Yannis Schumann
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_21 |
| git_last_commit: dedce04 |
| git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | 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 | | ||||||||
| kunpeng2 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.4.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.4.0.tar.gz |
| StartedAt: 2025-10-14 06:34:44 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 06:36:23 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 98.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* 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 31.355 1.334 24.137
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.4.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-10-14 06:36:02.993197 INFO::Formatting Data.
2025-10-14 06:36:02.99497 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:03.012293 INFO::Removing potential empty rows and columns
2025-10-14 06:36:03.768023 INFO::Found 0 missing values.
2025-10-14 06:36:03.772851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:03.77379 INFO::Done
2025-10-14 06:36:03.77458 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:03.789917 INFO::Starting hierarchical adjustment
2025-10-14 06:36:03.791078 INFO::Found 3 batches.
2025-10-14 06:36:03.79186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:03.793401 INFO::Using default BPPARAM
2025-10-14 06:36:03.794223 INFO::Processing subtree level 1
2025-10-14 06:36:03.932191 INFO::Adjusting the last 1 batches sequentially
2025-10-14 06:36:03.938843 INFO::Done
2025-10-14 06:36:03.939783 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:03.947577 INFO::ASW Batch was -0.072753116006083 prior to batch effect correction and is now -0.072753116006083 .
2025-10-14 06:36:03.953431 INFO::Total function execution time is 0.961031913757324 s and adjustment time is 0.147970914840698 s ( 15.4 )
2025-10-14 06:36:03.976877 INFO::Formatting Data.
2025-10-14 06:36:03.977926 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:03.979224 INFO::Removing potential empty rows and columns
2025-10-14 06:36:03.980989 INFO::Found 0 missing values.
2025-10-14 06:36:03.982404 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.
2025-10-14 06:36:03.999222 INFO::Formatting Data.
2025-10-14 06:36:04.000266 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:04.001612 INFO::Removing potential empty rows and columns
2025-10-14 06:36:04.003098 INFO::Found 0 missing values.
2025-10-14 06:36:04.004392 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.
2025-10-14 06:36:04.02742 INFO::Formatting Data.
2025-10-14 06:36:04.028489 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:04.030015 INFO::Removing potential empty rows and columns
2025-10-14 06:36:04.031509 INFO::Found 0 missing values.
2025-10-14 06:36:04.03297 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.
2025-10-14 06:36:04.039498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:04.040452 INFO::Done
2025-10-14 06:36:04.041236 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:04.044111 INFO::Starting hierarchical adjustment
2025-10-14 06:36:04.045289 INFO::Found 2 batches.
2025-10-14 06:36:04.046087 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:04.046995 INFO::Using default BPPARAM
2025-10-14 06:36:04.047742 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:04.049222 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 06:36:04.080918 INFO::Done
2025-10-14 06:36:04.081841 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:04.084849 INFO::ASW Batch was 0.0260743781813136 prior to batch effect correction and is now -0.119652397125998 .
2025-10-14 06:36:04.086069 INFO::Total function execution time is 0.0587069988250732 s and adjustment time is 0.0358443260192871 s ( 61.06 )
2025-10-14 06:36:04.089938 INFO::Formatting Data.
2025-10-14 06:36:04.090955 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:04.103469 INFO::Formatting Data.
2025-10-14 06:36:04.104527 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:04.105817 INFO::Removing potential empty rows and columns
2025-10-14 06:36:04.107373 INFO::Found 0 missing values.
2025-10-14 06:36:04.153783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:04.154977 INFO::Done
2025-10-14 06:36:04.15573 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:04.158614 INFO::Starting hierarchical adjustment
2025-10-14 06:36:04.159704 INFO::Found 2 batches.
2025-10-14 06:36:04.160495 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:04.161368 INFO::Using default BPPARAM
2025-10-14 06:36:04.162119 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:04.163425 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 06:36:04.185113 INFO::Done
2025-10-14 06:36:04.186013 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:04.188854 INFO::ASW Batch was -0.0855693156125914 prior to batch effect correction and is now -0.116610336365851 .
2025-10-14 06:36:04.189988 INFO::Total function execution time is 0.0865764617919922 s and adjustment time is 0.0256192684173584 s ( 29.59 )
2025-10-14 06:36:04.19145 INFO::Formatting Data.
2025-10-14 06:36:04.192311 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:04.193575 INFO::Removing potential empty rows and columns
2025-10-14 06:36:04.195054 INFO::Found 0 missing values.
2025-10-14 06:36:04.199294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:04.2002 INFO::Done
2025-10-14 06:36:04.201029 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:04.203875 INFO::Starting hierarchical adjustment
2025-10-14 06:36:04.205026 INFO::Found 2 batches.
2025-10-14 06:36:04.205812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:04.206678 INFO::Using default BPPARAM
2025-10-14 06:36:04.207442 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:04.208824 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 06:36:04.233243 INFO::Done
2025-10-14 06:36:04.234151 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:04.237099 INFO::ASW Batch was -0.0855693156125914 prior to batch effect correction and is now -0.116610336365851 .
2025-10-14 06:36:04.238317 INFO::Total function execution time is 0.0468449592590332 s and adjustment time is 0.0284132957458496 s ( 60.65 )
2025-10-14 06:36:08.272306 INFO::Formatting Data.
2025-10-14 06:36:08.273314 INFO::Recognized SummarizedExperiment
2025-10-14 06:36:08.274 INFO::Typecasting input to dataframe.
2025-10-14 06:36:08.314702 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:08.316125 INFO::Removing potential empty rows and columns
2025-10-14 06:36:08.321087 INFO::Found 0 missing values.
2025-10-14 06:36:08.331113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:08.332015 INFO::Done
2025-10-14 06:36:08.332795 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:08.337623 INFO::Starting hierarchical adjustment
2025-10-14 06:36:08.338619 INFO::Found 2 batches.
2025-10-14 06:36:08.339348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:08.340776 INFO::Using default BPPARAM
2025-10-14 06:36:08.341516 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:08.342858 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 06:36:08.420002 INFO::Done
2025-10-14 06:36:08.420918 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:08.425628 INFO::ASW Batch was -0.0157320066216908 prior to batch effect correction and is now -0.0879127709369746 .
2025-10-14 06:36:08.426737 INFO::Total function execution time is 0.154945135116577 s and adjustment time is 0.0815608501434326 s ( 52.64 )
2025-10-14 06:36:08.450206 INFO::Formatting Data.
2025-10-14 06:36:08.451141 INFO::Recognized SummarizedExperiment
2025-10-14 06:36:08.45187 INFO::Typecasting input to dataframe.
2025-10-14 06:36:08.464101 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:08.46562 INFO::Removing potential empty rows and columns
2025-10-14 06:36:08.470643 INFO::Found 0 missing values.
2025-10-14 06:36:08.480378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:08.481255 INFO::Done
2025-10-14 06:36:08.481974 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:08.486746 INFO::Starting hierarchical adjustment
2025-10-14 06:36:08.487795 INFO::Found 2 batches.
2025-10-14 06:36:08.488549 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:08.489356 INFO::Using default BPPARAM
2025-10-14 06:36:08.490058 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:08.491377 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 06:36:08.526016 INFO::Done
2025-10-14 06:36:08.526921 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:08.531778 INFO::ASW Batch was 0.00474484930171976 prior to batch effect correction and is now 0.00474484930171976 .
2025-10-14 06:36:08.533002 INFO::Total function execution time is 0.0827755928039551 s and adjustment time is 0.0383937358856201 s ( 46.38 )
2025-10-14 06:36:08.556352 INFO::Formatting Data.
2025-10-14 06:36:08.55731 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:08.558494 INFO::Removing potential empty rows and columns
2025-10-14 06:36:08.559839 INFO::Found 0 missing values.
