Yannis Schumann
| Snapshot Date: 2025-02-18 13:40 -0500 (Tue, 18 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0500 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-19 11:42 -0500 (Wed, 19 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.3.6 |
| Command: /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_1.3.6.tar.gz |
| StartedAt: 2025-02-18 18:58:17 -0500 (Tue, 18 Feb 2025) |
| EndedAt: 2025-02-18 18:59:44 -0500 (Tue, 18 Feb 2025) |
| EllapsedTime: 87.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 26.42 1.474 19.189
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.3.6’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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")
2025-02-18 18:59:23.148106 INFO::Formatting Data.
2025-02-18 18:59:23.15206 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:23.162985 INFO::Removing potential empty rows and columns
2025-02-18 18:59:23.462391 INFO::Found 0 missing values.
2025-02-18 18:59:23.466484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:23.467184 INFO::Done
2025-02-18 18:59:23.467718 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:23.482079 INFO::Starting hierarchical adjustment
2025-02-18 18:59:23.483282 INFO::Found 3 batches.
2025-02-18 18:59:23.484136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:23.485301 INFO::Using default BPPARAM
2025-02-18 18:59:23.485826 INFO::Processing subtree level 1
2025-02-18 18:59:23.644016 INFO::Adjusting the last 1 batches sequentially
2025-02-18 18:59:23.649999 INFO::Done
2025-02-18 18:59:23.650996 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:23.655746 INFO::ASW Batch was -0.151193794879938 prior to batch effect correction and is now -0.151193794879938 .
2025-02-18 18:59:23.657273 INFO::Total function execution time is 0.509680032730103 s and adjustment time is 0.166961908340454 s ( 32.76 )
2025-02-18 18:59:23.681072 INFO::Formatting Data.
2025-02-18 18:59:23.681859 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:23.682802 INFO::Removing potential empty rows and columns
2025-02-18 18:59:23.683906 INFO::Found 0 missing values.
2025-02-18 18:59:23.684849 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-18 18:59:23.695281 INFO::Formatting Data.
2025-02-18 18:59:23.696094 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:23.696987 INFO::Removing potential empty rows and columns
2025-02-18 18:59:23.697993 INFO::Found 0 missing values.
2025-02-18 18:59:23.698886 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-18 18:59:23.718515 INFO::Formatting Data.
2025-02-18 18:59:23.7193 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:23.720191 INFO::Removing potential empty rows and columns
2025-02-18 18:59:23.721145 INFO::Found 0 missing values.
2025-02-18 18:59:23.722456 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-18 18:59:23.726507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:23.727101 INFO::Done
2025-02-18 18:59:23.72759 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:23.729423 INFO::Starting hierarchical adjustment
2025-02-18 18:59:23.730099 INFO::Found 2 batches.
2025-02-18 18:59:23.73059 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:23.731176 INFO::Using default BPPARAM
2025-02-18 18:59:23.731656 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:23.732783 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:23.758567 INFO::Done
2025-02-18 18:59:23.759826 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:23.761839 INFO::ASW Batch was 0.00833595145762155 prior to batch effect correction and is now -0.104840299018643 .
2025-02-18 18:59:23.76261 INFO::Total function execution time is 0.0441679954528809 s and adjustment time is 0.0284619331359863 s ( 64.44 )
2025-02-18 18:59:23.765303 INFO::Formatting Data.
2025-02-18 18:59:23.765904 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:23.774184 INFO::Formatting Data.
2025-02-18 18:59:23.775135 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:23.776546 INFO::Removing potential empty rows and columns
2025-02-18 18:59:23.778076 INFO::Found 0 missing values.
2025-02-18 18:59:23.817971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:23.818903 INFO::Done
2025-02-18 18:59:23.819634 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:23.822226 INFO::Starting hierarchical adjustment
2025-02-18 18:59:23.823192 INFO::Found 2 batches.
2025-02-18 18:59:23.823898 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:23.824719 INFO::Using default BPPARAM
2025-02-18 18:59:23.825351 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:23.826178 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:23.84336 INFO::Done
2025-02-18 18:59:23.844426 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:23.846282 INFO::ASW Batch was 0.0106029205742719 prior to batch effect correction and is now -0.125619083508459 .
2025-02-18 18:59:23.847033 INFO::Total function execution time is 0.0729238986968994 s and adjustment time is 0.0203258991241455 s ( 27.87 )
2025-02-18 18:59:23.847951 INFO::Formatting Data.
2025-02-18 18:59:23.848474 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:23.849232 INFO::Removing potential empty rows and columns
2025-02-18 18:59:23.850091 INFO::Found 0 missing values.
2025-02-18 18:59:23.852644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:23.853149 INFO::Done
2025-02-18 18:59:23.853693 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:23.856148 INFO::Starting hierarchical adjustment
2025-02-18 18:59:23.857024 INFO::Found 2 batches.
2025-02-18 18:59:23.857665 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:23.858397 INFO::Using default BPPARAM
2025-02-18 18:59:23.859061 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:23.860409 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:23.877198 INFO::Done
2025-02-18 18:59:23.878144 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:23.880338 INFO::ASW Batch was 0.0106029205742719 prior to batch effect correction and is now -0.125619083508459 .
2025-02-18 18:59:23.881113 INFO::Total function execution time is 0.0331408977508545 s and adjustment time is 0.0202980041503906 s ( 61.25 )
2025-02-18 18:59:27.055053 INFO::Formatting Data.
2025-02-18 18:59:27.056004 INFO::Recognized SummarizedExperiment
2025-02-18 18:59:27.056748 INFO::Typecasting input to dataframe.
2025-02-18 18:59:27.093446 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:27.094753 INFO::Removing potential empty rows and columns
2025-02-18 18:59:27.097649 INFO::Found 0 missing values.
2025-02-18 18:59:27.103792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:27.104416 INFO::Done
2025-02-18 18:59:27.104891 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:27.108085 INFO::Starting hierarchical adjustment
2025-02-18 18:59:27.108789 INFO::Found 2 batches.
2025-02-18 18:59:27.109259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:27.11033 INFO::Using default BPPARAM
2025-02-18 18:59:27.110811 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:27.111712 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:27.164588 INFO::Done
2025-02-18 18:59:27.165272 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:27.168754 INFO::ASW Batch was 0.014879216193369 prior to batch effect correction and is now -0.0940931241641023 .
2025-02-18 18:59:27.169603 INFO::Total function execution time is 0.114989042282104 s and adjustment time is 0.0558998584747314 s ( 48.61 )
2025-02-18 18:59:27.193159 INFO::Formatting Data.
2025-02-18 18:59:27.194255 INFO::Recognized SummarizedExperiment
2025-02-18 18:59:27.195209 INFO::Typecasting input to dataframe.
2025-02-18 18:59:27.206568 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:27.208274 INFO::Removing potential empty rows and columns
2025-02-18 18:59:27.213543 INFO::Found 0 missing values.
2025-02-18 18:59:27.221715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:27.222728 INFO::Done
2025-02-18 18:59:27.223297 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:27.227244 INFO::Starting hierarchical adjustment
2025-02-18 18:59:27.228512 INFO::Found 2 batches.
2025-02-18 18:59:27.229254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:27.230167 INFO::Using default BPPARAM
2025-02-18 18:59:27.230871 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:27.232334 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:27.26312 INFO::Done
2025-02-18 18:59:27.263913 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:27.267683 INFO::ASW Batch was -0.0116296799642237 prior to batch effect correction and is now -0.0116296799642237 .
2025-02-18 18:59:27.268561 INFO::Total function execution time is 0.0754868984222412 s and adjustment time is 0.0348141193389893 s ( 46.12 )
2025-02-18 18:59:27.293136 INFO::Formatting Data.
2025-02-18 18:59:27.294509 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:27.295857 INFO::Removing potential empty rows and columns
2025-02-18 18:59:27.296875 INFO::Found 0 missing values.
