Yannis Schumann
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 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 2025-12-11 12:03 -0500 (Thu, 11 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| 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 | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2025-12-08 21:24:57 -0500 (Mon, 08 Dec 2025) |
| EndedAt: 2025-12-08 21:26:29 -0500 (Mon, 08 Dec 2025) |
| EllapsedTime: 92.1 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 24.076 1.569 17.802
* 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")
2025-12-08 21:25:49.513698 INFO::Formatting Data.
2025-12-08 21:25:49.514959 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:49.525622 INFO::Removing potential empty rows and columns
2025-12-08 21:25:49.762143 INFO::Found 0 missing values.
2025-12-08 21:25:49.765496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:49.766124 INFO::Done
2025-12-08 21:25:49.766662 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:49.77766 INFO::Starting hierarchical adjustment
2025-12-08 21:25:49.778465 INFO::Found 3 batches.
2025-12-08 21:25:49.77901 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:49.780104 INFO::Using default BPPARAM
2025-12-08 21:25:49.780645 INFO::Processing subtree level 1
2025-12-08 21:25:49.880301 INFO::Adjusting the last 1 batches sequentially
2025-12-08 21:25:49.882009 INFO::Done
2025-12-08 21:25:49.882639 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:49.885079 INFO::ASW Batch was -0.132005361323518 prior to batch effect correction and is now -0.132005361323518 .
2025-12-08 21:25:49.886125 INFO::Total function execution time is 0.373038053512573 s and adjustment time is 0.103705883026123 s ( 27.8 )
2025-12-08 21:25:49.899323 INFO::Formatting Data.
2025-12-08 21:25:49.90005 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:49.900952 INFO::Removing potential empty rows and columns
2025-12-08 21:25:49.902066 INFO::Found 0 missing values.
2025-12-08 21:25:49.902966 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.
2025-12-08 21:25:49.913495 INFO::Formatting Data.
2025-12-08 21:25:49.914179 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:49.915026 INFO::Removing potential empty rows and columns
2025-12-08 21:25:49.916027 INFO::Found 0 missing values.
2025-12-08 21:25:49.916939 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.
2025-12-08 21:25:49.932239 INFO::Formatting Data.
2025-12-08 21:25:49.932962 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:49.933874 INFO::Removing potential empty rows and columns
2025-12-08 21:25:49.934918 INFO::Found 0 missing values.
2025-12-08 21:25:49.935842 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.
2025-12-08 21:25:49.940252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:49.940806 INFO::Done
2025-12-08 21:25:49.941324 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:49.943285 INFO::Starting hierarchical adjustment
2025-12-08 21:25:49.943992 INFO::Found 2 batches.
2025-12-08 21:25:49.944517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:49.945144 INFO::Using default BPPARAM
2025-12-08 21:25:49.945674 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:49.946549 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-08 21:25:49.967164 INFO::Done
2025-12-08 21:25:49.967874 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:49.969919 INFO::ASW Batch was 0.0516293334960667 prior to batch effect correction and is now -0.126786235155241 .
2025-12-08 21:25:49.970721 INFO::Total function execution time is 0.0385358333587646 s and adjustment time is 0.0232789516448975 s ( 60.41 )
2025-12-08 21:25:49.973525 INFO::Formatting Data.
2025-12-08 21:25:49.974151 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:49.98294 INFO::Formatting Data.
2025-12-08 21:25:49.983644 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:49.984531 INFO::Removing potential empty rows and columns
2025-12-08 21:25:49.985615 INFO::Found 0 missing values.
2025-12-08 21:25:49.988558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:49.989101 INFO::Done
2025-12-08 21:25:49.989636 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:49.991673 INFO::Starting hierarchical adjustment
2025-12-08 21:25:49.992371 INFO::Found 2 batches.
2025-12-08 21:25:49.992926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:50.014128 INFO::Using default BPPARAM
2025-12-08 21:25:50.016304 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:50.017224 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-08 21:25:50.030627 INFO::Done
2025-12-08 21:25:50.031226 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:50.03309 INFO::ASW Batch was -0.0235463059036499 prior to batch effect correction and is now -0.121774692088432 .
2025-12-08 21:25:50.033802 INFO::Total function execution time is 0.0509061813354492 s and adjustment time is 0.0384011268615723 s ( 75.44 )
2025-12-08 21:25:50.034777 INFO::Formatting Data.
2025-12-08 21:25:50.035326 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:50.036111 INFO::Removing potential empty rows and columns
2025-12-08 21:25:50.037028 INFO::Found 0 missing values.
2025-12-08 21:25:50.039565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:50.040056 INFO::Done
2025-12-08 21:25:50.040532 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:50.042332 INFO::Starting hierarchical adjustment
2025-12-08 21:25:50.042987 INFO::Found 2 batches.
2025-12-08 21:25:50.043467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:50.04403 INFO::Using default BPPARAM
2025-12-08 21:25:50.044517 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:50.045319 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-08 21:25:50.070746 INFO::Done
2025-12-08 21:25:50.071591 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:50.073739 INFO::ASW Batch was -0.0235463059036499 prior to batch effect correction and is now -0.121774692088432 .
2025-12-08 21:25:50.074495 INFO::Total function execution time is 0.0397059917449951 s and adjustment time is 0.0278263092041016 s ( 70.08 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-08 21:25:53.045589 INFO::Formatting Data.
2025-12-08 21:25:53.046309 INFO::Recognized SummarizedExperiment
2025-12-08 21:25:53.0468 INFO::Typecasting input to dataframe.
2025-12-08 21:25:53.077191 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:53.078541 INFO::Removing potential empty rows and columns
2025-12-08 21:25:53.082566 INFO::Found 0 missing values.
2025-12-08 21:25:53.090028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:53.090684 INFO::Done
2025-12-08 21:25:53.091232 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:53.095086 INFO::Starting hierarchical adjustment
2025-12-08 21:25:53.095833 INFO::Found 2 batches.
2025-12-08 21:25:53.096359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:53.097548 INFO::Using default BPPARAM
2025-12-08 21:25:53.098106 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:53.099125 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-08 21:25:53.15801 INFO::Done
2025-12-08 21:25:53.158774 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:53.162435 INFO::ASW Batch was -0.00561298871473737 prior to batch effect correction and is now -0.0889533828890545 .
2025-12-08 21:25:53.16332 INFO::Total function execution time is 0.118050813674927 s and adjustment time is 0.0623018741607666 s ( 52.78 )
Warning: stack imbalance in '{', 73 then 75
2025-12-08 21:25:53.182653 INFO::Formatting Data.
2025-12-08 21:25:53.183418 INFO::Recognized SummarizedExperiment
2025-12-08 21:25:53.18397 INFO::Typecasting input to dataframe.
2025-12-08 21:25:53.193499 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:53.194733 INFO::Removing potential empty rows and columns
2025-12-08 21:25:53.198524 INFO::Found 0 missing values.
2025-12-08 21:25:53.205741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:53.206368 INFO::Done
2025-12-08 21:25:53.206904 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:53.21047 INFO::Starting hierarchical adjustment
2025-12-08 21:25:53.211198 INFO::Found 2 batches.
2025-12-08 21:25:53.211725 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:53.212311 INFO::Using default BPPARAM
2025-12-08 21:25:53.21284 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:53.213802 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-08 21:25:53.239067 INFO::Done
2025-12-08 21:25:53.239807 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:53.243376 INFO::ASW Batch was -0.0232998846916563 prior to batch effect correction and is now -0.0232998846916563 .
2025-12-08 21:25:53.244246 INFO::Total function execution time is 0.061586856842041 s and adjustment time is 0.0279669761657715 s ( 45.41 )
2025-12-08 21:25:53.272208 INFO::Formatting Data.
2025-12-08 21:25:53.273115 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:53.274065 INFO::Removing potential empty rows and columns
2025-12-08 21:25:53.275149 INFO::Found 0 missing values.
2025-12-08 21:25:53.278142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:53.278686 INFO::Done
2025-12-08 21:25:53.279202 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:53.281532 INFO::Starting hierarchical adjustment
2025-12-08 21:25:53.282271 INFO::Found 3 batches.
