Yannis Schumann
| Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-23 12:04 -0500 (Thu, 23 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
| 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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-01-20 20:01:17 -0500 (Mon, 20 Jan 2025) |
| EndedAt: 2025-01-20 20:02:43 -0500 (Mon, 20 Jan 2025) |
| EllapsedTime: 86.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.667 1.425 17.075
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-01-20 20:02:07.168787 INFO::Formatting Data.
2025-01-20 20:02:07.170082 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:07.181494 INFO::Removing potential empty rows and columns
2025-01-20 20:02:07.432651 INFO::Found 0 missing values.
2025-01-20 20:02:07.43619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:07.436822 INFO::Done
2025-01-20 20:02:07.437354 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:07.449014 INFO::Starting hierarchical adjustment
2025-01-20 20:02:07.449895 INFO::Found 3 batches.
2025-01-20 20:02:07.45044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:07.451619 INFO::Using default BPPARAM
2025-01-20 20:02:07.452172 INFO::Processing subtree level 1
2025-01-20 20:02:07.549034 INFO::Adjusting the last 1 batches sequentially
2025-01-20 20:02:07.550838 INFO::Done
2025-01-20 20:02:07.55149 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:07.554079 INFO::ASW Batch was 0.027503266712681 prior to batch effect correction and is now 0.027503266712681 .
2025-01-20 20:02:07.555124 INFO::Total function execution time is 0.386976957321167 s and adjustment time is 0.101132392883301 s ( 26.13 )
2025-01-20 20:02:07.568212 INFO::Formatting Data.
2025-01-20 20:02:07.56889 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:07.569752 INFO::Removing potential empty rows and columns
2025-01-20 20:02:07.570816 INFO::Found 0 missing values.
2025-01-20 20:02:07.571745 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.
2025-01-20 20:02:07.582466 INFO::Formatting Data.
2025-01-20 20:02:07.583098 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:07.58391 INFO::Removing potential empty rows and columns
2025-01-20 20:02:07.584911 INFO::Found 0 missing values.
2025-01-20 20:02:07.585767 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.
2025-01-20 20:02:07.601206 INFO::Formatting Data.
2025-01-20 20:02:07.601864 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:07.602676 INFO::Removing potential empty rows and columns
2025-01-20 20:02:07.603662 INFO::Found 0 missing values.
2025-01-20 20:02:07.604537 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.
2025-01-20 20:02:07.608932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:07.609442 INFO::Done
2025-01-20 20:02:07.609988 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:07.61196 INFO::Starting hierarchical adjustment
2025-01-20 20:02:07.61264 INFO::Found 2 batches.
2025-01-20 20:02:07.613142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:07.613734 INFO::Using default BPPARAM
2025-01-20 20:02:07.614247 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:07.615114 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:07.636704 INFO::Done
2025-01-20 20:02:07.63737 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:07.639319 INFO::ASW Batch was 0.146712121262698 prior to batch effect correction and is now -0.126141064816701 .
2025-01-20 20:02:07.640075 INFO::Total function execution time is 0.038898229598999 s and adjustment time is 0.02420973777771 s ( 62.24 )
2025-01-20 20:02:07.642682 INFO::Formatting Data.
2025-01-20 20:02:07.643288 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:07.651771 INFO::Formatting Data.
2025-01-20 20:02:07.652406 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:07.653256 INFO::Removing potential empty rows and columns
2025-01-20 20:02:07.654252 INFO::Found 0 missing values.
2025-01-20 20:02:07.65711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:07.657738 INFO::Done
2025-01-20 20:02:07.658282 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:07.660289 INFO::Starting hierarchical adjustment
2025-01-20 20:02:07.66098 INFO::Found 2 batches.
2025-01-20 20:02:07.661493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:07.662076 INFO::Using default BPPARAM
2025-01-20 20:02:07.662591 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:07.663586 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:07.678276 INFO::Done
2025-01-20 20:02:07.678973 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:07.680947 INFO::ASW Batch was -0.0391634335520421 prior to batch effect correction and is now -0.116133944769434 .
