Yannis Schumann
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:26 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2024-05-29 19:14:29 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 19:15:53 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 83.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* 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 27.203 1.597 19.633
* 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-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
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")
2024-05-29 19:15:32.230476 INFO::Formatting Data.
2024-05-29 19:15:32.234665 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:32.24984 INFO::Removing potential empty rows and columns
2024-05-29 19:15:32.554197 INFO::Found 0 missing values.
2024-05-29 19:15:32.558182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:32.558841 INFO::Done
2024-05-29 19:15:32.559361 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:32.572969 INFO::Starting hierarchical adjustment
2024-05-29 19:15:32.574142 INFO::Found 3 batches.
2024-05-29 19:15:32.574835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:32.575892 INFO::Using default BPPARAM
2024-05-29 19:15:32.576375 INFO::Processing subtree level 1
2024-05-29 19:15:32.746419 INFO::Adjusting the last 1 batches sequentially
2024-05-29 19:15:32.752353 INFO::Done
2024-05-29 19:15:32.753545 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:32.758291 INFO::ASW Batch was -0.0236836804802654 prior to batch effect correction and is now -0.0236836804802654 .
2024-05-29 19:15:32.759662 INFO::Total function execution time is 0.530833005905151 s and adjustment time is 0.178508043289185 s ( 33.63 )
2024-05-29 19:15:32.782733 INFO::Formatting Data.
2024-05-29 19:15:32.78399 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:32.785195 INFO::Removing potential empty rows and columns
2024-05-29 19:15:32.786298 INFO::Found 0 missing values.
2024-05-29 19:15:32.787238 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.
2024-05-29 19:15:32.799234 INFO::Formatting Data.
2024-05-29 19:15:32.800283 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:32.801725 INFO::Removing potential empty rows and columns
2024-05-29 19:15:32.802734 INFO::Found 0 missing values.
2024-05-29 19:15:32.803938 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.
2024-05-29 19:15:32.82522 INFO::Formatting Data.
2024-05-29 19:15:32.826392 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:32.827729 INFO::Removing potential empty rows and columns
2024-05-29 19:15:32.829229 INFO::Found 0 missing values.
2024-05-29 19:15:32.830446 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.
2024-05-29 19:15:32.835534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:32.836552 INFO::Done
2024-05-29 19:15:32.837379 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:32.840479 INFO::Starting hierarchical adjustment
2024-05-29 19:15:32.841549 INFO::Found 2 batches.
2024-05-29 19:15:32.842333 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:32.843188 INFO::Using default BPPARAM
2024-05-29 19:15:32.843785 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:32.84477 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:32.872568 INFO::Done
2024-05-29 19:15:32.873467 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:32.876485 INFO::ASW Batch was -0.0447036782685148 prior to batch effect correction and is now -0.0990133318214387 .
2024-05-29 19:15:32.877441 INFO::Total function execution time is 0.0523791313171387 s and adjustment time is 0.0312521457672119 s ( 59.67 )
2024-05-29 19:15:32.880204 INFO::Formatting Data.
2024-05-29 19:15:32.880838 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:32.893745 INFO::Formatting Data.
2024-05-29 19:15:32.894626 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:32.895519 INFO::Removing potential empty rows and columns
2024-05-29 19:15:32.896478 INFO::Found 0 missing values.
2024-05-29 19:15:32.899394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:32.900232 INFO::Done
2024-05-29 19:15:32.900835 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:32.903366 INFO::Starting hierarchical adjustment
2024-05-29 19:15:32.904256 INFO::Found 2 batches.
2024-05-29 19:15:32.904904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:32.905526 INFO::Using default BPPARAM
2024-05-29 19:15:32.905988 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:32.906817 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:32.923254 INFO::Done
2024-05-29 19:15:32.924248 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:32.926145 INFO::ASW Batch was 0.00119564159341603 prior to batch effect correction and is now -0.113617699045681 .
