Yannis Schumann
| Snapshot Date: 2025-03-13 13:00 -0400 (Thu, 13 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 2025-03-17 12:06 -0400 (Mon, 17 Mar 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" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4399 |
| 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: 2025-03-13 22:53:42 -0400 (Thu, 13 Mar 2025) |
| EndedAt: 2025-03-13 22:56:01 -0400 (Thu, 13 Mar 2025) |
| EllapsedTime: 139.0 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 8.64 0.69 18.72
* 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")
2025-03-13 22:54:48.037034 INFO::Formatting Data.
2025-03-13 22:54:48.039109 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:48.047997 INFO::Removing potential empty rows and columns
2025-03-13 22:54:48.264648 INFO::Found 0 missing values.
2025-03-13 22:54:48.26767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:54:48.268513 INFO::Done
2025-03-13 22:54:48.269238 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:54:48.282541 INFO::Starting hierarchical adjustment
2025-03-13 22:54:48.283583 INFO::Found 3 batches.
2025-03-13 22:54:48.284298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:54:48.285572 INFO::Using default BPPARAM
2025-03-13 22:54:48.286283 INFO::Processing subtree level 1
2025-03-13 22:54:51.005194 INFO::Adjusting the last 1 batches sequentially
2025-03-13 22:54:51.007343 INFO::Done
2025-03-13 22:54:51.008525 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:54:51.011532 INFO::ASW Batch was -0.11070269785726 prior to batch effect correction and is now -0.11070269785726 .
2025-03-13 22:54:51.013119 INFO::Total function execution time is 2.97667717933655 s and adjustment time is 2.72388696670532 s ( 91.51 )
2025-03-13 22:54:51.03171 INFO::Formatting Data.
2025-03-13 22:54:51.033214 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:51.034989 INFO::Removing potential empty rows and columns
2025-03-13 22:54:51.036918 INFO::Found 0 missing values.
2025-03-13 22:54:51.038678 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.
2025-03-13 22:54:51.053038 INFO::Formatting Data.
2025-03-13 22:54:51.054496 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:51.056201 INFO::Removing potential empty rows and columns
2025-03-13 22:54:51.058059 INFO::Found 0 missing values.
2025-03-13 22:54:51.05977 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.
2025-03-13 22:54:51.085094 INFO::Formatting Data.
2025-03-13 22:54:51.086611 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:51.088401 INFO::Removing potential empty rows and columns
2025-03-13 22:54:51.09028 INFO::Found 0 missing values.
2025-03-13 22:54:51.092101 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.
2025-03-13 22:54:51.098259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:54:51.099529 INFO::Done
2025-03-13 22:54:51.100736 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:54:51.103997 INFO::Starting hierarchical adjustment
2025-03-13 22:54:51.10544 INFO::Found 2 batches.
2025-03-13 22:54:51.106721 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:54:51.108007 INFO::Using default BPPARAM
2025-03-13 22:54:51.109174 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:54:51.110912 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:54:51.137707 INFO::Done
2025-03-13 22:54:51.139929 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:54:51.14324 INFO::ASW Batch was -0.0288975705434314 prior to batch effect correction and is now -0.122184066664854 .
2025-03-13 22:54:51.144814 INFO::Total function execution time is 0.0597989559173584 s and adjustment time is 0.0324540138244629 s ( 54.27 )
2025-03-13 22:54:51.148942 INFO::Formatting Data.
2025-03-13 22:54:51.150218 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:51.161459 INFO::Formatting Data.
2025-03-13 22:54:51.16284 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:51.164429 INFO::Removing potential empty rows and columns
2025-03-13 22:54:51.166146 INFO::Found 0 missing values.
2025-03-13 22:54:51.170065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:54:51.171208 INFO::Done
2025-03-13 22:54:51.172323 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:54:51.175476 INFO::Starting hierarchical adjustment
2025-03-13 22:54:51.176826 INFO::Found 2 batches.
2025-03-13 22:54:51.177938 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:54:51.179155 INFO::Using default BPPARAM
2025-03-13 22:54:51.180261 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:54:51.181934 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:54:51.201128 INFO::Done
2025-03-13 22:54:51.202444 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:54:51.205656 INFO::ASW Batch was -0.0033571715427306 prior to batch effect correction and is now -0.130700510406431 .
