Yannis Schumann
| Snapshot Date: 2024-10-09 14:00 -0400 (Wed, 09 Oct 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 2024-10-11 20:41 -0400 (Fri, 11 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
| 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 | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2024-10-10 01:29:36 -0400 (Thu, 10 Oct 2024) |
| EndedAt: 2024-10-10 01:32:17 -0400 (Thu, 10 Oct 2024) |
| EllapsedTime: 160.8 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 4.4.1 (2024-06-14)
* 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 ‘1.0.0’
* 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 46.385 2.837 41.303
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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")
2024-10-10 01:31:38.137748 INFO::Formatting Data.
2024-10-10 01:31:38.145216 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:38.183255 INFO::Removing potential empty rows and columns
2024-10-10 01:31:39.054076 INFO::Found 0 missing values.
2024-10-10 01:31:39.064944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:39.066529 INFO::Done
2024-10-10 01:31:39.067911 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:39.106254 INFO::Starting hierarchical adjustment
2024-10-10 01:31:39.110563 INFO::Found 3 batches.
2024-10-10 01:31:39.112115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:39.115014 INFO::Using default BPPARAM
2024-10-10 01:31:39.116607 INFO::Processing subtree level 1
2024-10-10 01:31:39.423204 INFO::Adjusting the last 1 batches sequentially
2024-10-10 01:31:39.429438 INFO::Done
2024-10-10 01:31:39.4313 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:39.439775 INFO::ASW Batch was -0.0116141935188797 prior to batch effect correction and is now -0.0116141935188797 .
2024-10-10 01:31:39.442888 INFO::Total function execution time is 1.30649709701538 s and adjustment time is 0.319442987442017 s ( 24.45 )
2024-10-10 01:31:39.483574 INFO::Formatting Data.
2024-10-10 01:31:39.485162 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:39.487254 INFO::Removing potential empty rows and columns
2024-10-10 01:31:39.493581 INFO::Found 0 missing values.
2024-10-10 01:31:39.49656 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.
2024-10-10 01:31:39.529183 INFO::Formatting Data.
2024-10-10 01:31:39.53066 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:39.532615 INFO::Removing potential empty rows and columns
2024-10-10 01:31:39.53535 INFO::Found 0 missing values.
2024-10-10 01:31:39.537707 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.
2024-10-10 01:31:39.58488 INFO::Formatting Data.
2024-10-10 01:31:39.586638 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:39.588695 INFO::Removing potential empty rows and columns
2024-10-10 01:31:39.591415 INFO::Found 0 missing values.
2024-10-10 01:31:39.59678 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.
2024-10-10 01:31:39.613672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:39.615059 INFO::Done
2024-10-10 01:31:39.616291 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:39.622028 INFO::Starting hierarchical adjustment
2024-10-10 01:31:39.624104 INFO::Found 2 batches.
2024-10-10 01:31:39.625513 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:39.627151 INFO::Using default BPPARAM
2024-10-10 01:31:39.62936 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:39.632107 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:39.697902 INFO::Done
2024-10-10 01:31:39.69934 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:39.705214 INFO::ASW Batch was 0.00999892385981413 prior to batch effect correction and is now -0.121527804681765 .
2024-10-10 01:31:39.707814 INFO::Total function execution time is 0.123015165328979 s and adjustment time is 0.0742149353027344 s ( 60.33 )
2024-10-10 01:31:39.715571 INFO::Formatting Data.
2024-10-10 01:31:39.717455 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:39.746581 INFO::Formatting Data.
2024-10-10 01:31:39.749703 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:39.752077 INFO::Removing potential empty rows and columns
2024-10-10 01:31:39.755192 INFO::Found 0 missing values.
2024-10-10 01:31:39.767907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:39.769283 INFO::Done
2024-10-10 01:31:39.771332 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:39.776546 INFO::Starting hierarchical adjustment
2024-10-10 01:31:39.778501 INFO::Found 2 batches.
2024-10-10 01:31:39.779813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:39.781479 INFO::Using default BPPARAM
2024-10-10 01:31:39.785931 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:39.788702 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:39.832497 INFO::Done
2024-10-10 01:31:39.833891 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:39.838707 INFO::ASW Batch was -0.010157690322551 prior to batch effect correction and is now -0.0851312206787074 .
