Yannis Schumann
| Snapshot Date: 2026-04-30 13:45 -0400 (Thu, 30 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-01 11:32 -0400 (Fri, 01 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4843 |
| 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 167/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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: 1.9.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz |
| StartedAt: 2026-04-30 21:35:22 -0400 (Thu, 30 Apr 2026) |
| EndedAt: 2026-04-30 21:36:54 -0400 (Thu, 30 Apr 2026) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-01 01:35:23 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 29.259 1.449 20.437
* 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-3.24-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.9.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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")
2026-04-30 21:36:17.554368 INFO::Formatting Data.
2026-04-30 21:36:17.555653 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:17.566561 INFO::Removing potential empty rows and columns
2026-04-30 21:36:17.802706 INFO::Found 0 missing values.
2026-04-30 21:36:17.80622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:17.80703 INFO::Done
2026-04-30 21:36:17.807668 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:17.821541 INFO::Starting hierarchical adjustment
2026-04-30 21:36:17.822505 INFO::Found 3 batches.
2026-04-30 21:36:17.823114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:17.824292 INFO::Using default BPPARAM
2026-04-30 21:36:17.824887 INFO::Processing subtree level 1
2026-04-30 21:36:17.921992 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:36:17.923737 INFO::Done
2026-04-30 21:36:17.924456 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:17.926912 INFO::ASW Batch was -0.0945932072510765 prior to batch effect correction and is now -0.0945932072510765 .
2026-04-30 21:36:17.927952 INFO::Total function execution time is 0.374197244644165 s and adjustment time is 0.101457118988037 s ( 27.11 )
2026-04-30 21:36:17.941194 INFO::Formatting Data.
2026-04-30 21:36:17.942089 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:17.943072 INFO::Removing potential empty rows and columns
2026-04-30 21:36:17.944227 INFO::Found 0 missing values.
2026-04-30 21:36:17.94521 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.
2026-04-30 21:36:17.956227 INFO::Formatting Data.
2026-04-30 21:36:17.957017 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:17.957941 INFO::Removing potential empty rows and columns
2026-04-30 21:36:17.959071 INFO::Found 0 missing values.
2026-04-30 21:36:17.960046 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.
2026-04-30 21:36:17.976564 INFO::Formatting Data.
2026-04-30 21:36:17.977406 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:17.978292 INFO::Removing potential empty rows and columns
2026-04-30 21:36:17.979342 INFO::Found 0 missing values.
2026-04-30 21:36:17.98027 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.
2026-04-30 21:36:17.984732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:17.985322 INFO::Done
2026-04-30 21:36:17.985902 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:17.987965 INFO::Starting hierarchical adjustment
2026-04-30 21:36:17.988715 INFO::Found 2 batches.
2026-04-30 21:36:17.989283 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:17.989977 INFO::Using default BPPARAM
2026-04-30 21:36:17.990566 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:17.991567 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:36:18.012651 INFO::Done
2026-04-30 21:36:18.013426 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:18.015521 INFO::ASW Batch was -0.00652692707577742 prior to batch effect correction and is now -0.105994329131924 .
2026-04-30 21:36:18.016322 INFO::Total function execution time is 0.0400352478027344 s and adjustment time is 0.0240523815155029 s ( 60.08 )
2026-04-30 21:36:18.019241 INFO::Formatting Data.
2026-04-30 21:36:18.019954 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:18.028945 INFO::Formatting Data.
2026-04-30 21:36:18.029691 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:18.030621 INFO::Removing potential empty rows and columns
2026-04-30 21:36:18.031717 INFO::Found 0 missing values.
2026-04-30 21:36:18.034726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:18.035294 INFO::Done
2026-04-30 21:36:18.035858 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:18.037978 INFO::Starting hierarchical adjustment
2026-04-30 21:36:18.038733 INFO::Found 2 batches.
2026-04-30 21:36:18.039297 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:18.039959 INFO::Using default BPPARAM
2026-04-30 21:36:18.040563 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:18.041543 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:36:18.057445 INFO::Done
2026-04-30 21:36:18.0582 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:18.060501 INFO::ASW Batch was 0.0115685602664394 prior to batch effect correction and is now -0.0900910386154279 .
