Yannis Schumann
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 10fd252 |
| git_last_commit_date: 2024-11-20 10:26:09 -0500 (Wed, 20 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:42 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 159/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.3 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.3.3 |
| 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_1.3.3.tar.gz |
| StartedAt: 2025-01-10 19:05:28 -0500 (Fri, 10 Jan 2025) |
| EndedAt: 2025-01-10 19:06:50 -0500 (Fri, 10 Jan 2025) |
| EllapsedTime: 82.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BERT.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.3’
* 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 ... WARNING
Undocumented code objects:
‘generate_truncated_dataset’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 26.453 1.431 18.912
* 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: 1 WARNING
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log’
for details.
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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")
2025-01-10 19:06:30.483492 INFO::Formatting Data.
2025-01-10 19:06:30.486539 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:30.501355 INFO::Removing potential empty rows and columns
2025-01-10 19:06:30.789931 INFO::Found 0 missing values.
2025-01-10 19:06:30.793126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:30.794066 INFO::Done
2025-01-10 19:06:30.794856 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:30.809079 INFO::Starting hierarchical adjustment
2025-01-10 19:06:30.810442 INFO::Found 3 batches.
2025-01-10 19:06:30.811237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:30.81276 INFO::Using default BPPARAM
2025-01-10 19:06:30.813584 INFO::Processing subtree level 1
2025-01-10 19:06:30.973258 INFO::Adjusting the last 1 batches sequentially
2025-01-10 19:06:30.977707 INFO::Done
2025-01-10 19:06:30.980168 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:30.987548 INFO::ASW Batch was -0.0808201127312085 prior to batch effect correction and is now -0.0808201127312085 .
2025-01-10 19:06:30.990521 INFO::Total function execution time is 0.506875991821289 s and adjustment time is 0.167593002319336 s ( 33.06 )
2025-01-10 19:06:31.015568 INFO::Formatting Data.
2025-01-10 19:06:31.016712 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:31.018074 INFO::Removing potential empty rows and columns
2025-01-10 19:06:31.019708 INFO::Found 0 missing values.
2025-01-10 19:06:31.020942 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.
2025-01-10 19:06:31.032158 INFO::Formatting Data.
2025-01-10 19:06:31.032955 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:31.033826 INFO::Removing potential empty rows and columns
2025-01-10 19:06:31.034813 INFO::Found 0 missing values.
2025-01-10 19:06:31.035789 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.
2025-01-10 19:06:31.059512 INFO::Formatting Data.
2025-01-10 19:06:31.060603 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:31.061947 INFO::Removing potential empty rows and columns
2025-01-10 19:06:31.063578 INFO::Found 0 missing values.
2025-01-10 19:06:31.064648 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.
2025-01-10 19:06:31.069609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:31.070497 INFO::Done
2025-01-10 19:06:31.071016 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:31.073146 INFO::Starting hierarchical adjustment
2025-01-10 19:06:31.073847 INFO::Found 2 batches.
2025-01-10 19:06:31.074543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:31.075443 INFO::Using default BPPARAM
2025-01-10 19:06:31.076195 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:31.077323 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:31.101892 INFO::Done
2025-01-10 19:06:31.102618 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:31.105022 INFO::ASW Batch was -0.0700927474811727 prior to batch effect correction and is now -0.119808105377159 .
2025-01-10 19:06:31.105828 INFO::Total function execution time is 0.0464670658111572 s and adjustment time is 0.0281469821929932 s ( 60.57 )
2025-01-10 19:06:31.108556 INFO::Formatting Data.
2025-01-10 19:06:31.109191 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:31.11982 INFO::Formatting Data.
2025-01-10 19:06:31.120905 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:31.122338 INFO::Removing potential empty rows and columns
2025-01-10 19:06:31.123869 INFO::Found 0 missing values.
2025-01-10 19:06:31.126526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:31.127084 INFO::Done
2025-01-10 19:06:31.127579 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:31.129759 INFO::Starting hierarchical adjustment
2025-01-10 19:06:31.130437 INFO::Found 2 batches.
2025-01-10 19:06:31.163337 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:31.166476 INFO::Using default BPPARAM
2025-01-10 19:06:31.167299 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:31.168579 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:31.184334 INFO::Done
2025-01-10 19:06:31.184974 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:31.187238 INFO::ASW Batch was -0.0210161815647597 prior to batch effect correction and is now -0.0890163102106993 .
2025-01-10 19:06:31.187981 INFO::Total function execution time is 0.0683269500732422 s and adjustment time is 0.0540080070495605 s ( 79.04 )
2025-01-10 19:06:31.18888 INFO::Formatting Data.
2025-01-10 19:06:31.189365 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:31.190108 INFO::Removing potential empty rows and columns
2025-01-10 19:06:31.191118 INFO::Found 0 missing values.
2025-01-10 19:06:31.193756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:31.194228 INFO::Done
2025-01-10 19:06:31.194664 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:31.196334 INFO::Starting hierarchical adjustment
2025-01-10 19:06:31.196924 INFO::Found 2 batches.
2025-01-10 19:06:31.197358 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:31.197859 INFO::Using default BPPARAM
2025-01-10 19:06:31.19828 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:31.19903 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:31.214967 INFO::Done
2025-01-10 19:06:31.215752 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:31.217693 INFO::ASW Batch was -0.0210161815647597 prior to batch effect correction and is now -0.0890163102106993 .
2025-01-10 19:06:31.218541 INFO::Total function execution time is 0.0295760631561279 s and adjustment time is 0.0181291103363037 s ( 61.3 )
2025-01-10 19:06:34.209911 INFO::Formatting Data.
2025-01-10 19:06:34.210693 INFO::Recognized SummarizedExperiment
2025-01-10 19:06:34.211306 INFO::Typecasting input to dataframe.
2025-01-10 19:06:34.237832 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:34.238979 INFO::Removing potential empty rows and columns
2025-01-10 19:06:34.242763 INFO::Found 0 missing values.
2025-01-10 19:06:34.249371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:34.250091 INFO::Done
2025-01-10 19:06:34.250532 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:34.253672 INFO::Starting hierarchical adjustment
2025-01-10 19:06:34.254661 INFO::Found 2 batches.
2025-01-10 19:06:34.255187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:34.256191 INFO::Using default BPPARAM
2025-01-10 19:06:34.256682 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:34.257833 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:34.312656 INFO::Done
2025-01-10 19:06:34.31333 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:34.316581 INFO::ASW Batch was 0.00678222661515151 prior to batch effect correction and is now -0.0909602293076797 .
2025-01-10 19:06:34.317407 INFO::Total function execution time is 0.107728958129883 s and adjustment time is 0.0582067966461182 s ( 54.03 )
2025-01-10 19:06:34.337611 INFO::Formatting Data.
2025-01-10 19:06:34.338598 INFO::Recognized SummarizedExperiment
2025-01-10 19:06:34.339349 INFO::Typecasting input to dataframe.
2025-01-10 19:06:34.350468 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:34.352149 INFO::Removing potential empty rows and columns
2025-01-10 19:06:34.355724 INFO::Found 0 missing values.
2025-01-10 19:06:34.362079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:34.362755 INFO::Done
2025-01-10 19:06:34.363263 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:34.366445 INFO::Starting hierarchical adjustment
2025-01-10 19:06:34.367138 INFO::Found 2 batches.
2025-01-10 19:06:34.367594 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:34.368105 INFO::Using default BPPARAM
2025-01-10 19:06:34.368558 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:34.369486 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:34.394379 INFO::Done
2025-01-10 19:06:34.39525 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:34.398548 INFO::ASW Batch was 0.0231603574001509 prior to batch effect correction and is now 0.0231603574001509 .
2025-01-10 19:06:34.399369 INFO::Total function execution time is 0.0617938041687012 s and adjustment time is 0.0273280143737793 s ( 44.22 )
2025-01-10 19:06:34.422708 INFO::Formatting Data.
2025-01-10 19:06:34.423814 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:34.424966 INFO::Removing potential empty rows and columns
2025-01-10 19:06:34.425882 INFO::Found 0 missing values.