2024-10-10 01:31:39.842373 INFO::Total function execution time is 0.095858097076416 s and adjustment time is 0.0544040203094482 s ( 56.75 )
2024-10-10 01:31:39.844983 INFO::Formatting Data.
2024-10-10 01:31:39.846602 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:39.848723 INFO::Removing potential empty rows and columns
2024-10-10 01:31:39.855173 INFO::Found 0 missing values.
2024-10-10 01:31:39.866263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:39.867992 INFO::Done
2024-10-10 01:31:39.869338 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:39.875019 INFO::Starting hierarchical adjustment
2024-10-10 01:31:39.876943 INFO::Found 2 batches.
2024-10-10 01:31:39.878249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:39.879727 INFO::Using default BPPARAM
2024-10-10 01:31:39.880966 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:39.883148 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:39.932179 INFO::Done
2024-10-10 01:31:39.937427 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:39.942601 INFO::ASW Batch was -0.010157690322551 prior to batch effect correction and is now -0.0851312206787074 .
2024-10-10 01:31:39.944678 INFO::Total function execution time is 0.0996711254119873 s and adjustment time is 0.0556120872497559 s ( 55.8 )
2024-10-10 01:31:46.172052 INFO::Formatting Data.
2024-10-10 01:31:46.173678 INFO::Recognized SummarizedExperiment
2024-10-10 01:31:46.179646 INFO::Typecasting input to dataframe.
2024-10-10 01:31:46.264376 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:46.266689 INFO::Removing potential empty rows and columns
2024-10-10 01:31:46.32778 INFO::Found 0 missing values.
2024-10-10 01:31:46.350674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:46.352041 INFO::Done
2024-10-10 01:31:46.35311 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:46.362924 INFO::Starting hierarchical adjustment
2024-10-10 01:31:46.364681 INFO::Found 2 batches.
2024-10-10 01:31:46.365827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:46.370147 INFO::Using default BPPARAM
2024-10-10 01:31:46.371427 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:46.373781 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:46.541252 INFO::Done
2024-10-10 01:31:46.544338 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:46.552333 INFO::ASW Batch was 0.0163477922480576 prior to batch effect correction and is now -0.118249653455066 .
2024-10-10 01:31:46.556356 INFO::Total function execution time is 0.383179903030396 s and adjustment time is 0.176897048950195 s ( 46.17 )
2024-10-10 01:31:46.602778 INFO::Formatting Data.
2024-10-10 01:31:46.604058 INFO::Recognized SummarizedExperiment
2024-10-10 01:31:46.60511 INFO::Typecasting input to dataframe.
2024-10-10 01:31:46.628842 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:46.631326 INFO::Removing potential empty rows and columns
2024-10-10 01:31:46.641586 INFO::Found 0 missing values.
2024-10-10 01:31:46.666915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:46.668263 INFO::Done
2024-10-10 01:31:46.66943 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:46.681294 INFO::Starting hierarchical adjustment
2024-10-10 01:31:46.683083 INFO::Found 2 batches.
2024-10-10 01:31:46.684369 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:46.686428 INFO::Using default BPPARAM
2024-10-10 01:31:46.687632 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:46.689847 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:46.758744 INFO::Done
2024-10-10 01:31:46.76321 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:46.771972 INFO::ASW Batch was -0.00635515875847674 prior to batch effect correction and is now -0.00635515875847674 .
2024-10-10 01:31:46.775277 INFO::Total function execution time is 0.172390937805176 s and adjustment time is 0.0760509967803955 s ( 44.12 )
2024-10-10 01:31:46.823626 INFO::Formatting Data.
2024-10-10 01:31:46.825076 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:46.826845 INFO::Removing potential empty rows and columns
2024-10-10 01:31:46.828953 INFO::Found 0 missing values.
2024-10-10 01:31:46.836818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:46.838358 INFO::Done
2024-10-10 01:31:46.839475 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:46.844818 INFO::Starting hierarchical adjustment
2024-10-10 01:31:46.846678 INFO::Found 3 batches.