2025-01-20 20:02:07.681704 INFO::Total function execution time is 0.0299408435821533 s and adjustment time is 0.0174131393432617 s ( 58.16 )
2025-01-20 20:02:07.682725 INFO::Formatting Data.
2025-01-20 20:02:07.683303 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:07.684132 INFO::Removing potential empty rows and columns
2025-01-20 20:02:07.685105 INFO::Found 0 missing values.
2025-01-20 20:02:07.687936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:07.688433 INFO::Done
2025-01-20 20:02:07.688913 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:07.690888 INFO::Starting hierarchical adjustment
2025-01-20 20:02:07.691546 INFO::Found 2 batches.
2025-01-20 20:02:07.692039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:07.692591 INFO::Using default BPPARAM
2025-01-20 20:02:07.693079 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:07.693924 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:07.708626 INFO::Done
2025-01-20 20:02:07.709208 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:07.711109 INFO::ASW Batch was -0.0391634335520421 prior to batch effect correction and is now -0.116133944769434 .
2025-01-20 20:02:07.711864 INFO::Total function execution time is 0.0291321277618408 s and adjustment time is 0.0172274112701416 s ( 59.14 )
2025-01-20 20:02:09.759109 INFO::Formatting Data.
2025-01-20 20:02:09.759799 INFO::Recognized SummarizedExperiment
2025-01-20 20:02:09.760249 INFO::Typecasting input to dataframe.
2025-01-20 20:02:09.788845 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:09.790002 INFO::Removing potential empty rows and columns
2025-01-20 20:02:09.793051 INFO::Found 0 missing values.
2025-01-20 20:02:09.798547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:09.799049 INFO::Done
2025-01-20 20:02:09.799459 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:09.80244 INFO::Starting hierarchical adjustment
2025-01-20 20:02:09.803041 INFO::Found 2 batches.
2025-01-20 20:02:09.803472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:09.80442 INFO::Using default BPPARAM
2025-01-20 20:02:09.80486 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:09.80567 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:09.853082 INFO::Done
2025-01-20 20:02:09.853702 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:09.856821 INFO::ASW Batch was -0.0188827668313369 prior to batch effect correction and is now -0.0920276601210838 .
2025-01-20 20:02:09.85757 INFO::Total function execution time is 0.0987858772277832 s and adjustment time is 0.0501387119293213 s ( 50.75 )
2025-01-20 20:02:09.873353 INFO::Formatting Data.
2025-01-20 20:02:09.874004 INFO::Recognized SummarizedExperiment
2025-01-20 20:02:09.874449 INFO::Typecasting input to dataframe.
2025-01-20 20:02:09.882407 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:09.883415 INFO::Removing potential empty rows and columns
2025-01-20 20:02:09.886374 INFO::Found 0 missing values.
2025-01-20 20:02:09.892173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:09.89266 INFO::Done
2025-01-20 20:02:09.8931 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:09.895999 INFO::Starting hierarchical adjustment
2025-01-20 20:02:09.896587 INFO::Found 2 batches.
2025-01-20 20:02:09.897034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:09.897517 INFO::Using default BPPARAM
2025-01-20 20:02:09.897951 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:09.89877 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:09.918785 INFO::Done
2025-01-20 20:02:09.919367 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:09.922285 INFO::ASW Batch was -0.00507956359156058 prior to batch effect correction and is now -0.00507956359156058 .
2025-01-20 20:02:09.922993 INFO::Total function execution time is 0.0496344566345215 s and adjustment time is 0.0223045349121094 s ( 44.94 )
2025-01-20 20:02:09.938354 INFO::Formatting Data.
2025-01-20 20:02:09.939024 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:09.939749 INFO::Removing potential empty rows and columns
2025-01-20 20:02:09.940596 INFO::Found 0 missing values.
2025-01-20 20:02:09.943112 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:09.943575 INFO::Done
2025-01-20 20:02:09.944038 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:09.945858 INFO::Starting hierarchical adjustment
2025-01-20 20:02:09.946539 INFO::Found 3 batches.
2025-01-20 20:02:09.947096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:09.947597 INFO::Using default BPPARAM
2025-01-20 20:02:09.948047 INFO::Processing subtree level 1
2025-01-20 20:02:10.097673 INFO::Adjusting the last 1 batches sequentially
2025-01-20 20:02:10.099653 INFO::Done
2025-01-20 20:02:10.100355 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:10.103003 INFO::ASW Batch was 0.0383593402932703 prior to batch effect correction and is now -0.155037959422595 .
2025-01-20 20:02:10.103966 INFO::Total function execution time is 0.165584564208984 s and adjustment time is 0.153209209442139 s ( 92.53 )
2025-01-20 20:02:10.119317 INFO::Skipping initial DF formatting
2025-01-20 20:02:10.120001 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:10.123924 INFO::Starting hierarchical adjustment
2025-01-20 20:02:10.12466 INFO::Found 5 batches.
2025-01-20 20:02:10.125196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:10.125774 INFO::Using default BPPARAM
2025-01-20 20:02:10.12632 INFO::Processing subtree level 1
2025-01-20 20:02:10.258257 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:10.259882 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:10.280055 INFO::Done
2025-01-20 20:02:10.280711 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:10.284837 INFO::ASW Batch was 0.482589695422912 prior to batch effect correction and is now 0.482589695422912 .
2025-01-20 20:02:10.285401 INFO::ASW Label was 0.38173793439105 prior to batch effect correction and is now 0.38173793439105 .
2025-01-20 20:02:10.286232 INFO::Total function execution time is 0.166994094848633 s and adjustment time is 0.155524492263794 s ( 93.13 )
2025-01-20 20:02:10.303546 INFO::Formatting Data.
2025-01-20 20:02:10.304428 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:10.305348 INFO::Removing potential empty rows and columns
2025-01-20 20:02:10.306357 INFO::Found 0 missing values.
2025-01-20 20:02:10.310498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:10.311052 INFO::Done
2025-01-20 20:02:10.31154 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:10.314571 INFO::Starting hierarchical adjustment
2025-01-20 20:02:10.315271 INFO::Found 5 batches.
2025-01-20 20:02:10.315783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:10.316382 INFO::Using default BPPARAM
2025-01-20 20:02:10.316897 INFO::Processing subtree level 1
2025-01-20 20:02:10.435236 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:10.436779 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:10.452593 INFO::Done
2025-01-20 20:02:10.453273 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:10.456366 INFO::ASW Batch was 0.467335958141719 prior to batch effect correction and is now -0.0907903002721949 .
2025-01-20 20:02:10.456952 INFO::ASW Label was 0.221909115522121 prior to batch effect correction and is now 0.824155102584306 .
2025-01-20 20:02:10.457746 INFO::Total function execution time is 0.154283285140991 s and adjustment time is 0.137421369552612 s ( 89.07 )
2025-01-20 20:02:10.458609 INFO::Formatting Data.
2025-01-20 20:02:10.459237 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:10.460105 INFO::Removing potential empty rows and columns
2025-01-20 20:02:10.461093 INFO::Found 0 missing values.
2025-01-20 20:02:10.465163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:10.465694 INFO::Done
2025-01-20 20:02:10.466217 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:10.469399 INFO::Starting hierarchical adjustment
2025-01-20 20:02:10.470122 INFO::Found 5 batches.
2025-01-20 20:02:10.470648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:10.471263 INFO::Using default BPPARAM
2025-01-20 20:02:10.471786 INFO::Processing subtree level 1
2025-01-20 20:02:10.594656 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:10.596275 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:10.611692 INFO::Done
2025-01-20 20:02:10.612411 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:10.615487 INFO::ASW Batch was 0.467335958141719 prior to batch effect correction and is now -0.0907903002721949 .
2025-01-20 20:02:10.616078 INFO::ASW Label was 0.221909115522121 prior to batch effect correction and is now 0.824155102584306 .
2025-01-20 20:02:10.616872 INFO::Total function execution time is 0.158259630203247 s and adjustment time is 0.141693830490112 s ( 89.53 )
2025-01-20 20:02:10.630041 INFO::Formatting Data.
2025-01-20 20:02:10.630793 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:10.631688 INFO::Removing potential empty rows and columns
2025-01-20 20:02:10.632671 INFO::Found 0 missing values.
2025-01-20 20:02:10.636852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:10.637372 INFO::Done
2025-01-20 20:02:10.637852 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:10.640688 INFO::Starting hierarchical adjustment
2025-01-20 20:02:10.641373 INFO::Found 5 batches.
2025-01-20 20:02:10.641895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:10.642495 INFO::Using default BPPARAM
2025-01-20 20:02:10.642992 INFO::Processing subtree level 1
2025-01-20 20:02:10.806166 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:10.80778 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:10.823462 INFO::Done
2025-01-20 20:02:10.824167 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:10.82732 INFO::ASW Batch was 0.495763445121042 prior to batch effect correction and is now -0.0759923291737437 .
2025-01-20 20:02:10.827924 INFO::ASW Label was 0.246793090843788 prior to batch effect correction and is now 0.832611876770701 .
2025-01-20 20:02:10.828719 INFO::Total function execution time is 0.198758363723755 s and adjustment time is 0.18219518661499 s ( 91.67 )
2025-01-20 20:02:10.829532 INFO::Formatting Data.
2025-01-20 20:02:10.830154 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:10.831028 INFO::Removing potential empty rows and columns
2025-01-20 20:02:10.831999 INFO::Found 0 missing values.
2025-01-20 20:02:10.836125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:10.836664 INFO::Done
2025-01-20 20:02:10.85553 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:10.85867 INFO::Starting hierarchical adjustment
2025-01-20 20:02:10.859451 INFO::Found 5 batches.
2025-01-20 20:02:10.859983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:10.860554 INFO::Using default BPPARAM
2025-01-20 20:02:10.861047 INFO::Processing subtree level 1
2025-01-20 20:02:10.996627 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:10.998322 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:11.015462 INFO::Done
2025-01-20 20:02:11.016248 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.019833 INFO::ASW Batch was 0.495763445121042 prior to batch effect correction and is now -0.0759923291737437 .
2025-01-20 20:02:11.020453 INFO::ASW Label was 0.246793090843788 prior to batch effect correction and is now 0.832611876770701 .
2025-01-20 20:02:11.021265 INFO::Total function execution time is 0.191725015640259 s and adjustment time is 0.156153440475464 s ( 81.45 )
2025-01-20 20:02:11.035991 INFO::Formatting Data.
2025-01-20 20:02:11.03679 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:11.037734 INFO::Removing potential empty rows and columns
2025-01-20 20:02:11.038879 INFO::Found 0 missing values.
2025-01-20 20:02:11.041867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:11.042376 INFO::Done
2025-01-20 20:02:11.042859 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:11.045838 INFO::Starting hierarchical adjustment
2025-01-20 20:02:11.046496 INFO::Found 2 batches.
2025-01-20 20:02:11.046996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:11.047558 INFO::Using default BPPARAM
2025-01-20 20:02:11.048043 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:11.048959 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:11.063699 INFO::Done
2025-01-20 20:02:11.064339 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.067288 INFO::ASW Batch was 0.422381346580671 prior to batch effect correction and is now -0.0240604524188743 .
2025-01-20 20:02:11.067858 INFO::ASW Label was 0.633992161716885 prior to batch effect correction and is now 0.926346275304748 .
2025-01-20 20:02:11.068643 INFO::Total function execution time is 0.0327980518341064 s and adjustment time is 0.0173346996307373 s ( 52.85 )
2025-01-20 20:02:11.06941 INFO::Formatting Data.