2025-01-10 19:06:34.428411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:34.429107 INFO::Done
2025-01-10 19:06:34.429659 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:34.43183 INFO::Starting hierarchical adjustment
2025-01-10 19:06:34.432458 INFO::Found 3 batches.
2025-01-10 19:06:34.432913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:34.43342 INFO::Using default BPPARAM
2025-01-10 19:06:34.433859 INFO::Processing subtree level 1
2025-01-10 19:06:34.643631 INFO::Adjusting the last 1 batches sequentially
2025-01-10 19:06:34.64903 INFO::Done
2025-01-10 19:06:34.651243 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:34.656183 INFO::ASW Batch was -0.0734176576245746 prior to batch effect correction and is now -0.146360639198535 .
2025-01-10 19:06:34.657699 INFO::Total function execution time is 0.234837055206299 s and adjustment time is 0.216645002365112 s ( 92.25 )
2025-01-10 19:06:34.68221 INFO::Skipping initial DF formatting
2025-01-10 19:06:34.682915 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:34.68761 INFO::Starting hierarchical adjustment
2025-01-10 19:06:34.688415 INFO::Found 5 batches.
2025-01-10 19:06:34.689941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:34.691029 INFO::Using default BPPARAM
2025-01-10 19:06:34.691539 INFO::Processing subtree level 1
2025-01-10 19:06:34.85353 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:34.858238 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:34.891419 INFO::Done
2025-01-10 19:06:34.892875 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:34.899862 INFO::ASW Batch was 0.489931709995936 prior to batch effect correction and is now 0.489931709995936 .
2025-01-10 19:06:34.900583 INFO::ASW Label was 0.366921044897393 prior to batch effect correction and is now 0.366921044897393 .
2025-01-10 19:06:34.902652 INFO::Total function execution time is 0.220134973526001 s and adjustment time is 0.203081130981445 s ( 92.25 )
2025-01-10 19:06:34.930449 INFO::Formatting Data.
2025-01-10 19:06:34.931218 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:34.932081 INFO::Removing potential empty rows and columns
2025-01-10 19:06:34.933504 INFO::Found 0 missing values.
2025-01-10 19:06:34.938077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:34.939177 INFO::Done
2025-01-10 19:06:34.93991 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:34.942873 INFO::Starting hierarchical adjustment
2025-01-10 19:06:34.94357 INFO::Found 5 batches.
2025-01-10 19:06:34.944063 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:34.944624 INFO::Using default BPPARAM
2025-01-10 19:06:34.945123 INFO::Processing subtree level 1
2025-01-10 19:06:35.084553 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:35.093235 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:35.123251 INFO::Done
2025-01-10 19:06:35.124345 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:35.128786 INFO::ASW Batch was 0.459007402160637 prior to batch effect correction and is now -0.0310186173250357 .
2025-01-10 19:06:35.129456 INFO::ASW Label was 0.294630022138641 prior to batch effect correction and is now 0.805018494297569 .
2025-01-10 19:06:35.13088 INFO::Total function execution time is 0.200191974639893 s and adjustment time is 0.179780006408691 s ( 89.8 )
2025-01-10 19:06:35.131723 INFO::Formatting Data.
2025-01-10 19:06:35.132292 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:35.133106 INFO::Removing potential empty rows and columns
2025-01-10 19:06:35.134834 INFO::Found 0 missing values.
2025-01-10 19:06:35.141775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:35.143402 INFO::Done
2025-01-10 19:06:35.144205 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:35.147728 INFO::Starting hierarchical adjustment
2025-01-10 19:06:35.148583 INFO::Found 5 batches.
2025-01-10 19:06:35.14934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:35.150179 INFO::Using default BPPARAM
2025-01-10 19:06:35.151195 INFO::Processing subtree level 1
2025-01-10 19:06:35.286206 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:35.29347 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:35.328193 INFO::Done
2025-01-10 19:06:35.330567 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:35.337777 INFO::ASW Batch was 0.459007402160637 prior to batch effect correction and is now -0.0310186173250357 .