2024-10-10 01:31:46.848019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:46.849356 INFO::Using default BPPARAM
2024-10-10 01:31:46.850462 INFO::Processing subtree level 1
2024-10-10 01:31:47.34509 INFO::Adjusting the last 1 batches sequentially
2024-10-10 01:31:47.355375 INFO::Done
2024-10-10 01:31:47.35897 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:47.373905 INFO::ASW Batch was -0.0864295931767436 prior to batch effect correction and is now -0.160098474339047 .
2024-10-10 01:31:47.379146 INFO::Total function execution time is 0.555458068847656 s and adjustment time is 0.509010076522827 s ( 91.64 )
2024-10-10 01:31:47.420083 INFO::Skipping initial DF formatting
2024-10-10 01:31:47.421679 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:47.431979 INFO::Starting hierarchical adjustment
2024-10-10 01:31:47.433975 INFO::Found 5 batches.
2024-10-10 01:31:47.435338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:47.437072 INFO::Using default BPPARAM
2024-10-10 01:31:47.438614 INFO::Processing subtree level 1
2024-10-10 01:31:47.846909 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:47.857341 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:47.939648 INFO::Done
2024-10-10 01:31:47.943561 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:47.964737 INFO::ASW Batch was 0.490759099331246 prior to batch effect correction and is now 0.490759099331246 .
2024-10-10 01:31:47.966913 INFO::ASW Label was 0.39140453527411 prior to batch effect correction and is now 0.39140453527411 .
2024-10-10 01:31:47.97602 INFO::Total function execution time is 0.555941104888916 s and adjustment time is 0.506031036376953 s ( 91.02 )
2024-10-10 01:31:48.032913 INFO::Formatting Data.
2024-10-10 01:31:48.03507 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:48.03879 INFO::Removing potential empty rows and columns
2024-10-10 01:31:48.044297 INFO::Found 0 missing values.
2024-10-10 01:31:48.057079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:48.058591 INFO::Done
2024-10-10 01:31:48.059896 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:48.069031 INFO::Starting hierarchical adjustment
2024-10-10 01:31:48.072477 INFO::Found 5 batches.
2024-10-10 01:31:48.073963 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:48.075713 INFO::Using default BPPARAM
2024-10-10 01:31:48.077173 INFO::Processing subtree level 1
2024-10-10 01:31:48.41557 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:48.43065 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:48.492294 INFO::Done
2024-10-10 01:31:48.49399 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:48.50259 INFO::ASW Batch was 0.318341501908847 prior to batch effect correction and is now -0.0850639356928555 .
2024-10-10 01:31:48.504464 INFO::ASW Label was 0.360636093792482 prior to batch effect correction and is now 0.838968243588525 .
2024-10-10 01:31:48.508157 INFO::Total function execution time is 0.47528600692749 s and adjustment time is 0.420202970504761 s ( 88.41 )
2024-10-10 01:31:48.511159 INFO::Formatting Data.
2024-10-10 01:31:48.513218 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:48.515963 INFO::Removing potential empty rows and columns
2024-10-10 01:31:48.520254 INFO::Found 0 missing values.
2024-10-10 01:31:48.534663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:48.536238 INFO::Done
2024-10-10 01:31:48.537601 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:48.545238 INFO::Starting hierarchical adjustment
2024-10-10 01:31:48.54719 INFO::Found 5 batches.
2024-10-10 01:31:48.548972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:48.550554 INFO::Using default BPPARAM
2024-10-10 01:31:48.552079 INFO::Processing subtree level 1
2024-10-10 01:31:48.883746 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:48.900581 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:48.96333 INFO::Done
2024-10-10 01:31:48.964809 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:48.973673 INFO::ASW Batch was 0.318341501908847 prior to batch effect correction and is now -0.0850639356928555 .
2024-10-10 01:31:48.975223 INFO::ASW Label was 0.360636093792482 prior to batch effect correction and is now 0.838968243588525 .
2024-10-10 01:31:48.97789 INFO::Total function execution time is 0.466248035430908 s and adjustment time is 0.416544914245605 s ( 89.34 )
2024-10-10 01:31:49.023363 INFO::Formatting Data.
2024-10-10 01:31:49.026161 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:49.029114 INFO::Removing potential empty rows and columns
2024-10-10 01:31:49.031941 INFO::Found 0 missing values.
2024-10-10 01:31:49.044595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:49.045975 INFO::Done
2024-10-10 01:31:49.047222 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:49.054398 INFO::Starting hierarchical adjustment
2024-10-10 01:31:49.056352 INFO::Found 5 batches.
2024-10-10 01:31:49.057759 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:49.059417 INFO::Using default BPPARAM
2024-10-10 01:31:49.060934 INFO::Processing subtree level 1
2024-10-10 01:31:49.382055 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:49.3966 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:49.453861 INFO::Done
2024-10-10 01:31:49.455703 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:49.466644 INFO::ASW Batch was 0.265015316898841 prior to batch effect correction and is now -0.0800877748470205 .
2024-10-10 01:31:49.468253 INFO::ASW Label was 0.454794407122781 prior to batch effect correction and is now 0.884151011473014 .
2024-10-10 01:31:49.47059 INFO::Total function execution time is 0.447260141372681 s and adjustment time is 0.397924184799194 s ( 88.97 )
2024-10-10 01:31:49.472847 INFO::Formatting Data.
2024-10-10 01:31:49.474299 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:49.476817 INFO::Removing potential empty rows and columns
2024-10-10 01:31:49.479494 INFO::Found 0 missing values.
2024-10-10 01:31:49.492475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:49.495513 INFO::Done
2024-10-10 01:31:49.497251 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:49.506595 INFO::Starting hierarchical adjustment
2024-10-10 01:31:49.508686 INFO::Found 5 batches.
2024-10-10 01:31:49.510361 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:49.51237 INFO::Using default BPPARAM
2024-10-10 01:31:49.514264 INFO::Processing subtree level 1
2024-10-10 01:31:49.845564 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:49.860375 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:49.922528 INFO::Done
2024-10-10 01:31:49.924188 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:49.933217 INFO::ASW Batch was 0.265015316898841 prior to batch effect correction and is now -0.0800877748470205 .
2024-10-10 01:31:49.934733 INFO::ASW Label was 0.454794407122781 prior to batch effect correction and is now 0.884151011473014 .
2024-10-10 01:31:49.937878 INFO::Total function execution time is 0.464514017105103 s and adjustment time is 0.41425895690918 s ( 89.18 )
2024-10-10 01:31:49.975948 INFO::Formatting Data.
2024-10-10 01:31:49.977709 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:49.980516 INFO::Removing potential empty rows and columns
2024-10-10 01:31:49.984459 INFO::Found 0 missing values.
2024-10-10 01:31:49.992642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:49.994096 INFO::Done
2024-10-10 01:31:49.995403 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:50.007229 INFO::Starting hierarchical adjustment
2024-10-10 01:31:50.009439 INFO::Found 2 batches.
2024-10-10 01:31:50.010809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:50.012565 INFO::Using default BPPARAM
2024-10-10 01:31:50.014251 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:50.01769 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:50.06111 INFO::Done
2024-10-10 01:31:50.062686 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:50.069976 INFO::ASW Batch was 0.307314946392543 prior to batch effect correction and is now 0.00352446198753447 .
2024-10-10 01:31:50.073065 INFO::ASW Label was 0.726157349730437 prior to batch effect correction and is now 0.92173182474184 .
2024-10-10 01:31:50.075033 INFO::Total function execution time is 0.09922194480896 s and adjustment time is 0.0522630214691162 s ( 52.67 )
2024-10-10 01:31:50.077209 INFO::Formatting Data.
2024-10-10 01:31:50.078794 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:50.081076 INFO::Removing potential empty rows and columns
2024-10-10 01:31:50.085368 INFO::Found 0 missing values.
2024-10-10 01:31:50.093925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:50.096656 INFO::Done
2024-10-10 01:31:50.098119 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:50.106393 INFO::Starting hierarchical adjustment
2024-10-10 01:31:50.108249 INFO::Found 2 batches.
2024-10-10 01:31:50.109571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:50.11109 INFO::Using default BPPARAM
2024-10-10 01:31:50.112362 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:50.114822 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:50.162822 INFO::Done
2024-10-10 01:31:50.164457 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:50.203143 INFO::ASW Batch was 0.307314946392543 prior to batch effect correction and is now 0.00352446198753447 .
2024-10-10 01:31:50.204721 INFO::ASW Label was 0.726157349730437 prior to batch effect correction and is now 0.92173182474184 .
2024-10-10 01:31:50.206701 INFO::Total function execution time is 0.129599094390869 s and adjustment time is 0.0549211502075195 s ( 42.38 )
2024-10-10 01:31:50.24592 INFO::Formatting Data.
2024-10-10 01:31:50.247597 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:50.250126 INFO::Removing potential empty rows and columns
2024-10-10 01:31:50.252591 INFO::Found 0 missing values.
2024-10-10 01:31:50.260711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:50.262194 INFO::Done
2024-10-10 01:31:50.263556 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:50.269891 INFO::Starting hierarchical adjustment
2024-10-10 01:31:50.272134 INFO::Found 2 batches.
2024-10-10 01:31:50.274162 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:50.27584 INFO::Using default BPPARAM
2024-10-10 01:31:50.27851 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:50.281188 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:50.396295 INFO::Done
2024-10-10 01:31:50.398154 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:50.405243 INFO::ASW Batch was 0.354772640077304 prior to batch effect correction and is now -0.135579721140036 .
2024-10-10 01:31:50.407533 INFO::Total function execution time is 0.161674022674561 s and adjustment time is 0.124803066253662 s ( 77.19 )
2024-10-10 01:31:50.45037 INFO::Formatting Data.
2024-10-10 01:31:50.452277 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:50.454797 INFO::Removing potential empty rows and columns
2024-10-10 01:31:50.457481 INFO::Found 0 missing values.
2024-10-10 01:31:50.463027 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.
2024-10-10 01:31:50.478559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:50.480207 INFO::Done
2024-10-10 01:31:50.481713 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:50.490207 INFO::Starting hierarchical adjustment
2024-10-10 01:31:50.4922 INFO::Found 2 batches.
2024-10-10 01:31:50.495959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:50.498172 INFO::Using default BPPARAM
2024-10-10 01:31:50.499537 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:50.50202 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:50.555373 INFO::Done
2024-10-10 01:31:50.556823 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:50.565193 INFO::ASW Batch was 0.85492688118268 prior to batch effect correction and is now 0.31007596609233 .
2024-10-10 01:31:50.566809 INFO::ASW Label was 0.109657714665718 prior to batch effect correction and is now 0.348344366020144 .
2024-10-10 01:31:50.568873 INFO::Total function execution time is 0.118633031845093 s and adjustment time is 0.0635941028594971 s ( 53.61 )
2024-10-10 01:31:50.572415 INFO::Formatting Data.
2024-10-10 01:31:50.574518 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:50.577327 INFO::Removing potential empty rows and columns
2024-10-10 01:31:50.580129 INFO::Found 0 missing values.
2024-10-10 01:31:50.582519 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.
2024-10-10 01:31:50.598334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:50.600046 INFO::Done
2024-10-10 01:31:50.601421 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:50.609855 INFO::Starting hierarchical adjustment
2024-10-10 01:31:50.612054 INFO::Found 2 batches.
2024-10-10 01:31:50.615492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:50.617376 INFO::Using default BPPARAM
2024-10-10 01:31:50.618784 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:50.621354 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:50.680554 INFO::Done
2024-10-10 01:31:50.68211 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:50.690612 INFO::ASW Batch was 0.85492688118268 prior to batch effect correction and is now 0.31007596609233 .
2024-10-10 01:31:50.692087 INFO::ASW Label was 0.109657714665718 prior to batch effect correction and is now 0.348344366020144 .
2024-10-10 01:31:50.694149 INFO::Total function execution time is 0.122954845428467 s and adjustment time is 0.0688989162445068 s ( 56.04 )
2024-10-10 01:31:51.397937 INFO::Formatting Data.
2024-10-10 01:31:51.399686 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:51.405515 INFO::Removing potential empty rows and columns
2024-10-10 01:31:51.408271 INFO::Found 0 missing values.
2024-10-10 01:31:51.41815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:51.419628 INFO::Done
2024-10-10 01:31:51.420951 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:51.428066 INFO::Starting hierarchical adjustment
2024-10-10 01:31:51.42997 INFO::Found 3 batches.
2024-10-10 01:31:51.43125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:51.432654 INFO::Using default BPPARAM
2024-10-10 01:31:51.433883 INFO::Processing subtree level 1
2024-10-10 01:31:51.738283 INFO::Adjusting the last 1 batches sequentially
2024-10-10 01:31:51.752779 INFO::Done
2024-10-10 01:31:51.754947 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:51.768682 INFO::ASW Batch was -0.0587984046246769 prior to batch effect correction and is now -0.0587984046246769 .
2024-10-10 01:31:51.771841 INFO::Total function execution time is 0.37394905090332 s and adjustment time is 0.323181867599487 s ( 86.42 )
2024-10-10 01:31:51.774802 INFO::Formatting Data.
2024-10-10 01:31:51.776489 INFO::Typecasting input to dataframe.
2024-10-10 01:31:51.778892 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:51.781459 INFO::Removing potential empty rows and columns
2024-10-10 01:31:51.785939 INFO::Found 0 missing values.
2024-10-10 01:31:51.794812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:51.796533 INFO::Done
2024-10-10 01:31:51.797915 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:51.803351 INFO::Starting hierarchical adjustment
2024-10-10 01:31:51.805346 INFO::Found 3 batches.
2024-10-10 01:31:51.806936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:51.808678 INFO::Using default BPPARAM
2024-10-10 01:31:51.810172 INFO::Processing subtree level 1
2024-10-10 01:31:52.109467 INFO::Adjusting the last 1 batches sequentially
2024-10-10 01:31:52.121016 INFO::Done
2024-10-10 01:31:52.12481 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:52.141025 INFO::ASW Batch was -0.0587984046246769 prior to batch effect correction and is now -0.0587984046246769 .
2024-10-10 01:31:52.145777 INFO::Total function execution time is 0.369971990585327 s and adjustment time is 0.316026926040649 s ( 85.42 )
2024-10-10 01:31:52.185171 INFO::Formatting Data.
2024-10-10 01:31:52.187108 INFO::Typecasting input to dataframe.
2024-10-10 01:31:52.189357 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:52.191779 INFO::Removing potential empty rows and columns
2024-10-10 01:31:52.196286 INFO::Found 0 missing values.
2024-10-10 01:31:52.206415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:52.207994 INFO::Done
2024-10-10 01:31:52.209444 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:52.2145 INFO::Starting hierarchical adjustment
2024-10-10 01:31:52.216476 INFO::Found 3 batches.
2024-10-10 01:31:52.218 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:52.219691 INFO::Using default BPPARAM
2024-10-10 01:31:52.221178 INFO::Processing subtree level 1
2024-10-10 01:31:52.524418 INFO::Adjusting the last 1 batches sequentially
2024-10-10 01:31:52.538015 INFO::Done
2024-10-10 01:31:52.539846 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:52.554425 INFO::ASW Batch was -0.028975388756532 prior to batch effect correction and is now -0.028975388756532 .
2024-10-10 01:31:52.558561 INFO::Total function execution time is 0.373349905014038 s and adjustment time is 0.321902990341187 s ( 86.22 )
2024-10-10 01:31:53.05322 INFO::Formatting Data.
2024-10-10 01:31:53.055009 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:53.057704 INFO::Removing potential empty rows and columns
2024-10-10 01:31:53.066076 INFO::Found 1000 missing values.
2024-10-10 01:31:53.143121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:53.144736 INFO::Done
2024-10-10 01:31:53.146794 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:53.161929 INFO::Starting hierarchical adjustment
2024-10-10 01:31:53.164031 INFO::Found 10 batches.
2024-10-10 01:31:53.16608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:53.167821 INFO::Using default BPPARAM
2024-10-10 01:31:53.169317 INFO::Processing subtree level 1
2024-10-10 01:31:53.715108 INFO::Processing subtree level 2
2024-10-10 01:31:54.406493 INFO::Adjusting the last 1 batches sequentially
2024-10-10 01:31:54.431793 INFO::Done
2024-10-10 01:31:54.434817 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:54.455577 INFO::ASW Batch was 0.5282726694394 prior to batch effect correction and is now 0.5282726694394 .
2024-10-10 01:31:54.457214 INFO::ASW Label was 0.287995531007343 prior to batch effect correction and is now 0.287995531007343 .
2024-10-10 01:31:54.46115 INFO::Total function execution time is 1.40796184539795 s and adjustment time is 1.26821112632751 s ( 90.07 )
2024-10-10 01:31:54.463775 INFO::Formatting Data.
2024-10-10 01:31:54.465427 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:54.468432 INFO::Removing potential empty rows and columns
2024-10-10 01:31:54.477374 INFO::Found 1000 missing values.
2024-10-10 01:31:54.551959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:54.553573 INFO::Done
2024-10-10 01:31:54.555038 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:54.567784 INFO::Starting hierarchical adjustment
2024-10-10 01:31:54.569762 INFO::Found 10 batches.
2024-10-10 01:31:56.070079 INFO::Set up parallel execution backend with 2 workers
2024-10-10 01:31:56.071414 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-10 01:31:58.015957 INFO::Adjusting the last 2 batches sequentially
2024-10-10 01:31:58.018243 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 01:31:58.072509 INFO::Done
2024-10-10 01:31:58.073885 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:58.089222 INFO::ASW Batch was 0.5282726694394 prior to batch effect correction and is now 0.5282726694394 .
2024-10-10 01:31:58.090555 INFO::ASW Label was 0.287995531007343 prior to batch effect correction and is now 0.287995531007343 .
2024-10-10 01:31:58.092243 INFO::Total function execution time is 3.62855792045593 s and adjustment time is 3.5031521320343 s ( 96.54 )
2024-10-10 01:31:58.544082 INFO::Formatting Data.
2024-10-10 01:31:58.545903 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:58.548252 INFO::Removing potential empty rows and columns
2024-10-10 01:31:58.551478 INFO::Found 0 missing values.
2024-10-10 01:31:58.564298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:58.56584 INFO::Done
2024-10-10 01:31:58.568335 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 01:31:58.575685 INFO::Starting hierarchical adjustment
2024-10-10 01:31:58.577696 INFO::Found 3 batches.
2024-10-10 01:31:58.579213 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 01:31:58.580953 INFO::Using default BPPARAM
2024-10-10 01:31:58.58254 INFO::Processing subtree level 1
2024-10-10 01:31:58.912757 INFO::Adjusting the last 1 batches sequentially
2024-10-10 01:31:58.927244 INFO::Done
2024-10-10 01:31:58.928812 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 01:31:58.947051 INFO::ASW Batch was 0.259167447221954 prior to batch effect correction and is now -0.151669910171616 .
2024-10-10 01:31:58.948717 INFO::ASW Label was -0.193993970190338 prior to batch effect correction and is now 0.0350143592374312 .
2024-10-10 01:31:58.952284 INFO::Total function execution time is 0.408208131790161 s and adjustment time is 0.349922895431519 s ( 85.72 )
2024-10-10 01:31:59.335494 INFO::Formatting Data.
2024-10-10 01:31:59.337063 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:59.339864 INFO::Removing potential empty rows and columns
2024-10-10 01:31:59.342652 INFO::Found 2 missing values.
2024-10-10 01:31:59.35307 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:59.354628 INFO::Done
2024-10-10 01:31:59.44728 INFO::Found NA in Reference column
2024-10-10 01:31:59.47854 INFO::Require at least two references per batch.
2024-10-10 01:31:59.552089 INFO::Formatting Data.
2024-10-10 01:31:59.553695 INFO::Recognized SummarizedExperiment
2024-10-10 01:31:59.555851 INFO::Typecasting input to dataframe.
2024-10-10 01:31:59.590792 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:59.593485 INFO::Removing potential empty rows and columns
2024-10-10 01:31:59.605703 INFO::Found 0 missing values.
2024-10-10 01:31:59.631867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:59.634564 INFO::Done
2024-10-10 01:31:59.686052 INFO::Formatting Data.
2024-10-10 01:31:59.687678 INFO::Recognized SummarizedExperiment
2024-10-10 01:31:59.688935 INFO::Typecasting input to dataframe.
2024-10-10 01:31:59.750057 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:59.752713 INFO::Removing potential empty rows and columns
2024-10-10 01:31:59.764944 INFO::Found 0 missing values.
2024-10-10 01:31:59.822813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:59.824446 INFO::Done
2024-10-10 01:31:59.880206 INFO::Formatting Data.
2024-10-10 01:31:59.906443 INFO::Recognized SummarizedExperiment
2024-10-10 01:31:59.908874 INFO::Typecasting input to dataframe.
2024-10-10 01:31:59.96046 INFO::Replacing NaNs with NAs.
2024-10-10 01:31:59.962836 INFO::Removing potential empty rows and columns
2024-10-10 01:31:59.968275 INFO::Found 0 missing values.
2024-10-10 01:31:59.970775 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.
2024-10-10 01:31:59.98601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:31:59.987788 INFO::Done
2024-10-10 01:32:00.020095 INFO::Formatting Data.
2024-10-10 01:32:00.021822 INFO::Replacing NaNs with NAs.
2024-10-10 01:32:00.023823 INFO::Removing potential empty rows and columns
2024-10-10 01:32:00.027053 INFO::Found 0 missing values.
2024-10-10 01:32:00.035337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:32:00.037019 INFO::Done
2024-10-10 01:32:00.077674 INFO::Formatting Data.
2024-10-10 01:32:00.082049 INFO::Replacing NaNs with NAs.
2024-10-10 01:32:00.084593 INFO::Removing potential empty rows and columns
2024-10-10 01:32:00.087587 INFO::Found 0 missing values.
2024-10-10 01:32:00.101387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:32:00.103093 INFO::Done
2024-10-10 01:32:00.206253 INFO::Formatting Data.
2024-10-10 01:32:00.207963 INFO::Replacing NaNs with NAs.
2024-10-10 01:32:00.210496 INFO::Removing potential empty rows and columns
2024-10-10 01:32:00.214778 INFO::Found 1 missing values.
2024-10-10 01:32:00.224313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:32:00.225862 INFO::Done
2024-10-10 01:32:00.29471 INFO::Formatting Data.
2024-10-10 01:32:00.29819 INFO::Replacing NaNs with NAs.
2024-10-10 01:32:00.301278 INFO::Removing potential empty rows and columns
2024-10-10 01:32:00.303718 INFO::Found 2 missing values.
2024-10-10 01:32:00.306024 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.
2024-10-10 01:32:00.313677 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:32:00.315281 INFO::Done
2024-10-10 01:32:00.358449 INFO::Formatting Data.
2024-10-10 01:32:00.360601 INFO::Replacing NaNs with NAs.
2024-10-10 01:32:00.363653 INFO::Removing potential empty rows and columns
2024-10-10 01:32:00.367772 INFO::Found 2 missing values.
2024-10-10 01:32:00.373011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:32:00.374584 INFO::Done
2024-10-10 01:32:00.41501 INFO::Formatting Data.
2024-10-10 01:32:00.416791 INFO::Typecasting input to dataframe.
2024-10-10 01:32:00.418896 INFO::Replacing NaNs with NAs.
2024-10-10 01:32:00.422123 INFO::Removing potential empty rows and columns
2024-10-10 01:32:00.425409 INFO::Found 0 missing values.
2024-10-10 01:32:00.435462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 01:32:00.436824 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.530 7.342 49.538
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 46.385 | 2.837 | 41.303 | |
| compute_asw | 0.060 | 0.002 | 0.076 | |
| count_existing | 0.028 | 0.003 | 0.036 | |
| generate_data_covariables | 0.028 | 0.003 | 0.035 | |
| generate_dataset | 0.024 | 0.002 | 0.034 | |