Yannis Schumann
| Snapshot Date: 2025-03-17 13:40 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0400 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-18 11:46 -0400 (Tue, 18 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4537 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4543 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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 161/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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. |
| Package: BERT |
| Version: 1.3.6 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-03-17 18:17:29 -0400 (Mon, 17 Mar 2025) |
| EndedAt: 2025-03-17 18:17:59 -0400 (Mon, 17 Mar 2025) |
| EllapsedTime: 30.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.505 0.409 6.806
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.3.6’ ** 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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-03-17 18:17:52.078068 INFO::Formatting Data.
2025-03-17 18:17:52.07974 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:52.085258 INFO::Removing potential empty rows and columns
2025-03-17 18:17:52.195106 INFO::Found 0 missing values.
2025-03-17 18:17:52.196404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:52.196669 INFO::Done
2025-03-17 18:17:52.196881 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:52.203003 INFO::Starting hierarchical adjustment
2025-03-17 18:17:52.20333 INFO::Found 3 batches.
2025-03-17 18:17:52.203525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:52.203955 INFO::Using default BPPARAM
2025-03-17 18:17:52.204154 INFO::Processing subtree level 1
2025-03-17 18:17:52.256715 INFO::Adjusting the last 1 batches sequentially
2025-03-17 18:17:52.257968 INFO::Done
2025-03-17 18:17:52.258233 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:52.259858 INFO::ASW Batch was -0.0844563823258968 prior to batch effect correction and is now -0.0844563823258968 .
2025-03-17 18:17:52.260505 INFO::Total function execution time is 0.182764053344727 s and adjustment time is 0.0547029972076416 s ( 29.93 )
2025-03-17 18:17:52.271112 INFO::Formatting Data.
2025-03-17 18:17:52.271449 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:52.271874 INFO::Removing potential empty rows and columns
2025-03-17 18:17:52.272534 INFO::Found 0 missing values.
2025-03-17 18:17:52.273039 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.
2025-03-17 18:17:52.277417 INFO::Formatting Data.
2025-03-17 18:17:52.277641 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:52.277914 INFO::Removing potential empty rows and columns
2025-03-17 18:17:52.278233 INFO::Found 0 missing values.
2025-03-17 18:17:52.278515 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.
2025-03-17 18:17:52.285776 INFO::Formatting Data.
2025-03-17 18:17:52.286036 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:52.286356 INFO::Removing potential empty rows and columns
2025-03-17 18:17:52.286695 INFO::Found 0 missing values.
2025-03-17 18:17:52.286993 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.
2025-03-17 18:17:52.288486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:52.288709 INFO::Done
2025-03-17 18:17:52.288892 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:52.289632 INFO::Starting hierarchical adjustment
2025-03-17 18:17:52.289897 INFO::Found 2 batches.
2025-03-17 18:17:52.290065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:52.290309 INFO::Using default BPPARAM
2025-03-17 18:17:52.290486 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:52.290767 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:52.301135 INFO::Done
2025-03-17 18:17:52.301359 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:52.302015 INFO::ASW Batch was -0.0278112371235171 prior to batch effect correction and is now -0.118856638280866 .
2025-03-17 18:17:52.302261 INFO::Total function execution time is 0.016510009765625 s and adjustment time is 0.011279821395874 s ( 68.32 )
2025-03-17 18:17:52.303314 INFO::Formatting Data.
2025-03-17 18:17:52.303527 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:52.306612 INFO::Formatting Data.
2025-03-17 18:17:52.306841 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:52.307107 INFO::Removing potential empty rows and columns
2025-03-17 18:17:52.3075 INFO::Found 0 missing values.
2025-03-17 18:17:52.327093 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:52.327377 INFO::Done
2025-03-17 18:17:52.32757 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:52.328297 INFO::Starting hierarchical adjustment
2025-03-17 18:17:52.328533 INFO::Found 2 batches.
2025-03-17 18:17:52.328717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:52.328926 INFO::Using default BPPARAM
2025-03-17 18:17:52.329079 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:52.329367 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:52.334342 INFO::Done
2025-03-17 18:17:52.334542 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:52.335181 INFO::ASW Batch was -0.013231902499135 prior to batch effect correction and is now -0.119299828046093 .