2024-05-29 19:15:32.926894 INFO::Total function execution time is 0.0335559844970703 s and adjustment time is 0.0191030502319336 s ( 56.93 )
2024-05-29 19:15:32.927835 INFO::Formatting Data.
2024-05-29 19:15:32.928371 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:32.929165 INFO::Removing potential empty rows and columns
2024-05-29 19:15:32.930098 INFO::Found 0 missing values.
2024-05-29 19:15:32.933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:32.933491 INFO::Done
2024-05-29 19:15:32.933955 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:32.935839 INFO::Starting hierarchical adjustment
2024-05-29 19:15:32.936461 INFO::Found 2 batches.
2024-05-29 19:15:32.936922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:32.93745 INFO::Using default BPPARAM
2024-05-29 19:15:32.937905 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:32.938753 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:32.95522 INFO::Done
2024-05-29 19:15:32.956152 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:32.958995 INFO::ASW Batch was 0.00119564159341603 prior to batch effect correction and is now -0.113617699045681 .
2024-05-29 19:15:32.960114 INFO::Total function execution time is 0.0321919918060303 s and adjustment time is 0.0188069343566895 s ( 58.42 )
2024-05-29 19:15:35.459908 INFO::Formatting Data.
2024-05-29 19:15:35.460786 INFO::Recognized SummarizedExperiment
2024-05-29 19:15:35.461537 INFO::Typecasting input to dataframe.
2024-05-29 19:15:36.262021 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:36.263757 INFO::Removing potential empty rows and columns
2024-05-29 19:15:36.267348 INFO::Found 0 missing values.
2024-05-29 19:15:36.275744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:36.276584 INFO::Done
2024-05-29 19:15:36.277258 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:36.281841 INFO::Starting hierarchical adjustment
2024-05-29 19:15:36.282587 INFO::Found 2 batches.
2024-05-29 19:15:36.283014 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:36.283962 INFO::Using default BPPARAM
2024-05-29 19:15:36.284414 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:36.285382 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:36.347954 INFO::Done
2024-05-29 19:15:36.348791 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:36.352748 INFO::ASW Batch was 0.0043479583398071 prior to batch effect correction and is now -0.093989549356053 .
2024-05-29 19:15:36.353468 INFO::Total function execution time is 0.89398980140686 s and adjustment time is 0.0654239654541016 s ( 7.32 )
2024-05-29 19:15:36.376599 INFO::Formatting Data.
2024-05-29 19:15:36.37752 INFO::Recognized SummarizedExperiment
2024-05-29 19:15:36.378214 INFO::Typecasting input to dataframe.
2024-05-29 19:15:36.388176 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:36.389201 INFO::Removing potential empty rows and columns
2024-05-29 19:15:36.391925 INFO::Found 0 missing values.
2024-05-29 19:15:36.397607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:36.398419 INFO::Done
2024-05-29 19:15:36.399109 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:36.403834 INFO::Starting hierarchical adjustment
2024-05-29 19:15:36.404816 INFO::Found 2 batches.
2024-05-29 19:15:36.405474 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:36.40614 INFO::Using default BPPARAM
2024-05-29 19:15:36.406553 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:36.407373 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:36.431235 INFO::Done
2024-05-29 19:15:36.431809 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:36.43484 INFO::ASW Batch was 0.00629941248248419 prior to batch effect correction and is now 0.00629941248248419 .
2024-05-29 19:15:36.435653 INFO::Total function execution time is 0.0590970516204834 s and adjustment time is 0.0266129970550537 s ( 45.03 )
2024-05-29 19:15:36.456318 INFO::Formatting Data.
2024-05-29 19:15:36.457348 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:36.458827 INFO::Removing potential empty rows and columns
2024-05-29 19:15:36.460199 INFO::Found 0 missing values.
2024-05-29 19:15:36.464105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:36.464868 INFO::Done
2024-05-29 19:15:36.465383 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:36.467572 INFO::Starting hierarchical adjustment
2024-05-29 19:15:36.468436 INFO::Found 3 batches.
