Yannis Schumann
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:33 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-04-01 11:45:02 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 11:46:28 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 86.0 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 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 27.95 1.463 20.944
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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")
2025-04-01 11:46:04.823894 INFO::Formatting Data.
2025-04-01 11:46:04.829166 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:04.841205 INFO::Removing potential empty rows and columns
2025-04-01 11:46:05.156796 INFO::Found 0 missing values.
2025-04-01 11:46:05.160199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:05.160834 INFO::Done
2025-04-01 11:46:05.161353 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:05.180358 INFO::Starting hierarchical adjustment
2025-04-01 11:46:05.181591 INFO::Found 3 batches.
2025-04-01 11:46:05.182122 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:05.183567 INFO::Using default BPPARAM
2025-04-01 11:46:05.184075 INFO::Processing subtree level 1
2025-04-01 11:46:05.342514 INFO::Adjusting the last 1 batches sequentially
2025-04-01 11:46:05.345769 INFO::Done
2025-04-01 11:46:05.346461 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:05.351287 INFO::ASW Batch was -0.0225035196197708 prior to batch effect correction and is now -0.0225035196197708 .
2025-04-01 11:46:05.353277 INFO::Total function execution time is 0.530410051345825 s and adjustment time is 0.16442084312439 s ( 31 )
2025-04-01 11:46:05.375836 INFO::Formatting Data.
2025-04-01 11:46:05.376858 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:05.377896 INFO::Removing potential empty rows and columns
2025-04-01 11:46:05.379278 INFO::Found 0 missing values.
2025-04-01 11:46:05.380519 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.
2025-04-01 11:46:05.394125 INFO::Formatting Data.
2025-04-01 11:46:05.39516 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:05.396122 INFO::Removing potential empty rows and columns
2025-04-01 11:46:05.397219 INFO::Found 0 missing values.
2025-04-01 11:46:05.398162 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.
2025-04-01 11:46:05.421876 INFO::Formatting Data.
2025-04-01 11:46:05.422852 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:05.424051 INFO::Removing potential empty rows and columns
2025-04-01 11:46:05.425145 INFO::Found 0 missing values.
2025-04-01 11:46:05.42619 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.
2025-04-01 11:46:05.431382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:05.432093 INFO::Done
2025-04-01 11:46:05.432857 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:05.435078 INFO::Starting hierarchical adjustment
2025-04-01 11:46:05.435761 INFO::Found 2 batches.
2025-04-01 11:46:05.436275 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:05.436989 INFO::Using default BPPARAM
2025-04-01 11:46:05.437448 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:05.438309 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:05.467311 INFO::Done
2025-04-01 11:46:05.468633 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:05.471854 INFO::ASW Batch was -0.00532252721401289 prior to batch effect correction and is now -0.126364882839917 .
2025-04-01 11:46:05.47317 INFO::Total function execution time is 0.051440954208374 s and adjustment time is 0.0314857959747314 s ( 61.21 )
2025-04-01 11:46:05.476622 INFO::Formatting Data.
2025-04-01 11:46:05.477273 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:05.488321 INFO::Formatting Data.
2025-04-01 11:46:05.489101 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:05.489962 INFO::Removing potential empty rows and columns
2025-04-01 11:46:05.491003 INFO::Found 0 missing values.
2025-04-01 11:46:05.493761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:05.494264 INFO::Done
2025-04-01 11:46:05.494698 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:05.49688 INFO::Starting hierarchical adjustment
2025-04-01 11:46:05.49757 INFO::Found 2 batches.
2025-04-01 11:46:05.498078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:05.498833 INFO::Using default BPPARAM
2025-04-01 11:46:05.49949 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:05.500334 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:05.517348 INFO::Done
2025-04-01 11:46:05.518406 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:05.520767 INFO::ASW Batch was -0.0491602916250095 prior to batch effect correction and is now -0.0917278107465516 .
2025-04-01 11:46:05.521687 INFO::Total function execution time is 0.0334231853485107 s and adjustment time is 0.0198380947113037 s ( 59.35 )
2025-04-01 11:46:05.522808 INFO::Formatting Data.
2025-04-01 11:46:05.523373 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:05.524238 INFO::Removing potential empty rows and columns
2025-04-01 11:46:05.525258 INFO::Found 0 missing values.
2025-04-01 11:46:05.528057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:05.528647 INFO::Done
2025-04-01 11:46:05.529112 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:05.531127 INFO::Starting hierarchical adjustment
2025-04-01 11:46:05.531851 INFO::Found 2 batches.
2025-04-01 11:46:05.532318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:05.532882 INFO::Using default BPPARAM
2025-04-01 11:46:05.533357 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:05.534181 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:05.550238 INFO::Done
2025-04-01 11:46:05.551369 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:05.55395 INFO::ASW Batch was -0.0491602916250095 prior to batch effect correction and is now -0.0917278107465516 .
2025-04-01 11:46:05.55492 INFO::Total function execution time is 0.0320911407470703 s and adjustment time is 0.018402099609375 s ( 57.34 )
2025-04-01 11:46:09.134891 INFO::Formatting Data.
2025-04-01 11:46:09.135704 INFO::Recognized SummarizedExperiment
2025-04-01 11:46:09.136758 INFO::Typecasting input to dataframe.
2025-04-01 11:46:09.172668 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:09.174023 INFO::Removing potential empty rows and columns
2025-04-01 11:46:09.177284 INFO::Found 0 missing values.
2025-04-01 11:46:09.183371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:09.183964 INFO::Done
2025-04-01 11:46:09.184381 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:09.187863 INFO::Starting hierarchical adjustment
2025-04-01 11:46:09.188731 INFO::Found 2 batches.
2025-04-01 11:46:09.189134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:09.190195 INFO::Using default BPPARAM
2025-04-01 11:46:09.19064 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:09.191487 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:09.244018 INFO::Done
2025-04-01 11:46:09.244819 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:09.248429 INFO::ASW Batch was -0.00813636263613329 prior to batch effect correction and is now -0.0945841599594202 .
2025-04-01 11:46:09.249249 INFO::Total function execution time is 0.114653825759888 s and adjustment time is 0.0555489063262939 s ( 48.45 )
2025-04-01 11:46:09.267411 INFO::Formatting Data.
2025-04-01 11:46:09.268216 INFO::Recognized SummarizedExperiment
2025-04-01 11:46:09.268702 INFO::Typecasting input to dataframe.
2025-04-01 11:46:09.279278 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:09.280626 INFO::Removing potential empty rows and columns
2025-04-01 11:46:09.284332 INFO::Found 0 missing values.
2025-04-01 11:46:09.291161 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:09.291806 INFO::Done
2025-04-01 11:46:09.2923 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:09.297446 INFO::Starting hierarchical adjustment
2025-04-01 11:46:09.29841 INFO::Found 2 batches.
2025-04-01 11:46:09.298932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:09.299529 INFO::Using default BPPARAM
2025-04-01 11:46:09.300001 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:09.301191 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:09.328197 INFO::Done
2025-04-01 11:46:09.329099 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:09.332968 INFO::ASW Batch was -0.00528947652450503 prior to batch effect correction and is now -0.00528947652450503 .
2025-04-01 11:46:09.333925 INFO::Total function execution time is 0.0665130615234375 s and adjustment time is 0.0299041271209717 s ( 44.96 )
2025-04-01 11:46:09.355777 INFO::Formatting Data.
2025-04-01 11:46:09.356721 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:09.357631 INFO::Removing potential empty rows and columns
2025-04-01 11:46:09.358622 INFO::Found 0 missing values.
2025-04-01 11:46:09.361318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:09.361814 INFO::Done
2025-04-01 11:46:09.362261 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:09.364239 INFO::Starting hierarchical adjustment
2025-04-01 11:46:09.364987 INFO::Found 3 batches.
2025-04-01 11:46:09.365435 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:09.365969 INFO::Using default BPPARAM
2025-04-01 11:46:09.366421 INFO::Processing subtree level 1
2025-04-01 11:46:09.539835 INFO::Adjusting the last 1 batches sequentially
2025-04-01 11:46:09.54801 INFO::Done
2025-04-01 11:46:09.549112 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:09.556199 INFO::ASW Batch was -0.0207202002368293 prior to batch effect correction and is now -0.168514549752658 .
2025-04-01 11:46:09.558225 INFO::Total function execution time is 0.202672958374023 s and adjustment time is 0.182991981506348 s ( 90.29 )
2025-04-01 11:46:09.577608 INFO::Skipping initial DF formatting
2025-04-01 11:46:09.579217 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:09.583992 INFO::Starting hierarchical adjustment
2025-04-01 11:46:09.584949 INFO::Found 5 batches.
2025-04-01 11:46:09.585504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:09.586212 INFO::Using default BPPARAM
2025-04-01 11:46:09.586751 INFO::Processing subtree level 1
2025-04-01 11:46:09.733337 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:09.739601 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:09.769878 INFO::Done
2025-04-01 11:46:09.770832 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:09.778364 INFO::ASW Batch was 0.519526278775908 prior to batch effect correction and is now 0.519526278775908 .
2025-04-01 11:46:09.780372 INFO::ASW Label was 0.35556331129303 prior to batch effect correction and is now 0.35556331129303 .
2025-04-01 11:46:09.781797 INFO::Total function execution time is 0.204479932785034 s and adjustment time is 0.18487811088562 s ( 90.41 )
2025-04-01 11:46:09.808005 INFO::Formatting Data.
2025-04-01 11:46:09.80966 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:09.810803 INFO::Removing potential empty rows and columns
2025-04-01 11:46:09.811902 INFO::Found 0 missing values.
2025-04-01 11:46:09.815566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:09.816119 INFO::Done
2025-04-01 11:46:09.816576 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:09.81939 INFO::Starting hierarchical adjustment
2025-04-01 11:46:09.820085 INFO::Found 5 batches.
2025-04-01 11:46:09.820557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:09.821194 INFO::Using default BPPARAM
2025-04-01 11:46:09.821671 INFO::Processing subtree level 1
2025-04-01 11:46:09.962191 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:09.965899 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:09.992487 INFO::Done
2025-04-01 11:46:09.993451 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:09.997884 INFO::ASW Batch was 0.271313360820714 prior to batch effect correction and is now -0.0964990574497185 .
2025-04-01 11:46:09.998654 INFO::ASW Label was 0.437827743959787 prior to batch effect correction and is now 0.880398968317525 .
2025-04-01 11:46:10.000059 INFO::Total function execution time is 0.19226598739624 s and adjustment time is 0.172466039657593 s ( 89.7 )
2025-04-01 11:46:10.001335 INFO::Formatting Data.
2025-04-01 11:46:10.001919 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:10.002829 INFO::Removing potential empty rows and columns
2025-04-01 11:46:10.003884 INFO::Found 0 missing values.
2025-04-01 11:46:10.007645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:10.008289 INFO::Done
2025-04-01 11:46:10.008793 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:10.011898 INFO::Starting hierarchical adjustment
2025-04-01 11:46:10.012704 INFO::Found 5 batches.
2025-04-01 11:46:10.0132 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:10.013935 INFO::Using default BPPARAM
2025-04-01 11:46:10.014427 INFO::Processing subtree level 1
2025-04-01 11:46:10.155921 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:10.160579 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:10.187815 INFO::Done
2025-04-01 11:46:10.188796 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:10.193717 INFO::ASW Batch was 0.271313360820714 prior to batch effect correction and is now -0.0964990574497185 .
2025-04-01 11:46:10.195309 INFO::ASW Label was 0.437827743959787 prior to batch effect correction and is now 0.880398968317525 .
2025-04-01 11:46:10.196742 INFO::Total function execution time is 0.195173025131226 s and adjustment time is 0.175175905227661 s ( 89.75 )
2025-04-01 11:46:10.218929 INFO::Formatting Data.
2025-04-01 11:46:10.220086 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:10.221141 INFO::Removing potential empty rows and columns
2025-04-01 11:46:10.222828 INFO::Found 0 missing values.
2025-04-01 11:46:10.226686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:10.227303 INFO::Done
2025-04-01 11:46:10.227815 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:10.230809 INFO::Starting hierarchical adjustment
2025-04-01 11:46:10.231693 INFO::Found 5 batches.
2025-04-01 11:46:10.232191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:10.232875 INFO::Using default BPPARAM
2025-04-01 11:46:10.233361 INFO::Processing subtree level 1
2025-04-01 11:46:10.365359 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:10.368448 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:10.387704 INFO::Done
2025-04-01 11:46:10.389114 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:10.393181 INFO::ASW Batch was 0.423314077248157 prior to batch effect correction and is now -0.0993964467381743 .
2025-04-01 11:46:10.393871 INFO::ASW Label was 0.269557405400308 prior to batch effect correction and is now 0.868447348533627 .
2025-04-01 11:46:10.39493 INFO::Total function execution time is 0.176185846328735 s and adjustment time is 0.156046867370605 s ( 88.57 )
2025-04-01 11:46:10.395727 INFO::Formatting Data.
2025-04-01 11:46:10.39627 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:10.397086 INFO::Removing potential empty rows and columns
2025-04-01 11:46:10.398099 INFO::Found 0 missing values.
2025-04-01 11:46:10.401689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:10.402278 INFO::Done
2025-04-01 11:46:10.40274 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:10.405477 INFO::Starting hierarchical adjustment
2025-04-01 11:46:10.406201 INFO::Found 5 batches.
2025-04-01 11:46:10.406666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:10.407375 INFO::Using default BPPARAM
2025-04-01 11:46:10.407869 INFO::Processing subtree level 1
2025-04-01 11:46:10.533538 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:10.536057 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:10.557113 INFO::Done
2025-04-01 11:46:10.558251 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:10.563155 INFO::ASW Batch was 0.423314077248157 prior to batch effect correction and is now -0.0993964467381743 .
2025-04-01 11:46:10.564079 INFO::ASW Label was 0.269557405400308 prior to batch effect correction and is now 0.868447348533627 .
2025-04-01 11:46:10.565359 INFO::Total function execution time is 0.169428825378418 s and adjustment time is 0.150976896286011 s ( 89.11 )
2025-04-01 11:46:10.582832 INFO::Formatting Data.
2025-04-01 11:46:10.583726 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:10.584651 INFO::Removing potential empty rows and columns
2025-04-01 11:46:10.585701 INFO::Found 0 missing values.
2025-04-01 11:46:10.588172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:10.588713 INFO::Done
2025-04-01 11:46:10.589183 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:10.591986 INFO::Starting hierarchical adjustment
2025-04-01 11:46:10.59275 INFO::Found 2 batches.
2025-04-01 11:46:10.593253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:10.593935 INFO::Using default BPPARAM
2025-04-01 11:46:10.594399 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:10.595336 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:10.610917 INFO::Done
2025-04-01 11:46:10.612061 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:10.6169 INFO::ASW Batch was 0.528856496695619 prior to batch effect correction and is now 0.0735284105250023 .
2025-04-01 11:46:10.617944 INFO::ASW Label was 0.579543664902895 prior to batch effect correction and is now 0.888198037701627 .
2025-04-01 11:46:10.619023 INFO::Total function execution time is 0.0362169742584229 s and adjustment time is 0.0182018280029297 s ( 50.26 )
2025-04-01 11:46:10.61982 INFO::Formatting Data.
2025-04-01 11:46:10.620838 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:10.621974 INFO::Removing potential empty rows and columns
2025-04-01 11:46:10.623031 INFO::Found 0 missing values.
2025-04-01 11:46:10.625666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:10.626206 INFO::Done
2025-04-01 11:46:10.626719 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:10.630654 INFO::Starting hierarchical adjustment
2025-04-01 11:46:10.632306 INFO::Found 2 batches.
2025-04-01 11:46:10.633142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:10.634139 INFO::Using default BPPARAM
2025-04-01 11:46:10.634745 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:10.635874 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:10.65133 INFO::Done
2025-04-01 11:46:10.652123 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:10.654994 INFO::ASW Batch was 0.528856496695619 prior to batch effect correction and is now 0.0735284105250023 .
2025-04-01 11:46:10.655546 INFO::ASW Label was 0.579543664902895 prior to batch effect correction and is now 0.888198037701627 .
2025-04-01 11:46:10.656268 INFO::Total function execution time is 0.0364260673522949 s and adjustment time is 0.0193140506744385 s ( 53.02 )
2025-04-01 11:46:10.668705 INFO::Formatting Data.
2025-04-01 11:46:10.669472 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:10.670302 INFO::Removing potential empty rows and columns
2025-04-01 11:46:10.671128 INFO::Found 0 missing values.
2025-04-01 11:46:10.673004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:10.673506 INFO::Done
2025-04-01 11:46:10.673978 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:10.675901 INFO::Starting hierarchical adjustment
2025-04-01 11:46:10.676552 INFO::Found 2 batches.
2025-04-01 11:46:10.677068 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:10.677587 INFO::Using default BPPARAM
2025-04-01 11:46:10.678042 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:10.678828 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:10.71417 INFO::Done
2025-04-01 11:46:10.715487 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:10.71807 INFO::ASW Batch was -0.0889820541673088 prior to batch effect correction and is now -0.127890257868062 .
2025-04-01 11:46:10.719005 INFO::Total function execution time is 0.0504000186920166 s and adjustment time is 0.0375330448150635 s ( 74.47 )
2025-04-01 11:46:10.732197 INFO::Formatting Data.
2025-04-01 11:46:10.732991 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:10.733849 INFO::Removing potential empty rows and columns
2025-04-01 11:46:10.734833 INFO::Found 0 missing values.
2025-04-01 11:46:10.73617 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.
2025-04-01 11:46:10.740461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:10.741104 INFO::Done
2025-04-01 11:46:10.741631 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:10.744564 INFO::Starting hierarchical adjustment
2025-04-01 11:46:10.745343 INFO::Found 2 batches.
2025-04-01 11:46:10.745796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:10.74635 INFO::Using default BPPARAM
2025-04-01 11:46:10.746834 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:10.747775 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:10.766297 INFO::Done
2025-04-01 11:46:10.767219 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:10.770462 INFO::ASW Batch was 0.470438542155339 prior to batch effect correction and is now 0.0324778064164211 .
2025-04-01 11:46:10.771275 INFO::ASW Label was 0.586314337262167 prior to batch effect correction and is now 0.897875508632242 .
2025-04-01 11:46:10.772189 INFO::Total function execution time is 0.0400738716125488 s and adjustment time is 0.0210440158843994 s ( 52.51 )
2025-04-01 11:46:10.772936 INFO::Formatting Data.
2025-04-01 11:46:10.774199 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:10.775634 INFO::Removing potential empty rows and columns
2025-04-01 11:46:10.776817 INFO::Found 0 missing values.
2025-04-01 11:46:10.778191 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.
2025-04-01 11:46:10.782846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:10.783445 INFO::Done
2025-04-01 11:46:10.783921 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:10.786792 INFO::Starting hierarchical adjustment
2025-04-01 11:46:10.787516 INFO::Found 2 batches.
2025-04-01 11:46:10.78891 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:10.789652 INFO::Using default BPPARAM
2025-04-01 11:46:10.790248 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:10.791381 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:10.809795 INFO::Done
2025-04-01 11:46:10.810982 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:10.814274 INFO::ASW Batch was 0.470438542155339 prior to batch effect correction and is now 0.0324778064164211 .
2025-04-01 11:46:10.815034 INFO::ASW Label was 0.586314337262167 prior to batch effect correction and is now 0.897875508632242 .
2025-04-01 11:46:10.815967 INFO::Total function execution time is 0.04292893409729 s and adjustment time is 0.0223588943481445 s ( 52.08 )
2025-04-01 11:46:11.034505 INFO::Formatting Data.
2025-04-01 11:46:11.035442 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:11.036349 INFO::Removing potential empty rows and columns
2025-04-01 11:46:11.037364 INFO::Found 0 missing values.
2025-04-01 11:46:11.040233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:11.040975 INFO::Done
2025-04-01 11:46:11.041563 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:11.044006 INFO::Starting hierarchical adjustment
2025-04-01 11:46:11.044794 INFO::Found 3 batches.
2025-04-01 11:46:11.045266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:11.045847 INFO::Using default BPPARAM
2025-04-01 11:46:11.046261 INFO::Processing subtree level 1
2025-04-01 11:46:11.164606 INFO::Adjusting the last 1 batches sequentially
2025-04-01 11:46:11.16763 INFO::Done
2025-04-01 11:46:11.168201 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:11.171206 INFO::ASW Batch was 0.147035501872434 prior to batch effect correction and is now 0.147035501872434 .
2025-04-01 11:46:11.172314 INFO::Total function execution time is 0.137856006622314 s and adjustment time is 0.123002052307129 s ( 89.23 )
2025-04-01 11:46:11.173419 INFO::Formatting Data.
2025-04-01 11:46:11.174044 INFO::Typecasting input to dataframe.
2025-04-01 11:46:11.174758 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:11.175687 INFO::Removing potential empty rows and columns
2025-04-01 11:46:11.176931 INFO::Found 0 missing values.
2025-04-01 11:46:11.18098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:11.181937 INFO::Done
2025-04-01 11:46:11.182521 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:11.185398 INFO::Starting hierarchical adjustment
2025-04-01 11:46:11.186206 INFO::Found 3 batches.
2025-04-01 11:46:11.186768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:11.187426 INFO::Using default BPPARAM
2025-04-01 11:46:11.187886 INFO::Processing subtree level 1
2025-04-01 11:46:11.501144 INFO::Adjusting the last 1 batches sequentially
2025-04-01 11:46:11.517267 INFO::Done
2025-04-01 11:46:11.518402 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:11.525644 INFO::ASW Batch was 0.147035501872434 prior to batch effect correction and is now 0.147035501872434 .
2025-04-01 11:46:11.526758 INFO::Total function execution time is 0.353301048278809 s and adjustment time is 0.331149816513062 s ( 93.73 )
2025-04-01 11:46:11.543256 INFO::Formatting Data.
2025-04-01 11:46:11.544536 INFO::Typecasting input to dataframe.
2025-04-01 11:46:11.545331 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:11.546527 INFO::Removing potential empty rows and columns
2025-04-01 11:46:11.548377 INFO::Found 0 missing values.
2025-04-01 11:46:11.551014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:11.551542 INFO::Done
2025-04-01 11:46:11.552019 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:11.553973 INFO::Starting hierarchical adjustment
2025-04-01 11:46:11.554684 INFO::Found 3 batches.
2025-04-01 11:46:11.555147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:11.556111 INFO::Using default BPPARAM
2025-04-01 11:46:11.556577 INFO::Processing subtree level 1
2025-04-01 11:46:11.8336 INFO::Adjusting the last 1 batches sequentially
2025-04-01 11:46:11.849318 INFO::Done
2025-04-01 11:46:11.850111 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:11.859475 INFO::ASW Batch was -0.084017002796459 prior to batch effect correction and is now -0.084017002796459 .
2025-04-01 11:46:11.862242 INFO::Total function execution time is 0.319103956222534 s and adjustment time is 0.294656038284302 s ( 92.34 )
2025-04-01 11:46:12.186889 INFO::Formatting Data.
2025-04-01 11:46:12.188228 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:12.189819 INFO::Removing potential empty rows and columns
2025-04-01 11:46:12.193897 INFO::Found 1000 missing values.
2025-04-01 11:46:12.223248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:12.22441 INFO::Done
2025-04-01 11:46:12.225047 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:12.235066 INFO::Starting hierarchical adjustment
2025-04-01 11:46:12.236739 INFO::Found 10 batches.
2025-04-01 11:46:12.237442 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:12.240375 INFO::Using default BPPARAM
2025-04-01 11:46:12.241152 INFO::Processing subtree level 1
2025-04-01 11:46:12.472173 INFO::Processing subtree level 2
2025-04-01 11:46:12.733432 INFO::Adjusting the last 1 batches sequentially
2025-04-01 11:46:12.73813 INFO::Done
2025-04-01 11:46:12.738979 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:12.750912 INFO::ASW Batch was 0.49371906922362 prior to batch effect correction and is now 0.49371906922362 .
2025-04-01 11:46:12.752172 INFO::ASW Label was 0.333321120951882 prior to batch effect correction and is now 0.333321120951882 .
2025-04-01 11:46:12.754001 INFO::Total function execution time is 0.56709098815918 s and adjustment time is 0.501710891723633 s ( 88.47 )
2025-04-01 11:46:12.755473 INFO::Formatting Data.
2025-04-01 11:46:12.756528 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:12.758813 INFO::Removing potential empty rows and columns
2025-04-01 11:46:12.763826 INFO::Found 1000 missing values.
2025-04-01 11:46:12.794824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:12.796397 INFO::Done
2025-04-01 11:46:12.797295 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:12.805794 INFO::Starting hierarchical adjustment
2025-04-01 11:46:12.807068 INFO::Found 10 batches.
2025-04-01 11:46:14.612454 INFO::Set up parallel execution backend with 2 workers
2025-04-01 11:46:14.613461 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-04-01 11:46:16.331815 INFO::Adjusting the last 2 batches sequentially
2025-04-01 11:46:16.333582 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 11:46:16.350548 INFO::Done
2025-04-01 11:46:16.351258 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:16.356875 INFO::ASW Batch was 0.49371906922362 prior to batch effect correction and is now 0.49371906922362 .
2025-04-01 11:46:16.35751 INFO::ASW Label was 0.333321120951882 prior to batch effect correction and is now 0.333321120951882 .
2025-04-01 11:46:16.35823 INFO::Total function execution time is 3.60287690162659 s and adjustment time is 3.54369711875916 s ( 98.36 )
2025-04-01 11:46:16.593279 INFO::Formatting Data.
2025-04-01 11:46:16.594398 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:16.595593 INFO::Removing potential empty rows and columns
2025-04-01 11:46:16.59732 INFO::Found 0 missing values.
2025-04-01 11:46:16.601271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:16.601922 INFO::Done
2025-04-01 11:46:16.602445 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 11:46:16.606095 INFO::Starting hierarchical adjustment
2025-04-01 11:46:16.606915 INFO::Found 3 batches.
2025-04-01 11:46:16.607463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 11:46:16.608209 INFO::Using default BPPARAM
2025-04-01 11:46:16.608732 INFO::Processing subtree level 1
2025-04-01 11:46:16.788714 INFO::Adjusting the last 1 batches sequentially
2025-04-01 11:46:16.796688 INFO::Done
2025-04-01 11:46:16.79766 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 11:46:16.805561 INFO::ASW Batch was 0.149214155389546 prior to batch effect correction and is now -0.169408908836492 .
2025-04-01 11:46:16.806403 INFO::ASW Label was -0.173489052718133 prior to batch effect correction and is now 0.0834919821580931 .
2025-04-01 11:46:16.808144 INFO::Total function execution time is 0.21489405632019 s and adjustment time is 0.189871072769165 s ( 88.36 )
2025-04-01 11:46:16.970438 INFO::Formatting Data.
2025-04-01 11:46:16.971585 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:16.973171 INFO::Removing potential empty rows and columns
2025-04-01 11:46:16.974529 INFO::Found 2 missing values.
2025-04-01 11:46:16.978164 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:16.978815 INFO::Done
2025-04-01 11:46:17.019562 INFO::Found NA in Reference column
2025-04-01 11:46:17.031633 INFO::Require at least two references per batch.
2025-04-01 11:46:17.064743 INFO::Formatting Data.
2025-04-01 11:46:17.065978 INFO::Recognized SummarizedExperiment
2025-04-01 11:46:17.066611 INFO::Typecasting input to dataframe.
2025-04-01 11:46:17.082577 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.084279 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.089179 INFO::Found 0 missing values.
2025-04-01 11:46:17.097154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.09787 INFO::Done
2025-04-01 11:46:17.121161 INFO::Formatting Data.
2025-04-01 11:46:17.122051 INFO::Recognized SummarizedExperiment
2025-04-01 11:46:17.122572 INFO::Typecasting input to dataframe.
2025-04-01 11:46:17.143719 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.14532 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.149792 INFO::Found 0 missing values.
2025-04-01 11:46:17.166486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.167625 INFO::Done
2025-04-01 11:46:17.188508 INFO::Formatting Data.
2025-04-01 11:46:17.18979 INFO::Recognized SummarizedExperiment
2025-04-01 11:46:17.190465 INFO::Typecasting input to dataframe.
2025-04-01 11:46:17.212655 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.214009 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.215307 INFO::Found 0 missing values.
2025-04-01 11:46:17.21648 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.
2025-04-01 11:46:17.221965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.222747 INFO::Done
2025-04-01 11:46:17.236931 INFO::Formatting Data.
2025-04-01 11:46:17.237971 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.23896 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.240115 INFO::Found 0 missing values.
2025-04-01 11:46:17.245262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.246297 INFO::Done
2025-04-01 11:46:17.262406 INFO::Formatting Data.
2025-04-01 11:46:17.263411 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.264353 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.265385 INFO::Found 0 missing values.
2025-04-01 11:46:17.26852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.269078 INFO::Done
2025-04-01 11:46:17.314649 INFO::Formatting Data.
2025-04-01 11:46:17.315718 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.31699 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.318291 INFO::Found 1 missing values.
2025-04-01 11:46:17.321452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.322109 INFO::Done
2025-04-01 11:46:17.345792 INFO::Formatting Data.
2025-04-01 11:46:17.346781 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.347702 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.348683 INFO::Found 2 missing values.
2025-04-01 11:46:17.349733 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.
2025-04-01 11:46:17.352396 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.353135 INFO::Done
2025-04-01 11:46:17.367036 INFO::Formatting Data.
2025-04-01 11:46:17.368018 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.36902 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.370004 INFO::Found 2 missing values.
2025-04-01 11:46:17.371746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.372291 INFO::Done
2025-04-01 11:46:17.386274 INFO::Formatting Data.
2025-04-01 11:46:17.387271 INFO::Typecasting input to dataframe.
2025-04-01 11:46:17.388116 INFO::Replacing NaNs with NAs.
2025-04-01 11:46:17.389103 INFO::Removing potential empty rows and columns
2025-04-01 11:46:17.390242 INFO::Found 0 missing values.
2025-04-01 11:46:17.393523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 11:46:17.394259 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.835 5.415 26.922
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.950 | 1.463 | 20.944 | |
| compute_asw | 0.031 | 0.002 | 0.034 | |
| count_existing | 0.016 | 0.001 | 0.018 | |
| generate_data_covariables | 0.014 | 0.002 | 0.017 | |
| generate_dataset | 0.014 | 0.002 | 0.015 | |