Yannis Schumann
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:29 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-03-31 23:11:42 -0400 (Mon, 31 Mar 2025) |
| EndedAt: 2025-03-31 23:14:00 -0400 (Mon, 31 Mar 2025) |
| EllapsedTime: 137.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.2.0'
* 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 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 9.17 0.55 18.6
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BERT' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2025-03-31 23:12:47.95841 INFO::Formatting Data.
2025-03-31 23:12:47.961453 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:47.977632 INFO::Removing potential empty rows and columns
2025-03-31 23:12:48.242155 INFO::Found 0 missing values.
2025-03-31 23:12:48.247482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:12:48.248878 INFO::Done
2025-03-31 23:12:48.250192 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:12:48.271216 INFO::Starting hierarchical adjustment
2025-03-31 23:12:48.27288 INFO::Found 3 batches.
2025-03-31 23:12:48.274219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:12:48.276133 INFO::Using default BPPARAM
2025-03-31 23:12:48.277282 INFO::Processing subtree level 1
2025-03-31 23:12:51.003965 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:12:51.006114 INFO::Done
2025-03-31 23:12:51.007309 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:12:51.010467 INFO::ASW Batch was -0.104023171016905 prior to batch effect correction and is now -0.104023171016905 .
2025-03-31 23:12:51.012151 INFO::Total function execution time is 3.05449295043945 s and adjustment time is 2.73352599143982 s ( 89.49 )
2025-03-31 23:12:51.032278 INFO::Formatting Data.
2025-03-31 23:12:51.033246 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:51.034889 INFO::Removing potential empty rows and columns
2025-03-31 23:12:51.036797 INFO::Found 0 missing values.
2025-03-31 23:12:51.038524 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.
2025-03-31 23:12:51.052388 INFO::Formatting Data.
2025-03-31 23:12:51.053849 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:51.055514 INFO::Removing potential empty rows and columns
2025-03-31 23:12:51.057327 INFO::Found 0 missing values.
2025-03-31 23:12:51.058978 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.
2025-03-31 23:12:51.084986 INFO::Formatting Data.
2025-03-31 23:12:51.086659 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:51.088551 INFO::Removing potential empty rows and columns
2025-03-31 23:12:51.090584 INFO::Found 0 missing values.
2025-03-31 23:12:51.092476 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.
2025-03-31 23:12:51.099075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:12:51.100531 INFO::Done
2025-03-31 23:12:51.101858 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:12:51.105441 INFO::Starting hierarchical adjustment
2025-03-31 23:12:51.107022 INFO::Found 2 batches.
2025-03-31 23:12:51.108436 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:12:51.109843 INFO::Using default BPPARAM
2025-03-31 23:12:51.111053 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:12:51.113003 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:12:51.141973 INFO::Done
2025-03-31 23:12:51.143537 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:12:51.147208 INFO::ASW Batch was 0.0539471893462642 prior to batch effect correction and is now -0.117252680572449 .
2025-03-31 23:12:51.148875 INFO::Total function execution time is 0.063988208770752 s and adjustment time is 0.0351529121398926 s ( 54.94 )
2025-03-31 23:12:51.153529 INFO::Formatting Data.
2025-03-31 23:12:51.155022 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:51.16798 INFO::Formatting Data.
2025-03-31 23:12:51.16958 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:51.171401 INFO::Removing potential empty rows and columns
2025-03-31 23:12:51.173326 INFO::Found 0 missing values.
2025-03-31 23:12:51.177737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:12:51.179062 INFO::Done
2025-03-31 23:12:51.180319 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:12:51.183885 INFO::Starting hierarchical adjustment
2025-03-31 23:12:51.185486 INFO::Found 2 batches.
2025-03-31 23:12:51.186701 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:12:51.188063 INFO::Using default BPPARAM
2025-03-31 23:12:51.189304 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:12:51.19121 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:12:51.212381 INFO::Done
2025-03-31 23:12:51.213864 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:12:51.217463 INFO::ASW Batch was -0.0113545425635434 prior to batch effect correction and is now -0.114197320095715 .