2024-05-29 19:15:36.469085 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:36.469826 INFO::Using default BPPARAM
2024-05-29 19:15:36.470465 INFO::Processing subtree level 1
2024-05-29 19:15:36.706324 INFO::Adjusting the last 1 batches sequentially
2024-05-29 19:15:36.71533 INFO::Done
2024-05-29 19:15:36.717615 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:36.725385 INFO::ASW Batch was -0.0732244714359182 prior to batch effect correction and is now -0.144059635592241 .
2024-05-29 19:15:36.727653 INFO::Total function execution time is 0.271270990371704 s and adjustment time is 0.247002124786377 s ( 91.05 )
2024-05-29 19:15:36.7528 INFO::Skipping initial DF formatting
2024-05-29 19:15:36.753497 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:36.759917 INFO::Starting hierarchical adjustment
2024-05-29 19:15:36.760736 INFO::Found 5 batches.
2024-05-29 19:15:36.76154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:36.762514 INFO::Using default BPPARAM
2024-05-29 19:15:36.764076 INFO::Processing subtree level 1
2024-05-29 19:15:36.990982 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:37.003668 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:37.042651 INFO::Done
2024-05-29 19:15:37.043624 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:37.05021 INFO::ASW Batch was 0.559535686262097 prior to batch effect correction and is now 0.559535686262097 .
2024-05-29 19:15:37.05107 INFO::ASW Label was 0.396766883237973 prior to batch effect correction and is now 0.396766883237973 .
2024-05-29 19:15:37.052338 INFO::Total function execution time is 0.29964804649353 s and adjustment time is 0.282031059265137 s ( 94.12 )
2024-05-29 19:15:37.07783 INFO::Formatting Data.
2024-05-29 19:15:37.078542 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:37.079804 INFO::Removing potential empty rows and columns
2024-05-29 19:15:37.081243 INFO::Found 0 missing values.
2024-05-29 19:15:37.086358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:37.087301 INFO::Done
2024-05-29 19:15:37.088033 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:37.090949 INFO::Starting hierarchical adjustment
2024-05-29 19:15:37.091889 INFO::Found 5 batches.
2024-05-29 19:15:37.092716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:37.093663 INFO::Using default BPPARAM
2024-05-29 19:15:37.094144 INFO::Processing subtree level 1
2024-05-29 19:15:37.243697 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:37.280279 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:37.316791 INFO::Done
2024-05-29 19:15:37.318264 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:37.321877 INFO::ASW Batch was 0.265884354043194 prior to batch effect correction and is now -0.0954275453663367 .
2024-05-29 19:15:37.322473 INFO::ASW Label was 0.368744738367899 prior to batch effect correction and is now 0.874278144262525 .
2024-05-29 19:15:37.324469 INFO::Total function execution time is 0.246664047241211 s and adjustment time is 0.225092887878418 s ( 91.25 )
2024-05-29 19:15:37.32591 INFO::Formatting Data.
2024-05-29 19:15:37.327346 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:37.328882 INFO::Removing potential empty rows and columns
2024-05-29 19:15:37.329921 INFO::Found 0 missing values.
2024-05-29 19:15:37.334623 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:37.335459 INFO::Done
2024-05-29 19:15:37.336253 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:37.339736 INFO::Starting hierarchical adjustment
2024-05-29 19:15:37.340406 INFO::Found 5 batches.
2024-05-29 19:15:37.341048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:37.341989 INFO::Using default BPPARAM
2024-05-29 19:15:37.342697 INFO::Processing subtree level 1
2024-05-29 19:15:37.496685 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:37.513351 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:37.545723 INFO::Done
2024-05-29 19:15:37.547348 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:37.552745 INFO::ASW Batch was 0.265884354043194 prior to batch effect correction and is now -0.0954275453663367 .
2024-05-29 19:15:37.553656 INFO::ASW Label was 0.368744738367899 prior to batch effect correction and is now 0.874278144262525 .
