Yannis Schumann
| Snapshot Date: 2025-03-03 13:00 -0500 (Mon, 03 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-06 12:09 -0500 (Thu, 06 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4769 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4504 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4527 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4480 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4416 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-03-04 11:58:07 -0500 (Tue, 04 Mar 2025) |
| EndedAt: 2025-03-04 11:59:26 -0500 (Tue, 04 Mar 2025) |
| EllapsedTime: 78.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 27.92 1.287 20.19
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-03-04 11:59:04.238733 INFO::Formatting Data.
2025-03-04 11:59:04.243529 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:04.257269 INFO::Removing potential empty rows and columns
2025-03-04 11:59:04.580533 INFO::Found 0 missing values.
2025-03-04 11:59:04.584221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:04.584962 INFO::Done
2025-03-04 11:59:04.585459 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:04.602377 INFO::Starting hierarchical adjustment
2025-03-04 11:59:04.603431 INFO::Found 3 batches.
2025-03-04 11:59:04.60396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:04.605286 INFO::Using default BPPARAM
2025-03-04 11:59:04.605838 INFO::Processing subtree level 1
2025-03-04 11:59:04.738219 INFO::Adjusting the last 1 batches sequentially
2025-03-04 11:59:04.741673 INFO::Done
2025-03-04 11:59:04.742685 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:04.746578 INFO::ASW Batch was -0.0436830896515515 prior to batch effect correction and is now -0.0436830896515515 .
2025-03-04 11:59:04.74789 INFO::Total function execution time is 0.51031494140625 s and adjustment time is 0.138427019119263 s ( 27.13 )
2025-03-04 11:59:04.767062 INFO::Formatting Data.
2025-03-04 11:59:04.767887 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:04.768818 INFO::Removing potential empty rows and columns
2025-03-04 11:59:04.769966 INFO::Found 0 missing values.
2025-03-04 11:59:04.770884 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.
2025-03-04 11:59:04.782942 INFO::Formatting Data.
2025-03-04 11:59:04.783759 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:04.784637 INFO::Removing potential empty rows and columns
2025-03-04 11:59:04.785641 INFO::Found 0 missing values.
2025-03-04 11:59:04.78651 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.
2025-03-04 11:59:04.803691 INFO::Formatting Data.
2025-03-04 11:59:04.804493 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:04.805319 INFO::Removing potential empty rows and columns
2025-03-04 11:59:04.806624 INFO::Found 0 missing values.
2025-03-04 11:59:04.807519 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.
2025-03-04 11:59:04.812085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:04.812659 INFO::Done
2025-03-04 11:59:04.81314 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:04.815231 INFO::Starting hierarchical adjustment
2025-03-04 11:59:04.815884 INFO::Found 2 batches.
2025-03-04 11:59:04.816332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:04.817003 INFO::Using default BPPARAM
2025-03-04 11:59:04.81747 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:04.818347 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:04.843616 INFO::Done
2025-03-04 11:59:04.844397 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:04.846683 INFO::ASW Batch was -0.0328114827622553 prior to batch effect correction and is now -0.119932450338705 .
2025-03-04 11:59:04.847542 INFO::Total function execution time is 0.0439839363098145 s and adjustment time is 0.0277879238128662 s ( 63.18 )
2025-03-04 11:59:04.850692 INFO::Formatting Data.
2025-03-04 11:59:04.851306 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:04.860127 INFO::Formatting Data.
2025-03-04 11:59:04.860809 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:04.861614 INFO::Removing potential empty rows and columns
2025-03-04 11:59:04.862567 INFO::Found 0 missing values.
2025-03-04 11:59:04.865407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:04.86592 INFO::Done
2025-03-04 11:59:04.866394 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:04.868316 INFO::Starting hierarchical adjustment
2025-03-04 11:59:04.868969 INFO::Found 2 batches.
2025-03-04 11:59:04.86942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:04.870107 INFO::Using default BPPARAM
2025-03-04 11:59:04.870743 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:04.871738 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:04.886509 INFO::Done
2025-03-04 11:59:04.887256 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:04.889861 INFO::ASW Batch was 0.0277530959830059 prior to batch effect correction and is now -0.0855258724694352 .
2025-03-04 11:59:04.89109 INFO::Total function execution time is 0.0309600830078125 s and adjustment time is 0.0176451206207275 s ( 56.99 )
2025-03-04 11:59:04.892469 INFO::Formatting Data.
2025-03-04 11:59:04.893134 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:04.894223 INFO::Removing potential empty rows and columns
2025-03-04 11:59:04.895465 INFO::Found 0 missing values.
2025-03-04 11:59:04.898534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:04.89915 INFO::Done
2025-03-04 11:59:04.899651 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:04.90175 INFO::Starting hierarchical adjustment
2025-03-04 11:59:04.902446 INFO::Found 2 batches.
2025-03-04 11:59:04.902915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:04.903477 INFO::Using default BPPARAM
2025-03-04 11:59:04.903928 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:04.904753 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:04.92045 INFO::Done
2025-03-04 11:59:04.921251 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:04.923437 INFO::ASW Batch was 0.0277530959830059 prior to batch effect correction and is now -0.0855258724694352 .
2025-03-04 11:59:04.924246 INFO::Total function execution time is 0.031843900680542 s and adjustment time is 0.0181088447570801 s ( 56.87 )
2025-03-04 11:59:08.313286 INFO::Formatting Data.
2025-03-04 11:59:08.314138 INFO::Recognized SummarizedExperiment
2025-03-04 11:59:08.314581 INFO::Typecasting input to dataframe.
2025-03-04 11:59:08.351105 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:08.352443 INFO::Removing potential empty rows and columns
2025-03-04 11:59:08.355704 INFO::Found 0 missing values.
2025-03-04 11:59:08.362117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:08.362824 INFO::Done
2025-03-04 11:59:08.363271 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:08.366964 INFO::Starting hierarchical adjustment
2025-03-04 11:59:08.367713 INFO::Found 2 batches.
2025-03-04 11:59:08.36815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:08.369282 INFO::Using default BPPARAM
2025-03-04 11:59:08.369707 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:08.370622 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:08.421981 INFO::Done
2025-03-04 11:59:08.422768 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:08.426421 INFO::ASW Batch was 0.000462974379563687 prior to batch effect correction and is now -0.0957073152073653 .
2025-03-04 11:59:08.427273 INFO::Total function execution time is 0.114341020584106 s and adjustment time is 0.0543529987335205 s ( 47.54 )
2025-03-04 11:59:08.446836 INFO::Formatting Data.
2025-03-04 11:59:08.447759 INFO::Recognized SummarizedExperiment
2025-03-04 11:59:08.448275 INFO::Typecasting input to dataframe.
2025-03-04 11:59:08.458952 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:08.460375 INFO::Removing potential empty rows and columns
2025-03-04 11:59:08.464148 INFO::Found 0 missing values.
2025-03-04 11:59:08.471151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:08.471876 INFO::Done
2025-03-04 11:59:08.472363 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:08.476412 INFO::Starting hierarchical adjustment
2025-03-04 11:59:08.477182 INFO::Found 2 batches.
2025-03-04 11:59:08.47765 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:08.478215 INFO::Using default BPPARAM
2025-03-04 11:59:08.478658 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:08.4796 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:08.504849 INFO::Done
2025-03-04 11:59:08.505634 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:08.509353 INFO::ASW Batch was 0.00717424579183766 prior to batch effect correction and is now 0.00717424579183766 .
2025-03-04 11:59:08.51035 INFO::Total function execution time is 0.0635759830474854 s and adjustment time is 0.0277450084686279 s ( 43.64 )
2025-03-04 11:59:08.53082 INFO::Formatting Data.
2025-03-04 11:59:08.531648 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:08.532544 INFO::Removing potential empty rows and columns
2025-03-04 11:59:08.533484 INFO::Found 0 missing values.
2025-03-04 11:59:08.536062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:08.536681 INFO::Done
2025-03-04 11:59:08.537129 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:08.539111 INFO::Starting hierarchical adjustment
2025-03-04 11:59:08.53974 INFO::Found 3 batches.