2025-03-31 23:12:51.21914 INFO::Total function execution time is 0.0512368679046631 s and adjustment time is 0.0271060466766357 s ( 52.9 )
2025-03-31 23:12:51.221236 INFO::Formatting Data.
2025-03-31 23:12:51.222635 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:51.224398 INFO::Removing potential empty rows and columns
2025-03-31 23:12:51.226224 INFO::Found 0 missing values.
2025-03-31 23:12:51.230105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:12:51.231195 INFO::Done
2025-03-31 23:12:51.232393 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:12:51.23604 INFO::Starting hierarchical adjustment
2025-03-31 23:12:51.237662 INFO::Found 2 batches.
2025-03-31 23:12:51.238823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:12:51.240003 INFO::Using default BPPARAM
2025-03-31 23:12:51.241112 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:12:51.242796 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:12:51.260689 INFO::Done
2025-03-31 23:12:51.261899 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:12:51.264776 INFO::ASW Batch was -0.0113545425635434 prior to batch effect correction and is now -0.114197320095715 .
2025-03-31 23:12:51.266108 INFO::Total function execution time is 0.0449330806732178 s and adjustment time is 0.0232470035552979 s ( 51.74 )
2025-03-31 23:12:53.730401 INFO::Formatting Data.
2025-03-31 23:12:53.731973 INFO::Recognized SummarizedExperiment
2025-03-31 23:12:53.733315 INFO::Typecasting input to dataframe.
2025-03-31 23:12:53.784171 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:53.786758 INFO::Removing potential empty rows and columns
2025-03-31 23:12:53.791901 INFO::Found 0 missing values.
2025-03-31 23:12:53.80083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:12:53.801858 INFO::Done
2025-03-31 23:12:53.802646 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:12:53.806675 INFO::Starting hierarchical adjustment
2025-03-31 23:12:53.807828 INFO::Found 2 batches.
2025-03-31 23:12:53.808957 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:12:53.810844 INFO::Using default BPPARAM
2025-03-31 23:12:53.81196 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:12:53.813569 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:12:53.858552 INFO::Done
2025-03-31 23:12:53.859441 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:12:53.863524 INFO::ASW Batch was 0.000533858056639421 prior to batch effect correction and is now -0.100666193065428 .
2025-03-31 23:12:53.864679 INFO::Total function execution time is 0.134847164154053 s and adjustment time is 0.0509340763092041 s ( 37.77 )
2025-03-31 23:12:54.592281 INFO::Formatting Data.
2025-03-31 23:12:54.593228 INFO::Recognized SummarizedExperiment
2025-03-31 23:12:54.593952 INFO::Typecasting input to dataframe.
2025-03-31 23:12:54.601912 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:54.603197 INFO::Removing potential empty rows and columns
2025-03-31 23:12:54.605962 INFO::Found 0 missing values.
2025-03-31 23:12:54.611448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:12:54.612272 INFO::Done
2025-03-31 23:12:54.613322 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:12:54.61883 INFO::Starting hierarchical adjustment
2025-03-31 23:12:54.619807 INFO::Found 2 batches.
2025-03-31 23:12:54.620531 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:12:54.621311 INFO::Using default BPPARAM
2025-03-31 23:12:54.622 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:12:54.623169 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:12:54.641745 INFO::Done
2025-03-31 23:12:54.642635 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:12:54.646472 INFO::ASW Batch was 0.00133352984717445 prior to batch effect correction and is now 0.00133352984717445 .
2025-03-31 23:12:54.647568 INFO::Total function execution time is 0.0552630424499512 s and adjustment time is 0.0220448970794678 s ( 39.89 )
2025-03-31 23:12:54.667392 INFO::Formatting Data.
2025-03-31 23:12:54.668396 INFO::Replacing NaNs with NAs.
2025-03-31 23:12:54.669488 INFO::Removing potential empty rows and columns
2025-03-31 23:12:54.670596 INFO::Found 0 missing values.
2025-03-31 23:12:54.673149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:12:54.673856 INFO::Done
2025-03-31 23:12:54.674543 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:12:54.676703 INFO::Starting hierarchical adjustment
2025-03-31 23:12:54.67758 INFO::Found 3 batches.
2025-03-31 23:12:54.678277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:12:54.679046 INFO::Using default BPPARAM
2025-03-31 23:12:54.679742 INFO::Processing subtree level 1
2025-03-31 23:13:04.454359 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:13:04.456331 INFO::Done
2025-03-31 23:13:04.457175 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:04.459423 INFO::ASW Batch was -0.102307848257445 prior to batch effect correction and is now -0.178991257345607 .
2025-03-31 23:13:04.460406 INFO::Total function execution time is 9.79310083389282 s and adjustment time is 9.77886390686035 s ( 99.85 )
2025-03-31 23:13:04.475486 INFO::Skipping initial DF formatting
2025-03-31 23:13:04.476373 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:04.48071 INFO::Starting hierarchical adjustment
2025-03-31 23:13:04.481703 INFO::Found 5 batches.
2025-03-31 23:13:04.482434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:04.483213 INFO::Using default BPPARAM
2025-03-31 23:13:04.483917 INFO::Processing subtree level 1
2025-03-31 23:13:07.382114 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:07.383721 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:07.398217 INFO::Done
2025-03-31 23:13:07.399103 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:07.403259 INFO::ASW Batch was 0.53140595787343 prior to batch effect correction and is now 0.53140595787343 .
2025-03-31 23:13:07.404111 INFO::ASW Label was 0.350623591736866 prior to batch effect correction and is now 0.350623591736866 .
2025-03-31 23:13:07.405099 INFO::Total function execution time is 2.92970514297485 s and adjustment time is 2.91663694381714 s ( 99.55 )
2025-03-31 23:13:07.422582 INFO::Formatting Data.
2025-03-31 23:13:07.423643 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:07.424813 INFO::Removing potential empty rows and columns
2025-03-31 23:13:07.425967 INFO::Found 0 missing values.
2025-03-31 23:13:07.429434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:07.430196 INFO::Done
2025-03-31 23:13:07.430904 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:07.433898 INFO::Starting hierarchical adjustment
2025-03-31 23:13:07.434846 INFO::Found 5 batches.
2025-03-31 23:13:07.435567 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:07.436336 INFO::Using default BPPARAM
2025-03-31 23:13:07.437035 INFO::Processing subtree level 1
2025-03-31 23:13:10.607568 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:10.609471 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:10.626865 INFO::Done
2025-03-31 23:13:10.628024 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:10.632218 INFO::ASW Batch was 0.517386459286766 prior to batch effect correction and is now -0.00760962854583084 .
2025-03-31 23:13:10.633148 INFO::ASW Label was 0.255797942061269 prior to batch effect correction and is now 0.757340824773338 .
2025-03-31 23:13:10.634271 INFO::Total function execution time is 3.21180391311646 s and adjustment time is 3.19213604927063 s ( 99.39 )
2025-03-31 23:13:10.635597 INFO::Formatting Data.
2025-03-31 23:13:10.636793 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:10.638272 INFO::Removing potential empty rows and columns
2025-03-31 23:13:10.639799 INFO::Found 0 missing values.
2025-03-31 23:13:10.644777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:10.645811 INFO::Done
2025-03-31 23:13:10.646801 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:10.65092 INFO::Starting hierarchical adjustment
2025-03-31 23:13:10.652226 INFO::Found 5 batches.
2025-03-31 23:13:10.653078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:10.653845 INFO::Using default BPPARAM
2025-03-31 23:13:10.654517 INFO::Processing subtree level 1
2025-03-31 23:13:13.73874 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:13.740904 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:13.759057 INFO::Done
2025-03-31 23:13:13.760373 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:13.765023 INFO::ASW Batch was 0.517386459286766 prior to batch effect correction and is now -0.00760962854583084 .
2025-03-31 23:13:13.76631 INFO::ASW Label was 0.255797942061269 prior to batch effect correction and is now 0.757340824773338 .
2025-03-31 23:13:13.767793 INFO::Total function execution time is 3.13220310211182 s and adjustment time is 3.10697603225708 s ( 99.19 )
2025-03-31 23:13:13.783287 INFO::Formatting Data.
2025-03-31 23:13:13.784372 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:13.785517 INFO::Removing potential empty rows and columns
2025-03-31 23:13:13.78662 INFO::Found 0 missing values.
2025-03-31 23:13:13.790034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:13.790792 INFO::Done
2025-03-31 23:13:13.791496 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:13.79452 INFO::Starting hierarchical adjustment
2025-03-31 23:13:13.795486 INFO::Found 5 batches.
2025-03-31 23:13:13.796239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:13.797452 INFO::Using default BPPARAM
2025-03-31 23:13:13.798606 INFO::Processing subtree level 1
2025-03-31 23:13:16.860143 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:16.861953 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:16.88019 INFO::Done
2025-03-31 23:13:16.881455 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:16.885915 INFO::ASW Batch was 0.539755863341902 prior to batch effect correction and is now -0.0905460799589016 .
2025-03-31 23:13:16.887118 INFO::ASW Label was 0.135055674119695 prior to batch effect correction and is now 0.829284670187856 .
2025-03-31 23:13:16.888508 INFO::Total function execution time is 3.10526990890503 s and adjustment time is 3.08476877212524 s ( 99.34 )
2025-03-31 23:13:16.889553 INFO::Formatting Data.
2025-03-31 23:13:16.890432 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:16.891469 INFO::Removing potential empty rows and columns
2025-03-31 23:13:16.892681 INFO::Found 0 missing values.
2025-03-31 23:13:16.896454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:16.897225 INFO::Done
2025-03-31 23:13:16.89791 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:16.900875 INFO::Starting hierarchical adjustment
2025-03-31 23:13:16.9018 INFO::Found 5 batches.
2025-03-31 23:13:16.902486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:16.903227 INFO::Using default BPPARAM
2025-03-31 23:13:16.903918 INFO::Processing subtree level 1
2025-03-31 23:13:20.081102 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:20.082593 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:20.100741 INFO::Done
2025-03-31 23:13:20.102075 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:20.106738 INFO::ASW Batch was 0.539755863341902 prior to batch effect correction and is now -0.0905460799589016 .
2025-03-31 23:13:20.107983 INFO::ASW Label was 0.135055674119695 prior to batch effect correction and is now 0.829284670187856 .
2025-03-31 23:13:20.10945 INFO::Total function execution time is 3.21984100341797 s and adjustment time is 3.19898986816406 s ( 99.35 )
2025-03-31 23:13:20.126383 INFO::Formatting Data.
2025-03-31 23:13:20.127596 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:20.129251 INFO::Removing potential empty rows and columns
2025-03-31 23:13:20.13084 INFO::Found 0 missing values.
2025-03-31 23:13:20.134662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:20.135843 INFO::Done
2025-03-31 23:13:20.136965 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:20.14188 INFO::Starting hierarchical adjustment
2025-03-31 23:13:20.143368 INFO::Found 2 batches.
2025-03-31 23:13:20.144592 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:20.145902 INFO::Using default BPPARAM
2025-03-31 23:13:20.147102 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:20.148907 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:20.168726 INFO::Done
2025-03-31 23:13:20.169613 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:20.172602 INFO::ASW Batch was 0.507423920670068 prior to batch effect correction and is now -0.0358375320009676 .
2025-03-31 23:13:20.1734 INFO::ASW Label was 0.583064373808801 prior to batch effect correction and is now 0.93119539045747 .
2025-03-31 23:13:20.174344 INFO::Total function execution time is 0.0480539798736572 s and adjustment time is 0.0255918502807617 s ( 53.26 )
2025-03-31 23:13:20.175264 INFO::Formatting Data.
2025-03-31 23:13:20.176138 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:20.177529 INFO::Removing potential empty rows and columns
2025-03-31 23:13:20.178971 INFO::Found 0 missing values.
2025-03-31 23:13:20.181875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:20.182628 INFO::Done
2025-03-31 23:13:20.183348 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:20.186527 INFO::Starting hierarchical adjustment
2025-03-31 23:13:20.187483 INFO::Found 2 batches.
2025-03-31 23:13:20.188187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:20.188944 INFO::Using default BPPARAM
2025-03-31 23:13:20.189629 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:20.190696 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:20.20655 INFO::Done
2025-03-31 23:13:20.207559 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:20.211789 INFO::ASW Batch was 0.507423920670068 prior to batch effect correction and is now -0.0358375320009676 .
2025-03-31 23:13:20.213106 INFO::ASW Label was 0.583064373808801 prior to batch effect correction and is now 0.93119539045747 .
2025-03-31 23:13:20.214369 INFO::Total function execution time is 0.0390689373016357 s and adjustment time is 0.0191550254821777 s ( 49.03 )
2025-03-31 23:13:20.23141 INFO::Formatting Data.
2025-03-31 23:13:20.23299 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:20.23463 INFO::Removing potential empty rows and columns
2025-03-31 23:13:20.235915 INFO::Found 0 missing values.
2025-03-31 23:13:20.238387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:20.239148 INFO::Done
2025-03-31 23:13:20.23999 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:20.242328 INFO::Starting hierarchical adjustment
2025-03-31 23:13:20.243333 INFO::Found 2 batches.
2025-03-31 23:13:20.244053 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:20.244832 INFO::Using default BPPARAM
2025-03-31 23:13:20.245575 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:20.24677 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:20.277214 INFO::Done
2025-03-31 23:13:20.278133 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:20.28053 INFO::ASW Batch was 0.19230420235292 prior to batch effect correction and is now -0.0901497595236681 .
2025-03-31 23:13:20.281536 INFO::Total function execution time is 0.0503017902374268 s and adjustment time is 0.0339779853820801 s ( 67.55 )
2025-03-31 23:13:20.296946 INFO::Formatting Data.
2025-03-31 23:13:20.298053 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:20.299192 INFO::Removing potential empty rows and columns
2025-03-31 23:13:20.300345 INFO::Found 0 missing values.
2025-03-31 23:13:20.301725 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.
2025-03-31 23:13:20.307437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:20.308602 INFO::Done
2025-03-31 23:13:20.309797 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:20.31479 INFO::Starting hierarchical adjustment
2025-03-31 23:13:20.3164 INFO::Found 2 batches.
2025-03-31 23:13:20.317668 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:20.319014 INFO::Using default BPPARAM
2025-03-31 23:13:20.320265 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:20.322133 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:20.34558 INFO::Done
2025-03-31 23:13:20.346963 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:20.351722 INFO::ASW Batch was 0.49763133180346 prior to batch effect correction and is now -0.0355016754920862 .
2025-03-31 23:13:20.353015 INFO::ASW Label was 0.567451035537874 prior to batch effect correction and is now 0.934742896128409 .
2025-03-31 23:13:20.354568 INFO::Total function execution time is 0.0576410293579102 s and adjustment time is 0.0294201374053955 s ( 51.04 )
2025-03-31 23:13:20.356077 INFO::Formatting Data.
2025-03-31 23:13:20.357317 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:20.359009 INFO::Removing potential empty rows and columns
2025-03-31 23:13:20.360861 INFO::Found 0 missing values.
2025-03-31 23:13:20.362608 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.
2025-03-31 23:13:20.36966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:20.370819 INFO::Done
2025-03-31 23:13:20.371745 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:20.375599 INFO::Starting hierarchical adjustment
2025-03-31 23:13:20.377222 INFO::Found 2 batches.
2025-03-31 23:13:20.378439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:20.379695 INFO::Using default BPPARAM
2025-03-31 23:13:20.380821 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:20.382573 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:20.399165 INFO::Done
2025-03-31 23:13:20.400491 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:20.404052 INFO::ASW Batch was 0.49763133180346 prior to batch effect correction and is now -0.0355016754920862 .
2025-03-31 23:13:20.404973 INFO::ASW Label was 0.567451035537874 prior to batch effect correction and is now 0.934742896128409 .
2025-03-31 23:13:20.406118 INFO::Total function execution time is 0.0500931739807129 s and adjustment time is 0.0221588611602783 s ( 44.24 )
2025-03-31 23:13:20.731611 INFO::Formatting Data.
2025-03-31 23:13:20.733274 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:20.735207 INFO::Removing potential empty rows and columns
2025-03-31 23:13:20.737269 INFO::Found 0 missing values.
2025-03-31 23:13:20.742619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:20.744087 INFO::Done
2025-03-31 23:13:20.74547 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:20.749114 INFO::Starting hierarchical adjustment
2025-03-31 23:13:20.750667 INFO::Found 3 batches.
2025-03-31 23:13:20.751935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:20.753265 INFO::Using default BPPARAM
2025-03-31 23:13:20.754506 INFO::Processing subtree level 1
2025-03-31 23:13:23.629841 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:13:23.632083 INFO::Done
2025-03-31 23:13:23.633321 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:23.636389 INFO::ASW Batch was 0.017122441044011 prior to batch effect correction and is now 0.017122441044011 .
2025-03-31 23:13:23.637853 INFO::Total function execution time is 2.90638780593872 s and adjustment time is 2.88164615631104 s ( 99.15 )
2025-03-31 23:13:23.639458 INFO::Formatting Data.
2025-03-31 23:13:23.640623 INFO::Typecasting input to dataframe.
2025-03-31 23:13:23.641933 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:23.643435 INFO::Removing potential empty rows and columns
2025-03-31 23:13:23.645086 INFO::Found 0 missing values.
2025-03-31 23:13:23.649132 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:23.650154 INFO::Done
2025-03-31 23:13:23.650856 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:23.652968 INFO::Starting hierarchical adjustment
2025-03-31 23:13:23.653832 INFO::Found 3 batches.
2025-03-31 23:13:23.654743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:23.655983 INFO::Using default BPPARAM
2025-03-31 23:13:23.657134 INFO::Processing subtree level 1
2025-03-31 23:13:26.612236 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:13:26.614464 INFO::Done
2025-03-31 23:13:26.615777 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:26.618857 INFO::ASW Batch was 0.017122441044011 prior to batch effect correction and is now 0.017122441044011 .
2025-03-31 23:13:26.620619 INFO::Total function execution time is 2.98116493225098 s and adjustment time is 2.960688829422 s ( 99.31 )
2025-03-31 23:13:26.642039 INFO::Formatting Data.
2025-03-31 23:13:26.643582 INFO::Typecasting input to dataframe.
2025-03-31 23:13:26.645251 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:26.646989 INFO::Removing potential empty rows and columns
2025-03-31 23:13:26.648724 INFO::Found 0 missing values.
2025-03-31 23:13:26.653448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:26.654771 INFO::Done
2025-03-31 23:13:26.655975 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:26.65947 INFO::Starting hierarchical adjustment
2025-03-31 23:13:26.660975 INFO::Found 3 batches.
2025-03-31 23:13:26.66217 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:26.66347 INFO::Using default BPPARAM
2025-03-31 23:13:26.664649 INFO::Processing subtree level 1
2025-03-31 23:13:29.57063 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:13:29.572835 INFO::Done
2025-03-31 23:13:29.574057 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:29.577056 INFO::ASW Batch was 0.00574922286973646 prior to batch effect correction and is now 0.00574922286973646 .
2025-03-31 23:13:29.578486 INFO::Total function execution time is 2.93658494949341 s and adjustment time is 2.91207218170166 s ( 99.17 )
2025-03-31 23:13:32.661297 INFO::Formatting Data.
2025-03-31 23:13:32.662304 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:32.663602 INFO::Removing potential empty rows and columns
2025-03-31 23:13:32.666097 INFO::Found 1000 missing values.
2025-03-31 23:13:32.681221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:32.682656 INFO::Done
2025-03-31 23:13:32.683915 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:32.693984 INFO::Starting hierarchical adjustment
2025-03-31 23:13:32.695831 INFO::Found 10 batches.
2025-03-31 23:13:32.697173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:32.698579 INFO::Using default BPPARAM
2025-03-31 23:13:32.699851 INFO::Processing subtree level 1
2025-03-31 23:13:35.720361 INFO::Processing subtree level 2
2025-03-31 23:13:38.740541 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:13:38.742907 INFO::Done
2025-03-31 23:13:38.744211 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:38.7533 INFO::ASW Batch was 0.48312189554252 prior to batch effect correction and is now 0.48312189554252 .
2025-03-31 23:13:38.754615 INFO::ASW Label was 0.330874854339232 prior to batch effect correction and is now 0.330874854339232 .
2025-03-31 23:13:38.756243 INFO::Total function execution time is 6.09496402740479 s and adjustment time is 6.04742097854614 s ( 99.22 )
2025-03-31 23:13:38.757705 INFO::Formatting Data.
2025-03-31 23:13:38.758959 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:38.760854 INFO::Removing potential empty rows and columns
2025-03-31 23:13:38.76463 INFO::Found 1000 missing values.
2025-03-31 23:13:38.780294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:38.781242 INFO::Done
2025-03-31 23:13:38.781985 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:38.788024 INFO::Starting hierarchical adjustment
2025-03-31 23:13:38.789056 INFO::Found 10 batches.
2025-03-31 23:13:39.525326 INFO::Set up parallel execution backend with 2 workers
2025-03-31 23:13:39.526289 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-31 23:13:42.448734 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:13:42.450888 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:13:42.474979 INFO::Done
2025-03-31 23:13:42.476336 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:42.485358 INFO::ASW Batch was 0.48312189554252 prior to batch effect correction and is now 0.48312189554252 .
2025-03-31 23:13:42.486723 INFO::ASW Label was 0.330874854339232 prior to batch effect correction and is now 0.330874854339232 .
2025-03-31 23:13:42.488267 INFO::Total function execution time is 3.73055601119995 s and adjustment time is 3.68599390983582 s ( 98.81 )
2025-03-31 23:13:45.547458 INFO::Formatting Data.
2025-03-31 23:13:45.548975 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:45.550703 INFO::Removing potential empty rows and columns
2025-03-31 23:13:45.552567 INFO::Found 0 missing values.
2025-03-31 23:13:45.55789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:45.559154 INFO::Done
2025-03-31 23:13:45.56041 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:13:45.564701 INFO::Starting hierarchical adjustment
2025-03-31 23:13:45.566146 INFO::Found 3 batches.
2025-03-31 23:13:45.567343 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:13:45.568577 INFO::Using default BPPARAM
2025-03-31 23:13:45.5697 INFO::Processing subtree level 1
2025-03-31 23:13:48.572107 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:13:48.574526 INFO::Done
2025-03-31 23:13:48.575865 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:13:48.580818 INFO::ASW Batch was 0.239632609464049 prior to batch effect correction and is now -0.192826825833082 .
2025-03-31 23:13:48.582319 INFO::ASW Label was -0.223194356469487 prior to batch effect correction and is now -0.12086497754882 .
2025-03-31 23:13:48.583521 INFO::Total function execution time is 3.03620910644531 s and adjustment time is 3.00858521461487 s ( 99.09 )
2025-03-31 23:13:48.791078 INFO::Formatting Data.
2025-03-31 23:13:48.792629 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:48.794387 INFO::Removing potential empty rows and columns
2025-03-31 23:13:48.796268 INFO::Found 2 missing values.
2025-03-31 23:13:48.800661 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:48.801916 INFO::Done
2025-03-31 23:13:48.858638 INFO::Found NA in Reference column
2025-03-31 23:13:48.877806 INFO::Require at least two references per batch.
2025-03-31 23:13:48.910826 INFO::Formatting Data.
2025-03-31 23:13:48.912312 INFO::Recognized SummarizedExperiment
2025-03-31 23:13:48.913589 INFO::Typecasting input to dataframe.
2025-03-31 23:13:48.927091 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:48.929181 INFO::Removing potential empty rows and columns
2025-03-31 23:13:48.934089 INFO::Found 0 missing values.
2025-03-31 23:13:48.943695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:48.945188 INFO::Done
2025-03-31 23:13:48.968552 INFO::Formatting Data.
2025-03-31 23:13:48.969973 INFO::Recognized SummarizedExperiment
2025-03-31 23:13:48.971126 INFO::Typecasting input to dataframe.
2025-03-31 23:13:48.996215 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:48.998442 INFO::Removing potential empty rows and columns
2025-03-31 23:13:49.003691 INFO::Found 0 missing values.
2025-03-31 23:13:49.018168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:49.019615 INFO::Done
2025-03-31 23:13:49.038312 INFO::Formatting Data.
2025-03-31 23:13:49.03925 INFO::Recognized SummarizedExperiment
2025-03-31 23:13:49.039964 INFO::Typecasting input to dataframe.
2025-03-31 23:13:49.054837 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:49.05651 INFO::Removing potential empty rows and columns
2025-03-31 23:13:49.057726 INFO::Found 0 missing values.
2025-03-31 23:13:49.058925 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.
2025-03-31 23:13:49.063417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:49.064339 INFO::Done
2025-03-31 23:13:49.078398 INFO::Formatting Data.
2025-03-31 23:13:49.079465 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:49.080557 INFO::Removing potential empty rows and columns
2025-03-31 23:13:49.081732 INFO::Found 0 missing values.
2025-03-31 23:13:49.084592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:49.08535 INFO::Done
2025-03-31 23:13:49.10366 INFO::Formatting Data.
2025-03-31 23:13:49.105281 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:49.107129 INFO::Removing potential empty rows and columns
2025-03-31 23:13:49.109054 INFO::Found 0 missing values.
2025-03-31 23:13:49.11403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:49.115443 INFO::Done
2025-03-31 23:13:49.170384 INFO::Formatting Data.
2025-03-31 23:13:49.171977 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:49.174051 INFO::Removing potential empty rows and columns
2025-03-31 23:13:49.176193 INFO::Found 1 missing values.
2025-03-31 23:13:49.180498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:49.181859 INFO::Done
2025-03-31 23:13:49.218891 INFO::Formatting Data.
2025-03-31 23:13:49.220476 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:49.22252 INFO::Removing potential empty rows and columns
2025-03-31 23:13:49.224687 INFO::Found 2 missing values.
2025-03-31 23:13:49.226719 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.
2025-03-31 23:13:49.230805 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:49.23222 INFO::Done
2025-03-31 23:13:49.253438 INFO::Formatting Data.
2025-03-31 23:13:49.255035 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:49.256876 INFO::Removing potential empty rows and columns
2025-03-31 23:13:49.258695 INFO::Found 2 missing values.
2025-03-31 23:13:49.261424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:49.262639 INFO::Done
2025-03-31 23:13:49.283606 INFO::Formatting Data.
2025-03-31 23:13:49.285202 INFO::Typecasting input to dataframe.
2025-03-31 23:13:49.286907 INFO::Replacing NaNs with NAs.
2025-03-31 23:13:49.288638 INFO::Removing potential empty rows and columns
2025-03-31 23:13:49.290523 INFO::Found 0 missing values.
2025-03-31 23:13:49.295098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:13:49.296457 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
31.92 1.37 77.53
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.17 | 0.55 | 18.60 | |
| compute_asw | 0.02 | 0.01 | 0.03 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0.02 | 0.00 | 0.02 | |