2024-05-29 19:15:37.557073 INFO::Total function execution time is 0.231071949005127 s and adjustment time is 0.205399990081787 s ( 88.89 )
2024-05-29 19:15:37.576023 INFO::Formatting Data.
2024-05-29 19:15:37.577171 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:37.578561 INFO::Removing potential empty rows and columns
2024-05-29 19:15:37.579908 INFO::Found 0 missing values.
2024-05-29 19:15:37.584047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:37.584634 INFO::Done
2024-05-29 19:15:37.585136 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:37.589259 INFO::Starting hierarchical adjustment
2024-05-29 19:15:37.590373 INFO::Found 5 batches.
2024-05-29 19:15:37.591142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:37.59213 INFO::Using default BPPARAM
2024-05-29 19:15:37.592705 INFO::Processing subtree level 1
2024-05-29 19:15:37.741739 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:37.756985 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:37.791083 INFO::Done
2024-05-29 19:15:37.79211 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:37.796736 INFO::ASW Batch was 0.222231494867817 prior to batch effect correction and is now -0.0277854731506118 .
2024-05-29 19:15:37.797385 INFO::ASW Label was 0.532122181424074 prior to batch effect correction and is now 0.836475387496078 .
2024-05-29 19:15:37.799527 INFO::Total function execution time is 0.223513841629028 s and adjustment time is 0.200862169265747 s ( 89.87 )
2024-05-29 19:15:37.800752 INFO::Formatting Data.
2024-05-29 19:15:37.801644 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:37.803053 INFO::Removing potential empty rows and columns
2024-05-29 19:15:37.804674 INFO::Found 0 missing values.
2024-05-29 19:15:37.808279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:37.809234 INFO::Done
2024-05-29 19:15:37.809993 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:37.813738 INFO::Starting hierarchical adjustment
2024-05-29 19:15:37.814675 INFO::Found 5 batches.
2024-05-29 19:15:37.81537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:37.816276 INFO::Using default BPPARAM
2024-05-29 19:15:37.817453 INFO::Processing subtree level 1
2024-05-29 19:15:37.972942 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:37.987938 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:38.022872 INFO::Done
2024-05-29 19:15:38.024778 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:38.029579 INFO::ASW Batch was 0.222231494867817 prior to batch effect correction and is now -0.0277854731506118 .
2024-05-29 19:15:38.030251 INFO::ASW Label was 0.532122181424074 prior to batch effect correction and is now 0.836475387496078 .
2024-05-29 19:15:38.032496 INFO::Total function execution time is 0.231642007827759 s and adjustment time is 0.208247900009155 s ( 89.9 )
2024-05-29 19:15:38.055312 INFO::Formatting Data.
2024-05-29 19:15:38.05618 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:38.057131 INFO::Removing potential empty rows and columns
2024-05-29 19:15:38.058111 INFO::Found 0 missing values.
2024-05-29 19:15:38.061691 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:38.062464 INFO::Done
2024-05-29 19:15:38.063167 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:38.067684 INFO::Starting hierarchical adjustment
2024-05-29 19:15:38.068776 INFO::Found 2 batches.
2024-05-29 19:15:38.069548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:38.070434 INFO::Using default BPPARAM
2024-05-29 19:15:38.071155 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:38.072067 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:38.087918 INFO::Done
2024-05-29 19:15:38.088929 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:38.092921 INFO::ASW Batch was 0.770113855328738 prior to batch effect correction and is now 0.113885585122452 .
2024-05-29 19:15:38.093807 INFO::ASW Label was 0.2774593562544 prior to batch effect correction and is now 0.725330187529109 .
2024-05-29 19:15:38.094889 INFO::Total function execution time is 0.0396621227264404 s and adjustment time is 0.0193359851837158 s ( 48.75 )
2024-05-29 19:15:38.095887 INFO::Formatting Data.
2024-05-29 19:15:38.096663 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:38.097812 INFO::Removing potential empty rows and columns
2024-05-29 19:15:38.099109 INFO::Found 0 missing values.