2025-10-14 06:36:08.563769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:08.564517 INFO::Done
2025-10-14 06:36:08.56523 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:08.567833 INFO::Starting hierarchical adjustment
2025-10-14 06:36:08.568855 INFO::Found 3 batches.
2025-10-14 06:36:08.56961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:08.570418 INFO::Using default BPPARAM
2025-10-14 06:36:08.571132 INFO::Processing subtree level 1
2025-10-14 06:36:08.863743 INFO::Adjusting the last 1 batches sequentially
2025-10-14 06:36:08.874316 INFO::Done
2025-10-14 06:36:08.875184 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:08.882632 INFO::ASW Batch was -0.066699778732597 prior to batch effect correction and is now -0.145616484054905 .
2025-10-14 06:36:08.883949 INFO::Total function execution time is 0.327625274658203 s and adjustment time is 0.305652618408203 s ( 93.29 )
2025-10-14 06:36:08.991571 INFO::Skipping initial DF formatting
2025-10-14 06:36:08.992532 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:08.998121 INFO::Starting hierarchical adjustment
2025-10-14 06:36:08.999221 INFO::Found 5 batches.
2025-10-14 06:36:08.999986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:09.000951 INFO::Using default BPPARAM
2025-10-14 06:36:09.001706 INFO::Processing subtree level 1
2025-10-14 06:36:09.288043 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:09.29474 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 06:36:09.347848 INFO::Done
2025-10-14 06:36:09.348886 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:09.355464 INFO::ASW Batch was 0.473988510303684 prior to batch effect correction and is now 0.473988510303684 .
2025-10-14 06:36:09.356422 INFO::ASW Label was 0.389722987092658 prior to batch effect correction and is now 0.389722987092658 .
2025-10-14 06:36:09.357768 INFO::Total function execution time is 0.366215705871582 s and adjustment time is 0.348808288574219 s ( 95.25 )
2025-10-14 06:36:09.385936 INFO::Formatting Data.
2025-10-14 06:36:09.387016 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:09.388417 INFO::Removing potential empty rows and columns
2025-10-14 06:36:09.390046 INFO::Found 0 missing values.
2025-10-14 06:36:09.396983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:09.397962 INFO::Done
2025-10-14 06:36:09.398792 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:09.403756 INFO::Starting hierarchical adjustment
2025-10-14 06:36:09.405066 INFO::Found 5 batches.
2025-10-14 06:36:09.405935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:09.406926 INFO::Using default BPPARAM
2025-10-14 06:36:09.407758 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.
2025-10-14 06:36:09.639284 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:09.649949 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 06:36:09.696372 INFO::Done
2025-10-14 06:36:09.69737 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:09.702095 INFO::ASW Batch was 0.379132201422552 prior to batch effect correction and is now -0.0726676705253565 .
2025-10-14 06:36:09.70306 INFO::ASW Label was 0.375640792286964 prior to batch effect correction and is now 0.798873409569227 .
2025-10-14 06:36:09.704335 INFO::Total function execution time is 0.31840443611145 s and adjustment time is 0.29153847694397 s ( 91.56 )
2025-10-14 06:36:09.70564 INFO::Formatting Data.
2025-10-14 06:36:09.70661 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:09.707929 INFO::Removing potential empty rows and columns
2025-10-14 06:36:09.709488 INFO::Found 0 missing values.
2025-10-14 06:36:09.71604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:09.717111 INFO::Done
2025-10-14 06:36:09.717956 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:09.722558 INFO::Starting hierarchical adjustment
2025-10-14 06:36:09.723807 INFO::Found 5 batches.
2025-10-14 06:36:09.724671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:09.725608 INFO::Using default BPPARAM
2025-10-14 06:36:09.726465 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.
2025-10-14 06:36:09.916996 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:09.91944 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 06:36:09.973287 INFO::Done
2025-10-14 06:36:09.974278 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:09.979126 INFO::ASW Batch was 0.379132201422552 prior to batch effect correction and is now -0.0726676705253565 .
2025-10-14 06:36:09.980003 INFO::ASW Label was 0.375640792286964 prior to batch effect correction and is now 0.798873409569227 .
2025-10-14 06:36:09.981313 INFO::Total function execution time is 0.275624513626099 s and adjustment time is 0.249724388122559 s ( 90.6 )
2025-10-14 06:36:10.007244 INFO::Formatting Data.
2025-10-14 06:36:10.008347 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:10.01392 INFO::Removing potential empty rows and columns
2025-10-14 06:36:10.015473 INFO::Found 0 missing values.
2025-10-14 06:36:10.030384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:10.03136 INFO::Done
2025-10-14 06:36:10.032154 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:10.044932 INFO::Starting hierarchical adjustment
2025-10-14 06:36:10.046239 INFO::Found 5 batches.
2025-10-14 06:36:10.047115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:10.048044 INFO::Using default BPPARAM
2025-10-14 06:36:10.053127 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.
2025-10-14 06:36:10.352112 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:10.362687 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 06:36:10.408568 INFO::Done
2025-10-14 06:36:10.409537 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:10.414136 INFO::ASW Batch was 0.506167042692058 prior to batch effect correction and is now -0.0903647602394863 .
2025-10-14 06:36:10.415072 INFO::ASW Label was 0.244714423997283 prior to batch effect correction and is now 0.816153610117824 .
2025-10-14 06:36:10.416263 INFO::Total function execution time is 0.409071207046509 s and adjustment time is 0.362570524215698 s ( 88.63 )
2025-10-14 06:36:10.417544 INFO::Formatting Data.
2025-10-14 06:36:10.418447 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:10.419725 INFO::Removing potential empty rows and columns
2025-10-14 06:36:10.421263 INFO::Found 0 missing values.
2025-10-14 06:36:10.427394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:10.428325 INFO::Done
2025-10-14 06:36:10.429135 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:10.433372 INFO::Starting hierarchical adjustment
2025-10-14 06:36:10.434536 INFO::Found 5 batches.
2025-10-14 06:36:10.435342 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:10.436285 INFO::Using default BPPARAM
2025-10-14 06:36:10.437107 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.
2025-10-14 06:36:10.621731 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:10.624111 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 06:36:10.678038 INFO::Done
2025-10-14 06:36:10.679057 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:10.685052 INFO::ASW Batch was 0.506167042692058 prior to batch effect correction and is now -0.0903647602394863 .
2025-10-14 06:36:10.686065 INFO::ASW Label was 0.244714423997283 prior to batch effect correction and is now 0.816153610117824 .
2025-10-14 06:36:10.687302 INFO::Total function execution time is 0.269733190536499 s and adjustment time is 0.243683338165283 s ( 90.34 )
2025-10-14 06:36:10.714828 INFO::Formatting Data.
2025-10-14 06:36:10.715852 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:10.721334 INFO::Removing potential empty rows and columns
2025-10-14 06:36:10.72293 INFO::Found 0 missing values.
2025-10-14 06:36:10.731233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:10.732121 INFO::Done
2025-10-14 06:36:10.737108 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:10.745513 INFO::Starting hierarchical adjustment
2025-10-14 06:36:10.746675 INFO::Found 2 batches.
2025-10-14 06:36:10.747451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:10.748367 INFO::Using default BPPARAM
2025-10-14 06:36:10.753363 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:10.754772 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 06:36:10.800951 INFO::Done
2025-10-14 06:36:10.801892 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:10.810262 INFO::ASW Batch was 0.554936578833166 prior to batch effect correction and is now -0.00267411611575116 .
2025-10-14 06:36:10.81119 INFO::ASW Label was 0.515460009757934 prior to batch effect correction and is now 0.907920139526189 .
2025-10-14 06:36:10.81232 INFO::Total function execution time is 0.0975453853607178 s and adjustment time is 0.0544850826263428 s ( 55.86 )
2025-10-14 06:36:10.813442 INFO::Formatting Data.
2025-10-14 06:36:10.814304 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:10.815516 INFO::Removing potential empty rows and columns
2025-10-14 06:36:10.816988 INFO::Found 0 missing values.
2025-10-14 06:36:10.82097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:10.821864 INFO::Done
2025-10-14 06:36:10.822632 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:10.82675 INFO::Starting hierarchical adjustment
2025-10-14 06:36:10.827847 INFO::Found 2 batches.
2025-10-14 06:36:10.82869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:10.829583 INFO::Using default BPPARAM
2025-10-14 06:36:10.830378 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:10.831733 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 06:36:10.853012 INFO::Done
2025-10-14 06:36:10.85396 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:10.858264 INFO::ASW Batch was 0.554936578833166 prior to batch effect correction and is now -0.00267411611575116 .
2025-10-14 06:36:10.859185 INFO::ASW Label was 0.515460009757934 prior to batch effect correction and is now 0.907920139526189 .
2025-10-14 06:36:10.860337 INFO::Total function execution time is 0.0468559265136719 s and adjustment time is 0.0253617763519287 s ( 54.13 )
2025-10-14 06:36:10.876529 INFO::Formatting Data.
2025-10-14 06:36:10.877534 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:10.878725 INFO::Removing potential empty rows and columns
2025-10-14 06:36:10.880006 INFO::Found 0 missing values.
2025-10-14 06:36:10.883065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:10.883862 INFO::Done
2025-10-14 06:36:10.884633 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:10.887338 INFO::Starting hierarchical adjustment
2025-10-14 06:36:10.888397 INFO::Found 2 batches.
2025-10-14 06:36:10.889192 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:10.890031 INFO::Using default BPPARAM
2025-10-14 06:36:10.890771 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:10.892098 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 06:36:10.937315 INFO::Done
2025-10-14 06:36:10.938202 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:10.940921 INFO::ASW Batch was -0.0556729602744859 prior to batch effect correction and is now -0.131691775208568 .
2025-10-14 06:36:10.942043 INFO::Total function execution time is 0.0655934810638428 s and adjustment time is 0.0491335391998291 s ( 74.91 )
2025-10-14 06:36:10.958507 INFO::Formatting Data.
2025-10-14 06:36:10.95952 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:10.960758 INFO::Removing potential empty rows and columns
2025-10-14 06:36:10.962173 INFO::Found 0 missing values.
2025-10-14 06:36:10.963737 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.
2025-10-14 06:36:10.970459 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:10.971358 INFO::Done
2025-10-14 06:36:10.972124 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:10.976158 INFO::Starting hierarchical adjustment
2025-10-14 06:36:10.977285 INFO::Found 2 batches.
2025-10-14 06:36:10.97806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:10.978893 INFO::Using default BPPARAM
2025-10-14 06:36:10.979615 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:10.981005 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 06:36:11.004562 INFO::Done
2025-10-14 06:36:11.005461 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:11.009458 INFO::ASW Batch was 0.629578126029613 prior to batch effect correction and is now 0.0667186847588858 .
2025-10-14 06:36:11.010349 INFO::ASW Label was 0.465261818628063 prior to batch effect correction and is now 0.858039769386805 .
2025-10-14 06:36:11.011422 INFO::Total function execution time is 0.0529932975769043 s and adjustment time is 0.0274505615234375 s ( 51.8 )
2025-10-14 06:36:11.012523 INFO::Formatting Data.
2025-10-14 06:36:11.013417 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:11.01471 INFO::Removing potential empty rows and columns
2025-10-14 06:36:11.016097 INFO::Found 0 missing values.
2025-10-14 06:36:11.017434 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.
2025-10-14 06:36:11.023988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:11.024919 INFO::Done
2025-10-14 06:36:11.025659 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:11.029702 INFO::Starting hierarchical adjustment
2025-10-14 06:36:11.030787 INFO::Found 2 batches.