2026-04-30 21:36:18.061412 INFO::Total function execution time is 0.0324559211730957 s and adjustment time is 0.0188343524932861 s ( 58.03 )
2026-04-30 21:36:18.062611 INFO::Formatting Data.
2026-04-30 21:36:18.063284 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:18.064216 INFO::Removing potential empty rows and columns
2026-04-30 21:36:18.065349 INFO::Found 0 missing values.
2026-04-30 21:36:18.068511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:18.06908 INFO::Done
2026-04-30 21:36:18.069677 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:18.071827 INFO::Starting hierarchical adjustment
2026-04-30 21:36:18.072707 INFO::Found 2 batches.
2026-04-30 21:36:18.07329 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:18.073988 INFO::Using default BPPARAM
2026-04-30 21:36:18.074614 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:18.075567 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:36:18.09101 INFO::Done
2026-04-30 21:36:18.091761 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:18.093889 INFO::ASW Batch was 0.0115685602664394 prior to batch effect correction and is now -0.0900910386154279 .
2026-04-30 21:36:18.094722 INFO::Total function execution time is 0.0321156978607178 s and adjustment time is 0.0184297561645508 s ( 57.39 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-30 21:36:21.1522 INFO::Formatting Data.
2026-04-30 21:36:21.153015 INFO::Recognized SummarizedExperiment
2026-04-30 21:36:21.15355 INFO::Typecasting input to dataframe.
2026-04-30 21:36:21.183665 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:21.184925 INFO::Removing potential empty rows and columns
2026-04-30 21:36:21.18823 INFO::Found 0 missing values.
2026-04-30 21:36:21.194474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:21.195064 INFO::Done
2026-04-30 21:36:21.19559 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:21.198762 INFO::Starting hierarchical adjustment
2026-04-30 21:36:21.199463 INFO::Found 2 batches.
2026-04-30 21:36:21.19997 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:21.200989 INFO::Using default BPPARAM
2026-04-30 21:36:21.201519 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:21.202445 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:36:21.252645 INFO::Done
2026-04-30 21:36:21.25356 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:21.257113 INFO::ASW Batch was 0.0240287040861538 prior to batch effect correction and is now -0.0931671672344177 .
2026-04-30 21:36:21.258051 INFO::Total function execution time is 0.106109857559204 s and adjustment time is 0.0532679557800293 s ( 50.2 )
Warning: stack imbalance in '{', 73 then 75
2026-04-30 21:36:21.27587 INFO::Formatting Data.
2026-04-30 21:36:21.276649 INFO::Recognized SummarizedExperiment
2026-04-30 21:36:21.277191 INFO::Typecasting input to dataframe.
2026-04-30 21:36:21.285609 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:21.286757 INFO::Removing potential empty rows and columns
2026-04-30 21:36:21.290004 INFO::Found 0 missing values.
2026-04-30 21:36:21.296288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:21.296899 INFO::Done
2026-04-30 21:36:21.297424 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:21.300652 INFO::Starting hierarchical adjustment
2026-04-30 21:36:21.301342 INFO::Found 2 batches.
2026-04-30 21:36:21.301897 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:21.302501 INFO::Using default BPPARAM
2026-04-30 21:36:21.303014 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:21.303985 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:36:21.329115 INFO::Done
2026-04-30 21:36:21.329947 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:21.333768 INFO::ASW Batch was 0.00726008689194418 prior to batch effect correction and is now 0.00726008689194418 .
2026-04-30 21:36:21.33474 INFO::Total function execution time is 0.0588293075561523 s and adjustment time is 0.0278332233428955 s ( 47.31 )
2026-04-30 21:36:21.354367 INFO::Formatting Data.
2026-04-30 21:36:21.35529 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:21.356238 INFO::Removing potential empty rows and columns
2026-04-30 21:36:21.357318 INFO::Found 0 missing values.
2026-04-30 21:36:21.360351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:21.360933 INFO::Done
2026-04-30 21:36:21.36149 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:21.363538 INFO::Starting hierarchical adjustment
2026-04-30 21:36:21.364265 INFO::Found 3 batches.
2026-04-30 21:36:21.364845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:21.365481 INFO::Using default BPPARAM
2026-04-30 21:36:21.366043 INFO::Processing subtree level 1
2026-04-30 21:36:21.496499 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:36:21.498436 INFO::Done
2026-04-30 21:36:21.499142 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:21.501734 INFO::ASW Batch was -0.0454032911962003 prior to batch effect correction and is now -0.158566707812385 .
2026-04-30 21:36:21.502712 INFO::Total function execution time is 0.148382425308228 s and adjustment time is 0.134273290634155 s ( 90.49 )
2026-04-30 21:36:21.51716 INFO::Skipping initial DF formatting
2026-04-30 21:36:21.517945 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:21.522159 INFO::Starting hierarchical adjustment
2026-04-30 21:36:21.523029 INFO::Found 5 batches.
2026-04-30 21:36:21.523635 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:21.524295 INFO::Using default BPPARAM
2026-04-30 21:36:21.524886 INFO::Processing subtree level 1
2026-04-30 21:36:21.642924 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:21.64509 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:36:21.667057 INFO::Done
2026-04-30 21:36:21.667999 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:21.672746 INFO::ASW Batch was 0.537093853275787 prior to batch effect correction and is now 0.537093853275787 .
2026-04-30 21:36:21.673484 INFO::ASW Label was 0.352354929222223 prior to batch effect correction and is now 0.352354929222223 .
2026-04-30 21:36:21.674474 INFO::Total function execution time is 0.157344341278076 s and adjustment time is 0.14414119720459 s ( 91.61 )
2026-04-30 21:36:21.693959 INFO::Formatting Data.
2026-04-30 21:36:21.694948 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:21.696003 INFO::Removing potential empty rows and columns
2026-04-30 21:36:21.697133 INFO::Found 0 missing values.
2026-04-30 21:36:21.701518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:21.702126 INFO::Done
2026-04-30 21:36:21.70271 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:21.706 INFO::Starting hierarchical adjustment
2026-04-30 21:36:21.706793 INFO::Found 5 batches.
2026-04-30 21:36:21.707363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:21.708063 INFO::Using default BPPARAM
2026-04-30 21:36:21.708656 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.
2026-04-30 21:36:21.815943 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:21.817743 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:36:21.834124 INFO::Done
2026-04-30 21:36:21.834905 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:21.838326 INFO::ASW Batch was 0.232402283726618 prior to batch effect correction and is now -0.0536162484283103 .
2026-04-30 21:36:21.839 INFO::ASW Label was 0.488749871004738 prior to batch effect correction and is now 0.80799822287152 .
2026-04-30 21:36:21.839904 INFO::Total function execution time is 0.14607310295105 s and adjustment time is 0.12746524810791 s ( 87.26 )
2026-04-30 21:36:21.840816 INFO::Formatting Data.
2026-04-30 21:36:21.841507 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:21.842449 INFO::Removing potential empty rows and columns
2026-04-30 21:36:21.843511 INFO::Found 0 missing values.
2026-04-30 21:36:21.847732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:21.848319 INFO::Done
2026-04-30 21:36:21.848911 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:21.851957 INFO::Starting hierarchical adjustment
2026-04-30 21:36:21.852736 INFO::Found 5 batches.
2026-04-30 21:36:21.853305 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:21.853977 INFO::Using default BPPARAM
2026-04-30 21:36:21.854563 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.
2026-04-30 21:36:21.952946 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:21.95475 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:36:21.971718 INFO::Done
2026-04-30 21:36:21.97253 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:21.97604 INFO::ASW Batch was 0.232402283726618 prior to batch effect correction and is now -0.0536162484283103 .
2026-04-30 21:36:21.976748 INFO::ASW Label was 0.488749871004738 prior to batch effect correction and is now 0.80799822287152 .
2026-04-30 21:36:21.977687 INFO::Total function execution time is 0.136856555938721 s and adjustment time is 0.119098663330078 s ( 87.02 )
2026-04-30 21:36:21.992755 INFO::Formatting Data.
2026-04-30 21:36:21.993595 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:21.994572 INFO::Removing potential empty rows and columns
2026-04-30 21:36:21.995618 INFO::Found 0 missing values.
2026-04-30 21:36:21.999835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.00044 INFO::Done
2026-04-30 21:36:22.000993 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.004069 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.004822 INFO::Found 5 batches.
2026-04-30 21:36:22.005402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.006076 INFO::Using default BPPARAM
2026-04-30 21:36:22.006656 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.
2026-04-30 21:36:22.111825 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:22.113743 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:36:22.13146 INFO::Done
2026-04-30 21:36:22.132333 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.136025 INFO::ASW Batch was 0.344921451879124 prior to batch effect correction and is now -0.0402687162420616 .
2026-04-30 21:36:22.136745 INFO::ASW Label was 0.44216464771824 prior to batch effect correction and is now 0.82211227990184 .
2026-04-30 21:36:22.137683 INFO::Total function execution time is 0.144987344741821 s and adjustment time is 0.126693725585938 s ( 87.38 )
2026-04-30 21:36:22.138658 INFO::Formatting Data.
2026-04-30 21:36:22.139346 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.140344 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.141464 INFO::Found 0 missing values.
2026-04-30 21:36:22.145883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.146502 INFO::Done
2026-04-30 21:36:22.14707 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.150448 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.151238 INFO::Found 5 batches.
2026-04-30 21:36:22.151835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.152531 INFO::Using default BPPARAM
2026-04-30 21:36:22.153106 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.
2026-04-30 21:36:22.26247 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:22.264239 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:36:22.280338 INFO::Done
2026-04-30 21:36:22.281142 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.284636 INFO::ASW Batch was 0.344921451879124 prior to batch effect correction and is now -0.0402687162420616 .
2026-04-30 21:36:22.285293 INFO::ASW Label was 0.44216464771824 prior to batch effect correction and is now 0.82211227990184 .
2026-04-30 21:36:22.2862 INFO::Total function execution time is 0.147573709487915 s and adjustment time is 0.129218101501465 s ( 87.56 )
2026-04-30 21:36:22.301309 INFO::Formatting Data.
2026-04-30 21:36:22.302199 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.303213 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.304308 INFO::Found 0 missing values.
2026-04-30 21:36:22.307226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.307832 INFO::Done
2026-04-30 21:36:22.308413 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.311485 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.312226 INFO::Found 2 batches.
2026-04-30 21:36:22.312823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.313504 INFO::Using default BPPARAM
2026-04-30 21:36:22.314071 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:22.315048 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:36:22.330235 INFO::Done
2026-04-30 21:36:22.331005 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.334152 INFO::ASW Batch was 0.319865743179955 prior to batch effect correction and is now 0.0328090298753343 .
2026-04-30 21:36:22.334833 INFO::ASW Label was 0.668311613587619 prior to batch effect correction and is now 0.89398651977181 .
2026-04-30 21:36:22.335681 INFO::Total function execution time is 0.0344760417938232 s and adjustment time is 0.0181243419647217 s ( 52.57 )
2026-04-30 21:36:22.336529 INFO::Formatting Data.
2026-04-30 21:36:22.337187 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.33814 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.339175 INFO::Found 0 missing values.
2026-04-30 21:36:22.342015 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.34261 INFO::Done
2026-04-30 21:36:22.343166 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.346244 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.34701 INFO::Found 2 batches.
2026-04-30 21:36:22.347589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.348245 INFO::Using default BPPARAM
2026-04-30 21:36:22.348829 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:22.349813 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-30 21:36:22.365341 INFO::Done
2026-04-30 21:36:22.366149 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.369304 INFO::ASW Batch was 0.319865743179955 prior to batch effect correction and is now 0.0328090298753343 .
2026-04-30 21:36:22.369977 INFO::ASW Label was 0.668311613587619 prior to batch effect correction and is now 0.89398651977181 .
2026-04-30 21:36:22.370816 INFO::Total function execution time is 0.0343129634857178 s and adjustment time is 0.0184469223022461 s ( 53.76 )
2026-04-30 21:36:22.383055 INFO::Formatting Data.
2026-04-30 21:36:22.383956 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.384927 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.385917 INFO::Found 0 missing values.
2026-04-30 21:36:22.38816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.388764 INFO::Done
2026-04-30 21:36:22.38932 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.391357 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.392119 INFO::Found 2 batches.
2026-04-30 21:36:22.392697 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.393333 INFO::Using default BPPARAM
2026-04-30 21:36:22.393921 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:22.394886 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:36:22.427669 INFO::Done
2026-04-30 21:36:22.428471 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.43067 INFO::ASW Batch was -0.0345542117438807 prior to batch effect correction and is now -0.17711275315192 .
2026-04-30 21:36:22.431563 INFO::Total function execution time is 0.0486502647399902 s and adjustment time is 0.0356593132019043 s ( 73.3 )
2026-04-30 21:36:22.444113 INFO::Formatting Data.
2026-04-30 21:36:22.444982 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.445932 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.446975 INFO::Found 0 missing values.
2026-04-30 21:36:22.448173 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.
2026-04-30 21:36:22.452955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.453582 INFO::Done
2026-04-30 21:36:22.45415 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.457229 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.457997 INFO::Found 2 batches.
2026-04-30 21:36:22.458576 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.459206 INFO::Using default BPPARAM
2026-04-30 21:36:22.45979 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:22.460771 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:36:22.477698 INFO::Done
2026-04-30 21:36:22.478522 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.481655 INFO::ASW Batch was 0.558796019342832 prior to batch effect correction and is now 0.0549596610875464 .
2026-04-30 21:36:22.48233 INFO::ASW Label was 0.484634432659087 prior to batch effect correction and is now 0.872952461967775 .
2026-04-30 21:36:22.483185 INFO::Total function execution time is 0.0391678810119629 s and adjustment time is 0.0198020935058594 s ( 50.56 )
2026-04-30 21:36:22.484051 INFO::Formatting Data.
2026-04-30 21:36:22.484715 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.485693 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.486753 INFO::Found 0 missing values.
2026-04-30 21:36:22.487743 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.
2026-04-30 21:36:22.492553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.493199 INFO::Done
2026-04-30 21:36:22.493792 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.496917 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.497689 INFO::Found 2 batches.
2026-04-30 21:36:22.49826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.498903 INFO::Using default BPPARAM
2026-04-30 21:36:22.499481 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:22.500483 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:36:22.517521 INFO::Done
2026-04-30 21:36:22.5183 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.521567 INFO::ASW Batch was 0.558796019342832 prior to batch effect correction and is now 0.0549596610875464 .
2026-04-30 21:36:22.522249 INFO::ASW Label was 0.484634432659087 prior to batch effect correction and is now 0.872952461967775 .
2026-04-30 21:36:22.523145 INFO::Total function execution time is 0.0391120910644531 s and adjustment time is 0.0199511051177979 s ( 51.01 )
2026-04-30 21:36:22.735218 INFO::Formatting Data.
2026-04-30 21:36:22.736128 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.737072 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.738169 INFO::Found 0 missing values.
2026-04-30 21:36:22.741401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.742 INFO::Done
2026-04-30 21:36:22.742573 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.744695 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.745451 INFO::Found 3 batches.
2026-04-30 21:36:22.746013 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.746653 INFO::Using default BPPARAM
2026-04-30 21:36:22.747216 INFO::Processing subtree level 1
2026-04-30 21:36:22.833623 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:36:22.835615 INFO::Done
2026-04-30 21:36:22.83631 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.838892 INFO::ASW Batch was -0.0685049797364234 prior to batch effect correction and is now -0.0685049797364234 .
2026-04-30 21:36:22.839873 INFO::Total function execution time is 0.104708909988403 s and adjustment time is 0.0903089046478271 s ( 86.25 )
2026-04-30 21:36:22.840918 INFO::Formatting Data.
2026-04-30 21:36:22.841626 INFO::Typecasting input to dataframe.
2026-04-30 21:36:22.842423 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.843386 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.844534 INFO::Found 0 missing values.
2026-04-30 21:36:22.847703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.848313 INFO::Done
2026-04-30 21:36:22.848895 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.851001 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.851751 INFO::Found 3 batches.
2026-04-30 21:36:22.85235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.853013 INFO::Using default BPPARAM
2026-04-30 21:36:22.853596 INFO::Processing subtree level 1
2026-04-30 21:36:22.941023 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:36:22.943295 INFO::Done
2026-04-30 21:36:22.944129 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:22.947156 INFO::ASW Batch was -0.0685049797364234 prior to batch effect correction and is now -0.0685049797364234 .
2026-04-30 21:36:22.948328 INFO::Total function execution time is 0.107351779937744 s and adjustment time is 0.091627836227417 s ( 85.35 )
2026-04-30 21:36:22.963708 INFO::Formatting Data.
2026-04-30 21:36:22.964704 INFO::Typecasting input to dataframe.
2026-04-30 21:36:22.965695 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:22.966736 INFO::Removing potential empty rows and columns
2026-04-30 21:36:22.967924 INFO::Found 0 missing values.
2026-04-30 21:36:22.971186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:22.971824 INFO::Done
2026-04-30 21:36:22.972424 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:22.974715 INFO::Starting hierarchical adjustment
2026-04-30 21:36:22.975505 INFO::Found 3 batches.
2026-04-30 21:36:22.976078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:22.976773 INFO::Using default BPPARAM
2026-04-30 21:36:22.977341 INFO::Processing subtree level 1
2026-04-30 21:36:23.068802 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:36:23.071033 INFO::Done
2026-04-30 21:36:23.071874 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:23.074886 INFO::ASW Batch was -0.0145817144037846 prior to batch effect correction and is now -0.0145817144037846 .
2026-04-30 21:36:23.075972 INFO::Total function execution time is 0.112658262252808 s and adjustment time is 0.0956504344940186 s ( 84.9 )
2026-04-30 21:36:23.22714 INFO::Formatting Data.
2026-04-30 21:36:23.228238 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:23.229591 INFO::Removing potential empty rows and columns
2026-04-30 21:36:23.23262 INFO::Found 1000 missing values.
2026-04-30 21:36:23.253121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:23.254072 INFO::Done
2026-04-30 21:36:23.254771 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:23.260816 INFO::Starting hierarchical adjustment
2026-04-30 21:36:23.261707 INFO::Found 10 batches.
2026-04-30 21:36:23.262308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:23.263011 INFO::Using default BPPARAM
2026-04-30 21:36:23.263612 INFO::Processing subtree level 1
2026-04-30 21:36:23.398627 INFO::Processing subtree level 2
2026-04-30 21:36:23.544498 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:36:23.546633 INFO::Done
2026-04-30 21:36:23.547361 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:23.553012 INFO::ASW Batch was 0.484649815521363 prior to batch effect correction and is now 0.484649815521363 .
2026-04-30 21:36:23.553761 INFO::ASW Label was 0.332469193842824 prior to batch effect correction and is now 0.332469193842824 .
2026-04-30 21:36:23.554764 INFO::Total function execution time is 0.327791452407837 s and adjustment time is 0.285098552703857 s ( 86.98 )
2026-04-30 21:36:23.555696 INFO::Formatting Data.
2026-04-30 21:36:23.556416 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:23.557719 INFO::Removing potential empty rows and columns
2026-04-30 21:36:23.560655 INFO::Found 1000 missing values.
2026-04-30 21:36:23.58069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:23.58151 INFO::Done
2026-04-30 21:36:23.582128 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:23.587771 INFO::Starting hierarchical adjustment
2026-04-30 21:36:23.588601 INFO::Found 10 batches.
2026-04-30 21:36:24.700219 INFO::Set up parallel execution backend with 2 workers
2026-04-30 21:36:24.712315 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-30 21:36:25.980865 INFO::Adjusting the last 2 batches sequentially
2026-04-30 21:36:25.983787 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-30 21:36:25.999902 INFO::Done
2026-04-30 21:36:26.000603 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:26.005022 INFO::ASW Batch was 0.484649815521363 prior to batch effect correction and is now 0.484649815521363 .
2026-04-30 21:36:26.005622 INFO::ASW Label was 0.332469193842824 prior to batch effect correction and is now 0.332469193842824 .
2026-04-30 21:36:26.006343 INFO::Total function execution time is 2.4506950378418 s and adjustment time is 2.41146278381348 s ( 98.4 )
2026-04-30 21:36:26.150464 INFO::Formatting Data.
2026-04-30 21:36:26.151292 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.152224 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.15332 INFO::Found 0 missing values.
2026-04-30 21:36:26.156981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.157552 INFO::Done
2026-04-30 21:36:26.158088 INFO::Acquiring quality metrics before batch effect correction.
2026-04-30 21:36:26.160802 INFO::Starting hierarchical adjustment
2026-04-30 21:36:26.161527 INFO::Found 3 batches.
2026-04-30 21:36:26.162076 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-30 21:36:26.162719 INFO::Using default BPPARAM
2026-04-30 21:36:26.163255 INFO::Processing subtree level 1
2026-04-30 21:36:26.263027 INFO::Adjusting the last 1 batches sequentially
2026-04-30 21:36:26.264984 INFO::Done
2026-04-30 21:36:26.265722 INFO::Acquiring quality metrics after batch effect correction.
2026-04-30 21:36:26.268976 INFO::ASW Batch was 0.179128682157305 prior to batch effect correction and is now -0.128498024729234 .
2026-04-30 21:36:26.269659 INFO::ASW Label was -0.237190574171814 prior to batch effect correction and is now -0.158442452547067 .
2026-04-30 21:36:26.270576 INFO::Total function execution time is 0.120184659957886 s and adjustment time is 0.103577136993408 s ( 86.18 )
2026-04-30 21:36:26.392175 INFO::Formatting Data.
2026-04-30 21:36:26.393138 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.394067 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.395149 INFO::Found 2 missing values.
2026-04-30 21:36:26.397954 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.398528 INFO::Done
2026-04-30 21:36:26.425181 INFO::Found NA in Reference column
2026-04-30 21:36:26.434668 INFO::Require at least two references per batch.
2026-04-30 21:36:26.454741 INFO::Formatting Data.
2026-04-30 21:36:26.455567 INFO::Recognized SummarizedExperiment
2026-04-30 21:36:26.456145 INFO::Typecasting input to dataframe.
2026-04-30 21:36:26.466087 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.467327 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.470853 INFO::Found 0 missing values.
2026-04-30 21:36:26.477564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.478168 INFO::Done
2026-04-30 21:36:26.493428 INFO::Formatting Data.
2026-04-30 21:36:26.494228 INFO::Recognized SummarizedExperiment
2026-04-30 21:36:26.494811 INFO::Typecasting input to dataframe.
2026-04-30 21:36:26.51172 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.512899 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.516564 INFO::Found 0 missing values.
2026-04-30 21:36:26.527475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.528129 INFO::Done
2026-04-30 21:36:26.543784 INFO::Formatting Data.
2026-04-30 21:36:26.544563 INFO::Recognized SummarizedExperiment
2026-04-30 21:36:26.545126 INFO::Typecasting input to dataframe.
2026-04-30 21:36:26.56106 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.5622 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.563325 INFO::Found 0 missing values.
2026-04-30 21:36:26.564279 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.
2026-04-30 21:36:26.568815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.569417 INFO::Done
2026-04-30 21:36:26.579556 INFO::Formatting Data.
2026-04-30 21:36:26.580307 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.581206 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.582255 INFO::Found 0 missing values.
2026-04-30 21:36:26.585076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.585647 INFO::Done
2026-04-30 21:36:26.597008 INFO::Formatting Data.
2026-04-30 21:36:26.597881 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.598813 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.599847 INFO::Found 0 missing values.
2026-04-30 21:36:26.602815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.603404 INFO::Done
2026-04-30 21:36:26.633245 INFO::Formatting Data.
2026-04-30 21:36:26.634141 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.635329 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.636604 INFO::Found 1 missing values.
2026-04-30 21:36:26.639299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.639919 INFO::Done
2026-04-30 21:36:26.659211 INFO::Formatting Data.
2026-04-30 21:36:26.660176 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.66123 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.66232 INFO::Found 2 missing values.
2026-04-30 21:36:26.663314 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.
2026-04-30 21:36:26.666118 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.666732 INFO::Done
2026-04-30 21:36:26.677146 INFO::Formatting Data.
2026-04-30 21:36:26.67796 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.678931 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.679935 INFO::Found 2 missing values.
2026-04-30 21:36:26.681745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.682315 INFO::Done
2026-04-30 21:36:26.693843 INFO::Formatting Data.
2026-04-30 21:36:26.69469 INFO::Typecasting input to dataframe.
2026-04-30 21:36:26.695553 INFO::Replacing NaNs with NAs.
2026-04-30 21:36:26.696485 INFO::Removing potential empty rows and columns
2026-04-30 21:36:26.697557 INFO::Found 0 missing values.
2026-04-30 21:36:26.700668 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-30 21:36:26.701241 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.385 3.244 20.417
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.259 | 1.449 | 20.437 | |
| compute_asw | 0.023 | 0.003 | 0.025 | |
| count_existing | 0.015 | 0.000 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.000 | 0.012 | |