2024-05-29 19:15:38.101875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:38.10235 INFO::Done
2024-05-29 19:15:38.102864 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:38.105464 INFO::Starting hierarchical adjustment
2024-05-29 19:15:38.106093 INFO::Found 2 batches.
2024-05-29 19:15:38.106581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:38.107095 INFO::Using default BPPARAM
2024-05-29 19:15:38.107551 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:38.108374 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:38.125531 INFO::Done
2024-05-29 19:15:38.126558 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:38.13069 INFO::ASW Batch was 0.770113855328738 prior to batch effect correction and is now 0.113885585122452 .
2024-05-29 19:15:38.131528 INFO::ASW Label was 0.2774593562544 prior to batch effect correction and is now 0.725330187529109 .
2024-05-29 19:15:38.132608 INFO::Total function execution time is 0.0366840362548828 s and adjustment time is 0.0194938182830811 s ( 53.14 )
2024-05-29 19:15:38.150527 INFO::Formatting Data.
2024-05-29 19:15:38.151357 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:38.152254 INFO::Removing potential empty rows and columns
2024-05-29 19:15:38.153082 INFO::Found 0 missing values.
2024-05-29 19:15:38.156022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:38.156912 INFO::Done
2024-05-29 19:15:38.157665 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:38.161001 INFO::Starting hierarchical adjustment
2024-05-29 19:15:38.161784 INFO::Found 2 batches.
2024-05-29 19:15:38.162271 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:38.162818 INFO::Using default BPPARAM
2024-05-29 19:15:38.163273 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:38.164116 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:38.199657 INFO::Done
2024-05-29 19:15:38.200621 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:38.202961 INFO::ASW Batch was -0.0503076885466598 prior to batch effect correction and is now -0.0741886460997746 .
2024-05-29 19:15:38.20374 INFO::Total function execution time is 0.0534241199493408 s and adjustment time is 0.0379350185394287 s ( 71.01 )
2024-05-29 19:15:38.220891 INFO::Formatting Data.
2024-05-29 19:15:38.221679 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:38.222889 INFO::Removing potential empty rows and columns
2024-05-29 19:15:38.224203 INFO::Found 0 missing values.
2024-05-29 19:15:38.225705 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.
2024-05-29 19:15:38.231234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:38.231813 INFO::Done
2024-05-29 19:15:38.232321 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:38.236296 INFO::Starting hierarchical adjustment
2024-05-29 19:15:38.237366 INFO::Found 2 batches.
2024-05-29 19:15:38.238121 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:38.238957 INFO::Using default BPPARAM
2024-05-29 19:15:38.239682 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:38.240711 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:38.258741 INFO::Done
2024-05-29 19:15:38.259376 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:38.261982 INFO::ASW Batch was 0.649033292252228 prior to batch effect correction and is now 0.257734273622022 .
2024-05-29 19:15:38.262526 INFO::ASW Label was 0.485505532083486 prior to batch effect correction and is now 0.744451361300655 .
2024-05-29 19:15:38.263228 INFO::Total function execution time is 0.0424320697784424 s and adjustment time is 0.021611213684082 s ( 50.93 )
2024-05-29 19:15:38.263909 INFO::Formatting Data.
2024-05-29 19:15:38.26447 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:38.265276 INFO::Removing potential empty rows and columns
2024-05-29 19:15:38.266124 INFO::Found 0 missing values.
2024-05-29 19:15:38.266939 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.
2024-05-29 19:15:38.270871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:38.271394 INFO::Done
2024-05-29 19:15:38.271953 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:38.276233 INFO::Starting hierarchical adjustment
2024-05-29 19:15:38.276967 INFO::Found 2 batches.
2024-05-29 19:15:38.277438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:38.278415 INFO::Using default BPPARAM
2024-05-29 19:15:38.27927 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:38.280698 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:38.297114 INFO::Done
2024-05-29 19:15:38.297744 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:38.300348 INFO::ASW Batch was 0.649033292252228 prior to batch effect correction and is now 0.257734273622022 .