2025-10-14 06:36:11.031546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:11.032454 INFO::Using default BPPARAM
2025-10-14 06:36:11.033229 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:11.034553 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 06:36:11.057481 INFO::Done
2025-10-14 06:36:11.05836 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:11.062336 INFO::ASW Batch was 0.629578126029613 prior to batch effect correction and is now 0.0667186847588858 .
2025-10-14 06:36:11.063195 INFO::ASW Label was 0.465261818628063 prior to batch effect correction and is now 0.858039769386805 .
2025-10-14 06:36:11.064279 INFO::Total function execution time is 0.0517299175262451 s and adjustment time is 0.0268895626068115 s ( 51.98 )
2025-10-14 06:36:11.355304 INFO::Formatting Data.
2025-10-14 06:36:11.356333 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:11.357575 INFO::Removing potential empty rows and columns
2025-10-14 06:36:11.359 INFO::Found 0 missing values.
2025-10-14 06:36:11.363357 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:11.364302 INFO::Done
2025-10-14 06:36:11.365099 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:11.368136 INFO::Starting hierarchical adjustment
2025-10-14 06:36:11.369348 INFO::Found 3 batches.
2025-10-14 06:36:11.370126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:11.370983 INFO::Using default BPPARAM
2025-10-14 06:36:11.371732 INFO::Processing subtree level 1
2025-10-14 06:36:11.482551 INFO::Adjusting the last 1 batches sequentially
2025-10-14 06:36:11.493285 INFO::Done
2025-10-14 06:36:11.49429 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:11.50194 INFO::ASW Batch was -0.0310793118223801 prior to batch effect correction and is now -0.0310793118223801 .
2025-10-14 06:36:11.503416 INFO::Total function execution time is 0.148087978363037 s and adjustment time is 0.124151229858398 s ( 83.84 )
2025-10-14 06:36:11.509088 INFO::Formatting Data.
2025-10-14 06:36:11.51016 INFO::Typecasting input to dataframe.
2025-10-14 06:36:11.51128 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:11.51675 INFO::Removing potential empty rows and columns
2025-10-14 06:36:11.51858 INFO::Found 0 missing values.
2025-10-14 06:36:11.527464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:11.528421 INFO::Done
2025-10-14 06:36:11.533497 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:11.536534 INFO::Starting hierarchical adjustment
2025-10-14 06:36:11.540747 INFO::Found 3 batches.
2025-10-14 06:36:11.541624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:11.542585 INFO::Using default BPPARAM
2025-10-14 06:36:11.543407 INFO::Processing subtree level 1
2025-10-14 06:36:11.673018 INFO::Adjusting the last 1 batches sequentially
2025-10-14 06:36:11.675359 INFO::Done
2025-10-14 06:36:11.67624 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:11.679705 INFO::ASW Batch was -0.0310793118223801 prior to batch effect correction and is now -0.0310793118223801 .
2025-10-14 06:36:11.681141 INFO::Total function execution time is 0.17209267616272 s and adjustment time is 0.134934425354004 s ( 78.41 )
2025-10-14 06:36:11.704898 INFO::Formatting Data.
2025-10-14 06:36:11.705987 INFO::Typecasting input to dataframe.
2025-10-14 06:36:11.707212 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:11.708591 INFO::Removing potential empty rows and columns
2025-10-14 06:36:11.710303 INFO::Found 0 missing values.
2025-10-14 06:36:11.719536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:11.72048 INFO::Done
2025-10-14 06:36:11.721246 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:11.723907 INFO::Starting hierarchical adjustment
2025-10-14 06:36:11.729173 INFO::Found 3 batches.
2025-10-14 06:36:11.730016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:11.730904 INFO::Using default BPPARAM
2025-10-14 06:36:11.731626 INFO::Processing subtree level 1
2025-10-14 06:36:11.913047 INFO::Adjusting the last 1 batches sequentially
2025-10-14 06:36:11.91555 INFO::Done
2025-10-14 06:36:11.916454 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:11.924342 INFO::ASW Batch was -0.00571228736769353 prior to batch effect correction and is now -0.00571228736769353 .
2025-10-14 06:36:11.930022 INFO::Total function execution time is 0.225101709365845 s and adjustment time is 0.186626672744751 s ( 82.91 )
2025-10-14 06:36:12.217952 INFO::Formatting Data.
2025-10-14 06:36:12.218989 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:12.220507 INFO::Removing potential empty rows and columns
2025-10-14 06:36:12.23697 INFO::Found 1000 missing values.
2025-10-14 06:36:12.293998 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:12.294918 INFO::Done
2025-10-14 06:36:12.295672 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:12.311517 INFO::Starting hierarchical adjustment
2025-10-14 06:36:12.316849 INFO::Found 10 batches.
2025-10-14 06:36:12.317756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:12.318659 INFO::Using default BPPARAM
2025-10-14 06:36:12.319433 INFO::Processing subtree level 1
2025-10-14 06:36:12.595338 INFO::Processing subtree level 2
2025-10-14 06:36:12.779293 INFO::Adjusting the last 1 batches sequentially
2025-10-14 06:36:12.794172 INFO::Done
2025-10-14 06:36:12.795133 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:12.811361 INFO::ASW Batch was 0.510787753862572 prior to batch effect correction and is now 0.510787753862572 .
2025-10-14 06:36:12.812378 INFO::ASW Label was 0.331889842184502 prior to batch effect correction and is now 0.331889842184501 .
2025-10-14 06:36:12.817988 INFO::Total function execution time is 0.600001335144043 s and adjustment time is 0.481678485870361 s ( 80.28 )
2025-10-14 06:36:12.819254 INFO::Formatting Data.
2025-10-14 06:36:12.820161 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:12.826224 INFO::Removing potential empty rows and columns
2025-10-14 06:36:12.834611 INFO::Found 1000 missing values.
2025-10-14 06:36:12.863009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:12.863944 INFO::Done
2025-10-14 06:36:12.864782 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:12.872388 INFO::Starting hierarchical adjustment
2025-10-14 06:36:12.873612 INFO::Found 10 batches.
2025-10-14 06:36:14.12891 INFO::Set up parallel execution backend with 2 workers
2025-10-14 06:36:14.131084 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-14 06:36:15.612023 INFO::Adjusting the last 2 batches sequentially
2025-10-14 06:36:15.614331 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 06:36:15.638779 INFO::Done
2025-10-14 06:36:15.639609 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:15.646148 INFO::ASW Batch was 0.510787753862572 prior to batch effect correction and is now 0.510787753862572 .
2025-10-14 06:36:15.646961 INFO::ASW Label was 0.331889842184502 prior to batch effect correction and is now 0.331889842184501 .
2025-10-14 06:36:15.647964 INFO::Total function execution time is 2.82875633239746 s and adjustment time is 2.76540923118591 s ( 97.76 )
2025-10-14 06:36:15.97104 INFO::Formatting Data.
2025-10-14 06:36:15.97218 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:15.97772 INFO::Removing potential empty rows and columns
2025-10-14 06:36:15.979366 INFO::Found 0 missing values.
2025-10-14 06:36:15.993442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:15.994352 INFO::Done
2025-10-14 06:36:15.995114 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 06:36:15.998989 INFO::Starting hierarchical adjustment
2025-10-14 06:36:16.000031 INFO::Found 3 batches.
2025-10-14 06:36:16.000827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 06:36:16.001731 INFO::Using default BPPARAM
2025-10-14 06:36:16.00249 INFO::Processing subtree level 1
2025-10-14 06:36:16.249068 INFO::Adjusting the last 1 batches sequentially
2025-10-14 06:36:16.25141 INFO::Done
2025-10-14 06:36:16.252321 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 06:36:16.265329 INFO::ASW Batch was 0.172340033280808 prior to batch effect correction and is now -0.145788253214213 .
2025-10-14 06:36:16.266327 INFO::ASW Label was -0.203783498742224 prior to batch effect correction and is now -0.028603650199762 .