2025-01-20 20:02:11.070011 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:11.070864 INFO::Removing potential empty rows and columns
2025-01-20 20:02:11.071856 INFO::Found 0 missing values.
2025-01-20 20:02:11.074549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:11.07509 INFO::Done
2025-01-20 20:02:11.075636 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:11.078532 INFO::Starting hierarchical adjustment
2025-01-20 20:02:11.079218 INFO::Found 2 batches.
2025-01-20 20:02:11.079713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:11.080306 INFO::Using default BPPARAM
2025-01-20 20:02:11.080819 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:11.081712 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:11.096407 INFO::Done
2025-01-20 20:02:11.097066 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.100022 INFO::ASW Batch was 0.422381346580671 prior to batch effect correction and is now -0.0240604524188743 .
2025-01-20 20:02:11.10059 INFO::ASW Label was 0.633992161716885 prior to batch effect correction and is now 0.926346275304748 .
2025-01-20 20:02:11.101358 INFO::Total function execution time is 0.0319671630859375 s and adjustment time is 0.0173232555389404 s ( 54.19 )
2025-01-20 20:02:11.112537 INFO::Formatting Data.
2025-01-20 20:02:11.113267 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:11.114099 INFO::Removing potential empty rows and columns
2025-01-20 20:02:11.115041 INFO::Found 0 missing values.
2025-01-20 20:02:11.117205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:11.117698 INFO::Done
2025-01-20 20:02:11.11818 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:11.120084 INFO::Starting hierarchical adjustment
2025-01-20 20:02:11.120759 INFO::Found 2 batches.
2025-01-20 20:02:11.121281 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:11.121853 INFO::Using default BPPARAM
2025-01-20 20:02:11.122339 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:11.123216 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:11.156116 INFO::Done
2025-01-20 20:02:11.15681 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.158936 INFO::ASW Batch was -0.128759546693371 prior to batch effect correction and is now -0.161778137742928 .
2025-01-20 20:02:11.159786 INFO::Total function execution time is 0.047309398651123 s and adjustment time is 0.0354709625244141 s ( 74.98 )
2025-01-20 20:02:11.171937 INFO::Formatting Data.
2025-01-20 20:02:11.172647 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:11.173546 INFO::Removing potential empty rows and columns
2025-01-20 20:02:11.174569 INFO::Found 0 missing values.
2025-01-20 20:02:11.175755 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.
2025-01-20 20:02:11.180406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:11.180933 INFO::Done
2025-01-20 20:02:11.181415 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:11.18434 INFO::Starting hierarchical adjustment
2025-01-20 20:02:11.185039 INFO::Found 2 batches.
2025-01-20 20:02:11.185548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:11.186113 INFO::Using default BPPARAM
2025-01-20 20:02:11.186593 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:11.18754 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:11.205372 INFO::Done
2025-01-20 20:02:11.206161 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.209199 INFO::ASW Batch was 0.497630509678003 prior to batch effect correction and is now -0.0364524824883033 .
2025-01-20 20:02:11.209831 INFO::ASW Label was 0.588882967524831 prior to batch effect correction and is now 0.944390395587309 .
2025-01-20 20:02:11.210575 INFO::Total function execution time is 0.0387318134307861 s and adjustment time is 0.0204606056213379 s ( 52.83 )
2025-01-20 20:02:11.211396 INFO::Formatting Data.
2025-01-20 20:02:11.21208 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:11.213112 INFO::Removing potential empty rows and columns
2025-01-20 20:02:11.214146 INFO::Found 0 missing values.
2025-01-20 20:02:11.215002 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.
2025-01-20 20:02:11.21935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:11.219862 INFO::Done
2025-01-20 20:02:11.220334 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:11.223118 INFO::Starting hierarchical adjustment
2025-01-20 20:02:11.223776 INFO::Found 2 batches.
2025-01-20 20:02:11.224279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:11.22484 INFO::Using default BPPARAM
2025-01-20 20:02:11.225326 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:11.226232 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:11.243252 INFO::Done
2025-01-20 20:02:11.244047 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.247158 INFO::ASW Batch was 0.497630509678003 prior to batch effect correction and is now -0.0364524824883033 .
2025-01-20 20:02:11.24772 INFO::ASW Label was 0.588882967524831 prior to batch effect correction and is now 0.944390395587309 .
2025-01-20 20:02:11.248508 INFO::Total function execution time is 0.0371289253234863 s and adjustment time is 0.0195662975311279 s ( 52.7 )
2025-01-20 20:02:11.448344 INFO::Formatting Data.
2025-01-20 20:02:11.449083 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:11.449916 INFO::Removing potential empty rows and columns
2025-01-20 20:02:11.450846 INFO::Found 0 missing values.
2025-01-20 20:02:11.453601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:11.454099 INFO::Done
2025-01-20 20:02:11.454563 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:11.456406 INFO::Starting hierarchical adjustment
2025-01-20 20:02:11.45706 INFO::Found 3 batches.
2025-01-20 20:02:11.457524 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:11.458071 INFO::Using default BPPARAM
2025-01-20 20:02:11.458525 INFO::Processing subtree level 1
2025-01-20 20:02:11.58882 INFO::Adjusting the last 1 batches sequentially
2025-01-20 20:02:11.590559 INFO::Done
2025-01-20 20:02:11.591187 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.593564 INFO::ASW Batch was -0.077616878255787 prior to batch effect correction and is now -0.077616878255787 .
2025-01-20 20:02:11.594501 INFO::Total function execution time is 0.146181583404541 s and adjustment time is 0.133604526519775 s ( 91.4 )
2025-01-20 20:02:11.595528 INFO::Formatting Data.
2025-01-20 20:02:11.596148 INFO::Typecasting input to dataframe.
2025-01-20 20:02:11.600681 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:11.602375 INFO::Removing potential empty rows and columns
2025-01-20 20:02:11.603535 INFO::Found 0 missing values.
2025-01-20 20:02:11.606681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:11.607232 INFO::Done
2025-01-20 20:02:11.607738 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:11.610147 INFO::Starting hierarchical adjustment
2025-01-20 20:02:11.610851 INFO::Found 3 batches.
2025-01-20 20:02:11.611363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:11.612003 INFO::Using default BPPARAM
2025-01-20 20:02:11.612506 INFO::Processing subtree level 1
2025-01-20 20:02:11.75325 INFO::Adjusting the last 1 batches sequentially
2025-01-20 20:02:11.75502 INFO::Done
2025-01-20 20:02:11.755625 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.758024 INFO::ASW Batch was -0.077616878255787 prior to batch effect correction and is now -0.077616878255787 .
2025-01-20 20:02:11.758992 INFO::Total function execution time is 0.16343355178833 s and adjustment time is 0.144295930862427 s ( 88.29 )
2025-01-20 20:02:11.772669 INFO::Formatting Data.
2025-01-20 20:02:11.773474 INFO::Typecasting input to dataframe.
2025-01-20 20:02:11.774319 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:11.77522 INFO::Removing potential empty rows and columns
2025-01-20 20:02:11.776279 INFO::Found 0 missing values.
2025-01-20 20:02:11.77927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:11.779794 INFO::Done
2025-01-20 20:02:11.780317 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:11.782295 INFO::Starting hierarchical adjustment
2025-01-20 20:02:11.782997 INFO::Found 3 batches.
2025-01-20 20:02:11.783499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:11.784104 INFO::Using default BPPARAM
2025-01-20 20:02:11.784596 INFO::Processing subtree level 1
2025-01-20 20:02:11.927257 INFO::Adjusting the last 1 batches sequentially
2025-01-20 20:02:11.929324 INFO::Done
2025-01-20 20:02:11.929994 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:11.932568 INFO::ASW Batch was -0.00659067407457999 prior to batch effect correction and is now -0.00659067407457999 .
2025-01-20 20:02:11.933526 INFO::Total function execution time is 0.160905361175537 s and adjustment time is 0.146441698074341 s ( 91.01 )
2025-01-20 20:02:12.095706 INFO::Formatting Data.
2025-01-20 20:02:12.09655 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:12.097714 INFO::Removing potential empty rows and columns
2025-01-20 20:02:12.100548 INFO::Found 1000 missing values.
2025-01-20 20:02:12.119066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:12.119831 INFO::Done
2025-01-20 20:02:12.120349 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:12.125708 INFO::Starting hierarchical adjustment
2025-01-20 20:02:12.126502 INFO::Found 10 batches.
2025-01-20 20:02:12.127114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:12.127691 INFO::Using default BPPARAM
2025-01-20 20:02:12.128177 INFO::Processing subtree level 1
2025-01-20 20:02:12.299794 INFO::Processing subtree level 2
2025-01-20 20:02:12.510494 INFO::Adjusting the last 1 batches sequentially
2025-01-20 20:02:12.513208 INFO::Done
2025-01-20 20:02:12.514105 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:12.52165 INFO::ASW Batch was 0.537102066910827 prior to batch effect correction and is now 0.537102066910827 .
2025-01-20 20:02:12.522547 INFO::ASW Label was 0.30416898964918 prior to batch effect correction and is now 0.30416898964918 .
2025-01-20 20:02:12.52376 INFO::Total function execution time is 0.428077697753906 s and adjustment time is 0.386815786361694 s ( 90.36 )
2025-01-20 20:02:12.524881 INFO::Formatting Data.
2025-01-20 20:02:12.525719 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:12.527712 INFO::Removing potential empty rows and columns
2025-01-20 20:02:12.531883 INFO::Found 1000 missing values.
2025-01-20 20:02:12.569669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:12.57117 INFO::Done
2025-01-20 20:02:12.572097 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:12.58111 INFO::Starting hierarchical adjustment
2025-01-20 20:02:12.582469 INFO::Found 10 batches.
2025-01-20 20:02:13.724952 INFO::Set up parallel execution backend with 2 workers
2025-01-20 20:02:13.726483 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-20 20:02:14.843818 INFO::Adjusting the last 2 batches sequentially
2025-01-20 20:02:14.845252 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-20 20:02:14.860574 INFO::Done
2025-01-20 20:02:14.861196 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:14.865617 INFO::ASW Batch was 0.537102066910827 prior to batch effect correction and is now 0.537102066910827 .
2025-01-20 20:02:14.866143 INFO::ASW Label was 0.30416898964918 prior to batch effect correction and is now 0.30416898964918 .
2025-01-20 20:02:14.866813 INFO::Total function execution time is 2.34203767776489 s and adjustment time is 2.27855253219604 s ( 97.29 )
2025-01-20 20:02:15.01067 INFO::Formatting Data.
2025-01-20 20:02:15.011525 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.01249 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.013585 INFO::Found 0 missing values.
2025-01-20 20:02:15.017315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.017838 INFO::Done
2025-01-20 20:02:15.018308 INFO::Acquiring quality metrics before batch effect correction.
2025-01-20 20:02:15.021032 INFO::Starting hierarchical adjustment
2025-01-20 20:02:15.021704 INFO::Found 3 batches.
2025-01-20 20:02:15.02224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-20 20:02:15.022812 INFO::Using default BPPARAM
2025-01-20 20:02:15.023286 INFO::Processing subtree level 1
2025-01-20 20:02:15.129322 INFO::Adjusting the last 1 batches sequentially
2025-01-20 20:02:15.13112 INFO::Done
2025-01-20 20:02:15.13175 INFO::Acquiring quality metrics after batch effect correction.
2025-01-20 20:02:15.135063 INFO::ASW Batch was 0.154517615727413 prior to batch effect correction and is now -0.171182841828391 .
2025-01-20 20:02:15.135635 INFO::ASW Label was -0.134397595841292 prior to batch effect correction and is now 0.0585277898643952 .
2025-01-20 20:02:15.136526 INFO::Total function execution time is 0.125905513763428 s and adjustment time is 0.109546184539795 s ( 87.01 )
2025-01-20 20:02:15.244781 INFO::Formatting Data.
2025-01-20 20:02:15.245551 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.246385 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.247342 INFO::Found 2 missing values.
2025-01-20 20:02:15.249964 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.25043 INFO::Done
2025-01-20 20:02:15.284869 INFO::Found NA in Reference column
2025-01-20 20:02:15.294184 INFO::Require at least two references per batch.
2025-01-20 20:02:15.314313 INFO::Formatting Data.
2025-01-20 20:02:15.315066 INFO::Recognized SummarizedExperiment
2025-01-20 20:02:15.315564 INFO::Typecasting input to dataframe.
2025-01-20 20:02:15.325858 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.327141 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.330615 INFO::Found 0 missing values.
2025-01-20 20:02:15.33692 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.337501 INFO::Done
2025-01-20 20:02:15.35205 INFO::Formatting Data.
2025-01-20 20:02:15.352787 INFO::Recognized SummarizedExperiment
2025-01-20 20:02:15.353329 INFO::Typecasting input to dataframe.
2025-01-20 20:02:15.371902 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.373166 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.376828 INFO::Found 0 missing values.
2025-01-20 20:02:15.388431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.389244 INFO::Done
2025-01-20 20:02:15.406873 INFO::Formatting Data.
2025-01-20 20:02:15.407638 INFO::Recognized SummarizedExperiment
2025-01-20 20:02:15.40817 INFO::Typecasting input to dataframe.
2025-01-20 20:02:15.426669 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.427745 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.428869 INFO::Found 0 missing values.
2025-01-20 20:02:15.429785 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.
2025-01-20 20:02:15.434606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.435157 INFO::Done
2025-01-20 20:02:15.445473 INFO::Formatting Data.
2025-01-20 20:02:15.446255 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.447131 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.448365 INFO::Found 0 missing values.
2025-01-20 20:02:15.4526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.453233 INFO::Done
2025-01-20 20:02:15.465432 INFO::Formatting Data.
2025-01-20 20:02:15.466351 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.467324 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.468472 INFO::Found 0 missing values.
2025-01-20 20:02:15.471747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.472328 INFO::Done
2025-01-20 20:02:15.504092 INFO::Formatting Data.
2025-01-20 20:02:15.504989 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.506457 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.508042 INFO::Found 1 missing values.
2025-01-20 20:02:15.5114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.511957 INFO::Done
2025-01-20 20:02:15.53089 INFO::Formatting Data.
2025-01-20 20:02:15.53176 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.532732 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.533778 INFO::Found 2 missing values.
2025-01-20 20:02:15.534818 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.
2025-01-20 20:02:15.537544 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.538128 INFO::Done
2025-01-20 20:02:15.549219 INFO::Formatting Data.
2025-01-20 20:02:15.550062 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.551014 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.552041 INFO::Found 2 missing values.
2025-01-20 20:02:15.55383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.554356 INFO::Done
2025-01-20 20:02:15.566075 INFO::Formatting Data.
2025-01-20 20:02:15.566885 INFO::Typecasting input to dataframe.
2025-01-20 20:02:15.567811 INFO::Replacing NaNs with NAs.
2025-01-20 20:02:15.56891 INFO::Removing potential empty rows and columns
2025-01-20 20:02:15.569952 INFO::Found 0 missing values.
2025-01-20 20:02:15.573246 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-20 20:02:15.573796 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.001 3.560 19.256
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.667 | 1.425 | 17.075 | |
| compute_asw | 0.023 | 0.001 | 0.025 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.011 | 0.001 | 0.013 | |
| generate_dataset | 0.013 | 0.001 | 0.012 | |