Yannis Schumann
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:04 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-12-11 22:18:35 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 22:20:03 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.242 1.156 16.529
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
2025-12-11 22:19:25.575333 INFO::Formatting Data.
2025-12-11 22:19:25.576546 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:25.587338 INFO::Removing potential empty rows and columns
2025-12-11 22:19:25.844312 INFO::Found 0 missing values.
2025-12-11 22:19:25.847804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:25.84843 INFO::Done
2025-12-11 22:19:25.848986 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:25.860461 INFO::Starting hierarchical adjustment
2025-12-11 22:19:25.861303 INFO::Found 3 batches.
2025-12-11 22:19:25.861857 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:25.862999 INFO::Using default BPPARAM
2025-12-11 22:19:25.863553 INFO::Processing subtree level 1
2025-12-11 22:19:25.963289 INFO::Adjusting the last 1 batches sequentially
2025-12-11 22:19:25.964988 INFO::Done
2025-12-11 22:19:25.965636 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:25.968186 INFO::ASW Batch was 0.0203462938769598 prior to batch effect correction and is now 0.0203462938769598 .
2025-12-11 22:19:25.969281 INFO::Total function execution time is 0.394558191299438 s and adjustment time is 0.103856801986694 s ( 26.32 )
2025-12-11 22:19:25.983876 INFO::Formatting Data.
2025-12-11 22:19:25.98478 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:25.985845 INFO::Removing potential empty rows and columns
2025-12-11 22:19:25.987091 INFO::Found 0 missing values.
2025-12-11 22:19:25.988112 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-11 22:19:25.99978 INFO::Formatting Data.
2025-12-11 22:19:26.000548 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:26.001489 INFO::Removing potential empty rows and columns
2025-12-11 22:19:26.002584 INFO::Found 0 missing values.
2025-12-11 22:19:26.003618 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-11 22:19:26.020258 INFO::Formatting Data.
2025-12-11 22:19:26.021019 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:26.021945 INFO::Removing potential empty rows and columns
2025-12-11 22:19:26.02302 INFO::Found 0 missing values.
2025-12-11 22:19:26.023981 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-11 22:19:26.028683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:26.029266 INFO::Done
2025-12-11 22:19:26.02981 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:26.031786 INFO::Starting hierarchical adjustment
2025-12-11 22:19:26.032512 INFO::Found 2 batches.
2025-12-11 22:19:26.03305 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:26.033698 INFO::Using default BPPARAM
2025-12-11 22:19:26.034235 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:26.03517 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-11 22:19:26.056561 INFO::Done
2025-12-11 22:19:26.057251 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:26.059311 INFO::ASW Batch was 0.00722490153502211 prior to batch effect correction and is now -0.106699040391722 .
2025-12-11 22:19:26.060107 INFO::Total function execution time is 0.0399191379547119 s and adjustment time is 0.0241470336914062 s ( 60.49 )
2025-12-11 22:19:26.062876 INFO::Formatting Data.
2025-12-11 22:19:26.063489 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:26.072478 INFO::Formatting Data.
2025-12-11 22:19:26.073213 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:26.074128 INFO::Removing potential empty rows and columns
2025-12-11 22:19:26.075218 INFO::Found 0 missing values.
2025-12-11 22:19:26.078226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:26.078777 INFO::Done
2025-12-11 22:19:26.079304 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:26.081302 INFO::Starting hierarchical adjustment
2025-12-11 22:19:26.082009 INFO::Found 2 batches.
2025-12-11 22:19:26.082546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:26.10698 INFO::Using default BPPARAM
2025-12-11 22:19:26.109265 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:26.110208 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:26.123995 INFO::Done
2025-12-11 22:19:26.124616 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:26.126484 INFO::ASW Batch was -0.00728545459142572 prior to batch effect correction and is now -0.134757373361455 .
2025-12-11 22:19:26.127229 INFO::Total function execution time is 0.0548136234283447 s and adjustment time is 0.0421140193939209 s ( 76.83 )
2025-12-11 22:19:26.128242 INFO::Formatting Data.
2025-12-11 22:19:26.128814 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:26.129596 INFO::Removing potential empty rows and columns
2025-12-11 22:19:26.13055 INFO::Found 0 missing values.
2025-12-11 22:19:26.133171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:26.133691 INFO::Done
2025-12-11 22:19:26.134179 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:26.136063 INFO::Starting hierarchical adjustment
2025-12-11 22:19:26.136752 INFO::Found 2 batches.
2025-12-11 22:19:26.137252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:26.137833 INFO::Using default BPPARAM
2025-12-11 22:19:26.138316 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:26.139168 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:26.153573 INFO::Done
2025-12-11 22:19:26.154228 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:26.156186 INFO::ASW Batch was -0.00728545459142572 prior to batch effect correction and is now -0.134757373361455 .
2025-12-11 22:19:26.156946 INFO::Total function execution time is 0.028700590133667 s and adjustment time is 0.0169191360473633 s ( 58.95 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-11 22:19:28.828936 INFO::Formatting Data.
2025-12-11 22:19:28.829603 INFO::Recognized SummarizedExperiment
2025-12-11 22:19:28.830064 INFO::Typecasting input to dataframe.
2025-12-11 22:19:28.85813 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:28.859331 INFO::Removing potential empty rows and columns
2025-12-11 22:19:28.863059 INFO::Found 0 missing values.
2025-12-11 22:19:28.870286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:28.870936 INFO::Done
2025-12-11 22:19:28.871474 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:28.875027 INFO::Starting hierarchical adjustment
2025-12-11 22:19:28.875762 INFO::Found 2 batches.
2025-12-11 22:19:28.876279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:28.877336 INFO::Using default BPPARAM
2025-12-11 22:19:28.877872 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:28.87884 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-11 22:19:28.935232 INFO::Done
2025-12-11 22:19:28.935944 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:28.939599 INFO::ASW Batch was 0.00576969488378202 prior to batch effect correction and is now -0.102670328258357 .
2025-12-11 22:19:28.94046 INFO::Total function execution time is 0.111794710159302 s and adjustment time is 0.0595822334289551 s ( 53.3 )
Warning: stack imbalance in '{', 73 then 75
2025-12-11 22:19:28.958807 INFO::Formatting Data.
2025-12-11 22:19:28.959557 INFO::Recognized SummarizedExperiment
2025-12-11 22:19:28.960101 INFO::Typecasting input to dataframe.
2025-12-11 22:19:28.969436 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:28.9707 INFO::Removing potential empty rows and columns
2025-12-11 22:19:28.97449 INFO::Found 0 missing values.
2025-12-11 22:19:28.981883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:28.98257 INFO::Done
2025-12-11 22:19:28.983119 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:28.986681 INFO::Starting hierarchical adjustment
2025-12-11 22:19:28.987413 INFO::Found 2 batches.
2025-12-11 22:19:28.987934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:28.988535 INFO::Using default BPPARAM
2025-12-11 22:19:28.989044 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:28.990041 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-11 22:19:29.015266 INFO::Done
2025-12-11 22:19:29.015987 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:29.019543 INFO::ASW Batch was 0.000335930086428931 prior to batch effect correction and is now 0.000335930086428931 .
2025-12-11 22:19:29.020401 INFO::Total function execution time is 0.0615811347961426 s and adjustment time is 0.0279746055603027 s ( 45.43 )
2025-12-11 22:19:29.038301 INFO::Formatting Data.
2025-12-11 22:19:29.039077 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:29.039961 INFO::Removing potential empty rows and columns
2025-12-11 22:19:29.040984 INFO::Found 0 missing values.
2025-12-11 22:19:29.043955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:29.044481 INFO::Done
2025-12-11 22:19:29.044993 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:29.046955 INFO::Starting hierarchical adjustment
2025-12-11 22:19:29.047628 INFO::Found 3 batches.
