Yannis Schumann
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:05 -0400 (Mon, 10 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" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| 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: 2025-03-06 20:34:06 -0500 (Thu, 06 Mar 2025) |
| EndedAt: 2025-03-06 20:35:34 -0500 (Thu, 06 Mar 2025) |
| EllapsedTime: 88.1 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 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 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 25.236 1.226 18.282
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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")
2025-03-06 20:34:56.767488 INFO::Formatting Data.
2025-03-06 20:34:56.768694 INFO::Replacing NaNs with NAs.
2025-03-06 20:34:56.779066 INFO::Removing potential empty rows and columns
2025-03-06 20:34:57.06549 INFO::Found 0 missing values.
2025-03-06 20:34:57.068926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:34:57.069487 INFO::Done
2025-03-06 20:34:57.069983 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:34:57.080949 INFO::Starting hierarchical adjustment
2025-03-06 20:34:57.081753 INFO::Found 3 batches.
2025-03-06 20:34:57.082255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:34:57.083362 INFO::Using default BPPARAM
2025-03-06 20:34:57.083896 INFO::Processing subtree level 1
2025-03-06 20:34:57.182784 INFO::Adjusting the last 1 batches sequentially
2025-03-06 20:34:57.184562 INFO::Done
2025-03-06 20:34:57.185234 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:34:57.187773 INFO::ASW Batch was -0.0741407005105284 prior to batch effect correction and is now -0.0741407005105284 .
2025-03-06 20:34:57.188807 INFO::Total function execution time is 0.421883821487427 s and adjustment time is 0.102970838546753 s ( 24.41 )
2025-03-06 20:34:57.202749 INFO::Formatting Data.
2025-03-06 20:34:57.203457 INFO::Replacing NaNs with NAs.
2025-03-06 20:34:57.204329 INFO::Removing potential empty rows and columns
2025-03-06 20:34:57.205358 INFO::Found 0 missing values.
2025-03-06 20:34:57.206278 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.
2025-03-06 20:34:57.216848 INFO::Formatting Data.
2025-03-06 20:34:57.217515 INFO::Replacing NaNs with NAs.
2025-03-06 20:34:57.218379 INFO::Removing potential empty rows and columns
2025-03-06 20:34:57.219375 INFO::Found 0 missing values.
2025-03-06 20:34:57.220273 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.
2025-03-06 20:34:57.23581 INFO::Formatting Data.
2025-03-06 20:34:57.236588 INFO::Replacing NaNs with NAs.
2025-03-06 20:34:57.237491 INFO::Removing potential empty rows and columns
2025-03-06 20:34:57.238523 INFO::Found 0 missing values.
2025-03-06 20:34:57.239463 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.
2025-03-06 20:34:57.243883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:34:57.244388 INFO::Done
2025-03-06 20:34:57.244928 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:34:57.246935 INFO::Starting hierarchical adjustment
2025-03-06 20:34:57.247612 INFO::Found 2 batches.
2025-03-06 20:34:57.248132 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:34:57.24875 INFO::Using default BPPARAM
2025-03-06 20:34:57.249256 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:34:57.250138 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:34:57.272272 INFO::Done
2025-03-06 20:34:57.272963 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:34:57.274904 INFO::ASW Batch was -0.0703783906578838 prior to batch effect correction and is now -0.12676310916118 .
2025-03-06 20:34:57.275671 INFO::Total function execution time is 0.0399396419525146 s and adjustment time is 0.0247786045074463 s ( 62.04 )
2025-03-06 20:34:57.27831 INFO::Formatting Data.
2025-03-06 20:34:57.278979 INFO::Replacing NaNs with NAs.
2025-03-06 20:34:57.287486 INFO::Formatting Data.
2025-03-06 20:34:57.288141 INFO::Replacing NaNs with NAs.
2025-03-06 20:34:57.288978 INFO::Removing potential empty rows and columns
2025-03-06 20:34:57.290039 INFO::Found 0 missing values.
2025-03-06 20:34:57.292793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:34:57.293298 INFO::Done
2025-03-06 20:34:57.29379 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:34:57.295708 INFO::Starting hierarchical adjustment
2025-03-06 20:34:57.296379 INFO::Found 2 batches.
2025-03-06 20:34:57.296894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:34:57.297478 INFO::Using default BPPARAM
2025-03-06 20:34:57.298028 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:34:57.298954 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:34:57.313984 INFO::Done
2025-03-06 20:34:57.31466 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:34:57.316636 INFO::ASW Batch was -0.055041217802036 prior to batch effect correction and is now -0.120536302156956 .
2025-03-06 20:34:57.317417 INFO::Total function execution time is 0.0299556255340576 s and adjustment time is 0.017723560333252 s ( 59.17 )
2025-03-06 20:34:57.318463 INFO::Formatting Data.
2025-03-06 20:34:57.319044 INFO::Replacing NaNs with NAs.
2025-03-06 20:34:57.319855 INFO::Removing potential empty rows and columns
2025-03-06 20:34:57.320856 INFO::Found 0 missing values.
2025-03-06 20:34:57.323627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:34:57.324136 INFO::Done
2025-03-06 20:34:57.324609 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:34:57.326617 INFO::Starting hierarchical adjustment
2025-03-06 20:34:57.327447 INFO::Found 2 batches.
2025-03-06 20:34:57.327951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:34:57.328501 INFO::Using default BPPARAM
2025-03-06 20:34:57.328995 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:34:57.32985 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:34:57.344667 INFO::Done
2025-03-06 20:34:57.345325 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:34:57.347322 INFO::ASW Batch was -0.055041217802036 prior to batch effect correction and is now -0.120536302156956 .
2025-03-06 20:34:57.348119 INFO::Total function execution time is 0.0296614170074463 s and adjustment time is 0.0173239707946777 s ( 58.41 )
2025-03-06 20:35:00.138976 INFO::Formatting Data.
2025-03-06 20:35:00.139772 INFO::Recognized SummarizedExperiment
2025-03-06 20:35:00.140292 INFO::Typecasting input to dataframe.
2025-03-06 20:35:00.195178 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:00.196946 INFO::Removing potential empty rows and columns
2025-03-06 20:35:00.200576 INFO::Found 0 missing values.
2025-03-06 20:35:00.206915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:00.207496 INFO::Done
2025-03-06 20:35:00.207993 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:00.211728 INFO::Starting hierarchical adjustment
2025-03-06 20:35:00.2124 INFO::Found 2 batches.
2025-03-06 20:35:00.212878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:00.214092 INFO::Using default BPPARAM
2025-03-06 20:35:00.214572 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:00.215499 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:00.272243 INFO::Done
2025-03-06 20:35:00.273099 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:00.276672 INFO::ASW Batch was 0.0147942003842911 prior to batch effect correction and is now -0.0944795395430153 .
2025-03-06 20:35:00.277606 INFO::Total function execution time is 0.138909578323364 s and adjustment time is 0.0599074363708496 s ( 43.13 )
2025-03-06 20:35:00.297185 INFO::Formatting Data.
2025-03-06 20:35:00.297924 INFO::Recognized SummarizedExperiment
2025-03-06 20:35:00.298425 INFO::Typecasting input to dataframe.
2025-03-06 20:35:00.308504 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:00.310046 INFO::Removing potential empty rows and columns
2025-03-06 20:35:00.313918 INFO::Found 0 missing values.
2025-03-06 20:35:00.321343 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:00.321994 INFO::Done
2025-03-06 20:35:00.322505 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:00.326234 INFO::Starting hierarchical adjustment
2025-03-06 20:35:00.32695 INFO::Found 2 batches.
2025-03-06 20:35:00.327443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:00.32803 INFO::Using default BPPARAM
2025-03-06 20:35:00.328512 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:00.329514 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:00.354687 INFO::Done
2025-03-06 20:35:00.355333 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:00.358744 INFO::ASW Batch was 7.02960383242978e-08 prior to batch effect correction and is now 7.02960383242978e-08 .
2025-03-06 20:35:00.359539 INFO::Total function execution time is 0.0623512268066406 s and adjustment time is 0.0278606414794922 s ( 44.68 )
2025-03-06 20:35:00.377141 INFO::Formatting Data.
2025-03-06 20:35:00.377896 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:00.37878 INFO::Removing potential empty rows and columns
2025-03-06 20:35:00.379766 INFO::Found 0 missing values.
2025-03-06 20:35:00.382631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:00.383149 INFO::Done
2025-03-06 20:35:00.383867 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:00.385813 INFO::Starting hierarchical adjustment
2025-03-06 20:35:00.386463 INFO::Found 3 batches.
2025-03-06 20:35:00.386966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:00.387517 INFO::Using default BPPARAM
2025-03-06 20:35:00.388011 INFO::Processing subtree level 1
2025-03-06 20:35:00.5173 INFO::Adjusting the last 1 batches sequentially
2025-03-06 20:35:00.519032 INFO::Done
2025-03-06 20:35:00.519638 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:00.521943 INFO::ASW Batch was -0.103855180125969 prior to batch effect correction and is now -0.178255953999808 .
2025-03-06 20:35:00.52281 INFO::Total function execution time is 0.145695209503174 s and adjustment time is 0.132686138153076 s ( 91.07 )
2025-03-06 20:35:00.53669 INFO::Skipping initial DF formatting
2025-03-06 20:35:00.537387 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:00.541314 INFO::Starting hierarchical adjustment
2025-03-06 20:35:00.542064 INFO::Found 5 batches.
2025-03-06 20:35:00.542578 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:00.543179 INFO::Using default BPPARAM
2025-03-06 20:35:00.543703 INFO::Processing subtree level 1
2025-03-06 20:35:00.662951 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:00.664571 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:00.6839 INFO::Done
2025-03-06 20:35:00.684645 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:00.688845 INFO::ASW Batch was 0.490390942077309 prior to batch effect correction and is now 0.490390942077309 .
2025-03-06 20:35:00.689429 INFO::ASW Label was 0.394950135910905 prior to batch effect correction and is now 0.394950135910905 .
2025-03-06 20:35:00.69026 INFO::Total function execution time is 0.153642892837524 s and adjustment time is 0.141953468322754 s ( 92.39 )
2025-03-06 20:35:00.707537 INFO::Formatting Data.
2025-03-06 20:35:00.708319 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:00.709225 INFO::Removing potential empty rows and columns
2025-03-06 20:35:00.710215 INFO::Found 0 missing values.
2025-03-06 20:35:00.714183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:00.714716 INFO::Done
2025-03-06 20:35:00.715206 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:00.718048 INFO::Starting hierarchical adjustment
2025-03-06 20:35:00.71873 INFO::Found 5 batches.
2025-03-06 20:35:00.719244 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:00.719823 INFO::Using default BPPARAM
2025-03-06 20:35:00.720315 INFO::Processing subtree level 1
2025-03-06 20:35:00.82936 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:00.831253 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:00.848332 INFO::Done
2025-03-06 20:35:00.849195 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:00.852662 INFO::ASW Batch was 0.410497347905809 prior to batch effect correction and is now 0.0019450272658264 .
2025-03-06 20:35:00.853323 INFO::ASW Label was 0.397186051036844 prior to batch effect correction and is now 0.788634654891208 .
2025-03-06 20:35:00.854197 INFO::Total function execution time is 0.146706342697144 s and adjustment time is 0.129696607589722 s ( 88.41 )
2025-03-06 20:35:00.855105 INFO::Formatting Data.
2025-03-06 20:35:00.855738 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:00.856629 INFO::Removing potential empty rows and columns
2025-03-06 20:35:00.857643 INFO::Found 0 missing values.
2025-03-06 20:35:00.861745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:00.862282 INFO::Done
2025-03-06 20:35:00.862783 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:00.865874 INFO::Starting hierarchical adjustment
2025-03-06 20:35:00.866559 INFO::Found 5 batches.
2025-03-06 20:35:00.867063 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:00.867643 INFO::Using default BPPARAM
2025-03-06 20:35:00.868152 INFO::Processing subtree level 1
2025-03-06 20:35:00.990842 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:00.992594 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:01.008476 INFO::Done
2025-03-06 20:35:01.009232 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.012488 INFO::ASW Batch was 0.410497347905809 prior to batch effect correction and is now 0.0019450272658264 .
2025-03-06 20:35:01.013082 INFO::ASW Label was 0.397186051036844 prior to batch effect correction and is now 0.788634654891208 .
2025-03-06 20:35:01.013907 INFO::Total function execution time is 0.158820867538452 s and adjustment time is 0.142044305801392 s ( 89.44 )
2025-03-06 20:35:01.027713 INFO::Formatting Data.
2025-03-06 20:35:01.028585 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.029587 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.030669 INFO::Found 0 missing values.
2025-03-06 20:35:01.034927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.035457 INFO::Done
2025-03-06 20:35:01.035962 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.03912 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.039835 INFO::Found 5 batches.
2025-03-06 20:35:01.040331 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.040934 INFO::Using default BPPARAM
2025-03-06 20:35:01.04144 INFO::Processing subtree level 1
2025-03-06 20:35:01.166295 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:01.168174 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:01.18569 INFO::Done
2025-03-06 20:35:01.186535 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.19013 INFO::ASW Batch was 0.469034935640142 prior to batch effect correction and is now -0.0876944910955271 .
2025-03-06 20:35:01.190866 INFO::ASW Label was 0.312627286294639 prior to batch effect correction and is now 0.856944864154607 .
2025-03-06 20:35:01.191783 INFO::Total function execution time is 0.164163112640381 s and adjustment time is 0.145949125289917 s ( 88.9 )
2025-03-06 20:35:01.192713 INFO::Formatting Data.
2025-03-06 20:35:01.193393 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.194355 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.195401 INFO::Found 0 missing values.
2025-03-06 20:35:01.199601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.200145 INFO::Done
2025-03-06 20:35:01.200658 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.20378 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.204491 INFO::Found 5 batches.
2025-03-06 20:35:01.205004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.205596 INFO::Using default BPPARAM
2025-03-06 20:35:01.206124 INFO::Processing subtree level 1
2025-03-06 20:35:01.332494 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:01.33424 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:01.35061 INFO::Done
2025-03-06 20:35:01.351411 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.354776 INFO::ASW Batch was 0.469034935640142 prior to batch effect correction and is now -0.0876944910955271 .
2025-03-06 20:35:01.3554 INFO::ASW Label was 0.312627286294639 prior to batch effect correction and is now 0.856944864154607 .
2025-03-06 20:35:01.357022 INFO::Total function execution time is 0.164204120635986 s and adjustment time is 0.146219730377197 s ( 89.05 )
2025-03-06 20:35:01.371464 INFO::Formatting Data.
2025-03-06 20:35:01.37235 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.373317 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.374367 INFO::Found 0 missing values.
2025-03-06 20:35:01.37718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.377717 INFO::Done
2025-03-06 20:35:01.37821 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.38131 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.382016 INFO::Found 2 batches.
2025-03-06 20:35:01.382517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.383148 INFO::Using default BPPARAM
2025-03-06 20:35:01.383824 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:01.384752 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:01.400561 INFO::Done
2025-03-06 20:35:01.401309 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.40425 INFO::ASW Batch was 0.350975060675701 prior to batch effect correction and is now 0.119310274540696 .
2025-03-06 20:35:01.40485 INFO::ASW Label was 0.724119487936082 prior to batch effect correction and is now 0.876170425171159 .
2025-03-06 20:35:01.405635 INFO::Total function execution time is 0.034306526184082 s and adjustment time is 0.0186660289764404 s ( 54.41 )
2025-03-06 20:35:01.406436 INFO::Formatting Data.
2025-03-06 20:35:01.407064 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.407914 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.408905 INFO::Found 0 missing values.
2025-03-06 20:35:01.411632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.412164 INFO::Done
2025-03-06 20:35:01.412669 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.415584 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.416277 INFO::Found 2 batches.
2025-03-06 20:35:01.416793 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.417379 INFO::Using default BPPARAM
2025-03-06 20:35:01.417892 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:01.418787 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:01.434263 INFO::Done
2025-03-06 20:35:01.434973 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.437994 INFO::ASW Batch was 0.350975060675701 prior to batch effect correction and is now 0.119310274540696 .
2025-03-06 20:35:01.438574 INFO::ASW Label was 0.724119487936082 prior to batch effect correction and is now 0.876170425171159 .
2025-03-06 20:35:01.439355 INFO::Total function execution time is 0.0329442024230957 s and adjustment time is 0.0181009769439697 s ( 54.94 )
2025-03-06 20:35:01.45107 INFO::Formatting Data.
2025-03-06 20:35:01.451838 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.452728 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.453621 INFO::Found 0 missing values.
2025-03-06 20:35:01.455793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.456296 INFO::Done
2025-03-06 20:35:01.456806 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.458798 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.459483 INFO::Found 2 batches.
2025-03-06 20:35:01.460003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.460586 INFO::Using default BPPARAM
2025-03-06 20:35:01.461092 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:01.461985 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:01.494605 INFO::Done
2025-03-06 20:35:01.495334 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.497313 INFO::ASW Batch was -0.107059885617274 prior to batch effect correction and is now -0.159341509111622 .
2025-03-06 20:35:01.498118 INFO::Total function execution time is 0.0471358299255371 s and adjustment time is 0.0352373123168945 s ( 74.76 )
2025-03-06 20:35:01.510315 INFO::Formatting Data.
2025-03-06 20:35:01.511143 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.512066 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.513064 INFO::Found 0 missing values.
2025-03-06 20:35:01.51427 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.
2025-03-06 20:35:01.51894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.519462 INFO::Done
2025-03-06 20:35:01.519968 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.522868 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.52354 INFO::Found 2 batches.
2025-03-06 20:35:01.524055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.524626 INFO::Using default BPPARAM
2025-03-06 20:35:01.525138 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:01.526077 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:01.542974 INFO::Done
2025-03-06 20:35:01.543695 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.546623 INFO::ASW Batch was 0.651719004420494 prior to batch effect correction and is now 0.104418480882259 .
2025-03-06 20:35:01.547203 INFO::ASW Label was 0.465375610795349 prior to batch effect correction and is now 0.841178960067904 .
2025-03-06 20:35:01.547981 INFO::Total function execution time is 0.037783145904541 s and adjustment time is 0.0195508003234863 s ( 51.74 )
2025-03-06 20:35:01.548782 INFO::Formatting Data.
2025-03-06 20:35:01.549395 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.550322 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.55131 INFO::Found 0 missing values.
2025-03-06 20:35:01.552216 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.
2025-03-06 20:35:01.556912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.557445 INFO::Done
2025-03-06 20:35:01.557953 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.560885 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.561567 INFO::Found 2 batches.
2025-03-06 20:35:01.562079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.562641 INFO::Using default BPPARAM
2025-03-06 20:35:01.563147 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:01.56406 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:01.581997 INFO::Done
2025-03-06 20:35:01.582776 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.585871 INFO::ASW Batch was 0.651719004420494 prior to batch effect correction and is now 0.104418480882259 .
2025-03-06 20:35:01.58648 INFO::ASW Label was 0.465375610795349 prior to batch effect correction and is now 0.841178960067904 .
2025-03-06 20:35:01.587299 INFO::Total function execution time is 0.0385403633117676 s and adjustment time is 0.020521879196167 s ( 53.25 )
2025-03-06 20:35:01.848297 INFO::Formatting Data.
2025-03-06 20:35:01.849247 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.850259 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.851382 INFO::Found 0 missing values.
2025-03-06 20:35:01.854599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.85517 INFO::Done
2025-03-06 20:35:01.85573 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.857934 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.85863 INFO::Found 3 batches.
2025-03-06 20:35:01.859149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.859783 INFO::Using default BPPARAM
2025-03-06 20:35:01.860281 INFO::Processing subtree level 1
2025-03-06 20:35:01.973591 INFO::Adjusting the last 1 batches sequentially
2025-03-06 20:35:01.975668 INFO::Done
2025-03-06 20:35:01.976429 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:01.979307 INFO::ASW Batch was -0.0131597926825139 prior to batch effect correction and is now -0.0131597926825139 .
2025-03-06 20:35:01.980368 INFO::Total function execution time is 0.132125854492188 s and adjustment time is 0.117142677307129 s ( 88.66 )
2025-03-06 20:35:01.981594 INFO::Formatting Data.
2025-03-06 20:35:01.982311 INFO::Typecasting input to dataframe.
2025-03-06 20:35:01.983172 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:01.984207 INFO::Removing potential empty rows and columns
2025-03-06 20:35:01.985445 INFO::Found 0 missing values.
2025-03-06 20:35:01.989003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:01.989594 INFO::Done
2025-03-06 20:35:01.990135 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:01.992372 INFO::Starting hierarchical adjustment
2025-03-06 20:35:01.993118 INFO::Found 3 batches.
2025-03-06 20:35:01.993637 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:01.994271 INFO::Using default BPPARAM
2025-03-06 20:35:01.994802 INFO::Processing subtree level 1
2025-03-06 20:35:02.111321 INFO::Adjusting the last 1 batches sequentially
2025-03-06 20:35:02.113364 INFO::Done
2025-03-06 20:35:02.114122 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:02.116802 INFO::ASW Batch was -0.0131597926825139 prior to batch effect correction and is now -0.0131597926825139 .
2025-03-06 20:35:02.117876 INFO::Total function execution time is 0.13627290725708 s and adjustment time is 0.120359420776367 s ( 88.32 )
2025-03-06 20:35:02.132702 INFO::Formatting Data.
2025-03-06 20:35:02.133707 INFO::Typecasting input to dataframe.
2025-03-06 20:35:02.134737 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:02.135861 INFO::Removing potential empty rows and columns
2025-03-06 20:35:02.137227 INFO::Found 0 missing values.
2025-03-06 20:35:02.140791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:02.14144 INFO::Done
2025-03-06 20:35:02.141998 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:02.144407 INFO::Starting hierarchical adjustment
2025-03-06 20:35:02.145286 INFO::Found 3 batches.
2025-03-06 20:35:02.145839 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:02.146486 INFO::Using default BPPARAM
2025-03-06 20:35:02.147024 INFO::Processing subtree level 1
2025-03-06 20:35:02.26935 INFO::Adjusting the last 1 batches sequentially
2025-03-06 20:35:02.271578 INFO::Done
2025-03-06 20:35:02.272386 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:02.275691 INFO::ASW Batch was 0.0357053875931949 prior to batch effect correction and is now 0.0357053875931949 .
2025-03-06 20:35:02.276756 INFO::Total function execution time is 0.144174337387085 s and adjustment time is 0.126399517059326 s ( 87.67 )
2025-03-06 20:35:02.463852 INFO::Formatting Data.
2025-03-06 20:35:02.464897 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:02.466419 INFO::Removing potential empty rows and columns
2025-03-06 20:35:02.469944 INFO::Found 1000 missing values.
2025-03-06 20:35:02.490985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:02.491878 INFO::Done
2025-03-06 20:35:02.492421 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:02.49861 INFO::Starting hierarchical adjustment
2025-03-06 20:35:02.499565 INFO::Found 10 batches.
2025-03-06 20:35:02.500131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:02.500771 INFO::Using default BPPARAM
2025-03-06 20:35:02.501301 INFO::Processing subtree level 1
2025-03-06 20:35:02.687838 INFO::Processing subtree level 2
2025-03-06 20:35:02.881591 INFO::Adjusting the last 1 batches sequentially
2025-03-06 20:35:02.883916 INFO::Done
2025-03-06 20:35:02.884629 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:02.891815 INFO::ASW Batch was 0.495165321631007 prior to batch effect correction and is now 0.495165321631007 .
2025-03-06 20:35:02.892821 INFO::ASW Label was 0.388097196482182 prior to batch effect correction and is now 0.388097196482182 .
2025-03-06 20:35:02.894 INFO::Total function execution time is 0.430271863937378 s and adjustment time is 0.384519577026367 s ( 89.37 )
2025-03-06 20:35:02.894999 INFO::Formatting Data.
2025-03-06 20:35:02.895774 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:02.897358 INFO::Removing potential empty rows and columns
2025-03-06 20:35:02.900572 INFO::Found 1000 missing values.
2025-03-06 20:35:02.921397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:02.922373 INFO::Done
2025-03-06 20:35:02.923007 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:02.929292 INFO::Starting hierarchical adjustment
2025-03-06 20:35:02.930221 INFO::Found 10 batches.
2025-03-06 20:35:04.119282 INFO::Set up parallel execution backend with 2 workers
2025-03-06 20:35:04.122435 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-06 20:35:05.473919 INFO::Adjusting the last 2 batches sequentially
2025-03-06 20:35:05.476424 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-06 20:35:05.493696 INFO::Done
2025-03-06 20:35:05.494492 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:05.499569 INFO::ASW Batch was 0.495165321631007 prior to batch effect correction and is now 0.495165321631007 .
2025-03-06 20:35:05.500197 INFO::ASW Label was 0.388097196482182 prior to batch effect correction and is now 0.388097196482182 .
2025-03-06 20:35:05.501001 INFO::Total function execution time is 2.60605335235596 s and adjustment time is 2.56358861923218 s ( 98.37 )
2025-03-06 20:35:05.662575 INFO::Formatting Data.
2025-03-06 20:35:05.663612 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:05.66472 INFO::Removing potential empty rows and columns
2025-03-06 20:35:05.665943 INFO::Found 0 missing values.
2025-03-06 20:35:05.66997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:05.670542 INFO::Done
2025-03-06 20:35:05.671072 INFO::Acquiring quality metrics before batch effect correction.
2025-03-06 20:35:05.674214 INFO::Starting hierarchical adjustment
2025-03-06 20:35:05.674946 INFO::Found 3 batches.
2025-03-06 20:35:05.675477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-06 20:35:05.676109 INFO::Using default BPPARAM
2025-03-06 20:35:05.676609 INFO::Processing subtree level 1
2025-03-06 20:35:05.801708 INFO::Adjusting the last 1 batches sequentially
2025-03-06 20:35:05.804035 INFO::Done
2025-03-06 20:35:05.804798 INFO::Acquiring quality metrics after batch effect correction.
2025-03-06 20:35:05.808874 INFO::ASW Batch was 0.0862888324005123 prior to batch effect correction and is now -0.154168732875812 .
2025-03-06 20:35:05.809679 INFO::ASW Label was -0.184211198870704 prior to batch effect correction and is now 0.0385691184432784 .
2025-03-06 20:35:05.810848 INFO::Total function execution time is 0.1483473777771 s and adjustment time is 0.129216194152832 s ( 87.1 )
2025-03-06 20:35:05.94307 INFO::Formatting Data.
2025-03-06 20:35:05.944029 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:05.944965 INFO::Removing potential empty rows and columns
2025-03-06 20:35:05.946033 INFO::Found 2 missing values.
2025-03-06 20:35:05.948881 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:05.94941 INFO::Done
2025-03-06 20:35:05.976393 INFO::Found NA in Reference column
2025-03-06 20:35:05.985429 INFO::Require at least two references per batch.
2025-03-06 20:35:06.014963 INFO::Formatting Data.
2025-03-06 20:35:06.015979 INFO::Recognized SummarizedExperiment
2025-03-06 20:35:06.016482 INFO::Typecasting input to dataframe.
2025-03-06 20:35:06.02686 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.02811 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.031595 INFO::Found 0 missing values.
2025-03-06 20:35:06.038245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.038859 INFO::Done
2025-03-06 20:35:06.054623 INFO::Formatting Data.
2025-03-06 20:35:06.055368 INFO::Recognized SummarizedExperiment
2025-03-06 20:35:06.055895 INFO::Typecasting input to dataframe.
2025-03-06 20:35:06.072745 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.073991 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.077405 INFO::Found 0 missing values.
2025-03-06 20:35:06.087997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.088663 INFO::Done
2025-03-06 20:35:06.103637 INFO::Formatting Data.
2025-03-06 20:35:06.104403 INFO::Recognized SummarizedExperiment
2025-03-06 20:35:06.104918 INFO::Typecasting input to dataframe.
2025-03-06 20:35:06.121515 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.122582 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.123698 INFO::Found 0 missing values.
2025-03-06 20:35:06.124593 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.
2025-03-06 20:35:06.12885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.129358 INFO::Done
2025-03-06 20:35:06.138919 INFO::Formatting Data.
2025-03-06 20:35:06.139612 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.14044 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.141377 INFO::Found 0 missing values.
2025-03-06 20:35:06.144295 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.144809 INFO::Done
2025-03-06 20:35:06.155559 INFO::Formatting Data.
2025-03-06 20:35:06.15631 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.157155 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.158129 INFO::Found 0 missing values.
2025-03-06 20:35:06.160918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.161434 INFO::Done
2025-03-06 20:35:06.18901 INFO::Formatting Data.
2025-03-06 20:35:06.18988 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.191002 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.19218 INFO::Found 1 missing values.
2025-03-06 20:35:06.194599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.195101 INFO::Done
2025-03-06 20:35:06.212245 INFO::Formatting Data.
2025-03-06 20:35:06.213041 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.213877 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.214799 INFO::Found 2 missing values.
2025-03-06 20:35:06.215666 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.
2025-03-06 20:35:06.217848 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.218341 INFO::Done
2025-03-06 20:35:06.227676 INFO::Formatting Data.
2025-03-06 20:35:06.228372 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.229227 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.23011 INFO::Found 2 missing values.
2025-03-06 20:35:06.231622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.232122 INFO::Done
2025-03-06 20:35:06.241872 INFO::Formatting Data.
2025-03-06 20:35:06.242548 INFO::Typecasting input to dataframe.
2025-03-06 20:35:06.243312 INFO::Replacing NaNs with NAs.
2025-03-06 20:35:06.244123 INFO::Removing potential empty rows and columns
2025-03-06 20:35:06.245104 INFO::Found 0 missing values.
2025-03-06 20:35:06.247883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-06 20:35:06.248368 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.800 3.840 20.124
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.236 | 1.226 | 18.282 | |
| compute_asw | 0.027 | 0.000 | 0.026 | |
| count_existing | 0.015 | 0.001 | 0.014 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |