Yannis Schumann
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 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 2025-12-22 12:04 -0500 (Mon, 22 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" | 4883 |
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-12-19 00:57:11 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 00:59:44 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 152.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 43.292 2.614 39.835
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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-apple-darwin20
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")
2025-12-19 00:59:04.266936 INFO::Formatting Data.
2025-12-19 00:59:04.272999 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:04.303714 INFO::Removing potential empty rows and columns
2025-12-19 00:59:05.096804 INFO::Found 0 missing values.
2025-12-19 00:59:05.109308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:05.112733 INFO::Done
2025-12-19 00:59:05.114166 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:05.143589 INFO::Starting hierarchical adjustment
2025-12-19 00:59:05.145676 INFO::Found 3 batches.
2025-12-19 00:59:05.147753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:05.150867 INFO::Using default BPPARAM
2025-12-19 00:59:05.152422 INFO::Processing subtree level 1
2025-12-19 00:59:05.416726 INFO::Adjusting the last 1 batches sequentially
2025-12-19 00:59:05.42371 INFO::Done
2025-12-19 00:59:05.425726 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:05.433129 INFO::ASW Batch was -0.0923783189285171 prior to batch effect correction and is now -0.0923783189285171 .
2025-12-19 00:59:05.43613 INFO::Total function execution time is 1.16971111297607 s and adjustment time is 0.278419017791748 s ( 23.8 )
2025-12-19 00:59:05.487493 INFO::Formatting Data.
2025-12-19 00:59:05.489585 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:05.491744 INFO::Removing potential empty rows and columns
2025-12-19 00:59:05.496246 INFO::Found 0 missing values.
2025-12-19 00:59:05.499704 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.
2025-12-19 00:59:05.534086 INFO::Formatting Data.
2025-12-19 00:59:05.535572 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:05.537443 INFO::Removing potential empty rows and columns
2025-12-19 00:59:05.540536 INFO::Found 0 missing values.
2025-12-19 00:59:05.543067 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.
2025-12-19 00:59:05.5872 INFO::Formatting Data.
2025-12-19 00:59:05.590611 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:05.602611 INFO::Removing potential empty rows and columns
2025-12-19 00:59:05.606054 INFO::Found 0 missing values.
2025-12-19 00:59:05.608484 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.
2025-12-19 00:59:05.622826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:05.624575 INFO::Done
2025-12-19 00:59:05.643453 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:05.648915 INFO::Starting hierarchical adjustment
2025-12-19 00:59:05.65113 INFO::Found 2 batches.
2025-12-19 00:59:05.652699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:05.65441 INFO::Using default BPPARAM
2025-12-19 00:59:05.655789 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:05.658417 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 00:59:05.716527 INFO::Done
2025-12-19 00:59:05.718053 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:05.723284 INFO::ASW Batch was -0.0619104946661605 prior to batch effect correction and is now -0.130405312762627 .
2025-12-19 00:59:05.726335 INFO::Total function execution time is 0.139117002487183 s and adjustment time is 0.0658440589904785 s ( 47.33 )
2025-12-19 00:59:05.742419 INFO::Formatting Data.
2025-12-19 00:59:05.744242 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:05.773948 INFO::Formatting Data.
2025-12-19 00:59:05.776338 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:05.778866 INFO::Removing potential empty rows and columns
2025-12-19 00:59:05.781959 INFO::Found 0 missing values.
2025-12-19 00:59:05.790399 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:05.791922 INFO::Done
2025-12-19 00:59:05.793473 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:05.85621 INFO::Starting hierarchical adjustment
2025-12-19 00:59:05.858273 INFO::Found 2 batches.
2025-12-19 00:59:05.859734 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:05.867824 INFO::Using default BPPARAM
2025-12-19 00:59:05.871021 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:05.874814 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 00:59:05.925355 INFO::Done
2025-12-19 00:59:05.927474 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:05.934432 INFO::ASW Batch was -0.0652290134474812 prior to batch effect correction and is now -0.117848390156397 .
2025-12-19 00:59:05.936597 INFO::Total function execution time is 0.162719964981079 s and adjustment time is 0.0672891139984131 s ( 41.35 )
2025-12-19 00:59:05.940122 INFO::Formatting Data.
2025-12-19 00:59:05.942027 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:05.944503 INFO::Removing potential empty rows and columns
2025-12-19 00:59:05.948928 INFO::Found 0 missing values.
2025-12-19 00:59:05.95767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:05.959234 INFO::Done
2025-12-19 00:59:05.960645 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:05.965695 INFO::Starting hierarchical adjustment
2025-12-19 00:59:05.96783 INFO::Found 2 batches.
2025-12-19 00:59:05.969477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:05.971109 INFO::Using default BPPARAM
2025-12-19 00:59:05.972478 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:05.974865 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 00:59:06.021413 INFO::Done
2025-12-19 00:59:06.029376 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:06.037057 INFO::ASW Batch was -0.0652290134474812 prior to batch effect correction and is now -0.117848390156397 .
2025-12-19 00:59:06.038964 INFO::Total function execution time is 0.0989089012145996 s and adjustment time is 0.0539278984069824 s ( 54.52 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-19 00:59:13.234511 INFO::Formatting Data.
2025-12-19 00:59:13.236066 INFO::Recognized SummarizedExperiment
2025-12-19 00:59:13.239041 INFO::Typecasting input to dataframe.
2025-12-19 00:59:13.314237 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:13.3169 INFO::Removing potential empty rows and columns
2025-12-19 00:59:13.330843 INFO::Found 0 missing values.
2025-12-19 00:59:13.3679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:13.369707 INFO::Done
2025-12-19 00:59:13.371092 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:13.382073 INFO::Starting hierarchical adjustment
2025-12-19 00:59:13.383966 INFO::Found 2 batches.
2025-12-19 00:59:13.38601 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:13.388373 INFO::Using default BPPARAM
2025-12-19 00:59:13.389634 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:13.391997 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 00:59:13.568869 INFO::Done
2025-12-19 00:59:13.570419 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:13.580118 INFO::ASW Batch was -0.0123747220307583 prior to batch effect correction and is now -0.0931907886309876 .
2025-12-19 00:59:13.582247 INFO::Total function execution time is 0.348318099975586 s and adjustment time is 0.185248136520386 s ( 53.18 )
Warning: stack imbalance in '{', 73 then 75
2025-12-19 00:59:13.660514 INFO::Formatting Data.
2025-12-19 00:59:13.662215 INFO::Recognized SummarizedExperiment
2025-12-19 00:59:13.663944 INFO::Typecasting input to dataframe.
2025-12-19 00:59:13.691627 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:13.694243 INFO::Removing potential empty rows and columns
2025-12-19 00:59:13.705127 INFO::Found 0 missing values.
2025-12-19 00:59:13.738466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:13.741837 INFO::Done
2025-12-19 00:59:13.743939 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:13.754583 INFO::Starting hierarchical adjustment
2025-12-19 00:59:13.758294 INFO::Found 2 batches.
2025-12-19 00:59:13.759685 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:13.76265 INFO::Using default BPPARAM
2025-12-19 00:59:13.764012 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:13.766447 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 00:59:13.852179 INFO::Done
2025-12-19 00:59:13.854015 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:13.864675 INFO::ASW Batch was 0.0211057616727883 prior to batch effect correction and is now 0.0211057616727883 .
2025-12-19 00:59:13.866611 INFO::Total function execution time is 0.207812070846558 s and adjustment time is 0.0961349010467529 s ( 46.26 )
2025-12-19 00:59:13.922816 INFO::Formatting Data.
2025-12-19 00:59:13.924453 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:13.926482 INFO::Removing potential empty rows and columns
2025-12-19 00:59:13.930564 INFO::Found 0 missing values.
2025-12-19 00:59:13.938581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:13.943548 INFO::Done
2025-12-19 00:59:13.952879 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:13.957982 INFO::Starting hierarchical adjustment
2025-12-19 00:59:13.959912 INFO::Found 3 batches.