2025-02-18 18:59:27.299694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:27.300624 INFO::Done
2025-02-18 18:59:27.301487 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:27.303609 INFO::Starting hierarchical adjustment
2025-02-18 18:59:27.304258 INFO::Found 3 batches.
2025-02-18 18:59:27.304846 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:27.305711 INFO::Using default BPPARAM
2025-02-18 18:59:27.306462 INFO::Processing subtree level 1
2025-02-18 18:59:27.701487 INFO::Adjusting the last 1 batches sequentially
2025-02-18 18:59:27.704791 INFO::Done
2025-02-18 18:59:27.70559 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:27.709897 INFO::ASW Batch was -0.0806338330161988 prior to batch effect correction and is now -0.126350307280279 .
2025-02-18 18:59:27.726095 INFO::Total function execution time is 0.426225900650024 s and adjustment time is 0.400624990463257 s ( 93.99 )
2025-02-18 18:59:27.858601 INFO::Skipping initial DF formatting
2025-02-18 18:59:27.859689 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:27.863413 INFO::Starting hierarchical adjustment
2025-02-18 18:59:27.864222 INFO::Found 5 batches.
2025-02-18 18:59:27.864733 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:27.86533 INFO::Using default BPPARAM
2025-02-18 18:59:27.865818 INFO::Processing subtree level 1
2025-02-18 18:59:28.110965 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:28.123476 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:28.160389 INFO::Done
2025-02-18 18:59:28.161171 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:28.169004 INFO::ASW Batch was 0.475967274545007 prior to batch effect correction and is now 0.475967274545007 .
2025-02-18 18:59:28.170112 INFO::ASW Label was 0.396711574781387 prior to batch effect correction and is now 0.396711574781387 .
2025-02-18 18:59:28.171679 INFO::Total function execution time is 0.313244104385376 s and adjustment time is 0.296292781829834 s ( 94.59 )
2025-02-18 18:59:28.198029 INFO::Formatting Data.
2025-02-18 18:59:28.199045 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:28.200825 INFO::Removing potential empty rows and columns
2025-02-18 18:59:28.202627 INFO::Found 0 missing values.
2025-02-18 18:59:28.208979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:28.209913 INFO::Done
2025-02-18 18:59:28.21078 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:28.215182 INFO::Starting hierarchical adjustment
2025-02-18 18:59:28.21644 INFO::Found 5 batches.
2025-02-18 18:59:28.217335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:28.21829 INFO::Using default BPPARAM
2025-02-18 18:59:28.219317 INFO::Processing subtree level 1
2025-02-18 18:59:28.40205 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:28.425579 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:28.47543 INFO::Done
2025-02-18 18:59:28.476519 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:28.481449 INFO::ASW Batch was 0.394504874107618 prior to batch effect correction and is now 0.00857660811785773 .
2025-02-18 18:59:28.482552 INFO::ASW Label was 0.508219176229876 prior to batch effect correction and is now 0.634721903979073 .
2025-02-18 18:59:28.484146 INFO::Total function execution time is 0.286118030548096 s and adjustment time is 0.259248018264771 s ( 90.61 )
2025-02-18 18:59:28.485265 INFO::Formatting Data.
2025-02-18 18:59:28.486361 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:28.487874 INFO::Removing potential empty rows and columns
2025-02-18 18:59:28.489027 INFO::Found 0 missing values.
2025-02-18 18:59:28.493759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:28.494428 INFO::Done
2025-02-18 18:59:28.494945 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:28.498598 INFO::Starting hierarchical adjustment
2025-02-18 18:59:28.49975 INFO::Found 5 batches.
2025-02-18 18:59:28.500578 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:28.501518 INFO::Using default BPPARAM
2025-02-18 18:59:28.502608 INFO::Processing subtree level 1
2025-02-18 18:59:28.690544 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:28.701861 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:28.733557 INFO::Done
2025-02-18 18:59:28.73437 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:28.739263 INFO::ASW Batch was 0.394504874107618 prior to batch effect correction and is now 0.00857660811785773 .
2025-02-18 18:59:28.740152 INFO::ASW Label was 0.508219176229876 prior to batch effect correction and is now 0.634721903979073 .
2025-02-18 18:59:28.741356 INFO::Total function execution time is 0.256132125854492 s and adjustment time is 0.234056949615479 s ( 91.38 )
2025-02-18 18:59:28.761129 INFO::Formatting Data.
2025-02-18 18:59:28.761953 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:28.763183 INFO::Removing potential empty rows and columns
2025-02-18 18:59:28.764618 INFO::Found 0 missing values.
2025-02-18 18:59:28.769654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:28.770556 INFO::Done
2025-02-18 18:59:28.771299 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:28.775243 INFO::Starting hierarchical adjustment
2025-02-18 18:59:28.776502 INFO::Found 5 batches.
2025-02-18 18:59:28.777646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:28.778496 INFO::Using default BPPARAM
2025-02-18 18:59:28.779895 INFO::Processing subtree level 1
2025-02-18 18:59:28.980555 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:28.987799 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:29.017352 INFO::Done
2025-02-18 18:59:29.018409 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:29.022354 INFO::ASW Batch was 0.327432471535738 prior to batch effect correction and is now -0.107618591195054 .
2025-02-18 18:59:29.02298 INFO::ASW Label was 0.430693154433765 prior to batch effect correction and is now 0.865133187388604 .
2025-02-18 18:59:29.023786 INFO::Total function execution time is 0.262734889984131 s and adjustment time is 0.241141080856323 s ( 91.78 )
2025-02-18 18:59:29.024949 INFO::Formatting Data.
2025-02-18 18:59:29.025564 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:29.026885 INFO::Removing potential empty rows and columns
2025-02-18 18:59:29.0286 INFO::Found 0 missing values.
2025-02-18 18:59:29.035883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:29.036537 INFO::Done
2025-02-18 18:59:29.037496 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:29.041988 INFO::Starting hierarchical adjustment
2025-02-18 18:59:29.0432 INFO::Found 5 batches.
2025-02-18 18:59:29.044053 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:29.045111 INFO::Using default BPPARAM
2025-02-18 18:59:29.046129 INFO::Processing subtree level 1
2025-02-18 18:59:29.192986 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:29.218956 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:29.252878 INFO::Done
2025-02-18 18:59:29.253925 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:29.258631 INFO::ASW Batch was 0.327432471535738 prior to batch effect correction and is now -0.107618591195054 .
2025-02-18 18:59:29.259579 INFO::ASW Label was 0.430693154433765 prior to batch effect correction and is now 0.865133187388604 .
2025-02-18 18:59:29.261257 INFO::Total function execution time is 0.235983848571777 s and adjustment time is 0.209923028945923 s ( 88.96 )
2025-02-18 18:59:29.281706 INFO::Formatting Data.
2025-02-18 18:59:29.282582 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:29.283573 INFO::Removing potential empty rows and columns
2025-02-18 18:59:29.28459 INFO::Found 0 missing values.
2025-02-18 18:59:29.288647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:29.289556 INFO::Done
2025-02-18 18:59:29.290377 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:29.294637 INFO::Starting hierarchical adjustment
2025-02-18 18:59:29.29544 INFO::Found 2 batches.
2025-02-18 18:59:29.29599 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:29.296902 INFO::Using default BPPARAM
2025-02-18 18:59:29.297682 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:29.298996 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:29.319723 INFO::Done
2025-02-18 18:59:29.320424 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:29.324689 INFO::ASW Batch was 0.414708064789131 prior to batch effect correction and is now 0.150028227473686 .
2025-02-18 18:59:29.325693 INFO::ASW Label was 0.728629192359571 prior to batch effect correction and is now 0.859202805472474 .
2025-02-18 18:59:29.326683 INFO::Total function execution time is 0.0451710224151611 s and adjustment time is 0.0244009494781494 s ( 54.02 )
2025-02-18 18:59:29.327808 INFO::Formatting Data.
2025-02-18 18:59:29.328401 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:29.329245 INFO::Removing potential empty rows and columns
2025-02-18 18:59:29.330181 INFO::Found 0 missing values.
2025-02-18 18:59:29.332728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:29.333387 INFO::Done
2025-02-18 18:59:29.33416 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:29.338487 INFO::Starting hierarchical adjustment
2025-02-18 18:59:29.339571 INFO::Found 2 batches.
2025-02-18 18:59:29.340364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:29.341253 INFO::Using default BPPARAM
2025-02-18 18:59:29.342015 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:29.343243 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:29.359913 INFO::Done
2025-02-18 18:59:29.360833 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:29.364653 INFO::ASW Batch was 0.414708064789131 prior to batch effect correction and is now 0.150028227473686 .
2025-02-18 18:59:29.365274 INFO::ASW Label was 0.728629192359571 prior to batch effect correction and is now 0.859202805472474 .
2025-02-18 18:59:29.366228 INFO::Total function execution time is 0.0383739471435547 s and adjustment time is 0.0205180644989014 s ( 53.47 )
2025-02-18 18:59:29.383109 INFO::Formatting Data.
2025-02-18 18:59:29.384265 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:29.385206 INFO::Removing potential empty rows and columns
2025-02-18 18:59:29.386269 INFO::Found 0 missing values.
2025-02-18 18:59:29.389394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:29.390182 INFO::Done
2025-02-18 18:59:29.390909 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:29.39337 INFO::Starting hierarchical adjustment
2025-02-18 18:59:29.394056 INFO::Found 2 batches.
2025-02-18 18:59:29.394905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:29.395506 INFO::Using default BPPARAM
2025-02-18 18:59:29.3962 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:29.397257 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:29.436928 INFO::Done
2025-02-18 18:59:29.437634 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:29.439636 INFO::ASW Batch was -0.0938170847986042 prior to batch effect correction and is now -0.163109269918437 .
2025-02-18 18:59:29.44044 INFO::Total function execution time is 0.0574150085449219 s and adjustment time is 0.0429730415344238 s ( 74.85 )
2025-02-18 18:59:29.457186 INFO::Formatting Data.
2025-02-18 18:59:29.457971 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:29.458928 INFO::Removing potential empty rows and columns
2025-02-18 18:59:29.459858 INFO::Found 0 missing values.
2025-02-18 18:59:29.460947 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-18 18:59:29.465337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:29.466082 INFO::Done
2025-02-18 18:59:29.466639 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:29.470563 INFO::Starting hierarchical adjustment
2025-02-18 18:59:29.47162 INFO::Found 2 batches.
2025-02-18 18:59:29.472389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:29.472954 INFO::Using default BPPARAM
2025-02-18 18:59:29.473436 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:29.474523 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:29.494031 INFO::Done
2025-02-18 18:59:29.494805 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:29.498453 INFO::ASW Batch was 0.284237619062405 prior to batch effect correction and is now 0.0842041802581729 .
2025-02-18 18:59:29.499253 INFO::ASW Label was 0.734931046696992 prior to batch effect correction and is now 0.837297633185059 .
2025-02-18 18:59:29.500007 INFO::Total function execution time is 0.0429179668426514 s and adjustment time is 0.0226211547851562 s ( 52.71 )
2025-02-18 18:59:29.501057 INFO::Formatting Data.
2025-02-18 18:59:29.501958 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:29.503018 INFO::Removing potential empty rows and columns
2025-02-18 18:59:29.504215 INFO::Found 0 missing values.
2025-02-18 18:59:29.50529 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-18 18:59:29.511995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:29.512739 INFO::Done
2025-02-18 18:59:29.513284 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:29.51702 INFO::Starting hierarchical adjustment
2025-02-18 18:59:29.518017 INFO::Found 2 batches.
2025-02-18 18:59:29.518764 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:29.519632 INFO::Using default BPPARAM
2025-02-18 18:59:29.520346 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:29.521718 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:29.540563 INFO::Done
2025-02-18 18:59:29.541316 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:29.54443 INFO::ASW Batch was 0.284237619062405 prior to batch effect correction and is now 0.0842041802581729 .
2025-02-18 18:59:29.545017 INFO::ASW Label was 0.734931046696992 prior to batch effect correction and is now 0.837297633185059 .
2025-02-18 18:59:29.545729 INFO::Total function execution time is 0.0447170734405518 s and adjustment time is 0.0227630138397217 s ( 50.9 )
2025-02-18 18:59:29.7991 INFO::Formatting Data.
2025-02-18 18:59:29.799868 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:29.800894 INFO::Removing potential empty rows and columns
2025-02-18 18:59:29.802133 INFO::Found 0 missing values.
2025-02-18 18:59:29.805394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:29.806193 INFO::Done
2025-02-18 18:59:29.806892 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:29.808791 INFO::Starting hierarchical adjustment
2025-02-18 18:59:29.809674 INFO::Found 3 batches.
2025-02-18 18:59:29.810418 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:29.811527 INFO::Using default BPPARAM
2025-02-18 18:59:29.812059 INFO::Processing subtree level 1
2025-02-18 18:59:29.929087 INFO::Adjusting the last 1 batches sequentially
2025-02-18 18:59:29.938073 INFO::Done
2025-02-18 18:59:29.94141 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:29.947858 INFO::ASW Batch was -0.0220704648785131 prior to batch effect correction and is now -0.0220704648785131 .
2025-02-18 18:59:29.95203 INFO::Total function execution time is 0.152844905853271 s and adjustment time is 0.12848687171936 s ( 84.06 )
2025-02-18 18:59:29.953862 INFO::Formatting Data.
2025-02-18 18:59:29.954872 INFO::Typecasting input to dataframe.
2025-02-18 18:59:29.95594 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:29.956878 INFO::Removing potential empty rows and columns
2025-02-18 18:59:29.959348 INFO::Found 0 missing values.
2025-02-18 18:59:29.962592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:29.963109 INFO::Done
2025-02-18 18:59:29.963676 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:29.965549 INFO::Starting hierarchical adjustment
2025-02-18 18:59:29.966252 INFO::Found 3 batches.
2025-02-18 18:59:29.966916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:29.967818 INFO::Using default BPPARAM
2025-02-18 18:59:29.968634 INFO::Processing subtree level 1
2025-02-18 18:59:30.075664 INFO::Adjusting the last 1 batches sequentially
2025-02-18 18:59:30.09341 INFO::Done
2025-02-18 18:59:30.094792 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:30.10653 INFO::ASW Batch was -0.0220704648785131 prior to batch effect correction and is now -0.0220704648785131 .
2025-02-18 18:59:30.110722 INFO::Total function execution time is 0.156183004379272 s and adjustment time is 0.127285003662109 s ( 81.5 )
2025-02-18 18:59:30.131749 INFO::Formatting Data.
2025-02-18 18:59:30.132586 INFO::Typecasting input to dataframe.
2025-02-18 18:59:30.133399 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:30.134246 INFO::Removing potential empty rows and columns
2025-02-18 18:59:30.136503 INFO::Found 0 missing values.
2025-02-18 18:59:30.139862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:30.1412 INFO::Done
2025-02-18 18:59:30.141792 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:30.143836 INFO::Starting hierarchical adjustment
2025-02-18 18:59:30.144711 INFO::Found 3 batches.
2025-02-18 18:59:30.145438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:30.146027 INFO::Using default BPPARAM
2025-02-18 18:59:30.146526 INFO::Processing subtree level 1
2025-02-18 18:59:30.251433 INFO::Adjusting the last 1 batches sequentially
2025-02-18 18:59:30.283106 INFO::Done
2025-02-18 18:59:30.285444 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:30.297766 INFO::ASW Batch was -0.084153792956304 prior to batch effect correction and is now -0.084153792956304 .
2025-02-18 18:59:30.303145 INFO::Total function execution time is 0.170037984848022 s and adjustment time is 0.138458013534546 s ( 81.43 )
2025-02-18 18:59:30.543325 INFO::Formatting Data.
2025-02-18 18:59:30.544517 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:30.547716 INFO::Removing potential empty rows and columns
2025-02-18 18:59:30.551359 INFO::Found 1000 missing values.
2025-02-18 18:59:30.57713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:30.578494 INFO::Done
2025-02-18 18:59:30.57941 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:30.586864 INFO::Starting hierarchical adjustment
2025-02-18 18:59:30.587766 INFO::Found 10 batches.
2025-02-18 18:59:30.588417 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:30.589356 INFO::Using default BPPARAM
2025-02-18 18:59:30.590089 INFO::Processing subtree level 1
2025-02-18 18:59:30.76307 INFO::Processing subtree level 2
2025-02-18 18:59:30.970045 INFO::Adjusting the last 1 batches sequentially
2025-02-18 18:59:30.982492 INFO::Done
2025-02-18 18:59:30.984017 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:30.998614 INFO::ASW Batch was 0.513985081236156 prior to batch effect correction and is now 0.513985081236156 .
2025-02-18 18:59:31.006005 INFO::ASW Label was 0.317347106651534 prior to batch effect correction and is now 0.317347106651534 .
2025-02-18 18:59:31.010188 INFO::Total function execution time is 0.467060089111328 s and adjustment time is 0.39483904838562 s ( 84.54 )
2025-02-18 18:59:31.011918 INFO::Formatting Data.
2025-02-18 18:59:31.013119 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:31.015733 INFO::Removing potential empty rows and columns
2025-02-18 18:59:31.020138 INFO::Found 1000 missing values.
2025-02-18 18:59:31.046942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:31.048473 INFO::Done
2025-02-18 18:59:31.050082 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:31.059526 INFO::Starting hierarchical adjustment
2025-02-18 18:59:31.060898 INFO::Found 10 batches.
2025-02-18 18:59:32.109579 INFO::Set up parallel execution backend with 2 workers
2025-02-18 18:59:32.110349 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-18 18:59:33.378059 INFO::Adjusting the last 2 batches sequentially
2025-02-18 18:59:33.379656 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-18 18:59:33.394036 INFO::Done
2025-02-18 18:59:33.394904 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:33.401286 INFO::ASW Batch was 0.513985081236156 prior to batch effect correction and is now 0.513985081236156 .
2025-02-18 18:59:33.402152 INFO::ASW Label was 0.317347106651534 prior to batch effect correction and is now 0.317347106651534 .
2025-02-18 18:59:33.403056 INFO::Total function execution time is 2.39134311676025 s and adjustment time is 2.3334698677063 s ( 97.58 )
2025-02-18 18:59:33.656584 INFO::Formatting Data.
2025-02-18 18:59:33.657697 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:33.658681 INFO::Removing potential empty rows and columns
2025-02-18 18:59:33.660315 INFO::Found 0 missing values.
2025-02-18 18:59:33.664075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:33.664602 INFO::Done
2025-02-18 18:59:33.665083 INFO::Acquiring quality metrics before batch effect correction.
2025-02-18 18:59:33.668508 INFO::Starting hierarchical adjustment
2025-02-18 18:59:33.669259 INFO::Found 3 batches.
2025-02-18 18:59:33.669958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-18 18:59:33.670968 INFO::Using default BPPARAM
2025-02-18 18:59:33.671506 INFO::Processing subtree level 1
2025-02-18 18:59:33.836373 INFO::Adjusting the last 1 batches sequentially
2025-02-18 18:59:33.854785 INFO::Done
2025-02-18 18:59:33.857971 INFO::Acquiring quality metrics after batch effect correction.
2025-02-18 18:59:33.869952 INFO::ASW Batch was 0.271864898499675 prior to batch effect correction and is now -0.17188157124919 .
2025-02-18 18:59:33.871017 INFO::ASW Label was -0.169897884441521 prior to batch effect correction and is now 0.0845662927074693 .
2025-02-18 18:59:33.874137 INFO::Total function execution time is 0.216787099838257 s and adjustment time is 0.1856689453125 s ( 85.65 )
2025-02-18 18:59:34.043287 INFO::Formatting Data.
2025-02-18 18:59:34.044078 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.04535 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.046912 INFO::Found 2 missing values.
2025-02-18 18:59:34.049749 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.050573 INFO::Done
2025-02-18 18:59:34.092761 INFO::Found NA in Reference column
2025-02-18 18:59:34.109036 INFO::Require at least two references per batch.
2025-02-18 18:59:34.13664 INFO::Formatting Data.
2025-02-18 18:59:34.137677 INFO::Recognized SummarizedExperiment
2025-02-18 18:59:34.138499 INFO::Typecasting input to dataframe.
2025-02-18 18:59:34.152576 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.153863 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.158174 INFO::Found 0 missing values.
2025-02-18 18:59:34.16789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.168848 INFO::Done
2025-02-18 18:59:34.186771 INFO::Formatting Data.
2025-02-18 18:59:34.187746 INFO::Recognized SummarizedExperiment
2025-02-18 18:59:34.188528 INFO::Typecasting input to dataframe.
2025-02-18 18:59:34.212294 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.21384 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.217948 INFO::Found 0 missing values.
2025-02-18 18:59:34.229311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.230318 INFO::Done
2025-02-18 18:59:34.250026 INFO::Formatting Data.
2025-02-18 18:59:34.251054 INFO::Recognized SummarizedExperiment
2025-02-18 18:59:34.251845 INFO::Typecasting input to dataframe.
2025-02-18 18:59:34.274238 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.275719 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.277353 INFO::Found 0 missing values.
2025-02-18 18:59:34.278698 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-18 18:59:34.283901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.284608 INFO::Done
2025-02-18 18:59:34.299461 INFO::Formatting Data.
2025-02-18 18:59:34.300624 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.301615 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.302562 INFO::Found 0 missing values.
2025-02-18 18:59:34.305081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.305851 INFO::Done
2025-02-18 18:59:34.323771 INFO::Formatting Data.
2025-02-18 18:59:34.324885 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.326161 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.327477 INFO::Found 0 missing values.
2025-02-18 18:59:34.330347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.331132 INFO::Done
2025-02-18 18:59:34.374525 INFO::Formatting Data.
2025-02-18 18:59:34.375593 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.376695 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.377806 INFO::Found 1 missing values.
2025-02-18 18:59:34.380484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.380998 INFO::Done
2025-02-18 18:59:34.408873 INFO::Formatting Data.
2025-02-18 18:59:34.409663 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.410517 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.411438 INFO::Found 2 missing values.
2025-02-18 18:59:34.41238 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-18 18:59:34.414515 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.415028 INFO::Done
2025-02-18 18:59:34.430047 INFO::Formatting Data.
2025-02-18 18:59:34.43117 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.43243 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.433719 INFO::Found 2 missing values.
2025-02-18 18:59:34.436018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.436772 INFO::Done
2025-02-18 18:59:34.452786 INFO::Formatting Data.
2025-02-18 18:59:34.45385 INFO::Typecasting input to dataframe.
2025-02-18 18:59:34.454962 INFO::Replacing NaNs with NAs.
2025-02-18 18:59:34.456122 INFO::Removing potential empty rows and columns
2025-02-18 18:59:34.457383 INFO::Found 0 missing values.
2025-02-18 18:59:34.461549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-18 18:59:34.462321 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.330 4.264 25.001
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.420 | 1.474 | 19.189 | |
| compute_asw | 0.029 | 0.002 | 0.032 | |
| count_existing | 0.017 | 0.001 | 0.019 | |
| generate_data_covariables | 0.016 | 0.001 | 0.018 | |
| generate_dataset | 0.013 | 0.001 | 0.015 | |