Yannis Schumann
| Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_21 |
| git_last_commit: dedce04 |
| git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-21 11:38 -0400 (Thu, 21 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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 | | ||||||||
| kunpeng2 | 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: 1.4.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.4.0.tar.gz |
| StartedAt: 2025-08-20 20:25:44 -0400 (Wed, 20 Aug 2025) |
| EndedAt: 2025-08-20 20:27:16 -0400 (Wed, 20 Aug 2025) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* 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 loading without being on the library search path ... 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 25.634 1.683 19.275
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.4.0’ ** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
2025-08-20 20:26:37.6274 INFO::Formatting Data.
2025-08-20 20:26:37.628926 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:37.640729 INFO::Removing potential empty rows and columns
2025-08-20 20:26:37.884955 INFO::Found 0 missing values.
2025-08-20 20:26:37.888535 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:37.889256 INFO::Done
2025-08-20 20:26:37.889855 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:37.901523 INFO::Starting hierarchical adjustment
2025-08-20 20:26:37.902458 INFO::Found 3 batches.
2025-08-20 20:26:37.903269 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:37.904898 INFO::Using default BPPARAM
2025-08-20 20:26:37.905699 INFO::Processing subtree level 1
2025-08-20 20:26:38.021893 INFO::Adjusting the last 1 batches sequentially
2025-08-20 20:26:38.023884 INFO::Done
2025-08-20 20:26:38.024617 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:38.027441 INFO::ASW Batch was 0.0377721166931235 prior to batch effect correction and is now 0.0377721166931235 .
2025-08-20 20:26:38.028604 INFO::Total function execution time is 0.401896476745605 s and adjustment time is 0.121601581573486 s ( 30.26 )
2025-08-20 20:26:38.043131 INFO::Formatting Data.
2025-08-20 20:26:38.043978 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:38.045024 INFO::Removing potential empty rows and columns
2025-08-20 20:26:38.046264 INFO::Found 0 missing values.
2025-08-20 20:26:38.047333 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.
2025-08-20 20:26:38.058588 INFO::Formatting Data.
2025-08-20 20:26:38.059407 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:38.060349 INFO::Removing potential empty rows and columns
2025-08-20 20:26:38.061425 INFO::Found 0 missing values.
2025-08-20 20:26:38.062394 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.
2025-08-20 20:26:38.079319 INFO::Formatting Data.
2025-08-20 20:26:38.080207 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:38.081191 INFO::Removing potential empty rows and columns
2025-08-20 20:26:38.082305 INFO::Found 0 missing values.
2025-08-20 20:26:38.083296 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.
2025-08-20 20:26:38.087927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:38.088508 INFO::Done
2025-08-20 20:26:38.089058 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:38.091234 INFO::Starting hierarchical adjustment
2025-08-20 20:26:38.091962 INFO::Found 2 batches.
2025-08-20 20:26:38.092505 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:38.093187 INFO::Using default BPPARAM
2025-08-20 20:26:38.093742 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:38.094736 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-20 20:26:38.118301 INFO::Done
2025-08-20 20:26:38.119206 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:38.121541 INFO::ASW Batch was -0.0285041000354522 prior to batch effect correction and is now -0.117158777024155 .
2025-08-20 20:26:38.122446 INFO::Total function execution time is 0.0432355403900146 s and adjustment time is 0.0264317989349365 s ( 61.13 )
2025-08-20 20:26:38.125678 INFO::Formatting Data.
2025-08-20 20:26:38.126358 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:38.135895 INFO::Formatting Data.
2025-08-20 20:26:38.136804 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:38.164164 INFO::Removing potential empty rows and columns
2025-08-20 20:26:38.1676 INFO::Found 0 missing values.
2025-08-20 20:26:38.170671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:38.17129 INFO::Done
2025-08-20 20:26:38.17184 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:38.173984 INFO::Starting hierarchical adjustment
2025-08-20 20:26:38.174722 INFO::Found 2 batches.
2025-08-20 20:26:38.175257 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:38.175901 INFO::Using default BPPARAM
2025-08-20 20:26:38.176438 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:38.177397 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-20 20:26:38.193092 INFO::Done
2025-08-20 20:26:38.193789 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:38.195936 INFO::ASW Batch was 0.203811688490708 prior to batch effect correction and is now -0.115518789943607 .
2025-08-20 20:26:38.196801 INFO::Total function execution time is 0.0609943866729736 s and adjustment time is 0.0185227394104004 s ( 30.37 )
2025-08-20 20:26:38.197876 INFO::Formatting Data.
2025-08-20 20:26:38.198484 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:38.199364 INFO::Removing potential empty rows and columns
2025-08-20 20:26:38.200371 INFO::Found 0 missing values.
2025-08-20 20:26:38.203218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:38.203784 INFO::Done
2025-08-20 20:26:38.2043 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:38.206375 INFO::Starting hierarchical adjustment
2025-08-20 20:26:38.207121 INFO::Found 2 batches.
2025-08-20 20:26:38.207657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:38.208275 INFO::Using default BPPARAM
2025-08-20 20:26:38.208813 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:38.209746 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-20 20:26:38.225312 INFO::Done
2025-08-20 20:26:38.226021 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:38.228117 INFO::ASW Batch was 0.203811688490708 prior to batch effect correction and is now -0.115518789943607 .
2025-08-20 20:26:38.228927 INFO::Total function execution time is 0.031038761138916 s and adjustment time is 0.0183281898498535 s ( 59.05 )
2025-08-20 20:26:42.121527 INFO::Formatting Data.
2025-08-20 20:26:42.122432 INFO::Recognized SummarizedExperiment
2025-08-20 20:26:42.122982 INFO::Typecasting input to dataframe.
2025-08-20 20:26:42.154972 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:42.156312 INFO::Removing potential empty rows and columns
2025-08-20 20:26:42.159635 INFO::Found 0 missing values.
2025-08-20 20:26:42.167248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:42.168066 INFO::Done
2025-08-20 20:26:42.168691 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:42.172794 INFO::Starting hierarchical adjustment
2025-08-20 20:26:42.173592 INFO::Found 2 batches.
2025-08-20 20:26:42.174148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:42.175384 INFO::Using default BPPARAM
2025-08-20 20:26:42.175947 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:42.177042 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-20 20:26:42.244337 INFO::Done
2025-08-20 20:26:42.245264 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:42.249716 INFO::ASW Batch was 0.0123526117149978 prior to batch effect correction and is now -0.089906390317986 .
2025-08-20 20:26:42.250779 INFO::Total function execution time is 0.129521608352661 s and adjustment time is 0.0708391666412354 s ( 54.69 )
2025-08-20 20:26:42.273002 INFO::Formatting Data.
2025-08-20 20:26:42.274154 INFO::Recognized SummarizedExperiment
2025-08-20 20:26:42.274808 INFO::Typecasting input to dataframe.
2025-08-20 20:26:42.286423 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:42.288194 INFO::Removing potential empty rows and columns
2025-08-20 20:26:42.29311 INFO::Found 0 missing values.
2025-08-20 20:26:42.300696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:42.301481 INFO::Done
2025-08-20 20:26:42.302156 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:42.306687 INFO::Starting hierarchical adjustment
2025-08-20 20:26:42.307608 INFO::Found 2 batches.
2025-08-20 20:26:42.308253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:42.30902 INFO::Using default BPPARAM
2025-08-20 20:26:42.309675 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:42.311025 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-20 20:26:42.338855 INFO::Done
2025-08-20 20:26:42.339668 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:42.343544 INFO::ASW Batch was 0.015201508151054 prior to batch effect correction and is now 0.015201508151054 .
2025-08-20 20:26:42.344521 INFO::Total function execution time is 0.071561336517334 s and adjustment time is 0.0314006805419922 s ( 43.88 )
2025-08-20 20:26:42.364168 INFO::Formatting Data.
2025-08-20 20:26:42.365083 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:42.366082 INFO::Removing potential empty rows and columns
2025-08-20 20:26:42.367177 INFO::Found 0 missing values.
2025-08-20 20:26:42.370542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:42.371119 INFO::Done
2025-08-20 20:26:42.371683 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:42.373849 INFO::Starting hierarchical adjustment
2025-08-20 20:26:42.37458 INFO::Found 3 batches.
2025-08-20 20:26:42.37514 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:42.37579 INFO::Using default BPPARAM
2025-08-20 20:26:42.376336 INFO::Processing subtree level 1
2025-08-20 20:26:42.72568 INFO::Adjusting the last 1 batches sequentially
2025-08-20 20:26:42.728375 INFO::Done
2025-08-20 20:26:42.729411 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:42.733138 INFO::ASW Batch was 0.00508323078510134 prior to batch effect correction and is now -0.145489511409789 .
2025-08-20 20:26:42.734567 INFO::Total function execution time is 0.370403051376343 s and adjustment time is 0.353904724121094 s ( 95.55 )
2025-08-20 20:26:42.82368 INFO::Skipping initial DF formatting
2025-08-20 20:26:42.824494 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:42.828638 INFO::Starting hierarchical adjustment
2025-08-20 20:26:42.829492 INFO::Found 5 batches.
2025-08-20 20:26:42.830096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:42.830743 INFO::Using default BPPARAM
2025-08-20 20:26:42.831274 INFO::Processing subtree level 1
2025-08-20 20:26:43.013537 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.016519 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-20 20:26:43.05496 INFO::Done
2025-08-20 20:26:43.056051 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:43.061595 INFO::ASW Batch was 0.477152662539296 prior to batch effect correction and is now 0.477152662539296 .
2025-08-20 20:26:43.062391 INFO::ASW Label was 0.421046390441586 prior to batch effect correction and is now 0.421046390441586 .
2025-08-20 20:26:43.063523 INFO::Total function execution time is 0.239908456802368 s and adjustment time is 0.225452661514282 s ( 93.97 )
2025-08-20 20:26:43.084665 INFO::Formatting Data.
2025-08-20 20:26:43.085655 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:43.086807 INFO::Removing potential empty rows and columns
2025-08-20 20:26:43.08808 INFO::Found 0 missing values.
2025-08-20 20:26:43.092719 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:43.093301 INFO::Done
2025-08-20 20:26:43.093931 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:43.0976 INFO::Starting hierarchical adjustment
2025-08-20 20:26:43.098425 INFO::Found 5 batches.
2025-08-20 20:26:43.09904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:43.099704 INFO::Using default BPPARAM
2025-08-20 20:26:43.10029 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.
2025-08-20 20:26:43.253479 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.255882 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-20 20:26:43.279973 INFO::Done
2025-08-20 20:26:43.281115 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:43.285946 INFO::ASW Batch was 0.281612105183148 prior to batch effect correction and is now -0.0379998146381353 .
2025-08-20 20:26:43.286685 INFO::ASW Label was 0.450989827173934 prior to batch effect correction and is now 0.81750185358901 .
2025-08-20 20:26:43.287635 INFO::Total function execution time is 0.203089475631714 s and adjustment time is 0.181665897369385 s ( 89.45 )
2025-08-20 20:26:43.288589 INFO::Formatting Data.
2025-08-20 20:26:43.289259 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:43.29021 INFO::Removing potential empty rows and columns
2025-08-20 20:26:43.291252 INFO::Found 0 missing values.
2025-08-20 20:26:43.295439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:43.296039 INFO::Done
2025-08-20 20:26:43.296605 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:43.299669 INFO::Starting hierarchical adjustment
2025-08-20 20:26:43.300415 INFO::Found 5 batches.
2025-08-20 20:26:43.300959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:43.301633 INFO::Using default BPPARAM
2025-08-20 20:26:43.302185 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.
2025-08-20 20:26:43.438103 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.439877 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-20 20:26:43.456386 INFO::Done
2025-08-20 20:26:43.457205 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:43.460728 INFO::ASW Batch was 0.281612105183148 prior to batch effect correction and is now -0.0379998146381353 .
2025-08-20 20:26:43.461335 INFO::ASW Label was 0.450989827173934 prior to batch effect correction and is now 0.81750185358901 .
2025-08-20 20:26:43.462199 INFO::Total function execution time is 0.173625946044922 s and adjustment time is 0.156080484390259 s ( 89.89 )
2025-08-20 20:26:43.476012 INFO::Formatting Data.
2025-08-20 20:26:43.476827 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:43.477789 INFO::Removing potential empty rows and columns
2025-08-20 20:26:43.478832 INFO::Found 0 missing values.
2025-08-20 20:26:43.482963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:43.483537 INFO::Done
2025-08-20 20:26:43.484086 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:43.487266 INFO::Starting hierarchical adjustment
2025-08-20 20:26:43.488064 INFO::Found 5 batches.
2025-08-20 20:26:43.488653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:43.489389 INFO::Using default BPPARAM
2025-08-20 20:26:43.48997 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.
2025-08-20 20:26:43.625163 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.62704 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-20 20:26:43.64393 INFO::Done
2025-08-20 20:26:43.64476 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:43.648241 INFO::ASW Batch was 0.604709542570176 prior to batch effect correction and is now -0.0992421496542332 .
2025-08-20 20:26:43.64893 INFO::ASW Label was 0.133069760120354 prior to batch effect correction and is now 0.807052974297909 .
2025-08-20 20:26:43.649792 INFO::Total function execution time is 0.173835039138794 s and adjustment time is 0.155973434448242 s ( 89.72 )
2025-08-20 20:26:43.65068 INFO::Formatting Data.
2025-08-20 20:26:43.651338 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:43.652261 INFO::Removing potential empty rows and columns
2025-08-20 20:26:43.653291 INFO::Found 0 missing values.
2025-08-20 20:26:43.657435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:43.658025 INFO::Done
2025-08-20 20:26:43.658574 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:43.661663 INFO::Starting hierarchical adjustment
2025-08-20 20:26:43.662397 INFO::Found 5 batches.
2025-08-20 20:26:43.662971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:43.663651 INFO::Using default BPPARAM
2025-08-20 20:26:43.664207 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.
2025-08-20 20:26:43.795321 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.797079 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-20 20:26:43.813898 INFO::Done
2025-08-20 20:26:43.814698 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:43.818177 INFO::ASW Batch was 0.604709542570176 prior to batch effect correction and is now -0.0992421496542332 .
2025-08-20 20:26:43.818831 INFO::ASW Label was 0.133069760120354 prior to batch effect correction and is now 0.807052974297909 .
2025-08-20 20:26:43.819721 INFO::Total function execution time is 0.169032096862793 s and adjustment time is 0.151610374450684 s ( 89.69 )
2025-08-20 20:26:43.834046 INFO::Formatting Data.
2025-08-20 20:26:43.834885 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:43.835911 INFO::Removing potential empty rows and columns
2025-08-20 20:26:43.836999 INFO::Found 0 missing values.
2025-08-20 20:26:43.839823 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:43.840408 INFO::Done
2025-08-20 20:26:43.840976 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:43.844166 INFO::Starting hierarchical adjustment
2025-08-20 20:26:43.844893 INFO::Found 2 batches.
2025-08-20 20:26:43.845442 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:43.846097 INFO::Using default BPPARAM
2025-08-20 20:26:43.846654 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.847558 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-20 20:26:43.863281 INFO::Done
2025-08-20 20:26:43.864048 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:43.86721 INFO::ASW Batch was 0.759224642470295 prior to batch effect correction and is now -0.0147996361801667 .
2025-08-20 20:26:43.86783 INFO::ASW Label was 0.244696934919601 prior to batch effect correction and is now 0.788524901675173 .
2025-08-20 20:26:43.868664 INFO::Total function execution time is 0.0347211360931396 s and adjustment time is 0.0185143947601318 s ( 53.32 )
2025-08-20 20:26:43.869504 INFO::Formatting Data.
2025-08-20 20:26:43.870169 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:43.871064 INFO::Removing potential empty rows and columns
2025-08-20 20:26:43.87207 INFO::Found 0 missing values.
2025-08-20 20:26:43.874773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:43.875308 INFO::Done
2025-08-20 20:26:43.875851 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:43.878776 INFO::Starting hierarchical adjustment
2025-08-20 20:26:43.87947 INFO::Found 2 batches.
2025-08-20 20:26:43.88001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:43.88063 INFO::Using default BPPARAM
2025-08-20 20:26:43.881142 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.882052 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-20 20:26:43.897539 INFO::Done
2025-08-20 20:26:43.898216 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:43.901289 INFO::ASW Batch was 0.759224642470295 prior to batch effect correction and is now -0.0147996361801667 .
2025-08-20 20:26:43.901907 INFO::ASW Label was 0.244696934919601 prior to batch effect correction and is now 0.788524901675173 .
2025-08-20 20:26:43.902722 INFO::Total function execution time is 0.0332267284393311 s and adjustment time is 0.0182104110717773 s ( 54.81 )
2025-08-20 20:26:43.914542 INFO::Formatting Data.
2025-08-20 20:26:43.915358 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:43.916296 INFO::Removing potential empty rows and columns
2025-08-20 20:26:43.917234 INFO::Found 0 missing values.
2025-08-20 20:26:43.919402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:43.91995 INFO::Done
2025-08-20 20:26:43.92046 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:43.922518 INFO::Starting hierarchical adjustment
2025-08-20 20:26:43.92324 INFO::Found 2 batches.
2025-08-20 20:26:43.923792 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:43.924401 INFO::Using default BPPARAM
2025-08-20 20:26:43.924937 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.925876 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-20 20:26:43.958896 INFO::Done
2025-08-20 20:26:43.959714 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:43.961925 INFO::ASW Batch was -0.161014803092986 prior to batch effect correction and is now -0.186053515313546 .
2025-08-20 20:26:43.962819 INFO::Total function execution time is 0.0483672618865967 s and adjustment time is 0.0357596874237061 s ( 73.93 )
2025-08-20 20:26:43.975485 INFO::Formatting Data.
2025-08-20 20:26:43.976277 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:43.977291 INFO::Removing potential empty rows and columns
2025-08-20 20:26:43.978338 INFO::Found 0 missing values.
2025-08-20 20:26:43.979557 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.
2025-08-20 20:26:43.98429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:43.984885 INFO::Done
2025-08-20 20:26:43.985435 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:43.988571 INFO::Starting hierarchical adjustment
2025-08-20 20:26:43.989283 INFO::Found 2 batches.
2025-08-20 20:26:43.989821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:43.990441 INFO::Using default BPPARAM
2025-08-20 20:26:43.991 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:43.992014 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-20 20:26:44.010028 INFO::Done
2025-08-20 20:26:44.010859 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:44.014055 INFO::ASW Batch was 0.257883162791147 prior to batch effect correction and is now 0.136327927229767 .
2025-08-20 20:26:44.01471 INFO::ASW Label was 0.765686532727401 prior to batch effect correction and is now 0.838723498813852 .
2025-08-20 20:26:44.015529 INFO::Total function execution time is 0.040132999420166 s and adjustment time is 0.0208718776702881 s ( 52.01 )
2025-08-20 20:26:44.016437 INFO::Formatting Data.
2025-08-20 20:26:44.01711 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:44.01809 INFO::Removing potential empty rows and columns
2025-08-20 20:26:44.01912 INFO::Found 0 missing values.
2025-08-20 20:26:44.020098 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.
2025-08-20 20:26:44.025152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:44.025796 INFO::Done
2025-08-20 20:26:44.026389 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:44.029744 INFO::Starting hierarchical adjustment
2025-08-20 20:26:44.030493 INFO::Found 2 batches.
2025-08-20 20:26:44.031073 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:44.031749 INFO::Using default BPPARAM
2025-08-20 20:26:44.032341 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:44.033332 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-20 20:26:44.052412 INFO::Done
2025-08-20 20:26:44.053203 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:44.056522 INFO::ASW Batch was 0.257883162791147 prior to batch effect correction and is now 0.136327927229767 .
2025-08-20 20:26:44.057161 INFO::ASW Label was 0.765686532727401 prior to batch effect correction and is now 0.838723498813852 .
2025-08-20 20:26:44.05817 INFO::Total function execution time is 0.0417487621307373 s and adjustment time is 0.0220365524291992 s ( 52.78 )
2025-08-20 20:26:44.273036 INFO::Formatting Data.
2025-08-20 20:26:44.273941 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:44.274911 INFO::Removing potential empty rows and columns
2025-08-20 20:26:44.275977 INFO::Found 0 missing values.
2025-08-20 20:26:44.279084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:44.279671 INFO::Done
2025-08-20 20:26:44.280194 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:44.282352 INFO::Starting hierarchical adjustment
2025-08-20 20:26:44.283066 INFO::Found 3 batches.
2025-08-20 20:26:44.283602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:44.284236 INFO::Using default BPPARAM
2025-08-20 20:26:44.284779 INFO::Processing subtree level 1
2025-08-20 20:26:44.380454 INFO::Adjusting the last 1 batches sequentially
2025-08-20 20:26:44.38231 INFO::Done
2025-08-20 20:26:44.382972 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:44.385526 INFO::ASW Batch was -0.0862745231350398 prior to batch effect correction and is now -0.0862745231350398 .
2025-08-20 20:26:44.386489 INFO::Total function execution time is 0.113547801971436 s and adjustment time is 0.0993678569793701 s ( 87.51 )
2025-08-20 20:26:44.387585 INFO::Formatting Data.
2025-08-20 20:26:44.388263 INFO::Typecasting input to dataframe.
2025-08-20 20:26:44.389038 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:44.390007 INFO::Removing potential empty rows and columns
2025-08-20 20:26:44.391131 INFO::Found 0 missing values.
2025-08-20 20:26:44.394243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:44.394812 INFO::Done
2025-08-20 20:26:44.395352 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:44.397598 INFO::Starting hierarchical adjustment
2025-08-20 20:26:44.398341 INFO::Found 3 batches.
2025-08-20 20:26:44.398889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:44.399529 INFO::Using default BPPARAM
2025-08-20 20:26:44.400076 INFO::Processing subtree level 1
2025-08-20 20:26:44.488322 INFO::Adjusting the last 1 batches sequentially
2025-08-20 20:26:44.490166 INFO::Done
2025-08-20 20:26:44.490866 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:44.493393 INFO::ASW Batch was -0.0862745231350398 prior to batch effect correction and is now -0.0862745231350398 .
2025-08-20 20:26:44.494363 INFO::Total function execution time is 0.106771469116211 s and adjustment time is 0.0919394493103027 s ( 86.11 )
2025-08-20 20:26:44.507898 INFO::Formatting Data.
2025-08-20 20:26:44.508756 INFO::Typecasting input to dataframe.
2025-08-20 20:26:44.50966 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:44.510648 INFO::Removing potential empty rows and columns
2025-08-20 20:26:44.511758 INFO::Found 0 missing values.
2025-08-20 20:26:44.514816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:44.515365 INFO::Done
2025-08-20 20:26:44.515907 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:44.517996 INFO::Starting hierarchical adjustment
2025-08-20 20:26:44.518725 INFO::Found 3 batches.
2025-08-20 20:26:44.519296 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:44.519949 INFO::Using default BPPARAM
2025-08-20 20:26:44.520486 INFO::Processing subtree level 1
2025-08-20 20:26:44.610351 INFO::Adjusting the last 1 batches sequentially
2025-08-20 20:26:44.61264 INFO::Done
2025-08-20 20:26:44.61343 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:44.616228 INFO::ASW Batch was -0.0903741307999046 prior to batch effect correction and is now -0.0903741307999046 .
2025-08-20 20:26:44.617292 INFO::Total function execution time is 0.109481334686279 s and adjustment time is 0.0940110683441162 s ( 85.87 )
2025-08-20 20:26:44.780865 INFO::Formatting Data.
2025-08-20 20:26:44.782203 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:44.783661 INFO::Removing potential empty rows and columns
2025-08-20 20:26:44.786946 INFO::Found 1000 missing values.
2025-08-20 20:26:44.806949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:44.807894 INFO::Done
2025-08-20 20:26:44.808535 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:44.815329 INFO::Starting hierarchical adjustment
2025-08-20 20:26:44.81623 INFO::Found 10 batches.
2025-08-20 20:26:44.816852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:44.817638 INFO::Using default BPPARAM
2025-08-20 20:26:44.818274 INFO::Processing subtree level 1
2025-08-20 20:26:44.979747 INFO::Processing subtree level 2
2025-08-20 20:26:45.134326 INFO::Adjusting the last 1 batches sequentially
2025-08-20 20:26:45.136709 INFO::Done
2025-08-20 20:26:45.137456 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:45.143701 INFO::ASW Batch was 0.453444319207596 prior to batch effect correction and is now 0.453444319207596 .
2025-08-20 20:26:45.144451 INFO::ASW Label was 0.362338676635056 prior to batch effect correction and is now 0.362338676635056 .
2025-08-20 20:26:45.145607 INFO::Total function execution time is 0.364997625350952 s and adjustment time is 0.320642948150635 s ( 87.85 )
2025-08-20 20:26:45.146587 INFO::Formatting Data.
2025-08-20 20:26:45.147425 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:45.148834 INFO::Removing potential empty rows and columns
2025-08-20 20:26:45.151803 INFO::Found 1000 missing values.
2025-08-20 20:26:45.172229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:45.173423 INFO::Done
2025-08-20 20:26:45.174159 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:45.180157 INFO::Starting hierarchical adjustment
2025-08-20 20:26:45.181033 INFO::Found 10 batches.
2025-08-20 20:26:46.705372 INFO::Set up parallel execution backend with 2 workers
2025-08-20 20:26:46.70835 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-20 20:26:48.143705 INFO::Adjusting the last 2 batches sequentially
2025-08-20 20:26:48.145824 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-20 20:26:48.162507 INFO::Done
2025-08-20 20:26:48.16325 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:48.167863 INFO::ASW Batch was 0.453444319207596 prior to batch effect correction and is now 0.453444319207596 .
2025-08-20 20:26:48.168434 INFO::ASW Label was 0.362338676635056 prior to batch effect correction and is now 0.362338676635056 .
2025-08-20 20:26:48.169171 INFO::Total function execution time is 3.02264332771301 s and adjustment time is 2.9816267490387 s ( 98.64 )
2025-08-20 20:26:48.33719 INFO::Formatting Data.
2025-08-20 20:26:48.338436 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.339911 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.341651 INFO::Found 0 missing values.
2025-08-20 20:26:48.348143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.349078 INFO::Done
2025-08-20 20:26:48.350013 INFO::Acquiring quality metrics before batch effect correction.
2025-08-20 20:26:48.354575 INFO::Starting hierarchical adjustment
2025-08-20 20:26:48.355744 INFO::Found 3 batches.
2025-08-20 20:26:48.35661 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-20 20:26:48.35766 INFO::Using default BPPARAM
2025-08-20 20:26:48.358528 INFO::Processing subtree level 1
2025-08-20 20:26:48.478335 INFO::Adjusting the last 1 batches sequentially
2025-08-20 20:26:48.481072 INFO::Done
2025-08-20 20:26:48.482045 INFO::Acquiring quality metrics after batch effect correction.
2025-08-20 20:26:48.486894 INFO::ASW Batch was 0.254367373500686 prior to batch effect correction and is now -0.162443312235797 .
2025-08-20 20:26:48.487826 INFO::ASW Label was -0.171867085161804 prior to batch effect correction and is now -0.0295643171326 .
2025-08-20 20:26:48.489171 INFO::Total function execution time is 0.152058362960815 s and adjustment time is 0.125558376312256 s ( 82.57 )
2025-08-20 20:26:48.626698 INFO::Formatting Data.
2025-08-20 20:26:48.627551 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.628465 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.629529 INFO::Found 2 missing values.
2025-08-20 20:26:48.63225 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.632779 INFO::Done
2025-08-20 20:26:48.65825 INFO::Found NA in Reference column
2025-08-20 20:26:48.667043 INFO::Require at least two references per batch.
2025-08-20 20:26:48.686446 INFO::Formatting Data.
2025-08-20 20:26:48.687236 INFO::Recognized SummarizedExperiment
2025-08-20 20:26:48.68777 INFO::Typecasting input to dataframe.
2025-08-20 20:26:48.697195 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.698387 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.701762 INFO::Found 0 missing values.
2025-08-20 20:26:48.708117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.708759 INFO::Done
2025-08-20 20:26:48.72377 INFO::Formatting Data.
2025-08-20 20:26:48.724501 INFO::Recognized SummarizedExperiment
2025-08-20 20:26:48.725038 INFO::Typecasting input to dataframe.
2025-08-20 20:26:48.742173 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.743453 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.746824 INFO::Found 0 missing values.
2025-08-20 20:26:48.756977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.757751 INFO::Done
2025-08-20 20:26:48.773077 INFO::Formatting Data.
2025-08-20 20:26:48.77389 INFO::Recognized SummarizedExperiment
2025-08-20 20:26:48.774425 INFO::Typecasting input to dataframe.
2025-08-20 20:26:48.790921 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.792052 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.793136 INFO::Found 0 missing values.
2025-08-20 20:26:48.794049 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.
2025-08-20 20:26:48.798269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.798834 INFO::Done
2025-08-20 20:26:48.808539 INFO::Formatting Data.
2025-08-20 20:26:48.809366 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.810237 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.811182 INFO::Found 0 missing values.
2025-08-20 20:26:48.81394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.814457 INFO::Done
2025-08-20 20:26:48.825267 INFO::Formatting Data.
2025-08-20 20:26:48.826077 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.826935 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.827917 INFO::Found 0 missing values.
2025-08-20 20:26:48.830689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.831233 INFO::Done
2025-08-20 20:26:48.859458 INFO::Formatting Data.
2025-08-20 20:26:48.860345 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.86139 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.862639 INFO::Found 1 missing values.
2025-08-20 20:26:48.865213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.865755 INFO::Done
2025-08-20 20:26:48.883723 INFO::Formatting Data.
2025-08-20 20:26:48.884567 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.885535 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.886585 INFO::Found 2 missing values.
2025-08-20 20:26:48.887526 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.
2025-08-20 20:26:48.889821 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.89034 INFO::Done
2025-08-20 20:26:48.899875 INFO::Formatting Data.
2025-08-20 20:26:48.900666 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.901574 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.902536 INFO::Found 2 missing values.
2025-08-20 20:26:48.904172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.904696 INFO::Done
2025-08-20 20:26:48.91498 INFO::Formatting Data.
2025-08-20 20:26:48.915744 INFO::Typecasting input to dataframe.
2025-08-20 20:26:48.916564 INFO::Replacing NaNs with NAs.
2025-08-20 20:26:48.917423 INFO::Removing potential empty rows and columns
2025-08-20 20:26:48.918404 INFO::Found 0 missing values.
2025-08-20 20:26:48.921265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-20 20:26:48.921791 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.219 5.118 22.946
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.634 | 1.683 | 19.275 | |
| compute_asw | 0.023 | 0.002 | 0.025 | |
| count_existing | 0.011 | 0.004 | 0.014 | |
| generate_data_covariables | 0.010 | 0.002 | 0.013 | |
| generate_dataset | 0.010 | 0.002 | 0.013 | |