Yannis Schumann
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-11 12:04 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-12-09 01:25:04 -0500 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 01:27:46 -0500 (Tue, 09 Dec 2025) |
| EllapsedTime: 161.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 43.541 2.731 42.262
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-12-09 01:27:08.315026 INFO::Formatting Data.
2025-12-09 01:27:08.321736 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:08.356483 INFO::Removing potential empty rows and columns
2025-12-09 01:27:09.095032 INFO::Found 0 missing values.
2025-12-09 01:27:09.103172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:09.104662 INFO::Done
2025-12-09 01:27:09.106186 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:09.136238 INFO::Starting hierarchical adjustment
2025-12-09 01:27:09.139415 INFO::Found 3 batches.
2025-12-09 01:27:09.140981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:09.143486 INFO::Using default BPPARAM
2025-12-09 01:27:09.144886 INFO::Processing subtree level 1
2025-12-09 01:27:09.4152 INFO::Adjusting the last 1 batches sequentially
2025-12-09 01:27:09.420715 INFO::Done
2025-12-09 01:27:09.422689 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:09.430661 INFO::ASW Batch was -0.0840294683200977 prior to batch effect correction and is now -0.0840294683200977 .
2025-12-09 01:27:09.432866 INFO::Total function execution time is 1.11928796768188 s and adjustment time is 0.282977104187012 s ( 25.28 )
2025-12-09 01:27:09.472947 INFO::Formatting Data.
2025-12-09 01:27:09.474687 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:09.476955 INFO::Removing potential empty rows and columns
2025-12-09 01:27:09.480709 INFO::Found 0 missing values.
2025-12-09 01:27:09.483357 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.
2025-12-09 01:27:09.515733 INFO::Formatting Data.
2025-12-09 01:27:09.517495 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:09.520148 INFO::Removing potential empty rows and columns
2025-12-09 01:27:09.524802 INFO::Found 0 missing values.
2025-12-09 01:27:09.527703 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.
2025-12-09 01:27:09.579467 INFO::Formatting Data.
2025-12-09 01:27:09.58135 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:09.583626 INFO::Removing potential empty rows and columns
2025-12-09 01:27:09.586442 INFO::Found 0 missing values.
2025-12-09 01:27:09.588956 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.
2025-12-09 01:27:09.602554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:09.604083 INFO::Done
2025-12-09 01:27:09.605824 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:09.610701 INFO::Starting hierarchical adjustment
2025-12-09 01:27:09.613835 INFO::Found 2 batches.
2025-12-09 01:27:09.615256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:09.616965 INFO::Using default BPPARAM
2025-12-09 01:27:09.618409 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:09.620932 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 01:27:09.683191 INFO::Done
2025-12-09 01:27:09.685188 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:09.69562 INFO::ASW Batch was -0.0190217775880801 prior to batch effect correction and is now -0.11777488880514 .
2025-12-09 01:27:09.698105 INFO::Total function execution time is 0.11864185333252 s and adjustment time is 0.0697479248046875 s ( 58.79 )
2025-12-09 01:27:09.705123 INFO::Formatting Data.
2025-12-09 01:27:09.706997 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:09.733877 INFO::Formatting Data.
2025-12-09 01:27:09.735656 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:09.738018 INFO::Removing potential empty rows and columns
2025-12-09 01:27:09.740887 INFO::Found 0 missing values.
2025-12-09 01:27:09.751069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:09.752541 INFO::Done
2025-12-09 01:27:09.753865 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:09.807252 INFO::Starting hierarchical adjustment
2025-12-09 01:27:09.809304 INFO::Found 2 batches.
2025-12-09 01:27:09.810718 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:09.812341 INFO::Using default BPPARAM
2025-12-09 01:27:09.815694 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:09.818101 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 01:27:09.863523 INFO::Done
2025-12-09 01:27:09.865226 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:09.869926 INFO::ASW Batch was -0.029920699517461 prior to batch effect correction and is now -0.126770824242285 .
2025-12-09 01:27:09.871829 INFO::Total function execution time is 0.138043880462646 s and adjustment time is 0.0546188354492188 s ( 39.57 )
2025-12-09 01:27:09.875027 INFO::Formatting Data.
2025-12-09 01:27:09.876489 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:09.878526 INFO::Removing potential empty rows and columns
2025-12-09 01:27:09.881126 INFO::Found 0 missing values.
2025-12-09 01:27:09.892202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:09.893643 INFO::Done
2025-12-09 01:27:09.894897 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:09.899808 INFO::Starting hierarchical adjustment
2025-12-09 01:27:09.901731 INFO::Found 2 batches.
2025-12-09 01:27:09.903064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:09.904663 INFO::Using default BPPARAM
2025-12-09 01:27:09.906064 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:09.908907 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 01:27:09.954279 INFO::Done
2025-12-09 01:27:09.957307 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:09.961864 INFO::ASW Batch was -0.029920699517461 prior to batch effect correction and is now -0.126770824242285 .
2025-12-09 01:27:09.964149 INFO::Total function execution time is 0.0891292095184326 s and adjustment time is 0.0529000759124756 s ( 59.35 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-09 01:27:17.043655 INFO::Formatting Data.
2025-12-09 01:27:17.045394 INFO::Recognized SummarizedExperiment
2025-12-09 01:27:17.046511 INFO::Typecasting input to dataframe.
2025-12-09 01:27:17.122959 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:17.125638 INFO::Removing potential empty rows and columns
2025-12-09 01:27:17.139515 INFO::Found 0 missing values.
2025-12-09 01:27:17.164176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:17.165738 INFO::Done
2025-12-09 01:27:17.167042 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:17.178999 INFO::Starting hierarchical adjustment
2025-12-09 01:27:17.182352 INFO::Found 2 batches.
2025-12-09 01:27:17.183803 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:17.186203 INFO::Using default BPPARAM
2025-12-09 01:27:17.187565 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:17.190002 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 01:27:17.3588 INFO::Done
2025-12-09 01:27:17.360303 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:17.370979 INFO::ASW Batch was -0.0030428456015259 prior to batch effect correction and is now -0.0919578395785749 .
2025-12-09 01:27:17.373065 INFO::Total function execution time is 0.330046892166138 s and adjustment time is 0.176854848861694 s ( 53.58 )
Warning: stack imbalance in '{', 73 then 75
2025-12-09 01:27:17.424964 INFO::Formatting Data.
2025-12-09 01:27:17.426377 INFO::Recognized SummarizedExperiment
2025-12-09 01:27:17.427595 INFO::Typecasting input to dataframe.
2025-12-09 01:27:17.459542 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:17.462191 INFO::Removing potential empty rows and columns
2025-12-09 01:27:17.4733 INFO::Found 0 missing values.
2025-12-09 01:27:17.496359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:17.497849 INFO::Done
2025-12-09 01:27:17.49915 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:17.509363 INFO::Starting hierarchical adjustment
2025-12-09 01:27:17.511343 INFO::Found 2 batches.
2025-12-09 01:27:17.512741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:17.51423 INFO::Using default BPPARAM
2025-12-09 01:27:17.515536 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:17.518022 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 01:27:17.606345 INFO::Done
2025-12-09 01:27:17.607826 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:17.618715 INFO::ASW Batch was -0.00895817026938563 prior to batch effect correction and is now -0.00895817026938563 .
2025-12-09 01:27:17.620861 INFO::Total function execution time is 0.195808887481689 s and adjustment time is 0.0954418182373047 s ( 48.74 )
2025-12-09 01:27:17.676624 INFO::Formatting Data.
2025-12-09 01:27:17.678435 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:17.68056 INFO::Removing potential empty rows and columns
2025-12-09 01:27:17.683105 INFO::Found 0 missing values.
2025-12-09 01:27:17.692218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:17.69372 INFO::Done
2025-12-09 01:27:17.694989 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:17.704004 INFO::Starting hierarchical adjustment
2025-12-09 01:27:17.705982 INFO::Found 3 batches.
2025-12-09 01:27:17.707434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:17.708992 INFO::Using default BPPARAM
2025-12-09 01:27:17.710465 INFO::Processing subtree level 1
2025-12-09 01:27:18.081712 INFO::Adjusting the last 1 batches sequentially
2025-12-09 01:27:18.097457 INFO::Done
2025-12-09 01:27:18.09934 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:18.112188 INFO::ASW Batch was -0.0698394030628583 prior to batch effect correction and is now -0.15739469525998 .
2025-12-09 01:27:18.11636 INFO::Total function execution time is 0.439413785934448 s and adjustment time is 0.391791105270386 s ( 89.16 )
2025-12-09 01:27:18.158933 INFO::Skipping initial DF formatting
2025-12-09 01:27:18.161482 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:18.171194 INFO::Starting hierarchical adjustment
2025-12-09 01:27:18.173065 INFO::Found 5 batches.
2025-12-09 01:27:18.174246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:18.175855 INFO::Using default BPPARAM
2025-12-09 01:27:18.177223 INFO::Processing subtree level 1
2025-12-09 01:27:18.789376 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:18.794633 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 01:27:18.894192 INFO::Done
2025-12-09 01:27:18.898877 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:18.9179 INFO::ASW Batch was 0.508351786835947 prior to batch effect correction and is now 0.508351786835947 .
2025-12-09 01:27:18.919629 INFO::ASW Label was 0.377167003815937 prior to batch effect correction and is now 0.377167003815937 .
2025-12-09 01:27:18.923576 INFO::Total function execution time is 0.764595031738281 s and adjustment time is 0.721467018127441 s ( 94.36 )
2025-12-09 01:27:19.092506 INFO::Formatting Data.
2025-12-09 01:27:19.094277 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:19.097247 INFO::Removing potential empty rows and columns
2025-12-09 01:27:19.099585 INFO::Found 0 missing values.
2025-12-09 01:27:19.110574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:19.112096 INFO::Done
2025-12-09 01:27:19.113417 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:19.120651 INFO::Starting hierarchical adjustment
2025-12-09 01:27:19.122549 INFO::Found 5 batches.
2025-12-09 01:27:19.123948 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:19.125626 INFO::Using default BPPARAM
2025-12-09 01:27:19.127002 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.
2025-12-09 01:27:19.483611 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:19.502042 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 01:27:19.572664 INFO::Done
2025-12-09 01:27:19.574459 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:19.583142 INFO::ASW Batch was 0.577313867204001 prior to batch effect correction and is now -0.0694411180040785 .
2025-12-09 01:27:19.584895 INFO::ASW Label was 0.271665178986545 prior to batch effect correction and is now 0.743635051323931 .
2025-12-09 01:27:19.587932 INFO::Total function execution time is 0.495373964309692 s and adjustment time is 0.450418949127197 s ( 90.93 )
2025-12-09 01:27:19.590346 INFO::Formatting Data.
2025-12-09 01:27:19.591997 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:19.594334 INFO::Removing potential empty rows and columns
2025-12-09 01:27:19.599567 INFO::Found 0 missing values.
2025-12-09 01:27:19.614653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:19.616321 INFO::Done
2025-12-09 01:27:19.617869 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:19.625923 INFO::Starting hierarchical adjustment
2025-12-09 01:27:19.628056 INFO::Found 5 batches.
2025-12-09 01:27:19.62959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:19.631329 INFO::Using default BPPARAM
2025-12-09 01:27:19.634136 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.
2025-12-09 01:27:19.960078 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:19.971983 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 01:27:20.028429 INFO::Done
2025-12-09 01:27:20.030145 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:20.038775 INFO::ASW Batch was 0.577313867204001 prior to batch effect correction and is now -0.0694411180040785 .
2025-12-09 01:27:20.040374 INFO::ASW Label was 0.271665178986545 prior to batch effect correction and is now 0.743635051323931 .
2025-12-09 01:27:20.042447 INFO::Total function execution time is 0.452086210250854 s and adjustment time is 0.4007568359375 s ( 88.65 )
2025-12-09 01:27:20.083359 INFO::Formatting Data.
2025-12-09 01:27:20.085221 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:20.088191 INFO::Removing potential empty rows and columns
2025-12-09 01:27:20.091738 INFO::Found 0 missing values.
2025-12-09 01:27:20.105492 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:20.107115 INFO::Done
2025-12-09 01:27:20.108673 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:20.116399 INFO::Starting hierarchical adjustment
2025-12-09 01:27:20.119131 INFO::Found 5 batches.
2025-12-09 01:27:20.120735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:20.122467 INFO::Using default BPPARAM
2025-12-09 01:27:20.1241 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.
2025-12-09 01:27:20.45805 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:20.46809 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 01:27:20.521729 INFO::Done
2025-12-09 01:27:20.523386 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:20.531388 INFO::ASW Batch was 0.309597619629314 prior to batch effect correction and is now -0.106781785778213 .
2025-12-09 01:27:20.533058 INFO::ASW Label was 0.401613068983939 prior to batch effect correction and is now 0.826836879523131 .
2025-12-09 01:27:20.535126 INFO::Total function execution time is 0.451849937438965 s and adjustment time is 0.403584003448486 s ( 89.32 )
2025-12-09 01:27:20.537708 INFO::Formatting Data.
2025-12-09 01:27:20.540232 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:20.542729 INFO::Removing potential empty rows and columns
2025-12-09 01:27:20.545382 INFO::Found 0 missing values.
2025-12-09 01:27:20.556996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:20.558672 INFO::Done
2025-12-09 01:27:20.560222 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:20.571167 INFO::Starting hierarchical adjustment
2025-12-09 01:27:20.573935 INFO::Found 5 batches.
2025-12-09 01:27:20.575616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:20.577341 INFO::Using default BPPARAM
2025-12-09 01:27:20.578841 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.
2025-12-09 01:27:20.918337 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:20.930345 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 01:27:20.985215 INFO::Done
2025-12-09 01:27:20.987093 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:20.996667 INFO::ASW Batch was 0.309597619629314 prior to batch effect correction and is now -0.106781785778213 .
2025-12-09 01:27:20.998263 INFO::ASW Label was 0.401613068983939 prior to batch effect correction and is now 0.826836879523131 .
2025-12-09 01:27:21.000396 INFO::Total function execution time is 0.462714195251465 s and adjustment time is 0.412078142166138 s ( 89.06 )
2025-12-09 01:27:21.039548 INFO::Formatting Data.
2025-12-09 01:27:21.041454 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:21.04434 INFO::Removing potential empty rows and columns
2025-12-09 01:27:21.047153 INFO::Found 0 missing values.
2025-12-09 01:27:21.055857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:21.057379 INFO::Done
2025-12-09 01:27:21.058719 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:21.067297 INFO::Starting hierarchical adjustment
2025-12-09 01:27:21.069338 INFO::Found 2 batches.
2025-12-09 01:27:21.070981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:21.07256 INFO::Using default BPPARAM
2025-12-09 01:27:21.074106 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:21.076741 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 01:27:21.121488 INFO::Done
2025-12-09 01:27:21.12309 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:21.130294 INFO::ASW Batch was 0.523608040441478 prior to batch effect correction and is now 0.0628333660229153 .
2025-12-09 01:27:21.131898 INFO::ASW Label was 0.459626410529062 prior to batch effect correction and is now 0.881700327493866 .
2025-12-09 01:27:21.134281 INFO::Total function execution time is 0.0948488712310791 s and adjustment time is 0.0525431632995605 s ( 55.4 )
2025-12-09 01:27:21.13633 INFO::Formatting Data.
2025-12-09 01:27:21.137926 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:21.140154 INFO::Removing potential empty rows and columns
2025-12-09 01:27:21.142787 INFO::Found 0 missing values.
2025-12-09 01:27:21.151087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:21.152589 INFO::Done
2025-12-09 01:27:21.153969 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:21.160452 INFO::Starting hierarchical adjustment
2025-12-09 01:27:21.162197 INFO::Found 2 batches.
2025-12-09 01:27:21.163421 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:21.165212 INFO::Using default BPPARAM
2025-12-09 01:27:21.169221 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:21.171646 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-09 01:27:21.217053 INFO::Done
2025-12-09 01:27:21.218612 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:21.226519 INFO::ASW Batch was 0.523608040441478 prior to batch effect correction and is now 0.0628333660229153 .
2025-12-09 01:27:21.228155 INFO::ASW Label was 0.459626410529062 prior to batch effect correction and is now 0.881700327493866 .
2025-12-09 01:27:21.230152 INFO::Total function execution time is 0.0938570499420166 s and adjustment time is 0.0551550388336182 s ( 58.76 )
2025-12-09 01:27:21.264263 INFO::Formatting Data.
2025-12-09 01:27:21.267328 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:21.270025 INFO::Removing potential empty rows and columns
2025-12-09 01:27:21.272446 INFO::Found 0 missing values.
2025-12-09 01:27:21.280212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:21.282188 INFO::Done
2025-12-09 01:27:21.283863 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:21.290541 INFO::Starting hierarchical adjustment
2025-12-09 01:27:21.292572 INFO::Found 2 batches.
2025-12-09 01:27:21.293947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:21.295565 INFO::Using default BPPARAM
2025-12-09 01:27:21.297023 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:21.299465 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 01:27:21.403994 INFO::Done
2025-12-09 01:27:21.405446 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:21.409911 INFO::ASW Batch was -0.0579130587421088 prior to batch effect correction and is now -0.163055287763593 .
2025-12-09 01:27:21.415673 INFO::Total function execution time is 0.151481866836548 s and adjustment time is 0.111816883087158 s ( 73.82 )
2025-12-09 01:27:21.468071 INFO::Formatting Data.
2025-12-09 01:27:21.475234 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:21.477736 INFO::Removing potential empty rows and columns
2025-12-09 01:27:21.480324 INFO::Found 0 missing values.
2025-12-09 01:27:21.483486 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.
2025-12-09 01:27:21.501649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:21.504265 INFO::Done
2025-12-09 01:27:21.509326 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:21.516533 INFO::Starting hierarchical adjustment
2025-12-09 01:27:21.518482 INFO::Found 2 batches.
2025-12-09 01:27:21.52138 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:21.523168 INFO::Using default BPPARAM
2025-12-09 01:27:21.524727 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:21.527444 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 01:27:21.582748 INFO::Done
2025-12-09 01:27:21.584357 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:21.595331 INFO::ASW Batch was 0.607259294633127 prior to batch effect correction and is now 0.0125313896098533 .
2025-12-09 01:27:21.596912 INFO::ASW Label was 0.500222089782482 prior to batch effect correction and is now 0.93127834050917 .
2025-12-09 01:27:21.598974 INFO::Total function execution time is 0.131072998046875 s and adjustment time is 0.0646121501922607 s ( 49.29 )
2025-12-09 01:27:21.601218 INFO::Formatting Data.
2025-12-09 01:27:21.60474 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:21.607333 INFO::Removing potential empty rows and columns
2025-12-09 01:27:21.609837 INFO::Found 0 missing values.
2025-12-09 01:27:21.612036 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.
2025-12-09 01:27:21.627835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:21.629526 INFO::Done
2025-12-09 01:27:21.630702 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:21.642274 INFO::Starting hierarchical adjustment
2025-12-09 01:27:21.644134 INFO::Found 2 batches.
2025-12-09 01:27:21.645509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:21.647054 INFO::Using default BPPARAM
2025-12-09 01:27:21.648427 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:21.652434 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 01:27:21.703329 INFO::Done
2025-12-09 01:27:21.704798 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:21.713399 INFO::ASW Batch was 0.607259294633127 prior to batch effect correction and is now 0.0125313896098533 .
2025-12-09 01:27:21.714927 INFO::ASW Label was 0.500222089782482 prior to batch effect correction and is now 0.93127834050917 .
2025-12-09 01:27:21.716846 INFO::Total function execution time is 0.115751028060913 s and adjustment time is 0.0595378875732422 s ( 51.44 )
2025-12-09 01:27:22.359095 INFO::Formatting Data.
2025-12-09 01:27:22.361078 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:22.363174 INFO::Removing potential empty rows and columns
2025-12-09 01:27:22.365804 INFO::Found 0 missing values.
2025-12-09 01:27:22.376202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:22.37771 INFO::Done
2025-12-09 01:27:22.379029 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:22.385188 INFO::Starting hierarchical adjustment
2025-12-09 01:27:22.38713 INFO::Found 3 batches.
2025-12-09 01:27:22.388604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:22.390235 INFO::Using default BPPARAM
2025-12-09 01:27:22.391689 INFO::Processing subtree level 1
2025-12-09 01:27:22.625334 INFO::Adjusting the last 1 batches sequentially
2025-12-09 01:27:22.634306 INFO::Done
2025-12-09 01:27:22.638192 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:22.650762 INFO::ASW Batch was -0.0904908329563391 prior to batch effect correction and is now -0.0904908329563391 .
2025-12-09 01:27:22.654959 INFO::Total function execution time is 0.294660091400146 s and adjustment time is 0.247480869293213 s ( 83.99 )
2025-12-09 01:27:22.658325 INFO::Formatting Data.
2025-12-09 01:27:22.662846 INFO::Typecasting input to dataframe.
2025-12-09 01:27:22.665914 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:22.668193 INFO::Removing potential empty rows and columns
2025-12-09 01:27:22.671212 INFO::Found 0 missing values.
2025-12-09 01:27:22.679251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:22.680741 INFO::Done
2025-12-09 01:27:22.682708 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:22.687861 INFO::Starting hierarchical adjustment
2025-12-09 01:27:22.689744 INFO::Found 3 batches.
2025-12-09 01:27:22.69231 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:22.694641 INFO::Using default BPPARAM
2025-12-09 01:27:22.696131 INFO::Processing subtree level 1
2025-12-09 01:27:22.936673 INFO::Adjusting the last 1 batches sequentially
2025-12-09 01:27:22.948242 INFO::Done
2025-12-09 01:27:22.95186 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:22.964337 INFO::ASW Batch was -0.0904908329563391 prior to batch effect correction and is now -0.0904908329563391 .
2025-12-09 01:27:22.96903 INFO::Total function execution time is 0.310176134109497 s and adjustment time is 0.258774995803833 s ( 83.43 )
2025-12-09 01:27:23.009473 INFO::Formatting Data.
2025-12-09 01:27:23.01142 INFO::Typecasting input to dataframe.
2025-12-09 01:27:23.013918 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:23.016752 INFO::Removing potential empty rows and columns
2025-12-09 01:27:23.019941 INFO::Found 0 missing values.
2025-12-09 01:27:23.028549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:23.030172 INFO::Done
2025-12-09 01:27:23.031664 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:23.036583 INFO::Starting hierarchical adjustment
2025-12-09 01:27:23.038591 INFO::Found 3 batches.
2025-12-09 01:27:23.040093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:23.041796 INFO::Using default BPPARAM
2025-12-09 01:27:23.043203 INFO::Processing subtree level 1
2025-12-09 01:27:23.280508 INFO::Adjusting the last 1 batches sequentially
2025-12-09 01:27:23.291971 INFO::Done
2025-12-09 01:27:23.293588 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:23.307427 INFO::ASW Batch was -0.110529944428461 prior to batch effect correction and is now -0.110529944428461 .
2025-12-09 01:27:23.310875 INFO::Total function execution time is 0.300447940826416 s and adjustment time is 0.253714084625244 s ( 84.45 )
2025-12-09 01:27:23.711357 INFO::Formatting Data.
2025-12-09 01:27:23.713595 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:23.716626 INFO::Removing potential empty rows and columns
2025-12-09 01:27:23.724918 INFO::Found 1000 missing values.
2025-12-09 01:27:23.788245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:23.789703 INFO::Done
2025-12-09 01:27:23.792134 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:23.806375 INFO::Starting hierarchical adjustment
2025-12-09 01:27:23.808345 INFO::Found 10 batches.
2025-12-09 01:27:23.810382 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:23.812136 INFO::Using default BPPARAM
2025-12-09 01:27:23.815134 INFO::Processing subtree level 1
2025-12-09 01:27:24.146165 INFO::Processing subtree level 2
2025-12-09 01:27:24.573772 INFO::Adjusting the last 1 batches sequentially
2025-12-09 01:27:24.589199 INFO::Done
2025-12-09 01:27:24.592155 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:24.612979 INFO::ASW Batch was 0.53566549262767 prior to batch effect correction and is now 0.53566549262767 .
2025-12-09 01:27:24.614564 INFO::ASW Label was 0.279725551659877 prior to batch effect correction and is now 0.279725551659877 .
2025-12-09 01:27:24.617544 INFO::Total function execution time is 0.906221151351929 s and adjustment time is 0.781198024749756 s ( 86.2 )
2025-12-09 01:27:24.61984 INFO::Formatting Data.
2025-12-09 01:27:24.62163 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:24.625647 INFO::Removing potential empty rows and columns
2025-12-09 01:27:24.633889 INFO::Found 1000 missing values.
2025-12-09 01:27:24.694545 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:24.696059 INFO::Done
2025-12-09 01:27:24.698028 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:24.713497 INFO::Starting hierarchical adjustment
2025-12-09 01:27:24.715993 INFO::Found 10 batches.
2025-12-09 01:27:26.122844 INFO::Set up parallel execution backend with 2 workers
2025-12-09 01:27:26.124101 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-09 01:27:28.003959 INFO::Adjusting the last 2 batches sequentially
2025-12-09 01:27:28.006603 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-09 01:27:28.055165 INFO::Done
2025-12-09 01:27:28.056528 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:28.068387 INFO::ASW Batch was 0.53566549262767 prior to batch effect correction and is now 0.53566549262767 .
2025-12-09 01:27:28.069745 INFO::ASW Label was 0.279725551659877 prior to batch effect correction and is now 0.279725551659877 .
2025-12-09 01:27:28.071325 INFO::Total function execution time is 3.4516270160675 s and adjustment time is 3.33962297439575 s ( 96.76 )
2025-12-09 01:27:28.483911 INFO::Formatting Data.
2025-12-09 01:27:28.487544 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:28.492628 INFO::Removing potential empty rows and columns
2025-12-09 01:27:28.49669 INFO::Found 0 missing values.
2025-12-09 01:27:28.510193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:28.511867 INFO::Done
2025-12-09 01:27:28.514319 INFO::Acquiring quality metrics before batch effect correction.
2025-12-09 01:27:28.521491 INFO::Starting hierarchical adjustment
2025-12-09 01:27:28.523381 INFO::Found 3 batches.
2025-12-09 01:27:28.524757 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-09 01:27:28.52649 INFO::Using default BPPARAM
2025-12-09 01:27:28.527974 INFO::Processing subtree level 1
2025-12-09 01:27:28.830097 INFO::Adjusting the last 1 batches sequentially
2025-12-09 01:27:28.842138 INFO::Done
2025-12-09 01:27:28.844677 INFO::Acquiring quality metrics after batch effect correction.
2025-12-09 01:27:28.860591 INFO::ASW Batch was 0.206686900681041 prior to batch effect correction and is now -0.144928415763131 .
2025-12-09 01:27:28.862857 INFO::ASW Label was -0.209929899392437 prior to batch effect correction and is now -0.0188369228965913 .
2025-12-09 01:27:28.866962 INFO::Total function execution time is 0.382887125015259 s and adjustment time is 0.318570137023926 s ( 83.2 )
2025-12-09 01:27:29.238203 INFO::Formatting Data.
2025-12-09 01:27:29.239968 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:29.242403 INFO::Removing potential empty rows and columns
2025-12-09 01:27:29.245354 INFO::Found 2 missing values.
2025-12-09 01:27:29.253764 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:29.25523 INFO::Done
2025-12-09 01:27:29.348234 INFO::Found NA in Reference column
2025-12-09 01:27:29.38002 INFO::Require at least two references per batch.
2025-12-09 01:27:29.444847 INFO::Formatting Data.
2025-12-09 01:27:29.44832 INFO::Recognized SummarizedExperiment
2025-12-09 01:27:29.449939 INFO::Typecasting input to dataframe.
2025-12-09 01:27:29.478868 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:29.481531 INFO::Removing potential empty rows and columns
2025-12-09 01:27:29.492869 INFO::Found 0 missing values.
2025-12-09 01:27:29.515653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:29.5171 INFO::Done
2025-12-09 01:27:29.560031 INFO::Formatting Data.
2025-12-09 01:27:29.561668 INFO::Recognized SummarizedExperiment
2025-12-09 01:27:29.56299 INFO::Typecasting input to dataframe.
2025-12-09 01:27:29.609588 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:29.612425 INFO::Removing potential empty rows and columns
2025-12-09 01:27:29.623534 INFO::Found 0 missing values.
2025-12-09 01:27:29.661683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:29.663209 INFO::Done
2025-12-09 01:27:29.714257 INFO::Formatting Data.
2025-12-09 01:27:29.716099 INFO::Recognized SummarizedExperiment
2025-12-09 01:27:29.717421 INFO::Typecasting input to dataframe.
2025-12-09 01:27:29.76546 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:29.767716 INFO::Removing potential empty rows and columns
2025-12-09 01:27:29.770607 INFO::Found 0 missing values.
2025-12-09 01:27:29.772904 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.
2025-12-09 01:27:29.786757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:29.788387 INFO::Done
2025-12-09 01:27:29.818705 INFO::Formatting Data.
2025-12-09 01:27:29.820441 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:29.823055 INFO::Removing potential empty rows and columns
2025-12-09 01:27:29.825883 INFO::Found 0 missing values.
2025-12-09 01:27:29.834275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:29.835617 INFO::Done
2025-12-09 01:27:29.874671 INFO::Formatting Data.
2025-12-09 01:27:29.876745 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:29.88345 INFO::Removing potential empty rows and columns
2025-12-09 01:27:29.886471 INFO::Found 0 missing values.
2025-12-09 01:27:29.896199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:29.897717 INFO::Done
2025-12-09 01:27:29.987709 INFO::Formatting Data.
2025-12-09 01:27:29.991742 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:29.994568 INFO::Removing potential empty rows and columns
2025-12-09 01:27:29.997945 INFO::Found 1 missing values.
2025-12-09 01:27:30.005849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:30.007384 INFO::Done
2025-12-09 01:27:30.062995 INFO::Formatting Data.
2025-12-09 01:27:30.068594 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:30.071024 INFO::Removing potential empty rows and columns
2025-12-09 01:27:30.07345 INFO::Found 2 missing values.
2025-12-09 01:27:30.075571 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.
2025-12-09 01:27:30.081741 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:30.083878 INFO::Done
2025-12-09 01:27:30.119452 INFO::Formatting Data.
2025-12-09 01:27:30.121223 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:30.12328 INFO::Removing potential empty rows and columns
2025-12-09 01:27:30.125464 INFO::Found 2 missing values.
2025-12-09 01:27:30.130979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:30.132678 INFO::Done
2025-12-09 01:27:30.167006 INFO::Formatting Data.
2025-12-09 01:27:30.168694 INFO::Typecasting input to dataframe.
2025-12-09 01:27:30.170695 INFO::Replacing NaNs with NAs.
2025-12-09 01:27:30.174908 INFO::Removing potential empty rows and columns
2025-12-09 01:27:30.177579 INFO::Found 0 missing values.
2025-12-09 01:27:30.187363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-09 01:27:30.18895 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.334 6.730 48.957
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.541 | 2.731 | 42.262 | |
| compute_asw | 0.055 | 0.003 | 0.107 | |
| count_existing | 0.027 | 0.001 | 0.039 | |
| generate_data_covariables | 0.026 | 0.002 | 0.052 | |
| generate_dataset | 0.025 | 0.003 | 0.061 | |