Yannis Schumann
| Snapshot Date: 2025-11-07 13:40 -0500 (Fri, 07 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-08 11:32 -0500 (Sat, 08 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4821 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2025-11-07 21:17:33 -0500 (Fri, 07 Nov 2025) |
| EndedAt: 2025-11-07 21:19:05 -0500 (Fri, 07 Nov 2025) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.7.0’
* 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 23.715 1.434 17.574
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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")
2025-11-07 21:18:26.255325 INFO::Formatting Data.
2025-11-07 21:18:26.256766 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:26.26849 INFO::Removing potential empty rows and columns
2025-11-07 21:18:26.525689 INFO::Found 0 missing values.
2025-11-07 21:18:26.529278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:26.530011 INFO::Done
2025-11-07 21:18:26.530596 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:26.542603 INFO::Starting hierarchical adjustment
2025-11-07 21:18:26.543566 INFO::Found 3 batches.
2025-11-07 21:18:26.544169 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:26.545369 INFO::Using default BPPARAM
2025-11-07 21:18:26.545937 INFO::Processing subtree level 1
2025-11-07 21:18:26.651699 INFO::Adjusting the last 1 batches sequentially
2025-11-07 21:18:26.653696 INFO::Done
2025-11-07 21:18:26.654506 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:26.657498 INFO::ASW Batch was -0.0664547304527257 prior to batch effect correction and is now -0.0664547304527257 .
2025-11-07 21:18:26.658751 INFO::Total function execution time is 0.404089450836182 s and adjustment time is 0.11030650138855 s ( 27.3 )
2025-11-07 21:18:26.674154 INFO::Formatting Data.
2025-11-07 21:18:26.675034 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:26.676055 INFO::Removing potential empty rows and columns
2025-11-07 21:18:26.677225 INFO::Found 0 missing values.
2025-11-07 21:18:26.678273 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.
2025-11-07 21:18:26.690984 INFO::Formatting Data.
2025-11-07 21:18:26.691931 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:26.693035 INFO::Removing potential empty rows and columns
2025-11-07 21:18:26.694355 INFO::Found 0 missing values.
2025-11-07 21:18:26.695495 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.
2025-11-07 21:18:26.714411 INFO::Formatting Data.
2025-11-07 21:18:26.715269 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:26.716214 INFO::Removing potential empty rows and columns
2025-11-07 21:18:26.717327 INFO::Found 0 missing values.
2025-11-07 21:18:26.718314 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.
2025-11-07 21:18:26.723018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:26.723589 INFO::Done
2025-11-07 21:18:26.724164 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:26.726364 INFO::Starting hierarchical adjustment
2025-11-07 21:18:26.727106 INFO::Found 2 batches.
2025-11-07 21:18:26.727666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:26.728356 INFO::Using default BPPARAM
2025-11-07 21:18:26.72891 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:26.729897 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-07 21:18:26.753002 INFO::Done
2025-11-07 21:18:26.753816 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:26.756096 INFO::ASW Batch was 0.0231074242466305 prior to batch effect correction and is now -0.114967272420182 .
2025-11-07 21:18:26.756979 INFO::Total function execution time is 0.0426490306854248 s and adjustment time is 0.0259995460510254 s ( 60.96 )
2025-11-07 21:18:26.759982 INFO::Formatting Data.
2025-11-07 21:18:26.760648 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:26.769773 INFO::Formatting Data.
2025-11-07 21:18:26.771336 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:26.772341 INFO::Removing potential empty rows and columns
2025-11-07 21:18:26.773448 INFO::Found 0 missing values.
2025-11-07 21:18:26.776591 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:26.777177 INFO::Done
2025-11-07 21:18:26.777728 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:26.780106 INFO::Starting hierarchical adjustment
2025-11-07 21:18:26.780863 INFO::Found 2 batches.
2025-11-07 21:18:26.781422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:26.782089 INFO::Using default BPPARAM
2025-11-07 21:18:26.782634 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:26.783726 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-07 21:18:26.829455 INFO::Done
2025-11-07 21:18:26.830164 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:26.83215 INFO::ASW Batch was 0.0218801524273081 prior to batch effect correction and is now -0.092758498642275 .
2025-11-07 21:18:26.832941 INFO::Total function execution time is 0.0632190704345703 s and adjustment time is 0.048741340637207 s ( 77.1 )
2025-11-07 21:18:26.833964 INFO::Formatting Data.
2025-11-07 21:18:26.834586 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:26.835464 INFO::Removing potential empty rows and columns
2025-11-07 21:18:26.836463 INFO::Found 0 missing values.
2025-11-07 21:18:26.83917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:26.83972 INFO::Done
2025-11-07 21:18:26.84023 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:26.84214 INFO::Starting hierarchical adjustment
2025-11-07 21:18:26.842825 INFO::Found 2 batches.
2025-11-07 21:18:26.843347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:26.843945 INFO::Using default BPPARAM
2025-11-07 21:18:26.844469 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:26.845371 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-07 21:18:26.859538 INFO::Done
2025-11-07 21:18:26.860207 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:26.862139 INFO::ASW Batch was 0.0218801524273081 prior to batch effect correction and is now -0.092758498642275 .
2025-11-07 21:18:26.862906 INFO::Total function execution time is 0.0289373397827148 s and adjustment time is 0.0168423652648926 s ( 58.2 )
2025-11-07 21:18:29.832181 INFO::Formatting Data.
2025-11-07 21:18:29.832928 INFO::Recognized SummarizedExperiment
2025-11-07 21:18:29.833414 INFO::Typecasting input to dataframe.
2025-11-07 21:18:29.861255 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:29.862398 INFO::Removing potential empty rows and columns
2025-11-07 21:18:29.865296 INFO::Found 0 missing values.
2025-11-07 21:18:29.870808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:29.87135 INFO::Done
2025-11-07 21:18:29.871815 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:29.874782 INFO::Starting hierarchical adjustment
2025-11-07 21:18:29.87541 INFO::Found 2 batches.
2025-11-07 21:18:29.875879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:29.876786 INFO::Using default BPPARAM
2025-11-07 21:18:29.87727 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:29.878138 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-07 21:18:29.92308 INFO::Done
2025-11-07 21:18:29.923733 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:29.926728 INFO::ASW Batch was 0.0148241626757501 prior to batch effect correction and is now -0.0865487356463167 .
2025-11-07 21:18:29.92751 INFO::Total function execution time is 0.0956175327301025 s and adjustment time is 0.0477626323699951 s ( 49.95 )
2025-11-07 21:18:29.943304 INFO::Formatting Data.
2025-11-07 21:18:29.943973 INFO::Recognized SummarizedExperiment
2025-11-07 21:18:29.944446 INFO::Typecasting input to dataframe.
2025-11-07 21:18:29.952366 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:29.953343 INFO::Removing potential empty rows and columns
2025-11-07 21:18:29.956295 INFO::Found 0 missing values.
2025-11-07 21:18:29.961966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:29.962464 INFO::Done
2025-11-07 21:18:29.962934 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:29.965886 INFO::Starting hierarchical adjustment
2025-11-07 21:18:29.966502 INFO::Found 2 batches.
2025-11-07 21:18:29.966972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:29.967495 INFO::Using default BPPARAM
2025-11-07 21:18:29.967957 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:29.96881 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-07 21:18:29.989821 INFO::Done
2025-11-07 21:18:29.990495 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:29.993949 INFO::ASW Batch was 0.00627352193844922 prior to batch effect correction and is now 0.00627352193844922 .
2025-11-07 21:18:29.994749 INFO::Total function execution time is 0.0514202117919922 s and adjustment time is 0.0234313011169434 s ( 45.57 )
2025-11-07 21:18:30.012293 INFO::Formatting Data.
2025-11-07 21:18:30.013106 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:30.014005 INFO::Removing potential empty rows and columns
2025-11-07 21:18:30.015023 INFO::Found 0 missing values.
2025-11-07 21:18:30.017907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:30.018439 INFO::Done
2025-11-07 21:18:30.019036 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:30.021026 INFO::Starting hierarchical adjustment
2025-11-07 21:18:30.021738 INFO::Found 3 batches.
2025-11-07 21:18:30.022276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:30.022876 INFO::Using default BPPARAM
2025-11-07 21:18:30.023416 INFO::Processing subtree level 1
2025-11-07 21:18:30.161293 INFO::Adjusting the last 1 batches sequentially
2025-11-07 21:18:30.163415 INFO::Done
2025-11-07 21:18:30.164196 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:30.167055 INFO::ASW Batch was -0.134675864961211 prior to batch effect correction and is now -0.188698609836621 .
2025-11-07 21:18:30.168102 INFO::Total function execution time is 0.155789136886597 s and adjustment time is 0.141773223876953 s ( 91 )
2025-11-07 21:18:30.183424 INFO::Skipping initial DF formatting
2025-11-07 21:18:30.184227 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:30.188532 INFO::Starting hierarchical adjustment
2025-11-07 21:18:30.189427 INFO::Found 5 batches.
2025-11-07 21:18:30.190027 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:30.190679 INFO::Using default BPPARAM
2025-11-07 21:18:30.191231 INFO::Processing subtree level 1
2025-11-07 21:18:30.315945 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:30.317717 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-07 21:18:30.337468 INFO::Done
2025-11-07 21:18:30.338233 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:30.342613 INFO::ASW Batch was 0.561702406668957 prior to batch effect correction and is now 0.561702406668957 .
2025-11-07 21:18:30.343264 INFO::ASW Label was 0.321273442045359 prior to batch effect correction and is now 0.321273442045359 .
2025-11-07 21:18:30.344154 INFO::Total function execution time is 0.16085958480835 s and adjustment time is 0.148220062255859 s ( 92.14 )
2025-11-07 21:18:30.362042 INFO::Formatting Data.
2025-11-07 21:18:30.362886 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:30.363816 INFO::Removing potential empty rows and columns
2025-11-07 21:18:30.364825 INFO::Found 0 missing values.
2025-11-07 21:18:30.368833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:30.369397 INFO::Done
2025-11-07 21:18:30.369949 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:30.372945 INFO::Starting hierarchical adjustment
2025-11-07 21:18:30.373654 INFO::Found 5 batches.
2025-11-07 21:18:30.374234 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:30.374886 INFO::Using default BPPARAM
2025-11-07 21:18:30.375421 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.
2025-11-07 21:18:30.481749 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:30.483534 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-07 21:18:30.500565 INFO::Done
2025-11-07 21:18:30.501366 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:30.504725 INFO::ASW Batch was 0.505639780121154 prior to batch effect correction and is now 0.00069660210644534 .
2025-11-07 21:18:30.505351 INFO::ASW Label was 0.328880163827494 prior to batch effect correction and is now 0.78044526412699 .
2025-11-07 21:18:30.506224 INFO::Total function execution time is 0.144280195236206 s and adjustment time is 0.12699556350708 s ( 88.02 )
2025-11-07 21:18:30.507098 INFO::Formatting Data.
2025-11-07 21:18:30.507727 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:30.508643 INFO::Removing potential empty rows and columns
2025-11-07 21:18:30.50965 INFO::Found 0 missing values.
2025-11-07 21:18:30.513821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:30.514418 INFO::Done
2025-11-07 21:18:30.514975 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:30.518091 INFO::Starting hierarchical adjustment
2025-11-07 21:18:30.518823 INFO::Found 5 batches.
2025-11-07 21:18:30.51937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:30.520045 INFO::Using default BPPARAM
2025-11-07 21:18:30.520607 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.
2025-11-07 21:18:30.632086 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:30.63382 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-07 21:18:30.650395 INFO::Done
2025-11-07 21:18:30.651199 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:30.654569 INFO::ASW Batch was 0.505639780121154 prior to batch effect correction and is now 0.00069660210644534 .
2025-11-07 21:18:30.655206 INFO::ASW Label was 0.328880163827494 prior to batch effect correction and is now 0.78044526412699 .
2025-11-07 21:18:30.656078 INFO::Total function execution time is 0.14898157119751 s and adjustment time is 0.131673336029053 s ( 88.38 )
2025-11-07 21:18:30.670052 INFO::Formatting Data.
2025-11-07 21:18:30.670926 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:30.671905 INFO::Removing potential empty rows and columns
2025-11-07 21:18:30.672977 INFO::Found 0 missing values.
2025-11-07 21:18:30.677202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:30.677768 INFO::Done
2025-11-07 21:18:30.678315 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:30.681622 INFO::Starting hierarchical adjustment
2025-11-07 21:18:30.682415 INFO::Found 5 batches.
2025-11-07 21:18:30.682979 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:30.683643 INFO::Using default BPPARAM
2025-11-07 21:18:30.684209 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.
2025-11-07 21:18:30.798394 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:30.800135 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-07 21:18:30.816921 INFO::Done
2025-11-07 21:18:30.817707 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:30.821114 INFO::ASW Batch was 0.227448982531706 prior to batch effect correction and is now -0.0628842551080434 .
2025-11-07 21:18:30.82179 INFO::ASW Label was 0.446906830131859 prior to batch effect correction and is now 0.853968784977271 .
2025-11-07 21:18:30.82264 INFO::Total function execution time is 0.152703762054443 s and adjustment time is 0.134614229202271 s ( 88.15 )
2025-11-07 21:18:30.823543 INFO::Formatting Data.
2025-11-07 21:18:30.8242 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:30.825124 INFO::Removing potential empty rows and columns
2025-11-07 21:18:30.826143 INFO::Found 0 missing values.
2025-11-07 21:18:30.830327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:30.830908 INFO::Done
2025-11-07 21:18:30.831434 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:30.834545 INFO::Starting hierarchical adjustment
2025-11-07 21:18:30.835269 INFO::Found 5 batches.
2025-11-07 21:18:30.835818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:30.836497 INFO::Using default BPPARAM
2025-11-07 21:18:30.837043 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.
2025-11-07 21:18:30.95076 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:30.952575 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-07 21:18:30.969708 INFO::Done
2025-11-07 21:18:30.970592 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:30.974062 INFO::ASW Batch was 0.227448982531706 prior to batch effect correction and is now -0.0628842551080434 .
2025-11-07 21:18:30.974719 INFO::ASW Label was 0.446906830131859 prior to batch effect correction and is now 0.853968784977271 .
2025-11-07 21:18:30.975582 INFO::Total function execution time is 0.15205454826355 s and adjustment time is 0.134529113769531 s ( 88.47 )
2025-11-07 21:18:30.990224 INFO::Formatting Data.
2025-11-07 21:18:30.99116 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:30.992175 INFO::Removing potential empty rows and columns
2025-11-07 21:18:30.993267 INFO::Found 0 missing values.
2025-11-07 21:18:30.996142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:30.996702 INFO::Done
2025-11-07 21:18:30.997503 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:31.000652 INFO::Starting hierarchical adjustment
2025-11-07 21:18:31.001392 INFO::Found 2 batches.
2025-11-07 21:18:31.001943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:31.002584 INFO::Using default BPPARAM
2025-11-07 21:18:31.003138 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:31.004085 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-07 21:18:31.019623 INFO::Done
2025-11-07 21:18:31.020396 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:31.023545 INFO::ASW Batch was 0.642634208132967 prior to batch effect correction and is now -0.00724476015229226 .
2025-11-07 21:18:31.024188 INFO::ASW Label was 0.427089888378695 prior to batch effect correction and is now 0.886461936959039 .
2025-11-07 21:18:31.025021 INFO::Total function execution time is 0.0349481105804443 s and adjustment time is 0.0183494091033936 s ( 52.5 )
2025-11-07 21:18:31.025896 INFO::Formatting Data.
2025-11-07 21:18:31.026538 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:31.027448 INFO::Removing potential empty rows and columns
2025-11-07 21:18:31.028457 INFO::Found 0 missing values.
2025-11-07 21:18:31.031514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:31.03207 INFO::Done
2025-11-07 21:18:31.03262 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:31.035655 INFO::Starting hierarchical adjustment
2025-11-07 21:18:31.036386 INFO::Found 2 batches.
2025-11-07 21:18:31.036929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:31.037549 INFO::Using default BPPARAM
2025-11-07 21:18:31.038095 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:31.039062 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-07 21:18:31.054667 INFO::Done
2025-11-07 21:18:31.055446 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:31.058532 INFO::ASW Batch was 0.642634208132967 prior to batch effect correction and is now -0.00724476015229226 .
2025-11-07 21:18:31.059149 INFO::ASW Label was 0.427089888378695 prior to batch effect correction and is now 0.886461936959039 .
2025-11-07 21:18:31.059975 INFO::Total function execution time is 0.0341143608093262 s and adjustment time is 0.0183925628662109 s ( 53.91 )
2025-11-07 21:18:31.071805 INFO::Formatting Data.
2025-11-07 21:18:31.072634 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:31.073575 INFO::Removing potential empty rows and columns
2025-11-07 21:18:31.074512 INFO::Found 0 missing values.
2025-11-07 21:18:31.076673 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:31.077222 INFO::Done
2025-11-07 21:18:31.077762 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:31.079793 INFO::Starting hierarchical adjustment
2025-11-07 21:18:31.08051 INFO::Found 2 batches.
2025-11-07 21:18:31.08105 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:31.081664 INFO::Using default BPPARAM
2025-11-07 21:18:31.0822 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:31.083103 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-07 21:18:31.11602 INFO::Done
2025-11-07 21:18:31.116853 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:31.119153 INFO::ASW Batch was 0.0171871111444433 prior to batch effect correction and is now -0.128481047554962 .
2025-11-07 21:18:31.12007 INFO::Total function execution time is 0.04836106300354 s and adjustment time is 0.0355992317199707 s ( 73.61 )
2025-11-07 21:18:31.133075 INFO::Formatting Data.
2025-11-07 21:18:31.134044 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:31.135065 INFO::Removing potential empty rows and columns
2025-11-07 21:18:31.136118 INFO::Found 0 missing values.
2025-11-07 21:18:31.137369 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.
2025-11-07 21:18:31.14222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:31.142819 INFO::Done
2025-11-07 21:18:31.143386 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:31.146548 INFO::Starting hierarchical adjustment
2025-11-07 21:18:31.147282 INFO::Found 2 batches.
2025-11-07 21:18:31.147824 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:31.148443 INFO::Using default BPPARAM
2025-11-07 21:18:31.148984 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:31.14999 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-07 21:18:31.16762 INFO::Done
2025-11-07 21:18:31.168411 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:31.171561 INFO::ASW Batch was 0.400760880656416 prior to batch effect correction and is now 0.077335024893585 .
2025-11-07 21:18:31.172213 INFO::ASW Label was 0.674735725191962 prior to batch effect correction and is now 0.87737938294871 .
2025-11-07 21:18:31.173032 INFO::Total function execution time is 0.0401175022125244 s and adjustment time is 0.0204346179962158 s ( 50.94 )
2025-11-07 21:18:31.173892 INFO::Formatting Data.
2025-11-07 21:18:31.174527 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:31.175481 INFO::Removing potential empty rows and columns
2025-11-07 21:18:31.176507 INFO::Found 0 missing values.
2025-11-07 21:18:31.177454 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.
2025-11-07 21:18:31.182221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:31.182786 INFO::Done
2025-11-07 21:18:31.183327 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:31.186407 INFO::Starting hierarchical adjustment
2025-11-07 21:18:31.187142 INFO::Found 2 batches.
2025-11-07 21:18:31.187674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:31.188335 INFO::Using default BPPARAM
2025-11-07 21:18:31.188876 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:31.189808 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-07 21:18:31.207625 INFO::Done
2025-11-07 21:18:31.208435 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:31.211603 INFO::ASW Batch was 0.400760880656416 prior to batch effect correction and is now 0.077335024893585 .
2025-11-07 21:18:31.21228 INFO::ASW Label was 0.674735725191962 prior to batch effect correction and is now 0.87737938294871 .
2025-11-07 21:18:31.213198 INFO::Total function execution time is 0.0393350124359131 s and adjustment time is 0.0205681324005127 s ( 52.29 )
2025-11-07 21:18:31.43112 INFO::Formatting Data.
2025-11-07 21:18:31.432142 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:31.43316 INFO::Removing potential empty rows and columns
2025-11-07 21:18:31.434282 INFO::Found 0 missing values.
2025-11-07 21:18:31.437548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:31.438167 INFO::Done
2025-11-07 21:18:31.438697 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:31.44102 INFO::Starting hierarchical adjustment
2025-11-07 21:18:31.44175 INFO::Found 3 batches.
2025-11-07 21:18:31.442306 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:31.442943 INFO::Using default BPPARAM
2025-11-07 21:18:31.443511 INFO::Processing subtree level 1
2025-11-07 21:18:31.541703 INFO::Adjusting the last 1 batches sequentially
2025-11-07 21:18:31.543776 INFO::Done
2025-11-07 21:18:31.544531 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:31.547246 INFO::ASW Batch was -0.0713428709941231 prior to batch effect correction and is now -0.0713428709941231 .
2025-11-07 21:18:31.548246 INFO::Total function execution time is 0.117244958877563 s and adjustment time is 0.102139949798584 s ( 87.12 )
2025-11-07 21:18:31.549433 INFO::Formatting Data.
2025-11-07 21:18:31.550123 INFO::Typecasting input to dataframe.
2025-11-07 21:18:31.550926 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:31.551926 INFO::Removing potential empty rows and columns
2025-11-07 21:18:31.553085 INFO::Found 0 missing values.
2025-11-07 21:18:31.556304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:31.556879 INFO::Done
2025-11-07 21:18:31.557633 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:31.559876 INFO::Starting hierarchical adjustment
2025-11-07 21:18:31.560636 INFO::Found 3 batches.
2025-11-07 21:18:31.5612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:31.561869 INFO::Using default BPPARAM
2025-11-07 21:18:31.562424 INFO::Processing subtree level 1
2025-11-07 21:18:31.658506 INFO::Adjusting the last 1 batches sequentially
2025-11-07 21:18:31.660599 INFO::Done
2025-11-07 21:18:31.661368 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:31.664104 INFO::ASW Batch was -0.0713428709941231 prior to batch effect correction and is now -0.0713428709941231 .
2025-11-07 21:18:31.665145 INFO::Total function execution time is 0.115686893463135 s and adjustment time is 0.100080966949463 s ( 86.51 )
2025-11-07 21:18:31.679373 INFO::Formatting Data.
2025-11-07 21:18:31.680352 INFO::Typecasting input to dataframe.
2025-11-07 21:18:31.681341 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:31.682344 INFO::Removing potential empty rows and columns
2025-11-07 21:18:31.683562 INFO::Found 0 missing values.
2025-11-07 21:18:31.686634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:31.687198 INFO::Done
2025-11-07 21:18:31.687733 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:31.689964 INFO::Starting hierarchical adjustment
2025-11-07 21:18:31.690685 INFO::Found 3 batches.
2025-11-07 21:18:31.691272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:31.691932 INFO::Using default BPPARAM
2025-11-07 21:18:31.692471 INFO::Processing subtree level 1
2025-11-07 21:18:31.784985 INFO::Adjusting the last 1 batches sequentially
2025-11-07 21:18:31.786899 INFO::Done
2025-11-07 21:18:31.787564 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:31.790181 INFO::ASW Batch was -0.107330767607959 prior to batch effect correction and is now -0.107330767607959 .
2025-11-07 21:18:31.791189 INFO::Total function execution time is 0.111918449401855 s and adjustment time is 0.0963165760040283 s ( 86.06 )
2025-11-07 21:18:31.965567 INFO::Formatting Data.
2025-11-07 21:18:31.967495 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:31.969712 INFO::Removing potential empty rows and columns
2025-11-07 21:18:31.975034 INFO::Found 1000 missing values.
2025-11-07 21:18:32.000944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:32.001921 INFO::Done
2025-11-07 21:18:32.002623 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:32.009264 INFO::Starting hierarchical adjustment
2025-11-07 21:18:32.010317 INFO::Found 10 batches.
2025-11-07 21:18:32.010945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:32.01173 INFO::Using default BPPARAM
2025-11-07 21:18:32.012352 INFO::Processing subtree level 1
2025-11-07 21:18:32.16176 INFO::Processing subtree level 2
2025-11-07 21:18:32.309023 INFO::Adjusting the last 1 batches sequentially
2025-11-07 21:18:32.311331 INFO::Done
2025-11-07 21:18:32.312089 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:32.31781 INFO::ASW Batch was 0.501513719412304 prior to batch effect correction and is now 0.501513719412304 .
2025-11-07 21:18:32.318617 INFO::ASW Label was 0.362609131128819 prior to batch effect correction and is now 0.362609131128819 .
2025-11-07 21:18:32.319722 INFO::Total function execution time is 0.354615211486816 s and adjustment time is 0.301273107528687 s ( 84.96 )
2025-11-07 21:18:32.32061 INFO::Formatting Data.
2025-11-07 21:18:32.321294 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:32.322617 INFO::Removing potential empty rows and columns
2025-11-07 21:18:32.325502 INFO::Found 1000 missing values.
2025-11-07 21:18:32.344799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:32.345685 INFO::Done
2025-11-07 21:18:32.346445 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:32.352216 INFO::Starting hierarchical adjustment
2025-11-07 21:18:32.353161 INFO::Found 10 batches.
2025-11-07 21:18:33.911402 INFO::Set up parallel execution backend with 2 workers
2025-11-07 21:18:33.9153 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-07 21:18:35.459931 INFO::Adjusting the last 2 batches sequentially
2025-11-07 21:18:35.463554 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-07 21:18:35.480518 INFO::Done
2025-11-07 21:18:35.48122 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:35.485876 INFO::ASW Batch was 0.501513719412304 prior to batch effect correction and is now 0.501513719412304 .
2025-11-07 21:18:35.486465 INFO::ASW Label was 0.362609131128819 prior to batch effect correction and is now 0.362609131128819 .
2025-11-07 21:18:35.487291 INFO::Total function execution time is 3.16670417785645 s and adjustment time is 3.12754464149475 s ( 98.76 )
2025-11-07 21:18:35.655363 INFO::Formatting Data.
2025-11-07 21:18:35.65615 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:35.657114 INFO::Removing potential empty rows and columns
2025-11-07 21:18:35.65821 INFO::Found 0 missing values.
2025-11-07 21:18:35.661761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:35.662332 INFO::Done
2025-11-07 21:18:35.662858 INFO::Acquiring quality metrics before batch effect correction.
2025-11-07 21:18:35.665515 INFO::Starting hierarchical adjustment
2025-11-07 21:18:35.6662 INFO::Found 3 batches.
2025-11-07 21:18:35.666709 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-07 21:18:35.667317 INFO::Using default BPPARAM
2025-11-07 21:18:35.667836 INFO::Processing subtree level 1
2025-11-07 21:18:35.783293 INFO::Adjusting the last 1 batches sequentially
2025-11-07 21:18:35.785347 INFO::Done
2025-11-07 21:18:35.786088 INFO::Acquiring quality metrics after batch effect correction.
2025-11-07 21:18:35.789523 INFO::ASW Batch was 0.277245873205609 prior to batch effect correction and is now -0.160619847771475 .
2025-11-07 21:18:35.790195 INFO::ASW Label was -0.15944205489548 prior to batch effect correction and is now 0.134354631598059 .
2025-11-07 21:18:35.791177 INFO::Total function execution time is 0.135823249816895 s and adjustment time is 0.119235754013062 s ( 87.79 )
2025-11-07 21:18:35.912836 INFO::Formatting Data.
2025-11-07 21:18:35.913777 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:35.914767 INFO::Removing potential empty rows and columns
2025-11-07 21:18:35.915896 INFO::Found 2 missing values.
2025-11-07 21:18:35.91893 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:35.919488 INFO::Done
2025-11-07 21:18:35.947228 INFO::Found NA in Reference column
2025-11-07 21:18:35.956688 INFO::Require at least two references per batch.
2025-11-07 21:18:35.977691 INFO::Formatting Data.
2025-11-07 21:18:35.978488 INFO::Recognized SummarizedExperiment
2025-11-07 21:18:35.979065 INFO::Typecasting input to dataframe.
2025-11-07 21:18:35.988854 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:35.990042 INFO::Removing potential empty rows and columns
2025-11-07 21:18:35.993687 INFO::Found 0 missing values.
2025-11-07 21:18:36.000477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.001109 INFO::Done
2025-11-07 21:18:36.016626 INFO::Formatting Data.
2025-11-07 21:18:36.017404 INFO::Recognized SummarizedExperiment
2025-11-07 21:18:36.017964 INFO::Typecasting input to dataframe.
2025-11-07 21:18:36.035605 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:36.036881 INFO::Removing potential empty rows and columns
2025-11-07 21:18:36.040474 INFO::Found 0 missing values.
2025-11-07 21:18:36.051701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.052412 INFO::Done
2025-11-07 21:18:36.067605 INFO::Formatting Data.
2025-11-07 21:18:36.068294 INFO::Recognized SummarizedExperiment
2025-11-07 21:18:36.068804 INFO::Typecasting input to dataframe.
2025-11-07 21:18:36.084805 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:36.085812 INFO::Removing potential empty rows and columns
2025-11-07 21:18:36.086904 INFO::Found 0 missing values.
2025-11-07 21:18:36.087788 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.
2025-11-07 21:18:36.09227 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.092812 INFO::Done
2025-11-07 21:18:36.102746 INFO::Formatting Data.
2025-11-07 21:18:36.103489 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:36.104338 INFO::Removing potential empty rows and columns
2025-11-07 21:18:36.10536 INFO::Found 0 missing values.
2025-11-07 21:18:36.108136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.108675 INFO::Done
2025-11-07 21:18:36.11907 INFO::Formatting Data.
2025-11-07 21:18:36.119826 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:36.120683 INFO::Removing potential empty rows and columns
2025-11-07 21:18:36.121621 INFO::Found 0 missing values.
2025-11-07 21:18:36.124333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.124905 INFO::Done
2025-11-07 21:18:36.152601 INFO::Formatting Data.
2025-11-07 21:18:36.153455 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:36.154483 INFO::Removing potential empty rows and columns
2025-11-07 21:18:36.155606 INFO::Found 1 missing values.
2025-11-07 21:18:36.158134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.158687 INFO::Done
2025-11-07 21:18:36.176335 INFO::Formatting Data.
2025-11-07 21:18:36.177213 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:36.178089 INFO::Removing potential empty rows and columns
2025-11-07 21:18:36.179004 INFO::Found 2 missing values.
2025-11-07 21:18:36.179921 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.
2025-11-07 21:18:36.182081 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.182621 INFO::Done
2025-11-07 21:18:36.191898 INFO::Formatting Data.
2025-11-07 21:18:36.192569 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:36.193397 INFO::Removing potential empty rows and columns
2025-11-07 21:18:36.194284 INFO::Found 2 missing values.
2025-11-07 21:18:36.195749 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.196263 INFO::Done
2025-11-07 21:18:36.205497 INFO::Formatting Data.
2025-11-07 21:18:36.206167 INFO::Typecasting input to dataframe.
2025-11-07 21:18:36.20698 INFO::Replacing NaNs with NAs.
2025-11-07 21:18:36.207795 INFO::Removing potential empty rows and columns
2025-11-07 21:18:36.20887 INFO::Found 0 missing values.
2025-11-07 21:18:36.21173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-07 21:18:36.212261 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.287 4.737 22.754
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.715 | 1.434 | 17.574 | |
| compute_asw | 0.025 | 0.000 | 0.026 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.001 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.011 | |