 0.0387930870056152 s and adjustment time is 0.0199134349822998 s ( 51.33 )
2025-02-14 20:04:34.680194 INFO::Formatting Data.
2025-02-14 20:04:34.680838 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:34.681778 INFO::Removing potential empty rows and columns
2025-02-14 20:04:34.682801 INFO::Found 0 missing values.
2025-02-14 20:04:34.683723 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.
2025-02-14 20:04:34.688277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:34.688854 INFO::Done
2025-02-14 20:04:34.689393 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:34.692265 INFO::Starting hierarchical adjustment
2025-02-14 20:04:34.692981 INFO::Found 2 batches.
2025-02-14 20:04:34.693667 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:34.694315 INFO::Using default BPPARAM
2025-02-14 20:04:34.694854 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:34.695792 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:34.768319 INFO::Done
2025-02-14 20:04:34.769116 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:34.772093 INFO::ASW Batch was 0.389665723650339 prior to batch effect correction and is now -0.0108933043508611 .
2025-02-14 20:04:34.772721 INFO::ASW Label was 0.631000049754882 prior to batch effect correction and is now 0.911940287904749 .
2025-02-14 20:04:34.773502 INFO::Total function execution time is 0.0933241844177246 s and adjustment time is 0.0754287242889404 s ( 80.82 )
2025-02-14 20:04:34.991536 INFO::Formatting Data.
2025-02-14 20:04:34.992509 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:34.993555 INFO::Removing potential empty rows and columns
2025-02-14 20:04:34.994734 INFO::Found 0 missing values.
2025-02-14 20:04:34.998192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:34.998857 INFO::Done
2025-02-14 20:04:34.999455 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:35.001635 INFO::Starting hierarchical adjustment
2025-02-14 20:04:35.002403 INFO::Found 3 batches.
2025-02-14 20:04:35.00296 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:35.003716 INFO::Using default BPPARAM
2025-02-14 20:04:35.004376 INFO::Processing subtree level 1
2025-02-14 20:04:35.116926 INFO::Adjusting the last 1 batches sequentially
2025-02-14 20:04:35.119016 INFO::Done
2025-02-14 20:04:35.119784 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:35.12239 INFO::ASW Batch was -0.100668704739262 prior to batch effect correction and is now -0.100668704739262 .
2025-02-14 20:04:35.12349 INFO::Total function execution time is 0.131999969482422 s and adjustment time is 0.116759777069092 s ( 88.45 )
2025-02-14 20:04:35.124651 INFO::Formatting Data.
2025-02-14 20:04:35.125384 INFO::Typecasting input to dataframe.
2025-02-14 20:04:35.126194 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:35.127362 INFO::Removing potential empty rows and columns
2025-02-14 20:04:35.12866 INFO::Found 0 missing values.
2025-02-14 20:04:35.132077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:35.132666 INFO::Done
2025-02-14 20:04:35.13323 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:35.135281 INFO::Starting hierarchical adjustment
2025-02-14 20:04:35.136007 INFO::Found 3 batches.
2025-02-14 20:04:35.13656 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:35.137232 INFO::Using default BPPARAM
2025-02-14 20:04:35.13777 INFO::Processing subtree level 1
2025-02-14 20:04:35.238039 INFO::Adjusting the last 1 batches sequentially
2025-02-14 20:04:35.240505 INFO::Done
2025-02-14 20:04:35.241483 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:35.244848 INFO::ASW Batch was -0.100668704739262 prior to batch effect correction and is now -0.100668704739262 .
2025-02-14 20:04:35.246195 INFO::Total function execution time is 0.121431350708008 s and adjustment time is 0.104615211486816 s ( 86.15 )
2025-02-14 20:04:35.265146 INFO::Formatting Data.
2025-02-14 20:04:35.266397 INFO::Typecasting input to dataframe.
2025-02-14 20:04:35.267759 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:35.269162 INFO::Removing potential empty rows and columns
2025-02-14 20:04:35.270776 INFO::Found 0 missing values.
2025-02-14 20:04:35.274199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:35.274796 INFO::Done
2025-02-14 20:04:35.275344 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:35.277442 INFO::Starting hierarchical adjustment
2025-02-14 20:04:35.278234 INFO::Found 3 batches.
2025-02-14 20:04:35.2788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:35.27943 INFO::Using default BPPARAM
2025-02-14 20:04:35.279974 INFO::Processing subtree level 1
2025-02-14 20:04:35.376832 INFO::Adjusting the last 1 batches sequentially
2025-02-14 20:04:35.378801 INFO::Done
2025-02-14 20:04:35.379487 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:35.382051 INFO::ASW Batch was -0.0665760304599689 prior to batch effect correction and is now -0.0665760304599689 .
2025-02-14 20:04:35.383089 INFO::Total function execution time is 0.118106603622437 s and adjustment time is 0.100704193115234 s ( 85.27 )
2025-02-14 20:04:35.547562 INFO::Formatting Data.
2025-02-14 20:04:35.548568 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:35.54995 INFO::Removing potential empty rows and columns
2025-02-14 20:04:35.553127 INFO::Found 1000 missing values.
2025-02-14 20:04:35.574245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:35.575159 INFO::Done
2025-02-14 20:04:35.575816 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:35.58175 INFO::Starting hierarchical adjustment
2025-02-14 20:04:35.582684 INFO::Found 10 batches.
2025-02-14 20:04:35.58328 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:35.584017 INFO::Using default BPPARAM
2025-02-14 20:04:35.584624 INFO::Processing subtree level 1
2025-02-14 20:04:35.748815 INFO::Processing subtree level 2
2025-02-14 20:04:35.933353 INFO::Adjusting the last 1 batches sequentially
2025-02-14 20:04:35.935807 INFO::Done
2025-02-14 20:04:35.936637 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:35.944009 INFO::ASW Batch was 0.487739683116811 prior to batch effect correction and is now 0.487739683116811 .
2025-02-14 20:04:35.944954 INFO::ASW Label was 0.351750544232377 prior to batch effect correction and is now 0.351750544232377 .
2025-02-14 20:04:35.946152 INFO::Total function execution time is 0.398609161376953 s and adjustment time is 0.353338003158569 s ( 88.64 )
2025-02-14 20:04:35.947217 INFO::Formatting Data.
2025-02-14 20:04:35.948103 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:35.949852 INFO::Removing potential empty rows and columns
2025-02-14 20:04:35.953354 INFO::Found 1000 missing values.
2025-02-14 20:04:35.976171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:35.977075 INFO::Done
2025-02-14 20:04:35.977761 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:35.983864 INFO::Starting hierarchical adjustment
2025-02-14 20:04:35.984753 INFO::Found 10 batches.
2025-02-14 20:04:37.061128 INFO::Set up parallel execution backend with 2 workers
2025-02-14 20:04:37.063154 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-14 20:04:38.146693 INFO::Adjusting the last 2 batches sequentially
2025-02-14 20:04:38.148869 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 20:04:38.164511 INFO::Done
2025-02-14 20:04:38.165159 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:38.169519 INFO::ASW Batch was 0.487739683116811 prior to batch effect correction and is now 0.487739683116811 .
2025-02-14 20:04:38.170061 INFO::ASW Label was 0.351750544232377 prior to batch effect correction and is now 0.351750544232377 .
2025-02-14 20:04:38.170808 INFO::Total function execution time is 2.22366690635681 s and adjustment time is 2.17992091178894 s ( 98.03 )
2025-02-14 20:04:38.318468 INFO::Formatting Data.
2025-02-14 20:04:38.319336 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.320248 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.321295 INFO::Found 0 missing values.
2025-02-14 20:04:38.324766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.325333 INFO::Done
2025-02-14 20:04:38.325844 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 20:04:38.32841 INFO::Starting hierarchical adjustment
2025-02-14 20:04:38.329092 INFO::Found 3 batches.
2025-02-14 20:04:38.329622 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 20:04:38.330204 INFO::Using default BPPARAM
2025-02-14 20:04:38.33072 INFO::Processing subtree level 1
2025-02-14 20:04:38.431686 INFO::Adjusting the last 1 batches sequentially
2025-02-14 20:04:38.433456 INFO::Done
2025-02-14 20:04:38.434112 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 20:04:38.437162 INFO::ASW Batch was 0.234634944583368 prior to batch effect correction and is now -0.119156208417712 .
2025-02-14 20:04:38.437835 INFO::ASW Label was -0.191076742692107 prior to batch effect correction and is now -0.0810302806855919 .
2025-02-14 20:04:38.438705 INFO::Total function execution time is 0.120299577713013 s and adjustment time is 0.104482889175415 s ( 86.85 )
2025-02-14 20:04:38.571876 INFO::Formatting Data.
2025-02-14 20:04:38.572803 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.573845 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.575019 INFO::Found 2 missing values.
2025-02-14 20:04:38.578052 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.578678 INFO::Done
2025-02-14 20:04:38.607379 INFO::Found NA in Reference column
2025-02-14 20:04:38.617429 INFO::Require at least two references per batch.
2025-02-14 20:04:38.638071 INFO::Formatting Data.
2025-02-14 20:04:38.638882 INFO::Recognized SummarizedExperiment
2025-02-14 20:04:38.639442 INFO::Typecasting input to dataframe.
2025-02-14 20:04:38.649549 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.650838 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.654697 INFO::Found 0 missing values.
2025-02-14 20:04:38.662049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.662812 INFO::Done
2025-02-14 20:04:38.678131 INFO::Formatting Data.
2025-02-14 20:04:38.67893 INFO::Recognized SummarizedExperiment
2025-02-14 20:04:38.679496 INFO::Typecasting input to dataframe.
2025-02-14 20:04:38.697726 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.699077 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.70328 INFO::Found 0 missing values.
2025-02-14 20:04:38.715036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.715811 INFO::Done
2025-02-14 20:04:38.731486 INFO::Formatting Data.
2025-02-14 20:04:38.732274 INFO::Recognized SummarizedExperiment
2025-02-14 20:04:38.732846 INFO::Typecasting input to dataframe.
2025-02-14 20:04:38.750249 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.751348 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.752506 INFO::Found 0 missing values.
2025-02-14 20:04:38.753554 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.
2025-02-14 20:04:38.758113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.758762 INFO::Done
2025-02-14 20:04:38.76914 INFO::Formatting Data.
2025-02-14 20:04:38.769978 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.770864 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.77192 INFO::Found 0 missing values.
2025-02-14 20:04:38.774673 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.775225 INFO::Done
2025-02-14 20:04:38.785769 INFO::Formatting Data.
2025-02-14 20:04:38.786629 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.787533 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.788505 INFO::Found 0 missing values.
2025-02-14 20:04:38.791264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.791817 INFO::Done
2025-02-14 20:04:38.820386 INFO::Formatting Data.
2025-02-14 20:04:38.821407 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.822547 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.823761 INFO::Found 1 missing values.
2025-02-14 20:04:38.826494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.827034 INFO::Done
2025-02-14 20:04:38.847003 INFO::Formatting Data.
2025-02-14 20:04:38.84795 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.848931 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.849921 INFO::Found 2 missing values.
2025-02-14 20:04:38.850842 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.
2025-02-14 20:04:38.853129 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.853727 INFO::Done
2025-02-14 20:04:38.863978 INFO::Formatting Data.
2025-02-14 20:04:38.864905 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.865825 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.86677 INFO::Found 2 missing values.
2025-02-14 20:04:38.868374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.868898 INFO::Done
2025-02-14 20:04:38.878751 INFO::Formatting Data.
2025-02-14 20:04:38.879625 INFO::Typecasting input to dataframe.
2025-02-14 20:04:38.880445 INFO::Replacing NaNs with NAs.
2025-02-14 20:04:38.881289 INFO::Removing potential empty rows and columns
2025-02-14 20:04:38.882291 INFO::Found 0 missing values.
2025-02-14 20:04:38.885154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 20:04:38.885715 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.810 3.621 21.090
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.627 | 1.387 | 17.975 | |
| compute_asw | 0.023 | 0.002 | 0.025 | |
| count_existing | 0.013 | 0.002 | 0.015 | |
| generate_data_covariables | 0.013 | 0.001 | 0.014 | |
| generate_dataset | 0.011 | 0.002 | 0.013 | |