2025-12-08 21:25:53.282802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:53.283417 INFO::Using default BPPARAM
2025-12-08 21:25:53.284075 INFO::Processing subtree level 1
2025-12-08 21:25:53.435131 INFO::Adjusting the last 1 batches sequentially
2025-12-08 21:25:53.437418 INFO::Done
2025-12-08 21:25:53.438225 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:53.44112 INFO::ASW Batch was -0.0311021442671878 prior to batch effect correction and is now -0.147081087825618 .
2025-12-08 21:25:53.442214 INFO::Total function execution time is 0.17003321647644 s and adjustment time is 0.155242919921875 s ( 91.3 )
2025-12-08 21:25:53.459913 INFO::Skipping initial DF formatting
2025-12-08 21:25:53.460959 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:53.46546 INFO::Starting hierarchical adjustment
2025-12-08 21:25:53.46636 INFO::Found 5 batches.
2025-12-08 21:25:53.466948 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:53.467613 INFO::Using default BPPARAM
2025-12-08 21:25:53.468148 INFO::Processing subtree level 1
2025-12-08 21:25:53.791606 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:53.793522 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-08 21:25:53.814895 INFO::Done
2025-12-08 21:25:53.815856 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:53.820666 INFO::ASW Batch was 0.516215669212764 prior to batch effect correction and is now 0.516215669212764 .
2025-12-08 21:25:53.821482 INFO::ASW Label was 0.376470766218485 prior to batch effect correction and is now 0.376470766218485 .
2025-12-08 21:25:53.822482 INFO::Total function execution time is 0.362740993499756 s and adjustment time is 0.3486647605896 s ( 96.12 )
2025-12-08 21:25:53.898522 INFO::Formatting Data.
2025-12-08 21:25:53.899521 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:53.900707 INFO::Removing potential empty rows and columns
2025-12-08 21:25:53.901981 INFO::Found 0 missing values.
2025-12-08 21:25:53.907777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:53.908434 INFO::Done
2025-12-08 21:25:53.909023 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:53.913053 INFO::Starting hierarchical adjustment
2025-12-08 21:25:53.91401 INFO::Found 5 batches.
2025-12-08 21:25:53.914726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:53.915542 INFO::Using default BPPARAM
2025-12-08 21:25:53.916404 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.
2025-12-08 21:25:54.086985 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.089011 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-08 21:25:54.107442 INFO::Done
2025-12-08 21:25:54.10828 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.112115 INFO::ASW Batch was 0.305780479547412 prior to batch effect correction and is now -0.0994278162479919 .
2025-12-08 21:25:54.112822 INFO::ASW Label was 0.471537021442616 prior to batch effect correction and is now 0.839178767306861 .
2025-12-08 21:25:54.113673 INFO::Total function execution time is 0.215315818786621 s and adjustment time is 0.193645477294922 s ( 89.94 )
2025-12-08 21:25:54.114625 INFO::Formatting Data.
2025-12-08 21:25:54.115265 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:54.116265 INFO::Removing potential empty rows and columns
2025-12-08 21:25:54.117384 INFO::Found 0 missing values.
2025-12-08 21:25:54.122109 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:54.122755 INFO::Done
2025-12-08 21:25:54.123314 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:54.126677 INFO::Starting hierarchical adjustment
2025-12-08 21:25:54.12741 INFO::Found 5 batches.
2025-12-08 21:25:54.127961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:54.128602 INFO::Using default BPPARAM
2025-12-08 21:25:54.129169 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.
2025-12-08 21:25:54.271386 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.273833 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-08 21:25:54.299103 INFO::Done
2025-12-08 21:25:54.30021 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.305299 INFO::ASW Batch was 0.305780479547412 prior to batch effect correction and is now -0.0994278162479919 .
2025-12-08 21:25:54.306242 INFO::ASW Label was 0.471537021442616 prior to batch effect correction and is now 0.839178767306861 .
2025-12-08 21:25:54.307499 INFO::Total function execution time is 0.192806243896484 s and adjustment time is 0.171773195266724 s ( 89.09 )
2025-12-08 21:25:54.329307 INFO::Formatting Data.
