Yannis Schumann
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:03 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 161/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.5.0 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-06-18 23:43:07 -0400 (Wed, 18 Jun 2025) |
| EndedAt: 2025-06-18 23:45:30 -0400 (Wed, 18 Jun 2025) |
| EllapsedTime: 142.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.5.0'
* 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 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 9.42 0.58 20.01
* 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: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'BERT' ... ** this is package 'BERT' version '1.5.0' ** 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 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2025-06-18 23:44:15.032019 INFO::Formatting Data.
2025-06-18 23:44:15.034962 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:15.050001 INFO::Removing potential empty rows and columns
2025-06-18 23:44:15.359408 INFO::Found 0 missing values.
2025-06-18 23:44:15.3626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:15.363515 INFO::Done
2025-06-18 23:44:15.364265 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:15.378852 INFO::Starting hierarchical adjustment
2025-06-18 23:44:15.380012 INFO::Found 3 batches.
2025-06-18 23:44:15.380809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:15.382119 INFO::Using default BPPARAM
2025-06-18 23:44:15.382887 INFO::Processing subtree level 1
2025-06-18 23:44:18.270947 INFO::Adjusting the last 1 batches sequentially
2025-06-18 23:44:18.273274 INFO::Done
2025-06-18 23:44:18.274664 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:18.278131 INFO::ASW Batch was -0.0743072079121826 prior to batch effect correction and is now -0.0743072079121826 .
2025-06-18 23:44:18.279875 INFO::Total function execution time is 3.2485191822052 s and adjustment time is 2.89342999458313 s ( 89.07 )
2025-06-18 23:44:18.302697 INFO::Formatting Data.
2025-06-18 23:44:18.304063 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:18.305784 INFO::Removing potential empty rows and columns
2025-06-18 23:44:18.307619 INFO::Found 0 missing values.
2025-06-18 23:44:18.309303 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.
2025-06-18 23:44:18.32235 INFO::Formatting Data.
2025-06-18 23:44:18.323406 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:18.324614 INFO::Removing potential empty rows and columns
2025-06-18 23:44:18.325803 INFO::Found 0 missing values.
2025-06-18 23:44:18.326881 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.
2025-06-18 23:44:18.342915 INFO::Formatting Data.
2025-06-18 23:44:18.343906 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:18.344969 INFO::Removing potential empty rows and columns
2025-06-18 23:44:18.34611 INFO::Found 0 missing values.
2025-06-18 23:44:18.347181 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.
2025-06-18 23:44:18.350826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:18.351569 INFO::Done
2025-06-18 23:44:18.352319 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:18.354458 INFO::Starting hierarchical adjustment
2025-06-18 23:44:18.355394 INFO::Found 2 batches.
2025-06-18 23:44:18.356199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:18.357167 INFO::Using default BPPARAM
2025-06-18 23:44:18.357969 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:18.359091 INFO::Adjusting sequential tree level 1 with 2 batches
2025-06-18 23:44:18.376014 INFO::Done
2025-06-18 23:44:18.376919 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:18.379247 INFO::ASW Batch was 0.00267652004017047 prior to batch effect correction and is now -0.114758896366746 .
2025-06-18 23:44:18.380277 INFO::Total function execution time is 0.0374460220336914 s and adjustment time is 0.020726203918457 s ( 55.35 )
2025-06-18 23:44:18.383163 INFO::Formatting Data.
2025-06-18 23:44:18.384102 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:18.391145 INFO::Formatting Data.
2025-06-18 23:44:18.391986 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:18.39299 INFO::Removing potential empty rows and columns
2025-06-18 23:44:18.394111 INFO::Found 0 missing values.
2025-06-18 23:44:18.396666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:18.397377 INFO::Done
2025-06-18 23:44:18.398186 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:18.400959 INFO::Starting hierarchical adjustment
2025-06-18 23:44:18.402212 INFO::Found 2 batches.
2025-06-18 23:44:18.40333 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:18.404562 INFO::Using default BPPARAM
2025-06-18 23:44:18.405681 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:18.407327 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:18.42341 INFO::Done
2025-06-18 23:44:18.424401 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:18.427143 INFO::ASW Batch was -0.0708624718066157 prior to batch effect correction and is now -0.121776612684001 .
2025-06-18 23:44:18.428238 INFO::Total function execution time is 0.0371420383453369 s and adjustment time is 0.0213758945465088 s ( 57.55 )
2025-06-18 23:44:18.429435 INFO::Formatting Data.
2025-06-18 23:44:18.430274 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:18.431841 INFO::Removing potential empty rows and columns
2025-06-18 23:44:18.433734 INFO::Found 0 missing values.
2025-06-18 23:44:18.438296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:18.439605 INFO::Done
2025-06-18 23:44:18.440888 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:18.44386 INFO::Starting hierarchical adjustment
2025-06-18 23:44:18.444803 INFO::Found 2 batches.
2025-06-18 23:44:18.445542 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:18.446386 INFO::Using default BPPARAM
2025-06-18 23:44:18.447102 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:18.448222 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:18.464949 INFO::Done
2025-06-18 23:44:18.466404 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:18.469996 INFO::ASW Batch was -0.0708624718066157 prior to batch effect correction and is now -0.121776612684001 .
2025-06-18 23:44:18.471719 INFO::Total function execution time is 0.0421459674835205 s and adjustment time is 0.020205020904541 s ( 47.94 )
2025-06-18 23:44:21.288332 INFO::Formatting Data.
2025-06-18 23:44:21.289852 INFO::Recognized SummarizedExperiment
2025-06-18 23:44:21.291214 INFO::Typecasting input to dataframe.
2025-06-18 23:44:21.338664 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:21.341015 INFO::Removing potential empty rows and columns
2025-06-18 23:44:21.346804 INFO::Found 0 missing values.
2025-06-18 23:44:21.357413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:21.35894 INFO::Done
2025-06-18 23:44:21.360399 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:21.367107 INFO::Starting hierarchical adjustment
2025-06-18 23:44:21.368798 INFO::Found 2 batches.
2025-06-18 23:44:21.370136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:21.37218 INFO::Using default BPPARAM
2025-06-18 23:44:21.373467 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:21.375593 INFO::Adjusting sequential tree level 1 with 2 batches
2025-06-18 23:44:22.275442 INFO::Done
2025-06-18 23:44:22.2768 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:22.283287 INFO::ASW Batch was -0.0110263585308044 prior to batch effect correction and is now -0.0900694616220854 .
2025-06-18 23:44:22.285131 INFO::Total function execution time is 0.997183084487915 s and adjustment time is 0.906898021697998 s ( 90.95 )
2025-06-18 23:44:22.316125 INFO::Formatting Data.
2025-06-18 23:44:22.317883 INFO::Recognized SummarizedExperiment
2025-06-18 23:44:22.319385 INFO::Typecasting input to dataframe.
2025-06-18 23:44:22.334057 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:22.336399 INFO::Removing potential empty rows and columns
2025-06-18 23:44:22.341359 INFO::Found 0 missing values.
2025-06-18 23:44:22.351418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:22.353139 INFO::Done
2025-06-18 23:44:22.354647 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:22.362185 INFO::Starting hierarchical adjustment
2025-06-18 23:44:22.364174 INFO::Found 2 batches.
2025-06-18 23:44:22.365699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:22.367314 INFO::Using default BPPARAM
2025-06-18 23:44:22.368773 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:22.371191 INFO::Adjusting sequential tree level 1 with 2 batches
2025-06-18 23:44:22.408951 INFO::Done
2025-06-18 23:44:22.410625 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:22.417913 INFO::ASW Batch was 0.00783933239034063 prior to batch effect correction and is now 0.00783933239034063 .
2025-06-18 23:44:22.419965 INFO::Total function execution time is 0.103766918182373 s and adjustment time is 0.0451040267944336 s ( 43.47 )
2025-06-18 23:44:22.45581 INFO::Formatting Data.
2025-06-18 23:44:22.457418 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:22.459232 INFO::Removing potential empty rows and columns
2025-06-18 23:44:22.461162 INFO::Found 0 missing values.
2025-06-18 23:44:22.46585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:22.467202 INFO::Done
2025-06-18 23:44:22.468471 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:22.471832 INFO::Starting hierarchical adjustment
2025-06-18 23:44:22.473301 INFO::Found 3 batches.
2025-06-18 23:44:22.474518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:22.475805 INFO::Using default BPPARAM
2025-06-18 23:44:22.477022 INFO::Processing subtree level 1
2025-06-18 23:44:33.291573 INFO::Adjusting the last 1 batches sequentially
2025-06-18 23:44:33.29352 INFO::Done
2025-06-18 23:44:33.294429 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:33.296861 INFO::ASW Batch was -0.124280441689552 prior to batch effect correction and is now -0.179505485023659 .
2025-06-18 23:44:33.297855 INFO::Total function execution time is 10.8422539234161 s and adjustment time is 10.8204491138458 s ( 99.8 )
2025-06-18 23:44:33.31553 INFO::Skipping initial DF formatting
2025-06-18 23:44:33.316875 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:33.322877 INFO::Starting hierarchical adjustment
2025-06-18 23:44:33.324064 INFO::Found 5 batches.
2025-06-18 23:44:33.325251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:33.326539 INFO::Using default BPPARAM
2025-06-18 23:44:33.327704 INFO::Processing subtree level 1
2025-06-18 23:44:36.461317 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:36.463004 INFO::Adjusting sequential tree level 1 with 2 batches
2025-06-18 23:44:36.48353 INFO::Done
2025-06-18 23:44:36.484815 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:36.491157 INFO::ASW Batch was 0.575703341203333 prior to batch effect correction and is now 0.575703341203333 .
2025-06-18 23:44:36.49245 INFO::ASW Label was 0.360506886599612 prior to batch effect correction and is now 0.360506886599612 .
2025-06-18 23:44:36.493819 INFO::Total function execution time is 3.178377866745 s and adjustment time is 3.15960311889648 s ( 99.41 )
2025-06-18 23:44:36.514843 INFO::Formatting Data.
2025-06-18 23:44:36.515965 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:36.517214 INFO::Removing potential empty rows and columns
2025-06-18 23:44:36.518376 INFO::Found 0 missing values.
2025-06-18 23:44:36.521894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:36.522638 INFO::Done
2025-06-18 23:44:36.523359 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:36.526631 INFO::Starting hierarchical adjustment
2025-06-18 23:44:36.527992 INFO::Found 5 batches.
2025-06-18 23:44:36.529207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:36.530517 INFO::Using default BPPARAM
2025-06-18 23:44:36.531728 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:39.866494 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:39.868372 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:39.883316 INFO::Done
2025-06-18 23:44:39.884734 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:39.889872 INFO::ASW Batch was 0.187065628212111 prior to batch effect correction and is now -0.0397643897017751 .
2025-06-18 23:44:39.89131 INFO::ASW Label was 0.535281454161223 prior to batch effect correction and is now 0.818223151377246 .
2025-06-18 23:44:39.892971 INFO::Total function execution time is 3.37811779975891 s and adjustment time is 3.35547208786011 s ( 99.33 )
2025-06-18 23:44:39.894573 INFO::Formatting Data.
2025-06-18 23:44:39.895937 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:39.897695 INFO::Removing potential empty rows and columns
2025-06-18 23:44:39.899495 INFO::Found 0 missing values.
2025-06-18 23:44:39.905517 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:39.906877 INFO::Done
2025-06-18 23:44:39.908113 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:39.913139 INFO::Starting hierarchical adjustment
2025-06-18 23:44:39.914733 INFO::Found 5 batches.
2025-06-18 23:44:39.915968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:39.917271 INFO::Using default BPPARAM
2025-06-18 23:44:39.918449 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:43.158118 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:43.15966 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:43.171823 INFO::Done
2025-06-18 23:44:43.172791 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:43.176171 INFO::ASW Batch was 0.187065628212111 prior to batch effect correction and is now -0.0397643897017751 .
2025-06-18 23:44:43.176978 INFO::ASW Label was 0.535281454161223 prior to batch effect correction and is now 0.818223151377246 .
2025-06-18 23:44:43.177936 INFO::Total function execution time is 3.28348302841187 s and adjustment time is 3.25737190246582 s ( 99.2 )
2025-06-18 23:44:43.193145 INFO::Formatting Data.
2025-06-18 23:44:43.194199 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:43.195464 INFO::Removing potential empty rows and columns
2025-06-18 23:44:43.1966 INFO::Found 0 missing values.
2025-06-18 23:44:43.200506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:43.201394 INFO::Done
2025-06-18 23:44:43.202141 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:43.205285 INFO::Starting hierarchical adjustment
2025-06-18 23:44:43.206212 INFO::Found 5 batches.
2025-06-18 23:44:43.206936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:43.207763 INFO::Using default BPPARAM
2025-06-18 23:44:43.208486 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:46.513919 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:46.515994 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:46.535261 INFO::Done
2025-06-18 23:44:46.536673 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:46.541642 INFO::ASW Batch was 0.499242174547815 prior to batch effect correction and is now -0.0897923475534185 .
2025-06-18 23:44:46.542994 INFO::ASW Label was 0.166375087150671 prior to batch effect correction and is now 0.808357326571255 .
2025-06-18 23:44:46.54451 INFO::Total function execution time is 3.35139799118042 s and adjustment time is 3.329097032547 s ( 99.33 )
2025-06-18 23:44:46.546023 INFO::Formatting Data.
2025-06-18 23:44:46.547282 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:46.548924 INFO::Removing potential empty rows and columns
2025-06-18 23:44:46.550619 INFO::Found 0 missing values.
2025-06-18 23:44:46.556346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:46.557501 INFO::Done
2025-06-18 23:44:46.558666 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:46.563373 INFO::Starting hierarchical adjustment
2025-06-18 23:44:46.564867 INFO::Found 5 batches.
2025-06-18 23:44:46.566045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:46.567301 INFO::Using default BPPARAM
2025-06-18 23:44:46.568437 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:49.827895 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:49.829799 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:49.846962 INFO::Done
2025-06-18 23:44:49.848214 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:49.852534 INFO::ASW Batch was 0.499242174547815 prior to batch effect correction and is now -0.0897923475534185 .
2025-06-18 23:44:49.853714 INFO::ASW Label was 0.166375087150671 prior to batch effect correction and is now 0.808357326571255 .
2025-06-18 23:44:49.855081 INFO::Total function execution time is 3.30909895896912 s and adjustment time is 3.28229999542236 s ( 99.19 )
2025-06-18 23:44:49.874194 INFO::Formatting Data.
2025-06-18 23:44:49.875192 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:49.876281 INFO::Removing potential empty rows and columns
2025-06-18 23:44:49.877403 INFO::Found 0 missing values.
2025-06-18 23:44:49.879843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:49.880571 INFO::Done
2025-06-18 23:44:49.88128 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:49.884335 INFO::Starting hierarchical adjustment
2025-06-18 23:44:49.885267 INFO::Found 2 batches.
2025-06-18 23:44:49.886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:49.886777 INFO::Using default BPPARAM
2025-06-18 23:44:49.887483 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:49.888583 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:49.900529 INFO::Done
2025-06-18 23:44:49.90137 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:49.904297 INFO::ASW Batch was 0.574415733973203 prior to batch effect correction and is now -0.0247877938637685 .
2025-06-18 23:44:49.905076 INFO::ASW Label was 0.493980073236702 prior to batch effect correction and is now 0.938673654542698 .
2025-06-18 23:44:49.906017 INFO::Total function execution time is 0.0319228172302246 s and adjustment time is 0.015408992767334 s ( 48.27 )
2025-06-18 23:44:49.906952 INFO::Formatting Data.
2025-06-18 23:44:49.907757 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:49.908791 INFO::Removing potential empty rows and columns
2025-06-18 23:44:49.909876 INFO::Found 0 missing values.
2025-06-18 23:44:49.912276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:49.913098 INFO::Done
2025-06-18 23:44:49.914296 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:49.917616 INFO::Starting hierarchical adjustment
2025-06-18 23:44:49.918511 INFO::Found 2 batches.
2025-06-18 23:44:49.919304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:49.920154 INFO::Using default BPPARAM
2025-06-18 23:44:49.920868 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:49.921985 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-06-18 23:44:49.934153 INFO::Done
2025-06-18 23:44:49.934981 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:49.938714 INFO::ASW Batch was 0.574415733973203 prior to batch effect correction and is now -0.0247877938637685 .
2025-06-18 23:44:49.93961 INFO::ASW Label was 0.493980073236702 prior to batch effect correction and is now 0.938673654542698 .
2025-06-18 23:44:49.940575 INFO::Total function execution time is 0.0336341857910156 s and adjustment time is 0.0157780647277832 s ( 46.91 )
2025-06-18 23:44:49.95534 INFO::Formatting Data.
2025-06-18 23:44:49.956388 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:49.957496 INFO::Removing potential empty rows and columns
2025-06-18 23:44:49.959016 INFO::Found 0 missing values.
2025-06-18 23:44:49.961143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:49.961878 INFO::Done
2025-06-18 23:44:49.96263 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:49.964693 INFO::Starting hierarchical adjustment
2025-06-18 23:44:49.965583 INFO::Found 2 batches.
2025-06-18 23:44:49.966318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:49.967114 INFO::Using default BPPARAM
2025-06-18 23:44:49.967851 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:49.969022 INFO::Adjusting sequential tree level 1 with 2 batches
2025-06-18 23:44:49.994547 INFO::Done
2025-06-18 23:44:49.995484 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:49.997607 INFO::ASW Batch was -0.053576411142475 prior to batch effect correction and is now -0.0735546888935507 .
2025-06-18 23:44:49.998604 INFO::Total function execution time is 0.0433552265167236 s and adjustment time is 0.0290648937225342 s ( 67.04 )
2025-06-18 23:44:50.01328 INFO::Formatting Data.
2025-06-18 23:44:50.014294 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:50.015414 INFO::Removing potential empty rows and columns
2025-06-18 23:44:50.016583 INFO::Found 0 missing values.
2025-06-18 23:44:50.017879 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.
2025-06-18 23:44:50.022016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:50.022787 INFO::Done
2025-06-18 23:44:50.02353 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:50.026767 INFO::Starting hierarchical adjustment
2025-06-18 23:44:50.027717 INFO::Found 2 batches.
2025-06-18 23:44:50.028546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:50.029395 INFO::Using default BPPARAM
2025-06-18 23:44:50.030166 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:50.031333 INFO::Adjusting sequential tree level 1 with 2 batches
2025-06-18 23:44:50.046674 INFO::Done
2025-06-18 23:44:50.047612 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:50.050922 INFO::ASW Batch was 0.393236095933698 prior to batch effect correction and is now -0.0249686825109519 .
2025-06-18 23:44:50.05176 INFO::ASW Label was 0.647138251708152 prior to batch effect correction and is now 0.945736415191597 .
2025-06-18 23:44:50.052797 INFO::Total function execution time is 0.0395917892456055 s and adjustment time is 0.0190949440002441 s ( 48.23 )
2025-06-18 23:44:50.053772 INFO::Formatting Data.
2025-06-18 23:44:50.054609 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:50.055704 INFO::Removing potential empty rows and columns
2025-06-18 23:44:50.056924 INFO::Found 0 missing values.
2025-06-18 23:44:50.058025 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.
2025-06-18 23:44:50.062212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:50.062994 INFO::Done
2025-06-18 23:44:50.06373 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:50.067004 INFO::Starting hierarchical adjustment
2025-06-18 23:44:50.068037 INFO::Found 2 batches.
2025-06-18 23:44:50.068844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:50.069726 INFO::Using default BPPARAM
2025-06-18 23:44:50.070512 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:44:50.071758 INFO::Adjusting sequential tree level 1 with 2 batches
2025-06-18 23:44:50.086465 INFO::Done
2025-06-18 23:44:50.08743 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:50.090789 INFO::ASW Batch was 0.393236095933698 prior to batch effect correction and is now -0.0249686825109519 .
2025-06-18 23:44:50.091642 INFO::ASW Label was 0.647138251708152 prior to batch effect correction and is now 0.945736415191597 .
2025-06-18 23:44:50.092676 INFO::Total function execution time is 0.0389049053192139 s and adjustment time is 0.0185770988464355 s ( 47.75 )
2025-06-18 23:44:50.394808 INFO::Formatting Data.
2025-06-18 23:44:50.395978 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:50.397254 INFO::Removing potential empty rows and columns
2025-06-18 23:44:50.398575 INFO::Found 0 missing values.
2025-06-18 23:44:50.401903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:50.402739 INFO::Done
2025-06-18 23:44:50.403527 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:50.405946 INFO::Starting hierarchical adjustment
2025-06-18 23:44:50.406963 INFO::Found 3 batches.
2025-06-18 23:44:50.407763 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:50.408671 INFO::Using default BPPARAM
2025-06-18 23:44:50.409819 INFO::Processing subtree level 1
2025-06-18 23:44:53.330364 INFO::Adjusting the last 1 batches sequentially
2025-06-18 23:44:53.332542 INFO::Done
2025-06-18 23:44:53.33383 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:53.336979 INFO::ASW Batch was 0.0277432385575646 prior to batch effect correction and is now 0.0277432385575646 .
2025-06-18 23:44:53.338544 INFO::Total function execution time is 2.94375991821289 s and adjustment time is 2.92569899559021 s ( 99.39 )
2025-06-18 23:44:53.340448 INFO::Formatting Data.
2025-06-18 23:44:53.341753 INFO::Typecasting input to dataframe.
2025-06-18 23:44:53.34315 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:53.344697 INFO::Removing potential empty rows and columns
2025-06-18 23:44:53.346392 INFO::Found 0 missing values.
2025-06-18 23:44:53.350866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:53.352273 INFO::Done
2025-06-18 23:44:53.35356 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:53.357182 INFO::Starting hierarchical adjustment
2025-06-18 23:44:53.358698 INFO::Found 3 batches.
2025-06-18 23:44:53.359921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:53.361172 INFO::Using default BPPARAM
2025-06-18 23:44:53.362337 INFO::Processing subtree level 1
2025-06-18 23:44:56.247009 INFO::Adjusting the last 1 batches sequentially
2025-06-18 23:44:56.249225 INFO::Done
2025-06-18 23:44:56.250588 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:56.253873 INFO::ASW Batch was 0.0277432385575646 prior to batch effect correction and is now 0.0277432385575646 .
2025-06-18 23:44:56.255458 INFO::Total function execution time is 2.91505813598633 s and adjustment time is 2.89079308509827 s ( 99.17 )
2025-06-18 23:44:56.276723 INFO::Formatting Data.
2025-06-18 23:44:56.278336 INFO::Typecasting input to dataframe.
2025-06-18 23:44:56.280057 INFO::Replacing NaNs with NAs.
2025-06-18 23:44:56.281744 INFO::Removing potential empty rows and columns
2025-06-18 23:44:56.283666 INFO::Found 0 missing values.
2025-06-18 23:44:56.287695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:44:56.288894 INFO::Done
2025-06-18 23:44:56.290049 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:44:56.293247 INFO::Starting hierarchical adjustment
2025-06-18 23:44:56.294662 INFO::Found 3 batches.
2025-06-18 23:44:56.295853 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:44:56.297134 INFO::Using default BPPARAM
2025-06-18 23:44:56.298317 INFO::Processing subtree level 1
2025-06-18 23:44:59.398081 INFO::Adjusting the last 1 batches sequentially
2025-06-18 23:44:59.40023 INFO::Done
2025-06-18 23:44:59.401545 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:44:59.405133 INFO::ASW Batch was -0.051159594468894 prior to batch effect correction and is now -0.051159594468894 .
2025-06-18 23:44:59.406778 INFO::Total function execution time is 3.13015198707581 s and adjustment time is 3.10575318336487 s ( 99.22 )
2025-06-18 23:45:02.318502 INFO::Formatting Data.
2025-06-18 23:45:02.320154 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:02.322211 INFO::Removing potential empty rows and columns
2025-06-18 23:45:02.32606 INFO::Found 1000 missing values.
2025-06-18 23:45:02.349438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:02.35087 INFO::Done
2025-06-18 23:45:02.352203 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:45:02.362234 INFO::Starting hierarchical adjustment
2025-06-18 23:45:02.363967 INFO::Found 10 batches.
2025-06-18 23:45:02.365258 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:45:02.366653 INFO::Using default BPPARAM
2025-06-18 23:45:02.367958 INFO::Processing subtree level 1
2025-06-18 23:45:05.803901 INFO::Processing subtree level 2
2025-06-18 23:45:08.909124 INFO::Adjusting the last 1 batches sequentially
2025-06-18 23:45:08.911487 INFO::Done
2025-06-18 23:45:08.912727 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:45:08.921667 INFO::ASW Batch was 0.625576298375171 prior to batch effect correction and is now 0.625576298375171 .
2025-06-18 23:45:08.922984 INFO::ASW Label was 0.267881718319833 prior to batch effect correction and is now 0.267881718319833 .
2025-06-18 23:45:08.924526 INFO::Total function execution time is 6.60613703727722 s and adjustment time is 6.54781103134155 s ( 99.12 )
2025-06-18 23:45:08.926006 INFO::Formatting Data.
2025-06-18 23:45:08.92727 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:08.929054 INFO::Removing potential empty rows and columns
2025-06-18 23:45:08.931991 INFO::Found 1000 missing values.
2025-06-18 23:45:08.947436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:08.948393 INFO::Done
2025-06-18 23:45:08.94915 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:45:08.955385 INFO::Starting hierarchical adjustment
2025-06-18 23:45:08.95641 INFO::Found 10 batches.
2025-06-18 23:45:09.743245 INFO::Set up parallel execution backend with 2 workers
2025-06-18 23:45:09.744924 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-06-18 23:45:12.851693 INFO::Adjusting the last 2 batches sequentially
2025-06-18 23:45:12.853949 INFO::Adjusting sequential tree level 1 with 2 batches
2025-06-18 23:45:12.879879 INFO::Done
2025-06-18 23:45:12.881237 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:45:12.890215 INFO::ASW Batch was 0.625576298375171 prior to batch effect correction and is now 0.625576298375171 .
2025-06-18 23:45:12.89158 INFO::ASW Label was 0.267881718319833 prior to batch effect correction and is now 0.267881718319833 .
2025-06-18 23:45:12.893127 INFO::Total function execution time is 3.96714401245117 s and adjustment time is 3.92355585098267 s ( 98.9 )
2025-06-18 23:45:15.839622 INFO::Formatting Data.
2025-06-18 23:45:15.840679 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:15.841817 INFO::Removing potential empty rows and columns
2025-06-18 23:45:15.842993 INFO::Found 0 missing values.
2025-06-18 23:45:15.846289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:15.847057 INFO::Done
2025-06-18 23:45:15.847777 INFO::Acquiring quality metrics before batch effect correction.
2025-06-18 23:45:15.850608 INFO::Starting hierarchical adjustment
2025-06-18 23:45:15.851527 INFO::Found 3 batches.
2025-06-18 23:45:15.852253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-06-18 23:45:15.853049 INFO::Using default BPPARAM
2025-06-18 23:45:15.853766 INFO::Processing subtree level 1
2025-06-18 23:45:19.011003 INFO::Adjusting the last 1 batches sequentially
2025-06-18 23:45:19.013312 INFO::Done
2025-06-18 23:45:19.014717 INFO::Acquiring quality metrics after batch effect correction.
2025-06-18 23:45:19.018427 INFO::ASW Batch was 0.183039061621433 prior to batch effect correction and is now -0.163040584050535 .
2025-06-18 23:45:19.019295 INFO::ASW Label was -0.184094123754263 prior to batch effect correction and is now -0.0695639089962724 .
2025-06-18 23:45:19.020357 INFO::Total function execution time is 3.18084383010864 s and adjustment time is 3.16186189651489 s ( 99.4 )
2025-06-18 23:45:19.214081 INFO::Formatting Data.
2025-06-18 23:45:19.215608 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.217345 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.219167 INFO::Found 2 missing values.
2025-06-18 23:45:19.223787 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.225093 INFO::Done
2025-06-18 23:45:19.279819 INFO::Found NA in Reference column
2025-06-18 23:45:19.298574 INFO::Require at least two references per batch.
2025-06-18 23:45:19.328173 INFO::Formatting Data.
2025-06-18 23:45:19.329429 INFO::Recognized SummarizedExperiment
2025-06-18 23:45:19.330568 INFO::Typecasting input to dataframe.
2025-06-18 23:45:19.342517 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.344622 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.348905 INFO::Found 0 missing values.
2025-06-18 23:45:19.357143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.358327 INFO::Done
2025-06-18 23:45:19.379396 INFO::Formatting Data.
2025-06-18 23:45:19.380649 INFO::Recognized SummarizedExperiment
2025-06-18 23:45:19.381733 INFO::Typecasting input to dataframe.
2025-06-18 23:45:19.404302 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.406397 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.411099 INFO::Found 0 missing values.
2025-06-18 23:45:19.423925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.425303 INFO::Done
2025-06-18 23:45:19.447466 INFO::Formatting Data.
2025-06-18 23:45:19.448933 INFO::Recognized SummarizedExperiment
2025-06-18 23:45:19.450232 INFO::Typecasting input to dataframe.
2025-06-18 23:45:19.47252 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.473773 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.474969 INFO::Found 0 missing values.
2025-06-18 23:45:19.476048 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.
2025-06-18 23:45:19.4801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.480849 INFO::Done
2025-06-18 23:45:19.498288 INFO::Formatting Data.
2025-06-18 23:45:19.499944 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.501754 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.503611 INFO::Found 0 missing values.
2025-06-18 23:45:19.508419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.509708 INFO::Done
2025-06-18 23:45:19.531607 INFO::Formatting Data.
2025-06-18 23:45:19.533259 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.535105 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.537062 INFO::Found 0 missing values.
2025-06-18 23:45:19.54169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.542997 INFO::Done
2025-06-18 23:45:19.600174 INFO::Formatting Data.
2025-06-18 23:45:19.601818 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.603795 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.605829 INFO::Found 1 missing values.
2025-06-18 23:45:19.609784 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.610994 INFO::Done
2025-06-18 23:45:19.646743 INFO::Formatting Data.
2025-06-18 23:45:19.648384 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.650201 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.652034 INFO::Found 2 missing values.
2025-06-18 23:45:19.653812 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.
2025-06-18 23:45:19.657477 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.658698 INFO::Done
2025-06-18 23:45:19.677588 INFO::Formatting Data.
2025-06-18 23:45:19.679119 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.680823 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.682552 INFO::Found 2 missing values.
2025-06-18 23:45:19.685187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.68634 INFO::Done
2025-06-18 23:45:19.705903 INFO::Formatting Data.
2025-06-18 23:45:19.707417 INFO::Typecasting input to dataframe.
2025-06-18 23:45:19.709112 INFO::Replacing NaNs with NAs.
2025-06-18 23:45:19.710832 INFO::Removing potential empty rows and columns
2025-06-18 23:45:19.712627 INFO::Found 0 missing values.
2025-06-18 23:45:19.716842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-06-18 23:45:19.718131 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
32.29 1.42 80.67
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.42 | 0.58 | 20.01 | |
| compute_asw | 0.03 | 0.00 | 0.04 | |
| count_existing | 0.02 | 0.00 | 0.01 | |
| generate_data_covariables | 0.01 | 0.00 | 0.02 | |
| generate_dataset | 0.00 | 0.02 | 0.01 | |