2025-03-13 22:54:51.207157 INFO::Total function execution time is 0.0457539558410645 s and adjustment time is 0.0244619846343994 s ( 53.46 )
2025-03-13 22:54:51.208993 INFO::Formatting Data.
2025-03-13 22:54:51.210222 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:51.211808 INFO::Removing potential empty rows and columns
2025-03-13 22:54:51.21356 INFO::Found 0 missing values.
2025-03-13 22:54:51.217641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:54:51.218801 INFO::Done
2025-03-13 22:54:51.219923 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:54:51.223066 INFO::Starting hierarchical adjustment
2025-03-13 22:54:51.224399 INFO::Found 2 batches.
2025-03-13 22:54:51.225503 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:54:51.226707 INFO::Using default BPPARAM
2025-03-13 22:54:51.227814 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:54:51.229531 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:54:51.248846 INFO::Done
2025-03-13 22:54:51.250216 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:54:51.253526 INFO::ASW Batch was -0.0033571715427306 prior to batch effect correction and is now -0.130700510406431 .
2025-03-13 22:54:51.255051 INFO::Total function execution time is 0.0460309982299805 s and adjustment time is 0.0246009826660156 s ( 53.44 )
2025-03-13 22:54:53.620056 INFO::Formatting Data.
2025-03-13 22:54:53.621001 INFO::Recognized SummarizedExperiment
2025-03-13 22:54:53.621736 INFO::Typecasting input to dataframe.
2025-03-13 22:54:53.651009 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:53.652506 INFO::Removing potential empty rows and columns
2025-03-13 22:54:53.655618 INFO::Found 0 missing values.
2025-03-13 22:54:53.661281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:54:53.662193 INFO::Done
2025-03-13 22:54:53.66294 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:54:53.666705 INFO::Starting hierarchical adjustment
2025-03-13 22:54:53.667609 INFO::Found 2 batches.
2025-03-13 22:54:53.668299 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:54:53.669572 INFO::Using default BPPARAM
2025-03-13 22:54:53.670285 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:54:53.671482 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:54:53.721236 INFO::Done
2025-03-13 22:54:53.722152 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:54:53.726199 INFO::ASW Batch was -0.00147168331254143 prior to batch effect correction and is now -0.0948640625181485 .
2025-03-13 22:54:53.727285 INFO::Total function execution time is 0.107517957687378 s and adjustment time is 0.0537319183349609 s ( 49.97 )
2025-03-13 22:54:54.407185 INFO::Formatting Data.
2025-03-13 22:54:54.408151 INFO::Recognized SummarizedExperiment
2025-03-13 22:54:54.408877 INFO::Typecasting input to dataframe.
2025-03-13 22:54:54.417024 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:54.418397 INFO::Removing potential empty rows and columns
2025-03-13 22:54:54.421284 INFO::Found 0 missing values.
2025-03-13 22:54:54.426571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:54:54.427443 INFO::Done
2025-03-13 22:54:54.428163 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:54:54.431838 INFO::Starting hierarchical adjustment
2025-03-13 22:54:54.432797 INFO::Found 2 batches.
2025-03-13 22:54:54.43352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:54:54.434283 INFO::Using default BPPARAM
2025-03-13 22:54:54.434978 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:54:54.43617 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:54:54.454472 INFO::Done
2025-03-13 22:54:54.455397 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:54:54.459177 INFO::ASW Batch was -0.0114906940470874 prior to batch effect correction and is now -0.0114906940470874 .
2025-03-13 22:54:54.460254 INFO::Total function execution time is 0.0530529022216797 s and adjustment time is 0.0217781066894531 s ( 41.05 )
2025-03-13 22:54:54.480657 INFO::Formatting Data.
2025-03-13 22:54:54.481634 INFO::Replacing NaNs with NAs.
2025-03-13 22:54:54.482699 INFO::Removing potential empty rows and columns
2025-03-13 22:54:54.483817 INFO::Found 0 missing values.
2025-03-13 22:54:54.48641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:54:54.487128 INFO::Done
2025-03-13 22:54:54.487888 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:54:54.490047 INFO::Starting hierarchical adjustment
2025-03-13 22:54:54.490937 INFO::Found 3 batches.
2025-03-13 22:54:54.491642 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:54:54.49241 INFO::Using default BPPARAM
2025-03-13 22:54:54.493109 INFO::Processing subtree level 1
2025-03-13 22:55:04.78746 INFO::Adjusting the last 1 batches sequentially
2025-03-13 22:55:04.789768 INFO::Done
2025-03-13 22:55:04.791078 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:04.794568 INFO::ASW Batch was 0.0573136482814748 prior to batch effect correction and is now -0.144478538282371 .
2025-03-13 22:55:04.796054 INFO::Total function execution time is 10.3153960704803 s and adjustment time is 10.2989020347595 s ( 99.84 )
2025-03-13 22:55:04.819537 INFO::Skipping initial DF formatting
2025-03-13 22:55:04.820909 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:04.827689 INFO::Starting hierarchical adjustment
2025-03-13 22:55:04.829298 INFO::Found 5 batches.
2025-03-13 22:55:04.830524 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:04.831823 INFO::Using default BPPARAM
2025-03-13 22:55:04.832989 INFO::Processing subtree level 1
2025-03-13 22:55:08.069141 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:08.071188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:08.092762 INFO::Done
2025-03-13 22:55:08.094003 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:08.100356 INFO::ASW Batch was 0.452087402675472 prior to batch effect correction and is now 0.452087402675472 .
2025-03-13 22:55:08.101737 INFO::ASW Label was 0.402828060724023 prior to batch effect correction and is now 0.402828060724023 .
2025-03-13 22:55:08.103345 INFO::Total function execution time is 3.28390192985535 s and adjustment time is 3.26367688179016 s ( 99.38 )
2025-03-13 22:55:08.132084 INFO::Formatting Data.
2025-03-13 22:55:08.133614 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:08.135341 INFO::Removing potential empty rows and columns
2025-03-13 22:55:08.137114 INFO::Found 0 missing values.
2025-03-13 22:55:08.142953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:08.144281 INFO::Done
2025-03-13 22:55:08.145517 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:08.150271 INFO::Starting hierarchical adjustment
2025-03-13 22:55:08.151776 INFO::Found 5 batches.
2025-03-13 22:55:08.15303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:08.154318 INFO::Using default BPPARAM
2025-03-13 22:55:08.155476 INFO::Processing subtree level 1
2025-03-13 22:55:11.425288 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:11.426938 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:11.443667 INFO::Done
2025-03-13 22:55:11.444868 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:11.44908 INFO::ASW Batch was 0.175403096056029 prior to batch effect correction and is now -0.0709326145517975 .
2025-03-13 22:55:11.450242 INFO::ASW Label was 0.557540425853286 prior to batch effect correction and is now 0.856187814175798 .
2025-03-13 22:55:11.451629 INFO::Total function execution time is 3.31966400146484 s and adjustment time is 3.29208993911743 s ( 99.17 )
2025-03-13 22:55:11.452817 INFO::Formatting Data.
2025-03-13 22:55:11.453648 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:11.454677 INFO::Removing potential empty rows and columns
2025-03-13 22:55:11.455735 INFO::Found 0 missing values.
2025-03-13 22:55:11.459378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:11.460634 INFO::Done
2025-03-13 22:55:11.461782 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:11.466606 INFO::Starting hierarchical adjustment
2025-03-13 22:55:11.468126 INFO::Found 5 batches.
2025-03-13 22:55:11.469371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:11.47065 INFO::Using default BPPARAM
2025-03-13 22:55:11.471796 INFO::Processing subtree level 1
2025-03-13 22:55:14.602003 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:14.604018 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:14.617701 INFO::Done
2025-03-13 22:55:14.618572 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:14.621641 INFO::ASW Batch was 0.175403096056029 prior to batch effect correction and is now -0.0709326145517975 .
2025-03-13 22:55:14.622435 INFO::ASW Label was 0.557540425853286 prior to batch effect correction and is now 0.856187814175798 .
2025-03-13 22:55:14.623388 INFO::Total function execution time is 3.17059302330017 s and adjustment time is 3.14983201026917 s ( 99.35 )
2025-03-13 22:55:14.63962 INFO::Formatting Data.
2025-03-13 22:55:14.641196 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:14.642899 INFO::Removing potential empty rows and columns
2025-03-13 22:55:14.644641 INFO::Found 0 missing values.
2025-03-13 22:55:14.650313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:14.651527 INFO::Done
2025-03-13 22:55:14.652693 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:14.657307 INFO::Starting hierarchical adjustment
2025-03-13 22:55:14.658766 INFO::Found 5 batches.
2025-03-13 22:55:14.659927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:14.661184 INFO::Using default BPPARAM
2025-03-13 22:55:14.662338 INFO::Processing subtree level 1
2025-03-13 22:55:17.778717 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:17.780427 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:17.792406 INFO::Done
2025-03-13 22:55:17.793253 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:17.796211 INFO::ASW Batch was 0.410540323530566 prior to batch effect correction and is now -0.076010796186065 .
2025-03-13 22:55:17.79697 INFO::ASW Label was 0.238550570480239 prior to batch effect correction and is now 0.849338802514097 .
2025-03-13 22:55:17.797871 INFO::Total function execution time is 3.15843796730042 s and adjustment time is 3.13387584686279 s ( 99.22 )
2025-03-13 22:55:17.798769 INFO::Formatting Data.
2025-03-13 22:55:17.799521 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:17.800494 INFO::Removing potential empty rows and columns
2025-03-13 22:55:17.801527 INFO::Found 0 missing values.
2025-03-13 22:55:17.804973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:17.80567 INFO::Done
2025-03-13 22:55:17.806376 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:17.809233 INFO::Starting hierarchical adjustment
2025-03-13 22:55:17.810066 INFO::Found 5 batches.
2025-03-13 22:55:17.810786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:17.811539 INFO::Using default BPPARAM
2025-03-13 22:55:17.812246 INFO::Processing subtree level 1
2025-03-13 22:55:20.649385 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:20.651382 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:20.663434 INFO::Done
2025-03-13 22:55:20.664321 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:20.667312 INFO::ASW Batch was 0.410540323530566 prior to batch effect correction and is now -0.076010796186065 .
2025-03-13 22:55:20.668102 INFO::ASW Label was 0.238550570480239 prior to batch effect correction and is now 0.849338802514097 .
2025-03-13 22:55:20.669041 INFO::Total function execution time is 2.87027311325073 s and adjustment time is 2.85345792770386 s ( 99.41 )
2025-03-13 22:55:20.684054 INFO::Formatting Data.
2025-03-13 22:55:20.685032 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:20.686144 INFO::Removing potential empty rows and columns
2025-03-13 22:55:20.687309 INFO::Found 0 missing values.
2025-03-13 22:55:20.68978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:20.690485 INFO::Done
2025-03-13 22:55:20.691165 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:20.694144 INFO::Starting hierarchical adjustment
2025-03-13 22:55:20.695055 INFO::Found 2 batches.
2025-03-13 22:55:20.695806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:20.696592 INFO::Using default BPPARAM
2025-03-13 22:55:20.697285 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:20.698409 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:20.710238 INFO::Done
2025-03-13 22:55:20.711063 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:20.713938 INFO::ASW Batch was 0.592402920587061 prior to batch effect correction and is now -0.0274009960964838 .
2025-03-13 22:55:20.714679 INFO::ASW Label was 0.428494680603241 prior to batch effect correction and is now 0.89810500116292 .
2025-03-13 22:55:20.7156 INFO::Total function execution time is 0.0316550731658936 s and adjustment time is 0.0153179168701172 s ( 48.39 )
2025-03-13 22:55:20.716534 INFO::Formatting Data.
2025-03-13 22:55:20.71733 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:20.718341 INFO::Removing potential empty rows and columns
2025-03-13 22:55:20.719409 INFO::Found 0 missing values.
2025-03-13 22:55:20.721811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:20.722514 INFO::Done
2025-03-13 22:55:20.723205 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:20.727005 INFO::Starting hierarchical adjustment
2025-03-13 22:55:20.72838 INFO::Found 2 batches.
2025-03-13 22:55:20.729549 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:20.730616 INFO::Using default BPPARAM
2025-03-13 22:55:20.731322 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:20.732384 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:20.74626 INFO::Done
2025-03-13 22:55:20.747144 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:20.750093 INFO::ASW Batch was 0.592402920587061 prior to batch effect correction and is now -0.0274009960964838 .
2025-03-13 22:55:20.750889 INFO::ASW Label was 0.428494680603241 prior to batch effect correction and is now 0.89810500116292 .
2025-03-13 22:55:20.751841 INFO::Total function execution time is 0.0353171825408936 s and adjustment time is 0.0181000232696533 s ( 51.25 )
2025-03-13 22:55:20.765761 INFO::Formatting Data.
2025-03-13 22:55:20.76677 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:20.767839 INFO::Removing potential empty rows and columns
2025-03-13 22:55:20.768904 INFO::Found 0 missing values.
2025-03-13 22:55:20.770993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:20.771748 INFO::Done
2025-03-13 22:55:20.77249 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:20.774579 INFO::Starting hierarchical adjustment
2025-03-13 22:55:20.775469 INFO::Found 2 batches.
2025-03-13 22:55:20.77618 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:20.776981 INFO::Using default BPPARAM
2025-03-13 22:55:20.777679 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:20.778753 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:20.804999 INFO::Done
2025-03-13 22:55:20.805881 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:20.808014 INFO::ASW Batch was 0.23502588550073 prior to batch effect correction and is now -0.103791052339392 .
2025-03-13 22:55:20.809009 INFO::Total function execution time is 0.0433390140533447 s and adjustment time is 0.0296289920806885 s ( 68.37 )
2025-03-13 22:55:20.823789 INFO::Formatting Data.
2025-03-13 22:55:20.824755 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:20.825834 INFO::Removing potential empty rows and columns
2025-03-13 22:55:20.826989 INFO::Found 0 missing values.
2025-03-13 22:55:20.828276 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.
2025-03-13 22:55:20.832441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:20.833193 INFO::Done
2025-03-13 22:55:20.833916 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:20.837568 INFO::Starting hierarchical adjustment
2025-03-13 22:55:20.838992 INFO::Found 2 batches.
2025-03-13 22:55:20.840149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:20.841403 INFO::Using default BPPARAM
2025-03-13 22:55:20.842611 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:20.844449 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:20.86527 INFO::Done
2025-03-13 22:55:20.866215 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:20.869551 INFO::ASW Batch was 0.692457436681722 prior to batch effect correction and is now 0.037716841442519 .
2025-03-13 22:55:20.870398 INFO::ASW Label was 0.385395897168672 prior to batch effect correction and is now 0.884908110183808 .
2025-03-13 22:55:20.871434 INFO::Total function execution time is 0.0477139949798584 s and adjustment time is 0.0265171527862549 s ( 55.58 )
2025-03-13 22:55:20.872574 INFO::Formatting Data.
2025-03-13 22:55:20.873829 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:20.875498 INFO::Removing potential empty rows and columns
2025-03-13 22:55:20.877356 INFO::Found 0 missing values.
2025-03-13 22:55:20.878871 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.
2025-03-13 22:55:20.883861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:20.884759 INFO::Done
2025-03-13 22:55:20.885543 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:20.888827 INFO::Starting hierarchical adjustment
2025-03-13 22:55:20.889806 INFO::Found 2 batches.
2025-03-13 22:55:20.890529 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:20.891536 INFO::Using default BPPARAM
2025-03-13 22:55:20.892315 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:20.893511 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:20.910546 INFO::Done
2025-03-13 22:55:20.91151 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:20.915078 INFO::ASW Batch was 0.692457436681722 prior to batch effect correction and is now 0.037716841442519 .
2025-03-13 22:55:20.915968 INFO::ASW Label was 0.385395897168672 prior to batch effect correction and is now 0.884908110183808 .
2025-03-13 22:55:20.917083 INFO::Total function execution time is 0.0445621013641357 s and adjustment time is 0.0208511352539062 s ( 46.79 )
2025-03-13 22:55:21.134596 INFO::Formatting Data.
2025-03-13 22:55:21.135723 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:21.137012 INFO::Removing potential empty rows and columns
2025-03-13 22:55:21.138364 INFO::Found 0 missing values.
2025-03-13 22:55:21.141703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:21.14257 INFO::Done
2025-03-13 22:55:21.143332 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:21.145801 INFO::Starting hierarchical adjustment
2025-03-13 22:55:21.14681 INFO::Found 3 batches.
2025-03-13 22:55:21.147565 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:21.148478 INFO::Using default BPPARAM
2025-03-13 22:55:21.149258 INFO::Processing subtree level 1
2025-03-13 22:55:23.91673 INFO::Adjusting the last 1 batches sequentially
2025-03-13 22:55:23.918908 INFO::Done
2025-03-13 22:55:23.920262 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:23.923697 INFO::ASW Batch was -0.0496393494355327 prior to batch effect correction and is now -0.0496393494355327 .
2025-03-13 22:55:23.925237 INFO::Total function execution time is 2.79070687294006 s and adjustment time is 2.77221393585205 s ( 99.34 )
2025-03-13 22:55:23.926922 INFO::Formatting Data.
2025-03-13 22:55:23.928151 INFO::Typecasting input to dataframe.
2025-03-13 22:55:23.929524 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:23.93106 INFO::Removing potential empty rows and columns
2025-03-13 22:55:23.932755 INFO::Found 0 missing values.
2025-03-13 22:55:23.936937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:23.937697 INFO::Done
2025-03-13 22:55:23.938415 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:23.940526 INFO::Starting hierarchical adjustment
2025-03-13 22:55:23.941363 INFO::Found 3 batches.
2025-03-13 22:55:23.942029 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:23.942758 INFO::Using default BPPARAM
2025-03-13 22:55:23.943431 INFO::Processing subtree level 1
2025-03-13 22:55:26.432738 INFO::Adjusting the last 1 batches sequentially
2025-03-13 22:55:26.434916 INFO::Done
2025-03-13 22:55:26.43612 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:26.439064 INFO::ASW Batch was -0.0496393494355327 prior to batch effect correction and is now -0.0496393494355327 .
2025-03-13 22:55:26.440482 INFO::Total function execution time is 2.51361012458801 s and adjustment time is 2.4936261177063 s ( 99.2 )
2025-03-13 22:55:26.458462 INFO::Formatting Data.
2025-03-13 22:55:26.459407 INFO::Typecasting input to dataframe.
2025-03-13 22:55:26.460382 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:26.461399 INFO::Removing potential empty rows and columns
2025-03-13 22:55:26.462508 INFO::Found 0 missing values.
2025-03-13 22:55:26.465034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:26.46579 INFO::Done
2025-03-13 22:55:26.466539 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:26.468642 INFO::Starting hierarchical adjustment
2025-03-13 22:55:26.46955 INFO::Found 3 batches.
2025-03-13 22:55:26.470248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:26.471001 INFO::Using default BPPARAM
2025-03-13 22:55:26.471685 INFO::Processing subtree level 1
2025-03-13 22:55:29.207854 INFO::Adjusting the last 1 batches sequentially
2025-03-13 22:55:29.209963 INFO::Done
2025-03-13 22:55:29.211155 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:29.214149 INFO::ASW Batch was -0.0377426631875795 prior to batch effect correction and is now -0.0377426631875795 .
2025-03-13 22:55:29.215594 INFO::Total function execution time is 2.75716805458069 s and adjustment time is 2.74053502082825 s ( 99.4 )
2025-03-13 22:55:32.351897 INFO::Formatting Data.
2025-03-13 22:55:32.352897 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:32.354127 INFO::Removing potential empty rows and columns
2025-03-13 22:55:32.356545 INFO::Found 1000 missing values.
2025-03-13 22:55:32.370733 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:32.371688 INFO::Done
2025-03-13 22:55:32.372426 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:32.378629 INFO::Starting hierarchical adjustment
2025-03-13 22:55:32.379757 INFO::Found 10 batches.
2025-03-13 22:55:32.380504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:32.381448 INFO::Using default BPPARAM
2025-03-13 22:55:32.382588 INFO::Processing subtree level 1
2025-03-13 22:55:35.45739 INFO::Processing subtree level 2
2025-03-13 22:55:38.245512 INFO::Adjusting the last 1 batches sequentially
2025-03-13 22:55:38.247856 INFO::Done
2025-03-13 22:55:38.248987 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:38.257576 INFO::ASW Batch was 0.44294168725024 prior to batch effect correction and is now 0.44294168725024 .
2025-03-13 22:55:38.258871 INFO::ASW Label was 0.378450773363845 prior to batch effect correction and is now 0.378450773363845 .
2025-03-13 22:55:38.260506 INFO::Total function execution time is 5.90863108634949 s and adjustment time is 5.86824083328247 s ( 99.32 )
2025-03-13 22:55:38.261884 INFO::Formatting Data.
2025-03-13 22:55:38.263048 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:38.264832 INFO::Removing potential empty rows and columns
2025-03-13 22:55:38.267483 INFO::Found 1000 missing values.
2025-03-13 22:55:38.282416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:38.283507 INFO::Done
2025-03-13 22:55:38.28464 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:38.29374 INFO::Starting hierarchical adjustment
2025-03-13 22:55:38.295264 INFO::Found 10 batches.
2025-03-13 22:55:39.141511 INFO::Set up parallel execution backend with 2 workers
2025-03-13 22:55:39.142905 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-13 22:55:42.333457 INFO::Adjusting the last 2 batches sequentially
2025-03-13 22:55:42.334908 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-13 22:55:42.349407 INFO::Done
2025-03-13 22:55:42.35028 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:42.356055 INFO::ASW Batch was 0.44294168725024 prior to batch effect correction and is now 0.44294168725024 .
2025-03-13 22:55:42.356884 INFO::ASW Label was 0.378450773363845 prior to batch effect correction and is now 0.378450773363845 .
2025-03-13 22:55:42.357838 INFO::Total function execution time is 4.09603905677795 s and adjustment time is 4.05440497398376 s ( 98.98 )
2025-03-13 22:55:45.289645 INFO::Formatting Data.
2025-03-13 22:55:45.291252 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:45.293128 INFO::Removing potential empty rows and columns
2025-03-13 22:55:45.295181 INFO::Found 0 missing values.
2025-03-13 22:55:45.30103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:45.302331 INFO::Done
2025-03-13 22:55:45.303527 INFO::Acquiring quality metrics before batch effect correction.
2025-03-13 22:55:45.308162 INFO::Starting hierarchical adjustment
2025-03-13 22:55:45.309769 INFO::Found 3 batches.
2025-03-13 22:55:45.310953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-13 22:55:45.312249 INFO::Using default BPPARAM
2025-03-13 22:55:45.313299 INFO::Processing subtree level 1
2025-03-13 22:55:48.435084 INFO::Adjusting the last 1 batches sequentially
2025-03-13 22:55:48.437522 INFO::Done
2025-03-13 22:55:48.438911 INFO::Acquiring quality metrics after batch effect correction.
2025-03-13 22:55:48.443213 INFO::ASW Batch was 0.192961917948245 prior to batch effect correction and is now -0.166192492033073 .
2025-03-13 22:55:48.444525 INFO::ASW Label was -0.151359274943537 prior to batch effect correction and is now 0.0294996731025795 .
2025-03-13 22:55:48.445945 INFO::Total function execution time is 3.15643787384033 s and adjustment time is 3.12799906730652 s ( 99.1 )
2025-03-13 22:55:48.647086 INFO::Formatting Data.
2025-03-13 22:55:48.648148 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:48.649334 INFO::Removing potential empty rows and columns
2025-03-13 22:55:48.650592 INFO::Found 2 missing values.
2025-03-13 22:55:48.653274 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:48.654019 INFO::Done
2025-03-13 22:55:48.696737 INFO::Found NA in Reference column
2025-03-13 22:55:48.713777 INFO::Require at least two references per batch.
2025-03-13 22:55:48.743857 INFO::Formatting Data.
2025-03-13 22:55:48.745258 INFO::Recognized SummarizedExperiment
2025-03-13 22:55:48.746592 INFO::Typecasting input to dataframe.
2025-03-13 22:55:48.761654 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:48.764012 INFO::Removing potential empty rows and columns
2025-03-13 22:55:48.769199 INFO::Found 0 missing values.
2025-03-13 22:55:48.775049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:48.775986 INFO::Done
2025-03-13 22:55:48.798296 INFO::Formatting Data.
2025-03-13 22:55:48.799782 INFO::Recognized SummarizedExperiment
2025-03-13 22:55:48.801081 INFO::Typecasting input to dataframe.
2025-03-13 22:55:48.824603 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:48.826927 INFO::Removing potential empty rows and columns
2025-03-13 22:55:48.830195 INFO::Found 0 missing values.
2025-03-13 22:55:48.838697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:48.839607 INFO::Done
2025-03-13 22:55:48.854524 INFO::Formatting Data.
2025-03-13 22:55:48.855484 INFO::Recognized SummarizedExperiment
2025-03-13 22:55:48.856265 INFO::Typecasting input to dataframe.
2025-03-13 22:55:48.873275 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:48.874484 INFO::Removing potential empty rows and columns
2025-03-13 22:55:48.875656 INFO::Found 0 missing values.
2025-03-13 22:55:48.876762 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.
2025-03-13 22:55:48.880558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:48.881296 INFO::Done
2025-03-13 22:55:48.894558 INFO::Formatting Data.
2025-03-13 22:55:48.895554 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:48.896651 INFO::Removing potential empty rows and columns
2025-03-13 22:55:48.897769 INFO::Found 0 missing values.
2025-03-13 22:55:48.900377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:48.901143 INFO::Done
2025-03-13 22:55:48.917359 INFO::Formatting Data.
2025-03-13 22:55:48.918949 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:48.920553 INFO::Removing potential empty rows and columns
2025-03-13 22:55:48.921698 INFO::Found 0 missing values.
2025-03-13 22:55:48.924377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:48.925101 INFO::Done
2025-03-13 22:55:48.960319 INFO::Formatting Data.
2025-03-13 22:55:48.961302 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:48.96249 INFO::Removing potential empty rows and columns
2025-03-13 22:55:48.963711 INFO::Found 1 missing values.
2025-03-13 22:55:48.966074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:48.966839 INFO::Done
2025-03-13 22:55:48.991751 INFO::Formatting Data.
2025-03-13 22:55:48.992738 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:48.993776 INFO::Removing potential empty rows and columns
2025-03-13 22:55:48.99484 INFO::Found 2 missing values.
2025-03-13 22:55:48.9959 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.
2025-03-13 22:55:48.998288 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:48.999425 INFO::Done
2025-03-13 22:55:49.018876 INFO::Formatting Data.
2025-03-13 22:55:49.020419 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:49.022188 INFO::Removing potential empty rows and columns
2025-03-13 22:55:49.023974 INFO::Found 2 missing values.
2025-03-13 22:55:49.02581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:49.026564 INFO::Done
2025-03-13 22:55:49.041572 INFO::Formatting Data.
2025-03-13 22:55:49.042942 INFO::Typecasting input to dataframe.
2025-03-13 22:55:49.04441 INFO::Replacing NaNs with NAs.
2025-03-13 22:55:49.045916 INFO::Removing potential empty rows and columns
2025-03-13 22:55:49.047551 INFO::Found 0 missing values.
2025-03-13 22:55:49.051533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-13 22:55:49.052594 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.54 1.42 76.45
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.64 | 0.69 | 18.72 | |
| compute_asw | 0.05 | 0.00 | 0.05 | |
| count_existing | 0.03 | 0.00 | 0.04 | |
| generate_data_covariables | 0.01 | 0.00 | 0.01 | |
| generate_dataset | 0.02 | 0.01 | 0.03 | |