Yannis Schumann
| Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 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 2025-08-04 11:47 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 2025-08-01 06:19:09 -0000 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 06:20:33 -0000 (Fri, 01 Aug 2025) |
| EllapsedTime: 84.1 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 31.212 1.516 22.77
* 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")
2025-08-01 06:20:16.788582 INFO::Formatting Data.
2025-08-01 06:20:16.790601 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:16.809665 INFO::Removing potential empty rows and columns
2025-08-01 06:20:17.244153 INFO::Found 0 missing values.
2025-08-01 06:20:17.249035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:17.2499 INFO::Done
2025-08-01 06:20:17.250628 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:17.266233 INFO::Starting hierarchical adjustment
2025-08-01 06:20:17.267506 INFO::Found 3 batches.
2025-08-01 06:20:17.268273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:17.269896 INFO::Using default BPPARAM
2025-08-01 06:20:17.270751 INFO::Processing subtree level 1
2025-08-01 06:20:17.401329 INFO::Adjusting the last 1 batches sequentially
2025-08-01 06:20:17.404003 INFO::Done
2025-08-01 06:20:17.405069 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:17.408881 INFO::ASW Batch was 0.035880199270537 prior to batch effect correction and is now 0.035880199270537 .
2025-08-01 06:20:17.410605 INFO::Total function execution time is 0.622929573059082 s and adjustment time is 0.136731386184692 s ( 21.95 )
2025-08-01 06:20:17.431457 INFO::Formatting Data.
2025-08-01 06:20:17.432515 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:17.433846 INFO::Removing potential empty rows and columns
2025-08-01 06:20:17.435608 INFO::Found 0 missing values.
2025-08-01 06:20:17.437011 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.
2025-08-01 06:20:17.452502 INFO::Formatting Data.
2025-08-01 06:20:17.453519 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:17.454787 INFO::Removing potential empty rows and columns
2025-08-01 06:20:17.456276 INFO::Found 0 missing values.
2025-08-01 06:20:17.457586 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.
2025-08-01 06:20:17.480049 INFO::Formatting Data.
2025-08-01 06:20:17.481067 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:17.482334 INFO::Removing potential empty rows and columns
2025-08-01 06:20:17.483865 INFO::Found 0 missing values.
2025-08-01 06:20:17.485277 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.
2025-08-01 06:20:17.491404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:17.492279 INFO::Done
2025-08-01 06:20:17.49305 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:17.495793 INFO::Starting hierarchical adjustment
2025-08-01 06:20:17.496906 INFO::Found 2 batches.
2025-08-01 06:20:17.49771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:17.498653 INFO::Using default BPPARAM
2025-08-01 06:20:17.499454 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:17.500918 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 06:20:17.532244 INFO::Done
2025-08-01 06:20:17.53317 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:17.535887 INFO::ASW Batch was -0.0688163606053636 prior to batch effect correction and is now -0.132237910660232 .
2025-08-01 06:20:17.537026 INFO::Total function execution time is 0.0570418834686279 s and adjustment time is 0.0355756282806396 s ( 62.37 )
2025-08-01 06:20:17.540663 INFO::Formatting Data.
2025-08-01 06:20:17.541565 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:17.563761 INFO::Formatting Data.
2025-08-01 06:20:17.564941 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:17.566193 INFO::Removing potential empty rows and columns
2025-08-01 06:20:17.567791 INFO::Found 0 missing values.
2025-08-01 06:20:17.619682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:17.620825 INFO::Done
2025-08-01 06:20:17.621566 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:17.624391 INFO::Starting hierarchical adjustment
2025-08-01 06:20:17.625478 INFO::Found 2 batches.
2025-08-01 06:20:17.626231 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:17.627086 INFO::Using default BPPARAM
2025-08-01 06:20:17.627837 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:17.629163 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 06:20:17.650918 INFO::Done
2025-08-01 06:20:17.651831 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:17.654609 INFO::ASW Batch was 0.0159645140308384 prior to batch effect correction and is now -0.121589554136527 .
2025-08-01 06:20:17.65573 INFO::Total function execution time is 0.0921273231506348 s and adjustment time is 0.0256292819976807 s ( 27.82 )
2025-08-01 06:20:17.657235 INFO::Formatting Data.
2025-08-01 06:20:17.658079 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:17.659286 INFO::Removing potential empty rows and columns
2025-08-01 06:20:17.660814 INFO::Found 0 missing values.
2025-08-01 06:20:17.665287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:17.666252 INFO::Done
2025-08-01 06:20:17.667057 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:17.670074 INFO::Starting hierarchical adjustment
2025-08-01 06:20:17.671282 INFO::Found 2 batches.
2025-08-01 06:20:17.672111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:17.673101 INFO::Using default BPPARAM
2025-08-01 06:20:17.673902 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:17.675318 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 06:20:17.697547 INFO::Done
2025-08-01 06:20:17.698458 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:17.701253 INFO::ASW Batch was 0.0159645140308384 prior to batch effect correction and is now -0.121589554136527 .
2025-08-01 06:20:17.70244 INFO::Total function execution time is 0.045173168182373 s and adjustment time is 0.0264780521392822 s ( 58.61 )
2025-08-01 06:20:21.926668 INFO::Formatting Data.
2025-08-01 06:20:21.927965 INFO::Recognized SummarizedExperiment
2025-08-01 06:20:21.928695 INFO::Typecasting input to dataframe.
2025-08-01 06:20:21.985282 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:21.987103 INFO::Removing potential empty rows and columns
2025-08-01 06:20:21.993062 INFO::Found 0 missing values.
2025-08-01 06:20:22.004718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:22.005713 INFO::Done
2025-08-01 06:20:22.006511 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:22.012523 INFO::Starting hierarchical adjustment
2025-08-01 06:20:22.013903 INFO::Found 2 batches.
2025-08-01 06:20:22.014737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:22.016351 INFO::Using default BPPARAM
2025-08-01 06:20:22.017382 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:22.018827 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 06:20:22.103883 INFO::Done
2025-08-01 06:20:22.104941 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:22.109921 INFO::ASW Batch was -0.0162783029219447 prior to batch effect correction and is now -0.090074477742543 .
2025-08-01 06:20:22.111259 INFO::Total function execution time is 0.185322284698486 s and adjustment time is 0.0902700424194336 s ( 48.71 )
2025-08-01 06:20:22.13889 INFO::Formatting Data.
2025-08-01 06:20:22.139901 INFO::Recognized SummarizedExperiment
2025-08-01 06:20:22.140755 INFO::Typecasting input to dataframe.
2025-08-01 06:20:22.15408 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:22.15565 INFO::Removing potential empty rows and columns
2025-08-01 06:20:22.160752 INFO::Found 0 missing values.
2025-08-01 06:20:22.170802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:22.171727 INFO::Done
2025-08-01 06:20:22.172564 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:22.177669 INFO::Starting hierarchical adjustment
2025-08-01 06:20:22.178822 INFO::Found 2 batches.
2025-08-01 06:20:22.179612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:22.180628 INFO::Using default BPPARAM
2025-08-01 06:20:22.181402 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:22.182838 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 06:20:22.218458 INFO::Done
2025-08-01 06:20:22.219394 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:22.224446 INFO::ASW Batch was 0.00610350680637756 prior to batch effect correction and is now 0.00610350680637756 .
2025-08-01 06:20:22.225793 INFO::Total function execution time is 0.0868690013885498 s and adjustment time is 0.0398516654968262 s ( 45.88 )
2025-08-01 06:20:22.252092 INFO::Formatting Data.
2025-08-01 06:20:22.253177 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:22.254493 INFO::Removing potential empty rows and columns
2025-08-01 06:20:22.256169 INFO::Found 0 missing values.
2025-08-01 06:20:22.261169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:22.262239 INFO::Done
2025-08-01 06:20:22.263221 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:22.266676 INFO::Starting hierarchical adjustment
2025-08-01 06:20:22.268027 INFO::Found 3 batches.
2025-08-01 06:20:22.268925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:22.269794 INFO::Using default BPPARAM
2025-08-01 06:20:22.270583 INFO::Processing subtree level 1
2025-08-01 06:20:22.606753 INFO::Adjusting the last 1 batches sequentially
2025-08-01 06:20:22.609252 INFO::Done
2025-08-01 06:20:22.610218 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:22.61383 INFO::ASW Batch was -0.152092968518603 prior to batch effect correction and is now -0.172846025687671 .
2025-08-01 06:20:22.615264 INFO::Total function execution time is 0.363188982009888 s and adjustment time is 0.341468572616577 s ( 94.02 )
2025-08-01 06:20:22.634766 INFO::Skipping initial DF formatting
2025-08-01 06:20:22.704861 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:22.711622 INFO::Starting hierarchical adjustment
2025-08-01 06:20:22.712888 INFO::Found 5 batches.
2025-08-01 06:20:22.713687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:22.714567 INFO::Using default BPPARAM
2025-08-01 06:20:22.715317 INFO::Processing subtree level 1
2025-08-01 06:20:22.920462 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:22.923291 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 06:20:22.961336 INFO::Done
2025-08-01 06:20:22.962426 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:22.969628 INFO::ASW Batch was 0.461149742563438 prior to batch effect correction and is now 0.461149742563438 .
2025-08-01 06:20:22.970565 INFO::ASW Label was 0.385513897527478 prior to batch effect correction and is now 0.385513897527478 .
2025-08-01 06:20:22.971967 INFO::Total function execution time is 0.337229251861572 s and adjustment time is 0.248666524887085 s ( 73.74 )
2025-08-01 06:20:23.00094 INFO::Formatting Data.
2025-08-01 06:20:23.002055 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:23.00335 INFO::Removing potential empty rows and columns
2025-08-01 06:20:23.004896 INFO::Found 0 missing values.
2025-08-01 06:20:23.011604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:23.01249 INFO::Done
2025-08-01 06:20:23.013322 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:23.017933 INFO::Starting hierarchical adjustment
2025-08-01 06:20:23.019058 INFO::Found 5 batches.
2025-08-01 06:20:23.019906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:23.020906 INFO::Using default BPPARAM
2025-08-01 06:20:23.021773 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.
2025-08-01 06:20:23.185162 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:23.187322 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 06:20:23.212382 INFO::Done
2025-08-01 06:20:23.21337 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:23.21814 INFO::ASW Batch was 0.324193181441377 prior to batch effect correction and is now -0.111685964321538 .
2025-08-01 06:20:23.219111 INFO::ASW Label was 0.316594480756699 prior to batch effect correction and is now 0.869880792779198 .
2025-08-01 06:20:23.220369 INFO::Total function execution time is 0.219453573226929 s and adjustment time is 0.193524122238159 s ( 88.18 )
2025-08-01 06:20:23.221677 INFO::Formatting Data.
2025-08-01 06:20:23.222581 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:23.223954 INFO::Removing potential empty rows and columns
2025-08-01 06:20:23.225555 INFO::Found 0 missing values.
2025-08-01 06:20:23.232111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:23.233118 INFO::Done
2025-08-01 06:20:23.233963 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:23.238446 INFO::Starting hierarchical adjustment
2025-08-01 06:20:23.239628 INFO::Found 5 batches.
2025-08-01 06:20:23.240484 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:23.241442 INFO::Using default BPPARAM
2025-08-01 06:20:23.242231 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.
2025-08-01 06:20:23.40784 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:23.410094 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 06:20:23.435796 INFO::Done
2025-08-01 06:20:23.436781 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:23.45055 INFO::ASW Batch was 0.324193181441377 prior to batch effect correction and is now -0.111685964321538 .
2025-08-01 06:20:23.451738 INFO::ASW Label was 0.316594480756699 prior to batch effect correction and is now 0.869880792779198 .
2025-08-01 06:20:23.453054 INFO::Total function execution time is 0.231359481811523 s and adjustment time is 0.196385860443115 s ( 84.88 )
2025-08-01 06:20:23.473987 INFO::Formatting Data.
2025-08-01 06:20:23.475102 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:23.47651 INFO::Removing potential empty rows and columns
2025-08-01 06:20:23.478082 INFO::Found 0 missing values.
2025-08-01 06:20:23.484569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:23.485554 INFO::Done
2025-08-01 06:20:23.486403 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:23.491066 INFO::Starting hierarchical adjustment
2025-08-01 06:20:23.492299 INFO::Found 5 batches.
2025-08-01 06:20:23.493191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:23.494229 INFO::Using default BPPARAM
2025-08-01 06:20:23.495088 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.
2025-08-01 06:20:23.655612 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:23.658475 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 06:20:23.683336 INFO::Done
2025-08-01 06:20:23.684361 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:23.689537 INFO::ASW Batch was 0.368044844376571 prior to batch effect correction and is now -0.0596206777999763 .
2025-08-01 06:20:23.690548 INFO::ASW Label was 0.413060724102284 prior to batch effect correction and is now 0.789233450850979 .
2025-08-01 06:20:23.691821 INFO::Total function execution time is 0.217875719070435 s and adjustment time is 0.191306114196777 s ( 87.81 )
2025-08-01 06:20:23.693203 INFO::Formatting Data.
2025-08-01 06:20:23.694197 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:23.695576 INFO::Removing potential empty rows and columns
2025-08-01 06:20:23.697239 INFO::Found 0 missing values.
2025-08-01 06:20:23.703939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:23.704992 INFO::Done
2025-08-01 06:20:23.705847 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:23.710453 INFO::Starting hierarchical adjustment
2025-08-01 06:20:23.711717 INFO::Found 5 batches.
2025-08-01 06:20:23.712678 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:23.71367 INFO::Using default BPPARAM
2025-08-01 06:20:23.714518 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.
2025-08-01 06:20:23.863613 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:23.865983 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 06:20:23.889487 INFO::Done
2025-08-01 06:20:23.890473 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:23.895205 INFO::ASW Batch was 0.368044844376571 prior to batch effect correction and is now -0.0596206777999763 .
2025-08-01 06:20:23.896205 INFO::ASW Label was 0.413060724102284 prior to batch effect correction and is now 0.789233450850979 .
2025-08-01 06:20:23.897497 INFO::Total function execution time is 0.204283714294434 s and adjustment time is 0.178032398223877 s ( 87.15 )
2025-08-01 06:20:23.917808 INFO::Formatting Data.
2025-08-01 06:20:23.918923 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:23.92034 INFO::Removing potential empty rows and columns
2025-08-01 06:20:23.921917 INFO::Found 0 missing values.
2025-08-01 06:20:23.926163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:23.927125 INFO::Done
2025-08-01 06:20:23.927947 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:23.932257 INFO::Starting hierarchical adjustment
2025-08-01 06:20:23.933458 INFO::Found 2 batches.
2025-08-01 06:20:23.934256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:23.935173 INFO::Using default BPPARAM
2025-08-01 06:20:23.935952 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:23.937404 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 06:20:23.959193 INFO::Done
2025-08-01 06:20:23.96015 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:23.964569 INFO::ASW Batch was 0.577258600401757 prior to batch effect correction and is now 0.0778665861565821 .
2025-08-01 06:20:23.965517 INFO::ASW Label was 0.449990599089559 prior to batch effect correction and is now 0.842537662928486 .
2025-08-01 06:20:23.966689 INFO::Total function execution time is 0.0489737987518311 s and adjustment time is 0.0259480476379395 s ( 52.98 )
2025-08-01 06:20:23.967818 INFO::Formatting Data.
2025-08-01 06:20:23.968754 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:23.970072 INFO::Removing potential empty rows and columns
2025-08-01 06:20:23.971562 INFO::Found 0 missing values.
2025-08-01 06:20:23.975754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:23.976745 INFO::Done
2025-08-01 06:20:23.977584 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:23.981954 INFO::Starting hierarchical adjustment
2025-08-01 06:20:23.983168 INFO::Found 2 batches.
2025-08-01 06:20:23.984038 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:23.985073 INFO::Using default BPPARAM
2025-08-01 06:20:23.985891 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:23.98734 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 06:20:24.009859 INFO::Done
2025-08-01 06:20:24.010818 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:24.015101 INFO::ASW Batch was 0.577258600401757 prior to batch effect correction and is now 0.0778665861565821 .
2025-08-01 06:20:24.016046 INFO::ASW Label was 0.449990599089559 prior to batch effect correction and is now 0.842537662928486 .
2025-08-01 06:20:24.017273 INFO::Total function execution time is 0.0494563579559326 s and adjustment time is 0.0269315242767334 s ( 54.46 )
2025-08-01 06:20:24.03401 INFO::Formatting Data.
2025-08-01 06:20:24.03508 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:24.036372 INFO::Removing potential empty rows and columns
2025-08-01 06:20:24.037791 INFO::Found 0 missing values.
2025-08-01 06:20:24.041071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:24.041959 INFO::Done
2025-08-01 06:20:24.04275 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:24.045537 INFO::Starting hierarchical adjustment
2025-08-01 06:20:24.04666 INFO::Found 2 batches.
2025-08-01 06:20:24.047487 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:24.048414 INFO::Using default BPPARAM
2025-08-01 06:20:24.049216 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:24.050585 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 06:20:24.097381 INFO::Done
2025-08-01 06:20:24.098336 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:24.101176 INFO::ASW Batch was 0.0376731793168171 prior to batch effect correction and is now -0.154086564793957 .
2025-08-01 06:20:24.102421 INFO::Total function execution time is 0.0684795379638672 s and adjustment time is 0.0509378910064697 s ( 74.38 )
2025-08-01 06:20:24.12011 INFO::Formatting Data.
2025-08-01 06:20:24.121261 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:24.122604 INFO::Removing potential empty rows and columns
2025-08-01 06:20:24.124124 INFO::Found 0 missing values.
2025-08-01 06:20:24.125901 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.
2025-08-01 06:20:24.133263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:24.134314 INFO::Done
2025-08-01 06:20:24.135123 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:24.139453 INFO::Starting hierarchical adjustment
2025-08-01 06:20:24.140686 INFO::Found 2 batches.
2025-08-01 06:20:24.141495 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:24.142359 INFO::Using default BPPARAM
2025-08-01 06:20:24.143133 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:24.144579 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 06:20:24.1686 INFO::Done
2025-08-01 06:20:24.169549 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:24.173782 INFO::ASW Batch was 0.759952887956799 prior to batch effect correction and is now -0.0166697419997371 .
2025-08-01 06:20:24.174769 INFO::ASW Label was 0.286227341685015 prior to batch effect correction and is now 0.881608102892351 .
2025-08-01 06:20:24.17593 INFO::Total function execution time is 0.0558958053588867 s and adjustment time is 0.0281369686126709 s ( 50.34 )
2025-08-01 06:20:24.177186 INFO::Formatting Data.
2025-08-01 06:20:24.178127 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:24.179526 INFO::Removing potential empty rows and columns
2025-08-01 06:20:24.181057 INFO::Found 0 missing values.
2025-08-01 06:20:24.182444 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.
2025-08-01 06:20:24.189665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:24.190678 INFO::Done
2025-08-01 06:20:24.191518 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:24.195827 INFO::Starting hierarchical adjustment
2025-08-01 06:20:24.197088 INFO::Found 2 batches.
2025-08-01 06:20:24.197925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:24.198823 INFO::Using default BPPARAM
2025-08-01 06:20:24.199597 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:24.201086 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 06:20:24.224634 INFO::Done
2025-08-01 06:20:24.225604 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:24.23004 INFO::ASW Batch was 0.759952887956799 prior to batch effect correction and is now -0.0166697419997371 .
2025-08-01 06:20:24.230965 INFO::ASW Label was 0.286227341685015 prior to batch effect correction and is now 0.881608102892351 .
2025-08-01 06:20:24.23205 INFO::Total function execution time is 0.054905891418457 s and adjustment time is 0.0277431011199951 s ( 50.53 )
2025-08-01 06:20:24.546104 INFO::Formatting Data.
2025-08-01 06:20:24.547237 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:24.54863 INFO::Removing potential empty rows and columns
2025-08-01 06:20:24.5502 INFO::Found 0 missing values.
2025-08-01 06:20:24.554839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:24.555811 INFO::Done
2025-08-01 06:20:24.556671 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:24.559687 INFO::Starting hierarchical adjustment
2025-08-01 06:20:24.560887 INFO::Found 3 batches.
2025-08-01 06:20:24.561741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:24.562648 INFO::Using default BPPARAM
2025-08-01 06:20:24.563468 INFO::Processing subtree level 1
2025-08-01 06:20:24.678698 INFO::Adjusting the last 1 batches sequentially
2025-08-01 06:20:24.681338 INFO::Done
2025-08-01 06:20:24.682301 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:24.685944 INFO::ASW Batch was -0.0494864893491913 prior to batch effect correction and is now -0.0494864893491913 .
2025-08-01 06:20:24.687527 INFO::Total function execution time is 0.14139199256897 s and adjustment time is 0.120687961578369 s ( 85.36 )
2025-08-01 06:20:24.689157 INFO::Formatting Data.
2025-08-01 06:20:24.690161 INFO::Typecasting input to dataframe.
2025-08-01 06:20:24.691632 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:24.693154 INFO::Removing potential empty rows and columns
2025-08-01 06:20:24.694831 INFO::Found 0 missing values.
2025-08-01 06:20:24.699612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:24.700606 INFO::Done
2025-08-01 06:20:24.701468 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:24.704381 INFO::Starting hierarchical adjustment
2025-08-01 06:20:24.705547 INFO::Found 3 batches.
2025-08-01 06:20:24.706353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:24.707282 INFO::Using default BPPARAM
2025-08-01 06:20:24.708076 INFO::Processing subtree level 1
2025-08-01 06:20:24.822594 INFO::Adjusting the last 1 batches sequentially
2025-08-01 06:20:24.82503 INFO::Done
2025-08-01 06:20:24.825899 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:24.82951 INFO::ASW Batch was -0.0494864893491913 prior to batch effect correction and is now -0.0494864893491913 .
2025-08-01 06:20:24.830943 INFO::Total function execution time is 0.141766309738159 s and adjustment time is 0.119700908660889 s ( 84.44 )
2025-08-01 06:20:24.848958 INFO::Formatting Data.
2025-08-01 06:20:24.84998 INFO::Typecasting input to dataframe.
2025-08-01 06:20:24.851131 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:24.852494 INFO::Removing potential empty rows and columns
2025-08-01 06:20:24.853991 INFO::Found 0 missing values.
2025-08-01 06:20:24.858208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:24.8591 INFO::Done
2025-08-01 06:20:24.859864 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:24.862677 INFO::Starting hierarchical adjustment
2025-08-01 06:20:24.863765 INFO::Found 3 batches.
2025-08-01 06:20:24.864577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:24.865489 INFO::Using default BPPARAM
2025-08-01 06:20:24.866256 INFO::Processing subtree level 1
2025-08-01 06:20:24.978269 INFO::Adjusting the last 1 batches sequentially
2025-08-01 06:20:24.980679 INFO::Done
2025-08-01 06:20:24.981548 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:24.985038 INFO::ASW Batch was -0.0634812516956319 prior to batch effect correction and is now -0.0634812516956319 .
2025-08-01 06:20:24.986426 INFO::Total function execution time is 0.137475490570068 s and adjustment time is 0.11711311340332 s ( 85.19 )
2025-08-01 06:20:25.171346 INFO::Formatting Data.
2025-08-01 06:20:25.172556 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:25.174234 INFO::Removing potential empty rows and columns
2025-08-01 06:20:25.178548 INFO::Found 1000 missing values.
2025-08-01 06:20:25.207488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:25.212531 INFO::Done
2025-08-01 06:20:25.214358 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:25.223198 INFO::Starting hierarchical adjustment
2025-08-01 06:20:25.224502 INFO::Found 10 batches.
2025-08-01 06:20:25.225359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:25.226354 INFO::Using default BPPARAM
2025-08-01 06:20:25.227189 INFO::Processing subtree level 1
2025-08-01 06:20:25.405087 INFO::Processing subtree level 2
2025-08-01 06:20:25.585216 INFO::Adjusting the last 1 batches sequentially
2025-08-01 06:20:25.587872 INFO::Done
2025-08-01 06:20:25.588883 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:25.596861 INFO::ASW Batch was 0.58175861395964 prior to batch effect correction and is now 0.58175861395964 .
2025-08-01 06:20:25.597857 INFO::ASW Label was 0.300417184853516 prior to batch effect correction and is now 0.300417184853516 .
2025-08-01 06:20:25.599258 INFO::Total function execution time is 0.427932977676392 s and adjustment time is 0.363672256469727 s ( 84.98 )
2025-08-01 06:20:25.600499 INFO::Formatting Data.
2025-08-01 06:20:25.601443 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:25.603238 INFO::Removing potential empty rows and columns
2025-08-01 06:20:25.607343 INFO::Found 1000 missing values.
2025-08-01 06:20:25.635052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:25.636008 INFO::Done
2025-08-01 06:20:25.636852 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:25.644638 INFO::Starting hierarchical adjustment
2025-08-01 06:20:25.64585 INFO::Found 10 batches.
2025-08-01 06:20:26.984317 INFO::Set up parallel execution backend with 2 workers
2025-08-01 06:20:26.986573 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-01 06:20:28.747303 INFO::Adjusting the last 2 batches sequentially
2025-08-01 06:20:28.749849 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 06:20:28.776256 INFO::Done
2025-08-01 06:20:28.777141 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:28.783969 INFO::ASW Batch was 0.58175861395964 prior to batch effect correction and is now 0.58175861395964 .
2025-08-01 06:20:28.784897 INFO::ASW Label was 0.300417184853516 prior to batch effect correction and is now 0.300417184853516 .
2025-08-01 06:20:28.785944 INFO::Total function execution time is 3.18549108505249 s and adjustment time is 3.13061261177063 s ( 98.28 )
2025-08-01 06:20:28.985153 INFO::Formatting Data.
2025-08-01 06:20:28.986353 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:28.987744 INFO::Removing potential empty rows and columns
2025-08-01 06:20:28.989479 INFO::Found 0 missing values.
2025-08-01 06:20:28.995432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:28.996406 INFO::Done
2025-08-01 06:20:28.997247 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 06:20:29.001268 INFO::Starting hierarchical adjustment
2025-08-01 06:20:29.002402 INFO::Found 3 batches.
2025-08-01 06:20:29.003207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 06:20:29.004128 INFO::Using default BPPARAM
2025-08-01 06:20:29.004997 INFO::Processing subtree level 1
2025-08-01 06:20:29.150755 INFO::Adjusting the last 1 batches sequentially
2025-08-01 06:20:29.153304 INFO::Done
2025-08-01 06:20:29.154238 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 06:20:29.158909 INFO::ASW Batch was 0.201166969080483 prior to batch effect correction and is now -0.164448661362533 .
2025-08-01 06:20:29.159893 INFO::ASW Label was -0.185041623511211 prior to batch effect correction and is now 0.0512411164108748 .
2025-08-01 06:20:29.161302 INFO::Total function execution time is 0.17616605758667 s and adjustment time is 0.151110649108887 s ( 85.78 )
2025-08-01 06:20:29.338595 INFO::Formatting Data.
2025-08-01 06:20:29.339749 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.341147 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.342742 INFO::Found 2 missing values.
2025-08-01 06:20:29.347203 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.348148 INFO::Done
2025-08-01 06:20:29.390566 INFO::Found NA in Reference column
2025-08-01 06:20:29.405047 INFO::Require at least two references per batch.
2025-08-01 06:20:29.435483 INFO::Formatting Data.
2025-08-01 06:20:29.436527 INFO::Recognized SummarizedExperiment
2025-08-01 06:20:29.437376 INFO::Typecasting input to dataframe.
2025-08-01 06:20:29.452169 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.453934 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.459872 INFO::Found 0 missing values.
2025-08-01 06:20:29.471431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.472411 INFO::Done
2025-08-01 06:20:29.494879 INFO::Formatting Data.
2025-08-01 06:20:29.49588 INFO::Recognized SummarizedExperiment
2025-08-01 06:20:29.496751 INFO::Typecasting input to dataframe.
2025-08-01 06:20:29.524209 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.525918 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.531746 INFO::Found 0 missing values.
2025-08-01 06:20:29.550452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.551389 INFO::Done
2025-08-01 06:20:29.574965 INFO::Formatting Data.
2025-08-01 06:20:29.575987 INFO::Recognized SummarizedExperiment
2025-08-01 06:20:29.576871 INFO::Typecasting input to dataframe.
2025-08-01 06:20:29.602397 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.603845 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.605544 INFO::Found 0 missing values.
2025-08-01 06:20:29.606903 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.
2025-08-01 06:20:29.613833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.614766 INFO::Done
2025-08-01 06:20:29.629983 INFO::Formatting Data.
2025-08-01 06:20:29.631139 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.632617 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.634244 INFO::Found 0 missing values.
2025-08-01 06:20:29.638919 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.63991 INFO::Done
2025-08-01 06:20:29.657575 INFO::Formatting Data.
2025-08-01 06:20:29.658664 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.659923 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.66155 INFO::Found 0 missing values.
2025-08-01 06:20:29.666237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.667162 INFO::Done
2025-08-01 06:20:29.713962 INFO::Formatting Data.
2025-08-01 06:20:29.715184 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.716888 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.718831 INFO::Found 1 missing values.
2025-08-01 06:20:29.723179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.724387 INFO::Done
2025-08-01 06:20:29.755093 INFO::Formatting Data.
2025-08-01 06:20:29.756293 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.757738 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.75935 INFO::Found 2 missing values.
2025-08-01 06:20:29.760882 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.
2025-08-01 06:20:29.76458 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.765668 INFO::Done
2025-08-01 06:20:29.780951 INFO::Formatting Data.
2025-08-01 06:20:29.781996 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.783206 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.784622 INFO::Found 2 missing values.
2025-08-01 06:20:29.787077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.787961 INFO::Done
2025-08-01 06:20:29.804274 INFO::Formatting Data.
2025-08-01 06:20:29.805422 INFO::Typecasting input to dataframe.
2025-08-01 06:20:29.806706 INFO::Replacing NaNs with NAs.
2025-08-01 06:20:29.807972 INFO::Removing potential empty rows and columns
2025-08-01 06:20:29.809548 INFO::Found 0 missing values.
2025-08-01 06:20:29.814025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 06:20:29.814952 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
23.297 5.080 28.297
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.212 | 1.516 | 22.770 | |
| compute_asw | 0.035 | 0.000 | 0.034 | |
| count_existing | 0.017 | 0.000 | 0.018 | |
| generate_data_covariables | 0.016 | 0.000 | 0.015 | |
| generate_dataset | 0.015 | 0.000 | 0.015 | |