Yannis Schumann
| Snapshot Date: 2025-10-05 13:45 -0400 (Sun, 05 Oct 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 2025-10-06 12:03 -0400 (Mon, 06 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 164/2341 | 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: 2025-10-05 21:26:08 -0400 (Sun, 05 Oct 2025) |
| EndedAt: 2025-10-05 21:28:11 -0400 (Sun, 05 Oct 2025) |
| EllapsedTime: 123.1 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 Patched (2025-08-23 r88802)
* 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 29.44 2.251 23.297
* 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 Patched (2025-08-23 r88802) -- "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")
2025-10-05 21:27:14.635375 INFO::Formatting Data.
2025-10-05 21:27:14.641204 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:14.657521 INFO::Removing potential empty rows and columns
2025-10-05 21:27:15.025029 INFO::Found 0 missing values.
2025-10-05 21:27:15.029304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:15.030032 INFO::Done
2025-10-05 21:27:15.030673 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:15.043761 INFO::Starting hierarchical adjustment
2025-10-05 21:27:15.044668 INFO::Found 3 batches.
2025-10-05 21:27:15.045308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:15.046638 INFO::Using default BPPARAM
2025-10-05 21:27:15.047295 INFO::Processing subtree level 1
2025-10-05 21:27:15.243179 INFO::Adjusting the last 1 batches sequentially
2025-10-05 21:27:15.249925 INFO::Done
2025-10-05 21:27:15.251022 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:15.255088 INFO::ASW Batch was -0.0963721373464726 prior to batch effect correction and is now -0.0963721373464726 .
2025-10-05 21:27:15.262788 INFO::Total function execution time is 0.628124713897705 s and adjustment time is 0.205362558364868 s ( 32.69 )
2025-10-05 21:27:15.304515 INFO::Formatting Data.
2025-10-05 21:27:15.308796 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:15.310437 INFO::Removing potential empty rows and columns
2025-10-05 21:27:15.316218 INFO::Found 0 missing values.
2025-10-05 21:27:15.317668 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.
2025-10-05 21:27:15.362167 INFO::Formatting Data.
2025-10-05 21:27:15.363234 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:15.368724 INFO::Removing potential empty rows and columns
2025-10-05 21:27:15.378392 INFO::Found 0 missing values.
2025-10-05 21:27:15.379795 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.
2025-10-05 21:27:15.461184 INFO::Formatting Data.
2025-10-05 21:27:15.465524 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:15.466666 INFO::Removing potential empty rows and columns
2025-10-05 21:27:15.47203 INFO::Found 0 missing values.
2025-10-05 21:27:15.473168 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.
2025-10-05 21:27:15.492512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:15.493226 INFO::Done
2025-10-05 21:27:15.493854 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:15.502295 INFO::Starting hierarchical adjustment
2025-10-05 21:27:15.503128 INFO::Found 2 batches.
2025-10-05 21:27:15.503739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:15.504468 INFO::Using default BPPARAM
2025-10-05 21:27:15.50509 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:15.512336 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-05 21:27:15.579887 INFO::Done
2025-10-05 21:27:15.580975 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:15.584052 INFO::ASW Batch was 0.0473623970792953 prior to batch effect correction and is now -0.100689819179628 .
2025-10-05 21:27:15.585238 INFO::Total function execution time is 0.124138593673706 s and adjustment time is 0.0768744945526123 s ( 61.93 )
2025-10-05 21:27:15.589417 INFO::Formatting Data.
2025-10-05 21:27:15.590366 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:15.605009 INFO::Formatting Data.
2025-10-05 21:27:15.606177 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:15.607515 INFO::Removing potential empty rows and columns
2025-10-05 21:27:15.609108 INFO::Found 0 missing values.
2025-10-05 21:27:15.613871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:15.614717 INFO::Done
2025-10-05 21:27:15.615527 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:15.618833 INFO::Starting hierarchical adjustment
2025-10-05 21:27:15.619952 INFO::Found 2 batches.
