Yannis Schumann
| Snapshot Date: 2025-01-23 13:00 -0500 (Thu, 23 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-27 12:10 -0500 (Mon, 27 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4395 |
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-01-24 12:09:35 -0500 (Fri, 24 Jan 2025) |
| EndedAt: 2025-01-24 12:10:43 -0500 (Fri, 24 Jan 2025) |
| EllapsedTime: 68.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* 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 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 26.293 1.152 19.333
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-01-24 12:10:30.486749 INFO::Formatting Data.
2025-01-24 12:10:30.490142 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:30.500669 INFO::Removing potential empty rows and columns
2025-01-24 12:10:30.70498 INFO::Found 0 missing values.
2025-01-24 12:10:30.70621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:30.706422 INFO::Done
2025-01-24 12:10:30.706603 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:30.711975 INFO::Starting hierarchical adjustment
2025-01-24 12:10:30.712398 INFO::Found 3 batches.
2025-01-24 12:10:30.712615 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:30.71306 INFO::Using default BPPARAM
2025-01-24 12:10:30.713246 INFO::Processing subtree level 1
2025-01-24 12:10:30.756109 INFO::Adjusting the last 1 batches sequentially
2025-01-24 12:10:30.757985 INFO::Done
2025-01-24 12:10:30.758221 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:30.759842 INFO::ASW Batch was -0.070715607278782 prior to batch effect correction and is now -0.070715607278782 .
2025-01-24 12:10:30.76038 INFO::Total function execution time is 0.274761915206909 s and adjustment time is 0.0456700325012207 s ( 16.62 )
2025-01-24 12:10:30.766498 INFO::Formatting Data.
2025-01-24 12:10:30.76676 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:30.76708 INFO::Removing potential empty rows and columns
2025-01-24 12:10:30.767465 INFO::Found 0 missing values.
2025-01-24 12:10:30.767771 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-01-24 12:10:30.771808 INFO::Formatting Data.
2025-01-24 12:10:30.772083 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:30.772377 INFO::Removing potential empty rows and columns
2025-01-24 12:10:30.772705 INFO::Found 0 missing values.
2025-01-24 12:10:30.773 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-01-24 12:10:30.778845 INFO::Formatting Data.
2025-01-24 12:10:30.779099 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:30.779386 INFO::Removing potential empty rows and columns
2025-01-24 12:10:30.779831 INFO::Found 0 missing values.
2025-01-24 12:10:30.780125 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-01-24 12:10:30.782002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:30.782302 INFO::Done
2025-01-24 12:10:30.782519 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:30.783417 INFO::Starting hierarchical adjustment
2025-01-24 12:10:30.783707 INFO::Found 2 batches.
2025-01-24 12:10:30.783999 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:30.78428 INFO::Using default BPPARAM
2025-01-24 12:10:30.784457 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:30.784799 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:30.79474 INFO::Done
2025-01-24 12:10:30.79504 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:30.79587 INFO::ASW Batch was -0.00703085145449732 prior to batch effect correction and is now -0.11974578624352 .
2025-01-24 12:10:30.796236 INFO::Total function execution time is 0.0173940658569336 s and adjustment time is 0.0110759735107422 s ( 63.68 )
2025-01-24 12:10:30.797465 INFO::Formatting Data.
2025-01-24 12:10:30.797736 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:30.801527 INFO::Formatting Data.
2025-01-24 12:10:30.801878 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:30.802219 INFO::Removing potential empty rows and columns
2025-01-24 12:10:30.802626 INFO::Found 0 missing values.
2025-01-24 12:10:30.803715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:30.803947 INFO::Done
2025-01-24 12:10:30.804123 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:30.8049 INFO::Starting hierarchical adjustment
2025-01-24 12:10:30.805173 INFO::Found 2 batches.
2025-01-24 12:10:30.805347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:30.805595 INFO::Using default BPPARAM
2025-01-24 12:10:30.805841 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:30.806174 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:30.811693 INFO::Done
2025-01-24 12:10:30.811967 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:30.81271 INFO::ASW Batch was -0.0485048768989238 prior to batch effect correction and is now -0.123405301855536 .
2025-01-24 12:10:30.813001 INFO::Total function execution time is 0.0115420818328857 s and adjustment time is 0.00656294822692871 s ( 56.86 )
2025-01-24 12:10:30.81335 INFO::Formatting Data.
2025-01-24 12:10:30.813526 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:30.81382 INFO::Removing potential empty rows and columns
2025-01-24 12:10:30.81416 INFO::Found 0 missing values.
2025-01-24 12:10:30.815383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:30.815847 INFO::Done
2025-01-24 12:10:30.816375 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:30.818247 INFO::Starting hierarchical adjustment
2025-01-24 12:10:30.818941 INFO::Found 2 batches.
2025-01-24 12:10:30.819402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:30.819933 INFO::Using default BPPARAM
2025-01-24 12:10:30.820372 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:30.821188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:30.834834 INFO::Done
2025-01-24 12:10:30.835439 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:30.837286 INFO::ASW Batch was -0.0485048768989238 prior to batch effect correction and is now -0.123405301855536 .
2025-01-24 12:10:30.838029 INFO::Total function execution time is 0.0245778560638428 s and adjustment time is 0.0160121917724609 s ( 65.15 )
2025-01-24 12:10:32.782154 INFO::Formatting Data.
2025-01-24 12:10:32.782822 INFO::Recognized SummarizedExperiment
2025-01-24 12:10:32.783247 INFO::Typecasting input to dataframe.
2025-01-24 12:10:32.812073 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:32.813071 INFO::Removing potential empty rows and columns
2025-01-24 12:10:32.815947 INFO::Found 0 missing values.
2025-01-24 12:10:32.821901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:32.822466 INFO::Done
2025-01-24 12:10:32.822692 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:32.824608 INFO::Starting hierarchical adjustment
2025-01-24 12:10:32.82526 INFO::Found 2 batches.
2025-01-24 12:10:32.825692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:32.826592 INFO::Using default BPPARAM
2025-01-24 12:10:32.827016 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:32.827841 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:32.873191 INFO::Done
2025-01-24 12:10:32.873752 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:32.876909 INFO::ASW Batch was -0.0210331401963548 prior to batch effect correction and is now -0.0906605535100262 .
2025-01-24 12:10:32.877614 INFO::Total function execution time is 0.095970869064331 s and adjustment time is 0.0480449199676514 s ( 50.06 )
2025-01-24 12:10:32.887227 INFO::Formatting Data.
2025-01-24 12:10:32.887548 INFO::Recognized SummarizedExperiment
2025-01-24 12:10:32.887716 INFO::Typecasting input to dataframe.
2025-01-24 12:10:32.890934 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:32.891341 INFO::Removing potential empty rows and columns
2025-01-24 12:10:32.892529 INFO::Found 0 missing values.
2025-01-24 12:10:32.894839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:32.895056 INFO::Done
2025-01-24 12:10:32.895214 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:32.896495 INFO::Starting hierarchical adjustment
2025-01-24 12:10:32.896732 INFO::Found 2 batches.
2025-01-24 12:10:32.896882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:32.89707 INFO::Using default BPPARAM
2025-01-24 12:10:32.897244 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:32.897542 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:32.915226 INFO::Done
2025-01-24 12:10:32.915808 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:32.91923 INFO::ASW Batch was -0.00408839796438427 prior to batch effect correction and is now -0.00408839796438427 .
2025-01-24 12:10:32.919959 INFO::Total function execution time is 0.0326569080352783 s and adjustment time is 0.0184581279754639 s ( 56.52 )
2025-01-24 12:10:32.936875 INFO::Formatting Data.
2025-01-24 12:10:32.937534 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:32.938646 INFO::Removing potential empty rows and columns
2025-01-24 12:10:32.939662 INFO::Found 0 missing values.
2025-01-24 12:10:32.943445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:32.944026 INFO::Done
2025-01-24 12:10:32.944467 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:32.946202 INFO::Starting hierarchical adjustment
2025-01-24 12:10:32.946841 INFO::Found 3 batches.
2025-01-24 12:10:32.947261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:32.947756 INFO::Using default BPPARAM
2025-01-24 12:10:32.948157 INFO::Processing subtree level 1
2025-01-24 12:10:33.100318 INFO::Adjusting the last 1 batches sequentially
2025-01-24 12:10:33.103611 INFO::Done
2025-01-24 12:10:33.104208 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:33.112296 INFO::ASW Batch was -0.0909524713256237 prior to batch effect correction and is now -0.179608180617678 .
2025-01-24 12:10:33.125278 INFO::Total function execution time is 0.188236951828003 s and adjustment time is 0.156888008117676 s ( 83.35 )
2025-01-24 12:10:33.182436 INFO::Skipping initial DF formatting
2025-01-24 12:10:33.183335 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:33.18792 INFO::Starting hierarchical adjustment
2025-01-24 12:10:33.191415 INFO::Found 5 batches.
2025-01-24 12:10:33.192338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:33.193091 INFO::Using default BPPARAM
2025-01-24 12:10:33.193621 INFO::Processing subtree level 1
2025-01-24 12:10:33.376432 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:33.379968 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:33.406123 INFO::Done
2025-01-24 12:10:33.407096 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:33.414411 INFO::ASW Batch was 0.612174527162705 prior to batch effect correction and is now 0.612174527162705 .
2025-01-24 12:10:33.415219 INFO::ASW Label was 0.331632461844724 prior to batch effect correction and is now 0.331632461844724 .
2025-01-24 12:10:33.416602 INFO::Total function execution time is 0.2342369556427 s and adjustment time is 0.215090036392212 s ( 91.83 )
2025-01-24 12:10:33.447521 INFO::Formatting Data.
2025-01-24 12:10:33.448405 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:33.449336 INFO::Removing potential empty rows and columns
2025-01-24 12:10:33.469013 INFO::Found 0 missing values.
2025-01-24 12:10:33.47874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:33.47963 INFO::Done
2025-01-24 12:10:33.480165 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:33.502649 INFO::Starting hierarchical adjustment
2025-01-24 12:10:33.504528 INFO::Found 5 batches.
2025-01-24 12:10:33.523278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:33.524372 INFO::Using default BPPARAM
2025-01-24 12:10:33.525137 INFO::Processing subtree level 1
2025-01-24 12:10:33.640764 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:33.644064 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:33.66674 INFO::Done
2025-01-24 12:10:33.667639 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:33.671684 INFO::ASW Batch was 0.409033311743506 prior to batch effect correction and is now -0.0287363518630133 .
2025-01-24 12:10:33.672367 INFO::ASW Label was 0.386567342223559 prior to batch effect correction and is now 0.755600892020865 .
2025-01-24 12:10:33.673347 INFO::Total function execution time is 0.2258620262146 s and adjustment time is 0.162693977355957 s ( 72.03 )
2025-01-24 12:10:33.695089 INFO::Formatting Data.
2025-01-24 12:10:33.69701 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:33.698613 INFO::Removing potential empty rows and columns
2025-01-24 12:10:33.699983 INFO::Found 0 missing values.
2025-01-24 12:10:33.703828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:33.704489 INFO::Done
2025-01-24 12:10:33.705003 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:33.70854 INFO::Starting hierarchical adjustment
2025-01-24 12:10:33.709468 INFO::Found 5 batches.
2025-01-24 12:10:33.710006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:33.710936 INFO::Using default BPPARAM
2025-01-24 12:10:33.711564 INFO::Processing subtree level 1
2025-01-24 12:10:33.821763 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:33.824937 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:33.85518 INFO::Done
2025-01-24 12:10:33.856126 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:33.869579 INFO::ASW Batch was 0.409033311743506 prior to batch effect correction and is now -0.0287363518630133 .
2025-01-24 12:10:33.870684 INFO::ASW Label was 0.386567342223559 prior to batch effect correction and is now 0.755600892020865 .
2025-01-24 12:10:33.871822 INFO::Total function execution time is 0.181352138519287 s and adjustment time is 0.145827054977417 s ( 80.41 )
2025-01-24 12:10:33.910627 INFO::Formatting Data.
2025-01-24 12:10:33.9115 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:33.912444 INFO::Removing potential empty rows and columns
2025-01-24 12:10:33.91365 INFO::Found 0 missing values.
2025-01-24 12:10:33.917262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:33.93743 INFO::Done
2025-01-24 12:10:33.94214 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:33.946165 INFO::Starting hierarchical adjustment
2025-01-24 12:10:33.946971 INFO::Found 5 batches.
2025-01-24 12:10:33.94745 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:33.948085 INFO::Using default BPPARAM
2025-01-24 12:10:33.948526 INFO::Processing subtree level 1
2025-01-24 12:10:34.090477 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:34.091868 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:34.099765 INFO::Done
2025-01-24 12:10:34.100084 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.101692 INFO::ASW Batch was 0.400276120134194 prior to batch effect correction and is now -0.0749334482491263 .
2025-01-24 12:10:34.101941 INFO::ASW Label was 0.399354193060774 prior to batch effect correction and is now 0.891745373509579 .
2025-01-24 12:10:34.10232 INFO::Total function execution time is 0.19192099571228 s and adjustment time is 0.153013944625854 s ( 79.73 )
2025-01-24 12:10:34.102625 INFO::Formatting Data.
2025-01-24 12:10:34.10282 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.103128 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.103505 INFO::Found 0 missing values.
2025-01-24 12:10:34.115098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.11698 INFO::Done
2025-01-24 12:10:34.117759 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.120743 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.121481 INFO::Found 5 batches.
2025-01-24 12:10:34.122018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.122619 INFO::Using default BPPARAM
2025-01-24 12:10:34.123137 INFO::Processing subtree level 1
2025-01-24 12:10:34.184727 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:34.185616 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:34.193838 INFO::Done
2025-01-24 12:10:34.194198 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.195659 INFO::ASW Batch was 0.400276120134194 prior to batch effect correction and is now -0.0749334482491263 .
2025-01-24 12:10:34.195879 INFO::ASW Label was 0.399354193060774 prior to batch effect correction and is now 0.891745373509579 .
2025-01-24 12:10:34.196205 INFO::Total function execution time is 0.0935449600219727 s and adjustment time is 0.0715711116790771 s ( 76.51 )
2025-01-24 12:10:34.202107 INFO::Formatting Data.
2025-01-24 12:10:34.202415 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.202772 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.203174 INFO::Found 0 missing values.
2025-01-24 12:10:34.204108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.20434 INFO::Done
2025-01-24 12:10:34.20451 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.205533 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.205818 INFO::Found 2 batches.
2025-01-24 12:10:34.206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.206229 INFO::Using default BPPARAM
2025-01-24 12:10:34.206387 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:34.206752 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:34.217157 INFO::Done
2025-01-24 12:10:34.217459 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.218474 INFO::ASW Batch was 0.296312342872831 prior to batch effect correction and is now 0.0496123782278417 .
2025-01-24 12:10:34.218695 INFO::ASW Label was 0.778292095862846 prior to batch effect correction and is now 0.921341531750531 .
2025-01-24 12:10:34.219052 INFO::Total function execution time is 0.0169918537139893 s and adjustment time is 0.0113749504089355 s ( 66.94 )
2025-01-24 12:10:34.219301 INFO::Formatting Data.
2025-01-24 12:10:34.219481 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.219758 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.220067 INFO::Found 0 missing values.
2025-01-24 12:10:34.220896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.221079 INFO::Done
2025-01-24 12:10:34.221242 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.222155 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.222373 INFO::Found 2 batches.
2025-01-24 12:10:34.222533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.222728 INFO::Using default BPPARAM
2025-01-24 12:10:34.222893 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:34.223201 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:34.228634 INFO::Done
2025-01-24 12:10:34.228938 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.230001 INFO::ASW Batch was 0.296312342872831 prior to batch effect correction and is now 0.0496123782278417 .
2025-01-24 12:10:34.230226 INFO::ASW Label was 0.778292095862846 prior to batch effect correction and is now 0.921341531750531 .
2025-01-24 12:10:34.230498 INFO::Total function execution time is 0.011181116104126 s and adjustment time is 0.00627803802490234 s ( 56.15 )
2025-01-24 12:10:34.234909 INFO::Formatting Data.
2025-01-24 12:10:34.235191 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.235485 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.235806 INFO::Found 0 missing values.
2025-01-24 12:10:34.236484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.236653 INFO::Done
2025-01-24 12:10:34.236811 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.237454 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.237683 INFO::Found 2 batches.
2025-01-24 12:10:34.237848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.238038 INFO::Using default BPPARAM
2025-01-24 12:10:34.238191 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:34.238481 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:34.25022 INFO::Done
2025-01-24 12:10:34.250493 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.251184 INFO::ASW Batch was -0.0793085858664846 prior to batch effect correction and is now -0.176592630363788 .
2025-01-24 12:10:34.251481 INFO::Total function execution time is 0.0166130065917969 s and adjustment time is 0.0125608444213867 s ( 75.61 )
2025-01-24 12:10:34.255962 INFO::Formatting Data.
2025-01-24 12:10:34.256243 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.256553 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.256889 INFO::Found 0 missing values.
2025-01-24 12:10:34.257367 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-01-24 12:10:34.258907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.259115 INFO::Done
2025-01-24 12:10:34.259289 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.260236 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.260449 INFO::Found 2 batches.
2025-01-24 12:10:34.260613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.260797 INFO::Using default BPPARAM
2025-01-24 12:10:34.260938 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:34.261231 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:34.272027 INFO::Done
2025-01-24 12:10:34.272694 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.275383 INFO::ASW Batch was 0.28299256185477 prior to batch effect correction and is now 0.104519869842119 .
2025-01-24 12:10:34.275942 INFO::ASW Label was 0.533556251407029 prior to batch effect correction and is now 0.828970991671703 .
2025-01-24 12:10:34.27662 INFO::Total function execution time is 0.0206060409545898 s and adjustment time is 0.0115430355072021 s ( 56.02 )
2025-01-24 12:10:34.277344 INFO::Formatting Data.
2025-01-24 12:10:34.27785 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.278636 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.279497 INFO::Found 0 missing values.
2025-01-24 12:10:34.280271 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-01-24 12:10:34.28407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.284588 INFO::Done
2025-01-24 12:10:34.285064 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.287658 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.288346 INFO::Found 2 batches.
2025-01-24 12:10:34.28879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.289401 INFO::Using default BPPARAM
2025-01-24 12:10:34.289876 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:34.290719 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:34.308987 INFO::Done
2025-01-24 12:10:34.309641 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.312319 INFO::ASW Batch was 0.28299256185477 prior to batch effect correction and is now 0.104519869842119 .
2025-01-24 12:10:34.312891 INFO::ASW Label was 0.533556251407029 prior to batch effect correction and is now 0.828970991671703 .
2025-01-24 12:10:34.313606 INFO::Total function execution time is 0.0363130569458008 s and adjustment time is 0.0207588672637939 s ( 57.17 )
2025-01-24 12:10:34.537127 INFO::Formatting Data.
2025-01-24 12:10:34.537937 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.538769 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.539813 INFO::Found 0 missing values.
2025-01-24 12:10:34.542538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.54372 INFO::Done
2025-01-24 12:10:34.544594 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.547602 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.548688 INFO::Found 3 batches.
2025-01-24 12:10:34.549255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.549851 INFO::Using default BPPARAM
2025-01-24 12:10:34.550339 INFO::Processing subtree level 1
2025-01-24 12:10:34.690029 INFO::Adjusting the last 1 batches sequentially
2025-01-24 12:10:34.693141 INFO::Done
2025-01-24 12:10:34.693813 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.697207 INFO::ASW Batch was -0.054677569145815 prior to batch effect correction and is now -0.054677569145815 .
2025-01-24 12:10:34.698691 INFO::Total function execution time is 0.161535024642944 s and adjustment time is 0.144639015197754 s ( 89.54 )
2025-01-24 12:10:34.700144 INFO::Formatting Data.
2025-01-24 12:10:34.700796 INFO::Typecasting input to dataframe.
2025-01-24 12:10:34.701567 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.70257 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.703761 INFO::Found 0 missing values.
2025-01-24 12:10:34.70665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.707221 INFO::Done
2025-01-24 12:10:34.707771 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.709908 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.710633 INFO::Found 3 batches.
2025-01-24 12:10:34.711105 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.711744 INFO::Using default BPPARAM
2025-01-24 12:10:34.712192 INFO::Processing subtree level 1
2025-01-24 12:10:34.870251 INFO::Adjusting the last 1 batches sequentially
2025-01-24 12:10:34.876203 INFO::Done
2025-01-24 12:10:34.876947 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:34.882531 INFO::ASW Batch was -0.054677569145815 prior to batch effect correction and is now -0.054677569145815 .
2025-01-24 12:10:34.885209 INFO::Total function execution time is 0.18454098701477 s and adjustment time is 0.165648937225342 s ( 89.76 )
2025-01-24 12:10:34.907362 INFO::Formatting Data.
2025-01-24 12:10:34.908725 INFO::Typecasting input to dataframe.
2025-01-24 12:10:34.909541 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:34.910714 INFO::Removing potential empty rows and columns
2025-01-24 12:10:34.911946 INFO::Found 0 missing values.
2025-01-24 12:10:34.914281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:34.914718 INFO::Done
2025-01-24 12:10:34.915129 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:34.920546 INFO::Starting hierarchical adjustment
2025-01-24 12:10:34.921308 INFO::Found 3 batches.
2025-01-24 12:10:34.921671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:34.922215 INFO::Using default BPPARAM
2025-01-24 12:10:34.923039 INFO::Processing subtree level 1
2025-01-24 12:10:35.096972 INFO::Adjusting the last 1 batches sequentially
2025-01-24 12:10:35.098284 INFO::Done
2025-01-24 12:10:35.098569 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:35.099976 INFO::ASW Batch was -0.0794790272112803 prior to batch effect correction and is now -0.0794790272112803 .
2025-01-24 12:10:35.100535 INFO::Total function execution time is 0.193465948104858 s and adjustment time is 0.177118062973022 s ( 91.55 )
2025-01-24 12:10:35.264166 INFO::Formatting Data.
2025-01-24 12:10:35.264686 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:35.265145 INFO::Removing potential empty rows and columns
2025-01-24 12:10:35.266372 INFO::Found 1000 missing values.
2025-01-24 12:10:35.274927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:35.275263 INFO::Done
2025-01-24 12:10:35.275473 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:35.27772 INFO::Starting hierarchical adjustment
2025-01-24 12:10:35.278033 INFO::Found 10 batches.
2025-01-24 12:10:35.278208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:35.278446 INFO::Using default BPPARAM
2025-01-24 12:10:35.278731 INFO::Processing subtree level 1
2025-01-24 12:10:35.346307 INFO::Processing subtree level 2
2025-01-24 12:10:35.487828 INFO::Adjusting the last 1 batches sequentially
2025-01-24 12:10:35.489456 INFO::Done
2025-01-24 12:10:35.489694 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:35.493072 INFO::ASW Batch was 0.458498102743458 prior to batch effect correction and is now 0.458498102743458 .
2025-01-24 12:10:35.493936 INFO::ASW Label was 0.361774342817905 prior to batch effect correction and is now 0.361774342817905 .
2025-01-24 12:10:35.494319 INFO::Total function execution time is 0.23019003868103 s and adjustment time is 0.211477994918823 s ( 91.87 )
2025-01-24 12:10:35.494616 INFO::Formatting Data.
2025-01-24 12:10:35.494815 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:35.495226 INFO::Removing potential empty rows and columns
2025-01-24 12:10:35.496214 INFO::Found 1000 missing values.
2025-01-24 12:10:35.502424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:35.502715 INFO::Done
2025-01-24 12:10:35.502892 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:35.505357 INFO::Starting hierarchical adjustment
2025-01-24 12:10:35.505721 INFO::Found 10 batches.
2025-01-24 12:10:36.087899 INFO::Set up parallel execution backend with 2 workers
2025-01-24 12:10:36.088583 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-24 12:10:36.839972 INFO::Adjusting the last 2 batches sequentially
2025-01-24 12:10:36.84057 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-24 12:10:36.846642 INFO::Done
2025-01-24 12:10:36.846913 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:36.848953 INFO::ASW Batch was 0.458498102743458 prior to batch effect correction and is now 0.458498102743458 .
2025-01-24 12:10:36.84918 INFO::ASW Label was 0.361774342817905 prior to batch effect correction and is now 0.361774342817905 .
2025-01-24 12:10:36.849436 INFO::Total function execution time is 1.35482311248779 s and adjustment time is 1.34097504615784 s ( 98.98 )
2025-01-24 12:10:36.94658 INFO::Formatting Data.
2025-01-24 12:10:36.946899 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:36.947228 INFO::Removing potential empty rows and columns
2025-01-24 12:10:36.947632 INFO::Found 0 missing values.
2025-01-24 12:10:36.948846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:36.949033 INFO::Done
2025-01-24 12:10:36.94919 INFO::Acquiring quality metrics before batch effect correction.
2025-01-24 12:10:36.950145 INFO::Starting hierarchical adjustment
2025-01-24 12:10:36.950377 INFO::Found 3 batches.
2025-01-24 12:10:36.950534 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-24 12:10:36.950744 INFO::Using default BPPARAM
2025-01-24 12:10:36.950895 INFO::Processing subtree level 1
2025-01-24 12:10:37.010208 INFO::Adjusting the last 1 batches sequentially
2025-01-24 12:10:37.011298 INFO::Done
2025-01-24 12:10:37.011505 INFO::Acquiring quality metrics after batch effect correction.
2025-01-24 12:10:37.013689 INFO::ASW Batch was 0.185654922169878 prior to batch effect correction and is now -0.128033996221014 .
2025-01-24 12:10:37.013929 INFO::ASW Label was -0.165586233351365 prior to batch effect correction and is now -0.00534317184623015 .
2025-01-24 12:10:37.014385 INFO::Total function execution time is 0.067828893661499 s and adjustment time is 0.0609660148620605 s ( 89.88 )
2025-01-24 12:10:37.069553 INFO::Formatting Data.
2025-01-24 12:10:37.069926 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.070285 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.070742 INFO::Found 2 missing values.
2025-01-24 12:10:37.071937 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.072163 INFO::Done
2025-01-24 12:10:37.087663 INFO::Found NA in Reference column
2025-01-24 12:10:37.093174 INFO::Require at least two references per batch.
2025-01-24 12:10:37.115661 INFO::Formatting Data.
2025-01-24 12:10:37.116385 INFO::Recognized SummarizedExperiment
2025-01-24 12:10:37.116866 INFO::Typecasting input to dataframe.
2025-01-24 12:10:37.127388 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.128324 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.129677 INFO::Found 0 missing values.
2025-01-24 12:10:37.132282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.132523 INFO::Done
2025-01-24 12:10:37.138877 INFO::Formatting Data.
2025-01-24 12:10:37.139164 INFO::Recognized SummarizedExperiment
2025-01-24 12:10:37.13935 INFO::Typecasting input to dataframe.
2025-01-24 12:10:37.146055 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.146544 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.148081 INFO::Found 0 missing values.
2025-01-24 12:10:37.153225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.153485 INFO::Done
2025-01-24 12:10:37.159434 INFO::Formatting Data.
2025-01-24 12:10:37.159709 INFO::Recognized SummarizedExperiment
2025-01-24 12:10:37.159891 INFO::Typecasting input to dataframe.
2025-01-24 12:10:37.176424 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.177417 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.178387 INFO::Found 0 missing values.
2025-01-24 12:10:37.17923 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-01-24 12:10:37.183205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.18375 INFO::Done
2025-01-24 12:10:37.19388 INFO::Formatting Data.
2025-01-24 12:10:37.194605 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.19541 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.196356 INFO::Found 0 missing values.
2025-01-24 12:10:37.19885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.199397 INFO::Done
2025-01-24 12:10:37.208362 INFO::Formatting Data.
2025-01-24 12:10:37.208659 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.208938 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.209267 INFO::Found 0 missing values.
2025-01-24 12:10:37.210173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.210339 INFO::Done
2025-01-24 12:10:37.23627 INFO::Formatting Data.
2025-01-24 12:10:37.237005 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.237909 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.238898 INFO::Found 1 missing values.
2025-01-24 12:10:37.241038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.241512 INFO::Done
2025-01-24 12:10:37.257816 INFO::Formatting Data.
2025-01-24 12:10:37.258118 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.258402 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.25871 INFO::Found 2 missing values.
2025-01-24 12:10:37.258995 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-01-24 12:10:37.259714 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.259887 INFO::Done
2025-01-24 12:10:37.263515 INFO::Formatting Data.
2025-01-24 12:10:37.263769 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.264048 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.264343 INFO::Found 2 missing values.
2025-01-24 12:10:37.264899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.265059 INFO::Done
2025-01-24 12:10:37.268861 INFO::Formatting Data.
2025-01-24 12:10:37.269122 INFO::Typecasting input to dataframe.
2025-01-24 12:10:37.269371 INFO::Replacing NaNs with NAs.
2025-01-24 12:10:37.269638 INFO::Removing potential empty rows and columns
2025-01-24 12:10:37.269948 INFO::Found 0 missing values.
2025-01-24 12:10:37.270836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-24 12:10:37.271005 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
13.168 2.445 16.582
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.293 | 1.152 | 19.333 | |
| compute_asw | 0.030 | 0.001 | 0.031 | |
| count_existing | 0.016 | 0.002 | 0.018 | |
| generate_data_covariables | 0.014 | 0.002 | 0.016 | |
| generate_dataset | 0.014 | 0.002 | 0.015 | |