Yannis Schumann
| Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-03 12:03 -0400 (Wed, 03 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4826 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 163/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-09-02 21:16:11 -0400 (Tue, 02 Sep 2025) |
| EndedAt: 2025-09-02 21:18:21 -0400 (Tue, 02 Sep 2025) |
| EllapsedTime: 129.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 29.815 1.425 22.824
* 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-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-09-02 21:17:24.341171 INFO::Formatting Data.
2025-09-02 21:17:24.342773 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:24.356017 INFO::Removing potential empty rows and columns
2025-09-02 21:17:24.830144 INFO::Found 0 missing values.
2025-09-02 21:17:24.834243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:24.835058 INFO::Done
2025-09-02 21:17:24.835709 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:24.849238 INFO::Starting hierarchical adjustment
2025-09-02 21:17:24.850317 INFO::Found 3 batches.
2025-09-02 21:17:24.851018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:24.852374 INFO::Using default BPPARAM
2025-09-02 21:17:24.853085 INFO::Processing subtree level 1
2025-09-02 21:17:24.986387 INFO::Adjusting the last 1 batches sequentially
2025-09-02 21:17:24.988655 INFO::Done
2025-09-02 21:17:24.989474 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:24.992565 INFO::ASW Batch was 0.0429748261267926 prior to batch effect correction and is now 0.0429748261267926 .
2025-09-02 21:17:24.993897 INFO::Total function execution time is 0.653436899185181 s and adjustment time is 0.138548851013184 s ( 21.2 )
2025-09-02 21:17:25.012753 INFO::Formatting Data.
2025-09-02 21:17:25.01366 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:25.014708 INFO::Removing potential empty rows and columns
2025-09-02 21:17:25.016012 INFO::Found 0 missing values.
2025-09-02 21:17:25.017084 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.
2025-09-02 21:17:25.029607 INFO::Formatting Data.
2025-09-02 21:17:25.030446 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:25.031463 INFO::Removing potential empty rows and columns
2025-09-02 21:17:25.032706 INFO::Found 0 missing values.
2025-09-02 21:17:25.033816 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.
2025-09-02 21:17:25.052392 INFO::Formatting Data.
2025-09-02 21:17:25.053232 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:25.054227 INFO::Removing potential empty rows and columns
2025-09-02 21:17:25.055405 INFO::Found 0 missing values.
2025-09-02 21:17:25.056434 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.
2025-09-02 21:17:25.061399 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:25.062018 INFO::Done
2025-09-02 21:17:25.062594 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:25.064857 INFO::Starting hierarchical adjustment
2025-09-02 21:17:25.065636 INFO::Found 2 batches.
2025-09-02 21:17:25.066249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:25.066969 INFO::Using default BPPARAM
2025-09-02 21:17:25.06755 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:25.068602 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 21:17:25.098659 INFO::Done
2025-09-02 21:17:25.099487 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:25.101842 INFO::ASW Batch was -0.0448508063902842 prior to batch effect correction and is now -0.11101438687428 .
2025-09-02 21:17:25.102768 INFO::Total function execution time is 0.0504505634307861 s and adjustment time is 0.0331549644470215 s ( 65.72 )
2025-09-02 21:17:25.105948 INFO::Formatting Data.
2025-09-02 21:17:25.10668 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:25.11737 INFO::Formatting Data.
2025-09-02 21:17:25.118136 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:25.119155 INFO::Removing potential empty rows and columns
2025-09-02 21:17:25.120373 INFO::Found 0 missing values.
2025-09-02 21:17:25.123761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:25.124385 INFO::Done
2025-09-02 21:17:25.125003 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:25.127467 INFO::Starting hierarchical adjustment
2025-09-02 21:17:25.128293 INFO::Found 2 batches.
2025-09-02 21:17:25.128957 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:25.129685 INFO::Using default BPPARAM
2025-09-02 21:17:25.130328 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:25.135476 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 21:17:25.18386 INFO::Done
2025-09-02 21:17:25.184632 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:25.186987 INFO::ASW Batch was 0.0493902869346758 prior to batch effect correction and is now -0.115212980259946 .
2025-09-02 21:17:25.187893 INFO::Total function execution time is 0.0705399513244629 s and adjustment time is 0.0556991100311279 s ( 78.96 )
2025-09-02 21:17:25.189058 INFO::Formatting Data.
2025-09-02 21:17:25.189735 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:25.190673 INFO::Removing potential empty rows and columns
2025-09-02 21:17:25.195878 INFO::Found 0 missing values.
2025-09-02 21:17:25.198939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:25.19952 INFO::Done
2025-09-02 21:17:25.200092 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:25.202183 INFO::Starting hierarchical adjustment
2025-09-02 21:17:25.202945 INFO::Found 2 batches.
2025-09-02 21:17:25.203509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:25.204163 INFO::Using default BPPARAM
2025-09-02 21:17:25.204726 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:25.205678 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 21:17:25.222123 INFO::Done
2025-09-02 21:17:25.222833 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:25.22502 INFO::ASW Batch was 0.0493902869346758 prior to batch effect correction and is now -0.115212980259946 .
2025-09-02 21:17:25.225893 INFO::Total function execution time is 0.0368146896362305 s and adjustment time is 0.0193328857421875 s ( 52.51 )
2025-09-02 21:17:29.755083 INFO::Formatting Data.
2025-09-02 21:17:29.755931 INFO::Recognized SummarizedExperiment
2025-09-02 21:17:29.756513 INFO::Typecasting input to dataframe.
2025-09-02 21:17:29.792481 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:29.794024 INFO::Removing potential empty rows and columns
2025-09-02 21:17:29.799395 INFO::Found 0 missing values.
2025-09-02 21:17:29.809496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:29.810339 INFO::Done
2025-09-02 21:17:29.811008 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:29.815771 INFO::Starting hierarchical adjustment
2025-09-02 21:17:29.816692 INFO::Found 2 batches.
2025-09-02 21:17:29.817357 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:29.818678 INFO::Using default BPPARAM
2025-09-02 21:17:29.81936 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:29.820577 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 21:17:29.894628 INFO::Done
2025-09-02 21:17:29.895514 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:29.900301 INFO::ASW Batch was -0.00311079750397629 prior to batch effect correction and is now -0.0970556136163158 .
2025-09-02 21:17:29.901428 INFO::Total function execution time is 0.146666526794434 s and adjustment time is 0.0780978202819824 s ( 53.25 )
2025-09-02 21:17:29.924584 INFO::Formatting Data.
2025-09-02 21:17:29.925484 INFO::Recognized SummarizedExperiment
2025-09-02 21:17:29.926149 INFO::Typecasting input to dataframe.
2025-09-02 21:17:29.937946 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:29.939402 INFO::Removing potential empty rows and columns
2025-09-02 21:17:29.945298 INFO::Found 0 missing values.
2025-09-02 21:17:29.957123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:29.958159 INFO::Done
2025-09-02 21:17:29.958888 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:29.96371 INFO::Starting hierarchical adjustment
2025-09-02 21:17:29.964691 INFO::Found 2 batches.
2025-09-02 21:17:29.965364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:29.966122 INFO::Using default BPPARAM
2025-09-02 21:17:29.966784 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:29.968049 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 21:17:30.0083 INFO::Done
2025-09-02 21:17:30.009413 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:30.015712 INFO::ASW Batch was 0.0112741448808465 prior to batch effect correction and is now 0.0112741448808465 .
2025-09-02 21:17:30.017134 INFO::Total function execution time is 0.0924627780914307 s and adjustment time is 0.0437395572662354 s ( 47.31 )
2025-09-02 21:17:30.044157 INFO::Formatting Data.
2025-09-02 21:17:30.045177 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:30.046297 INFO::Removing potential empty rows and columns
2025-09-02 21:17:30.047598 INFO::Found 0 missing values.
2025-09-02 21:17:30.051412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:30.05209 INFO::Done
2025-09-02 21:17:30.052732 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:30.055247 INFO::Starting hierarchical adjustment
2025-09-02 21:17:30.056133 INFO::Found 3 batches.
2025-09-02 21:17:30.056773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:30.057379 INFO::Using default BPPARAM
2025-09-02 21:17:30.057915 INFO::Processing subtree level 1
2025-09-02 21:17:30.268456 INFO::Adjusting the last 1 batches sequentially
2025-09-02 21:17:30.274286 INFO::Done
2025-09-02 21:17:30.275015 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:30.277646 INFO::ASW Batch was -0.132433363271843 prior to batch effect correction and is now -0.168931112388645 .
2025-09-02 21:17:30.278731 INFO::Total function execution time is 0.234641313552856 s and adjustment time is 0.218337774276733 s ( 93.05 )
2025-09-02 21:17:30.294743 INFO::Skipping initial DF formatting
2025-09-02 21:17:30.295588 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:30.300164 INFO::Starting hierarchical adjustment
2025-09-02 21:17:30.30112 INFO::Found 5 batches.
2025-09-02 21:17:30.301785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:30.302518 INFO::Using default BPPARAM
2025-09-02 21:17:30.303191 INFO::Processing subtree level 1
2025-09-02 21:17:30.61911 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:30.621588 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 21:17:30.661165 INFO::Done
2025-09-02 21:17:30.662073 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:30.724407 INFO::ASW Batch was 0.478255334279447 prior to batch effect correction and is now 0.478255334279447 .
2025-09-02 21:17:30.726523 INFO::ASW Label was 0.398187520303198 prior to batch effect correction and is now 0.398187520303198 .
2025-09-02 21:17:30.727738 INFO::Total function execution time is 0.433065891265869 s and adjustment time is 0.360167980194092 s ( 83.17 )
2025-09-02 21:17:30.748206 INFO::Formatting Data.
2025-09-02 21:17:30.749294 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:30.750444 INFO::Removing potential empty rows and columns
2025-09-02 21:17:30.751658 INFO::Found 0 missing values.
2025-09-02 21:17:30.756961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:30.75768 INFO::Done
2025-09-02 21:17:30.758337 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:30.762408 INFO::Starting hierarchical adjustment
2025-09-02 21:17:30.76339 INFO::Found 5 batches.
2025-09-02 21:17:30.764046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:30.76488 INFO::Using default BPPARAM
2025-09-02 21:17:30.765574 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.
2025-09-02 21:17:31.080752 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:31.089536 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 21:17:31.125509 INFO::Done
2025-09-02 21:17:31.126455 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:31.130549 INFO::ASW Batch was 0.542594805833754 prior to batch effect correction and is now -0.0368823904943899 .
2025-09-02 21:17:31.131357 INFO::ASW Label was 0.231290028138245 prior to batch effect correction and is now 0.731658707486488 .
2025-09-02 21:17:31.132375 INFO::Total function execution time is 0.384278059005737 s and adjustment time is 0.362305164337158 s ( 94.28 )
2025-09-02 21:17:31.133522 INFO::Formatting Data.
2025-09-02 21:17:31.134335 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:31.135482 INFO::Removing potential empty rows and columns
2025-09-02 21:17:31.136796 INFO::Found 0 missing values.
2025-09-02 21:17:31.142128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:31.142894 INFO::Done
2025-09-02 21:17:31.14352 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:31.147413 INFO::Starting hierarchical adjustment
2025-09-02 21:17:31.148416 INFO::Found 5 batches.
2025-09-02 21:17:31.149095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:31.14985 INFO::Using default BPPARAM
2025-09-02 21:17:31.150506 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.
2025-09-02 21:17:31.396147 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:31.398518 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 21:17:31.424358 INFO::Done
2025-09-02 21:17:31.425528 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:31.430928 INFO::ASW Batch was 0.542594805833754 prior to batch effect correction and is now -0.0368823904943899 .
2025-09-02 21:17:31.432008 INFO::ASW Label was 0.231290028138245 prior to batch effect correction and is now 0.731658707486488 .
2025-09-02 21:17:31.433297 INFO::Total function execution time is 0.299720287322998 s and adjustment time is 0.276095390319824 s ( 92.12 )
2025-09-02 21:17:31.454439 INFO::Formatting Data.
2025-09-02 21:17:31.455755 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:31.4573 INFO::Removing potential empty rows and columns
2025-09-02 21:17:31.458941 INFO::Found 0 missing values.
2025-09-02 21:17:31.465864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:31.466812 INFO::Done
2025-09-02 21:17:31.467649 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:31.472317 INFO::Starting hierarchical adjustment
2025-09-02 21:17:31.473434 INFO::Found 5 batches.
2025-09-02 21:17:31.47425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:31.475164 INFO::Using default BPPARAM
2025-09-02 21:17:31.475965 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.
2025-09-02 21:17:31.697825 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:31.700662 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 21:17:31.738949 INFO::Done
2025-09-02 21:17:31.739942 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:31.744522 INFO::ASW Batch was 0.467846977432228 prior to batch effect correction and is now -0.0685751583871662 .
2025-09-02 21:17:31.745417 INFO::ASW Label was 0.313090025888294 prior to batch effect correction and is now 0.851247908195971 .
2025-09-02 21:17:31.746533 INFO::Total function execution time is 0.29224967956543 s and adjustment time is 0.265702247619629 s ( 90.92 )
2025-09-02 21:17:31.747685 INFO::Formatting Data.
2025-09-02 21:17:31.74851 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:31.749688 INFO::Removing potential empty rows and columns
2025-09-02 21:17:31.751048 INFO::Found 0 missing values.
2025-09-02 21:17:31.756056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:31.756627 INFO::Done
2025-09-02 21:17:31.757165 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:31.761036 INFO::Starting hierarchical adjustment
2025-09-02 21:17:31.761956 INFO::Found 5 batches.
2025-09-02 21:17:31.762621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:31.763446 INFO::Using default BPPARAM
2025-09-02 21:17:31.764122 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.
2025-09-02 21:17:32.049543 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:32.051997 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 21:17:32.07779 INFO::Done
2025-09-02 21:17:32.079217 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:32.084435 INFO::ASW Batch was 0.467846977432228 prior to batch effect correction and is now -0.0685751583871662 .
2025-09-02 21:17:32.085404 INFO::ASW Label was 0.313090025888294 prior to batch effect correction and is now 0.851247908195971 .
2025-09-02 21:17:32.086781 INFO::Total function execution time is 0.339020967483521 s and adjustment time is 0.315930366516113 s ( 93.19 )
2025-09-02 21:17:32.107169 INFO::Formatting Data.
2025-09-02 21:17:32.108343 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:32.109816 INFO::Removing potential empty rows and columns
2025-09-02 21:17:32.111414 INFO::Found 0 missing values.
2025-09-02 21:17:32.115877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:32.116693 INFO::Done
2025-09-02 21:17:32.117512 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:32.122065 INFO::Starting hierarchical adjustment
2025-09-02 21:17:32.123138 INFO::Found 2 batches.
2025-09-02 21:17:32.123946 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:32.124912 INFO::Using default BPPARAM
2025-09-02 21:17:32.125732 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:32.127158 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 21:17:32.150875 INFO::Done
2025-09-02 21:17:32.151993 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:32.156552 INFO::ASW Batch was 0.620742839746317 prior to batch effect correction and is now -0.0138805957121553 .
2025-09-02 21:17:32.15745 INFO::ASW Label was 0.398606246043138 prior to batch effect correction and is now 0.846258287516144 .
2025-09-02 21:17:32.158657 INFO::Total function execution time is 0.0515913963317871 s and adjustment time is 0.0278782844543457 s ( 54.04 )
2025-09-02 21:17:32.159883 INFO::Formatting Data.
2025-09-02 21:17:32.160846 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:32.16216 INFO::Removing potential empty rows and columns
2025-09-02 21:17:32.16365 INFO::Found 0 missing values.
2025-09-02 21:17:32.167895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:32.168686 INFO::Done
2025-09-02 21:17:32.169521 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:32.173911 INFO::Starting hierarchical adjustment
2025-09-02 21:17:32.174964 INFO::Found 2 batches.
2025-09-02 21:17:32.17577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:32.17669 INFO::Using default BPPARAM
2025-09-02 21:17:32.177515 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:32.178934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 21:17:32.202201 INFO::Done
2025-09-02 21:17:32.203261 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:32.207706 INFO::ASW Batch was 0.620742839746317 prior to batch effect correction and is now -0.0138805957121553 .
2025-09-02 21:17:32.20861 INFO::ASW Label was 0.398606246043138 prior to batch effect correction and is now 0.846258287516144 .
2025-09-02 21:17:32.209821 INFO::Total function execution time is 0.0499629974365234 s and adjustment time is 0.0274171829223633 s ( 54.87 )
2025-09-02 21:17:32.22564 INFO::Formatting Data.
2025-09-02 21:17:32.226608 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:32.227724 INFO::Removing potential empty rows and columns
2025-09-02 21:17:32.228925 INFO::Found 0 missing values.
2025-09-02 21:17:32.231568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:32.232243 INFO::Done
2025-09-02 21:17:32.232891 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:32.235235 INFO::Starting hierarchical adjustment
2025-09-02 21:17:32.236099 INFO::Found 2 batches.
2025-09-02 21:17:32.236757 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:32.237491 INFO::Using default BPPARAM
2025-09-02 21:17:32.238136 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:32.239223 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 21:17:32.278147 INFO::Done
2025-09-02 21:17:32.279027 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:32.281419 INFO::ASW Batch was 0.113842934667497 prior to batch effect correction and is now -0.0830417756652187 .
2025-09-02 21:17:32.282417 INFO::Total function execution time is 0.0568771362304688 s and adjustment time is 0.0421886444091797 s ( 74.18 )
2025-09-02 21:17:32.296506 INFO::Formatting Data.
2025-09-02 21:17:32.297425 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:32.2985 INFO::Removing potential empty rows and columns
2025-09-02 21:17:32.299755 INFO::Found 0 missing values.
2025-09-02 21:17:32.301108 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.
2025-09-02 21:17:32.306828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:32.307488 INFO::Done
2025-09-02 21:17:32.308132 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:32.311661 INFO::Starting hierarchical adjustment
2025-09-02 21:17:32.312522 INFO::Found 2 batches.
2025-09-02 21:17:32.313175 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:32.3139 INFO::Using default BPPARAM
2025-09-02 21:17:32.314521 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:32.315643 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 21:17:32.336583 INFO::Done
2025-09-02 21:17:32.337556 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:32.342007 INFO::ASW Batch was 0.506299931903669 prior to batch effect correction and is now 0.099648184687579 .
2025-09-02 21:17:32.342934 INFO::ASW Label was 0.580853248595402 prior to batch effect correction and is now 0.855806199411689 .
2025-09-02 21:17:32.344145 INFO::Total function execution time is 0.0476725101470947 s and adjustment time is 0.0242035388946533 s ( 50.77 )
2025-09-02 21:17:32.345411 INFO::Formatting Data.
2025-09-02 21:17:32.346395 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:32.347834 INFO::Removing potential empty rows and columns
2025-09-02 21:17:32.349426 INFO::Found 0 missing values.
2025-09-02 21:17:32.35085 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.
2025-09-02 21:17:32.358184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:32.359061 INFO::Done
2025-09-02 21:17:32.359912 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:32.364482 INFO::Starting hierarchical adjustment
2025-09-02 21:17:32.365585 INFO::Found 2 batches.
2025-09-02 21:17:32.36645 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:32.367433 INFO::Using default BPPARAM
2025-09-02 21:17:32.368282 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:32.369845 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 21:17:32.391035 INFO::Done
2025-09-02 21:17:32.391901 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:32.395492 INFO::ASW Batch was 0.506299931903669 prior to batch effect correction and is now 0.099648184687579 .
2025-09-02 21:17:32.396245 INFO::ASW Label was 0.580853248595402 prior to batch effect correction and is now 0.855806199411689 .
2025-09-02 21:17:32.397206 INFO::Total function execution time is 0.0518703460693359 s and adjustment time is 0.0256946086883545 s ( 49.54 )
2025-09-02 21:17:32.740155 INFO::Formatting Data.
2025-09-02 21:17:32.741302 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:32.742622 INFO::Removing potential empty rows and columns
2025-09-02 21:17:32.74413 INFO::Found 0 missing values.
2025-09-02 21:17:32.74868 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:32.74949 INFO::Done
2025-09-02 21:17:32.750278 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:32.753163 INFO::Starting hierarchical adjustment
2025-09-02 21:17:32.754169 INFO::Found 3 batches.
2025-09-02 21:17:32.754951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:32.755858 INFO::Using default BPPARAM
2025-09-02 21:17:32.756629 INFO::Processing subtree level 1
2025-09-02 21:17:32.896871 INFO::Adjusting the last 1 batches sequentially
2025-09-02 21:17:32.902725 INFO::Done
2025-09-02 21:17:32.903781 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:32.907181 INFO::ASW Batch was -0.082384906457282 prior to batch effect correction and is now -0.082384906457282 .
2025-09-02 21:17:32.908505 INFO::Total function execution time is 0.168385028839111 s and adjustment time is 0.148714780807495 s ( 88.32 )
2025-09-02 21:17:32.910022 INFO::Formatting Data.
2025-09-02 21:17:32.910961 INFO::Typecasting input to dataframe.
2025-09-02 21:17:32.912067 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:32.913416 INFO::Removing potential empty rows and columns
2025-09-02 21:17:32.91503 INFO::Found 0 missing values.
2025-09-02 21:17:32.919538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:32.920339 INFO::Done
2025-09-02 21:17:32.921094 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:32.923875 INFO::Starting hierarchical adjustment
2025-09-02 21:17:32.92486 INFO::Found 3 batches.
2025-09-02 21:17:32.925609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:32.92655 INFO::Using default BPPARAM
2025-09-02 21:17:32.927324 INFO::Processing subtree level 1
2025-09-02 21:17:33.064681 INFO::Adjusting the last 1 batches sequentially
2025-09-02 21:17:33.067216 INFO::Done
2025-09-02 21:17:33.071257 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:33.081985 INFO::ASW Batch was -0.082384906457282 prior to batch effect correction and is now -0.082384906457282 .
2025-09-02 21:17:33.083518 INFO::Total function execution time is 0.173445701599121 s and adjustment time is 0.142528772354126 s ( 82.17 )
2025-09-02 21:17:33.114096 INFO::Formatting Data.
2025-09-02 21:17:33.115276 INFO::Typecasting input to dataframe.
2025-09-02 21:17:33.116555 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:33.117908 INFO::Removing potential empty rows and columns
2025-09-02 21:17:33.119526 INFO::Found 0 missing values.
2025-09-02 21:17:33.124202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:33.125015 INFO::Done
2025-09-02 21:17:33.125809 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:33.128789 INFO::Starting hierarchical adjustment
2025-09-02 21:17:33.129839 INFO::Found 3 batches.
2025-09-02 21:17:33.130627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:33.131567 INFO::Using default BPPARAM
2025-09-02 21:17:33.132386 INFO::Processing subtree level 1
2025-09-02 21:17:33.376129 INFO::Adjusting the last 1 batches sequentially
2025-09-02 21:17:33.382484 INFO::Done
2025-09-02 21:17:33.383344 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:33.386388 INFO::ASW Batch was -0.122020598340697 prior to batch effect correction and is now -0.122020598340697 .
2025-09-02 21:17:33.38755 INFO::Total function execution time is 0.273546934127808 s and adjustment time is 0.252848386764526 s ( 92.43 )
2025-09-02 21:17:33.684014 INFO::Formatting Data.
2025-09-02 21:17:33.685453 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:33.691495 INFO::Removing potential empty rows and columns
2025-09-02 21:17:33.703326 INFO::Found 1000 missing values.
2025-09-02 21:17:33.765091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:33.770387 INFO::Done
2025-09-02 21:17:33.771474 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:33.791744 INFO::Starting hierarchical adjustment
2025-09-02 21:17:33.793195 INFO::Found 10 batches.
2025-09-02 21:17:33.794147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:33.799186 INFO::Using default BPPARAM
2025-09-02 21:17:33.800054 INFO::Processing subtree level 1
2025-09-02 21:17:34.235554 INFO::Processing subtree level 2
2025-09-02 21:17:34.474185 INFO::Adjusting the last 1 batches sequentially
2025-09-02 21:17:34.483997 INFO::Done
2025-09-02 21:17:34.485036 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:34.514387 INFO::ASW Batch was 0.517708183081977 prior to batch effect correction and is now 0.517708183081977 .
2025-09-02 21:17:34.515813 INFO::ASW Label was 0.316092801759024 prior to batch effect correction and is now 0.316092801759024 .
2025-09-02 21:17:34.517421 INFO::Total function execution time is 0.833503246307373 s and adjustment time is 0.691106796264648 s ( 82.92 )
2025-09-02 21:17:34.518955 INFO::Formatting Data.
2025-09-02 21:17:34.52003 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:34.522012 INFO::Removing potential empty rows and columns
2025-09-02 21:17:34.526711 INFO::Found 1000 missing values.
2025-09-02 21:17:34.558329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:34.559415 INFO::Done
2025-09-02 21:17:34.560283 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:34.568691 INFO::Starting hierarchical adjustment
2025-09-02 21:17:34.570003 INFO::Found 10 batches.
2025-09-02 21:17:35.914539 INFO::Set up parallel execution backend with 2 workers
2025-09-02 21:17:35.916867 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-02 21:17:37.740558 INFO::Adjusting the last 2 batches sequentially
2025-09-02 21:17:37.743435 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 21:17:37.770122 INFO::Done
2025-09-02 21:17:37.771116 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:37.785885 INFO::ASW Batch was 0.517708183081977 prior to batch effect correction and is now 0.517708183081977 .
2025-09-02 21:17:37.786943 INFO::ASW Label was 0.316092801759024 prior to batch effect correction and is now 0.316092801759024 .
2025-09-02 21:17:37.788051 INFO::Total function execution time is 3.26921010017395 s and adjustment time is 3.2003972530365 s ( 97.9 )
2025-09-02 21:17:38.095261 INFO::Formatting Data.
2025-09-02 21:17:38.096611 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.098206 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.100067 INFO::Found 0 missing values.
2025-09-02 21:17:38.106508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.107484 INFO::Done
2025-09-02 21:17:38.108384 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 21:17:38.112893 INFO::Starting hierarchical adjustment
2025-09-02 21:17:38.114028 INFO::Found 3 batches.
2025-09-02 21:17:38.114896 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 21:17:38.115917 INFO::Using default BPPARAM
2025-09-02 21:17:38.116794 INFO::Processing subtree level 1
2025-09-02 21:17:38.290448 INFO::Adjusting the last 1 batches sequentially
2025-09-02 21:17:38.293232 INFO::Done
2025-09-02 21:17:38.294337 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 21:17:38.307792 INFO::ASW Batch was 0.213492602841209 prior to batch effect correction and is now -0.136892264277513 .
2025-09-02 21:17:38.309013 INFO::ASW Label was -0.194795973604951 prior to batch effect correction and is now 0.125160087229418 .
2025-09-02 21:17:38.314631 INFO::Total function execution time is 0.219372510910034 s and adjustment time is 0.179423093795776 s ( 81.79 )
2025-09-02 21:17:38.514251 INFO::Formatting Data.
2025-09-02 21:17:38.515464 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.516865 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.51846 INFO::Found 2 missing values.
2025-09-02 21:17:38.52302 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.523846 INFO::Done
2025-09-02 21:17:38.56542 INFO::Found NA in Reference column
2025-09-02 21:17:38.579803 INFO::Require at least two references per batch.
2025-09-02 21:17:38.611087 INFO::Formatting Data.
2025-09-02 21:17:38.612252 INFO::Recognized SummarizedExperiment
2025-09-02 21:17:38.613092 INFO::Typecasting input to dataframe.
2025-09-02 21:17:38.629808 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.631763 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.63745 INFO::Found 0 missing values.
2025-09-02 21:17:38.649234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.650441 INFO::Done
2025-09-02 21:17:38.679192 INFO::Formatting Data.
2025-09-02 21:17:38.680187 INFO::Recognized SummarizedExperiment
2025-09-02 21:17:38.68084 INFO::Typecasting input to dataframe.
2025-09-02 21:17:38.703176 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.704696 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.70904 INFO::Found 0 missing values.
2025-09-02 21:17:38.722621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.723558 INFO::Done
2025-09-02 21:17:38.743664 INFO::Formatting Data.
2025-09-02 21:17:38.744639 INFO::Recognized SummarizedExperiment
2025-09-02 21:17:38.745294 INFO::Typecasting input to dataframe.
2025-09-02 21:17:38.767294 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.768666 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.770293 INFO::Found 0 missing values.
2025-09-02 21:17:38.77159 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.
2025-09-02 21:17:38.777423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.778254 INFO::Done
2025-09-02 21:17:38.791024 INFO::Formatting Data.
2025-09-02 21:17:38.79199 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.793113 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.794481 INFO::Found 0 missing values.
2025-09-02 21:17:38.798554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.799206 INFO::Done
2025-09-02 21:17:38.813921 INFO::Formatting Data.
2025-09-02 21:17:38.814956 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.816232 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.817708 INFO::Found 0 missing values.
2025-09-02 21:17:38.82145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.822079 INFO::Done
2025-09-02 21:17:38.859942 INFO::Formatting Data.
2025-09-02 21:17:38.860974 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.862271 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.863739 INFO::Found 1 missing values.
2025-09-02 21:17:38.866817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.867439 INFO::Done
2025-09-02 21:17:38.903253 INFO::Formatting Data.
2025-09-02 21:17:38.90455 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.905703 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.906994 INFO::Found 2 missing values.
2025-09-02 21:17:38.908121 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.
2025-09-02 21:17:38.9109 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.911557 INFO::Done
2025-09-02 21:17:38.924638 INFO::Formatting Data.
2025-09-02 21:17:38.925865 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.927097 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.928417 INFO::Found 2 missing values.
2025-09-02 21:17:38.930543 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.931182 INFO::Done
2025-09-02 21:17:38.945337 INFO::Formatting Data.
2025-09-02 21:17:38.946492 INFO::Typecasting input to dataframe.
2025-09-02 21:17:38.947604 INFO::Replacing NaNs with NAs.
2025-09-02 21:17:38.948814 INFO::Removing potential empty rows and columns
2025-09-02 21:17:38.95014 INFO::Found 0 missing values.
2025-09-02 21:17:38.95374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 21:17:38.954374 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.776 5.260 30.672
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.815 | 1.425 | 22.824 | |
| compute_asw | 0.038 | 0.001 | 0.038 | |
| count_existing | 0.020 | 0.001 | 0.021 | |
| generate_data_covariables | 0.018 | 0.000 | 0.019 | |
| generate_dataset | 0.018 | 0.000 | 0.018 | |