2025-10-05 21:27:15.620749 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:15.621663 INFO::Using default BPPARAM
2025-10-05 21:27:15.622481 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:15.623902 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-05 21:27:15.690742 INFO::Done
2025-10-05 21:27:15.691745 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:15.694698 INFO::ASW Batch was 0.128996782218898 prior to batch effect correction and is now -0.0885127133516963 .
2025-10-05 21:27:15.695821 INFO::Total function execution time is 0.0908987522125244 s and adjustment time is 0.071014404296875 s ( 78.12 )
2025-10-05 21:27:15.697396 INFO::Formatting Data.
2025-10-05 21:27:15.698251 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:15.699454 INFO::Removing potential empty rows and columns
2025-10-05 21:27:15.700915 INFO::Found 0 missing values.
2025-10-05 21:27:15.705077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:15.705824 INFO::Done
2025-10-05 21:27:15.706566 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:15.709405 INFO::Starting hierarchical adjustment
2025-10-05 21:27:15.710395 INFO::Found 2 batches.
2025-10-05 21:27:15.711148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:15.712009 INFO::Using default BPPARAM
2025-10-05 21:27:15.712775 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:15.714037 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-05 21:27:15.737629 INFO::Done
2025-10-05 21:27:15.738638 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:15.741637 INFO::ASW Batch was 0.128996782218898 prior to batch effect correction and is now -0.0885127133516963 .
2025-10-05 21:27:15.742765 INFO::Total function execution time is 0.0453510284423828 s and adjustment time is 0.0274131298065186 s ( 60.45 )
2025-10-05 21:27:20.853017 INFO::Formatting Data.
2025-10-05 21:27:20.857173 INFO::Recognized SummarizedExperiment
2025-10-05 21:27:20.857921 INFO::Typecasting input to dataframe.
2025-10-05 21:27:20.892882 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:20.894364 INFO::Removing potential empty rows and columns
2025-10-05 21:27:20.898961 INFO::Found 0 missing values.
2025-10-05 21:27:20.919297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:20.920392 INFO::Done
2025-10-05 21:27:20.9211 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:20.926063 INFO::Starting hierarchical adjustment
2025-10-05 21:27:20.92699 INFO::Found 2 batches.
2025-10-05 21:27:20.927625 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:20.929436 INFO::Using default BPPARAM
2025-10-05 21:27:20.930085 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:20.931325 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-05 21:27:21.002937 INFO::Done
2025-10-05 21:27:21.003743 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:21.008008 INFO::ASW Batch was 0.0276284086229428 prior to batch effect correction and is now -0.0960882191858933 .
2025-10-05 21:27:21.009024 INFO::Total function execution time is 0.156328439712524 s and adjustment time is 0.0761346817016602 s ( 48.7 )
2025-10-05 21:27:21.032612 INFO::Formatting Data.
2025-10-05 21:27:21.03348 INFO::Recognized SummarizedExperiment
2025-10-05 21:27:21.034107 INFO::Typecasting input to dataframe.
2025-10-05 21:27:21.045867 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:21.047266 INFO::Removing potential empty rows and columns
2025-10-05 21:27:21.051788 INFO::Found 0 missing values.
2025-10-05 21:27:21.060555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:21.061255 INFO::Done
2025-10-05 21:27:21.061867 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:21.066169 INFO::Starting hierarchical adjustment
2025-10-05 21:27:21.066996 INFO::Found 2 batches.
2025-10-05 21:27:21.067617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:21.068316 INFO::Using default BPPARAM
2025-10-05 21:27:21.068917 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:21.07005 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-05 21:27:21.103726 INFO::Done
2025-10-05 21:27:21.104708 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:21.110331 INFO::ASW Batch was 0.0272896535186854 prior to batch effect correction and is now 0.0272896535186854 .
2025-10-05 21:27:21.111618 INFO::Total function execution time is 0.0789334774017334 s and adjustment time is 0.0368349552154541 s ( 46.67 )
2025-10-05 21:27:21.139066 INFO::Formatting Data.
2025-10-05 21:27:21.140216 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:21.141689 INFO::Removing potential empty rows and columns
2025-10-05 21:27:21.143264 INFO::Found 0 missing values.
2025-10-05 21:27:21.147746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:21.148552 INFO::Done
2025-10-05 21:27:21.149303 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:21.152151 INFO::Starting hierarchical adjustment
2025-10-05 21:27:21.15307 INFO::Found 3 batches.
2025-10-05 21:27:21.153787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:21.154628 INFO::Using default BPPARAM
2025-10-05 21:27:21.155342 INFO::Processing subtree level 1
2025-10-05 21:27:21.382039 INFO::Adjusting the last 1 batches sequentially
2025-10-05 21:27:21.387612 INFO::Done
2025-10-05 21:27:21.388553 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:21.39588 INFO::ASW Batch was -0.119530296295137 prior to batch effect correction and is now -0.161481491367131 .
2025-10-05 21:27:21.400228 INFO::Total function execution time is 0.25817346572876 s and adjustment time is 0.234694242477417 s ( 90.91 )
2025-10-05 21:27:21.436971 INFO::Skipping initial DF formatting
2025-10-05 21:27:21.442178 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:21.447295 INFO::Starting hierarchical adjustment
2025-10-05 21:27:21.44925 INFO::Found 5 batches.
2025-10-05 21:27:21.449987 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:21.450755 INFO::Using default BPPARAM
2025-10-05 21:27:21.451397 INFO::Processing subtree level 1
2025-10-05 21:27:21.933337 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:21.93945 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-05 21:27:21.98816 INFO::Done
2025-10-05 21:27:21.989055 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:22.113443 INFO::ASW Batch was 0.507391354930823 prior to batch effect correction and is now 0.507391354930823 .
2025-10-05 21:27:22.114421 INFO::ASW Label was 0.38094576329303 prior to batch effect correction and is now 0.38094576329303 .
2025-10-05 21:27:22.115522 INFO::Total function execution time is 0.678632497787476 s and adjustment time is 0.540020942687988 s ( 79.57 )
2025-10-05 21:27:22.136589 INFO::Formatting Data.
2025-10-05 21:27:22.137583 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:22.138988 INFO::Removing potential empty rows and columns
2025-10-05 21:27:22.140524 INFO::Found 0 missing values.
2025-10-05 21:27:22.146502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:22.147204 INFO::Done
2025-10-05 21:27:22.147748 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:22.151336 INFO::Starting hierarchical adjustment
2025-10-05 21:27:22.1522 INFO::Found 5 batches.
2025-10-05 21:27:22.152835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:22.153633 INFO::Using default BPPARAM
2025-10-05 21:27:22.154308 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.
2025-10-05 21:27:22.343898 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:22.345791 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-05 21:27:22.366717 INFO::Done
2025-10-05 21:27:22.367724 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:22.371984 INFO::ASW Batch was 0.454302243204358 prior to batch effect correction and is now -0.0649554346102208 .
2025-10-05 21:27:22.372774 INFO::ASW Label was 0.548000967952834 prior to batch effect correction and is now 0.589645929199952 .
2025-10-05 21:27:22.373827 INFO::Total function execution time is 0.237309217453003 s and adjustment time is 0.214668750762939 s ( 90.46 )
2025-10-05 21:27:22.374968 INFO::Formatting Data.
2025-10-05 21:27:22.375854 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:22.377 INFO::Removing potential empty rows and columns
2025-10-05 21:27:22.378342 INFO::Found 0 missing values.
2025-10-05 21:27:22.383342 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:22.383986 INFO::Done
2025-10-05 21:27:22.384642 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:22.38836 INFO::Starting hierarchical adjustment
2025-10-05 21:27:22.389201 INFO::Found 5 batches.
2025-10-05 21:27:22.389802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:22.390515 INFO::Using default BPPARAM
2025-10-05 21:27:22.391099 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.
2025-10-05 21:27:22.596081 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:22.598409 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-05 21:27:22.658261 INFO::Done
2025-10-05 21:27:22.659473 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:22.664267 INFO::ASW Batch was 0.454302243204358 prior to batch effect correction and is now -0.0649554346102208 .
2025-10-05 21:27:22.665209 INFO::ASW Label was 0.548000967952834 prior to batch effect correction and is now 0.589645929199952 .
2025-10-05 21:27:22.666404 INFO::Total function execution time is 0.291417837142944 s and adjustment time is 0.265108108520508 s ( 90.97 )
2025-10-05 21:27:22.685995 INFO::Formatting Data.
2025-10-05 21:27:22.687153 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:22.688485 INFO::Removing potential empty rows and columns
2025-10-05 21:27:22.689912 INFO::Found 0 missing values.
2025-10-05 21:27:22.696262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:22.697098 INFO::Done
2025-10-05 21:27:22.697863 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:22.702257 INFO::Starting hierarchical adjustment
2025-10-05 21:27:22.703323 INFO::Found 5 batches.
2025-10-05 21:27:22.704108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:22.705027 INFO::Using default BPPARAM
2025-10-05 21:27:22.705831 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.
2025-10-05 21:27:22.996593 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:22.99901 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-05 21:27:23.046247 INFO::Done
2025-10-05 21:27:23.047369 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:23.052161 INFO::ASW Batch was 0.378081640055298 prior to batch effect correction and is now -0.0757412382739183 .
2025-10-05 21:27:23.053188 INFO::ASW Label was 0.304392565226575 prior to batch effect correction and is now 0.845933407334387 .
2025-10-05 21:27:23.05447 INFO::Total function execution time is 0.368554830551147 s and adjustment time is 0.335093975067139 s ( 90.92 )
2025-10-05 21:27:23.055579 INFO::Formatting Data.
2025-10-05 21:27:23.05634 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:23.057509 INFO::Removing potential empty rows and columns
2025-10-05 21:27:23.059005 INFO::Found 0 missing values.
2025-10-05 21:27:23.064637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:23.065462 INFO::Done
2025-10-05 21:27:23.066328 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:23.070546 INFO::Starting hierarchical adjustment
2025-10-05 21:27:23.07145 INFO::Found 5 batches.
2025-10-05 21:27:23.072238 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:23.073289 INFO::Using default BPPARAM
2025-10-05 21:27:23.074152 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.
2025-10-05 21:27:23.393493 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:23.395406 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-05 21:27:23.445265 INFO::Done
2025-10-05 21:27:23.446695 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:23.451473 INFO::ASW Batch was 0.378081640055298 prior to batch effect correction and is now -0.0757412382739183 .
2025-10-05 21:27:23.452348 INFO::ASW Label was 0.304392565226575 prior to batch effect correction and is now 0.845933407334387 .
2025-10-05 21:27:23.453563 INFO::Total function execution time is 0.397928237915039 s and adjustment time is 0.37389612197876 s ( 93.96 )
2025-10-05 21:27:23.473394 INFO::Formatting Data.
2025-10-05 21:27:23.474517 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:23.475863 INFO::Removing potential empty rows and columns
2025-10-05 21:27:23.477374 INFO::Found 0 missing values.
2025-10-05 21:27:23.481548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:23.482345 INFO::Done
2025-10-05 21:27:23.483101 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:23.487458 INFO::Starting hierarchical adjustment
2025-10-05 21:27:23.488478 INFO::Found 2 batches.
2025-10-05 21:27:23.489284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:23.490221 INFO::Using default BPPARAM
2025-10-05 21:27:23.491034 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:23.492397 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-05 21:27:23.515153 INFO::Done
2025-10-05 21:27:23.51608 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:23.520329 INFO::ASW Batch was 0.733879101691016 prior to batch effect correction and is now 0.111629686224257 .
2025-10-05 21:27:23.521153 INFO::ASW Label was 0.372831652870355 prior to batch effect correction and is now 0.848554997726675 .
2025-10-05 21:27:23.522305 INFO::Total function execution time is 0.0490026473999023 s and adjustment time is 0.0268540382385254 s ( 54.8 )
2025-10-05 21:27:23.523483 INFO::Formatting Data.
2025-10-05 21:27:23.524429 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:23.525703 INFO::Removing potential empty rows and columns
2025-10-05 21:27:23.52716 INFO::Found 0 missing values.
2025-10-05 21:27:23.53129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:23.532094 INFO::Done
2025-10-05 21:27:23.532889 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:23.537276 INFO::Starting hierarchical adjustment
2025-10-05 21:27:23.538298 INFO::Found 2 batches.
2025-10-05 21:27:23.539054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:23.539947 INFO::Using default BPPARAM
2025-10-05 21:27:23.540727 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:23.542044 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-05 21:27:23.562976 INFO::Done
2025-10-05 21:27:23.563729 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:23.56699 INFO::ASW Batch was 0.733879101691016 prior to batch effect correction and is now 0.111629686224257 .
2025-10-05 21:27:23.567661 INFO::ASW Label was 0.372831652870355 prior to batch effect correction and is now 0.848554997726675 .
2025-10-05 21:27:23.56853 INFO::Total function execution time is 0.0451259613037109 s and adjustment time is 0.0249073505401611 s ( 55.2 )
2025-10-05 21:27:23.580889 INFO::Formatting Data.
2025-10-05 21:27:23.581711 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:23.582699 INFO::Removing potential empty rows and columns
2025-10-05 21:27:23.583732 INFO::Found 0 missing values.
2025-10-05 21:27:23.586063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:23.586696 INFO::Done
2025-10-05 21:27:23.587285 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:23.5894 INFO::Starting hierarchical adjustment
2025-10-05 21:27:23.590181 INFO::Found 2 batches.
2025-10-05 21:27:23.59077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:23.591446 INFO::Using default BPPARAM
2025-10-05 21:27:23.592021 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:23.593007 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-05 21:27:23.62874 INFO::Done
2025-10-05 21:27:23.629547 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:23.631727 INFO::ASW Batch was -0.0983004767811787 prior to batch effect correction and is now -0.137530165658407 .
2025-10-05 21:27:23.632636 INFO::Total function execution time is 0.0518198013305664 s and adjustment time is 0.0386905670166016 s ( 74.66 )
2025-10-05 21:27:23.645516 INFO::Formatting Data.
2025-10-05 21:27:23.646339 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:23.647338 INFO::Removing potential empty rows and columns
2025-10-05 21:27:23.648477 INFO::Found 0 missing values.
2025-10-05 21:27:23.649804 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.
2025-10-05 21:27:23.654956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:23.655578 INFO::Done
2025-10-05 21:27:23.65616 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:23.659424 INFO::Starting hierarchical adjustment
2025-10-05 21:27:23.660218 INFO::Found 2 batches.
2025-10-05 21:27:23.660808 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:23.661486 INFO::Using default BPPARAM
2025-10-05 21:27:23.662064 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:23.663098 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-05 21:27:23.681685 INFO::Done
2025-10-05 21:27:23.682441 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:23.685699 INFO::ASW Batch was 0.512561039703786 prior to batch effect correction and is now 0.0774667838034717 .
2025-10-05 21:27:23.686405 INFO::ASW Label was 0.587807233338174 prior to batch effect correction and is now 0.8581217162716 .
2025-10-05 21:27:23.687275 INFO::Total function execution time is 0.0418155193328857 s and adjustment time is 0.0216178894042969 s ( 51.7 )
2025-10-05 21:27:23.688175 INFO::Formatting Data.
2025-10-05 21:27:23.688875 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:23.689896 INFO::Removing potential empty rows and columns
2025-10-05 21:27:23.690996 INFO::Found 0 missing values.
2025-10-05 21:27:23.692021 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.
2025-10-05 21:27:23.697136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:23.697807 INFO::Done
2025-10-05 21:27:23.698395 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:23.701684 INFO::Starting hierarchical adjustment
2025-10-05 21:27:23.702497 INFO::Found 2 batches.
2025-10-05 21:27:23.703077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:23.703754 INFO::Using default BPPARAM
2025-10-05 21:27:23.704356 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:23.705398 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-05 21:27:23.723832 INFO::Done
2025-10-05 21:27:23.724572 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:23.727784 INFO::ASW Batch was 0.512561039703786 prior to batch effect correction and is now 0.0774667838034717 .
2025-10-05 21:27:23.728447 INFO::ASW Label was 0.587807233338174 prior to batch effect correction and is now 0.8581217162716 .
2025-10-05 21:27:23.729316 INFO::Total function execution time is 0.0411784648895264 s and adjustment time is 0.0214848518371582 s ( 52.17 )
2025-10-05 21:27:24.070597 INFO::Formatting Data.
2025-10-05 21:27:24.071883 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:24.073729 INFO::Removing potential empty rows and columns
2025-10-05 21:27:24.075465 INFO::Found 0 missing values.
2025-10-05 21:27:24.080695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:24.081612 INFO::Done
2025-10-05 21:27:24.082497 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:24.085795 INFO::Starting hierarchical adjustment
2025-10-05 21:27:24.086973 INFO::Found 3 batches.
2025-10-05 21:27:24.087865 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:24.088881 INFO::Using default BPPARAM
2025-10-05 21:27:24.089743 INFO::Processing subtree level 1
2025-10-05 21:27:24.278324 INFO::Adjusting the last 1 batches sequentially
2025-10-05 21:27:24.280437 INFO::Done
2025-10-05 21:27:24.281195 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:24.287088 INFO::ASW Batch was -0.0776553849173241 prior to batch effect correction and is now -0.0776553849173241 .
2025-10-05 21:27:24.291234 INFO::Total function execution time is 0.217723608016968 s and adjustment time is 0.193695545196533 s ( 88.96 )
2025-10-05 21:27:24.292526 INFO::Formatting Data.
2025-10-05 21:27:24.293321 INFO::Typecasting input to dataframe.
2025-10-05 21:27:24.298255 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:24.299414 INFO::Removing potential empty rows and columns
2025-10-05 21:27:24.300725 INFO::Found 0 missing values.
2025-10-05 21:27:24.304424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:24.305058 INFO::Done
2025-10-05 21:27:24.307757 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:24.315213 INFO::Starting hierarchical adjustment
2025-10-05 21:27:24.316463 INFO::Found 3 batches.
2025-10-05 21:27:24.320431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:24.321506 INFO::Using default BPPARAM
2025-10-05 21:27:24.32242 INFO::Processing subtree level 1
2025-10-05 21:27:24.590126 INFO::Adjusting the last 1 batches sequentially
2025-10-05 21:27:24.596316 INFO::Done
2025-10-05 21:27:24.597231 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:24.604235 INFO::ASW Batch was -0.0776553849173241 prior to batch effect correction and is now -0.0776553849173241 .
2025-10-05 21:27:24.605444 INFO::Total function execution time is 0.31287670135498 s and adjustment time is 0.276048183441162 s ( 88.23 )
2025-10-05 21:27:24.635631 INFO::Formatting Data.
2025-10-05 21:27:24.636727 INFO::Typecasting input to dataframe.
2025-10-05 21:27:24.637847 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:24.639055 INFO::Removing potential empty rows and columns
2025-10-05 21:27:24.643413 INFO::Found 0 missing values.
2025-10-05 21:27:24.650237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:24.650904 INFO::Done
2025-10-05 21:27:24.651537 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:24.654038 INFO::Starting hierarchical adjustment
2025-10-05 21:27:24.654858 INFO::Found 3 batches.
2025-10-05 21:27:24.655478 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:24.656187 INFO::Using default BPPARAM
2025-10-05 21:27:24.656812 INFO::Processing subtree level 1
2025-10-05 21:27:24.804931 INFO::Adjusting the last 1 batches sequentially
2025-10-05 21:27:24.810538 INFO::Done
2025-10-05 21:27:24.811526 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:24.822221 INFO::ASW Batch was -0.0901715304969281 prior to batch effect correction and is now -0.0901715304969281 .
2025-10-05 21:27:24.82373 INFO::Total function execution time is 0.188135862350464 s and adjustment time is 0.155780553817749 s ( 82.8 )
2025-10-05 21:27:25.070005 INFO::Formatting Data.
2025-10-05 21:27:25.071179 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:25.07286 INFO::Removing potential empty rows and columns
2025-10-05 21:27:25.0772 INFO::Found 1000 missing values.
2025-10-05 21:27:25.107816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:25.10884 INFO::Done
2025-10-05 21:27:25.109723 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:25.117942 INFO::Starting hierarchical adjustment
2025-10-05 21:27:25.119096 INFO::Found 10 batches.
2025-10-05 21:27:25.120214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:25.121191 INFO::Using default BPPARAM
2025-10-05 21:27:25.122012 INFO::Processing subtree level 1
2025-10-05 21:27:25.393383 INFO::Processing subtree level 2
2025-10-05 21:27:25.606875 INFO::Adjusting the last 1 batches sequentially
2025-10-05 21:27:25.613148 INFO::Done
2025-10-05 21:27:25.613999 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:25.631549 INFO::ASW Batch was 0.484190728555975 prior to batch effect correction and is now 0.484190728555975 .
2025-10-05 21:27:25.632655 INFO::ASW Label was 0.337006904304735 prior to batch effect correction and is now 0.337006904304735 .
2025-10-05 21:27:25.633997 INFO::Total function execution time is 0.564084053039551 s and adjustment time is 0.494250059127808 s ( 87.62 )
2025-10-05 21:27:25.635286 INFO::Formatting Data.
2025-10-05 21:27:25.636251 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:25.63795 INFO::Removing potential empty rows and columns
2025-10-05 21:27:25.642166 INFO::Found 1000 missing values.
2025-10-05 21:27:25.670819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:25.671894 INFO::Done
2025-10-05 21:27:25.672764 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:25.680761 INFO::Starting hierarchical adjustment
2025-10-05 21:27:25.681893 INFO::Found 10 batches.
2025-10-05 21:27:27.048752 INFO::Set up parallel execution backend with 2 workers
2025-10-05 21:27:27.051052 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-05 21:27:28.756214 INFO::Adjusting the last 2 batches sequentially
2025-10-05 21:27:28.758539 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-05 21:27:28.785518 INFO::Done
2025-10-05 21:27:28.7865 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:28.793492 INFO::ASW Batch was 0.484190728555975 prior to batch effect correction and is now 0.484190728555975 .
2025-10-05 21:27:28.794376 INFO::ASW Label was 0.337006904304735 prior to batch effect correction and is now 0.337006904304735 .
2025-10-05 21:27:28.795478 INFO::Total function execution time is 3.1602737903595 s and adjustment time is 3.10383105278015 s ( 98.21 )
2025-10-05 21:27:29.050374 INFO::Formatting Data.
2025-10-05 21:27:29.051461 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.052764 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.054325 INFO::Found 0 missing values.
2025-10-05 21:27:29.059734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.060475 INFO::Done
2025-10-05 21:27:29.061194 INFO::Acquiring quality metrics before batch effect correction.
2025-10-05 21:27:29.064428 INFO::Starting hierarchical adjustment
2025-10-05 21:27:29.065242 INFO::Found 3 batches.
2025-10-05 21:27:29.065843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-05 21:27:29.066547 INFO::Using default BPPARAM
2025-10-05 21:27:29.067158 INFO::Processing subtree level 1
2025-10-05 21:27:29.230419 INFO::Adjusting the last 1 batches sequentially
2025-10-05 21:27:29.232504 INFO::Done
2025-10-05 21:27:29.237396 INFO::Acquiring quality metrics after batch effect correction.
2025-10-05 21:27:29.246757 INFO::ASW Batch was 0.153897606581584 prior to batch effect correction and is now -0.16733674613859 .
2025-10-05 21:27:29.247853 INFO::ASW Label was -0.187046832732339 prior to batch effect correction and is now 0.032473928455335 .
2025-10-05 21:27:29.249308 INFO::Total function execution time is 0.19892406463623 s and adjustment time is 0.167409420013428 s ( 84.16 )
2025-10-05 21:27:29.440758 INFO::Formatting Data.
2025-10-05 21:27:29.441943 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.443265 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.444839 INFO::Found 2 missing values.
2025-10-05 21:27:29.449283 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.450096 INFO::Done
2025-10-05 21:27:29.490551 INFO::Found NA in Reference column
2025-10-05 21:27:29.504602 INFO::Require at least two references per batch.
2025-10-05 21:27:29.536027 INFO::Formatting Data.
2025-10-05 21:27:29.537071 INFO::Recognized SummarizedExperiment
2025-10-05 21:27:29.537863 INFO::Typecasting input to dataframe.
2025-10-05 21:27:29.552433 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.554072 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.559628 INFO::Found 0 missing values.
2025-10-05 21:27:29.570257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.571129 INFO::Done
2025-10-05 21:27:29.594486 INFO::Formatting Data.
2025-10-05 21:27:29.595511 INFO::Recognized SummarizedExperiment
2025-10-05 21:27:29.596315 INFO::Typecasting input to dataframe.
2025-10-05 21:27:29.622835 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.624656 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.630363 INFO::Found 0 missing values.
2025-10-05 21:27:29.647974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.648906 INFO::Done
2025-10-05 21:27:29.672524 INFO::Formatting Data.
2025-10-05 21:27:29.673568 INFO::Recognized SummarizedExperiment
2025-10-05 21:27:29.674414 INFO::Typecasting input to dataframe.
2025-10-05 21:27:29.700377 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.701874 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.703519 INFO::Found 0 missing values.
2025-10-05 21:27:29.70487 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.
2025-10-05 21:27:29.711768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.7126 INFO::Done
2025-10-05 21:27:29.727218 INFO::Formatting Data.
2025-10-05 21:27:29.728445 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.729789 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.731268 INFO::Found 0 missing values.
2025-10-05 21:27:29.735734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.736565 INFO::Done
2025-10-05 21:27:29.754568 INFO::Formatting Data.
2025-10-05 21:27:29.755858 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.757242 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.7588 INFO::Found 0 missing values.
2025-10-05 21:27:29.763506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.764397 INFO::Done
2025-10-05 21:27:29.811725 INFO::Formatting Data.
2025-10-05 21:27:29.813055 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.814723 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.816628 INFO::Found 1 missing values.
2025-10-05 21:27:29.820991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.821884 INFO::Done
2025-10-05 21:27:29.849832 INFO::Formatting Data.
2025-10-05 21:27:29.850997 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.852296 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.853725 INFO::Found 2 missing values.
2025-10-05 21:27:29.855026 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.
2025-10-05 21:27:29.858527 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.85934 INFO::Done
2025-10-05 21:27:29.873264 INFO::Formatting Data.
2025-10-05 21:27:29.874294 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.875613 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.877095 INFO::Found 2 missing values.
2025-10-05 21:27:29.879526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.880347 INFO::Done
2025-10-05 21:27:29.895303 INFO::Formatting Data.
2025-10-05 21:27:29.896314 INFO::Typecasting input to dataframe.
2025-10-05 21:27:29.897412 INFO::Replacing NaNs with NAs.
2025-10-05 21:27:29.898562 INFO::Removing potential empty rows and columns
2025-10-05 21:27:29.899928 INFO::Found 0 missing values.
2025-10-05 21:27:29.904259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-05 21:27:29.905027 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
23.507 5.466 33.441
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.440 | 2.251 | 23.297 | |
| compute_asw | 0.030 | 0.001 | 0.030 | |
| count_existing | 0.016 | 0.001 | 0.018 | |
| generate_data_covariables | 0.016 | 0.000 | 0.028 | |
| generate_dataset | 0.015 | 0.001 | 0.016 | |