2025-12-11 22:19:29.048144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:29.048728 INFO::Using default BPPARAM
2025-12-11 22:19:29.049232 INFO::Processing subtree level 1
2025-12-11 22:19:29.185753 INFO::Adjusting the last 1 batches sequentially
2025-12-11 22:19:29.187589 INFO::Done
2025-12-11 22:19:29.188226 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:29.1907 INFO::ASW Batch was -0.0755484404574134 prior to batch effect correction and is now -0.178679087472715 .
2025-12-11 22:19:29.191632 INFO::Total function execution time is 0.153326988220215 s and adjustment time is 0.140059471130371 s ( 91.35 )
2025-12-11 22:19:29.206269 INFO::Skipping initial DF formatting
2025-12-11 22:19:29.206993 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:29.211024 INFO::Starting hierarchical adjustment
2025-12-11 22:19:29.211827 INFO::Found 5 batches.
2025-12-11 22:19:29.21236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:29.212979 INFO::Using default BPPARAM
2025-12-11 22:19:29.213515 INFO::Processing subtree level 1
2025-12-11 22:19:29.562601 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:29.564371 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-11 22:19:29.5847 INFO::Done
2025-12-11 22:19:29.585557 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:29.645937 INFO::ASW Batch was 0.499348166918851 prior to batch effect correction and is now 0.499348166918851 .
2025-12-11 22:19:29.646755 INFO::ASW Label was 0.367772209277552 prior to batch effect correction and is now 0.367772209277552 .
2025-12-11 22:19:29.647684 INFO::Total function execution time is 0.441468000411987 s and adjustment time is 0.372972011566162 s ( 84.48 )
2025-12-11 22:19:29.666046 INFO::Formatting Data.
2025-12-11 22:19:29.666957 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:29.667989 INFO::Removing potential empty rows and columns
2025-12-11 22:19:29.669135 INFO::Found 0 missing values.
2025-12-11 22:19:29.673762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:29.674417 INFO::Done
2025-12-11 22:19:29.675096 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:29.678623 INFO::Starting hierarchical adjustment
2025-12-11 22:19:29.67942 INFO::Found 5 batches.
2025-12-11 22:19:29.680017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:29.680796 INFO::Using default BPPARAM
2025-12-11 22:19:29.681427 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:29.840246 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:29.842093 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:29.861152 INFO::Done
2025-12-11 22:19:29.861988 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:29.865935 INFO::ASW Batch was 0.541532646769778 prior to batch effect correction and is now -0.0971534707068139 .
2025-12-11 22:19:29.866662 INFO::ASW Label was 0.21539349138927 prior to batch effect correction and is now 0.795067664736978 .
2025-12-11 22:19:29.867592 INFO::Total function execution time is 0.20164155960083 s and adjustment time is 0.181856155395508 s ( 90.19 )
2025-12-11 22:19:29.868613 INFO::Formatting Data.
2025-12-11 22:19:29.869305 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:29.870303 INFO::Removing potential empty rows and columns
2025-12-11 22:19:29.871465 INFO::Found 0 missing values.
2025-12-11 22:19:29.876147 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:29.876756 INFO::Done
2025-12-11 22:19:29.877318 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:29.880777 INFO::Starting hierarchical adjustment
2025-12-11 22:19:29.881544 INFO::Found 5 batches.
2025-12-11 22:19:29.882085 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:29.88276 INFO::Using default BPPARAM
2025-12-11 22:19:29.883307 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:30.022102 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:30.023864 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:30.041663 INFO::Done
2025-12-11 22:19:30.04249 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:30.046191 INFO::ASW Batch was 0.541532646769778 prior to batch effect correction and is now -0.0971534707068139 .
2025-12-11 22:19:30.046866 INFO::ASW Label was 0.21539349138927 prior to batch effect correction and is now 0.795067664736978 .
2025-12-11 22:19:30.047761 INFO::Total function execution time is 0.179187774658203 s and adjustment time is 0.160224676132202 s ( 89.42 )
2025-12-11 22:19:30.063024 INFO::Formatting Data.
2025-12-11 22:19:30.063936 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:30.064931 INFO::Removing potential empty rows and columns
2025-12-11 22:19:30.066022 INFO::Found 0 missing values.
2025-12-11 22:19:30.070304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:30.070899 INFO::Done
2025-12-11 22:19:30.071447 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:30.075304 INFO::Starting hierarchical adjustment
2025-12-11 22:19:30.076169 INFO::Found 5 batches.
2025-12-11 22:19:30.076774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:30.077482 INFO::Using default BPPARAM
2025-12-11 22:19:30.078186 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:30.22331 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:30.225144 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:30.242649 INFO::Done
2025-12-11 22:19:30.243465 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:30.24708 INFO::ASW Batch was 0.57738580768196 prior to batch effect correction and is now -0.0804499130602052 .
2025-12-11 22:19:30.247782 INFO::ASW Label was 0.182899677033163 prior to batch effect correction and is now 0.744088743979882 .
2025-12-11 22:19:30.248653 INFO::Total function execution time is 0.185750246047974 s and adjustment time is 0.166618824005127 s ( 89.7 )
2025-12-11 22:19:30.249548 INFO::Formatting Data.
2025-12-11 22:19:30.250206 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:30.251167 INFO::Removing potential empty rows and columns
2025-12-11 22:19:30.252213 INFO::Found 0 missing values.
2025-12-11 22:19:30.256423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:30.257016 INFO::Done
2025-12-11 22:19:30.257554 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:30.260803 INFO::Starting hierarchical adjustment
2025-12-11 22:19:30.261609 INFO::Found 5 batches.
2025-12-11 22:19:30.262177 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:30.262841 INFO::Using default BPPARAM
2025-12-11 22:19:30.263402 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:30.399073 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:30.400821 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:30.419088 INFO::Done
2025-12-11 22:19:30.419908 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:30.423417 INFO::ASW Batch was 0.57738580768196 prior to batch effect correction and is now -0.0804499130602052 .
2025-12-11 22:19:30.438114 INFO::ASW Label was 0.182899677033163 prior to batch effect correction and is now 0.744088743979882 .
2025-12-11 22:19:30.439925 INFO::Total function execution time is 0.19027304649353 s and adjustment time is 0.157600164413452 s ( 82.83 )
2025-12-11 22:19:30.462967 INFO::Formatting Data.
2025-12-11 22:19:30.463846 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:30.465135 INFO::Removing potential empty rows and columns
2025-12-11 22:19:30.466428 INFO::Found 0 missing values.
2025-12-11 22:19:30.46969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:30.470278 INFO::Done
2025-12-11 22:19:30.470861 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:30.475334 INFO::Starting hierarchical adjustment
2025-12-11 22:19:30.476129 INFO::Found 2 batches.
2025-12-11 22:19:30.47672 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:30.47754 INFO::Using default BPPARAM
2025-12-11 22:19:30.47812 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:30.479096 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:30.500284 INFO::Done
2025-12-11 22:19:30.501059 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:30.504286 INFO::ASW Batch was 0.683054555994135 prior to batch effect correction and is now -0.0338352063040001 .
2025-12-11 22:19:30.504927 INFO::ASW Label was 0.382627069107593 prior to batch effect correction and is now 0.921892150947826 .
2025-12-11 22:19:30.505759 INFO::Total function execution time is 0.0429036617279053 s and adjustment time is 0.0242931842803955 s ( 56.62 )
2025-12-11 22:19:30.506613 INFO::Formatting Data.
2025-12-11 22:19:30.507264 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:30.508211 INFO::Removing potential empty rows and columns
2025-12-11 22:19:30.509241 INFO::Found 0 missing values.
2025-12-11 22:19:30.511996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:30.512586 INFO::Done
2025-12-11 22:19:30.513143 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:30.51622 INFO::Starting hierarchical adjustment
2025-12-11 22:19:30.516976 INFO::Found 2 batches.
2025-12-11 22:19:30.517547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:30.518191 INFO::Using default BPPARAM
2025-12-11 22:19:30.518721 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:30.519706 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-11 22:19:30.535076 INFO::Done
2025-12-11 22:19:30.535757 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:30.538887 INFO::ASW Batch was 0.683054555994135 prior to batch effect correction and is now -0.0338352063040001 .
2025-12-11 22:19:30.539535 INFO::ASW Label was 0.382627069107593 prior to batch effect correction and is now 0.921892150947826 .
2025-12-11 22:19:30.540374 INFO::Total function execution time is 0.0337789058685303 s and adjustment time is 0.0182428359985352 s ( 54.01 )
2025-12-11 22:19:30.552674 INFO::Formatting Data.
2025-12-11 22:19:30.553496 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:30.554483 INFO::Removing potential empty rows and columns
2025-12-11 22:19:30.555585 INFO::Found 0 missing values.
2025-12-11 22:19:30.557815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:30.558383 INFO::Done
2025-12-11 22:19:30.558934 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:30.561136 INFO::Starting hierarchical adjustment
2025-12-11 22:19:30.561935 INFO::Found 2 batches.
2025-12-11 22:19:30.562493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:30.563147 INFO::Using default BPPARAM
2025-12-11 22:19:30.563713 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:30.564711 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-11 22:19:30.603695 INFO::Done
2025-12-11 22:19:30.604468 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:30.606662 INFO::ASW Batch was -0.134112576989365 prior to batch effect correction and is now -0.137421345923986 .
2025-12-11 22:19:30.607586 INFO::Total function execution time is 0.0549912452697754 s and adjustment time is 0.0418784618377686 s ( 76.15 )
2025-12-11 22:19:30.620214 INFO::Formatting Data.
2025-12-11 22:19:30.620996 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:30.621909 INFO::Removing potential empty rows and columns
2025-12-11 22:19:30.62297 INFO::Found 0 missing values.
2025-12-11 22:19:30.624331 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-11 22:19:30.629196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:30.629783 INFO::Done
2025-12-11 22:19:30.630329 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:30.633559 INFO::Starting hierarchical adjustment
2025-12-11 22:19:30.634323 INFO::Found 2 batches.
2025-12-11 22:19:30.634904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:30.635551 INFO::Using default BPPARAM
2025-12-11 22:19:30.6361 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:30.637109 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-11 22:19:30.654613 INFO::Done
2025-12-11 22:19:30.655331 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:30.658484 INFO::ASW Batch was 0.673079099698199 prior to batch effect correction and is now 0.0742346123699922 .
2025-12-11 22:19:30.659129 INFO::ASW Label was 0.413235218518419 prior to batch effect correction and is now 0.856949537351107 .
2025-12-11 22:19:30.659966 INFO::Total function execution time is 0.0398144721984863 s and adjustment time is 0.0204081535339355 s ( 51.26 )
2025-12-11 22:19:30.660848 INFO::Formatting Data.
2025-12-11 22:19:30.661533 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:30.662552 INFO::Removing potential empty rows and columns
2025-12-11 22:19:30.663617 INFO::Found 0 missing values.
2025-12-11 22:19:30.664604 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-11 22:19:30.669415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:30.67001 INFO::Done
2025-12-11 22:19:30.670595 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:30.673818 INFO::Starting hierarchical adjustment
2025-12-11 22:19:30.674537 INFO::Found 2 batches.
2025-12-11 22:19:30.675111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:30.675762 INFO::Using default BPPARAM
2025-12-11 22:19:30.676303 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:30.677335 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-11 22:19:30.694977 INFO::Done
2025-12-11 22:19:30.695676 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:30.698837 INFO::ASW Batch was 0.673079099698199 prior to batch effect correction and is now 0.0742346123699922 .
2025-12-11 22:19:30.699453 INFO::ASW Label was 0.413235218518419 prior to batch effect correction and is now 0.856949537351107 .
2025-12-11 22:19:30.700289 INFO::Total function execution time is 0.0394673347473145 s and adjustment time is 0.0205864906311035 s ( 52.16 )
2025-12-11 22:19:30.92063 INFO::Formatting Data.
2025-12-11 22:19:30.921492 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:30.922418 INFO::Removing potential empty rows and columns
2025-12-11 22:19:30.923533 INFO::Found 0 missing values.
2025-12-11 22:19:30.926574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:30.927123 INFO::Done
2025-12-11 22:19:30.927661 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:30.929841 INFO::Starting hierarchical adjustment
2025-12-11 22:19:30.930554 INFO::Found 3 batches.
2025-12-11 22:19:30.931089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:30.93172 INFO::Using default BPPARAM
2025-12-11 22:19:30.932236 INFO::Processing subtree level 1
2025-12-11 22:19:31.031869 INFO::Adjusting the last 1 batches sequentially
2025-12-11 22:19:31.033805 INFO::Done
2025-12-11 22:19:31.034487 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:31.037167 INFO::ASW Batch was 0.0356043643726413 prior to batch effect correction and is now 0.0356043643726413 .
2025-12-11 22:19:31.038198 INFO::Total function execution time is 0.11766505241394 s and adjustment time is 0.103381633758545 s ( 87.86 )
2025-12-11 22:19:31.039293 INFO::Formatting Data.
2025-12-11 22:19:31.039998 INFO::Typecasting input to dataframe.
2025-12-11 22:19:31.040793 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:31.041784 INFO::Removing potential empty rows and columns
2025-12-11 22:19:31.042944 INFO::Found 0 missing values.
2025-12-11 22:19:31.046168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:31.046752 INFO::Done
2025-12-11 22:19:31.047293 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:31.049528 INFO::Starting hierarchical adjustment
2025-12-11 22:19:31.050281 INFO::Found 3 batches.
2025-12-11 22:19:31.050828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:31.05146 INFO::Using default BPPARAM
2025-12-11 22:19:31.052006 INFO::Processing subtree level 1
2025-12-11 22:19:31.184572 INFO::Adjusting the last 1 batches sequentially
2025-12-11 22:19:31.186753 INFO::Done
2025-12-11 22:19:31.187564 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:31.190497 INFO::ASW Batch was 0.0356043643726413 prior to batch effect correction and is now 0.0356043643726413 .
2025-12-11 22:19:31.191584 INFO::Total function execution time is 0.152258634567261 s and adjustment time is 0.136605739593506 s ( 89.72 )
2025-12-11 22:19:31.205775 INFO::Formatting Data.
2025-12-11 22:19:31.206657 INFO::Typecasting input to dataframe.
2025-12-11 22:19:31.20759 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:31.208582 INFO::Removing potential empty rows and columns
2025-12-11 22:19:31.209755 INFO::Found 0 missing values.
2025-12-11 22:19:31.21301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:31.213602 INFO::Done
2025-12-11 22:19:31.214159 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:31.216383 INFO::Starting hierarchical adjustment
2025-12-11 22:19:31.217132 INFO::Found 3 batches.
2025-12-11 22:19:31.217686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:31.218343 INFO::Using default BPPARAM
2025-12-11 22:19:31.218891 INFO::Processing subtree level 1
2025-12-11 22:19:31.314382 INFO::Adjusting the last 1 batches sequentially
2025-12-11 22:19:31.316987 INFO::Done
2025-12-11 22:19:31.317981 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:31.321605 INFO::ASW Batch was -0.0954210086246633 prior to batch effect correction and is now -0.0954210086246633 .
2025-12-11 22:19:31.322938 INFO::Total function execution time is 0.117173194885254 s and adjustment time is 0.0999410152435303 s ( 85.29 )
2025-12-11 22:19:31.494784 INFO::Formatting Data.
2025-12-11 22:19:31.495979 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:31.497683 INFO::Removing potential empty rows and columns
2025-12-11 22:19:31.501928 INFO::Found 1000 missing values.
2025-12-11 22:19:31.530526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:31.53167 INFO::Done
2025-12-11 22:19:31.532573 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:31.540873 INFO::Starting hierarchical adjustment
2025-12-11 22:19:31.542345 INFO::Found 10 batches.
2025-12-11 22:19:31.543341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:31.544424 INFO::Using default BPPARAM
2025-12-11 22:19:31.545268 INFO::Processing subtree level 1
2025-12-11 22:19:31.70141 INFO::Processing subtree level 2
2025-12-11 22:19:31.843842 INFO::Adjusting the last 1 batches sequentially
2025-12-11 22:19:31.845815 INFO::Done
2025-12-11 22:19:31.846475 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:31.852025 INFO::ASW Batch was 0.489342843876924 prior to batch effect correction and is now 0.489342843876924 .
2025-12-11 22:19:31.852711 INFO::ASW Label was 0.320296037961069 prior to batch effect correction and is now 0.320296037961069 .
2025-12-11 22:19:31.853634 INFO::Total function execution time is 0.359059810638428 s and adjustment time is 0.303788185119629 s ( 84.61 )
2025-12-11 22:19:31.854473 INFO::Formatting Data.
2025-12-11 22:19:31.855114 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:31.85641 INFO::Removing potential empty rows and columns
2025-12-11 22:19:31.859197 INFO::Found 1000 missing values.
2025-12-11 22:19:31.878151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:31.878955 INFO::Done
2025-12-11 22:19:31.879522 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:31.885117 INFO::Starting hierarchical adjustment
2025-12-11 22:19:31.885948 INFO::Found 10 batches.
2025-12-11 22:19:33.112748 INFO::Set up parallel execution backend with 2 workers
2025-12-11 22:19:33.114658 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-11 22:19:34.166153 INFO::Adjusting the last 2 batches sequentially
2025-12-11 22:19:34.168039 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-11 22:19:34.184433 INFO::Done
2025-12-11 22:19:34.185148 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:34.189729 INFO::ASW Batch was 0.489342843876924 prior to batch effect correction and is now 0.489342843876924 .
2025-12-11 22:19:34.190305 INFO::ASW Label was 0.320296037961069 prior to batch effect correction and is now 0.320296037961069 .
2025-12-11 22:19:34.191035 INFO::Total function execution time is 2.33661341667175 s and adjustment time is 2.29861187934875 s ( 98.37 )
2025-12-11 22:19:34.334445 INFO::Formatting Data.
2025-12-11 22:19:34.335229 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.336124 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.337137 INFO::Found 0 missing values.
2025-12-11 22:19:34.340639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.341156 INFO::Done
2025-12-11 22:19:34.341651 INFO::Acquiring quality metrics before batch effect correction.
2025-12-11 22:19:34.344309 INFO::Starting hierarchical adjustment
2025-12-11 22:19:34.344984 INFO::Found 3 batches.
2025-12-11 22:19:34.345464 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-11 22:19:34.346048 INFO::Using default BPPARAM
2025-12-11 22:19:34.346555 INFO::Processing subtree level 1
2025-12-11 22:19:34.448185 INFO::Adjusting the last 1 batches sequentially
2025-12-11 22:19:34.449902 INFO::Done
2025-12-11 22:19:34.450498 INFO::Acquiring quality metrics after batch effect correction.
2025-12-11 22:19:34.453576 INFO::ASW Batch was 0.207527360518068 prior to batch effect correction and is now -0.181414712958118 .
2025-12-11 22:19:34.454159 INFO::ASW Label was -0.169113780883906 prior to batch effect correction and is now -0.135400742006731 .
2025-12-11 22:19:34.45505 INFO::Total function execution time is 0.120689868927002 s and adjustment time is 0.105036735534668 s ( 87.03 )
2025-12-11 22:19:34.572827 INFO::Formatting Data.
2025-12-11 22:19:34.573674 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.574595 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.575596 INFO::Found 2 missing values.
2025-12-11 22:19:34.578314 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.578819 INFO::Done
2025-12-11 22:19:34.604948 INFO::Found NA in Reference column
2025-12-11 22:19:34.613903 INFO::Require at least two references per batch.
2025-12-11 22:19:34.633209 INFO::Formatting Data.
2025-12-11 22:19:34.633961 INFO::Recognized SummarizedExperiment
2025-12-11 22:19:34.634473 INFO::Typecasting input to dataframe.
2025-12-11 22:19:34.643569 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.64469 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.647965 INFO::Found 0 missing values.
2025-12-11 22:19:34.654307 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.654869 INFO::Done
2025-12-11 22:19:34.669871 INFO::Formatting Data.
2025-12-11 22:19:34.670561 INFO::Recognized SummarizedExperiment
2025-12-11 22:19:34.671053 INFO::Typecasting input to dataframe.
2025-12-11 22:19:34.687376 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.688558 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.691903 INFO::Found 0 missing values.
2025-12-11 22:19:34.702066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.702737 INFO::Done
2025-12-11 22:19:34.717665 INFO::Formatting Data.
2025-12-11 22:19:34.718363 INFO::Recognized SummarizedExperiment
2025-12-11 22:19:34.718864 INFO::Typecasting input to dataframe.
2025-12-11 22:19:34.734207 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.735236 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.736248 INFO::Found 0 missing values.
2025-12-11 22:19:34.73712 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-11 22:19:34.741265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.741783 INFO::Done
2025-12-11 22:19:34.75159 INFO::Formatting Data.
2025-12-11 22:19:34.752318 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.75315 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.754082 INFO::Found 0 missing values.
2025-12-11 22:19:34.756742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.757226 INFO::Done
2025-12-11 22:19:34.76847 INFO::Formatting Data.
2025-12-11 22:19:34.769418 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.77028 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.77125 INFO::Found 0 missing values.
2025-12-11 22:19:34.774057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.77457 INFO::Done
2025-12-11 22:19:34.805287 INFO::Formatting Data.
2025-12-11 22:19:34.806228 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.807307 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.808471 INFO::Found 1 missing values.
2025-12-11 22:19:34.811385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.811922 INFO::Done
2025-12-11 22:19:34.831632 INFO::Formatting Data.
2025-12-11 22:19:34.832519 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.833444 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.834393 INFO::Found 2 missing values.
2025-12-11 22:19:34.835292 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-11 22:19:34.837527 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.83804 INFO::Done
2025-12-11 22:19:34.848796 INFO::Formatting Data.
2025-12-11 22:19:34.849648 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.850574 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.851525 INFO::Found 2 missing values.
2025-12-11 22:19:34.853163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.853708 INFO::Done
2025-12-11 22:19:34.864498 INFO::Formatting Data.
2025-12-11 22:19:34.865352 INFO::Typecasting input to dataframe.
2025-12-11 22:19:34.866264 INFO::Replacing NaNs with NAs.
2025-12-11 22:19:34.867141 INFO::Removing potential empty rows and columns
2025-12-11 22:19:34.868134 INFO::Found 0 missing values.
2025-12-11 22:19:34.870927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-11 22:19:34.871433 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.917 3.573 20.151
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.242 | 1.156 | 16.529 | |
| compute_asw | 0.022 | 0.003 | 0.025 | |
| count_existing | 0.011 | 0.003 | 0.014 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |