Yannis Schumann
| Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-03 12:07 -0400 (Wed, 03 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4826 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 163/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2025-09-02 04:21:29 -0000 (Tue, 02 Sep 2025) |
| EndedAt: 2025-09-02 04:22:49 -0000 (Tue, 02 Sep 2025) |
| EllapsedTime: 79.8 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_1.5.0.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 ‘1.5.0’
* 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 27.641 1.593 20.165
* 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 ‘1.5.0’ ** 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 4.5.0 (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")
2025-09-02 04:22:31.984103 INFO::Formatting Data.
2025-09-02 04:22:31.986696 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:32.022231 INFO::Removing potential empty rows and columns
2025-09-02 04:22:32.647001 INFO::Found 0 missing values.
2025-09-02 04:22:32.651818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:32.652696 INFO::Done
2025-09-02 04:22:32.653515 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:32.669242 INFO::Starting hierarchical adjustment
2025-09-02 04:22:32.670451 INFO::Found 3 batches.
2025-09-02 04:22:32.671233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:32.672824 INFO::Using default BPPARAM
2025-09-02 04:22:32.673671 INFO::Processing subtree level 1
2025-09-02 04:22:32.803361 INFO::Adjusting the last 1 batches sequentially
2025-09-02 04:22:32.805929 INFO::Done
2025-09-02 04:22:32.806828 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:32.810601 INFO::ASW Batch was -0.108812562729275 prior to batch effect correction and is now -0.108812562729275 .
2025-09-02 04:22:32.812333 INFO::Total function execution time is 0.829266786575317 s and adjustment time is 0.135725975036621 s ( 16.37 )
2025-09-02 04:22:32.833081 INFO::Formatting Data.
2025-09-02 04:22:32.834144 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:32.835433 INFO::Removing potential empty rows and columns
2025-09-02 04:22:32.837083 INFO::Found 0 missing values.
2025-09-02 04:22:32.838476 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-09-02 04:22:32.855148 INFO::Formatting Data.
2025-09-02 04:22:32.856215 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:32.858344 INFO::Removing potential empty rows and columns
2025-09-02 04:22:32.860133 INFO::Found 0 missing values.
2025-09-02 04:22:32.861719 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-09-02 04:22:32.886382 INFO::Formatting Data.
2025-09-02 04:22:32.887439 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:32.888728 INFO::Removing potential empty rows and columns
2025-09-02 04:22:32.890322 INFO::Found 0 missing values.
2025-09-02 04:22:32.891677 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-09-02 04:22:32.898502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:32.899436 INFO::Done
2025-09-02 04:22:32.900169 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:32.903028 INFO::Starting hierarchical adjustment
2025-09-02 04:22:32.90409 INFO::Found 2 batches.
2025-09-02 04:22:32.904914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:32.905818 INFO::Using default BPPARAM
2025-09-02 04:22:32.906588 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:32.907944 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 04:22:32.939481 INFO::Done
2025-09-02 04:22:32.94037 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:32.943104 INFO::ASW Batch was -0.0295843029021526 prior to batch effect correction and is now -0.127603508800055 .
2025-09-02 04:22:32.944216 INFO::Total function execution time is 0.0579519271850586 s and adjustment time is 0.0355789661407471 s ( 61.39 )
2025-09-02 04:22:32.948 INFO::Formatting Data.
2025-09-02 04:22:32.948992 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:32.961375 INFO::Formatting Data.
2025-09-02 04:22:32.962381 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:32.96359 INFO::Removing potential empty rows and columns
2025-09-02 04:22:32.965134 INFO::Found 0 missing values.
2025-09-02 04:22:32.969445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:32.970338 INFO::Done
2025-09-02 04:22:32.971106 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:32.974173 INFO::Starting hierarchical adjustment
2025-09-02 04:22:32.975291 INFO::Found 2 batches.
2025-09-02 04:22:32.976088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:32.977081 INFO::Using default BPPARAM
2025-09-02 04:22:32.977859 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:32.979284 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:33.04135 INFO::Done
2025-09-02 04:22:33.042245 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:33.045088 INFO::ASW Batch was 0.0433770385748948 prior to batch effect correction and is now -0.111680163090845 .
2025-09-02 04:22:33.04627 INFO::Total function execution time is 0.0849599838256836 s and adjustment time is 0.0662639141082764 s ( 77.99 )
2025-09-02 04:22:33.047796 INFO::Formatting Data.
2025-09-02 04:22:33.04865 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:33.049955 INFO::Removing potential empty rows and columns
2025-09-02 04:22:33.051435 INFO::Found 0 missing values.
2025-09-02 04:22:33.05559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:33.056442 INFO::Done
2025-09-02 04:22:33.057264 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:33.060023 INFO::Starting hierarchical adjustment
2025-09-02 04:22:33.061126 INFO::Found 2 batches.
2025-09-02 04:22:33.061893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:33.06274 INFO::Using default BPPARAM
2025-09-02 04:22:33.063462 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:33.064834 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:33.086273 INFO::Done
2025-09-02 04:22:33.087163 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:33.089982 INFO::ASW Batch was 0.0433770385748948 prior to batch effect correction and is now -0.111680163090845 .
2025-09-02 04:22:33.091087 INFO::Total function execution time is 0.0432651042938232 s and adjustment time is 0.0253772735595703 s ( 58.66 )
2025-09-02 04:22:37.21023 INFO::Formatting Data.
2025-09-02 04:22:37.211227 INFO::Recognized SummarizedExperiment
2025-09-02 04:22:37.211876 INFO::Typecasting input to dataframe.
2025-09-02 04:22:37.255556 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:37.257217 INFO::Removing potential empty rows and columns
2025-09-02 04:22:37.262431 INFO::Found 0 missing values.
2025-09-02 04:22:37.272643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:37.273596 INFO::Done
2025-09-02 04:22:37.274327 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:37.279593 INFO::Starting hierarchical adjustment
2025-09-02 04:22:37.280722 INFO::Found 2 batches.
2025-09-02 04:22:37.281518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:37.282962 INFO::Using default BPPARAM
2025-09-02 04:22:37.283701 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:37.285064 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 04:22:37.364136 INFO::Done
2025-09-02 04:22:37.365144 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:37.370258 INFO::ASW Batch was 0.0121723837152456 prior to batch effect correction and is now -0.0916823276107927 .
2025-09-02 04:22:37.371537 INFO::Total function execution time is 0.161925792694092 s and adjustment time is 0.0836038589477539 s ( 51.63 )
2025-09-02 04:22:37.398249 INFO::Formatting Data.
2025-09-02 04:22:37.399206 INFO::Recognized SummarizedExperiment
2025-09-02 04:22:37.399966 INFO::Typecasting input to dataframe.
2025-09-02 04:22:37.413082 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:37.414635 INFO::Removing potential empty rows and columns
2025-09-02 04:22:37.419909 INFO::Found 0 missing values.
2025-09-02 04:22:37.430171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:37.431059 INFO::Done
2025-09-02 04:22:37.431785 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:37.436691 INFO::Starting hierarchical adjustment
2025-09-02 04:22:37.437869 INFO::Found 2 batches.
2025-09-02 04:22:37.438618 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:37.439466 INFO::Using default BPPARAM
2025-09-02 04:22:37.440183 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:37.44159 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 04:22:37.476406 INFO::Done
2025-09-02 04:22:37.477371 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:37.482322 INFO::ASW Batch was 0.0282352544483969 prior to batch effect correction and is now 0.0282352544483969 .
2025-09-02 04:22:37.483581 INFO::Total function execution time is 0.085310697555542 s and adjustment time is 0.0387229919433594 s ( 45.39 )
2025-09-02 04:22:37.508947 INFO::Formatting Data.
2025-09-02 04:22:37.509944 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:37.511118 INFO::Removing potential empty rows and columns
2025-09-02 04:22:37.512502 INFO::Found 0 missing values.
2025-09-02 04:22:37.516708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:37.517677 INFO::Done
2025-09-02 04:22:37.518433 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:37.521189 INFO::Starting hierarchical adjustment
2025-09-02 04:22:37.522227 INFO::Found 3 batches.
2025-09-02 04:22:37.522966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:37.523813 INFO::Using default BPPARAM
2025-09-02 04:22:37.524569 INFO::Processing subtree level 1
2025-09-02 04:22:37.695479 INFO::Adjusting the last 1 batches sequentially
2025-09-02 04:22:37.698163 INFO::Done
2025-09-02 04:22:37.699199 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:37.702959 INFO::ASW Batch was -0.0351804610599064 prior to batch effect correction and is now -0.163408921496046 .
2025-09-02 04:22:37.704466 INFO::Total function execution time is 0.195542573928833 s and adjustment time is 0.176076173782349 s ( 90.04 )
2025-09-02 04:22:37.725532 INFO::Skipping initial DF formatting
2025-09-02 04:22:37.726517 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:37.732323 INFO::Starting hierarchical adjustment
2025-09-02 04:22:37.733635 INFO::Found 5 batches.
2025-09-02 04:22:37.734503 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:37.735425 INFO::Using default BPPARAM
2025-09-02 04:22:37.736259 INFO::Processing subtree level 1
2025-09-02 04:22:38.001175 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:38.003584 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 04:22:38.033808 INFO::Done
2025-09-02 04:22:38.035065 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:38.041666 INFO::ASW Batch was 0.628174012318689 prior to batch effect correction and is now 0.628174012318689 .
2025-09-02 04:22:38.042759 INFO::ASW Label was 0.351815758729806 prior to batch effect correction and is now 0.351815758729806 .
2025-09-02 04:22:38.044134 INFO::Total function execution time is 0.318609476089478 s and adjustment time is 0.300389528274536 s ( 94.28 )
2025-09-02 04:22:38.146512 INFO::Formatting Data.
2025-09-02 04:22:38.147761 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:38.149311 INFO::Removing potential empty rows and columns
2025-09-02 04:22:38.151045 INFO::Found 0 missing values.
2025-09-02 04:22:38.158058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:38.159049 INFO::Done
2025-09-02 04:22:38.159863 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:38.164589 INFO::Starting hierarchical adjustment
2025-09-02 04:22:38.16597 INFO::Found 5 batches.
2025-09-02 04:22:38.166911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:38.167915 INFO::Using default BPPARAM
2025-09-02 04:22:38.168866 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:38.34091 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:38.343555 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:38.371525 INFO::Done
2025-09-02 04:22:38.372513 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:38.377694 INFO::ASW Batch was 0.336971339402311 prior to batch effect correction and is now -0.101952890564072 .
2025-09-02 04:22:38.378681 INFO::ASW Label was 0.447980670719379 prior to batch effect correction and is now 0.887391528037951 .
2025-09-02 04:22:38.379908 INFO::Total function execution time is 0.233494758605957 s and adjustment time is 0.205804824829102 s ( 88.14 )
2025-09-02 04:22:38.381297 INFO::Formatting Data.
2025-09-02 04:22:38.382254 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:38.383593 INFO::Removing potential empty rows and columns
2025-09-02 04:22:38.385306 INFO::Found 0 missing values.
2025-09-02 04:22:38.392274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:38.393343 INFO::Done
2025-09-02 04:22:38.394288 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:38.398923 INFO::Starting hierarchical adjustment
2025-09-02 04:22:38.400067 INFO::Found 5 batches.
2025-09-02 04:22:38.400907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:38.401837 INFO::Using default BPPARAM
2025-09-02 04:22:38.402642 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:38.569452 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:38.57163 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:38.596133 INFO::Done
2025-09-02 04:22:38.597213 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:38.602011 INFO::ASW Batch was 0.336971339402311 prior to batch effect correction and is now -0.101952890564072 .
2025-09-02 04:22:38.602973 INFO::ASW Label was 0.447980670719379 prior to batch effect correction and is now 0.887391528037951 .
2025-09-02 04:22:38.60415 INFO::Total function execution time is 0.222843408584595 s and adjustment time is 0.196219205856323 s ( 88.05 )
2025-09-02 04:22:38.624705 INFO::Formatting Data.
2025-09-02 04:22:38.625832 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:38.627137 INFO::Removing potential empty rows and columns
2025-09-02 04:22:38.628667 INFO::Found 0 missing values.
2025-09-02 04:22:38.634983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:38.635919 INFO::Done
2025-09-02 04:22:38.636691 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:38.641103 INFO::Starting hierarchical adjustment
2025-09-02 04:22:38.6423 INFO::Found 5 batches.
2025-09-02 04:22:38.643128 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:38.644028 INFO::Using default BPPARAM
2025-09-02 04:22:38.644846 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:38.799087 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:38.801412 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:38.82468 INFO::Done
2025-09-02 04:22:38.82567 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:38.830552 INFO::ASW Batch was 0.427988400425301 prior to batch effect correction and is now -0.087725594840736 .
2025-09-02 04:22:38.831582 INFO::ASW Label was 0.195115029329761 prior to batch effect correction and is now 0.825576497244702 .
2025-09-02 04:22:38.832899 INFO::Total function execution time is 0.208165645599365 s and adjustment time is 0.182587385177612 s ( 87.71 )
2025-09-02 04:22:38.834235 INFO::Formatting Data.
2025-09-02 04:22:38.835262 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:38.836651 INFO::Removing potential empty rows and columns
2025-09-02 04:22:38.838354 INFO::Found 0 missing values.
2025-09-02 04:22:38.845169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:38.846177 INFO::Done
2025-09-02 04:22:38.847009 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:38.851681 INFO::Starting hierarchical adjustment
2025-09-02 04:22:38.853033 INFO::Found 5 batches.
2025-09-02 04:22:38.853922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:38.854871 INFO::Using default BPPARAM
2025-09-02 04:22:38.855696 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:39.015031 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:39.017509 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:39.043902 INFO::Done
2025-09-02 04:22:39.045104 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:39.050117 INFO::ASW Batch was 0.427988400425301 prior to batch effect correction and is now -0.087725594840736 .
2025-09-02 04:22:39.051126 INFO::ASW Label was 0.195115029329761 prior to batch effect correction and is now 0.825576497244702 .
2025-09-02 04:22:39.052487 INFO::Total function execution time is 0.218248605728149 s and adjustment time is 0.191156387329102 s ( 87.59 )
2025-09-02 04:22:39.081264 INFO::Formatting Data.
2025-09-02 04:22:39.082506 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:39.083955 INFO::Removing potential empty rows and columns
2025-09-02 04:22:39.085752 INFO::Found 0 missing values.
2025-09-02 04:22:39.090608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:39.091637 INFO::Done
2025-09-02 04:22:39.092494 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:39.097344 INFO::Starting hierarchical adjustment
2025-09-02 04:22:39.098626 INFO::Found 2 batches.
2025-09-02 04:22:39.099511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:39.1005 INFO::Using default BPPARAM
2025-09-02 04:22:39.10145 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:39.10296 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:39.127436 INFO::Done
2025-09-02 04:22:39.128486 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:39.133487 INFO::ASW Batch was 0.466277564430207 prior to batch effect correction and is now -0.00757926012528663 .
2025-09-02 04:22:39.13458 INFO::ASW Label was 0.485128414804514 prior to batch effect correction and is now 0.876155193517843 .
2025-09-02 04:22:39.135856 INFO::Total function execution time is 0.0546877384185791 s and adjustment time is 0.0290462970733643 s ( 53.11 )
2025-09-02 04:22:39.13724 INFO::Formatting Data.
2025-09-02 04:22:39.138315 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:39.139808 INFO::Removing potential empty rows and columns
2025-09-02 04:22:39.141589 INFO::Found 0 missing values.
2025-09-02 04:22:39.146497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:39.147589 INFO::Done
2025-09-02 04:22:39.148517 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:39.153545 INFO::Starting hierarchical adjustment
2025-09-02 04:22:39.154902 INFO::Found 2 batches.
2025-09-02 04:22:39.155896 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:39.156996 INFO::Using default BPPARAM
2025-09-02 04:22:39.157927 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:39.159498 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-02 04:22:39.184378 INFO::Done
2025-09-02 04:22:39.185571 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:39.19064 INFO::ASW Batch was 0.466277564430207 prior to batch effect correction and is now -0.00757926012528663 .
2025-09-02 04:22:39.191734 INFO::ASW Label was 0.485128414804514 prior to batch effect correction and is now 0.876155193517843 .
2025-09-02 04:22:39.193159 INFO::Total function execution time is 0.0559229850769043 s and adjustment time is 0.0297143459320068 s ( 53.13 )
2025-09-02 04:22:39.211768 INFO::Formatting Data.
2025-09-02 04:22:39.213004 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:39.214595 INFO::Removing potential empty rows and columns
2025-09-02 04:22:39.216296 INFO::Found 0 missing values.
2025-09-02 04:22:39.220035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:39.22109 INFO::Done
2025-09-02 04:22:39.221988 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:39.225209 INFO::Starting hierarchical adjustment
2025-09-02 04:22:39.226531 INFO::Found 2 batches.
2025-09-02 04:22:39.227453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:39.22851 INFO::Using default BPPARAM
2025-09-02 04:22:39.229518 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:39.23113 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 04:22:39.283738 INFO::Done
2025-09-02 04:22:39.28492 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:39.288147 INFO::ASW Batch was 0.105267414900906 prior to batch effect correction and is now -0.161464524462348 .
2025-09-02 04:22:39.289689 INFO::Total function execution time is 0.0779438018798828 s and adjustment time is 0.0574429035186768 s ( 73.7 )
2025-09-02 04:22:39.309455 INFO::Formatting Data.
2025-09-02 04:22:39.310698 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:39.312178 INFO::Removing potential empty rows and columns
2025-09-02 04:22:39.314018 INFO::Found 0 missing values.
2025-09-02 04:22:39.315983 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-09-02 04:22:39.324223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:39.325335 INFO::Done
2025-09-02 04:22:39.326256 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:39.331064 INFO::Starting hierarchical adjustment
2025-09-02 04:22:39.332362 INFO::Found 2 batches.
2025-09-02 04:22:39.333354 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:39.334369 INFO::Using default BPPARAM
2025-09-02 04:22:39.335228 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:39.336819 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 04:22:39.364078 INFO::Done
2025-09-02 04:22:39.365234 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:39.370098 INFO::ASW Batch was 0.637092176996533 prior to batch effect correction and is now -0.0293746165876163 .
2025-09-02 04:22:39.371145 INFO::ASW Label was 0.432701889641691 prior to batch effect correction and is now 0.920442626530814 .
2025-09-02 04:22:39.372444 INFO::Total function execution time is 0.0630514621734619 s and adjustment time is 0.0319528579711914 s ( 50.68 )
2025-09-02 04:22:39.373831 INFO::Formatting Data.
2025-09-02 04:22:39.374925 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:39.376466 INFO::Removing potential empty rows and columns
2025-09-02 04:22:39.37822 INFO::Found 0 missing values.
2025-09-02 04:22:39.379759 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-09-02 04:22:39.387853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:39.388995 INFO::Done
2025-09-02 04:22:39.389903 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:39.39482 INFO::Starting hierarchical adjustment
2025-09-02 04:22:39.39607 INFO::Found 2 batches.
2025-09-02 04:22:39.397048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:39.398023 INFO::Using default BPPARAM
2025-09-02 04:22:39.398876 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:39.400456 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 04:22:39.426848 INFO::Done
2025-09-02 04:22:39.427915 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:39.433016 INFO::ASW Batch was 0.637092176996533 prior to batch effect correction and is now -0.0293746165876163 .
2025-09-02 04:22:39.43415 INFO::ASW Label was 0.432701889641691 prior to batch effect correction and is now 0.920442626530814 .
2025-09-02 04:22:39.435559 INFO::Total function execution time is 0.0617213249206543 s and adjustment time is 0.0309915542602539 s ( 50.21 )
2025-09-02 04:22:39.755711 INFO::Formatting Data.
2025-09-02 04:22:39.756877 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:39.758083 INFO::Removing potential empty rows and columns
2025-09-02 04:22:39.759523 INFO::Found 0 missing values.
2025-09-02 04:22:39.763931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:39.764793 INFO::Done
2025-09-02 04:22:39.765563 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:39.768463 INFO::Starting hierarchical adjustment
2025-09-02 04:22:39.769521 INFO::Found 3 batches.
2025-09-02 04:22:39.770262 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:39.771165 INFO::Using default BPPARAM
2025-09-02 04:22:39.771904 INFO::Processing subtree level 1
2025-09-02 04:22:39.892873 INFO::Adjusting the last 1 batches sequentially
2025-09-02 04:22:39.895382 INFO::Done
2025-09-02 04:22:39.896348 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:39.900033 INFO::ASW Batch was -0.147996415409251 prior to batch effect correction and is now -0.147996415409251 .
2025-09-02 04:22:39.901666 INFO::Total function execution time is 0.146121740341187 s and adjustment time is 0.126023054122925 s ( 86.25 )
2025-09-02 04:22:39.903309 INFO::Formatting Data.
2025-09-02 04:22:39.904341 INFO::Typecasting input to dataframe.
2025-09-02 04:22:39.905683 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:39.907116 INFO::Removing potential empty rows and columns
2025-09-02 04:22:39.908883 INFO::Found 0 missing values.
2025-09-02 04:22:39.913672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:39.914801 INFO::Done
2025-09-02 04:22:39.915616 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:39.918386 INFO::Starting hierarchical adjustment
2025-09-02 04:22:39.919439 INFO::Found 3 batches.
2025-09-02 04:22:39.92019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:39.921326 INFO::Using default BPPARAM
2025-09-02 04:22:39.922173 INFO::Processing subtree level 1
2025-09-02 04:22:40.030493 INFO::Adjusting the last 1 batches sequentially
2025-09-02 04:22:40.032945 INFO::Done
2025-09-02 04:22:40.033825 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:40.037405 INFO::ASW Batch was -0.147996415409251 prior to batch effect correction and is now -0.147996415409251 .
2025-09-02 04:22:40.038836 INFO::Total function execution time is 0.135538816452026 s and adjustment time is 0.113623857498169 s ( 83.83 )
2025-09-02 04:22:40.057324 INFO::Formatting Data.
2025-09-02 04:22:40.058336 INFO::Typecasting input to dataframe.
2025-09-02 04:22:40.059479 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:40.060703 INFO::Removing potential empty rows and columns
2025-09-02 04:22:40.062251 INFO::Found 0 missing values.
2025-09-02 04:22:40.066647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:40.067529 INFO::Done
2025-09-02 04:22:40.06829 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:40.071147 INFO::Starting hierarchical adjustment
2025-09-02 04:22:40.072189 INFO::Found 3 batches.
2025-09-02 04:22:40.073022 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:40.073924 INFO::Using default BPPARAM
2025-09-02 04:22:40.074683 INFO::Processing subtree level 1
2025-09-02 04:22:40.187792 INFO::Adjusting the last 1 batches sequentially
2025-09-02 04:22:40.190188 INFO::Done
2025-09-02 04:22:40.191007 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:40.194398 INFO::ASW Batch was -0.0187023499271121 prior to batch effect correction and is now -0.0187023499271121 .
2025-09-02 04:22:40.195729 INFO::Total function execution time is 0.138440847396851 s and adjustment time is 0.118223190307617 s ( 85.4 )
2025-09-02 04:22:40.381532 INFO::Formatting Data.
2025-09-02 04:22:40.382571 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:40.384042 INFO::Removing potential empty rows and columns
2025-09-02 04:22:40.387895 INFO::Found 1000 missing values.
2025-09-02 04:22:40.414978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:40.415964 INFO::Done
2025-09-02 04:22:40.416865 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:40.424452 INFO::Starting hierarchical adjustment
2025-09-02 04:22:40.42572 INFO::Found 10 batches.
2025-09-02 04:22:40.426527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:40.427413 INFO::Using default BPPARAM
2025-09-02 04:22:40.428188 INFO::Processing subtree level 1
2025-09-02 04:22:40.591496 INFO::Processing subtree level 2
2025-09-02 04:22:40.775751 INFO::Adjusting the last 1 batches sequentially
2025-09-02 04:22:40.778485 INFO::Done
2025-09-02 04:22:40.779377 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:40.787303 INFO::ASW Batch was 0.437026734894492 prior to batch effect correction and is now 0.437026734894492 .
2025-09-02 04:22:40.788303 INFO::ASW Label was 0.339055253338086 prior to batch effect correction and is now 0.339055253338086 .
2025-09-02 04:22:40.789737 INFO::Total function execution time is 0.408198356628418 s and adjustment time is 0.353025197982788 s ( 86.48 )
2025-09-02 04:22:40.791008 INFO::Formatting Data.
2025-09-02 04:22:40.791933 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:40.793735 INFO::Removing potential empty rows and columns
2025-09-02 04:22:40.797851 INFO::Found 1000 missing values.
2025-09-02 04:22:40.825254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:40.82626 INFO::Done
2025-09-02 04:22:40.827034 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:40.834895 INFO::Starting hierarchical adjustment
2025-09-02 04:22:40.83615 INFO::Found 10 batches.
2025-09-02 04:22:42.139531 INFO::Set up parallel execution backend with 2 workers
2025-09-02 04:22:42.146637 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-02 04:22:43.548445 INFO::Adjusting the last 2 batches sequentially
2025-09-02 04:22:43.55106 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-02 04:22:43.577779 INFO::Done
2025-09-02 04:22:43.578754 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:43.586209 INFO::ASW Batch was 0.437026734894492 prior to batch effect correction and is now 0.437026734894492 .
2025-09-02 04:22:43.587217 INFO::ASW Label was 0.339055253338086 prior to batch effect correction and is now 0.339055253338086 .
2025-09-02 04:22:43.588482 INFO::Total function execution time is 2.79744982719421 s and adjustment time is 2.74185085296631 s ( 98.01 )
2025-09-02 04:22:43.780943 INFO::Formatting Data.
2025-09-02 04:22:43.781969 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:43.783236 INFO::Removing potential empty rows and columns
2025-09-02 04:22:43.784795 INFO::Found 0 missing values.
2025-09-02 04:22:43.790294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:43.791152 INFO::Done
2025-09-02 04:22:43.791894 INFO::Acquiring quality metrics before batch effect correction.
2025-09-02 04:22:43.795738 INFO::Starting hierarchical adjustment
2025-09-02 04:22:43.79687 INFO::Found 3 batches.
2025-09-02 04:22:43.797646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-02 04:22:43.79854 INFO::Using default BPPARAM
2025-09-02 04:22:43.799309 INFO::Processing subtree level 1
2025-09-02 04:22:43.932008 INFO::Adjusting the last 1 batches sequentially
2025-09-02 04:22:43.934348 INFO::Done
2025-09-02 04:22:43.935195 INFO::Acquiring quality metrics after batch effect correction.
2025-09-02 04:22:43.93973 INFO::ASW Batch was 0.309457283211749 prior to batch effect correction and is now -0.126914771529328 .
2025-09-02 04:22:43.940734 INFO::ASW Label was -0.218431192933613 prior to batch effect correction and is now -0.0235790560366626 .
2025-09-02 04:22:43.94207 INFO::Total function execution time is 0.1612229347229 s and adjustment time is 0.137749433517456 s ( 85.44 )
2025-09-02 04:22:44.114765 INFO::Formatting Data.
2025-09-02 04:22:44.115845 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.117133 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.118659 INFO::Found 2 missing values.
2025-09-02 04:22:44.122963 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.123889 INFO::Done
2025-09-02 04:22:44.163191 INFO::Found NA in Reference column
2025-09-02 04:22:44.176574 INFO::Require at least two references per batch.
2025-09-02 04:22:44.206057 INFO::Formatting Data.
2025-09-02 04:22:44.206982 INFO::Recognized SummarizedExperiment
2025-09-02 04:22:44.207701 INFO::Typecasting input to dataframe.
2025-09-02 04:22:44.221889 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.223472 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.228646 INFO::Found 0 missing values.
2025-09-02 04:22:44.238991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.239928 INFO::Done
2025-09-02 04:22:44.262052 INFO::Formatting Data.
2025-09-02 04:22:44.263019 INFO::Recognized SummarizedExperiment
2025-09-02 04:22:44.263776 INFO::Typecasting input to dataframe.
2025-09-02 04:22:44.290199 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.291825 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.297063 INFO::Found 0 missing values.
2025-09-02 04:22:44.314056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.314951 INFO::Done
2025-09-02 04:22:44.346923 INFO::Formatting Data.
2025-09-02 04:22:44.348024 INFO::Recognized SummarizedExperiment
2025-09-02 04:22:44.348803 INFO::Typecasting input to dataframe.
2025-09-02 04:22:44.374938 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.376319 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.377907 INFO::Found 0 missing values.
2025-09-02 04:22:44.379136 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-09-02 04:22:44.385605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.38648 INFO::Done
2025-09-02 04:22:44.40156 INFO::Formatting Data.
2025-09-02 04:22:44.402617 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.403847 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.405332 INFO::Found 0 missing values.
2025-09-02 04:22:44.40969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.410564 INFO::Done
2025-09-02 04:22:44.426864 INFO::Formatting Data.
2025-09-02 04:22:44.427847 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.429103 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.430566 INFO::Found 0 missing values.
2025-09-02 04:22:44.435011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.435886 INFO::Done
2025-09-02 04:22:44.481971 INFO::Formatting Data.
2025-09-02 04:22:44.483088 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.484578 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.48643 INFO::Found 1 missing values.
2025-09-02 04:22:44.490507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.491477 INFO::Done
2025-09-02 04:22:44.520948 INFO::Formatting Data.
2025-09-02 04:22:44.521992 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.523149 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.524505 INFO::Found 2 missing values.
2025-09-02 04:22:44.525798 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-09-02 04:22:44.529181 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.530117 INFO::Done
2025-09-02 04:22:44.54465 INFO::Formatting Data.
2025-09-02 04:22:44.545817 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.547064 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.548409 INFO::Found 2 missing values.
2025-09-02 04:22:44.550817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.551645 INFO::Done
2025-09-02 04:22:44.567179 INFO::Formatting Data.
2025-09-02 04:22:44.568213 INFO::Typecasting input to dataframe.
2025-09-02 04:22:44.569366 INFO::Replacing NaNs with NAs.
2025-09-02 04:22:44.570554 INFO::Removing potential empty rows and columns
2025-09-02 04:22:44.571979 INFO::Found 0 missing values.
2025-09-02 04:22:44.576102 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-02 04:22:44.576925 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.937 5.120 25.804
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.641 | 1.593 | 20.165 | |
| compute_asw | 0.033 | 0.000 | 0.033 | |
| count_existing | 0.017 | 0.000 | 0.017 | |
| generate_data_covariables | 0.015 | 0.000 | 0.015 | |
| generate_dataset | 0.015 | 0.000 | 0.015 | |