2025-03-04 11:59:08.540181 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:08.540738 INFO::Using default BPPARAM
2025-03-04 11:59:08.541178 INFO::Processing subtree level 1
2025-03-04 11:59:08.726829 INFO::Adjusting the last 1 batches sequentially
2025-03-04 11:59:08.731089 INFO::Done
2025-03-04 11:59:08.732493 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:08.738641 INFO::ASW Batch was -0.104233970293061 prior to batch effect correction and is now -0.167875503953555 .
2025-03-04 11:59:08.7411 INFO::Total function execution time is 0.21015191078186 s and adjustment time is 0.191445112228394 s ( 91.1 )
2025-03-04 11:59:08.763808 INFO::Skipping initial DF formatting
2025-03-04 11:59:08.764778 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:08.770328 INFO::Starting hierarchical adjustment
2025-03-04 11:59:08.771413 INFO::Found 5 batches.
2025-03-04 11:59:08.77198 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:08.772811 INFO::Using default BPPARAM
2025-03-04 11:59:08.773375 INFO::Processing subtree level 1
2025-03-04 11:59:08.918341 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:08.92264 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:08.945475 INFO::Done
2025-03-04 11:59:08.946585 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:08.951825 INFO::ASW Batch was 0.521220632798477 prior to batch effect correction and is now 0.521220632798477 .
2025-03-04 11:59:08.952502 INFO::ASW Label was 0.399172227406322 prior to batch effect correction and is now 0.399172227406322 .
2025-03-04 11:59:08.954056 INFO::Total function execution time is 0.190364122390747 s and adjustment time is 0.174220085144043 s ( 91.52 )
2025-03-04 11:59:08.974506 INFO::Formatting Data.
2025-03-04 11:59:08.9753 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:08.976202 INFO::Removing potential empty rows and columns
2025-03-04 11:59:08.977225 INFO::Found 0 missing values.
2025-03-04 11:59:08.980921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:08.981493 INFO::Done
2025-03-04 11:59:08.981976 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:08.984864 INFO::Starting hierarchical adjustment
2025-03-04 11:59:08.985605 INFO::Found 5 batches.
2025-03-04 11:59:08.986096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:08.986759 INFO::Using default BPPARAM
2025-03-04 11:59:08.987232 INFO::Processing subtree level 1
2025-03-04 11:59:09.116078 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.122862 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.153147 INFO::Done
2025-03-04 11:59:09.154189 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.159841 INFO::ASW Batch was 0.411132165320754 prior to batch effect correction and is now -0.0542343618520384 .
2025-03-04 11:59:09.160831 INFO::ASW Label was 0.321402563363362 prior to batch effect correction and is now 0.797183972251272 .
2025-03-04 11:59:09.162507 INFO::Total function execution time is 0.187845945358276 s and adjustment time is 0.167572021484375 s ( 89.21 )
2025-03-04 11:59:09.163964 INFO::Formatting Data.
2025-03-04 11:59:09.164901 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:09.16621 INFO::Removing potential empty rows and columns
2025-03-04 11:59:09.167763 INFO::Found 0 missing values.
2025-03-04 11:59:09.172376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:09.173077 INFO::Done
2025-03-04 11:59:09.173574 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:09.176606 INFO::Starting hierarchical adjustment
2025-03-04 11:59:09.17736 INFO::Found 5 batches.
2025-03-04 11:59:09.177792 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:09.178431 INFO::Using default BPPARAM
2025-03-04 11:59:09.178888 INFO::Processing subtree level 1
2025-03-04 11:59:09.303153 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.307211 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.335467 INFO::Done
2025-03-04 11:59:09.336428 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.341715 INFO::ASW Batch was 0.411132165320754 prior to batch effect correction and is now -0.0542343618520384 .
2025-03-04 11:59:09.342407 INFO::ASW Label was 0.321402563363362 prior to batch effect correction and is now 0.797183972251272 .
2025-03-04 11:59:09.343491 INFO::Total function execution time is 0.179605007171631 s and adjustment time is 0.15822696685791 s ( 88.1 )
2025-03-04 11:59:09.358625 INFO::Formatting Data.
2025-03-04 11:59:09.359418 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:09.360295 INFO::Removing potential empty rows and columns
2025-03-04 11:59:09.361335 INFO::Found 0 missing values.
2025-03-04 11:59:09.364865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:09.365419 INFO::Done
2025-03-04 11:59:09.365906 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:09.36874 INFO::Starting hierarchical adjustment
2025-03-04 11:59:09.369443 INFO::Found 5 batches.
2025-03-04 11:59:09.369893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:09.37048 INFO::Using default BPPARAM
2025-03-04 11:59:09.37091 INFO::Processing subtree level 1
2025-03-04 11:59:09.514687 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.520019 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.545898 INFO::Done
2025-03-04 11:59:09.54714 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.55117 INFO::ASW Batch was 0.34240753581416 prior to batch effect correction and is now -0.059523110153099 .
2025-03-04 11:59:09.551854 INFO::ASW Label was 0.37075295405119 prior to batch effect correction and is now 0.86919762114605 .
2025-03-04 11:59:09.553782 INFO::Total function execution time is 0.194942951202393 s and adjustment time is 0.17656397819519 s ( 90.57 )
2025-03-04 11:59:09.554672 INFO::Formatting Data.
2025-03-04 11:59:09.555225 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:09.556367 INFO::Removing potential empty rows and columns
2025-03-04 11:59:09.557661 INFO::Found 0 missing values.
2025-03-04 11:59:09.562971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:09.563913 INFO::Done
2025-03-04 11:59:09.564537 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:09.568261 INFO::Starting hierarchical adjustment
2025-03-04 11:59:09.569244 INFO::Found 5 batches.
2025-03-04 11:59:09.569752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:09.570439 INFO::Using default BPPARAM
2025-03-04 11:59:09.57092 INFO::Processing subtree level 1
2025-03-04 11:59:09.690483 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.696052 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.718049 INFO::Done
2025-03-04 11:59:09.718847 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.722921 INFO::ASW Batch was 0.34240753581416 prior to batch effect correction and is now -0.059523110153099 .
2025-03-04 11:59:09.723559 INFO::ASW Label was 0.37075295405119 prior to batch effect correction and is now 0.86919762114605 .
2025-03-04 11:59:09.724694 INFO::Total function execution time is 0.169964075088501 s and adjustment time is 0.148977994918823 s ( 87.65 )
2025-03-04 11:59:09.740666 INFO::Formatting Data.
2025-03-04 11:59:09.741448 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:09.742335 INFO::Removing potential empty rows and columns
2025-03-04 11:59:09.743363 INFO::Found 0 missing values.
2025-03-04 11:59:09.745772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:09.746328 INFO::Done
2025-03-04 11:59:09.746789 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:09.749577 INFO::Starting hierarchical adjustment
2025-03-04 11:59:09.750332 INFO::Found 2 batches.
2025-03-04 11:59:09.750837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:09.751462 INFO::Using default BPPARAM
2025-03-04 11:59:09.751912 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.752745 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.767621 INFO::Done
2025-03-04 11:59:09.768392 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.771132 INFO::ASW Batch was 0.447037863731468 prior to batch effect correction and is now -0.0224393928129253 .
2025-03-04 11:59:09.771677 INFO::ASW Label was 0.594129228725653 prior to batch effect correction and is now 0.94325082013671 .
2025-03-04 11:59:09.772422 INFO::Total function execution time is 0.0319209098815918 s and adjustment time is 0.0173988342285156 s ( 54.51 )
2025-03-04 11:59:09.773081 INFO::Formatting Data.
2025-03-04 11:59:09.773602 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:09.774353 INFO::Removing potential empty rows and columns
2025-03-04 11:59:09.775231 INFO::Found 0 missing values.
2025-03-04 11:59:09.777658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:09.778153 INFO::Done
2025-03-04 11:59:09.778589 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:09.781112 INFO::Starting hierarchical adjustment
2025-03-04 11:59:09.781751 INFO::Found 2 batches.
2025-03-04 11:59:09.782217 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:09.782777 INFO::Using default BPPARAM
2025-03-04 11:59:09.783197 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.783982 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.798148 INFO::Done
2025-03-04 11:59:09.798822 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.801543 INFO::ASW Batch was 0.447037863731468 prior to batch effect correction and is now -0.0224393928129253 .
2025-03-04 11:59:09.802084 INFO::ASW Label was 0.594129228725653 prior to batch effect correction and is now 0.94325082013671 .
2025-03-04 11:59:09.802791 INFO::Total function execution time is 0.0296900272369385 s and adjustment time is 0.0164878368377686 s ( 55.53 )
2025-03-04 11:59:09.81492 INFO::Formatting Data.
2025-03-04 11:59:09.815682 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:09.817083 INFO::Removing potential empty rows and columns
2025-03-04 11:59:09.817931 INFO::Found 0 missing values.
2025-03-04 11:59:09.819814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:09.820297 INFO::Done
2025-03-04 11:59:09.820746 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:09.822661 INFO::Starting hierarchical adjustment
2025-03-04 11:59:09.823282 INFO::Found 2 batches.
2025-03-04 11:59:09.823746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:09.824286 INFO::Using default BPPARAM
2025-03-04 11:59:09.824714 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.825456 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.858291 INFO::Done
2025-03-04 11:59:09.859066 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.86101 INFO::ASW Batch was 0.307499974715094 prior to batch effect correction and is now -0.117512582131955 .
2025-03-04 11:59:09.861814 INFO::Total function execution time is 0.0470261573791504 s and adjustment time is 0.0350830554962158 s ( 74.6 )
2025-03-04 11:59:09.874947 INFO::Formatting Data.
2025-03-04 11:59:09.875777 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:09.876651 INFO::Removing potential empty rows and columns
2025-03-04 11:59:09.87764 INFO::Found 0 missing values.
2025-03-04 11:59:09.879044 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.
2025-03-04 11:59:09.883435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:09.884179 INFO::Done
2025-03-04 11:59:09.884664 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:09.88751 INFO::Starting hierarchical adjustment
2025-03-04 11:59:09.888185 INFO::Found 2 batches.
2025-03-04 11:59:09.888657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:09.889212 INFO::Using default BPPARAM
2025-03-04 11:59:09.889657 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.890559 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.906851 INFO::Done
2025-03-04 11:59:09.907591 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.910552 INFO::ASW Batch was 0.593670871592167 prior to batch effect correction and is now -0.0176661732347578 .
2025-03-04 11:59:09.911196 INFO::ASW Label was 0.489493642224582 prior to batch effect correction and is now 0.910162422104958 .
2025-03-04 11:59:09.911952 INFO::Total function execution time is 0.0371429920196533 s and adjustment time is 0.0187499523162842 s ( 50.48 )
2025-03-04 11:59:09.912631 INFO::Formatting Data.
2025-03-04 11:59:09.91315 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:09.914093 INFO::Removing potential empty rows and columns
2025-03-04 11:59:09.915016 INFO::Found 0 missing values.
2025-03-04 11:59:09.915904 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.
2025-03-04 11:59:09.920135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:09.92077 INFO::Done
2025-03-04 11:59:09.921256 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:09.924646 INFO::Starting hierarchical adjustment
2025-03-04 11:59:09.925536 INFO::Found 2 batches.
2025-03-04 11:59:09.925994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:09.9266 INFO::Using default BPPARAM
2025-03-04 11:59:09.927042 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:09.927976 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:09.944561 INFO::Done
2025-03-04 11:59:09.945357 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:09.948347 INFO::ASW Batch was 0.593670871592167 prior to batch effect correction and is now -0.0176661732347578 .
2025-03-04 11:59:09.94903 INFO::ASW Label was 0.489493642224582 prior to batch effect correction and is now 0.910162422104958 .
2025-03-04 11:59:09.949818 INFO::Total function execution time is 0.0371568202972412 s and adjustment time is 0.0191271305084229 s ( 51.48 )
2025-03-04 11:59:10.170934 INFO::Formatting Data.
2025-03-04 11:59:10.171837 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:10.172744 INFO::Removing potential empty rows and columns
2025-03-04 11:59:10.173763 INFO::Found 0 missing values.
2025-03-04 11:59:10.176394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:10.176925 INFO::Done
2025-03-04 11:59:10.177381 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:10.179452 INFO::Starting hierarchical adjustment
2025-03-04 11:59:10.180233 INFO::Found 3 batches.
2025-03-04 11:59:10.180729 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:10.181295 INFO::Using default BPPARAM
2025-03-04 11:59:10.181849 INFO::Processing subtree level 1
2025-03-04 11:59:10.288813 INFO::Adjusting the last 1 batches sequentially
2025-03-04 11:59:10.293273 INFO::Done
2025-03-04 11:59:10.294248 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:10.298359 INFO::ASW Batch was -0.108599490427102 prior to batch effect correction and is now -0.108599490427102 .
2025-03-04 11:59:10.300378 INFO::Total function execution time is 0.129479885101318 s and adjustment time is 0.113174915313721 s ( 87.41 )
2025-03-04 11:59:10.301465 INFO::Formatting Data.
2025-03-04 11:59:10.30203 INFO::Typecasting input to dataframe.
2025-03-04 11:59:10.302704 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:10.303529 INFO::Removing potential empty rows and columns
2025-03-04 11:59:10.304579 INFO::Found 0 missing values.
2025-03-04 11:59:10.307279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:10.307853 INFO::Done
2025-03-04 11:59:10.308371 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:10.311798 INFO::Starting hierarchical adjustment
2025-03-04 11:59:10.313893 INFO::Found 3 batches.
2025-03-04 11:59:10.314754 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:10.31556 INFO::Using default BPPARAM
2025-03-04 11:59:10.316122 INFO::Processing subtree level 1
2025-03-04 11:59:10.553996 INFO::Adjusting the last 1 batches sequentially
2025-03-04 11:59:10.557627 INFO::Done
2025-03-04 11:59:10.558376 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:10.573189 INFO::ASW Batch was -0.108599490427102 prior to batch effect correction and is now -0.108599490427102 .
2025-03-04 11:59:10.576939 INFO::Total function execution time is 0.275251150131226 s and adjustment time is 0.244163036346436 s ( 88.71 )
2025-03-04 11:59:10.599499 INFO::Formatting Data.
2025-03-04 11:59:10.600442 INFO::Typecasting input to dataframe.
2025-03-04 11:59:10.601344 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:10.603393 INFO::Removing potential empty rows and columns
2025-03-04 11:59:10.605501 INFO::Found 0 missing values.
2025-03-04 11:59:10.609101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:10.609771 INFO::Done
2025-03-04 11:59:10.610289 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:10.612943 INFO::Starting hierarchical adjustment
2025-03-04 11:59:10.613665 INFO::Found 3 batches.
2025-03-04 11:59:10.614135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:10.614881 INFO::Using default BPPARAM
2025-03-04 11:59:10.615451 INFO::Processing subtree level 1
2025-03-04 11:59:10.855489 INFO::Adjusting the last 1 batches sequentially
2025-03-04 11:59:10.859807 INFO::Done
2025-03-04 11:59:10.86128 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:10.877769 INFO::ASW Batch was 0.0172894955557296 prior to batch effect correction and is now 0.0172894955557296 .
2025-03-04 11:59:10.880661 INFO::Total function execution time is 0.281290054321289 s and adjustment time is 0.246225833892822 s ( 87.53 )
2025-03-04 11:59:11.174306 INFO::Formatting Data.
2025-03-04 11:59:11.175268 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:11.176888 INFO::Removing potential empty rows and columns
2025-03-04 11:59:11.179814 INFO::Found 1000 missing values.
2025-03-04 11:59:11.200208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:11.201066 INFO::Done
2025-03-04 11:59:11.201599 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:11.207757 INFO::Starting hierarchical adjustment
2025-03-04 11:59:11.208577 INFO::Found 10 batches.
2025-03-04 11:59:11.209079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:11.209724 INFO::Using default BPPARAM
2025-03-04 11:59:11.210257 INFO::Processing subtree level 1
2025-03-04 11:59:11.381162 INFO::Processing subtree level 2
2025-03-04 11:59:11.598569 INFO::Adjusting the last 1 batches sequentially
2025-03-04 11:59:11.602134 INFO::Done
2025-03-04 11:59:11.60269 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:11.610039 INFO::ASW Batch was 0.553060220387509 prior to batch effect correction and is now 0.553060220387509 .
2025-03-04 11:59:11.610725 INFO::ASW Label was 0.299701903106815 prior to batch effect correction and is now 0.299701903106815 .
2025-03-04 11:59:11.611718 INFO::Total function execution time is 0.437546014785767 s and adjustment time is 0.393732070922852 s ( 89.99 )
2025-03-04 11:59:11.61252 INFO::Formatting Data.
2025-03-04 11:59:11.613382 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:11.614437 INFO::Removing potential empty rows and columns
2025-03-04 11:59:11.617509 INFO::Found 1000 missing values.
2025-03-04 11:59:11.635653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:11.63655 INFO::Done
2025-03-04 11:59:11.637114 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:11.643287 INFO::Starting hierarchical adjustment
2025-03-04 11:59:11.644146 INFO::Found 10 batches.
2025-03-04 11:59:12.832978 INFO::Set up parallel execution backend with 2 workers
2025-03-04 11:59:12.83402 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-04 11:59:14.244579 INFO::Adjusting the last 2 batches sequentially
2025-03-04 11:59:14.24654 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-04 11:59:14.266433 INFO::Done
2025-03-04 11:59:14.267198 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:14.272864 INFO::ASW Batch was 0.553060220387509 prior to batch effect correction and is now 0.553060220387509 .
2025-03-04 11:59:14.273496 INFO::ASW Label was 0.299701903106815 prior to batch effect correction and is now 0.299701903106815 .
2025-03-04 11:59:14.274246 INFO::Total function execution time is 2.66172504425049 s and adjustment time is 2.62239718437195 s ( 98.52 )
2025-03-04 11:59:14.461181 INFO::Formatting Data.
2025-03-04 11:59:14.46222 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:14.463397 INFO::Removing potential empty rows and columns
2025-03-04 11:59:14.464952 INFO::Found 0 missing values.
2025-03-04 11:59:14.469087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:14.46975 INFO::Done
2025-03-04 11:59:14.470235 INFO::Acquiring quality metrics before batch effect correction.
2025-03-04 11:59:14.473125 INFO::Starting hierarchical adjustment
2025-03-04 11:59:14.473915 INFO::Found 3 batches.
2025-03-04 11:59:14.474409 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-04 11:59:14.475028 INFO::Using default BPPARAM
2025-03-04 11:59:14.475503 INFO::Processing subtree level 1
2025-03-04 11:59:14.606006 INFO::Adjusting the last 1 batches sequentially
2025-03-04 11:59:14.611524 INFO::Done
2025-03-04 11:59:14.612599 INFO::Acquiring quality metrics after batch effect correction.
2025-03-04 11:59:14.61989 INFO::ASW Batch was 0.205721730616766 prior to batch effect correction and is now -0.153281155650182 .
2025-03-04 11:59:14.620673 INFO::ASW Label was -0.141225397112113 prior to batch effect correction and is now 0.136553017145368 .
2025-03-04 11:59:14.622158 INFO::Total function execution time is 0.161128997802734 s and adjustment time is 0.137711048126221 s ( 85.47 )
2025-03-04 11:59:14.768437 INFO::Formatting Data.
2025-03-04 11:59:14.769362 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:14.770237 INFO::Removing potential empty rows and columns
2025-03-04 11:59:14.771325 INFO::Found 2 missing values.
2025-03-04 11:59:14.775136 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:14.776259 INFO::Done
2025-03-04 11:59:14.810757 INFO::Found NA in Reference column
2025-03-04 11:59:14.82186 INFO::Require at least two references per batch.
2025-03-04 11:59:14.845388 INFO::Formatting Data.
2025-03-04 11:59:14.846374 INFO::Recognized SummarizedExperiment
2025-03-04 11:59:14.847013 INFO::Typecasting input to dataframe.
2025-03-04 11:59:14.859669 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:14.861189 INFO::Removing potential empty rows and columns
2025-03-04 11:59:14.865156 INFO::Found 0 missing values.
2025-03-04 11:59:14.872531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:14.873246 INFO::Done
2025-03-04 11:59:14.890225 INFO::Formatting Data.
2025-03-04 11:59:14.891069 INFO::Recognized SummarizedExperiment
2025-03-04 11:59:14.891636 INFO::Typecasting input to dataframe.
2025-03-04 11:59:14.910527 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:14.911996 INFO::Removing potential empty rows and columns
2025-03-04 11:59:14.915924 INFO::Found 0 missing values.
2025-03-04 11:59:14.928451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:14.92933 INFO::Done
2025-03-04 11:59:14.946788 INFO::Formatting Data.
2025-03-04 11:59:14.947728 INFO::Recognized SummarizedExperiment
2025-03-04 11:59:14.948355 INFO::Typecasting input to dataframe.
2025-03-04 11:59:14.96822 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:14.969453 INFO::Removing potential empty rows and columns
2025-03-04 11:59:14.970591 INFO::Found 0 missing values.
2025-03-04 11:59:14.971579 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.
2025-03-04 11:59:14.976278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:14.976909 INFO::Done
2025-03-04 11:59:14.98956 INFO::Formatting Data.
2025-03-04 11:59:14.990465 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:14.991327 INFO::Removing potential empty rows and columns
2025-03-04 11:59:14.992297 INFO::Found 0 missing values.
2025-03-04 11:59:14.995324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:14.996115 INFO::Done
2025-03-04 11:59:15.010988 INFO::Formatting Data.
2025-03-04 11:59:15.011907 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:15.012825 INFO::Removing potential empty rows and columns
2025-03-04 11:59:15.013815 INFO::Found 0 missing values.
2025-03-04 11:59:15.016565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:15.017115 INFO::Done
2025-03-04 11:59:15.051227 INFO::Formatting Data.
2025-03-04 11:59:15.052126 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:15.053199 INFO::Removing potential empty rows and columns
2025-03-04 11:59:15.054469 INFO::Found 1 missing values.
2025-03-04 11:59:15.057148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:15.057711 INFO::Done
2025-03-04 11:59:15.078993 INFO::Formatting Data.
2025-03-04 11:59:15.079879 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:15.080709 INFO::Removing potential empty rows and columns
2025-03-04 11:59:15.081582 INFO::Found 2 missing values.
2025-03-04 11:59:15.082407 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.
2025-03-04 11:59:15.084752 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:15.085412 INFO::Done
2025-03-04 11:59:15.09757 INFO::Formatting Data.
2025-03-04 11:59:15.098481 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:15.099373 INFO::Removing potential empty rows and columns
2025-03-04 11:59:15.100282 INFO::Found 2 missing values.
2025-03-04 11:59:15.102145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:15.102739 INFO::Done
2025-03-04 11:59:15.115186 INFO::Formatting Data.
2025-03-04 11:59:15.116085 INFO::Typecasting input to dataframe.
2025-03-04 11:59:15.116918 INFO::Replacing NaNs with NAs.
2025-03-04 11:59:15.117877 INFO::Removing potential empty rows and columns
2025-03-04 11:59:15.118914 INFO::Found 0 missing values.
2025-03-04 11:59:15.123649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-04 11:59:15.124908 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.579 3.828 21.204
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.920 | 1.287 | 20.190 | |
| compute_asw | 0.011 | 0.001 | 0.015 | |
| count_existing | 0.007 | 0.001 | 0.008 | |
| generate_data_covariables | 0.005 | 0.000 | 0.006 | |
| generate_dataset | 0.006 | 0.000 | 0.006 | |