2025-01-10 19:06:35.338955 INFO::ASW Label was 0.294630022138641 prior to batch effect correction and is now 0.805018494297569 .
2025-01-10 19:06:35.339849 INFO::Total function execution time is 0.208083868026733 s and adjustment time is 0.179810047149658 s ( 86.41 )
2025-01-10 19:06:35.35838 INFO::Formatting Data.
2025-01-10 19:06:35.359109 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:35.359963 INFO::Removing potential empty rows and columns
2025-01-10 19:06:35.361222 INFO::Found 0 missing values.
2025-01-10 19:06:35.36548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:35.36605 INFO::Done
2025-01-10 19:06:35.366563 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:35.369309 INFO::Starting hierarchical adjustment
2025-01-10 19:06:35.369962 INFO::Found 5 batches.
2025-01-10 19:06:35.370432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:35.370995 INFO::Using default BPPARAM
2025-01-10 19:06:35.371683 INFO::Processing subtree level 1
2025-01-10 19:06:35.506411 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:35.51286 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:35.540962 INFO::Done
2025-01-10 19:06:35.54249 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:35.547041 INFO::ASW Batch was 0.391482123156519 prior to batch effect correction and is now -0.105115335862117 .
2025-01-10 19:06:35.54765 INFO::ASW Label was 0.142091432923187 prior to batch effect correction and is now 0.762509107038679 .
2025-01-10 19:06:35.548703 INFO::Total function execution time is 0.190382957458496 s and adjustment time is 0.171049118041992 s ( 89.84 )
2025-01-10 19:06:35.54947 INFO::Formatting Data.
2025-01-10 19:06:35.550002 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:35.550825 INFO::Removing potential empty rows and columns
2025-01-10 19:06:35.552536 INFO::Found 0 missing values.
2025-01-10 19:06:35.556347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:35.556846 INFO::Done
2025-01-10 19:06:35.557314 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:35.559916 INFO::Starting hierarchical adjustment
2025-01-10 19:06:35.560552 INFO::Found 5 batches.
2025-01-10 19:06:35.561004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:35.561553 INFO::Using default BPPARAM
2025-01-10 19:06:35.562222 INFO::Processing subtree level 1
2025-01-10 19:06:35.701308 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:35.709453 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:35.742554 INFO::Done
2025-01-10 19:06:35.744183 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:35.748868 INFO::ASW Batch was 0.391482123156519 prior to batch effect correction and is now -0.105115335862117 .
2025-01-10 19:06:35.749948 INFO::ASW Label was 0.142091432923187 prior to batch effect correction and is now 0.762509107038679 .
2025-01-10 19:06:35.751217 INFO::Total function execution time is 0.201633930206299 s and adjustment time is 0.182084798812866 s ( 90.3 )
2025-01-10 19:06:35.773342 INFO::Formatting Data.
2025-01-10 19:06:35.774479 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:35.775822 INFO::Removing potential empty rows and columns
2025-01-10 19:06:35.778029 INFO::Found 0 missing values.
2025-01-10 19:06:35.780899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:35.78214 INFO::Done
2025-01-10 19:06:35.782624 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:35.785186 INFO::Starting hierarchical adjustment
2025-01-10 19:06:35.785861 INFO::Found 2 batches.
2025-01-10 19:06:35.786477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:35.787014 INFO::Using default BPPARAM
2025-01-10 19:06:35.787477 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:35.788277 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:35.801605 INFO::Done
2025-01-10 19:06:35.802485 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:35.806408 INFO::ASW Batch was 0.533790711512535 prior to batch effect correction and is now 0.134149129105892 .
2025-01-10 19:06:35.807395 INFO::ASW Label was 0.614619487797894 prior to batch effect correction and is now 0.850954548329114 .
2025-01-10 19:06:35.808481 INFO::Total function execution time is 0.0352721214294434 s and adjustment time is 0.0158500671386719 s ( 44.94 )
2025-01-10 19:06:35.809526 INFO::Formatting Data.
2025-01-10 19:06:35.810435 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:35.812016 INFO::Removing potential empty rows and columns
2025-01-10 19:06:35.81351 INFO::Found 0 missing values.