2024-05-29 19:15:38.300894 INFO::ASW Label was 0.485505532083486 prior to batch effect correction and is now 0.744451361300655 .
2024-05-29 19:15:38.301691 INFO::Total function execution time is 0.0376970767974854 s and adjustment time is 0.0202457904815674 s ( 53.71 )
2024-05-29 19:15:38.567574 INFO::Formatting Data.
2024-05-29 19:15:38.568357 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:38.569204 INFO::Removing potential empty rows and columns
2024-05-29 19:15:38.570289 INFO::Found 0 missing values.
2024-05-29 19:15:38.573466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:38.573963 INFO::Done
2024-05-29 19:15:38.574414 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:38.576213 INFO::Starting hierarchical adjustment
2024-05-29 19:15:38.576817 INFO::Found 3 batches.
2024-05-29 19:15:38.577288 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:38.577802 INFO::Using default BPPARAM
2024-05-29 19:15:38.578344 INFO::Processing subtree level 1
2024-05-29 19:15:38.690198 INFO::Adjusting the last 1 batches sequentially
2024-05-29 19:15:38.707142 INFO::Done
2024-05-29 19:15:38.708514 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:38.718878 INFO::ASW Batch was -0.134869227892353 prior to batch effect correction and is now -0.134869227892353 .
2024-05-29 19:15:38.72321 INFO::Total function execution time is 0.154650926589966 s and adjustment time is 0.130366086959839 s ( 84.3 )
2024-05-29 19:15:38.725003 INFO::Formatting Data.
2024-05-29 19:15:38.726618 INFO::Typecasting input to dataframe.
2024-05-29 19:15:38.728271 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:38.730224 INFO::Removing potential empty rows and columns
2024-05-29 19:15:38.731506 INFO::Found 0 missing values.
2024-05-29 19:15:38.734765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:38.735301 INFO::Done
2024-05-29 19:15:38.73579 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:38.737949 INFO::Starting hierarchical adjustment
2024-05-29 19:15:38.739571 INFO::Found 3 batches.
2024-05-29 19:15:38.740304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:38.741127 INFO::Using default BPPARAM
2024-05-29 19:15:38.742349 INFO::Processing subtree level 1
2024-05-29 19:15:38.864071 INFO::Adjusting the last 1 batches sequentially
2024-05-29 19:15:38.887787 INFO::Done
2024-05-29 19:15:38.890776 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:38.901544 INFO::ASW Batch was -0.134869227892353 prior to batch effect correction and is now -0.134869227892353 .
2024-05-29 19:15:38.905182 INFO::Total function execution time is 0.179525136947632 s and adjustment time is 0.148350954055786 s ( 82.64 )
2024-05-29 19:15:38.932011 INFO::Formatting Data.
2024-05-29 19:15:38.933514 INFO::Typecasting input to dataframe.
2024-05-29 19:15:38.934753 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:38.936598 INFO::Removing potential empty rows and columns
2024-05-29 19:15:38.938912 INFO::Found 0 missing values.
2024-05-29 19:15:38.941956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:38.942491 INFO::Done
2024-05-29 19:15:38.943093 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:38.94495 INFO::Starting hierarchical adjustment
2024-05-29 19:15:38.945582 INFO::Found 3 batches.
2024-05-29 19:15:38.946172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:38.9468 INFO::Using default BPPARAM
2024-05-29 19:15:38.947296 INFO::Processing subtree level 1
2024-05-29 19:15:39.091706 INFO::Adjusting the last 1 batches sequentially
2024-05-29 19:15:39.099935 INFO::Done
2024-05-29 19:15:39.100606 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:39.108897 INFO::ASW Batch was -0.0701759002794632 prior to batch effect correction and is now -0.0701759002794632 .
2024-05-29 19:15:39.11091 INFO::Total function execution time is 0.178963899612427 s and adjustment time is 0.154433965682983 s ( 86.29 )
2024-05-29 19:15:39.349408 INFO::Formatting Data.
2024-05-29 19:15:39.351867 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:39.35361 INFO::Removing potential empty rows and columns
2024-05-29 19:15:39.357955 INFO::Found 1000 missing values.
2024-05-29 19:15:39.380659 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:39.382067 INFO::Done
2024-05-29 19:15:39.382679 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:39.389147 INFO::Starting hierarchical adjustment
2024-05-29 19:15:39.390889 INFO::Found 10 batches.
2024-05-29 19:15:39.391645 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:39.392257 INFO::Using default BPPARAM
2024-05-29 19:15:39.392769 INFO::Processing subtree level 1
2024-05-29 19:15:39.575534 INFO::Processing subtree level 2
2024-05-29 19:15:39.79312 INFO::Adjusting the last 1 batches sequentially
2024-05-29 19:15:39.809039 INFO::Done
2024-05-29 19:15:39.810086 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:39.828083 INFO::ASW Batch was 0.46914463124919 prior to batch effect correction and is now 0.46914463124919 .
2024-05-29 19:15:39.829604 INFO::ASW Label was 0.368447044194847 prior to batch effect correction and is now 0.368447044194847 .
2024-05-29 19:15:39.833807 INFO::Total function execution time is 0.483448028564453 s and adjustment time is 0.418397903442383 s ( 86.54 )
2024-05-29 19:15:39.836131 INFO::Formatting Data.
2024-05-29 19:15:39.838466 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:39.841848 INFO::Removing potential empty rows and columns
2024-05-29 19:15:39.84744 INFO::Found 1000 missing values.
2024-05-29 19:15:39.872893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:39.873888 INFO::Done
2024-05-29 19:15:39.874641 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:39.8826 INFO::Starting hierarchical adjustment
2024-05-29 19:15:39.88379 INFO::Found 10 batches.
2024-05-29 19:15:40.916676 INFO::Set up parallel execution backend with 2 workers
2024-05-29 19:15:40.917712 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-29 19:15:42.279375 INFO::Adjusting the last 2 batches sequentially
2024-05-29 19:15:42.281134 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-29 19:15:42.300086 INFO::Done
2024-05-29 19:15:42.300688 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:42.305409 INFO::ASW Batch was 0.46914463124919 prior to batch effect correction and is now 0.46914463124919 .
2024-05-29 19:15:42.306165 INFO::ASW Label was 0.368447044194847 prior to batch effect correction and is now 0.368447044194847 .
2024-05-29 19:15:42.307145 INFO::Total function execution time is 2.47117018699646 s and adjustment time is 2.41655802726746 s ( 97.79 )
2024-05-29 19:15:42.566255 INFO::Formatting Data.
2024-05-29 19:15:42.56764 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:42.569069 INFO::Removing potential empty rows and columns
2024-05-29 19:15:42.570732 INFO::Found 0 missing values.
2024-05-29 19:15:42.57725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:42.578316 INFO::Done
2024-05-29 19:15:42.579118 INFO::Acquiring quality metrics before batch effect correction.
2024-05-29 19:15:42.582585 INFO::Starting hierarchical adjustment
2024-05-29 19:15:42.584061 INFO::Found 3 batches.
2024-05-29 19:15:42.584908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-29 19:15:42.585853 INFO::Using default BPPARAM
2024-05-29 19:15:42.586381 INFO::Processing subtree level 1
2024-05-29 19:15:42.768735 INFO::Adjusting the last 1 batches sequentially
2024-05-29 19:15:42.780374 INFO::Done
2024-05-29 19:15:42.782449 INFO::Acquiring quality metrics after batch effect correction.
2024-05-29 19:15:42.798562 INFO::ASW Batch was 0.259465113706493 prior to batch effect correction and is now -0.165491658389128 .
2024-05-29 19:15:42.800457 INFO::ASW Label was -0.163776036714807 prior to batch effect correction and is now -0.0129680587145208 .
2024-05-29 19:15:42.805124 INFO::Total function execution time is 0.23822283744812 s and adjustment time is 0.196442127227783 s ( 82.46 )
2024-05-29 19:15:42.995511 INFO::Formatting Data.
2024-05-29 19:15:42.996584 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:42.997601 INFO::Removing potential empty rows and columns
2024-05-29 19:15:42.999103 INFO::Found 2 missing values.
2024-05-29 19:15:43.003969 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.004887 INFO::Done
2024-05-29 19:15:43.047323 INFO::Found NA in Reference column
2024-05-29 19:15:43.064314 INFO::Require at least two references per batch.
2024-05-29 19:15:43.092529 INFO::Formatting Data.
2024-05-29 19:15:43.093257 INFO::Recognized SummarizedExperiment
2024-05-29 19:15:43.093748 INFO::Typecasting input to dataframe.
2024-05-29 19:15:43.10342 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.104598 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.108581 INFO::Found 0 missing values.
2024-05-29 19:15:43.117457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.118435 INFO::Done
2024-05-29 19:15:43.134517 INFO::Formatting Data.
2024-05-29 19:15:43.135548 INFO::Recognized SummarizedExperiment
2024-05-29 19:15:43.136326 INFO::Typecasting input to dataframe.
2024-05-29 19:15:43.159692 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.161408 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.165802 INFO::Found 0 missing values.
2024-05-29 19:15:43.17999 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.181083 INFO::Done
2024-05-29 19:15:43.203291 INFO::Formatting Data.
2024-05-29 19:15:43.204005 INFO::Recognized SummarizedExperiment
2024-05-29 19:15:43.204491 INFO::Typecasting input to dataframe.
2024-05-29 19:15:43.228676 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.230281 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.232105 INFO::Found 0 missing values.
2024-05-29 19:15:43.23386 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.
2024-05-29 19:15:43.239753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.240735 INFO::Done
2024-05-29 19:15:43.258459 INFO::Formatting Data.
2024-05-29 19:15:43.259763 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.260853 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.262061 INFO::Found 0 missing values.
2024-05-29 19:15:43.266101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.266909 INFO::Done
2024-05-29 19:15:43.285896 INFO::Formatting Data.
2024-05-29 19:15:43.28717 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.2885 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.289909 INFO::Found 0 missing values.
2024-05-29 19:15:43.294097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.294791 INFO::Done
2024-05-29 19:15:43.340951 INFO::Formatting Data.
2024-05-29 19:15:43.342199 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.343711 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.345338 INFO::Found 1 missing values.
2024-05-29 19:15:43.349364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.350154 INFO::Done
2024-05-29 19:15:43.380902 INFO::Formatting Data.
2024-05-29 19:15:43.381944 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.38285 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.383721 INFO::Found 2 missing values.
2024-05-29 19:15:43.384549 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.
2024-05-29 19:15:43.388075 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.388905 INFO::Done
2024-05-29 19:15:43.405875 INFO::Formatting Data.
2024-05-29 19:15:43.407045 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.408298 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.409616 INFO::Found 2 missing values.
2024-05-29 19:15:43.411968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.412742 INFO::Done
2024-05-29 19:15:43.431201 INFO::Formatting Data.
2024-05-29 19:15:43.432473 INFO::Typecasting input to dataframe.
2024-05-29 19:15:43.433738 INFO::Replacing NaNs with NAs.
2024-05-29 19:15:43.435084 INFO::Removing potential empty rows and columns
2024-05-29 19:15:43.436358 INFO::Found 0 missing values.
2024-05-29 19:15:43.440328 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-29 19:15:43.440999 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.029 4.050 24.482
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.203 | 1.597 | 19.633 | |
| compute_asw | 0.028 | 0.002 | 0.029 | |
| count_existing | 0.018 | 0.001 | 0.019 | |
| generate_data_covariables | 0.015 | 0.001 | 0.017 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |