Yannis Schumann
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:00 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| 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: 2025-12-01 21:48:05 -0500 (Mon, 01 Dec 2025) |
| EndedAt: 2025-12-01 21:49:34 -0500 (Mon, 01 Dec 2025) |
| EllapsedTime: 89.1 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 24.592 1.516 17.845
* 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")
2025-12-01 21:48:57.527997 INFO::Formatting Data.
2025-12-01 21:48:57.529267 INFO::Replacing NaNs with NAs.
2025-12-01 21:48:57.540257 INFO::Removing potential empty rows and columns
2025-12-01 21:48:57.782958 INFO::Found 0 missing values.
2025-12-01 21:48:57.786569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:48:57.787282 INFO::Done
2025-12-01 21:48:57.787868 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:48:57.799337 INFO::Starting hierarchical adjustment
2025-12-01 21:48:57.800194 INFO::Found 3 batches.
2025-12-01 21:48:57.800767 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:48:57.80202 INFO::Using default BPPARAM
2025-12-01 21:48:57.802611 INFO::Processing subtree level 1
2025-12-01 21:48:57.899119 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:48:57.900792 INFO::Done
2025-12-01 21:48:57.901414 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:48:57.903774 INFO::ASW Batch was -0.0729922161097779 prior to batch effect correction and is now -0.0729922161097779 .
2025-12-01 21:48:57.904765 INFO::Total function execution time is 0.377454996109009 s and adjustment time is 0.100764513015747 s ( 26.7 )
2025-12-01 21:48:57.918095 INFO::Formatting Data.
2025-12-01 21:48:57.918857 INFO::Replacing NaNs with NAs.
2025-12-01 21:48:57.919859 INFO::Removing potential empty rows and columns
2025-12-01 21:48:57.921046 INFO::Found 0 missing values.
2025-12-01 21:48:57.92202 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.
2025-12-01 21:48:57.932928 INFO::Formatting Data.
2025-12-01 21:48:57.93367 INFO::Replacing NaNs with NAs.
2025-12-01 21:48:57.934574 INFO::Removing potential empty rows and columns
2025-12-01 21:48:57.935634 INFO::Found 0 missing values.
2025-12-01 21:48:57.936581 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.
2025-12-01 21:48:57.952783 INFO::Formatting Data.
2025-12-01 21:48:57.953537 INFO::Replacing NaNs with NAs.
2025-12-01 21:48:57.954422 INFO::Removing potential empty rows and columns
2025-12-01 21:48:57.955472 INFO::Found 0 missing values.
2025-12-01 21:48:57.956398 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.
2025-12-01 21:48:57.960972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:48:57.961543 INFO::Done
2025-12-01 21:48:57.962093 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:48:57.964094 INFO::Starting hierarchical adjustment
2025-12-01 21:48:57.964836 INFO::Found 2 batches.
2025-12-01 21:48:57.965374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:48:57.966051 INFO::Using default BPPARAM
2025-12-01 21:48:57.966595 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:48:57.967502 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:48:57.988547 INFO::Done
2025-12-01 21:48:57.989221 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:48:57.991275 INFO::ASW Batch was -0.000951536305663473 prior to batch effect correction and is now -0.0729073188582419 .
2025-12-01 21:48:57.992077 INFO::Total function execution time is 0.0394158363342285 s and adjustment time is 0.0238094329833984 s ( 60.41 )
2025-12-01 21:48:57.994847 INFO::Formatting Data.
2025-12-01 21:48:57.995459 INFO::Replacing NaNs with NAs.
2025-12-01 21:48:58.004275 INFO::Formatting Data.
2025-12-01 21:48:58.005002 INFO::Replacing NaNs with NAs.
2025-12-01 21:48:58.005918 INFO::Removing potential empty rows and columns
2025-12-01 21:48:58.006981 INFO::Found 0 missing values.
2025-12-01 21:48:58.009935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:48:58.010468 INFO::Done
2025-12-01 21:48:58.011018 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:48:58.012999 INFO::Starting hierarchical adjustment
2025-12-01 21:48:58.013722 INFO::Found 2 batches.
2025-12-01 21:48:58.014262 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:48:58.034756 INFO::Using default BPPARAM
2025-12-01 21:48:58.036882 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:48:58.03782 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:48:58.051238 INFO::Done
2025-12-01 21:48:58.051846 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:48:58.053794 INFO::ASW Batch was 0.025154502514427 prior to batch effect correction and is now -0.109615790569749 .
2025-12-01 21:48:58.054516 INFO::Total function execution time is 0.0502727031707764 s and adjustment time is 0.0376851558685303 s ( 74.96 )
2025-12-01 21:48:58.055476 INFO::Formatting Data.
2025-12-01 21:48:58.056044 INFO::Replacing NaNs with NAs.
2025-12-01 21:48:58.056827 INFO::Removing potential empty rows and columns
2025-12-01 21:48:58.057766 INFO::Found 0 missing values.
2025-12-01 21:48:58.060299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:48:58.060803 INFO::Done
2025-12-01 21:48:58.061275 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:48:58.063094 INFO::Starting hierarchical adjustment
2025-12-01 21:48:58.06375 INFO::Found 2 batches.
2025-12-01 21:48:58.064224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:48:58.064788 INFO::Using default BPPARAM
2025-12-01 21:48:58.065264 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:48:58.0661 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:48:58.079545 INFO::Done
2025-12-01 21:48:58.080131 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:48:58.08197 INFO::ASW Batch was 0.025154502514427 prior to batch effect correction and is now -0.109615790569749 .
2025-12-01 21:48:58.082705 INFO::Total function execution time is 0.0272278785705566 s and adjustment time is 0.0159025192260742 s ( 58.41 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-01 21:49:00.97909 INFO::Formatting Data.
2025-12-01 21:49:00.979864 INFO::Recognized SummarizedExperiment
2025-12-01 21:49:00.980341 INFO::Typecasting input to dataframe.
2025-12-01 21:49:01.010272 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:01.011599 INFO::Removing potential empty rows and columns
2025-12-01 21:49:01.015424 INFO::Found 0 missing values.
2025-12-01 21:49:01.022726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:01.023365 INFO::Done
2025-12-01 21:49:01.023946 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:01.027684 INFO::Starting hierarchical adjustment
2025-12-01 21:49:01.028416 INFO::Found 2 batches.
2025-12-01 21:49:01.028948 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:01.030082 INFO::Using default BPPARAM
2025-12-01 21:49:01.030638 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:01.031638 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:49:01.089715 INFO::Done
2025-12-01 21:49:01.090492 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:01.094308 INFO::ASW Batch was 0.00544258607306884 prior to batch effect correction and is now -0.0892078688659403 .
2025-12-01 21:49:01.095217 INFO::Total function execution time is 0.116430044174194 s and adjustment time is 0.0614109039306641 s ( 52.74 )
Warning: stack imbalance in '{', 73 then 75
2025-12-01 21:49:01.11497 INFO::Formatting Data.
2025-12-01 21:49:01.11582 INFO::Recognized SummarizedExperiment
2025-12-01 21:49:01.116366 INFO::Typecasting input to dataframe.
2025-12-01 21:49:01.12626 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:01.127521 INFO::Removing potential empty rows and columns
2025-12-01 21:49:01.131347 INFO::Found 0 missing values.
2025-12-01 21:49:01.138815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:01.139454 INFO::Done
2025-12-01 21:49:01.14002 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:01.143858 INFO::Starting hierarchical adjustment
2025-12-01 21:49:01.144599 INFO::Found 2 batches.
2025-12-01 21:49:01.145118 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:01.145738 INFO::Using default BPPARAM
2025-12-01 21:49:01.146269 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:01.14732 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:49:01.173429 INFO::Done
2025-12-01 21:49:01.174325 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:01.178171 INFO::ASW Batch was -0.0333726387939773 prior to batch effect correction and is now -0.0333726387939773 .
2025-12-01 21:49:01.179093 INFO::Total function execution time is 0.0641355514526367 s and adjustment time is 0.0289237499237061 s ( 45.1 )
2025-12-01 21:49:01.198843 INFO::Formatting Data.
2025-12-01 21:49:01.199709 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:01.200664 INFO::Removing potential empty rows and columns
2025-12-01 21:49:01.20173 INFO::Found 0 missing values.
2025-12-01 21:49:01.204842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:01.205384 INFO::Done
2025-12-01 21:49:01.20593 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:01.208074 INFO::Starting hierarchical adjustment
2025-12-01 21:49:01.2088 INFO::Found 3 batches.
2025-12-01 21:49:01.209311 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:01.209935 INFO::Using default BPPARAM
2025-12-01 21:49:01.210445 INFO::Processing subtree level 1
2025-12-01 21:49:01.346313 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:49:01.348364 INFO::Done
2025-12-01 21:49:01.349018 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:01.351582 INFO::ASW Batch was -0.136593666649737 prior to batch effect correction and is now -0.158648383222616 .
2025-12-01 21:49:01.352479 INFO::Total function execution time is 0.153713703155518 s and adjustment time is 0.139709234237671 s ( 90.89 )
2025-12-01 21:49:01.367538 INFO::Skipping initial DF formatting
2025-12-01 21:49:01.368216 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:01.3723 INFO::Starting hierarchical adjustment
2025-12-01 21:49:01.373075 INFO::Found 5 batches.
2025-12-01 21:49:01.37362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:01.374249 INFO::Using default BPPARAM
2025-12-01 21:49:01.374796 INFO::Processing subtree level 1
2025-12-01 21:49:01.604286 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:01.60612 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:49:01.626559 INFO::Done
2025-12-01 21:49:01.627385 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:01.631971 INFO::ASW Batch was 0.515430183505491 prior to batch effect correction and is now 0.515430183505491 .
2025-12-01 21:49:01.632642 INFO::ASW Label was 0.360104772072748 prior to batch effect correction and is now 0.360104772072748 .
2025-12-01 21:49:01.633757 INFO::Total function execution time is 0.266206979751587 s and adjustment time is 0.253567934036255 s ( 95.25 )
2025-12-01 21:49:01.709453 INFO::Formatting Data.
2025-12-01 21:49:01.710368 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:01.711373 INFO::Removing potential empty rows and columns
2025-12-01 21:49:01.712492 INFO::Found 0 missing values.
2025-12-01 21:49:01.716739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:01.717297 INFO::Done
2025-12-01 21:49:01.717852 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:01.72105 INFO::Starting hierarchical adjustment
2025-12-01 21:49:01.721848 INFO::Found 5 batches.
2025-12-01 21:49:01.722378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:01.723009 INFO::Using default BPPARAM
2025-12-01 21:49:01.723559 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.
2025-12-01 21:49:01.848083 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:01.8499 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:49:01.868657 INFO::Done
2025-12-01 21:49:01.869464 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:01.873283 INFO::ASW Batch was 0.35531686884712 prior to batch effect correction and is now -0.0930651597970165 .
2025-12-01 21:49:01.873952 INFO::ASW Label was 0.330474885185893 prior to batch effect correction and is now 0.886003869234208 .
2025-12-01 21:49:01.874847 INFO::Total function execution time is 0.165512800216675 s and adjustment time is 0.146904230117798 s ( 88.76 )
2025-12-01 21:49:01.875808 INFO::Formatting Data.
2025-12-01 21:49:01.876472 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:01.877491 INFO::Removing potential empty rows and columns
2025-12-01 21:49:01.878647 INFO::Found 0 missing values.
2025-12-01 21:49:01.883386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:01.884061 INFO::Done
2025-12-01 21:49:01.884604 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:01.887931 INFO::Starting hierarchical adjustment
2025-12-01 21:49:01.888697 INFO::Found 5 batches.
2025-12-01 21:49:01.889264 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:01.889925 INFO::Using default BPPARAM
2025-12-01 21:49:01.890498 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.
2025-12-01 21:49:02.006115 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:02.00788 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:49:02.025481 INFO::Done
2025-12-01 21:49:02.026182 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.029668 INFO::ASW Batch was 0.35531686884712 prior to batch effect correction and is now -0.0930651597970165 .
2025-12-01 21:49:02.030283 INFO::ASW Label was 0.330474885185893 prior to batch effect correction and is now 0.886003869234208 .
2025-12-01 21:49:02.031142 INFO::Total function execution time is 0.155349731445312 s and adjustment time is 0.13692307472229 s ( 88.14 )
2025-12-01 21:49:02.045583 INFO::Formatting Data.
2025-12-01 21:49:02.046346 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.047231 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.048226 INFO::Found 0 missing values.
2025-12-01 21:49:02.052186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.052759 INFO::Done
2025-12-01 21:49:02.053253 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.056249 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.056929 INFO::Found 5 batches.
2025-12-01 21:49:02.057433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.058061 INFO::Using default BPPARAM
2025-12-01 21:49:02.058571 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.
2025-12-01 21:49:02.170418 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:02.171975 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:49:02.191709 INFO::Done
2025-12-01 21:49:02.192533 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.196035 INFO::ASW Batch was 0.403683702575748 prior to batch effect correction and is now -0.0931860980038815 .
2025-12-01 21:49:02.196689 INFO::ASW Label was 0.325010325776287 prior to batch effect correction and is now 0.875907119367759 .
2025-12-01 21:49:02.197533 INFO::Total function execution time is 0.152075529098511 s and adjustment time is 0.134840250015259 s ( 88.67 )
2025-12-01 21:49:02.19842 INFO::Formatting Data.
2025-12-01 21:49:02.199102 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.200053 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.201133 INFO::Found 0 missing values.
2025-12-01 21:49:02.205362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.20594 INFO::Done
2025-12-01 21:49:02.206491 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.209551 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.210275 INFO::Found 5 batches.
2025-12-01 21:49:02.210824 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.211524 INFO::Using default BPPARAM
2025-12-01 21:49:02.212075 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.
2025-12-01 21:49:02.337052 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:02.338934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:49:02.357769 INFO::Done
2025-12-01 21:49:02.358664 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.362347 INFO::ASW Batch was 0.403683702575748 prior to batch effect correction and is now -0.0931860980038815 .
2025-12-01 21:49:02.363172 INFO::ASW Label was 0.325010325776287 prior to batch effect correction and is now 0.875907119367759 .
2025-12-01 21:49:02.364254 INFO::Total function execution time is 0.165805339813232 s and adjustment time is 0.147612571716309 s ( 89.03 )
2025-12-01 21:49:02.380057 INFO::Formatting Data.
2025-12-01 21:49:02.380914 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.38194 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.38306 INFO::Found 0 missing values.
2025-12-01 21:49:02.386077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.386685 INFO::Done
2025-12-01 21:49:02.387243 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.390422 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.391198 INFO::Found 2 batches.
2025-12-01 21:49:02.391791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.392442 INFO::Using default BPPARAM
2025-12-01 21:49:02.393034 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:02.394001 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:49:02.40911 INFO::Done
2025-12-01 21:49:02.409767 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.412681 INFO::ASW Batch was 0.613436248910789 prior to batch effect correction and is now 0.0330067796532968 .
2025-12-01 21:49:02.413263 INFO::ASW Label was 0.478171643806446 prior to batch effect correction and is now 0.897041680692791 .
2025-12-01 21:49:02.414035 INFO::Total function execution time is 0.0340638160705566 s and adjustment time is 0.01806640625 s ( 53.04 )
2025-12-01 21:49:02.414807 INFO::Formatting Data.
2025-12-01 21:49:02.415403 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.416256 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.417226 INFO::Found 0 missing values.
2025-12-01 21:49:02.419805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.42032 INFO::Done
2025-12-01 21:49:02.420832 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.423657 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.424344 INFO::Found 2 batches.
2025-12-01 21:49:02.424877 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.425461 INFO::Using default BPPARAM
2025-12-01 21:49:02.42598 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:02.426857 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-01 21:49:02.441023 INFO::Done
2025-12-01 21:49:02.441654 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.444496 INFO::ASW Batch was 0.613436248910789 prior to batch effect correction and is now 0.0330067796532968 .
2025-12-01 21:49:02.445103 INFO::ASW Label was 0.478171643806446 prior to batch effect correction and is now 0.897041680692791 .
2025-12-01 21:49:02.445856 INFO::Total function execution time is 0.031064510345459 s and adjustment time is 0.016817569732666 s ( 54.14 )
2025-12-01 21:49:02.456623 INFO::Formatting Data.
2025-12-01 21:49:02.457344 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.458195 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.459093 INFO::Found 0 missing values.
2025-12-01 21:49:02.461127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.461658 INFO::Done
2025-12-01 21:49:02.462148 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.464004 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.464682 INFO::Found 2 batches.
2025-12-01 21:49:02.465189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.465777 INFO::Using default BPPARAM
2025-12-01 21:49:02.466291 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:02.467146 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:49:02.49774 INFO::Done
2025-12-01 21:49:02.498404 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.500281 INFO::ASW Batch was -0.0595455267150024 prior to batch effect correction and is now -0.123466970556085 .
2025-12-01 21:49:02.50107 INFO::Total function execution time is 0.0446083545684814 s and adjustment time is 0.03318190574646 s ( 74.38 )
2025-12-01 21:49:02.512304 INFO::Formatting Data.
2025-12-01 21:49:02.513027 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.513864 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.514817 INFO::Found 0 missing values.
2025-12-01 21:49:02.515934 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.
2025-12-01 21:49:02.520282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.520822 INFO::Done
2025-12-01 21:49:02.521311 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.524145 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.524823 INFO::Found 2 batches.
2025-12-01 21:49:02.525329 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.525909 INFO::Using default BPPARAM
2025-12-01 21:49:02.52641 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:02.527308 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:49:02.542981 INFO::Done
2025-12-01 21:49:02.543612 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.546381 INFO::ASW Batch was 0.596088930494821 prior to batch effect correction and is now -0.0211978432015633 .
2025-12-01 21:49:02.546961 INFO::ASW Label was 0.43511392322524 prior to batch effect correction and is now 0.919096718263526 .
2025-12-01 21:49:02.547701 INFO::Total function execution time is 0.0354712009429932 s and adjustment time is 0.0182766914367676 s ( 51.53 )
2025-12-01 21:49:02.548458 INFO::Formatting Data.
2025-12-01 21:49:02.549061 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.549934 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.550913 INFO::Found 0 missing values.
2025-12-01 21:49:02.551796 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.
2025-12-01 21:49:02.556045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.556579 INFO::Done
2025-12-01 21:49:02.557082 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.559812 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.560472 INFO::Found 2 batches.
2025-12-01 21:49:02.560987 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.561555 INFO::Using default BPPARAM
2025-12-01 21:49:02.562056 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:02.562933 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:49:02.578521 INFO::Done
2025-12-01 21:49:02.57914 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.581881 INFO::ASW Batch was 0.596088930494821 prior to batch effect correction and is now -0.0211978432015633 .
2025-12-01 21:49:02.582417 INFO::ASW Label was 0.43511392322524 prior to batch effect correction and is now 0.919096718263526 .
2025-12-01 21:49:02.583165 INFO::Total function execution time is 0.0347127914428711 s and adjustment time is 0.0181560516357422 s ( 52.3 )
2025-12-01 21:49:02.79009 INFO::Formatting Data.
2025-12-01 21:49:02.790894 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.791806 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.792867 INFO::Found 0 missing values.
2025-12-01 21:49:02.795866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.796399 INFO::Done
2025-12-01 21:49:02.796941 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.798942 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.799644 INFO::Found 3 batches.
2025-12-01 21:49:02.800168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.800785 INFO::Using default BPPARAM
2025-12-01 21:49:02.801316 INFO::Processing subtree level 1
2025-12-01 21:49:02.878793 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:49:02.880483 INFO::Done
2025-12-01 21:49:02.881125 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.883487 INFO::ASW Batch was 0.0441991803895233 prior to batch effect correction and is now 0.0441991803895233 .
2025-12-01 21:49:02.884414 INFO::Total function execution time is 0.0943758487701416 s and adjustment time is 0.0809793472290039 s ( 85.81 )
2025-12-01 21:49:02.885427 INFO::Formatting Data.
2025-12-01 21:49:02.886094 INFO::Typecasting input to dataframe.
2025-12-01 21:49:02.88687 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.887784 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.888854 INFO::Found 0 missing values.
2025-12-01 21:49:02.891909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.892448 INFO::Done
2025-12-01 21:49:02.892984 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:02.894946 INFO::Starting hierarchical adjustment
2025-12-01 21:49:02.895659 INFO::Found 3 batches.
2025-12-01 21:49:02.896189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:02.896814 INFO::Using default BPPARAM
2025-12-01 21:49:02.897357 INFO::Processing subtree level 1
2025-12-01 21:49:02.97418 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:49:02.975924 INFO::Done
2025-12-01 21:49:02.976594 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:02.978972 INFO::ASW Batch was 0.0441991803895233 prior to batch effect correction and is now 0.0441991803895233 .
2025-12-01 21:49:02.979878 INFO::Total function execution time is 0.0944488048553467 s and adjustment time is 0.080402135848999 s ( 85.13 )
2025-12-01 21:49:02.99243 INFO::Formatting Data.
2025-12-01 21:49:02.993263 INFO::Typecasting input to dataframe.
2025-12-01 21:49:02.994106 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:02.995015 INFO::Removing potential empty rows and columns
2025-12-01 21:49:02.996076 INFO::Found 0 missing values.
2025-12-01 21:49:02.999052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:02.999599 INFO::Done
2025-12-01 21:49:03.00012 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:03.002099 INFO::Starting hierarchical adjustment
2025-12-01 21:49:03.002816 INFO::Found 3 batches.
2025-12-01 21:49:03.003352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:03.003965 INFO::Using default BPPARAM
2025-12-01 21:49:03.004502 INFO::Processing subtree level 1
2025-12-01 21:49:03.082407 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:49:03.084231 INFO::Done
2025-12-01 21:49:03.084915 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:03.08745 INFO::ASW Batch was -0.0512995028798648 prior to batch effect correction and is now -0.0512995028798648 .
2025-12-01 21:49:03.088425 INFO::Total function execution time is 0.0960352420806885 s and adjustment time is 0.0815291404724121 s ( 84.9 )
2025-12-01 21:49:03.217616 INFO::Formatting Data.
2025-12-01 21:49:03.218359 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:03.219435 INFO::Removing potential empty rows and columns
2025-12-01 21:49:03.222198 INFO::Found 1000 missing values.
2025-12-01 21:49:03.241225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:03.241971 INFO::Done
2025-12-01 21:49:03.242546 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:03.248052 INFO::Starting hierarchical adjustment
2025-12-01 21:49:03.248847 INFO::Found 10 batches.
2025-12-01 21:49:03.249374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:03.250005 INFO::Using default BPPARAM
2025-12-01 21:49:03.250559 INFO::Processing subtree level 1
2025-12-01 21:49:03.366608 INFO::Processing subtree level 2
2025-12-01 21:49:03.501242 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:49:03.503204 INFO::Done
2025-12-01 21:49:03.503868 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:03.50929 INFO::ASW Batch was 0.497626074776292 prior to batch effect correction and is now 0.497626074776292 .
2025-12-01 21:49:03.509938 INFO::ASW Label was 0.332624692523515 prior to batch effect correction and is now 0.332624692523515 .
2025-12-01 21:49:03.510849 INFO::Total function execution time is 0.293287038803101 s and adjustment time is 0.25449800491333 s ( 86.77 )
2025-12-01 21:49:03.511706 INFO::Formatting Data.
2025-12-01 21:49:03.512352 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:03.513481 INFO::Removing potential empty rows and columns
2025-12-01 21:49:03.516391 INFO::Found 1000 missing values.
2025-12-01 21:49:03.535449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:03.536187 INFO::Done
2025-12-01 21:49:03.536768 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:03.54219 INFO::Starting hierarchical adjustment
2025-12-01 21:49:03.542971 INFO::Found 10 batches.
2025-12-01 21:49:04.650894 INFO::Set up parallel execution backend with 2 workers
2025-12-01 21:49:04.653062 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-01 21:49:05.766855 INFO::Adjusting the last 2 batches sequentially
2025-12-01 21:49:05.768609 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-01 21:49:05.784231 INFO::Done
2025-12-01 21:49:05.784858 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:05.789208 INFO::ASW Batch was 0.497626074776292 prior to batch effect correction and is now 0.497626074776292 .
2025-12-01 21:49:05.789751 INFO::ASW Label was 0.332624692523515 prior to batch effect correction and is now 0.332624692523515 .
2025-12-01 21:49:05.790429 INFO::Total function execution time is 2.27877044677734 s and adjustment time is 2.24140095710754 s ( 98.36 )
2025-12-01 21:49:05.926409 INFO::Formatting Data.
2025-12-01 21:49:05.927297 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:05.928281 INFO::Removing potential empty rows and columns
2025-12-01 21:49:05.929403 INFO::Found 0 missing values.
2025-12-01 21:49:05.933129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:05.933699 INFO::Done
2025-12-01 21:49:05.934208 INFO::Acquiring quality metrics before batch effect correction.
2025-12-01 21:49:05.93717 INFO::Starting hierarchical adjustment
2025-12-01 21:49:05.937927 INFO::Found 3 batches.
2025-12-01 21:49:05.93845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-01 21:49:05.93909 INFO::Using default BPPARAM
2025-12-01 21:49:05.93964 INFO::Processing subtree level 1
2025-12-01 21:49:06.038007 INFO::Adjusting the last 1 batches sequentially
2025-12-01 21:49:06.039765 INFO::Done
2025-12-01 21:49:06.040401 INFO::Acquiring quality metrics after batch effect correction.
2025-12-01 21:49:06.043519 INFO::ASW Batch was 0.185053818697693 prior to batch effect correction and is now -0.144689852097677 .
2025-12-01 21:49:06.044137 INFO::ASW Label was -0.214161363997662 prior to batch effect correction and is now -0.0459402855679582 .
2025-12-01 21:49:06.044996 INFO::Total function execution time is 0.118738412857056 s and adjustment time is 0.101977586746216 s ( 85.88 )
2025-12-01 21:49:06.167092 INFO::Formatting Data.
2025-12-01 21:49:06.168088 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.168979 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.170008 INFO::Found 2 missing values.
2025-12-01 21:49:06.172781 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.173289 INFO::Done
2025-12-01 21:49:06.198907 INFO::Found NA in Reference column
2025-12-01 21:49:06.207761 INFO::Require at least two references per batch.
2025-12-01 21:49:06.227888 INFO::Formatting Data.
2025-12-01 21:49:06.228592 INFO::Recognized SummarizedExperiment
2025-12-01 21:49:06.229102 INFO::Typecasting input to dataframe.
2025-12-01 21:49:06.238844 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.239903 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.243107 INFO::Found 0 missing values.
2025-12-01 21:49:06.249256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.24981 INFO::Done
2025-12-01 21:49:06.26429 INFO::Formatting Data.
2025-12-01 21:49:06.264955 INFO::Recognized SummarizedExperiment
2025-12-01 21:49:06.265447 INFO::Typecasting input to dataframe.
2025-12-01 21:49:06.281478 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.282628 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.285901 INFO::Found 0 missing values.
2025-12-01 21:49:06.295768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.296354 INFO::Done
2025-12-01 21:49:06.310766 INFO::Formatting Data.
2025-12-01 21:49:06.311423 INFO::Recognized SummarizedExperiment
2025-12-01 21:49:06.311919 INFO::Typecasting input to dataframe.
2025-12-01 21:49:06.327138 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.328092 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.329098 INFO::Found 0 missing values.
2025-12-01 21:49:06.329962 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.
2025-12-01 21:49:06.334006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.334504 INFO::Done
2025-12-01 21:49:06.34388 INFO::Formatting Data.
2025-12-01 21:49:06.344573 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.345359 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.346275 INFO::Found 0 missing values.
2025-12-01 21:49:06.348889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.349378 INFO::Done
2025-12-01 21:49:06.360042 INFO::Formatting Data.
2025-12-01 21:49:06.360747 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.361564 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.362496 INFO::Found 0 missing values.
2025-12-01 21:49:06.365154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.365678 INFO::Done
2025-12-01 21:49:06.393038 INFO::Formatting Data.
2025-12-01 21:49:06.393825 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.394823 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.396004 INFO::Found 1 missing values.
2025-12-01 21:49:06.398564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.399083 INFO::Done
2025-12-01 21:49:06.416352 INFO::Formatting Data.
2025-12-01 21:49:06.417215 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.418049 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.418928 INFO::Found 2 missing values.
2025-12-01 21:49:06.419784 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.
2025-12-01 21:49:06.421899 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.4224 INFO::Done
2025-12-01 21:49:06.431695 INFO::Formatting Data.
2025-12-01 21:49:06.432374 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.433196 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.43409 INFO::Found 2 missing values.
2025-12-01 21:49:06.435609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.436104 INFO::Done
2025-12-01 21:49:06.445687 INFO::Formatting Data.
2025-12-01 21:49:06.446368 INFO::Typecasting input to dataframe.
2025-12-01 21:49:06.447113 INFO::Replacing NaNs with NAs.
2025-12-01 21:49:06.447916 INFO::Removing potential empty rows and columns
2025-12-01 21:49:06.448841 INFO::Found 0 missing values.
2025-12-01 21:49:06.451457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-01 21:49:06.451968 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.235 3.116 20.198
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.592 | 1.516 | 17.845 | |
| compute_asw | 0.024 | 0.002 | 0.026 | |
| count_existing | 0.013 | 0.003 | 0.015 | |
| generate_data_covariables | 0.012 | 0.002 | 0.013 | |
| generate_dataset | 0.012 | 0.001 | 0.012 | |