2025-01-10 19:06:35.885793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:35.886832 INFO::Done
2025-01-10 19:06:35.887647 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:35.891942 INFO::Starting hierarchical adjustment
2025-01-10 19:06:35.892672 INFO::Found 2 batches.
2025-01-10 19:06:35.893154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:35.893665 INFO::Using default BPPARAM
2025-01-10 19:06:35.894115 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:35.894918 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:35.912859 INFO::Done
2025-01-10 19:06:35.91366 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:35.916377 INFO::ASW Batch was 0.533790711512535 prior to batch effect correction and is now 0.134149129105892 .
2025-01-10 19:06:35.916994 INFO::ASW Label was 0.614619487797894 prior to batch effect correction and is now 0.850954548329114 .
2025-01-10 19:06:35.917713 INFO::Total function execution time is 0.108250856399536 s and adjustment time is 0.0202920436859131 s ( 18.75 )
2025-01-10 19:06:35.933909 INFO::Formatting Data.
2025-01-10 19:06:35.934735 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:35.935625 INFO::Removing potential empty rows and columns
2025-01-10 19:06:35.936539 INFO::Found 0 missing values.
2025-01-10 19:06:35.938575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:35.939088 INFO::Done
2025-01-10 19:06:35.93958 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:35.941464 INFO::Starting hierarchical adjustment
2025-01-10 19:06:35.942162 INFO::Found 2 batches.
2025-01-10 19:06:35.94268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:35.943266 INFO::Using default BPPARAM
2025-01-10 19:06:35.943778 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:35.944932 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:35.976026 INFO::Done
2025-01-10 19:06:35.976976 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:35.97937 INFO::ASW Batch was -0.124918162497165 prior to batch effect correction and is now -0.148707579911678 .
2025-01-10 19:06:35.980354 INFO::Total function execution time is 0.0464730262756348 s and adjustment time is 0.0339450836181641 s ( 73.04 )
2025-01-10 19:06:35.997902 INFO::Formatting Data.
2025-01-10 19:06:35.99864 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:35.999465 INFO::Removing potential empty rows and columns
2025-01-10 19:06:36.000353 INFO::Found 0 missing values.
2025-01-10 19:06:36.001425 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.
2025-01-10 19:06:36.005642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:36.006169 INFO::Done
2025-01-10 19:06:36.006635 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:36.009132 INFO::Starting hierarchical adjustment
2025-01-10 19:06:36.009748 INFO::Found 2 batches.
2025-01-10 19:06:36.010398 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:36.01125 INFO::Using default BPPARAM
2025-01-10 19:06:36.011741 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:36.01261 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:36.031476 INFO::Done
2025-01-10 19:06:36.032179 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:36.034915 INFO::ASW Batch was 0.314205946524543 prior to batch effect correction and is now 0.063984588215069 .
2025-01-10 19:06:36.035558 INFO::ASW Label was 0.710991780434262 prior to batch effect correction and is now 0.889358689697781 .
2025-01-10 19:06:36.036325 INFO::Total function execution time is 0.0384809970855713 s and adjustment time is 0.0218050479888916 s ( 56.66 )
2025-01-10 19:06:36.037035 INFO::Formatting Data.
2025-01-10 19:06:36.037615 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:36.038546 INFO::Removing potential empty rows and columns
2025-01-10 19:06:36.039434 INFO::Found 0 missing values.
2025-01-10 19:06:36.04026 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.
2025-01-10 19:06:36.044058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:36.044576 INFO::Done
2025-01-10 19:06:36.04503 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:36.048357 INFO::Starting hierarchical adjustment
2025-01-10 19:06:36.049358 INFO::Found 2 batches.
2025-01-10 19:06:36.050081 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:36.050897 INFO::Using default BPPARAM
2025-01-10 19:06:36.0516 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:36.052891 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:36.07323 INFO::Done
2025-01-10 19:06:36.074175 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:36.078182 INFO::ASW Batch was 0.314205946524543 prior to batch effect correction and is now 0.063984588215069 .
2025-01-10 19:06:36.079035 INFO::ASW Label was 0.710991780434262 prior to batch effect correction and is now 0.889358689697781 .
2025-01-10 19:06:36.080101 INFO::Total function execution time is 0.0430190563201904 s and adjustment time is 0.0240190029144287 s ( 55.83 )
2025-01-10 19:06:36.347248 INFO::Formatting Data.
2025-01-10 19:06:36.348084 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:36.348954 INFO::Removing potential empty rows and columns
2025-01-10 19:06:36.35011 INFO::Found 0 missing values.
2025-01-10 19:06:36.354475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:36.35521 INFO::Done
2025-01-10 19:06:36.355728 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:36.357584 INFO::Starting hierarchical adjustment
2025-01-10 19:06:36.358242 INFO::Found 3 batches.
2025-01-10 19:06:36.358711 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:36.359233 INFO::Using default BPPARAM
2025-01-10 19:06:36.359695 INFO::Processing subtree level 1
2025-01-10 19:06:36.520393 INFO::Adjusting the last 1 batches sequentially
2025-01-10 19:06:36.536602 INFO::Done
2025-01-10 19:06:36.53829 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:36.545456 INFO::ASW Batch was -0.0876958894540284 prior to batch effect correction and is now -0.0876958894540284 .
2025-01-10 19:06:36.54816 INFO::Total function execution time is 0.200154066085815 s and adjustment time is 0.178388833999634 s ( 89.13 )
2025-01-10 19:06:36.551152 INFO::Formatting Data.
2025-01-10 19:06:36.552956 INFO::Typecasting input to dataframe.
2025-01-10 19:06:36.554306 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:36.555674 INFO::Removing potential empty rows and columns
2025-01-10 19:06:36.559172 INFO::Found 0 missing values.
2025-01-10 19:06:36.564766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:36.565689 INFO::Done
2025-01-10 19:06:36.566959 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:36.569838 INFO::Starting hierarchical adjustment
2025-01-10 19:06:36.570898 INFO::Found 3 batches.
2025-01-10 19:06:36.571638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:36.572509 INFO::Using default BPPARAM
2025-01-10 19:06:36.573203 INFO::Processing subtree level 1
2025-01-10 19:06:36.717835 INFO::Adjusting the last 1 batches sequentially
2025-01-10 19:06:36.724957 INFO::Done
2025-01-10 19:06:36.727444 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:36.735046 INFO::ASW Batch was -0.0876958894540284 prior to batch effect correction and is now -0.0876958894540284 .
2025-01-10 19:06:36.737705 INFO::Total function execution time is 0.186382055282593 s and adjustment time is 0.154248952865601 s ( 82.76 )
2025-01-10 19:06:36.762447 INFO::Formatting Data.
2025-01-10 19:06:36.763216 INFO::Typecasting input to dataframe.
2025-01-10 19:06:36.763998 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:36.765252 INFO::Removing potential empty rows and columns
2025-01-10 19:06:36.766544 INFO::Found 0 missing values.
2025-01-10 19:06:36.769323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:36.770118 INFO::Done
2025-01-10 19:06:36.770872 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:36.773518 INFO::Starting hierarchical adjustment
2025-01-10 19:06:36.774476 INFO::Found 3 batches.
2025-01-10 19:06:36.774978 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:36.775531 INFO::Using default BPPARAM
2025-01-10 19:06:36.776204 INFO::Processing subtree level 1
2025-01-10 19:06:36.920533 INFO::Adjusting the last 1 batches sequentially
2025-01-10 19:06:36.929845 INFO::Done
2025-01-10 19:06:36.933184 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:36.940627 INFO::ASW Batch was -0.0620204206543705 prior to batch effect correction and is now -0.0620204206543705 .
2025-01-10 19:06:36.945331 INFO::Total function execution time is 0.181818008422852 s and adjustment time is 0.155538082122803 s ( 85.55 )
2025-01-10 19:06:37.200099 INFO::Formatting Data.
2025-01-10 19:06:37.201348 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:37.203241 INFO::Removing potential empty rows and columns
2025-01-10 19:06:37.207277 INFO::Found 1000 missing values.
2025-01-10 19:06:37.227722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:37.228872 INFO::Done
2025-01-10 19:06:37.229696 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:37.2361 INFO::Starting hierarchical adjustment
2025-01-10 19:06:37.236951 INFO::Found 10 batches.
2025-01-10 19:06:37.237515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:37.238378 INFO::Using default BPPARAM
2025-01-10 19:06:37.23907 INFO::Processing subtree level 1
2025-01-10 19:06:37.450885 INFO::Processing subtree level 2
2025-01-10 19:06:37.674898 INFO::Adjusting the last 1 batches sequentially
2025-01-10 19:06:37.684994 INFO::Done
2025-01-10 19:06:37.686447 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:37.697037 INFO::ASW Batch was 0.532629874642415 prior to batch effect correction and is now 0.532629874642415 .
2025-01-10 19:06:37.698225 INFO::ASW Label was 0.29045956669941 prior to batch effect correction and is now 0.29045956669941 .
2025-01-10 19:06:37.702292 INFO::Total function execution time is 0.501772880554199 s and adjustment time is 0.448172807693481 s ( 89.32 )
2025-01-10 19:06:37.704537 INFO::Formatting Data.
2025-01-10 19:06:37.705257 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:37.706441 INFO::Removing potential empty rows and columns
2025-01-10 19:06:37.711293 INFO::Found 1000 missing values.
2025-01-10 19:06:37.730399 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:37.73129 INFO::Done
2025-01-10 19:06:37.731824 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:37.736952 INFO::Starting hierarchical adjustment
2025-01-10 19:06:37.738276 INFO::Found 10 batches.
2025-01-10 19:06:38.750877 INFO::Set up parallel execution backend with 2 workers
2025-01-10 19:06:38.751752 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-10 19:06:39.972294 INFO::Adjusting the last 2 batches sequentially
2025-01-10 19:06:39.973958 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 19:06:39.995791 INFO::Done
2025-01-10 19:06:39.996656 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:40.004936 INFO::ASW Batch was 0.532629874642415 prior to batch effect correction and is now 0.532629874642415 .
2025-01-10 19:06:40.00577 INFO::ASW Label was 0.29045956669941 prior to batch effect correction and is now 0.29045956669941 .
2025-01-10 19:06:40.00673 INFO::Total function execution time is 2.30225586891174 s and adjustment time is 2.25810194015503 s ( 98.08 )
2025-01-10 19:06:40.258126 INFO::Formatting Data.
2025-01-10 19:06:40.259581 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.261293 INFO::Removing potential empty rows and columns
2025-01-10 19:06:40.262757 INFO::Found 0 missing values.
2025-01-10 19:06:40.266654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:40.267228 INFO::Done
2025-01-10 19:06:40.267798 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 19:06:40.270768 INFO::Starting hierarchical adjustment
2025-01-10 19:06:40.271635 INFO::Found 3 batches.
2025-01-10 19:06:40.272102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 19:06:40.272775 INFO::Using default BPPARAM
2025-01-10 19:06:40.273509 INFO::Processing subtree level 1
2025-01-10 19:06:40.436932 INFO::Adjusting the last 1 batches sequentially
2025-01-10 19:06:40.444798 INFO::Done
2025-01-10 19:06:40.447852 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 19:06:40.454236 INFO::ASW Batch was 0.187572947762013 prior to batch effect correction and is now -0.136380306343233 .
2025-01-10 19:06:40.455837 INFO::ASW Label was -0.16531761217287 prior to batch effect correction and is now 0.142029351467257 .
2025-01-10 19:06:40.458997 INFO::Total function execution time is 0.200890064239502 s and adjustment time is 0.173210859298706 s ( 86.22 )
2025-01-10 19:06:40.636179 INFO::Formatting Data.
2025-01-10 19:06:40.636978 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.637859 INFO::Removing potential empty rows and columns
2025-01-10 19:06:40.638815 INFO::Found 2 missing values.
2025-01-10 19:06:40.641264 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:40.64176 INFO::Done
2025-01-10 19:06:40.684809 INFO::Found NA in Reference column
2025-01-10 19:06:40.699133 INFO::Require at least two references per batch.
2025-01-10 19:06:40.726749 INFO::Formatting Data.
2025-01-10 19:06:40.727693 INFO::Recognized SummarizedExperiment
2025-01-10 19:06:40.728728 INFO::Typecasting input to dataframe.
2025-01-10 19:06:40.740298 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.741893 INFO::Removing potential empty rows and columns
2025-01-10 19:06:40.746005 INFO::Found 0 missing values.
2025-01-10 19:06:40.754444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:40.755159 INFO::Done
2025-01-10 19:06:40.773099 INFO::Formatting Data.
2025-01-10 19:06:40.773786 INFO::Recognized SummarizedExperiment
2025-01-10 19:06:40.77427 INFO::Typecasting input to dataframe.
2025-01-10 19:06:40.797985 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.799213 INFO::Removing potential empty rows and columns
2025-01-10 19:06:40.803462 INFO::Found 0 missing values.
2025-01-10 19:06:40.813603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:40.814253 INFO::Done
2025-01-10 19:06:40.834414 INFO::Formatting Data.
2025-01-10 19:06:40.835476 INFO::Recognized SummarizedExperiment
2025-01-10 19:06:40.836289 INFO::Typecasting input to dataframe.
2025-01-10 19:06:40.860221 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.861165 INFO::Removing potential empty rows and columns
2025-01-10 19:06:40.862106 INFO::Found 0 missing values.
2025-01-10 19:06:40.862939 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.
2025-01-10 19:06:40.866983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:40.867521 INFO::Done
2025-01-10 19:06:40.882348 INFO::Formatting Data.
2025-01-10 19:06:40.883625 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.884455 INFO::Removing potential empty rows and columns
2025-01-10 19:06:40.885332 INFO::Found 0 missing values.
2025-01-10 19:06:40.889077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:40.889856 INFO::Done
2025-01-10 19:06:40.906081 INFO::Formatting Data.
2025-01-10 19:06:40.907127 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.908257 INFO::Removing potential empty rows and columns
2025-01-10 19:06:40.909479 INFO::Found 0 missing values.
2025-01-10 19:06:40.91302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:40.913808 INFO::Done
2025-01-10 19:06:40.958885 INFO::Formatting Data.
2025-01-10 19:06:40.960165 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.961871 INFO::Removing potential empty rows and columns
2025-01-10 19:06:40.963796 INFO::Found 1 missing values.
2025-01-10 19:06:40.966944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:40.967821 INFO::Done
2025-01-10 19:06:40.997098 INFO::Formatting Data.
2025-01-10 19:06:40.998078 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:40.999414 INFO::Removing potential empty rows and columns
2025-01-10 19:06:41.000912 INFO::Found 2 missing values.
2025-01-10 19:06:41.002344 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.
2025-01-10 19:06:41.005767 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:41.006527 INFO::Done
2025-01-10 19:06:41.020982 INFO::Formatting Data.
2025-01-10 19:06:41.022495 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:41.024295 INFO::Removing potential empty rows and columns
2025-01-10 19:06:41.026137 INFO::Found 2 missing values.
2025-01-10 19:06:41.028828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:41.029912 INFO::Done
2025-01-10 19:06:41.046382 INFO::Formatting Data.
2025-01-10 19:06:41.047139 INFO::Typecasting input to dataframe.
2025-01-10 19:06:41.047869 INFO::Replacing NaNs with NAs.
2025-01-10 19:06:41.048765 INFO::Removing potential empty rows and columns
2025-01-10 19:06:41.04976 INFO::Found 0 missing values.
2025-01-10 19:06:41.052572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 19:06:41.053102 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
>
> proc.time()
user system elapsed
19.119 3.740 23.338
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.453 | 1.431 | 18.912 | |
| compute_asw | 0.032 | 0.002 | 0.034 | |
| count_existing | 0.014 | 0.002 | 0.015 | |
| generate_data_covariables | 0.01 | 0.00 | 0.01 | |
| generate_dataset | 0.010 | 0.001 | 0.011 | |