2025-12-08 21:25:54.330532 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:54.331961 INFO::Removing potential empty rows and columns
2025-12-08 21:25:54.33348 INFO::Found 0 missing values.
2025-12-08 21:25:54.340163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:54.340985 INFO::Done
2025-12-08 21:25:54.34188 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:54.346592 INFO::Starting hierarchical adjustment
2025-12-08 21:25:54.347642 INFO::Found 5 batches.
2025-12-08 21:25:54.348411 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:54.349347 INFO::Using default BPPARAM
2025-12-08 21:25:54.350158 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.
2025-12-08 21:25:54.504042 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.505941 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-08 21:25:54.529021 INFO::Done
2025-12-08 21:25:54.529934 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.533873 INFO::ASW Batch was 0.355655532323085 prior to batch effect correction and is now -0.0225981127388092 .
2025-12-08 21:25:54.534587 INFO::ASW Label was 0.399358364876213 prior to batch effect correction and is now 0.755997674961065 .
2025-12-08 21:25:54.535554 INFO::Total function execution time is 0.206385612487793 s and adjustment time is 0.181570053100586 s ( 87.98 )
2025-12-08 21:25:54.53648 INFO::Formatting Data.
2025-12-08 21:25:54.537178 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:54.538225 INFO::Removing potential empty rows and columns
2025-12-08 21:25:54.539418 INFO::Found 0 missing values.
2025-12-08 21:25:54.544321 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:54.544954 INFO::Done
2025-12-08 21:25:54.545501 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:54.549143 INFO::Starting hierarchical adjustment
2025-12-08 21:25:54.549956 INFO::Found 5 batches.
2025-12-08 21:25:54.550548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:54.551238 INFO::Using default BPPARAM
2025-12-08 21:25:54.551854 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.
2025-12-08 21:25:54.693322 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.695029 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-08 21:25:54.712245 INFO::Done
2025-12-08 21:25:54.713164 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.717243 INFO::ASW Batch was 0.355655532323085 prior to batch effect correction and is now -0.0225981127388092 .
2025-12-08 21:25:54.717941 INFO::ASW Label was 0.399358364876213 prior to batch effect correction and is now 0.755997674961065 .
2025-12-08 21:25:54.719053 INFO::Total function execution time is 0.182538032531738 s and adjustment time is 0.162391901016235 s ( 88.96 )
2025-12-08 21:25:54.73415 INFO::Formatting Data.
2025-12-08 21:25:54.734995 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:54.735996 INFO::Removing potential empty rows and columns
2025-12-08 21:25:54.737165 INFO::Found 0 missing values.
2025-12-08 21:25:54.740146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:54.740748 INFO::Done
2025-12-08 21:25:54.741302 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:54.744554 INFO::Starting hierarchical adjustment
2025-12-08 21:25:54.745322 INFO::Found 2 batches.
2025-12-08 21:25:54.745923 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:54.746594 INFO::Using default BPPARAM
2025-12-08 21:25:54.747175 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.748156 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-08 21:25:54.763749 INFO::Done
2025-12-08 21:25:54.764405 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.767429 INFO::ASW Batch was 0.522334373059142 prior to batch effect correction and is now 0.037346194017208 .
2025-12-08 21:25:54.768039 INFO::ASW Label was 0.558808413245548 prior to batch effect correction and is now 0.903484882413705 .
2025-12-08 21:25:54.768834 INFO::Total function execution time is 0.0347945690155029 s and adjustment time is 0.018582820892334 s ( 53.41 )
2025-12-08 21:25:54.769624 INFO::Formatting Data.
2025-12-08 21:25:54.770231 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:54.771098 INFO::Removing potential empty rows and columns
2025-12-08 21:25:54.772084 INFO::Found 0 missing values.
2025-12-08 21:25:54.77474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:54.775275 INFO::Done
2025-12-08 21:25:54.775811 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:54.778758 INFO::Starting hierarchical adjustment
2025-12-08 21:25:54.779462 INFO::Found 2 batches.
2025-12-08 21:25:54.779993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:54.780584 INFO::Using default BPPARAM
2025-12-08 21:25:54.781105 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.781973 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-08 21:25:54.796652 INFO::Done
2025-12-08 21:25:54.797314 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.800315 INFO::ASW Batch was 0.522334373059142 prior to batch effect correction and is now 0.037346194017208 .
2025-12-08 21:25:54.800928 INFO::ASW Label was 0.558808413245548 prior to batch effect correction and is now 0.903484882413705 .
2025-12-08 21:25:54.801702 INFO::Total function execution time is 0.0321025848388672 s and adjustment time is 0.0173244476318359 s ( 53.97 )
2025-12-08 21:25:54.813017 INFO::Formatting Data.
2025-12-08 21:25:54.813773 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:54.814647 INFO::Removing potential empty rows and columns
2025-12-08 21:25:54.815567 INFO::Found 0 missing values.
2025-12-08 21:25:54.817616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:54.818136 INFO::Done
2025-12-08 21:25:54.818651 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:54.820565 INFO::Starting hierarchical adjustment
2025-12-08 21:25:54.821264 INFO::Found 2 batches.
2025-12-08 21:25:54.821795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:54.822355 INFO::Using default BPPARAM
2025-12-08 21:25:54.822872 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.823745 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-08 21:25:54.854964 INFO::Done
2025-12-08 21:25:54.855664 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.857609 INFO::ASW Batch was 0.20266701079719 prior to batch effect correction and is now -0.135383719717614 .
2025-12-08 21:25:54.858425 INFO::Total function execution time is 0.0454823970794678 s and adjustment time is 0.0338268280029297 s ( 74.37 )
2025-12-08 21:25:54.86992 INFO::Formatting Data.
2025-12-08 21:25:54.870692 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:54.871555 INFO::Removing potential empty rows and columns
2025-12-08 21:25:54.872518 INFO::Found 0 missing values.
2025-12-08 21:25:54.873643 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.
2025-12-08 21:25:54.878036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:54.878588 INFO::Done
2025-12-08 21:25:54.879088 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:54.881942 INFO::Starting hierarchical adjustment
2025-12-08 21:25:54.882636 INFO::Found 2 batches.
2025-12-08 21:25:54.883149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:54.883742 INFO::Using default BPPARAM
2025-12-08 21:25:54.884235 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.885145 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-08 21:25:54.901197 INFO::Done
2025-12-08 21:25:54.901881 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.904767 INFO::ASW Batch was 0.738900035297981 prior to batch effect correction and is now 0.0812755640774907 .
2025-12-08 21:25:54.905366 INFO::ASW Label was 0.248076708098828 prior to batch effect correction and is now 0.768408286080885 .
2025-12-08 21:25:54.906113 INFO::Total function execution time is 0.0362784862518311 s and adjustment time is 0.0186893939971924 s ( 51.52 )
2025-12-08 21:25:54.906886 INFO::Formatting Data.
2025-12-08 21:25:54.907466 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:54.90834 INFO::Removing potential empty rows and columns
2025-12-08 21:25:54.909289 INFO::Found 0 missing values.
2025-12-08 21:25:54.910206 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.
2025-12-08 21:25:54.914607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:54.915191 INFO::Done
2025-12-08 21:25:54.915717 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:54.918623 INFO::Starting hierarchical adjustment
2025-12-08 21:25:54.919334 INFO::Found 2 batches.
2025-12-08 21:25:54.919858 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:54.920464 INFO::Using default BPPARAM
2025-12-08 21:25:54.920975 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:54.921887 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-08 21:25:54.938456 INFO::Done
2025-12-08 21:25:54.939169 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:54.942195 INFO::ASW Batch was 0.738900035297981 prior to batch effect correction and is now 0.0812755640774907 .
2025-12-08 21:25:54.942819 INFO::ASW Label was 0.248076708098828 prior to batch effect correction and is now 0.768408286080885 .
2025-12-08 21:25:54.943604 INFO::Total function execution time is 0.0367159843444824 s and adjustment time is 0.0192360877990723 s ( 52.39 )
2025-12-08 21:25:55.145213 INFO::Formatting Data.
2025-12-08 21:25:55.146087 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:55.147032 INFO::Removing potential empty rows and columns
2025-12-08 21:25:55.148169 INFO::Found 0 missing values.
2025-12-08 21:25:55.151216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:55.151768 INFO::Done
2025-12-08 21:25:55.152291 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:55.154354 INFO::Starting hierarchical adjustment
2025-12-08 21:25:55.155054 INFO::Found 3 batches.
2025-12-08 21:25:55.155573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:55.156308 INFO::Using default BPPARAM
2025-12-08 21:25:55.156847 INFO::Processing subtree level 1
2025-12-08 21:25:55.251097 INFO::Adjusting the last 1 batches sequentially
2025-12-08 21:25:55.253114 INFO::Done
2025-12-08 21:25:55.253761 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:55.256393 INFO::ASW Batch was -0.0842664061422089 prior to batch effect correction and is now -0.0842664061422089 .
2025-12-08 21:25:55.257396 INFO::Total function execution time is 0.112239122390747 s and adjustment time is 0.098179817199707 s ( 87.47 )
2025-12-08 21:25:55.258465 INFO::Formatting Data.
2025-12-08 21:25:55.259127 INFO::Typecasting input to dataframe.
2025-12-08 21:25:55.259905 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:55.260886 INFO::Removing potential empty rows and columns
2025-12-08 21:25:55.262001 INFO::Found 0 missing values.
2025-12-08 21:25:55.265139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:55.265715 INFO::Done
2025-12-08 21:25:55.26624 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:55.268299 INFO::Starting hierarchical adjustment
2025-12-08 21:25:55.269068 INFO::Found 3 batches.
2025-12-08 21:25:55.269616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:55.270234 INFO::Using default BPPARAM
2025-12-08 21:25:55.270788 INFO::Processing subtree level 1
2025-12-08 21:25:55.362015 INFO::Adjusting the last 1 batches sequentially
2025-12-08 21:25:55.364142 INFO::Done
2025-12-08 21:25:55.364902 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:55.367808 INFO::ASW Batch was -0.0842664061422089 prior to batch effect correction and is now -0.0842664061422089 .
2025-12-08 21:25:55.368858 INFO::Total function execution time is 0.110342741012573 s and adjustment time is 0.095186710357666 s ( 86.26 )
2025-12-08 21:25:55.383754 INFO::Formatting Data.
2025-12-08 21:25:55.384998 INFO::Typecasting input to dataframe.
2025-12-08 21:25:55.386012 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:55.387038 INFO::Removing potential empty rows and columns
2025-12-08 21:25:55.388218 INFO::Found 0 missing values.
2025-12-08 21:25:55.391375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:55.391958 INFO::Done
2025-12-08 21:25:55.39248 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:55.394764 INFO::Starting hierarchical adjustment
2025-12-08 21:25:55.395487 INFO::Found 3 batches.
2025-12-08 21:25:55.396037 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:55.396662 INFO::Using default BPPARAM
2025-12-08 21:25:55.397204 INFO::Processing subtree level 1
2025-12-08 21:25:55.486629 INFO::Adjusting the last 1 batches sequentially
2025-12-08 21:25:55.488741 INFO::Done
2025-12-08 21:25:55.489486 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:55.49231 INFO::ASW Batch was -0.12751823951727 prior to batch effect correction and is now -0.12751823951727 .
2025-12-08 21:25:55.493352 INFO::Total function execution time is 0.1098473072052 s and adjustment time is 0.0933582782745361 s ( 84.99 )
2025-12-08 21:25:55.665331 INFO::Formatting Data.
2025-12-08 21:25:55.666282 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:55.66798 INFO::Removing potential empty rows and columns
2025-12-08 21:25:55.671001 INFO::Found 1000 missing values.
2025-12-08 21:25:55.690409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:55.6913 INFO::Done
2025-12-08 21:25:55.6919 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:55.697762 INFO::Starting hierarchical adjustment
2025-12-08 21:25:55.698613 INFO::Found 10 batches.
2025-12-08 21:25:55.699186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:55.699897 INFO::Using default BPPARAM
2025-12-08 21:25:55.700461 INFO::Processing subtree level 1
2025-12-08 21:25:55.864921 INFO::Processing subtree level 2
2025-12-08 21:25:56.015118 INFO::Adjusting the last 1 batches sequentially
2025-12-08 21:25:56.017426 INFO::Done
2025-12-08 21:25:56.018267 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:56.02479 INFO::ASW Batch was 0.480297669260966 prior to batch effect correction and is now 0.480297669260966 .
2025-12-08 21:25:56.025541 INFO::ASW Label was 0.335058959833921 prior to batch effect correction and is now 0.335058959833921 .
2025-12-08 21:25:56.026609 INFO::Total function execution time is 0.361371755599976 s and adjustment time is 0.318949937820435 s ( 88.26 )
2025-12-08 21:25:56.027561 INFO::Formatting Data.
2025-12-08 21:25:56.028257 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:56.02966 INFO::Removing potential empty rows and columns
2025-12-08 21:25:56.032747 INFO::Found 1000 missing values.
2025-12-08 21:25:56.054028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:56.05493 INFO::Done
2025-12-08 21:25:56.055554 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:56.061841 INFO::Starting hierarchical adjustment
2025-12-08 21:25:56.062653 INFO::Found 10 batches.
2025-12-08 21:25:57.661568 INFO::Set up parallel execution backend with 2 workers
2025-12-08 21:25:57.664305 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-08 21:25:59.188768 INFO::Adjusting the last 2 batches sequentially
2025-12-08 21:25:59.190898 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-08 21:25:59.208285 INFO::Done
2025-12-08 21:25:59.20902 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:59.21379 INFO::ASW Batch was 0.480297669260966 prior to batch effect correction and is now 0.480297669260966 .
2025-12-08 21:25:59.214404 INFO::ASW Label was 0.335058959833921 prior to batch effect correction and is now 0.335058959833921 .
2025-12-08 21:25:59.215186 INFO::Total function execution time is 3.18768405914307 s and adjustment time is 3.1457691192627 s ( 98.69 )
2025-12-08 21:25:59.38355 INFO::Formatting Data.
2025-12-08 21:25:59.384569 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:59.385756 INFO::Removing potential empty rows and columns
2025-12-08 21:25:59.386952 INFO::Found 0 missing values.
2025-12-08 21:25:59.390812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:59.391379 INFO::Done
2025-12-08 21:25:59.391923 INFO::Acquiring quality metrics before batch effect correction.
2025-12-08 21:25:59.394889 INFO::Starting hierarchical adjustment
2025-12-08 21:25:59.395656 INFO::Found 3 batches.
2025-12-08 21:25:59.396195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-08 21:25:59.396847 INFO::Using default BPPARAM
2025-12-08 21:25:59.397382 INFO::Processing subtree level 1
2025-12-08 21:25:59.517321 INFO::Adjusting the last 1 batches sequentially
2025-12-08 21:25:59.51944 INFO::Done
2025-12-08 21:25:59.520222 INFO::Acquiring quality metrics after batch effect correction.
2025-12-08 21:25:59.524067 INFO::ASW Batch was 0.156312298071829 prior to batch effect correction and is now -0.133317772757949 .
2025-12-08 21:25:59.5248 INFO::ASW Label was -0.165422662338303 prior to batch effect correction and is now 0.045079015770447 .
2025-12-08 21:25:59.525846 INFO::Total function execution time is 0.142444372177124 s and adjustment time is 0.123934984207153 s ( 87.01 )
2025-12-08 21:25:59.705752 INFO::Formatting Data.
2025-12-08 21:25:59.707129 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:59.708337 INFO::Removing potential empty rows and columns
2025-12-08 21:25:59.709738 INFO::Found 2 missing values.
2025-12-08 21:25:59.713611 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:59.714272 INFO::Done
2025-12-08 21:25:59.751841 INFO::Found NA in Reference column
2025-12-08 21:25:59.764915 INFO::Require at least two references per batch.
2025-12-08 21:25:59.793244 INFO::Formatting Data.
2025-12-08 21:25:59.794275 INFO::Recognized SummarizedExperiment
2025-12-08 21:25:59.795038 INFO::Typecasting input to dataframe.
2025-12-08 21:25:59.808257 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:59.809944 INFO::Removing potential empty rows and columns
2025-12-08 21:25:59.81505 INFO::Found 0 missing values.
2025-12-08 21:25:59.825101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:59.825995 INFO::Done
2025-12-08 21:25:59.847407 INFO::Formatting Data.
2025-12-08 21:25:59.848516 INFO::Recognized SummarizedExperiment
2025-12-08 21:25:59.849249 INFO::Typecasting input to dataframe.
2025-12-08 21:25:59.874093 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:59.875772 INFO::Removing potential empty rows and columns
2025-12-08 21:25:59.88078 INFO::Found 0 missing values.
2025-12-08 21:25:59.896775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:59.897757 INFO::Done
2025-12-08 21:25:59.919082 INFO::Formatting Data.
2025-12-08 21:25:59.920142 INFO::Recognized SummarizedExperiment
2025-12-08 21:25:59.920886 INFO::Typecasting input to dataframe.
2025-12-08 21:25:59.944555 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:59.946047 INFO::Removing potential empty rows and columns
2025-12-08 21:25:59.947574 INFO::Found 0 missing values.
2025-12-08 21:25:59.948832 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.
2025-12-08 21:25:59.955079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:59.955963 INFO::Done
2025-12-08 21:25:59.970417 INFO::Formatting Data.
2025-12-08 21:25:59.971626 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:59.972825 INFO::Removing potential empty rows and columns
2025-12-08 21:25:59.974127 INFO::Found 0 missing values.
2025-12-08 21:25:59.977968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:59.978663 INFO::Done
2025-12-08 21:25:59.992783 INFO::Formatting Data.
2025-12-08 21:25:59.99403 INFO::Replacing NaNs with NAs.
2025-12-08 21:25:59.995065 INFO::Removing potential empty rows and columns
2025-12-08 21:25:59.996215 INFO::Found 0 missing values.
2025-12-08 21:25:59.999301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:25:59.999861 INFO::Done
2025-12-08 21:26:00.034315 INFO::Formatting Data.
2025-12-08 21:26:00.035335 INFO::Replacing NaNs with NAs.
2025-12-08 21:26:00.036473 INFO::Removing potential empty rows and columns
2025-12-08 21:26:00.037705 INFO::Found 1 missing values.
2025-12-08 21:26:00.040659 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:26:00.041225 INFO::Done
2025-12-08 21:26:00.06228 INFO::Formatting Data.
2025-12-08 21:26:00.063191 INFO::Replacing NaNs with NAs.
2025-12-08 21:26:00.06418 INFO::Removing potential empty rows and columns
2025-12-08 21:26:00.065206 INFO::Found 2 missing values.
2025-12-08 21:26:00.066159 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.
2025-12-08 21:26:00.068522 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:26:00.069066 INFO::Done
2025-12-08 21:26:00.080195 INFO::Formatting Data.
2025-12-08 21:26:00.081076 INFO::Replacing NaNs with NAs.
2025-12-08 21:26:00.082024 INFO::Removing potential empty rows and columns
2025-12-08 21:26:00.082966 INFO::Found 2 missing values.
2025-12-08 21:26:00.084638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:26:00.0852 INFO::Done
2025-12-08 21:26:00.098232 INFO::Formatting Data.
2025-12-08 21:26:00.099303 INFO::Typecasting input to dataframe.
2025-12-08 21:26:00.100302 INFO::Replacing NaNs with NAs.
2025-12-08 21:26:00.101271 INFO::Removing potential empty rows and columns
2025-12-08 21:26:00.102349 INFO::Found 0 missing values.
2025-12-08 21:26:00.10533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-08 21:26:00.105896 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.243 4.942 21.723
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.076 | 1.569 | 17.802 | |
| compute_asw | 0.024 | 0.001 | 0.025 | |
| count_existing | 0.012 | 0.001 | 0.013 | |
| generate_data_covariables | 0.010 | 0.001 | 0.011 | |
| generate_dataset | 0.010 | 0.001 | 0.011 | |