Yannis Schumann
| Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 Jan 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 2025-01-16 12:09 -0500 (Thu, 16 Jan 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" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4387 |
| 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 | NA | ||||||||||
|
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: 2025-01-14 12:06:17 -0500 (Tue, 14 Jan 2025) |
| EndedAt: 2025-01-14 12:07:35 -0500 (Tue, 14 Jan 2025) |
| EllapsedTime: 77.6 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 28.916 1.305 20.576
* 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")
2025-01-14 12:07:17.658603 INFO::Formatting Data.
2025-01-14 12:07:17.662903 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:17.675843 INFO::Removing potential empty rows and columns
2025-01-14 12:07:17.984225 INFO::Found 0 missing values.
2025-01-14 12:07:17.988159 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:17.989021 INFO::Done
2025-01-14 12:07:17.989578 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:18.008484 INFO::Starting hierarchical adjustment
2025-01-14 12:07:18.010078 INFO::Found 3 batches.
2025-01-14 12:07:18.010871 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:18.012314 INFO::Using default BPPARAM
2025-01-14 12:07:18.018455 INFO::Processing subtree level 1
2025-01-14 12:07:18.158101 INFO::Adjusting the last 1 batches sequentially
2025-01-14 12:07:18.163067 INFO::Done
2025-01-14 12:07:18.163903 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:18.171672 INFO::ASW Batch was -0.0258612121437001 prior to batch effect correction and is now -0.0258612121437001 .
2025-01-14 12:07:18.173646 INFO::Total function execution time is 0.515980005264282 s and adjustment time is 0.15333104133606 s ( 29.72 )
2025-01-14 12:07:18.204461 INFO::Formatting Data.
2025-01-14 12:07:18.205474 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:18.209313 INFO::Removing potential empty rows and columns
2025-01-14 12:07:18.210956 INFO::Found 0 missing values.
2025-01-14 12:07:18.212661 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.
2025-01-14 12:07:18.234014 INFO::Formatting Data.
2025-01-14 12:07:18.23514 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:18.236122 INFO::Removing potential empty rows and columns
2025-01-14 12:07:18.237944 INFO::Found 0 missing values.
2025-01-14 12:07:18.240073 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.
2025-01-14 12:07:18.271619 INFO::Formatting Data.
2025-01-14 12:07:18.273464 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:18.275212 INFO::Removing potential empty rows and columns
2025-01-14 12:07:18.283571 INFO::Found 0 missing values.
2025-01-14 12:07:18.287242 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.
2025-01-14 12:07:18.295277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:18.296285 INFO::Done
2025-01-14 12:07:18.296912 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:18.299671 INFO::Starting hierarchical adjustment
2025-01-14 12:07:18.300584 INFO::Found 2 batches.
2025-01-14 12:07:18.301194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:18.302109 INFO::Using default BPPARAM
2025-01-14 12:07:18.302731 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:18.303869 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:18.331426 INFO::Done
2025-01-14 12:07:18.33224 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:18.334635 INFO::ASW Batch was 0.00631423021550755 prior to batch effect correction and is now -0.120686386213391 .
2025-01-14 12:07:18.335637 INFO::Total function execution time is 0.0641078948974609 s and adjustment time is 0.030958890914917 s ( 48.29 )
2025-01-14 12:07:18.339149 INFO::Formatting Data.
2025-01-14 12:07:18.339839 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:18.350309 INFO::Formatting Data.
2025-01-14 12:07:18.351186 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:18.352117 INFO::Removing potential empty rows and columns
2025-01-14 12:07:18.353205 INFO::Found 0 missing values.
2025-01-14 12:07:18.355948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:18.356498 INFO::Done
2025-01-14 12:07:18.35698 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:18.359087 INFO::Starting hierarchical adjustment
2025-01-14 12:07:18.359926 INFO::Found 2 batches.
2025-01-14 12:07:18.360448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:18.361217 INFO::Using default BPPARAM
2025-01-14 12:07:18.36177 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:18.362772 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:18.379366 INFO::Done
2025-01-14 12:07:18.380179 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:18.382356 INFO::ASW Batch was -0.0406407775431816 prior to batch effect correction and is now -0.103411613551132 .
2025-01-14 12:07:18.383215 INFO::Total function execution time is 0.0330171585083008 s and adjustment time is 0.0195529460906982 s ( 59.22 )
2025-01-14 12:07:18.384221 INFO::Formatting Data.
2025-01-14 12:07:18.384757 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:18.385556 INFO::Removing potential empty rows and columns
2025-01-14 12:07:18.386517 INFO::Found 0 missing values.
2025-01-14 12:07:18.389319 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:18.389857 INFO::Done
2025-01-14 12:07:18.390337 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:18.394155 INFO::Starting hierarchical adjustment
2025-01-14 12:07:18.395506 INFO::Found 2 batches.
2025-01-14 12:07:18.396293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:18.397058 INFO::Using default BPPARAM
2025-01-14 12:07:18.397678 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:18.398854 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:18.415627 INFO::Done
2025-01-14 12:07:18.416403 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:18.41896 INFO::ASW Batch was -0.0406407775431816 prior to batch effect correction and is now -0.103411613551132 .
2025-01-14 12:07:18.42006 INFO::Total function execution time is 0.0357949733734131 s and adjustment time is 0.0204119682312012 s ( 57.02 )
2025-01-14 12:07:21.890942 INFO::Formatting Data.
2025-01-14 12:07:21.891772 INFO::Recognized SummarizedExperiment
2025-01-14 12:07:21.892199 INFO::Typecasting input to dataframe.
2025-01-14 12:07:21.917281 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:21.917991 INFO::Removing potential empty rows and columns
2025-01-14 12:07:21.919345 INFO::Found 0 missing values.
2025-01-14 12:07:21.924221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:21.924948 INFO::Done
2025-01-14 12:07:21.925636 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:21.929108 INFO::Starting hierarchical adjustment
2025-01-14 12:07:21.929606 INFO::Found 2 batches.
2025-01-14 12:07:21.929846 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:21.930577 INFO::Using default BPPARAM
2025-01-14 12:07:21.930871 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:21.93177 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:21.963268 INFO::Done
2025-01-14 12:07:21.963725 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:21.965503 INFO::ASW Batch was -0.00286058041473487 prior to batch effect correction and is now -0.0971220391217036 .
2025-01-14 12:07:21.96599 INFO::Total function execution time is 0.0754120349884033 s and adjustment time is 0.0337178707122803 s ( 44.71 )
2025-01-14 12:07:21.974857 INFO::Formatting Data.
2025-01-14 12:07:21.975308 INFO::Recognized SummarizedExperiment
2025-01-14 12:07:21.975504 INFO::Typecasting input to dataframe.
2025-01-14 12:07:21.984961 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:21.985994 INFO::Removing potential empty rows and columns
2025-01-14 12:07:21.987874 INFO::Found 0 missing values.
2025-01-14 12:07:21.991731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:21.992133 INFO::Done
2025-01-14 12:07:21.992382 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:21.994486 INFO::Starting hierarchical adjustment
2025-01-14 12:07:21.994926 INFO::Found 2 batches.
2025-01-14 12:07:21.995122 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:21.995364 INFO::Using default BPPARAM
2025-01-14 12:07:21.995548 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:21.99599 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.010021 INFO::Done
2025-01-14 12:07:22.010518 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.012392 INFO::ASW Batch was 0.00187592096362028 prior to batch effect correction and is now 0.00187592096362028 .
2025-01-14 12:07:22.012839 INFO::Total function execution time is 0.0380218029022217 s and adjustment time is 0.0151078701019287 s ( 39.73 )
2025-01-14 12:07:22.032216 INFO::Formatting Data.
2025-01-14 12:07:22.033031 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.033888 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.034812 INFO::Found 0 missing values.
2025-01-14 12:07:22.037392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.037924 INFO::Done
2025-01-14 12:07:22.038384 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.040348 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.040971 INFO::Found 3 batches.
2025-01-14 12:07:22.041409 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.041923 INFO::Using default BPPARAM
2025-01-14 12:07:22.042491 INFO::Processing subtree level 1
2025-01-14 12:07:22.162252 INFO::Adjusting the last 1 batches sequentially
2025-01-14 12:07:22.164637 INFO::Done
2025-01-14 12:07:22.164957 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.169462 INFO::ASW Batch was -0.00815344336178064 prior to batch effect correction and is now -0.162056832982606 .
2025-01-14 12:07:22.170864 INFO::Total function execution time is 0.138689041137695 s and adjustment time is 0.123807907104492 s ( 89.27 )
2025-01-14 12:07:22.19019 INFO::Skipping initial DF formatting
2025-01-14 12:07:22.191108 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.195442 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.196315 INFO::Found 5 batches.
2025-01-14 12:07:22.196823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.197541 INFO::Using default BPPARAM
2025-01-14 12:07:22.198056 INFO::Processing subtree level 1
2025-01-14 12:07:22.307325 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.312067 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.332757 INFO::Done
2025-01-14 12:07:22.333697 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.337587 INFO::ASW Batch was 0.51621439311372 prior to batch effect correction and is now 0.51621439311372 .
2025-01-14 12:07:22.338246 INFO::ASW Label was 0.331806840290359 prior to batch effect correction and is now 0.331806840290359 .
2025-01-14 12:07:22.338937 INFO::Total function execution time is 0.148922204971313 s and adjustment time is 0.136569976806641 s ( 91.71 )
2025-01-14 12:07:22.351179 INFO::Formatting Data.
2025-01-14 12:07:22.351685 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.352147 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.352687 INFO::Found 0 missing values.
2025-01-14 12:07:22.354308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.354595 INFO::Done
2025-01-14 12:07:22.354808 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.356915 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.357362 INFO::Found 5 batches.
2025-01-14 12:07:22.357584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.3579 INFO::Using default BPPARAM
2025-01-14 12:07:22.358258 INFO::Processing subtree level 1
2025-01-14 12:07:22.445424 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.450031 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.466679 INFO::Done
2025-01-14 12:07:22.467243 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.470723 INFO::ASW Batch was 0.205510996783549 prior to batch effect correction and is now -0.0625263670876252 .
2025-01-14 12:07:22.47118 INFO::ASW Label was 0.476068528094566 prior to batch effect correction and is now 0.860620692021759 .
2025-01-14 12:07:22.471803 INFO::Total function execution time is 0.120697975158691 s and adjustment time is 0.109379053115845 s ( 90.62 )
2025-01-14 12:07:22.472377 INFO::Formatting Data.
2025-01-14 12:07:22.472624 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.473234 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.473763 INFO::Found 0 missing values.
2025-01-14 12:07:22.475275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.475516 INFO::Done
2025-01-14 12:07:22.475713 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.476974 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.477313 INFO::Found 5 batches.
2025-01-14 12:07:22.477533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.477882 INFO::Using default BPPARAM
2025-01-14 12:07:22.478106 INFO::Processing subtree level 1
2025-01-14 12:07:22.583908 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.589394 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.611322 INFO::Done
2025-01-14 12:07:22.612353 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.616334 INFO::ASW Batch was 0.205510996783549 prior to batch effect correction and is now -0.0625263670876252 .
2025-01-14 12:07:22.616834 INFO::ASW Label was 0.476068528094566 prior to batch effect correction and is now 0.860620692021759 .
2025-01-14 12:07:22.617294 INFO::Total function execution time is 0.144876003265381 s and adjustment time is 0.1339271068573 s ( 92.44 )
2025-01-14 12:07:22.626647 INFO::Formatting Data.
2025-01-14 12:07:22.627512 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.628266 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.628854 INFO::Found 0 missing values.
2025-01-14 12:07:22.630816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.631181 INFO::Done
2025-01-14 12:07:22.6314 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.632904 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.633308 INFO::Found 5 batches.
2025-01-14 12:07:22.633487 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.63377 INFO::Using default BPPARAM
2025-01-14 12:07:22.634022 INFO::Processing subtree level 1
2025-01-14 12:07:22.708118 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.712027 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.72647 INFO::Done
2025-01-14 12:07:22.727109 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.729677 INFO::ASW Batch was 0.416062869857596 prior to batch effect correction and is now -0.092218778852407 .
2025-01-14 12:07:22.730148 INFO::ASW Label was 0.332294444415114 prior to batch effect correction and is now 0.837568687213688 .
2025-01-14 12:07:22.730739 INFO::Total function execution time is 0.10425591468811 s and adjustment time is 0.0931439399719238 s ( 89.34 )
2025-01-14 12:07:22.731328 INFO::Formatting Data.
2025-01-14 12:07:22.731664 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.732192 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.732715 INFO::Found 0 missing values.
2025-01-14 12:07:22.734838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.735265 INFO::Done
2025-01-14 12:07:22.735479 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.736981 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.73739 INFO::Found 5 batches.
2025-01-14 12:07:22.737582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.737867 INFO::Using default BPPARAM
2025-01-14 12:07:22.738067 INFO::Processing subtree level 1
2025-01-14 12:07:22.812092 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.816116 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.832511 INFO::Done
2025-01-14 12:07:22.833848 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.838194 INFO::ASW Batch was 0.416062869857596 prior to batch effect correction and is now -0.092218778852407 .
2025-01-14 12:07:22.838929 INFO::ASW Label was 0.332294444415114 prior to batch effect correction and is now 0.837568687213688 .
2025-01-14 12:07:22.840735 INFO::Total function execution time is 0.108840942382812 s and adjustment time is 0.0949831008911133 s ( 87.27 )
2025-01-14 12:07:22.857701 INFO::Formatting Data.
2025-01-14 12:07:22.858244 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.85873 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.859252 INFO::Found 0 missing values.
2025-01-14 12:07:22.860311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.860523 INFO::Done
2025-01-14 12:07:22.86073 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.862163 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.862624 INFO::Found 2 batches.
2025-01-14 12:07:22.862848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.863194 INFO::Using default BPPARAM
2025-01-14 12:07:22.863399 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.863822 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.871276 INFO::Done
2025-01-14 12:07:22.87169 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.873062 INFO::ASW Batch was 0.441587016517434 prior to batch effect correction and is now -0.00782173098687987 .
2025-01-14 12:07:22.873327 INFO::ASW Label was 0.545904239533328 prior to batch effect correction and is now 0.903520340115983 .
2025-01-14 12:07:22.873678 INFO::Total function execution time is 0.0161240100860596 s and adjustment time is 0.00871992111206055 s ( 54.08 )
2025-01-14 12:07:22.874003 INFO::Formatting Data.
2025-01-14 12:07:22.874206 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.874547 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.874941 INFO::Found 0 missing values.
2025-01-14 12:07:22.87592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.876121 INFO::Done
2025-01-14 12:07:22.876309 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.877548 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.87807 INFO::Found 2 batches.
2025-01-14 12:07:22.878279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.878558 INFO::Using default BPPARAM
2025-01-14 12:07:22.878761 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.887262 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.893593 INFO::Done
2025-01-14 12:07:22.900084 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.901795 INFO::ASW Batch was 0.441587016517434 prior to batch effect correction and is now -0.00782173098687987 .
2025-01-14 12:07:22.902092 INFO::ASW Label was 0.545904239533328 prior to batch effect correction and is now 0.903520340115983 .
2025-01-14 12:07:22.902369 INFO::Total function execution time is 0.0283660888671875 s and adjustment time is 0.0156271457672119 s ( 55.09 )
2025-01-14 12:07:22.935355 INFO::Formatting Data.
2025-01-14 12:07:22.935918 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.936252 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.936684 INFO::Found 0 missing values.
2025-01-14 12:07:22.937482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.937714 INFO::Done
2025-01-14 12:07:22.937888 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.938647 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.938889 INFO::Found 2 batches.
2025-01-14 12:07:22.939051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.939237 INFO::Using default BPPARAM
2025-01-14 12:07:22.939448 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.939817 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.951493 INFO::Done
2025-01-14 12:07:22.951747 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.952427 INFO::ASW Batch was 0.0892835051440957 prior to batch effect correction and is now -0.106598259049695 .
2025-01-14 12:07:22.952687 INFO::Total function execution time is 0.017423152923584 s and adjustment time is 0.0126340389251709 s ( 72.51 )
2025-01-14 12:07:22.957594 INFO::Formatting Data.
2025-01-14 12:07:22.957876 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.958167 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.958479 INFO::Found 0 missing values.
2025-01-14 12:07:22.95892 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.
2025-01-14 12:07:22.960368 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.960558 INFO::Done
2025-01-14 12:07:22.960715 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.961659 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.961904 INFO::Found 2 batches.
2025-01-14 12:07:22.96206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.962256 INFO::Using default BPPARAM
2025-01-14 12:07:22.962403 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.962714 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.968573 INFO::Done
2025-01-14 12:07:22.968854 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.969914 INFO::ASW Batch was 0.475511092566035 prior to batch effect correction and is now -0.0366853688592034 .
2025-01-14 12:07:22.970223 INFO::ASW Label was 0.62615141455578 prior to batch effect correction and is now 0.955009034287109 .
2025-01-14 12:07:22.970497 INFO::Total function execution time is 0.0129249095916748 s and adjustment time is 0.00670194625854492 s ( 51.85 )
2025-01-14 12:07:22.97074 INFO::Formatting Data.
2025-01-14 12:07:22.970924 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:22.971235 INFO::Removing potential empty rows and columns
2025-01-14 12:07:22.971622 INFO::Found 0 missing values.
2025-01-14 12:07:22.972019 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.
2025-01-14 12:07:22.973608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:22.973836 INFO::Done
2025-01-14 12:07:22.974006 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:22.974997 INFO::Starting hierarchical adjustment
2025-01-14 12:07:22.975299 INFO::Found 2 batches.
2025-01-14 12:07:22.975465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:22.975655 INFO::Using default BPPARAM
2025-01-14 12:07:22.975812 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:22.976095 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:22.984363 INFO::Done
2025-01-14 12:07:22.984998 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:22.986521 INFO::ASW Batch was 0.475511092566035 prior to batch effect correction and is now -0.0366853688592034 .
2025-01-14 12:07:22.988244 INFO::ASW Label was 0.62615141455578 prior to batch effect correction and is now 0.955009034287109 .
2025-01-14 12:07:22.988683 INFO::Total function execution time is 0.0179269313812256 s and adjustment time is 0.0090339183807373 s ( 50.39 )
2025-01-14 12:07:23.125824 INFO::Formatting Data.
2025-01-14 12:07:23.126318 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:23.126676 INFO::Removing potential empty rows and columns
2025-01-14 12:07:23.127128 INFO::Found 0 missing values.
2025-01-14 12:07:23.128567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:23.129117 INFO::Done
2025-01-14 12:07:23.129575 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:23.130768 INFO::Starting hierarchical adjustment
2025-01-14 12:07:23.131136 INFO::Found 3 batches.
2025-01-14 12:07:23.131349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:23.131638 INFO::Using default BPPARAM
2025-01-14 12:07:23.13186 INFO::Processing subtree level 1
2025-01-14 12:07:23.177788 INFO::Adjusting the last 1 batches sequentially
2025-01-14 12:07:23.179227 INFO::Done
2025-01-14 12:07:23.179462 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:23.182336 INFO::ASW Batch was -0.0901566406576416 prior to batch effect correction and is now -0.0901566406576416 .
2025-01-14 12:07:23.183274 INFO::Total function execution time is 0.0574769973754883 s and adjustment time is 0.0481550693511963 s ( 83.78 )
2025-01-14 12:07:23.184173 INFO::Formatting Data.
2025-01-14 12:07:23.184709 INFO::Typecasting input to dataframe.
2025-01-14 12:07:23.185321 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:23.186076 INFO::Removing potential empty rows and columns
2025-01-14 12:07:23.187218 INFO::Found 0 missing values.
2025-01-14 12:07:23.189783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:23.190289 INFO::Done
2025-01-14 12:07:23.190939 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:23.192118 INFO::Starting hierarchical adjustment
2025-01-14 12:07:23.192468 INFO::Found 3 batches.
2025-01-14 12:07:23.193141 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:23.19374 INFO::Using default BPPARAM
2025-01-14 12:07:23.19404 INFO::Processing subtree level 1
2025-01-14 12:07:23.314475 INFO::Adjusting the last 1 batches sequentially
2025-01-14 12:07:23.316027 INFO::Done
2025-01-14 12:07:23.316647 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:23.322659 INFO::ASW Batch was -0.0901566406576416 prior to batch effect correction and is now -0.0901566406576416 .
2025-01-14 12:07:23.324094 INFO::Total function execution time is 0.139641046524048 s and adjustment time is 0.123598098754883 s ( 88.51 )
2025-01-14 12:07:23.33556 INFO::Formatting Data.
2025-01-14 12:07:23.335906 INFO::Typecasting input to dataframe.
2025-01-14 12:07:23.336218 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:23.337523 INFO::Removing potential empty rows and columns
2025-01-14 12:07:23.338805 INFO::Found 0 missing values.
2025-01-14 12:07:23.341697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:23.342226 INFO::Done
2025-01-14 12:07:23.342916 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:23.344411 INFO::Starting hierarchical adjustment
2025-01-14 12:07:23.344651 INFO::Found 3 batches.
2025-01-14 12:07:23.344941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:23.345155 INFO::Using default BPPARAM
2025-01-14 12:07:23.345318 INFO::Processing subtree level 1
2025-01-14 12:07:23.478551 INFO::Adjusting the last 1 batches sequentially
2025-01-14 12:07:23.479939 INFO::Done
2025-01-14 12:07:23.480236 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:23.487946 INFO::ASW Batch was 0.0302295073141798 prior to batch effect correction and is now 0.0302295073141798 .
2025-01-14 12:07:23.489079 INFO::Total function execution time is 0.153398990631104 s and adjustment time is 0.135317087173462 s ( 88.21 )
2025-01-14 12:07:23.646664 INFO::Formatting Data.
2025-01-14 12:07:23.647288 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:23.647977 INFO::Removing potential empty rows and columns
2025-01-14 12:07:23.649462 INFO::Found 1000 missing values.
2025-01-14 12:07:23.659719 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:23.660281 INFO::Done
2025-01-14 12:07:23.660536 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:23.663475 INFO::Starting hierarchical adjustment
2025-01-14 12:07:23.663977 INFO::Found 10 batches.
2025-01-14 12:07:23.664256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:23.664584 INFO::Using default BPPARAM
2025-01-14 12:07:23.664911 INFO::Processing subtree level 1
2025-01-14 12:07:23.784124 INFO::Processing subtree level 2
2025-01-14 12:07:24.022276 INFO::Adjusting the last 1 batches sequentially
2025-01-14 12:07:24.023947 INFO::Done
2025-01-14 12:07:24.024293 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:24.028148 INFO::ASW Batch was 0.50675487564663 prior to batch effect correction and is now 0.50675487564663 .
2025-01-14 12:07:24.028443 INFO::ASW Label was 0.305477154225533 prior to batch effect correction and is now 0.305477154225533 .
2025-01-14 12:07:24.028939 INFO::Total function execution time is 0.38227391242981 s and adjustment time is 0.360082864761353 s ( 94.19 )
2025-01-14 12:07:24.029494 INFO::Formatting Data.
2025-01-14 12:07:24.02974 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:24.03031 INFO::Removing potential empty rows and columns
2025-01-14 12:07:24.031565 INFO::Found 1000 missing values.
2025-01-14 12:07:24.039301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:24.039635 INFO::Done
2025-01-14 12:07:24.039848 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:24.042215 INFO::Starting hierarchical adjustment
2025-01-14 12:07:24.042573 INFO::Found 10 batches.
2025-01-14 12:07:24.549329 INFO::Set up parallel execution backend with 2 workers
2025-01-14 12:07:24.54962 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-14 12:07:25.189719 INFO::Adjusting the last 2 batches sequentially
2025-01-14 12:07:25.190502 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 12:07:25.199703 INFO::Done
2025-01-14 12:07:25.199941 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:25.202673 INFO::ASW Batch was 0.50675487564663 prior to batch effect correction and is now 0.50675487564663 .
2025-01-14 12:07:25.203725 INFO::ASW Label was 0.305477154225533 prior to batch effect correction and is now 0.305477154225533 .
2025-01-14 12:07:25.204512 INFO::Total function execution time is 1.17496609687805 s and adjustment time is 1.15718293190002 s ( 98.49 )
2025-01-14 12:07:25.293285 INFO::Formatting Data.
2025-01-14 12:07:25.293764 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.294216 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.294959 INFO::Found 0 missing values.
2025-01-14 12:07:25.296409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.296642 INFO::Done
2025-01-14 12:07:25.296985 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 12:07:25.298181 INFO::Starting hierarchical adjustment
2025-01-14 12:07:25.298681 INFO::Found 3 batches.
2025-01-14 12:07:25.299134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 12:07:25.299661 INFO::Using default BPPARAM
2025-01-14 12:07:25.299859 INFO::Processing subtree level 1
2025-01-14 12:07:25.367158 INFO::Adjusting the last 1 batches sequentially
2025-01-14 12:07:25.369954 INFO::Done
2025-01-14 12:07:25.371303 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 12:07:25.374826 INFO::ASW Batch was 0.250953256959942 prior to batch effect correction and is now -0.169646446127974 .
2025-01-14 12:07:25.375242 INFO::ASW Label was -0.200304179527985 prior to batch effect correction and is now -0.0192743023492933 .
2025-01-14 12:07:25.379225 INFO::Total function execution time is 0.085874080657959 s and adjustment time is 0.07151198387146 s ( 83.28 )
2025-01-14 12:07:25.460949 INFO::Formatting Data.
2025-01-14 12:07:25.461428 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.461812 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.462358 INFO::Found 2 missing values.
2025-01-14 12:07:25.463792 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.464052 INFO::Done
2025-01-14 12:07:25.480568 INFO::Found NA in Reference column
2025-01-14 12:07:25.486155 INFO::Require at least two references per batch.
2025-01-14 12:07:25.498564 INFO::Formatting Data.
2025-01-14 12:07:25.499048 INFO::Recognized SummarizedExperiment
2025-01-14 12:07:25.499361 INFO::Typecasting input to dataframe.
2025-01-14 12:07:25.503811 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.504333 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.506814 INFO::Found 0 missing values.
2025-01-14 12:07:25.513645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.514235 INFO::Done
2025-01-14 12:07:25.523475 INFO::Formatting Data.
2025-01-14 12:07:25.524204 INFO::Recognized SummarizedExperiment
2025-01-14 12:07:25.524575 INFO::Typecasting input to dataframe.
2025-01-14 12:07:25.532593 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.533111 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.534476 INFO::Found 0 missing values.
2025-01-14 12:07:25.54028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.541014 INFO::Done
2025-01-14 12:07:25.548491 INFO::Formatting Data.
2025-01-14 12:07:25.548803 INFO::Recognized SummarizedExperiment
2025-01-14 12:07:25.549103 INFO::Typecasting input to dataframe.
2025-01-14 12:07:25.557977 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.558695 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.559337 INFO::Found 0 missing values.
2025-01-14 12:07:25.559858 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.
2025-01-14 12:07:25.562195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.562622 INFO::Done
2025-01-14 12:07:25.569995 INFO::Formatting Data.
2025-01-14 12:07:25.570479 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.570915 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.571596 INFO::Found 0 missing values.
2025-01-14 12:07:25.573701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.574078 INFO::Done
2025-01-14 12:07:25.581794 INFO::Formatting Data.
2025-01-14 12:07:25.582112 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.582795 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.583344 INFO::Found 0 missing values.
2025-01-14 12:07:25.585403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.585915 INFO::Done
2025-01-14 12:07:25.613271 INFO::Formatting Data.
2025-01-14 12:07:25.613564 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.613907 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.614293 INFO::Found 1 missing values.
2025-01-14 12:07:25.615092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.615257 INFO::Done
2025-01-14 12:07:25.630393 INFO::Formatting Data.
2025-01-14 12:07:25.630687 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.630994 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.631307 INFO::Found 2 missing values.
2025-01-14 12:07:25.631642 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.
2025-01-14 12:07:25.63287 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.633096 INFO::Done
2025-01-14 12:07:25.637806 INFO::Formatting Data.
2025-01-14 12:07:25.638071 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.638658 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.639103 INFO::Found 2 missing values.
2025-01-14 12:07:25.640044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.640332 INFO::Done
2025-01-14 12:07:25.645981 INFO::Formatting Data.
2025-01-14 12:07:25.646669 INFO::Typecasting input to dataframe.
2025-01-14 12:07:25.646983 INFO::Replacing NaNs with NAs.
2025-01-14 12:07:25.647466 INFO::Removing potential empty rows and columns
2025-01-14 12:07:25.647875 INFO::Found 0 missing values.
2025-01-14 12:07:25.648965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 12:07:25.649224 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.899 2.790 21.835
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.916 | 1.305 | 20.576 | |
| compute_asw | 0.030 | 0.002 | 0.032 | |
| count_existing | 0.016 | 0.001 | 0.017 | |
| generate_data_covariables | 0.014 | 0.001 | 0.015 | |
| generate_dataset | 0.013 | 0.002 | 0.015 | |