2025-03-17 18:17:52.335423 INFO::Total function execution time is 0.0288209915161133 s and adjustment time is 0.00585603713989258 s ( 20.32 )
2025-03-17 18:17:52.335765 INFO::Formatting Data.
2025-03-17 18:17:52.335938 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:52.336186 INFO::Removing potential empty rows and columns
2025-03-17 18:17:52.336484 INFO::Found 0 missing values.
2025-03-17 18:17:52.337346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:52.337511 INFO::Done
2025-03-17 18:17:52.337672 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:52.33828 INFO::Starting hierarchical adjustment
2025-03-17 18:17:52.338506 INFO::Found 2 batches.
2025-03-17 18:17:52.338668 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:52.338858 INFO::Using default BPPARAM
2025-03-17 18:17:52.339029 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:52.339282 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:52.343953 INFO::Done
2025-03-17 18:17:52.344152 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:52.344801 INFO::ASW Batch was -0.013231902499135 prior to batch effect correction and is now -0.119299828046093 .
2025-03-17 18:17:52.345046 INFO::Total function execution time is 0.00927281379699707 s and adjustment time is 0.00548887252807617 s ( 59.19 )
2025-03-17 18:17:53.546915 INFO::Formatting Data.
2025-03-17 18:17:53.547164 INFO::Recognized SummarizedExperiment
2025-03-17 18:17:53.547324 INFO::Typecasting input to dataframe.
2025-03-17 18:17:53.557886 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:53.558307 INFO::Removing potential empty rows and columns
2025-03-17 18:17:53.559429 INFO::Found 0 missing values.
2025-03-17 18:17:53.561502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:53.561672 INFO::Done
2025-03-17 18:17:53.561825 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:53.563023 INFO::Starting hierarchical adjustment
2025-03-17 18:17:53.563248 INFO::Found 2 batches.
2025-03-17 18:17:53.5634 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:53.563717 INFO::Using default BPPARAM
2025-03-17 18:17:53.563869 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:53.56415 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:53.582143 INFO::Done
2025-03-17 18:17:53.582389 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:53.583607 INFO::ASW Batch was -0.00283092676750476 prior to batch effect correction and is now -0.0905882936148023 .
2025-03-17 18:17:53.58387 INFO::Total function execution time is 0.0370559692382812 s and adjustment time is 0.0189230442047119 s ( 51.07 )
2025-03-17 18:17:53.590133 INFO::Formatting Data.
2025-03-17 18:17:53.59036 INFO::Recognized SummarizedExperiment
2025-03-17 18:17:53.59052 INFO::Typecasting input to dataframe.
2025-03-17 18:17:53.593437 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:53.593788 INFO::Removing potential empty rows and columns
2025-03-17 18:17:53.594908 INFO::Found 0 missing values.
2025-03-17 18:17:53.596967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:53.597129 INFO::Done
2025-03-17 18:17:53.597285 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:53.598511 INFO::Starting hierarchical adjustment
2025-03-17 18:17:53.598724 INFO::Found 2 batches.
2025-03-17 18:17:53.598876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:53.599055 INFO::Using default BPPARAM
2025-03-17 18:17:53.599199 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:53.599491 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:53.60739 INFO::Done
2025-03-17 18:17:53.607611 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:53.60878 INFO::ASW Batch was -0.0100152989839148 prior to batch effect correction and is now -0.0100152989839148 .
2025-03-17 18:17:53.609069 INFO::Total function execution time is 0.0189321041107178 s and adjustment time is 0.00870990753173828 s ( 46.01 )
2025-03-17 18:17:53.616498 INFO::Formatting Data.
2025-03-17 18:17:53.616759 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:53.617037 INFO::Removing potential empty rows and columns
2025-03-17 18:17:53.617345 INFO::Found 0 missing values.
2025-03-17 18:17:53.618626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:53.618919 INFO::Done
2025-03-17 18:17:53.619101 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:53.619783 INFO::Starting hierarchical adjustment
2025-03-17 18:17:53.619996 INFO::Found 3 batches.
2025-03-17 18:17:53.620147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:53.620329 INFO::Using default BPPARAM
2025-03-17 18:17:53.620475 INFO::Processing subtree level 1
2025-03-17 18:17:53.745541 INFO::Adjusting the last 1 batches sequentially
2025-03-17 18:17:53.750668 INFO::Done
2025-03-17 18:17:53.751073 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:53.753457 INFO::ASW Batch was 0.00417104897705823 prior to batch effect correction and is now -0.154328843098395 .
2025-03-17 18:17:53.755237 INFO::Total function execution time is 0.138103008270264 s and adjustment time is 0.130689144134521 s ( 94.63 )
2025-03-17 18:17:53.796469 INFO::Skipping initial DF formatting
2025-03-17 18:17:53.79679 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:53.798407 INFO::Starting hierarchical adjustment
2025-03-17 18:17:53.798681 INFO::Found 5 batches.
2025-03-17 18:17:53.798851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:53.799093 INFO::Using default BPPARAM
2025-03-17 18:17:53.799252 INFO::Processing subtree level 1
2025-03-17 18:17:53.875416 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:53.885075 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:53.899007 INFO::Done
2025-03-17 18:17:53.908433 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:53.924104 INFO::ASW Batch was 0.547774964465748 prior to batch effect correction and is now 0.547774964465748 .
2025-03-17 18:17:53.925871 INFO::ASW Label was 0.381489561460241 prior to batch effect correction and is now 0.381489561460241 .
2025-03-17 18:17:53.930333 INFO::Total function execution time is 0.133806943893433 s and adjustment time is 0.100368022918701 s ( 75.01 )
2025-03-17 18:17:53.940532 INFO::Formatting Data.
2025-03-17 18:17:53.940839 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:53.941214 INFO::Removing potential empty rows and columns
2025-03-17 18:17:53.94248 INFO::Found 0 missing values.
2025-03-17 18:17:53.944724 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:53.94502 INFO::Done
2025-03-17 18:17:53.94528 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:53.946777 INFO::Starting hierarchical adjustment
2025-03-17 18:17:53.947068 INFO::Found 5 batches.
2025-03-17 18:17:53.947268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:53.947586 INFO::Using default BPPARAM
2025-03-17 18:17:53.947908 INFO::Processing subtree level 1
2025-03-17 18:17:54.01758 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.019304 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.029655 INFO::Done
2025-03-17 18:17:54.030161 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.03198 INFO::ASW Batch was 0.35885253484605 prior to batch effect correction and is now -0.109848902353055 .
2025-03-17 18:17:54.032253 INFO::ASW Label was 0.318455634548644 prior to batch effect correction and is now 0.87201187883364 .
2025-03-17 18:17:54.03289 INFO::Total function execution time is 0.0922930240631104 s and adjustment time is 0.0826389789581299 s ( 89.54 )
2025-03-17 18:17:54.033357 INFO::Formatting Data.
2025-03-17 18:17:54.03363 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.034136 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.034565 INFO::Found 0 missing values.
2025-03-17 18:17:54.036513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.036888 INFO::Done
2025-03-17 18:17:54.037169 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.038594 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.038939 INFO::Found 5 batches.
2025-03-17 18:17:54.039168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.039481 INFO::Using default BPPARAM
2025-03-17 18:17:54.039814 INFO::Processing subtree level 1
2025-03-17 18:17:54.113141 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.1158 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.125629 INFO::Done
2025-03-17 18:17:54.125912 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.127512 INFO::ASW Batch was 0.35885253484605 prior to batch effect correction and is now -0.109848902353055 .
2025-03-17 18:17:54.12789 INFO::ASW Label was 0.318455634548644 prior to batch effect correction and is now 0.87201187883364 .
2025-03-17 18:17:54.1282 INFO::Total function execution time is 0.0948100090026855 s and adjustment time is 0.0867431163787842 s ( 91.49 )
2025-03-17 18:17:54.134962 INFO::Formatting Data.
2025-03-17 18:17:54.135219 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.135529 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.135883 INFO::Found 0 missing values.
2025-03-17 18:17:54.137236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.137433 INFO::Done
2025-03-17 18:17:54.13762 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.138837 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.139098 INFO::Found 5 batches.
2025-03-17 18:17:54.139287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.139524 INFO::Using default BPPARAM
2025-03-17 18:17:54.139794 INFO::Processing subtree level 1
2025-03-17 18:17:54.196243 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.199053 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.206749 INFO::Done
2025-03-17 18:17:54.207174 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.208938 INFO::ASW Batch was 0.472291242643339 prior to batch effect correction and is now -0.0357149243470035 .
2025-03-17 18:17:54.20917 INFO::ASW Label was 0.355894522443421 prior to batch effect correction and is now 0.746267095198434 .
2025-03-17 18:17:54.209511 INFO::Total function execution time is 0.0745298862457275 s and adjustment time is 0.0676991939544678 s ( 90.83 )
2025-03-17 18:17:54.209867 INFO::Formatting Data.
2025-03-17 18:17:54.21008 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.210387 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.210777 INFO::Found 0 missing values.
2025-03-17 18:17:54.212549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.212828 INFO::Done
2025-03-17 18:17:54.213037 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.214276 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.214589 INFO::Found 5 batches.
2025-03-17 18:17:54.214782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.215028 INFO::Using default BPPARAM
2025-03-17 18:17:54.215249 INFO::Processing subtree level 1
2025-03-17 18:17:54.270427 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.290004 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.299168 INFO::Done
2025-03-17 18:17:54.299621 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.301376 INFO::ASW Batch was 0.472291242643339 prior to batch effect correction and is now -0.0357149243470035 .
2025-03-17 18:17:54.30179 INFO::ASW Label was 0.355894522443421 prior to batch effect correction and is now 0.746267095198434 .
2025-03-17 18:17:54.302269 INFO::Total function execution time is 0.0922298431396484 s and adjustment time is 0.0846271514892578 s ( 91.76 )
2025-03-17 18:17:54.311156 INFO::Formatting Data.
2025-03-17 18:17:54.311489 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.311862 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.312334 INFO::Found 0 missing values.
2025-03-17 18:17:54.313472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.313672 INFO::Done
2025-03-17 18:17:54.313876 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.315077 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.315349 INFO::Found 2 batches.
2025-03-17 18:17:54.31555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.31582 INFO::Using default BPPARAM
2025-03-17 18:17:54.316001 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.316312 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.324491 INFO::Done
2025-03-17 18:17:54.324765 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.325808 INFO::ASW Batch was 0.259133320682713 prior to batch effect correction and is now 0.131576251248711 .
2025-03-17 18:17:54.326012 INFO::ASW Label was 0.767027751546399 prior to batch effect correction and is now 0.848703338723442 .
2025-03-17 18:17:54.326304 INFO::Total function execution time is 0.0151770114898682 s and adjustment time is 0.00916504859924316 s ( 60.39 )
2025-03-17 18:17:54.326579 INFO::Formatting Data.
2025-03-17 18:17:54.326776 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.327045 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.327371 INFO::Found 0 missing values.
2025-03-17 18:17:54.328333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.328525 INFO::Done
2025-03-17 18:17:54.328694 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.329579 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.32985 INFO::Found 2 batches.
2025-03-17 18:17:54.330027 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.330214 INFO::Using default BPPARAM
2025-03-17 18:17:54.330379 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.330672 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.335883 INFO::Done
2025-03-17 18:17:54.336103 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.337101 INFO::ASW Batch was 0.259133320682713 prior to batch effect correction and is now 0.131576251248711 .
2025-03-17 18:17:54.337303 INFO::ASW Label was 0.767027751546399 prior to batch effect correction and is now 0.848703338723442 .
2025-03-17 18:17:54.337557 INFO::Total function execution time is 0.0109691619873047 s and adjustment time is 0.006072998046875 s ( 55.36 )
2025-03-17 18:17:54.342711 INFO::Formatting Data.
2025-03-17 18:17:54.342962 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.343273 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.343579 INFO::Found 0 missing values.
2025-03-17 18:17:54.344332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.344538 INFO::Done
2025-03-17 18:17:54.344717 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.345397 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.345651 INFO::Found 2 batches.
2025-03-17 18:17:54.345848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.346087 INFO::Using default BPPARAM
2025-03-17 18:17:54.346262 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.346577 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.359523 INFO::Done
2025-03-17 18:17:54.359811 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.360586 INFO::ASW Batch was -0.0289823437985068 prior to batch effect correction and is now -0.106131528378979 .
2025-03-17 18:17:54.360924 INFO::Total function execution time is 0.0182199478149414 s and adjustment time is 0.0139031410217285 s ( 76.31 )
2025-03-17 18:17:54.366982 INFO::Formatting Data.
2025-03-17 18:17:54.367274 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.367597 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.367944 INFO::Found 0 missing values.
2025-03-17 18:17:54.368369 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.
2025-03-17 18:17:54.369883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.370073 INFO::Done
2025-03-17 18:17:54.370256 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.371448 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.37171 INFO::Found 2 batches.
2025-03-17 18:17:54.371902 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.372128 INFO::Using default BPPARAM
2025-03-17 18:17:54.372317 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.372636 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.378561 INFO::Done
2025-03-17 18:17:54.378809 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.379806 INFO::ASW Batch was 0.230928227041786 prior to batch effect correction and is now -0.00279572318707122 .
2025-03-17 18:17:54.380013 INFO::ASW Label was 0.811527149603582 prior to batch effect correction and is now 0.942990069490041 .
2025-03-17 18:17:54.38029 INFO::Total function execution time is 0.0133349895477295 s and adjustment time is 0.00689697265625 s ( 51.72 )
2025-03-17 18:17:54.380565 INFO::Formatting Data.
2025-03-17 18:17:54.380789 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.381092 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.381416 INFO::Found 0 missing values.
2025-03-17 18:17:54.381721 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.
2025-03-17 18:17:54.383181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.383366 INFO::Done
2025-03-17 18:17:54.383544 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.384449 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.384689 INFO::Found 2 batches.
2025-03-17 18:17:54.384875 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.385074 INFO::Using default BPPARAM
2025-03-17 18:17:54.385237 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:54.385517 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:54.390636 INFO::Done
2025-03-17 18:17:54.390839 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.391689 INFO::ASW Batch was 0.230928227041786 prior to batch effect correction and is now -0.00279572318707122 .
2025-03-17 18:17:54.391891 INFO::ASW Label was 0.811527149603582 prior to batch effect correction and is now 0.942990069490041 .
2025-03-17 18:17:54.392129 INFO::Total function execution time is 0.0115580558776855 s and adjustment time is 0.00598716735839844 s ( 51.8 )
2025-03-17 18:17:54.458863 INFO::Formatting Data.
2025-03-17 18:17:54.459194 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.45952 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.45988 INFO::Found 0 missing values.
2025-03-17 18:17:54.46085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.461039 INFO::Done
2025-03-17 18:17:54.461237 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.462004 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.462225 INFO::Found 3 batches.
2025-03-17 18:17:54.462395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.462591 INFO::Using default BPPARAM
2025-03-17 18:17:54.462751 INFO::Processing subtree level 1
2025-03-17 18:17:54.504727 INFO::Adjusting the last 1 batches sequentially
2025-03-17 18:17:54.506154 INFO::Done
2025-03-17 18:17:54.506417 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.507999 INFO::ASW Batch was 0.00777314459515662 prior to batch effect correction and is now 0.00777314459515662 .
2025-03-17 18:17:54.508652 INFO::Total function execution time is 0.0498268604278564 s and adjustment time is 0.0439701080322266 s ( 88.25 )
2025-03-17 18:17:54.509032 INFO::Formatting Data.
2025-03-17 18:17:54.509236 INFO::Typecasting input to dataframe.
2025-03-17 18:17:54.509485 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.509795 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.510199 INFO::Found 0 missing values.
2025-03-17 18:17:54.511227 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.511428 INFO::Done
2025-03-17 18:17:54.511809 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.512407 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.512623 INFO::Found 3 batches.
2025-03-17 18:17:54.512784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.512999 INFO::Using default BPPARAM
2025-03-17 18:17:54.513306 INFO::Processing subtree level 1
2025-03-17 18:17:54.557569 INFO::Adjusting the last 1 batches sequentially
2025-03-17 18:17:54.559177 INFO::Done
2025-03-17 18:17:54.559423 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.561355 INFO::ASW Batch was 0.00777314459515662 prior to batch effect correction and is now 0.00777314459515662 .
2025-03-17 18:17:54.562861 INFO::Total function execution time is 0.0537419319152832 s and adjustment time is 0.0465810298919678 s ( 86.68 )
2025-03-17 18:17:54.571317 INFO::Formatting Data.
2025-03-17 18:17:54.571567 INFO::Typecasting input to dataframe.
2025-03-17 18:17:54.57185 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.57219 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.572622 INFO::Found 0 missing values.
2025-03-17 18:17:54.573729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.573917 INFO::Done
2025-03-17 18:17:54.574085 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.574742 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.574962 INFO::Found 3 batches.
2025-03-17 18:17:54.575131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.575369 INFO::Using default BPPARAM
2025-03-17 18:17:54.575541 INFO::Processing subtree level 1
2025-03-17 18:17:54.618088 INFO::Adjusting the last 1 batches sequentially
2025-03-17 18:17:54.619753 INFO::Done
2025-03-17 18:17:54.620018 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.621578 INFO::ASW Batch was -0.113664533297067 prior to batch effect correction and is now -0.113664533297067 .
2025-03-17 18:17:54.622252 INFO::Total function execution time is 0.0509228706359863 s and adjustment time is 0.0448319911956787 s ( 88.04 )
2025-03-17 18:17:54.689851 INFO::Formatting Data.
2025-03-17 18:17:54.690147 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.690595 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.691649 INFO::Found 1000 missing values.
2025-03-17 18:17:54.697649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.69789 INFO::Done
2025-03-17 18:17:54.698069 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.700236 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.700638 INFO::Found 10 batches.
2025-03-17 18:17:54.700855 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:54.701127 INFO::Using default BPPARAM
2025-03-17 18:17:54.701491 INFO::Processing subtree level 1
2025-03-17 18:17:54.762558 INFO::Processing subtree level 2
2025-03-17 18:17:54.824418 INFO::Adjusting the last 1 batches sequentially
2025-03-17 18:17:54.827285 INFO::Done
2025-03-17 18:17:54.827674 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:54.830638 INFO::ASW Batch was 0.47669750803606 prior to batch effect correction and is now 0.47669750803606 .
2025-03-17 18:17:54.830869 INFO::ASW Label was 0.335567354557766 prior to batch effect correction and is now 0.335567354557766 .
2025-03-17 18:17:54.831475 INFO::Total function execution time is 0.141640901565552 s and adjustment time is 0.126708030700684 s ( 89.46 )
2025-03-17 18:17:54.83177 INFO::Formatting Data.
2025-03-17 18:17:54.832226 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:54.832642 INFO::Removing potential empty rows and columns
2025-03-17 18:17:54.833729 INFO::Found 1000 missing values.
2025-03-17 18:17:54.839359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:54.83956 INFO::Done
2025-03-17 18:17:54.839728 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:54.841638 INFO::Starting hierarchical adjustment
2025-03-17 18:17:54.841887 INFO::Found 10 batches.
2025-03-17 18:17:55.279762 INFO::Set up parallel execution backend with 2 workers
2025-03-17 18:17:55.280054 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-17 18:17:55.824604 INFO::Adjusting the last 2 batches sequentially
2025-03-17 18:17:55.825225 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 18:17:55.830724 INFO::Done
2025-03-17 18:17:55.830936 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:55.832687 INFO::ASW Batch was 0.47669750803606 prior to batch effect correction and is now 0.47669750803606 .
2025-03-17 18:17:55.832862 INFO::ASW Label was 0.335567354557766 prior to batch effect correction and is now 0.335567354557766 .
2025-03-17 18:17:55.833097 INFO::Total function execution time is 1.00132989883423 s and adjustment time is 0.988885164260864 s ( 98.76 )
2025-03-17 18:17:55.897357 INFO::Formatting Data.
2025-03-17 18:17:55.897621 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:55.897947 INFO::Removing potential empty rows and columns
2025-03-17 18:17:55.898356 INFO::Found 0 missing values.
2025-03-17 18:17:55.899836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:55.900008 INFO::Done
2025-03-17 18:17:55.900182 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 18:17:55.901223 INFO::Starting hierarchical adjustment
2025-03-17 18:17:55.90151 INFO::Found 3 batches.
2025-03-17 18:17:55.901736 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 18:17:55.901994 INFO::Using default BPPARAM
2025-03-17 18:17:55.902165 INFO::Processing subtree level 1
2025-03-17 18:17:55.9516 INFO::Adjusting the last 1 batches sequentially
2025-03-17 18:17:55.953025 INFO::Done
2025-03-17 18:17:55.953251 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 18:17:55.954867 INFO::ASW Batch was 0.19516099829541 prior to batch effect correction and is now -0.141456709448242 .
2025-03-17 18:17:55.955393 INFO::ASW Label was -0.203256003715013 prior to batch effect correction and is now -0.0203513485719679 .
2025-03-17 18:17:55.956098 INFO::Total function execution time is 0.0587661266326904 s and adjustment time is 0.0515708923339844 s ( 87.76 )
2025-03-17 18:17:56.025516 INFO::Formatting Data.
2025-03-17 18:17:56.025844 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.02619 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.026621 INFO::Found 2 missing values.
2025-03-17 18:17:56.027602 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.027789 INFO::Done
2025-03-17 18:17:56.042426 INFO::Found NA in Reference column
2025-03-17 18:17:56.051856 INFO::Require at least two references per batch.
2025-03-17 18:17:56.068488 INFO::Formatting Data.
2025-03-17 18:17:56.068799 INFO::Recognized SummarizedExperiment
2025-03-17 18:17:56.069027 INFO::Typecasting input to dataframe.
2025-03-17 18:17:56.073451 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.073867 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.075223 INFO::Found 0 missing values.
2025-03-17 18:17:56.077735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.077941 INFO::Done
2025-03-17 18:17:56.085636 INFO::Formatting Data.
2025-03-17 18:17:56.085885 INFO::Recognized SummarizedExperiment
2025-03-17 18:17:56.086226 INFO::Typecasting input to dataframe.
2025-03-17 18:17:56.09351 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.093927 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.095182 INFO::Found 0 missing values.
2025-03-17 18:17:56.101906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.102168 INFO::Done
2025-03-17 18:17:56.10757 INFO::Formatting Data.
2025-03-17 18:17:56.107824 INFO::Recognized SummarizedExperiment
2025-03-17 18:17:56.107998 INFO::Typecasting input to dataframe.
2025-03-17 18:17:56.11342 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.113752 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.114109 INFO::Found 0 missing values.
2025-03-17 18:17:56.11441 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.
2025-03-17 18:17:56.115819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.11601 INFO::Done
2025-03-17 18:17:56.120437 INFO::Formatting Data.
2025-03-17 18:17:56.120697 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.12098 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.121309 INFO::Found 0 missing values.
2025-03-17 18:17:56.122332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.122523 INFO::Done
2025-03-17 18:17:56.127262 INFO::Formatting Data.
2025-03-17 18:17:56.127528 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.127799 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.128128 INFO::Found 0 missing values.
2025-03-17 18:17:56.129093 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.129268 INFO::Done
2025-03-17 18:17:56.14337 INFO::Formatting Data.
2025-03-17 18:17:56.143673 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.144086 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.144545 INFO::Found 1 missing values.
2025-03-17 18:17:56.145627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.146282 INFO::Done
2025-03-17 18:17:56.155263 INFO::Formatting Data.
2025-03-17 18:17:56.15555 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.157214 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.157753 INFO::Found 2 missing values.
2025-03-17 18:17:56.158332 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.
2025-03-17 18:17:56.159539 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.15978 INFO::Done
2025-03-17 18:17:56.16459 INFO::Formatting Data.
2025-03-17 18:17:56.164866 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.16519 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.165629 INFO::Found 2 missing values.
2025-03-17 18:17:56.166271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.166527 INFO::Done
2025-03-17 18:17:56.172125 INFO::Formatting Data.
2025-03-17 18:17:56.172528 INFO::Typecasting input to dataframe.
2025-03-17 18:17:56.172859 INFO::Replacing NaNs with NAs.
2025-03-17 18:17:56.173168 INFO::Removing potential empty rows and columns
2025-03-17 18:17:56.17357 INFO::Found 0 missing values.
2025-03-17 18:17:56.17478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 18:17:56.175061 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.682 1.717 8.609
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.505 | 0.409 | 6.806 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.004 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |