Yannis Schumann
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:02 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-12-02 06:56:17 -0000 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 06:58:38 -0000 (Tue, 02 Dec 2025) |
| EllapsedTime: 140.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 27.531 1.248 21.333
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-12-02 06:58:17.632118 INFO::Formatting Data.
2025-12-02 06:58:17.634025 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:17.651391 INFO::Removing potential empty rows and columns
2025-12-02 06:58:18.656718 INFO::Found 0 missing values.
2025-12-02 06:58:18.662238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:18.66331 INFO::Done
2025-12-02 06:58:18.664281 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:18.681011 INFO::Starting hierarchical adjustment
2025-12-02 06:58:18.68233 INFO::Found 3 batches.
2025-12-02 06:58:18.683356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:18.68516 INFO::Using default BPPARAM
2025-12-02 06:58:18.686172 INFO::Processing subtree level 1
2025-12-02 06:58:18.824474 INFO::Adjusting the last 1 batches sequentially
2025-12-02 06:58:18.831053 INFO::Done
2025-12-02 06:58:18.831961 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:18.839794 INFO::ASW Batch was -0.0824359544380119 prior to batch effect correction and is now -0.0824359544380119 .
2025-12-02 06:58:18.84558 INFO::Total function execution time is 1.21422648429871 s and adjustment time is 0.149023771286011 s ( 12.27 )
2025-12-02 06:58:18.866599 INFO::Formatting Data.
2025-12-02 06:58:18.86761 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:18.868902 INFO::Removing potential empty rows and columns
2025-12-02 06:58:18.87048 INFO::Found 0 missing values.
2025-12-02 06:58:18.87183 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-02 06:58:18.887115 INFO::Formatting Data.
2025-12-02 06:58:18.888094 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:18.889359 INFO::Removing potential empty rows and columns
2025-12-02 06:58:18.890901 INFO::Found 0 missing values.
2025-12-02 06:58:18.892198 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-02 06:58:18.914293 INFO::Formatting Data.
2025-12-02 06:58:18.915294 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:18.916482 INFO::Removing potential empty rows and columns
2025-12-02 06:58:18.917993 INFO::Found 0 missing values.
2025-12-02 06:58:18.919338 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-02 06:58:18.925898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:18.926875 INFO::Done
2025-12-02 06:58:18.92768 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:18.930596 INFO::Starting hierarchical adjustment
2025-12-02 06:58:18.931738 INFO::Found 2 batches.
2025-12-02 06:58:18.932523 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:18.933477 INFO::Using default BPPARAM
2025-12-02 06:58:18.934273 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:18.935765 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-02 06:58:18.967293 INFO::Done
2025-12-02 06:58:18.968254 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:18.971341 INFO::ASW Batch was 0.0744677223084184 prior to batch effect correction and is now -0.0894723739835669 .
2025-12-02 06:58:18.972549 INFO::Total function execution time is 0.058286190032959 s and adjustment time is 0.0357623100280762 s ( 61.36 )
2025-12-02 06:58:18.976331 INFO::Formatting Data.
2025-12-02 06:58:18.97733 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:18.989895 INFO::Formatting Data.
2025-12-02 06:58:18.99097 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:18.992233 INFO::Removing potential empty rows and columns
2025-12-02 06:58:18.993791 INFO::Found 0 missing values.
2025-12-02 06:58:18.998258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:18.999239 INFO::Done
2025-12-02 06:58:19.000046 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:19.002991 INFO::Starting hierarchical adjustment
2025-12-02 06:58:19.004158 INFO::Found 2 batches.
2025-12-02 06:58:19.005006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:19.005969 INFO::Using default BPPARAM
2025-12-02 06:58:19.006899 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:19.008417 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:19.067947 INFO::Done
2025-12-02 06:58:19.06884 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:19.071597 INFO::ASW Batch was -0.00957328129478926 prior to batch effect correction and is now -0.11571271279897 .
2025-12-02 06:58:19.072684 INFO::Total function execution time is 0.0828678607940674 s and adjustment time is 0.0640127658843994 s ( 77.25 )
2025-12-02 06:58:19.074208 INFO::Formatting Data.
2025-12-02 06:58:19.075103 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:19.076334 INFO::Removing potential empty rows and columns
2025-12-02 06:58:19.077804 INFO::Found 0 missing values.
2025-12-02 06:58:19.084071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:19.084975 INFO::Done
2025-12-02 06:58:19.085758 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:19.088623 INFO::Starting hierarchical adjustment
2025-12-02 06:58:19.090063 INFO::Found 2 batches.
2025-12-02 06:58:19.090895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:19.091753 INFO::Using default BPPARAM
2025-12-02 06:58:19.092514 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:19.093878 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:19.115596 INFO::Done
2025-12-02 06:58:19.1165 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:19.119354 INFO::ASW Batch was -0.00957328129478926 prior to batch effect correction and is now -0.11571271279897 .
2025-12-02 06:58:19.12045 INFO::Total function execution time is 0.0462276935577393 s and adjustment time is 0.0257198810577393 s ( 55.64 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-02 06:58:23.082592 INFO::Formatting Data.
2025-12-02 06:58:23.083463 INFO::Recognized SummarizedExperiment
2025-12-02 06:58:23.084152 INFO::Typecasting input to dataframe.
2025-12-02 06:58:23.124331 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:23.125875 INFO::Removing potential empty rows and columns
2025-12-02 06:58:23.131015 INFO::Found 0 missing values.
2025-12-02 06:58:23.141046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:23.141954 INFO::Done
2025-12-02 06:58:23.142792 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:23.147732 INFO::Starting hierarchical adjustment
2025-12-02 06:58:23.148883 INFO::Found 2 batches.
2025-12-02 06:58:23.149692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:23.151157 INFO::Using default BPPARAM
2025-12-02 06:58:23.151951 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:23.153364 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-02 06:58:23.231609 INFO::Done
2025-12-02 06:58:23.232494 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:23.237352 INFO::ASW Batch was -0.00266148113345453 prior to batch effect correction and is now -0.0910198947737411 .
2025-12-02 06:58:23.238603 INFO::Total function execution time is 0.156392097473145 s and adjustment time is 0.0829606056213379 s ( 53.05 )
Warning: stack imbalance in '{', 73 then 75
2025-12-02 06:58:23.264328 INFO::Formatting Data.
2025-12-02 06:58:23.265307 INFO::Recognized SummarizedExperiment
2025-12-02 06:58:23.266084 INFO::Typecasting input to dataframe.
2025-12-02 06:58:23.279259 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:23.2809 INFO::Removing potential empty rows and columns
2025-12-02 06:58:23.286208 INFO::Found 0 missing values.
2025-12-02 06:58:23.296661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:23.297627 INFO::Done
2025-12-02 06:58:23.298415 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:23.303358 INFO::Starting hierarchical adjustment
2025-12-02 06:58:23.304458 INFO::Found 2 batches.
2025-12-02 06:58:23.305279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:23.306165 INFO::Using default BPPARAM
2025-12-02 06:58:23.30699 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:23.308412 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-02 06:58:23.343138 INFO::Done
2025-12-02 06:58:23.344028 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:23.348921 INFO::ASW Batch was 0.0150292556248822 prior to batch effect correction and is now 0.0150292556248822 .
2025-12-02 06:58:23.350111 INFO::Total function execution time is 0.0857467651367188 s and adjustment time is 0.0388550758361816 s ( 45.31 )
2025-12-02 06:58:23.374707 INFO::Formatting Data.
2025-12-02 06:58:23.375685 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:23.376883 INFO::Removing potential empty rows and columns
2025-12-02 06:58:23.378315 INFO::Found 0 missing values.
2025-12-02 06:58:23.382653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:23.383513 INFO::Done
2025-12-02 06:58:23.384276 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:23.387024 INFO::Starting hierarchical adjustment
2025-12-02 06:58:23.388016 INFO::Found 3 batches.
2025-12-02 06:58:23.388799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:23.389671 INFO::Using default BPPARAM
2025-12-02 06:58:23.390435 INFO::Processing subtree level 1
2025-12-02 06:58:23.667257 INFO::Adjusting the last 1 batches sequentially
2025-12-02 06:58:23.689941 INFO::Done
2025-12-02 06:58:23.690952 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:23.701888 INFO::ASW Batch was -0.0693685448115647 prior to batch effect correction and is now -0.173143948264369 .
2025-12-02 06:58:23.703316 INFO::Total function execution time is 0.328673362731934 s and adjustment time is 0.302090406417847 s ( 91.91 )
2025-12-02 06:58:23.758945 INFO::Skipping initial DF formatting
2025-12-02 06:58:23.75991 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:23.77399 INFO::Starting hierarchical adjustment
2025-12-02 06:58:23.775252 INFO::Found 5 batches.
2025-12-02 06:58:23.776034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:23.781042 INFO::Using default BPPARAM
2025-12-02 06:58:23.781936 INFO::Processing subtree level 1
2025-12-02 06:58:24.114903 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:24.121161 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-02 06:58:24.171416 INFO::Done
2025-12-02 06:58:24.172308 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:24.181124 INFO::ASW Batch was 0.488707295525226 prior to batch effect correction and is now 0.488707295525226 .
2025-12-02 06:58:24.182069 INFO::ASW Label was 0.359360249975763 prior to batch effect correction and is now 0.359360249975763 .
2025-12-02 06:58:24.183374 INFO::Total function execution time is 0.424452781677246 s and adjustment time is 0.396404027938843 s ( 93.39 )
2025-12-02 06:58:24.277948 INFO::Formatting Data.
2025-12-02 06:58:24.279006 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:24.280334 INFO::Removing potential empty rows and columns
2025-12-02 06:58:24.281827 INFO::Found 0 missing values.
2025-12-02 06:58:24.288039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:24.288905 INFO::Done
2025-12-02 06:58:24.28965 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:24.293772 INFO::Starting hierarchical adjustment
2025-12-02 06:58:24.294995 INFO::Found 5 batches.
2025-12-02 06:58:24.295785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:24.296695 INFO::Using default BPPARAM
2025-12-02 06:58:24.297522 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:24.577213 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:24.579613 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:24.633569 INFO::Done
2025-12-02 06:58:24.634593 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:24.64382 INFO::ASW Batch was 0.498227575179091 prior to batch effect correction and is now -0.0969768105784661 .
2025-12-02 06:58:24.648878 INFO::ASW Label was 0.282542303847637 prior to batch effect correction and is now 0.827181847884708 .
2025-12-02 06:58:24.650208 INFO::Total function execution time is 0.372270584106445 s and adjustment time is 0.338765144348145 s ( 91 )
2025-12-02 06:58:24.651539 INFO::Formatting Data.
2025-12-02 06:58:24.652454 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:24.658133 INFO::Removing potential empty rows and columns
2025-12-02 06:58:24.660104 INFO::Found 0 missing values.
2025-12-02 06:58:24.675616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:24.676565 INFO::Done
2025-12-02 06:58:24.681572 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:24.690421 INFO::Starting hierarchical adjustment
2025-12-02 06:58:24.691632 INFO::Found 5 batches.
2025-12-02 06:58:24.692431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:24.697516 INFO::Using default BPPARAM
2025-12-02 06:58:24.698393 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:24.979266 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:24.989777 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:25.035115 INFO::Done
2025-12-02 06:58:25.036047 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:25.041587 INFO::ASW Batch was 0.498227575179091 prior to batch effect correction and is now -0.0969768105784661 .
2025-12-02 06:58:25.042581 INFO::ASW Label was 0.282542303847637 prior to batch effect correction and is now 0.827181847884708 .
2025-12-02 06:58:25.043787 INFO::Total function execution time is 0.392198801040649 s and adjustment time is 0.343708992004395 s ( 87.64 )
2025-12-02 06:58:25.077773 INFO::Formatting Data.
2025-12-02 06:58:25.078901 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:25.0802 INFO::Removing potential empty rows and columns
2025-12-02 06:58:25.082482 INFO::Found 0 missing values.
2025-12-02 06:58:25.089962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:25.090932 INFO::Done
2025-12-02 06:58:25.09177 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:25.096358 INFO::Starting hierarchical adjustment
2025-12-02 06:58:25.097574 INFO::Found 5 batches.
2025-12-02 06:58:25.098395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:25.099344 INFO::Using default BPPARAM
2025-12-02 06:58:25.100128 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:25.401225 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:25.40349 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:25.451237 INFO::Done
2025-12-02 06:58:25.452178 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:25.464947 INFO::ASW Batch was 0.574675267555699 prior to batch effect correction and is now -0.0517361768660013 .
2025-12-02 06:58:25.465928 INFO::ASW Label was 0.130891240698585 prior to batch effect correction and is now 0.815538334028697 .
2025-12-02 06:58:25.467122 INFO::Total function execution time is 0.389425039291382 s and adjustment time is 0.353884220123291 s ( 90.87 )
2025-12-02 06:58:25.468277 INFO::Formatting Data.
2025-12-02 06:58:25.473276 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:25.474677 INFO::Removing potential empty rows and columns
2025-12-02 06:58:25.476134 INFO::Found 0 missing values.
2025-12-02 06:58:25.490674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:25.491576 INFO::Done
2025-12-02 06:58:25.492342 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:25.500597 INFO::Starting hierarchical adjustment
2025-12-02 06:58:25.505829 INFO::Found 5 batches.
2025-12-02 06:58:25.506675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:25.507586 INFO::Using default BPPARAM
2025-12-02 06:58:25.508351 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:25.747708 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:25.758258 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:25.782147 INFO::Done
2025-12-02 06:58:25.783148 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:25.787837 INFO::ASW Batch was 0.574675267555699 prior to batch effect correction and is now -0.0517361768660013 .
2025-12-02 06:58:25.788727 INFO::ASW Label was 0.130891240698585 prior to batch effect correction and is now 0.815538334028697 .
2025-12-02 06:58:25.790061 INFO::Total function execution time is 0.321649789810181 s and adjustment time is 0.276551246643066 s ( 85.98 )
2025-12-02 06:58:25.813769 INFO::Formatting Data.
2025-12-02 06:58:25.814848 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:25.816103 INFO::Removing potential empty rows and columns
2025-12-02 06:58:25.818101 INFO::Found 0 missing values.
2025-12-02 06:58:25.822248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:25.823115 INFO::Done
2025-12-02 06:58:25.82391 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:25.82808 INFO::Starting hierarchical adjustment
2025-12-02 06:58:25.829153 INFO::Found 2 batches.
2025-12-02 06:58:25.831855 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:25.832821 INFO::Using default BPPARAM
2025-12-02 06:58:25.833632 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:25.835487 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:25.857068 INFO::Done
2025-12-02 06:58:25.857954 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:25.867282 INFO::ASW Batch was 0.478249661266897 prior to batch effect correction and is now 0.113144277194384 .
2025-12-02 06:58:25.868306 INFO::ASW Label was 0.578722341801855 prior to batch effect correction and is now 0.831122180933045 .
2025-12-02 06:58:25.869515 INFO::Total function execution time is 0.0557968616485596 s and adjustment time is 0.0281147956848145 s ( 50.39 )
2025-12-02 06:58:25.870725 INFO::Formatting Data.
2025-12-02 06:58:25.871659 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:25.872989 INFO::Removing potential empty rows and columns
2025-12-02 06:58:25.874533 INFO::Found 0 missing values.
2025-12-02 06:58:25.878762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:25.879599 INFO::Done
2025-12-02 06:58:25.880393 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:25.884682 INFO::Starting hierarchical adjustment
2025-12-02 06:58:25.885807 INFO::Found 2 batches.
2025-12-02 06:58:25.886636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:25.887558 INFO::Using default BPPARAM
2025-12-02 06:58:25.888359 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:25.88977 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-02 06:58:25.911664 INFO::Done
2025-12-02 06:58:25.912577 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:25.916806 INFO::ASW Batch was 0.478249661266897 prior to batch effect correction and is now 0.113144277194384 .
2025-12-02 06:58:25.917718 INFO::ASW Label was 0.578722341801855 prior to batch effect correction and is now 0.831122180933045 .
2025-12-02 06:58:25.918883 INFO::Total function execution time is 0.0481929779052734 s and adjustment time is 0.026066780090332 s ( 54.09 )
2025-12-02 06:58:25.935639 INFO::Formatting Data.
2025-12-02 06:58:25.936653 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:25.937925 INFO::Removing potential empty rows and columns
2025-12-02 06:58:25.939323 INFO::Found 0 missing values.
2025-12-02 06:58:25.94259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:25.943418 INFO::Done
2025-12-02 06:58:25.944225 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:25.947052 INFO::Starting hierarchical adjustment
2025-12-02 06:58:25.948094 INFO::Found 2 batches.
2025-12-02 06:58:25.948933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:25.949867 INFO::Using default BPPARAM
2025-12-02 06:58:25.950703 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:25.952013 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-02 06:58:25.998346 INFO::Done
2025-12-02 06:58:25.999311 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:26.002079 INFO::ASW Batch was -0.0539277852640116 prior to batch effect correction and is now -0.0955687883770985 .
2025-12-02 06:58:26.003257 INFO::Total function execution time is 0.0676817893981934 s and adjustment time is 0.0504517555236816 s ( 74.54 )
2025-12-02 06:58:26.020313 INFO::Formatting Data.
2025-12-02 06:58:26.021365 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:26.022615 INFO::Removing potential empty rows and columns
2025-12-02 06:58:26.024064 INFO::Found 0 missing values.
2025-12-02 06:58:26.025688 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-02 06:58:26.032687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:26.033585 INFO::Done
2025-12-02 06:58:26.034389 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:26.038891 INFO::Starting hierarchical adjustment
2025-12-02 06:58:26.040036 INFO::Found 2 batches.
2025-12-02 06:58:26.040894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:26.041881 INFO::Using default BPPARAM
2025-12-02 06:58:26.042789 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:26.044115 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-02 06:58:26.06765 INFO::Done
2025-12-02 06:58:26.068557 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:26.072577 INFO::ASW Batch was 0.457122517399463 prior to batch effect correction and is now -0.0220522813975732 .
2025-12-02 06:58:26.073427 INFO::ASW Label was 0.60522057752852 prior to batch effect correction and is now 0.9360026839684 .
2025-12-02 06:58:26.074541 INFO::Total function execution time is 0.0542705059051514 s and adjustment time is 0.0278551578521729 s ( 51.33 )
2025-12-02 06:58:26.075671 INFO::Formatting Data.
2025-12-02 06:58:26.076549 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:26.077863 INFO::Removing potential empty rows and columns
2025-12-02 06:58:26.079309 INFO::Found 0 missing values.
2025-12-02 06:58:26.080578 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-02 06:58:26.087338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:26.088152 INFO::Done
2025-12-02 06:58:26.088958 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:26.093006 INFO::Starting hierarchical adjustment
2025-12-02 06:58:26.094005 INFO::Found 2 batches.
2025-12-02 06:58:26.094836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:26.095723 INFO::Using default BPPARAM
2025-12-02 06:58:26.096497 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:26.097871 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-02 06:58:26.121525 INFO::Done
2025-12-02 06:58:26.122433 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:26.126521 INFO::ASW Batch was 0.457122517399463 prior to batch effect correction and is now -0.0220522813975732 .
2025-12-02 06:58:26.127366 INFO::ASW Label was 0.60522057752852 prior to batch effect correction and is now 0.9360026839684 .
2025-12-02 06:58:26.128487 INFO::Total function execution time is 0.0528252124786377 s and adjustment time is 0.0276954174041748 s ( 52.43 )
2025-12-02 06:58:26.424482 INFO::Formatting Data.
2025-12-02 06:58:26.425485 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:26.426673 INFO::Removing potential empty rows and columns
2025-12-02 06:58:26.428075 INFO::Found 0 missing values.
2025-12-02 06:58:26.432279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:26.433085 INFO::Done
2025-12-02 06:58:26.433797 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:26.436481 INFO::Starting hierarchical adjustment
2025-12-02 06:58:26.43746 INFO::Found 3 batches.
2025-12-02 06:58:26.438173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:26.439027 INFO::Using default BPPARAM
2025-12-02 06:58:26.439749 INFO::Processing subtree level 1
2025-12-02 06:58:26.547079 INFO::Adjusting the last 1 batches sequentially
2025-12-02 06:58:26.557758 INFO::Done
2025-12-02 06:58:26.558776 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:26.566312 INFO::ASW Batch was -0.0991747445318142 prior to batch effect correction and is now -0.0991747445318142 .
2025-12-02 06:58:26.567739 INFO::Total function execution time is 0.143296003341675 s and adjustment time is 0.120441436767578 s ( 84.05 )
2025-12-02 06:58:26.573326 INFO::Formatting Data.
2025-12-02 06:58:26.574407 INFO::Typecasting input to dataframe.
2025-12-02 06:58:26.575567 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:26.580987 INFO::Removing potential empty rows and columns
2025-12-02 06:58:26.582798 INFO::Found 0 missing values.
2025-12-02 06:58:26.591663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:26.592664 INFO::Done
2025-12-02 06:58:26.596559 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:26.599524 INFO::Starting hierarchical adjustment
2025-12-02 06:58:26.600562 INFO::Found 3 batches.
2025-12-02 06:58:26.60135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:26.602229 INFO::Using default BPPARAM
2025-12-02 06:58:26.60304 INFO::Processing subtree level 1
2025-12-02 06:58:26.708024 INFO::Adjusting the last 1 batches sequentially
2025-12-02 06:58:26.718745 INFO::Done
2025-12-02 06:58:26.719652 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:26.72735 INFO::ASW Batch was -0.0991747445318142 prior to batch effect correction and is now -0.0991747445318142 .
2025-12-02 06:58:26.73286 INFO::Total function execution time is 0.155468225479126 s and adjustment time is 0.118355274200439 s ( 76.13 )
2025-12-02 06:58:26.764314 INFO::Formatting Data.
2025-12-02 06:58:26.765394 INFO::Typecasting input to dataframe.
2025-12-02 06:58:26.766571 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:26.767764 INFO::Removing potential empty rows and columns
2025-12-02 06:58:26.769269 INFO::Found 0 missing values.
2025-12-02 06:58:26.773507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:26.77431 INFO::Done
2025-12-02 06:58:26.775112 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:26.777772 INFO::Starting hierarchical adjustment
2025-12-02 06:58:26.778785 INFO::Found 3 batches.
2025-12-02 06:58:26.779528 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:26.780393 INFO::Using default BPPARAM
2025-12-02 06:58:26.785491 INFO::Processing subtree level 1
2025-12-02 06:58:26.92002 INFO::Adjusting the last 1 batches sequentially
2025-12-02 06:58:26.926816 INFO::Done
2025-12-02 06:58:26.927803 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:26.935757 INFO::ASW Batch was 0.109683204871924 prior to batch effect correction and is now 0.109683204871924 .
2025-12-02 06:58:26.941392 INFO::Total function execution time is 0.177029609680176 s and adjustment time is 0.148203372955322 s ( 83.72 )
2025-12-02 06:58:27.178696 INFO::Formatting Data.
2025-12-02 06:58:27.179937 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:27.181803 INFO::Removing potential empty rows and columns
2025-12-02 06:58:27.186308 INFO::Found 1000 missing values.
2025-12-02 06:58:27.215137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:27.216074 INFO::Done
2025-12-02 06:58:27.216888 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:27.22435 INFO::Starting hierarchical adjustment
2025-12-02 06:58:27.225528 INFO::Found 10 batches.
2025-12-02 06:58:27.226314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:27.227215 INFO::Using default BPPARAM
2025-12-02 06:58:27.227978 INFO::Processing subtree level 1
2025-12-02 06:58:27.493191 INFO::Processing subtree level 2
2025-12-02 06:58:27.710184 INFO::Adjusting the last 1 batches sequentially
2025-12-02 06:58:27.712612 INFO::Done
2025-12-02 06:58:27.717651 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:27.733542 INFO::ASW Batch was 0.535063260023931 prior to batch effect correction and is now 0.535063260023931 .
2025-12-02 06:58:27.734477 INFO::ASW Label was 0.297698957992012 prior to batch effect correction and is now 0.297698957992012 .
2025-12-02 06:58:27.735759 INFO::Total function execution time is 0.557165384292603 s and adjustment time is 0.487320899963379 s ( 87.46 )
2025-12-02 06:58:27.741111 INFO::Formatting Data.
2025-12-02 06:58:27.742139 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:27.743787 INFO::Removing potential empty rows and columns
2025-12-02 06:58:27.750628 INFO::Found 1000 missing values.
2025-12-02 06:58:27.777745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:27.778711 INFO::Done
2025-12-02 06:58:27.779469 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:27.786925 INFO::Starting hierarchical adjustment
2025-12-02 06:58:27.788047 INFO::Found 10 batches.
2025-12-02 06:58:28.724396 INFO::Set up parallel execution backend with 2 workers
2025-12-02 06:58:28.726553 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-02 06:58:30.233959 INFO::Adjusting the last 2 batches sequentially
2025-12-02 06:58:30.236083 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-02 06:58:30.259086 INFO::Done
2025-12-02 06:58:30.25987 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:30.266106 INFO::ASW Batch was 0.535063260023931 prior to batch effect correction and is now 0.535063260023931 .
2025-12-02 06:58:30.266961 INFO::ASW Label was 0.297698957992012 prior to batch effect correction and is now 0.297698957992012 .
2025-12-02 06:58:30.267934 INFO::Total function execution time is 2.53106546401978 s and adjustment time is 2.47126030921936 s ( 97.64 )
2025-12-02 06:58:30.56924 INFO::Formatting Data.
2025-12-02 06:58:30.570324 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:30.571611 INFO::Removing potential empty rows and columns
2025-12-02 06:58:30.577265 INFO::Found 0 missing values.
2025-12-02 06:58:30.586996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:30.587883 INFO::Done
2025-12-02 06:58:30.588619 INFO::Acquiring quality metrics before batch effect correction.
2025-12-02 06:58:30.596604 INFO::Starting hierarchical adjustment
2025-12-02 06:58:30.601824 INFO::Found 3 batches.
2025-12-02 06:58:30.602626 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-02 06:58:30.603495 INFO::Using default BPPARAM
2025-12-02 06:58:30.604248 INFO::Processing subtree level 1
2025-12-02 06:58:30.768557 INFO::Adjusting the last 1 batches sequentially
2025-12-02 06:58:30.779114 INFO::Done
2025-12-02 06:58:30.779951 INFO::Acquiring quality metrics after batch effect correction.
2025-12-02 06:58:30.78857 INFO::ASW Batch was 0.196874096968526 prior to batch effect correction and is now -0.153698440648364 .
2025-12-02 06:58:30.793732 INFO::ASW Label was -0.167775138178259 prior to batch effect correction and is now 0.0904542479765936 .
2025-12-02 06:58:30.795096 INFO::Total function execution time is 0.22587776184082 s and adjustment time is 0.177511692047119 s ( 78.59 )
2025-12-02 06:58:30.973673 INFO::Formatting Data.
2025-12-02 06:58:30.974751 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:30.975946 INFO::Removing potential empty rows and columns
2025-12-02 06:58:30.977406 INFO::Found 2 missing values.
2025-12-02 06:58:30.981527 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:30.982293 INFO::Done
2025-12-02 06:58:31.020309 INFO::Found NA in Reference column
2025-12-02 06:58:31.033364 INFO::Require at least two references per batch.
2025-12-02 06:58:31.061844 INFO::Formatting Data.
2025-12-02 06:58:31.062821 INFO::Recognized SummarizedExperiment
2025-12-02 06:58:31.063535 INFO::Typecasting input to dataframe.
2025-12-02 06:58:31.07691 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.078421 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.083552 INFO::Found 0 missing values.
2025-12-02 06:58:31.093637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.094536 INFO::Done
2025-12-02 06:58:31.116051 INFO::Formatting Data.
2025-12-02 06:58:31.11701 INFO::Recognized SummarizedExperiment
2025-12-02 06:58:31.117735 INFO::Typecasting input to dataframe.
2025-12-02 06:58:31.141713 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.143272 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.148368 INFO::Found 0 missing values.
2025-12-02 06:58:31.1738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.174978 INFO::Done
2025-12-02 06:58:31.198903 INFO::Formatting Data.
2025-12-02 06:58:31.19984 INFO::Recognized SummarizedExperiment
2025-12-02 06:58:31.200546 INFO::Typecasting input to dataframe.
2025-12-02 06:58:31.22368 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.224975 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.2264 INFO::Found 0 missing values.
2025-12-02 06:58:31.227604 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-02 06:58:31.233632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.234407 INFO::Done
2025-12-02 06:58:31.247589 INFO::Formatting Data.
2025-12-02 06:58:31.24853 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.24965 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.251037 INFO::Found 0 missing values.
2025-12-02 06:58:31.255037 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.255807 INFO::Done
2025-12-02 06:58:31.270662 INFO::Formatting Data.
2025-12-02 06:58:31.271667 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.272806 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.274204 INFO::Found 0 missing values.
2025-12-02 06:58:31.278419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.279325 INFO::Done
2025-12-02 06:58:31.319856 INFO::Formatting Data.
2025-12-02 06:58:31.320884 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.322218 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.323835 INFO::Found 1 missing values.
2025-12-02 06:58:31.327551 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.328362 INFO::Done
2025-12-02 06:58:31.354888 INFO::Formatting Data.
2025-12-02 06:58:31.355933 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.357091 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.35839 INFO::Found 2 missing values.
2025-12-02 06:58:31.359637 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-02 06:58:31.362858 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.363609 INFO::Done
2025-12-02 06:58:31.377272 INFO::Formatting Data.
2025-12-02 06:58:31.378251 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.379426 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.380726 INFO::Found 2 missing values.
2025-12-02 06:58:31.382984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.383724 INFO::Done
2025-12-02 06:58:31.398216 INFO::Formatting Data.
2025-12-02 06:58:31.399223 INFO::Typecasting input to dataframe.
2025-12-02 06:58:31.400289 INFO::Replacing NaNs with NAs.
2025-12-02 06:58:31.401444 INFO::Removing potential empty rows and columns
2025-12-02 06:58:31.40293 INFO::Found 0 missing values.
2025-12-02 06:58:31.407031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-02 06:58:31.407771 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.451 3.851 28.652
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.531 | 1.248 | 21.333 | |
| compute_asw | 0.034 | 0.000 | 0.034 | |
| count_existing | 0.018 | 0.000 | 0.018 | |
| generate_data_covariables | 0.015 | 0.000 | 0.016 | |
| generate_dataset | 0.014 | 0.000 | 0.014 | |