2025-10-14 06:36:16.267593 INFO::Total function execution time is 0.296603441238403 s and adjustment time is 0.251579284667969 s ( 84.82 )
2025-10-14 06:36:16.485686 INFO::Formatting Data.
2025-10-14 06:36:16.486756 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.48803 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.489673 INFO::Found 2 missing values.
2025-10-14 06:36:16.494165 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.49505 INFO::Done
2025-10-14 06:36:16.535745 INFO::Found NA in Reference column
2025-10-14 06:36:16.549901 INFO::Require at least two references per batch.
2025-10-14 06:36:16.579743 INFO::Formatting Data.
2025-10-14 06:36:16.580743 INFO::Recognized SummarizedExperiment
2025-10-14 06:36:16.581532 INFO::Typecasting input to dataframe.
2025-10-14 06:36:16.595991 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.597646 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.603497 INFO::Found 0 missing values.
2025-10-14 06:36:16.614851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.61579 INFO::Done
2025-10-14 06:36:16.638005 INFO::Formatting Data.
2025-10-14 06:36:16.638978 INFO::Recognized SummarizedExperiment
2025-10-14 06:36:16.639746 INFO::Typecasting input to dataframe.
2025-10-14 06:36:16.665364 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.667015 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.672852 INFO::Found 0 missing values.
2025-10-14 06:36:16.691261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.692196 INFO::Done
2025-10-14 06:36:16.71402 INFO::Formatting Data.
2025-10-14 06:36:16.714999 INFO::Recognized SummarizedExperiment
2025-10-14 06:36:16.715757 INFO::Typecasting input to dataframe.
2025-10-14 06:36:16.739768 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.741154 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.742686 INFO::Found 0 missing values.
2025-10-14 06:36:16.743974 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.
2025-10-14 06:36:16.750682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.751552 INFO::Done
2025-10-14 06:36:16.765737 INFO::Formatting Data.
2025-10-14 06:36:16.766771 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.767961 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.76944 INFO::Found 0 missing values.
2025-10-14 06:36:16.773934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.774885 INFO::Done
2025-10-14 06:36:16.791238 INFO::Formatting Data.
2025-10-14 06:36:16.792285 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.793555 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.794988 INFO::Found 0 missing values.
2025-10-14 06:36:16.799329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.800144 INFO::Done
2025-10-14 06:36:16.843879 INFO::Formatting Data.
2025-10-14 06:36:16.844987 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.846439 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.848167 INFO::Found 1 missing values.
2025-10-14 06:36:16.85209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.853077 INFO::Done
2025-10-14 06:36:16.88244 INFO::Formatting Data.
2025-10-14 06:36:16.88348 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.884742 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.886077 INFO::Found 2 missing values.
2025-10-14 06:36:16.887357 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.
2025-10-14 06:36:16.8908 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.891609 INFO::Done
2025-10-14 06:36:16.905961 INFO::Formatting Data.
2025-10-14 06:36:16.907001 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.908623 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.909986 INFO::Found 2 missing values.
2025-10-14 06:36:16.912318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.913502 INFO::Done
2025-10-14 06:36:16.92934 INFO::Formatting Data.
2025-10-14 06:36:16.930433 INFO::Typecasting input to dataframe.
2025-10-14 06:36:16.931676 INFO::Replacing NaNs with NAs.
2025-10-14 06:36:16.932993 INFO::Removing potential empty rows and columns
2025-10-14 06:36:16.934529 INFO::Found 0 missing values.
2025-10-14 06:36:16.939017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 06:36:16.939928 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.651 4.338 29.708
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.355 | 1.334 | 24.137 | |
| compute_asw | 0.037 | 0.000 | 0.057 | |
| count_existing | 0.020 | 0.000 | 0.044 | |
| generate_data_covariables | 0.018 | 0.000 | 0.024 | |
| generate_dataset | 0.017 | 0.000 | 0.016 | |