2025-12-19 00:59:13.96141 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:13.965577 INFO::Using default BPPARAM
2025-12-19 00:59:13.967083 INFO::Processing subtree level 1
2025-12-19 00:59:14.339419 INFO::Adjusting the last 1 batches sequentially
2025-12-19 00:59:14.349167 INFO::Done
2025-12-19 00:59:14.352016 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:14.362225 INFO::ASW Batch was -0.116213839217694 prior to batch effect correction and is now -0.176663782449826 .
2025-12-19 00:59:14.365989 INFO::Total function execution time is 0.442477941513062 s and adjustment time is 0.389638185501099 s ( 88.06 )
2025-12-19 00:59:14.418438 INFO::Skipping initial DF formatting
2025-12-19 00:59:14.420659 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:14.432177 INFO::Starting hierarchical adjustment
2025-12-19 00:59:14.434968 INFO::Found 5 batches.
2025-12-19 00:59:14.436754 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:14.43876 INFO::Using default BPPARAM
2025-12-19 00:59:14.440192 INFO::Processing subtree level 1
2025-12-19 00:59:15.060415 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:15.070927 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 00:59:15.153435 INFO::Done
2025-12-19 00:59:15.156806 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:15.177038 INFO::ASW Batch was 0.498434331468251 prior to batch effect correction and is now 0.498434331468251 .
2025-12-19 00:59:15.17856 INFO::ASW Label was 0.404869137815366 prior to batch effect correction and is now 0.404869137815366 .
2025-12-19 00:59:15.183257 INFO::Total function execution time is 0.764037132263184 s and adjustment time is 0.719309091567993 s ( 94.15 )
2025-12-19 00:59:15.35414 INFO::Formatting Data.
2025-12-19 00:59:15.356896 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:15.359356 INFO::Removing potential empty rows and columns
2025-12-19 00:59:15.363465 INFO::Found 0 missing values.
2025-12-19 00:59:15.373576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:15.374988 INFO::Done
2025-12-19 00:59:15.376307 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:15.383094 INFO::Starting hierarchical adjustment
2025-12-19 00:59:15.384968 INFO::Found 5 batches.
2025-12-19 00:59:15.38626 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:15.387867 INFO::Using default BPPARAM
2025-12-19 00:59:15.389341 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.
2025-12-19 00:59:15.765871 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:15.78224 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 00:59:15.842579 INFO::Done
2025-12-19 00:59:15.844453 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:15.853468 INFO::ASW Batch was 0.523864367278324 prior to batch effect correction and is now -0.0505981455673501 .
2025-12-19 00:59:15.855318 INFO::ASW Label was 0.235873185170598 prior to batch effect correction and is now 0.798311525624341 .
2025-12-19 00:59:15.858345 INFO::Total function execution time is 0.503484010696411 s and adjustment time is 0.457919120788574 s ( 90.95 )
2025-12-19 00:59:15.861042 INFO::Formatting Data.
2025-12-19 00:59:15.862649 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:15.865088 INFO::Removing potential empty rows and columns
2025-12-19 00:59:15.868162 INFO::Found 0 missing values.
2025-12-19 00:59:15.880714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:15.882449 INFO::Done
2025-12-19 00:59:15.884237 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:15.892093 INFO::Starting hierarchical adjustment
2025-12-19 00:59:15.894705 INFO::Found 5 batches.
2025-12-19 00:59:15.896396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:15.898415 INFO::Using default BPPARAM
2025-12-19 00:59:15.900168 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.
2025-12-19 00:59:16.256102 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:16.26294 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 00:59:16.328808 INFO::Done
2025-12-19 00:59:16.330864 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:16.340185 INFO::ASW Batch was 0.523864367278324 prior to batch effect correction and is now -0.0505981455673501 .
2025-12-19 00:59:16.341848 INFO::ASW Label was 0.235873185170598 prior to batch effect correction and is now 0.798311525624341 .
2025-12-19 00:59:16.344012 INFO::Total function execution time is 0.483083009719849 s and adjustment time is 0.434633016586304 s ( 89.97 )
2025-12-19 00:59:16.383861 INFO::Formatting Data.
2025-12-19 00:59:16.385611 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:16.387743 INFO::Removing potential empty rows and columns
2025-12-19 00:59:16.390737 INFO::Found 0 missing values.
2025-12-19 00:59:16.402561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:16.404459 INFO::Done
2025-12-19 00:59:16.406337 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:16.415076 INFO::Starting hierarchical adjustment
2025-12-19 00:59:16.417177 INFO::Found 5 batches.
2025-12-19 00:59:16.423311 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:16.425375 INFO::Using default BPPARAM
2025-12-19 00:59:16.428247 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.
2025-12-19 00:59:16.793287 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:16.803887 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 00:59:16.875982 INFO::Done
2025-12-19 00:59:16.878788 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:16.888511 INFO::ASW Batch was 0.407569131872402 prior to batch effect correction and is now -0.0570141130331799 .
2025-12-19 00:59:16.890123 INFO::ASW Label was 0.407876014411107 prior to batch effect correction and is now 0.809831042737242 .
2025-12-19 00:59:16.8921 INFO::Total function execution time is 0.508252143859863 s and adjustment time is 0.459228038787842 s ( 90.35 )
2025-12-19 00:59:16.894043 INFO::Formatting Data.
2025-12-19 00:59:16.895586 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:16.897748 INFO::Removing potential empty rows and columns
2025-12-19 00:59:16.900787 INFO::Found 0 missing values.
2025-12-19 00:59:16.912583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:16.914211 INFO::Done
2025-12-19 00:59:16.915461 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:16.92285 INFO::Starting hierarchical adjustment
2025-12-19 00:59:16.929084 INFO::Found 5 batches.
2025-12-19 00:59:16.931828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:16.933655 INFO::Using default BPPARAM
2025-12-19 00:59:16.935623 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.
2025-12-19 00:59:17.266445 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:17.277563 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 00:59:17.33736 INFO::Done
2025-12-19 00:59:17.339057 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:17.3489 INFO::ASW Batch was 0.407569131872402 prior to batch effect correction and is now -0.0570141130331799 .
2025-12-19 00:59:17.350853 INFO::ASW Label was 0.407876014411107 prior to batch effect correction and is now 0.809831042737242 .
2025-12-19 00:59:17.377519 INFO::Total function execution time is 0.483346939086914 s and adjustment time is 0.408727884292603 s ( 84.56 )
2025-12-19 00:59:17.422351 INFO::Formatting Data.
2025-12-19 00:59:17.424118 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:17.426902 INFO::Removing potential empty rows and columns
2025-12-19 00:59:17.431253 INFO::Found 0 missing values.
2025-12-19 00:59:17.439869 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:17.4414 INFO::Done
2025-12-19 00:59:17.444666 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:17.452283 INFO::Starting hierarchical adjustment
2025-12-19 00:59:17.454297 INFO::Found 2 batches.
2025-12-19 00:59:17.457153 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:17.458858 INFO::Using default BPPARAM
2025-12-19 00:59:17.460322 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:17.462999 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 00:59:17.507034 INFO::Done
2025-12-19 00:59:17.51245 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:17.52214 INFO::ASW Batch was 0.589886406966416 prior to batch effect correction and is now -0.0351083781527547 .
2025-12-19 00:59:17.524204 INFO::ASW Label was 0.464895585043537 prior to batch effect correction and is now 0.904242818695357 .
2025-12-19 00:59:17.526687 INFO::Total function execution time is 0.10442590713501 s and adjustment time is 0.0531380176544189 s ( 50.89 )
2025-12-19 00:59:17.528733 INFO::Formatting Data.
2025-12-19 00:59:17.530444 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:17.532839 INFO::Removing potential empty rows and columns
2025-12-19 00:59:17.535368 INFO::Found 0 missing values.
2025-12-19 00:59:17.543022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:17.544576 INFO::Done
2025-12-19 00:59:17.546029 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:17.553868 INFO::Starting hierarchical adjustment
2025-12-19 00:59:17.555813 INFO::Found 2 batches.
2025-12-19 00:59:17.557159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:17.55872 INFO::Using default BPPARAM
2025-12-19 00:59:17.560078 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:17.562493 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-19 00:59:17.612179 INFO::Done
2025-12-19 00:59:17.617193 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:17.624585 INFO::ASW Batch was 0.589886406966416 prior to batch effect correction and is now -0.0351083781527547 .
2025-12-19 00:59:17.626065 INFO::ASW Label was 0.464895585043537 prior to batch effect correction and is now 0.904242818695357 .
2025-12-19 00:59:17.628178 INFO::Total function execution time is 0.0994400978088379 s and adjustment time is 0.056685209274292 s ( 57 )
2025-12-19 00:59:17.660256 INFO::Formatting Data.
2025-12-19 00:59:17.662064 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:17.664264 INFO::Removing potential empty rows and columns
2025-12-19 00:59:17.666667 INFO::Found 0 missing values.
2025-12-19 00:59:17.67227 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:17.67381 INFO::Done
2025-12-19 00:59:17.675188 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:17.679887 INFO::Starting hierarchical adjustment
2025-12-19 00:59:17.681836 INFO::Found 2 batches.
2025-12-19 00:59:17.683471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:17.685122 INFO::Using default BPPARAM
2025-12-19 00:59:17.686571 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:17.688907 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 00:59:17.767392 INFO::Done
2025-12-19 00:59:17.768728 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:17.774517 INFO::ASW Batch was -0.107671532994243 prior to batch effect correction and is now -0.171566104883672 .
2025-12-19 00:59:17.776913 INFO::Total function execution time is 0.116791963577271 s and adjustment time is 0.0859379768371582 s ( 73.58 )
2025-12-19 00:59:17.815535 INFO::Formatting Data.
2025-12-19 00:59:17.817326 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:17.825442 INFO::Removing potential empty rows and columns
2025-12-19 00:59:17.828144 INFO::Found 0 missing values.
2025-12-19 00:59:17.830681 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.
2025-12-19 00:59:17.849749 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:17.851278 INFO::Done
2025-12-19 00:59:17.852609 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:17.861616 INFO::Starting hierarchical adjustment
2025-12-19 00:59:17.86423 INFO::Found 2 batches.
2025-12-19 00:59:17.865625 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:17.867071 INFO::Using default BPPARAM
2025-12-19 00:59:17.868335 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:17.870568 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 00:59:17.931385 INFO::Done
2025-12-19 00:59:17.932828 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:17.939848 INFO::ASW Batch was 0.60123590090564 prior to batch effect correction and is now 0.12378229866739 .
2025-12-19 00:59:17.941428 INFO::ASW Label was 0.470522970558404 prior to batch effect correction and is now 0.808469193248119 .
2025-12-19 00:59:17.943301 INFO::Total function execution time is 0.127907037734985 s and adjustment time is 0.0677409172058105 s ( 52.96 )
2025-12-19 00:59:17.945144 INFO::Formatting Data.
2025-12-19 00:59:17.946513 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:17.948579 INFO::Removing potential empty rows and columns
2025-12-19 00:59:17.955119 INFO::Found 0 missing values.
2025-12-19 00:59:17.957332 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.
2025-12-19 00:59:17.971377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:17.972823 INFO::Done
2025-12-19 00:59:17.975557 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:17.982672 INFO::Starting hierarchical adjustment
2025-12-19 00:59:17.984548 INFO::Found 2 batches.
2025-12-19 00:59:17.98977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:17.991398 INFO::Using default BPPARAM
2025-12-19 00:59:17.992733 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:17.995327 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 00:59:18.055914 INFO::Done
2025-12-19 00:59:18.058202 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:18.065653 INFO::ASW Batch was 0.60123590090564 prior to batch effect correction and is now 0.12378229866739 .
2025-12-19 00:59:18.072996 INFO::ASW Label was 0.470522970558404 prior to batch effect correction and is now 0.808469193248119 .
2025-12-19 00:59:18.076618 INFO::Total function execution time is 0.13139796257019 s and adjustment time is 0.0710940361022949 s ( 54.11 )
2025-12-19 00:59:18.795878 INFO::Formatting Data.
2025-12-19 00:59:18.797346 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:18.799242 INFO::Removing potential empty rows and columns
2025-12-19 00:59:18.801819 INFO::Found 0 missing values.
2025-12-19 00:59:18.816597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:18.818097 INFO::Done
2025-12-19 00:59:18.819367 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:18.828293 INFO::Starting hierarchical adjustment
2025-12-19 00:59:18.838805 INFO::Found 3 batches.
2025-12-19 00:59:18.840417 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:18.84296 INFO::Using default BPPARAM
2025-12-19 00:59:18.844461 INFO::Processing subtree level 1
2025-12-19 00:59:19.084486 INFO::Adjusting the last 1 batches sequentially
2025-12-19 00:59:19.092302 INFO::Done
2025-12-19 00:59:19.094337 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:19.104875 INFO::ASW Batch was -0.0854905943777348 prior to batch effect correction and is now -0.0854905943777348 .
2025-12-19 00:59:19.108211 INFO::Total function execution time is 0.31145191192627 s and adjustment time is 0.253931999206543 s ( 81.53 )
2025-12-19 00:59:19.11159 INFO::Formatting Data.
2025-12-19 00:59:19.119186 INFO::Typecasting input to dataframe.
2025-12-19 00:59:19.125946 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:19.129445 INFO::Removing potential empty rows and columns
2025-12-19 00:59:19.132261 INFO::Found 0 missing values.
2025-12-19 00:59:19.144062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:19.145584 INFO::Done
2025-12-19 00:59:19.147451 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:19.152756 INFO::Starting hierarchical adjustment
2025-12-19 00:59:19.15482 INFO::Found 3 batches.
2025-12-19 00:59:19.156217 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:19.159226 INFO::Using default BPPARAM
2025-12-19 00:59:19.160844 INFO::Processing subtree level 1
2025-12-19 00:59:19.388846 INFO::Adjusting the last 1 batches sequentially
2025-12-19 00:59:19.396388 INFO::Done
2025-12-19 00:59:19.399571 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:19.410366 INFO::ASW Batch was -0.0854905943777348 prior to batch effect correction and is now -0.0854905943777348 .
2025-12-19 00:59:19.414855 INFO::Total function execution time is 0.30240797996521 s and adjustment time is 0.242061853408813 s ( 80.04 )
2025-12-19 00:59:19.470943 INFO::Formatting Data.
2025-12-19 00:59:19.47267 INFO::Typecasting input to dataframe.
2025-12-19 00:59:19.474768 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:19.478596 INFO::Removing potential empty rows and columns
2025-12-19 00:59:19.485755 INFO::Found 0 missing values.
2025-12-19 00:59:19.494682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:19.499616 INFO::Done
2025-12-19 00:59:19.501188 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:19.505967 INFO::Starting hierarchical adjustment
2025-12-19 00:59:19.508476 INFO::Found 3 batches.
2025-12-19 00:59:19.510452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:19.512057 INFO::Using default BPPARAM
2025-12-19 00:59:19.513414 INFO::Processing subtree level 1
2025-12-19 00:59:19.74126 INFO::Adjusting the last 1 batches sequentially
2025-12-19 00:59:19.749819 INFO::Done
2025-12-19 00:59:19.752223 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:19.761703 INFO::ASW Batch was 0.00160558886505169 prior to batch effect correction and is now 0.00160558886505169 .
2025-12-19 00:59:19.76629 INFO::Total function execution time is 0.295156955718994 s and adjustment time is 0.241717100143433 s ( 81.89 )
2025-12-19 00:59:20.160568 INFO::Formatting Data.
2025-12-19 00:59:20.164753 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:20.169027 INFO::Removing potential empty rows and columns
2025-12-19 00:59:20.178194 INFO::Found 1000 missing values.
2025-12-19 00:59:20.242788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:20.24443 INFO::Done
2025-12-19 00:59:20.245858 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:20.263989 INFO::Starting hierarchical adjustment
2025-12-19 00:59:20.266013 INFO::Found 10 batches.
2025-12-19 00:59:20.268001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:20.272457 INFO::Using default BPPARAM
2025-12-19 00:59:20.274777 INFO::Processing subtree level 1
2025-12-19 00:59:20.597302 INFO::Processing subtree level 2
2025-12-19 00:59:21.030159 INFO::Adjusting the last 1 batches sequentially
2025-12-19 00:59:21.043012 INFO::Done
2025-12-19 00:59:21.046492 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:21.068553 INFO::ASW Batch was 0.486956659701936 prior to batch effect correction and is now 0.486956659701936 .
2025-12-19 00:59:21.070589 INFO::ASW Label was 0.311844527684688 prior to batch effect correction and is now 0.311844527684688 .
2025-12-19 00:59:21.076895 INFO::Total function execution time is 0.915087938308716 s and adjustment time is 0.777360916137695 s ( 84.95 )
2025-12-19 00:59:21.080062 INFO::Formatting Data.
2025-12-19 00:59:21.081541 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:21.085847 INFO::Removing potential empty rows and columns
2025-12-19 00:59:21.096232 INFO::Found 1000 missing values.
2025-12-19 00:59:21.156249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:21.157624 INFO::Done
2025-12-19 00:59:21.158863 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:21.171931 INFO::Starting hierarchical adjustment
2025-12-19 00:59:21.173936 INFO::Found 10 batches.
2025-12-19 00:59:22.640495 INFO::Set up parallel execution backend with 2 workers
2025-12-19 00:59:22.641819 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-19 00:59:24.669898 INFO::Adjusting the last 2 batches sequentially
2025-12-19 00:59:24.672238 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-19 00:59:24.719485 INFO::Done
2025-12-19 00:59:24.7229 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:24.737963 INFO::ASW Batch was 0.486956659701936 prior to batch effect correction and is now 0.486956659701936 .
2025-12-19 00:59:24.739399 INFO::ASW Label was 0.311844527684688 prior to batch effect correction and is now 0.311844527684688 .
2025-12-19 00:59:24.741076 INFO::Total function execution time is 3.66110801696777 s and adjustment time is 3.5459349155426 s ( 96.85 )
2025-12-19 00:59:25.146605 INFO::Formatting Data.
2025-12-19 00:59:25.148473 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:25.152016 INFO::Removing potential empty rows and columns
2025-12-19 00:59:25.154765 INFO::Found 0 missing values.
2025-12-19 00:59:25.168597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:25.170111 INFO::Done
2025-12-19 00:59:25.171435 INFO::Acquiring quality metrics before batch effect correction.
2025-12-19 00:59:25.177963 INFO::Starting hierarchical adjustment
2025-12-19 00:59:25.180487 INFO::Found 3 batches.
2025-12-19 00:59:25.182064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-19 00:59:25.183791 INFO::Using default BPPARAM
2025-12-19 00:59:25.185248 INFO::Processing subtree level 1
2025-12-19 00:59:25.476637 INFO::Adjusting the last 1 batches sequentially
2025-12-19 00:59:25.484849 INFO::Done
2025-12-19 00:59:25.487577 INFO::Acquiring quality metrics after batch effect correction.
2025-12-19 00:59:25.504261 INFO::ASW Batch was 0.237496214129452 prior to batch effect correction and is now -0.160118802144646 .
2025-12-19 00:59:25.506496 INFO::ASW Label was -0.145307051735801 prior to batch effect correction and is now 0.0570441847426864 .
2025-12-19 00:59:25.508799 INFO::Total function execution time is 0.362397909164429 s and adjustment time is 0.304759979248047 s ( 84.1 )
2025-12-19 00:59:25.8832 INFO::Formatting Data.
2025-12-19 00:59:25.884977 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:25.889057 INFO::Removing potential empty rows and columns
2025-12-19 00:59:25.892365 INFO::Found 2 missing values.
2025-12-19 00:59:25.901224 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:25.903829 INFO::Done
2025-12-19 00:59:25.980392 INFO::Found NA in Reference column
2025-12-19 00:59:26.006328 INFO::Require at least two references per batch.
2025-12-19 00:59:26.065045 INFO::Formatting Data.
2025-12-19 00:59:26.06656 INFO::Recognized SummarizedExperiment
2025-12-19 00:59:26.067806 INFO::Typecasting input to dataframe.
2025-12-19 00:59:26.100505 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.10314 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.114649 INFO::Found 0 missing values.
2025-12-19 00:59:26.139539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.140832 INFO::Done
2025-12-19 00:59:26.185323 INFO::Formatting Data.
2025-12-19 00:59:26.187663 INFO::Recognized SummarizedExperiment
2025-12-19 00:59:26.189128 INFO::Typecasting input to dataframe.
2025-12-19 00:59:26.246699 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.250462 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.261384 INFO::Found 0 missing values.
2025-12-19 00:59:26.304806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.306274 INFO::Done
2025-12-19 00:59:26.353923 INFO::Formatting Data.
2025-12-19 00:59:26.355536 INFO::Recognized SummarizedExperiment
2025-12-19 00:59:26.356844 INFO::Typecasting input to dataframe.
2025-12-19 00:59:26.407355 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.40949 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.412205 INFO::Found 0 missing values.
2025-12-19 00:59:26.4145 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.
2025-12-19 00:59:26.428605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.431093 INFO::Done
2025-12-19 00:59:26.462519 INFO::Formatting Data.
2025-12-19 00:59:26.464985 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.467116 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.47024 INFO::Found 0 missing values.
2025-12-19 00:59:26.478341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.479796 INFO::Done
2025-12-19 00:59:26.51345 INFO::Formatting Data.
2025-12-19 00:59:26.515265 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.517607 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.521516 INFO::Found 0 missing values.
2025-12-19 00:59:26.529572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.531887 INFO::Done
2025-12-19 00:59:26.626726 INFO::Formatting Data.
2025-12-19 00:59:26.628388 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.630678 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.635617 INFO::Found 1 missing values.
2025-12-19 00:59:26.642459 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.645023 INFO::Done
2025-12-19 00:59:26.703721 INFO::Formatting Data.
2025-12-19 00:59:26.70546 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.707523 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.711651 INFO::Found 2 missing values.
2025-12-19 00:59:26.714065 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.
2025-12-19 00:59:26.719894 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.722669 INFO::Done
2025-12-19 00:59:26.75114 INFO::Formatting Data.
2025-12-19 00:59:26.752905 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.754817 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.756949 INFO::Found 2 missing values.
2025-12-19 00:59:26.763734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.765112 INFO::Done
2025-12-19 00:59:26.79683 INFO::Formatting Data.
2025-12-19 00:59:26.798542 INFO::Typecasting input to dataframe.
2025-12-19 00:59:26.800549 INFO::Replacing NaNs with NAs.
2025-12-19 00:59:26.80265 INFO::Removing potential empty rows and columns
2025-12-19 00:59:26.806163 INFO::Found 0 missing values.
2025-12-19 00:59:26.814288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-19 00:59:26.816262 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
34.835 6.715 47.583
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.292 | 2.614 | 39.835 | |
| compute_asw | 0.055 | 0.004 | 0.067 | |
| count_existing | 0.028 | 0.001 | 0.033 | |
| generate_data_covariables | 0.025 | 0.002 | 0.029 | |
| generate_dataset | 0.025 | 0.002 | 0.030 | |