Yannis Schumann
| Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 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 2024-06-07 20:26 -0400 (Fri, 07 Jun 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" | 4755 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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 | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 2024-06-05 18:56:24 -0400 (Wed, 05 Jun 2024) |
| EndedAt: 2024-06-05 18:57:47 -0400 (Wed, 05 Jun 2024) |
| EllapsedTime: 82.8 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 4.4.0 (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 26.888 1.415 19.365
* 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")
2024-06-05 18:57:26.598692 INFO::Formatting Data.
2024-06-05 18:57:26.602506 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:26.619171 INFO::Removing potential empty rows and columns
2024-06-05 18:57:26.938655 INFO::Found 0 missing values.
2024-06-05 18:57:26.943034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:26.943971 INFO::Done
2024-06-05 18:57:26.94475 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:26.959715 INFO::Starting hierarchical adjustment
2024-06-05 18:57:26.960576 INFO::Found 3 batches.
2024-06-05 18:57:26.961108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:26.962182 INFO::Using default BPPARAM
2024-06-05 18:57:26.96268 INFO::Processing subtree level 1
2024-06-05 18:57:27.109439 INFO::Adjusting the last 1 batches sequentially
2024-06-05 18:57:27.115655 INFO::Done
2024-06-05 18:57:27.117458 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:27.125332 INFO::ASW Batch was -0.0582947389424232 prior to batch effect correction and is now -0.0582947389424232 .
2024-06-05 18:57:27.12794 INFO::Total function execution time is 0.529858827590942 s and adjustment time is 0.155169010162354 s ( 29.28 )
2024-06-05 18:57:27.149591 INFO::Formatting Data.
2024-06-05 18:57:27.150794 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:27.152362 INFO::Removing potential empty rows and columns
2024-06-05 18:57:27.154156 INFO::Found 0 missing values.
2024-06-05 18:57:27.155662 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.
2024-06-05 18:57:27.170911 INFO::Formatting Data.
2024-06-05 18:57:27.171994 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:27.173283 INFO::Removing potential empty rows and columns
2024-06-05 18:57:27.174882 INFO::Found 0 missing values.
2024-06-05 18:57:27.176104 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.
2024-06-05 18:57:27.1999 INFO::Formatting Data.
2024-06-05 18:57:27.200878 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:27.202367 INFO::Removing potential empty rows and columns
2024-06-05 18:57:27.203442 INFO::Found 0 missing values.
2024-06-05 18:57:27.204336 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.
2024-06-05 18:57:27.208162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:27.208886 INFO::Done
2024-06-05 18:57:27.20959 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:27.211511 INFO::Starting hierarchical adjustment
2024-06-05 18:57:27.212121 INFO::Found 2 batches.
2024-06-05 18:57:27.212571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:27.213156 INFO::Using default BPPARAM
2024-06-05 18:57:27.213616 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:27.214484 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:27.244336 INFO::Done
2024-06-05 18:57:27.24524 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:27.24792 INFO::ASW Batch was -0.0478377946899071 prior to batch effect correction and is now -0.111212798055114 .
2024-06-05 18:57:27.248973 INFO::Total function execution time is 0.0490989685058594 s and adjustment time is 0.0322508811950684 s ( 65.69 )
2024-06-05 18:57:27.252293 INFO::Formatting Data.
2024-06-05 18:57:27.252908 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:27.261633 INFO::Formatting Data.
2024-06-05 18:57:27.262707 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:27.263971 INFO::Removing potential empty rows and columns
2024-06-05 18:57:27.265385 INFO::Found 0 missing values.
2024-06-05 18:57:27.269821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:27.27081 INFO::Done
2024-06-05 18:57:27.271706 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:27.274667 INFO::Starting hierarchical adjustment
2024-06-05 18:57:27.275692 INFO::Found 2 batches.
2024-06-05 18:57:27.27643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:27.277277 INFO::Using default BPPARAM
2024-06-05 18:57:27.277987 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:27.27931 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:27.301576 INFO::Done
2024-06-05 18:57:27.302454 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:27.305062 INFO::ASW Batch was 0.0794335277767872 prior to batch effect correction and is now -0.118619025767522 .
2024-06-05 18:57:27.305872 INFO::Total function execution time is 0.0443799495697021 s and adjustment time is 0.026047945022583 s ( 58.69 )
2024-06-05 18:57:27.307377 INFO::Formatting Data.
2024-06-05 18:57:27.308231 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:27.309472 INFO::Removing potential empty rows and columns
2024-06-05 18:57:27.310891 INFO::Found 0 missing values.
2024-06-05 18:57:27.314748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:27.315584 INFO::Done
2024-06-05 18:57:27.316262 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:27.318402 INFO::Starting hierarchical adjustment
2024-06-05 18:57:27.319022 INFO::Found 2 batches.
2024-06-05 18:57:27.319522 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:27.320052 INFO::Using default BPPARAM
2024-06-05 18:57:27.320497 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:27.321308 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:27.339525 INFO::Done
2024-06-05 18:57:27.340238 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:27.342453 INFO::ASW Batch was 0.0794335277767872 prior to batch effect correction and is now -0.118619025767522 .
2024-06-05 18:57:27.343584 INFO::Total function execution time is 0.0362429618835449 s and adjustment time is 0.020582914352417 s ( 56.79 )
2024-06-05 18:57:29.800145 INFO::Formatting Data.
2024-06-05 18:57:29.800767 INFO::Recognized SummarizedExperiment
2024-06-05 18:57:29.801215 INFO::Typecasting input to dataframe.
2024-06-05 18:57:30.605068 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:30.60609 INFO::Removing potential empty rows and columns
2024-06-05 18:57:30.608577 INFO::Found 0 missing values.
2024-06-05 18:57:30.613301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:30.613819 INFO::Done
2024-06-05 18:57:30.614228 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:30.616928 INFO::Starting hierarchical adjustment
2024-06-05 18:57:30.617494 INFO::Found 2 batches.
2024-06-05 18:57:30.617883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:30.618744 INFO::Using default BPPARAM
2024-06-05 18:57:30.619151 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:30.61995 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:30.659319 INFO::Done
2024-06-05 18:57:30.659897 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:30.662638 INFO::ASW Batch was 0.00310758544498938 prior to batch effect correction and is now -0.0880179764153268 .
2024-06-05 18:57:30.66333 INFO::Total function execution time is 0.863456010818481 s and adjustment time is 0.0418930053710938 s ( 4.85 )
2024-06-05 18:57:30.684249 INFO::Formatting Data.
2024-06-05 18:57:30.685018 INFO::Recognized SummarizedExperiment
2024-06-05 18:57:30.685912 INFO::Typecasting input to dataframe.
2024-06-05 18:57:30.696553 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:30.69811 INFO::Removing potential empty rows and columns
2024-06-05 18:57:30.702628 INFO::Found 0 missing values.
2024-06-05 18:57:30.708775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:30.709648 INFO::Done
2024-06-05 18:57:30.710406 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:30.715174 INFO::Starting hierarchical adjustment
2024-06-05 18:57:30.716111 INFO::Found 2 batches.
2024-06-05 18:57:30.716788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:30.717607 INFO::Using default BPPARAM
2024-06-05 18:57:30.718237 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:30.719503 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:30.745741 INFO::Done
2024-06-05 18:57:30.746706 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:30.751059 INFO::ASW Batch was -0.0097809784084004 prior to batch effect correction and is now -0.0097809784084004 .
2024-06-05 18:57:30.75212 INFO::Total function execution time is 0.0678009986877441 s and adjustment time is 0.0298230648040771 s ( 43.99 )
2024-06-05 18:57:30.775875 INFO::Formatting Data.
2024-06-05 18:57:30.776523 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:30.777235 INFO::Removing potential empty rows and columns
2024-06-05 18:57:30.777989 INFO::Found 0 missing values.
2024-06-05 18:57:30.78011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:30.780522 INFO::Done
2024-06-05 18:57:30.780914 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:30.782483 INFO::Starting hierarchical adjustment
2024-06-05 18:57:30.783024 INFO::Found 3 batches.
2024-06-05 18:57:30.783425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:30.783886 INFO::Using default BPPARAM
2024-06-05 18:57:30.784291 INFO::Processing subtree level 1
2024-06-05 18:57:31.00178 INFO::Adjusting the last 1 batches sequentially
2024-06-05 18:57:31.018676 INFO::Done
2024-06-05 18:57:31.020355 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:31.052987 INFO::ASW Batch was -0.101173185513041 prior to batch effect correction and is now -0.154844166338596 .
2024-06-05 18:57:31.057359 INFO::Total function execution time is 0.281387090682983 s and adjustment time is 0.235130786895752 s ( 83.56 )
2024-06-05 18:57:31.084148 INFO::Skipping initial DF formatting
2024-06-05 18:57:31.086899 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:31.092758 INFO::Starting hierarchical adjustment
2024-06-05 18:57:31.094061 INFO::Found 5 batches.
2024-06-05 18:57:31.09492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:31.095578 INFO::Using default BPPARAM
2024-06-05 18:57:31.09609 INFO::Processing subtree level 1
2024-06-05 18:57:31.286037 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:31.295885 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:31.338414 INFO::Done
2024-06-05 18:57:31.339443 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:31.346588 INFO::ASW Batch was 0.544126146339937 prior to batch effect correction and is now 0.544126146339937 .
2024-06-05 18:57:31.34763 INFO::ASW Label was 0.356352634328628 prior to batch effect correction and is now 0.356352634328628 .
2024-06-05 18:57:31.349462 INFO::Total function execution time is 0.265388011932373 s and adjustment time is 0.244570016860962 s ( 92.16 )
2024-06-05 18:57:31.373372 INFO::Formatting Data.
2024-06-05 18:57:31.374543 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:31.375905 INFO::Removing potential empty rows and columns
2024-06-05 18:57:31.376894 INFO::Found 0 missing values.
2024-06-05 18:57:31.382455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:31.383366 INFO::Done
2024-06-05 18:57:31.38415 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:31.387971 INFO::Starting hierarchical adjustment
2024-06-05 18:57:31.389065 INFO::Found 5 batches.
2024-06-05 18:57:31.389821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:31.39069 INFO::Using default BPPARAM
2024-06-05 18:57:31.391437 INFO::Processing subtree level 1
2024-06-05 18:57:31.552914 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:31.564143 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:31.602493 INFO::Done
2024-06-05 18:57:31.603744 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:31.6094 INFO::ASW Batch was 0.265475816360555 prior to batch effect correction and is now -0.096063837083032 .
2024-06-05 18:57:31.611064 INFO::ASW Label was 0.439051694329726 prior to batch effect correction and is now 0.88741755070214 .
2024-06-05 18:57:31.613614 INFO::Total function execution time is 0.24005389213562 s and adjustment time is 0.2136390209198 s ( 89 )
2024-06-05 18:57:31.614673 INFO::Formatting Data.
2024-06-05 18:57:31.615332 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:31.616894 INFO::Removing potential empty rows and columns
2024-06-05 18:57:31.618155 INFO::Found 0 missing values.
2024-06-05 18:57:31.622783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:31.623635 INFO::Done
2024-06-05 18:57:31.624187 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:31.627276 INFO::Starting hierarchical adjustment
2024-06-05 18:57:31.628281 INFO::Found 5 batches.
2024-06-05 18:57:31.628862 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:31.62964 INFO::Using default BPPARAM
2024-06-05 18:57:31.630352 INFO::Processing subtree level 1
2024-06-05 18:57:31.759258 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:31.776474 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:31.812058 INFO::Done
2024-06-05 18:57:31.813186 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:31.821408 INFO::ASW Batch was 0.265475816360555 prior to batch effect correction and is now -0.096063837083032 .
2024-06-05 18:57:31.822319 INFO::ASW Label was 0.439051694329726 prior to batch effect correction and is now 0.88741755070214 .
2024-06-05 18:57:31.82349 INFO::Total function execution time is 0.208842992782593 s and adjustment time is 0.184090852737427 s ( 88.15 )
2024-06-05 18:57:31.844131 INFO::Formatting Data.
2024-06-05 18:57:31.844994 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:31.846934 INFO::Removing potential empty rows and columns
2024-06-05 18:57:31.848515 INFO::Found 0 missing values.
2024-06-05 18:57:31.853555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:31.854162 INFO::Done
2024-06-05 18:57:31.854991 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:31.858199 INFO::Starting hierarchical adjustment
2024-06-05 18:57:31.859374 INFO::Found 5 batches.
2024-06-05 18:57:31.859983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:31.860788 INFO::Using default BPPARAM
2024-06-05 18:57:31.861437 INFO::Processing subtree level 1
2024-06-05 18:57:32.020548 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:32.029039 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:32.062971 INFO::Done
2024-06-05 18:57:32.063933 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:32.069177 INFO::ASW Batch was 0.316978618400299 prior to batch effect correction and is now -0.0132298023819675 .
2024-06-05 18:57:32.070058 INFO::ASW Label was 0.428963726501276 prior to batch effect correction and is now 0.757062905791 .
2024-06-05 18:57:32.071596 INFO::Total function execution time is 0.227205991744995 s and adjustment time is 0.204093217849731 s ( 89.83 )
2024-06-05 18:57:32.072756 INFO::Formatting Data.
2024-06-05 18:57:32.073341 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:32.07468 INFO::Removing potential empty rows and columns
2024-06-05 18:57:32.076325 INFO::Found 0 missing values.
2024-06-05 18:57:32.081548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:32.082388 INFO::Done
2024-06-05 18:57:32.083105 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:32.08641 INFO::Starting hierarchical adjustment
2024-06-05 18:57:32.087422 INFO::Found 5 batches.
2024-06-05 18:57:32.087908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:32.088545 INFO::Using default BPPARAM
2024-06-05 18:57:32.089053 INFO::Processing subtree level 1
2024-06-05 18:57:32.235286 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:32.247331 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:32.283088 INFO::Done
2024-06-05 18:57:32.283783 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:32.288154 INFO::ASW Batch was 0.316978618400299 prior to batch effect correction and is now -0.0132298023819675 .
2024-06-05 18:57:32.289287 INFO::ASW Label was 0.428963726501276 prior to batch effect correction and is now 0.757062905791 .
2024-06-05 18:57:32.291019 INFO::Total function execution time is 0.218183994293213 s and adjustment time is 0.196042060852051 s ( 89.85 )
2024-06-05 18:57:32.312503 INFO::Formatting Data.
2024-06-05 18:57:32.313287 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:32.314478 INFO::Removing potential empty rows and columns
2024-06-05 18:57:32.316303 INFO::Found 0 missing values.
2024-06-05 18:57:32.31874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:32.319213 INFO::Done
2024-06-05 18:57:32.31968 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:32.324153 INFO::Starting hierarchical adjustment
2024-06-05 18:57:32.325321 INFO::Found 2 batches.
2024-06-05 18:57:32.326156 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:32.327112 INFO::Using default BPPARAM
2024-06-05 18:57:32.327863 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:32.329217 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:32.349826 INFO::Done
2024-06-05 18:57:32.350758 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:32.355016 INFO::ASW Batch was 0.530468629051731 prior to batch effect correction and is now 0.204614693797764 .
2024-06-05 18:57:32.355956 INFO::ASW Label was 0.659350627174316 prior to batch effect correction and is now 0.775966442757434 .
2024-06-05 18:57:32.357097 INFO::Total function execution time is 0.0446209907531738 s and adjustment time is 0.0247039794921875 s ( 55.36 )
2024-06-05 18:57:32.358072 INFO::Formatting Data.
2024-06-05 18:57:32.358675 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:32.359471 INFO::Removing potential empty rows and columns
2024-06-05 18:57:32.360324 INFO::Found 0 missing values.
2024-06-05 18:57:32.36369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:32.364395 INFO::Done
2024-06-05 18:57:32.365098 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:32.367933 INFO::Starting hierarchical adjustment
2024-06-05 18:57:32.368552 INFO::Found 2 batches.
2024-06-05 18:57:32.369021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:32.369542 INFO::Using default BPPARAM
2024-06-05 18:57:32.369974 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:32.371432 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:32.391888 INFO::Done
2024-06-05 18:57:32.392943 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:32.396717 INFO::ASW Batch was 0.530468629051731 prior to batch effect correction and is now 0.204614693797764 .
2024-06-05 18:57:32.397279 INFO::ASW Label was 0.659350627174316 prior to batch effect correction and is now 0.775966442757434 .
2024-06-05 18:57:32.397978 INFO::Total function execution time is 0.0399529933929443 s and adjustment time is 0.023374080657959 s ( 58.5 )
2024-06-05 18:57:32.413906 INFO::Formatting Data.
2024-06-05 18:57:32.414669 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:32.415488 INFO::Removing potential empty rows and columns
2024-06-05 18:57:32.416282 INFO::Found 0 missing values.
2024-06-05 18:57:32.41817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:32.418636 INFO::Done
2024-06-05 18:57:32.419084 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:32.420803 INFO::Starting hierarchical adjustment
2024-06-05 18:57:32.42142 INFO::Found 2 batches.
2024-06-05 18:57:32.421882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:32.42239 INFO::Using default BPPARAM
2024-06-05 18:57:32.422835 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:32.423936 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:32.462082 INFO::Done
2024-06-05 18:57:32.463049 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:32.465798 INFO::ASW Batch was 0.0153672253379649 prior to batch effect correction and is now -0.108006992515554 .
2024-06-05 18:57:32.466962 INFO::Total function execution time is 0.0531039237976074 s and adjustment time is 0.0406739711761475 s ( 76.59 )
2024-06-05 18:57:32.486281 INFO::Formatting Data.
2024-06-05 18:57:32.487377 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:32.488626 INFO::Removing potential empty rows and columns
2024-06-05 18:57:32.489877 INFO::Found 0 missing values.
2024-06-05 18:57:32.491383 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.
2024-06-05 18:57:32.497508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:32.498441 INFO::Done
2024-06-05 18:57:32.499233 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:32.50281 INFO::Starting hierarchical adjustment
2024-06-05 18:57:32.50377 INFO::Found 2 batches.
2024-06-05 18:57:32.50439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:32.505088 INFO::Using default BPPARAM
2024-06-05 18:57:32.505555 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:32.506425 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:32.527654 INFO::Done
2024-06-05 18:57:32.528555 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:32.532615 INFO::ASW Batch was 0.469876227484442 prior to batch effect correction and is now 0.00776985149519255 .
2024-06-05 18:57:32.533356 INFO::ASW Label was 0.608824530234378 prior to batch effect correction and is now 0.933946471252259 .
2024-06-05 18:57:32.534304 INFO::Total function execution time is 0.0481669902801514 s and adjustment time is 0.0240800380706787 s ( 49.99 )
2024-06-05 18:57:32.535222 INFO::Formatting Data.
2024-06-05 18:57:32.536 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:32.537238 INFO::Removing potential empty rows and columns
2024-06-05 18:57:32.538516 INFO::Found 0 missing values.
2024-06-05 18:57:32.539694 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.
2024-06-05 18:57:32.546526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:32.547496 INFO::Done
2024-06-05 18:57:32.548296 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:32.552409 INFO::Starting hierarchical adjustment
2024-06-05 18:57:32.55365 INFO::Found 2 batches.
2024-06-05 18:57:32.55442 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:32.555227 INFO::Using default BPPARAM
2024-06-05 18:57:32.555903 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:32.5572 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:32.579797 INFO::Done
2024-06-05 18:57:32.580435 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:32.583037 INFO::ASW Batch was 0.469876227484442 prior to batch effect correction and is now 0.00776985149519255 .
2024-06-05 18:57:32.583554 INFO::ASW Label was 0.608824530234378 prior to batch effect correction and is now 0.933946471252259 .
2024-06-05 18:57:32.584599 INFO::Total function execution time is 0.049400806427002 s and adjustment time is 0.026453971862793 s ( 53.55 )
2024-06-05 18:57:32.833448 INFO::Formatting Data.
2024-06-05 18:57:32.834468 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:32.835605 INFO::Removing potential empty rows and columns
2024-06-05 18:57:32.836779 INFO::Found 0 missing values.
2024-06-05 18:57:32.840605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:32.841096 INFO::Done
2024-06-05 18:57:32.841537 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:32.843238 INFO::Starting hierarchical adjustment
2024-06-05 18:57:32.84406 INFO::Found 3 batches.
2024-06-05 18:57:32.84466 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:32.845192 INFO::Using default BPPARAM
2024-06-05 18:57:32.845948 INFO::Processing subtree level 1
2024-06-05 18:57:32.96105 INFO::Adjusting the last 1 batches sequentially
2024-06-05 18:57:32.970274 INFO::Done
2024-06-05 18:57:32.97562 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:32.988106 INFO::ASW Batch was -0.0338950216557712 prior to batch effect correction and is now -0.0338950216557712 .
2024-06-05 18:57:32.991788 INFO::Total function execution time is 0.157934188842773 s and adjustment time is 0.126265048980713 s ( 79.95 )
2024-06-05 18:57:32.993837 INFO::Formatting Data.
2024-06-05 18:57:32.995381 INFO::Typecasting input to dataframe.
2024-06-05 18:57:32.996504 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:32.998432 INFO::Removing potential empty rows and columns
2024-06-05 18:57:33.000553 INFO::Found 0 missing values.
2024-06-05 18:57:33.004488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:33.005013 INFO::Done
2024-06-05 18:57:33.005475 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:33.008147 INFO::Starting hierarchical adjustment
2024-06-05 18:57:33.009117 INFO::Found 3 batches.
2024-06-05 18:57:33.009797 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:33.013711 INFO::Using default BPPARAM
2024-06-05 18:57:33.015163 INFO::Processing subtree level 1
2024-06-05 18:57:33.149686 INFO::Adjusting the last 1 batches sequentially
2024-06-05 18:57:33.157552 INFO::Done
2024-06-05 18:57:33.159175 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:33.173332 INFO::ASW Batch was -0.0338950216557712 prior to batch effect correction and is now -0.0338950216557712 .
2024-06-05 18:57:33.17745 INFO::Total function execution time is 0.182932138442993 s and adjustment time is 0.148553133010864 s ( 81.21 )
2024-06-05 18:57:33.201333 INFO::Formatting Data.
2024-06-05 18:57:33.203161 INFO::Typecasting input to dataframe.
2024-06-05 18:57:33.204025 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:33.204837 INFO::Removing potential empty rows and columns
2024-06-05 18:57:33.207427 INFO::Found 0 missing values.
2024-06-05 18:57:33.211205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:33.211892 INFO::Done
2024-06-05 18:57:33.212912 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:33.214682 INFO::Starting hierarchical adjustment
2024-06-05 18:57:33.215551 INFO::Found 3 batches.
2024-06-05 18:57:33.216256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:33.218179 INFO::Using default BPPARAM
2024-06-05 18:57:33.218915 INFO::Processing subtree level 1
2024-06-05 18:57:33.339806 INFO::Adjusting the last 1 batches sequentially
2024-06-05 18:57:33.354892 INFO::Done
2024-06-05 18:57:33.357363 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:33.376063 INFO::ASW Batch was -0.138083285687668 prior to batch effect correction and is now -0.138083285687668 .
2024-06-05 18:57:33.380769 INFO::Total function execution time is 0.178491830825806 s and adjustment time is 0.139443159103394 s ( 78.12 )
2024-06-05 18:57:33.651713 INFO::Formatting Data.
2024-06-05 18:57:33.652943 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:33.654582 INFO::Removing potential empty rows and columns
2024-06-05 18:57:33.657978 INFO::Found 1000 missing values.
2024-06-05 18:57:33.684901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:33.685855 INFO::Done
2024-06-05 18:57:33.68662 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:33.693522 INFO::Starting hierarchical adjustment
2024-06-05 18:57:33.694665 INFO::Found 10 batches.
2024-06-05 18:57:33.695384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:33.6969 INFO::Using default BPPARAM
2024-06-05 18:57:33.697652 INFO::Processing subtree level 1
2024-06-05 18:57:33.889739 INFO::Processing subtree level 2
2024-06-05 18:57:34.103629 INFO::Adjusting the last 1 batches sequentially
2024-06-05 18:57:34.113503 INFO::Done
2024-06-05 18:57:34.115577 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:34.134291 INFO::ASW Batch was 0.524259124680066 prior to batch effect correction and is now 0.524259124680066 .
2024-06-05 18:57:34.135309 INFO::ASW Label was 0.316179272947352 prior to batch effect correction and is now 0.316179272947352 .
2024-06-05 18:57:34.139784 INFO::Total function execution time is 0.487725019454956 s and adjustment time is 0.418398857116699 s ( 85.79 )
2024-06-05 18:57:34.142116 INFO::Formatting Data.
2024-06-05 18:57:34.143266 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:34.147032 INFO::Removing potential empty rows and columns
2024-06-05 18:57:34.151875 INFO::Found 1000 missing values.
2024-06-05 18:57:34.178622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:34.17956 INFO::Done
2024-06-05 18:57:34.180437 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:34.186685 INFO::Starting hierarchical adjustment
2024-06-05 18:57:34.187886 INFO::Found 10 batches.
2024-06-05 18:57:35.161854 INFO::Set up parallel execution backend with 2 workers
2024-06-05 18:57:35.162451 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-05 18:57:36.456573 INFO::Adjusting the last 2 batches sequentially
2024-06-05 18:57:36.458353 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-05 18:57:36.480609 INFO::Done
2024-06-05 18:57:36.481585 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:36.48949 INFO::ASW Batch was 0.524259124680066 prior to batch effect correction and is now 0.524259124680066 .
2024-06-05 18:57:36.490373 INFO::ASW Label was 0.316179272947352 prior to batch effect correction and is now 0.316179272947352 .
2024-06-05 18:57:36.491436 INFO::Total function execution time is 2.3493959903717 s and adjustment time is 2.29294800758362 s ( 97.6 )
2024-06-05 18:57:36.739061 INFO::Formatting Data.
2024-06-05 18:57:36.740267 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:36.741861 INFO::Removing potential empty rows and columns
2024-06-05 18:57:36.744116 INFO::Found 0 missing values.
2024-06-05 18:57:36.74961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:36.750461 INFO::Done
2024-06-05 18:57:36.751241 INFO::Acquiring quality metrics before batch effect correction.
2024-06-05 18:57:36.755297 INFO::Starting hierarchical adjustment
2024-06-05 18:57:36.756026 INFO::Found 3 batches.
2024-06-05 18:57:36.756504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-05 18:57:36.757067 INFO::Using default BPPARAM
2024-06-05 18:57:36.75764 INFO::Processing subtree level 1
2024-06-05 18:57:36.931542 INFO::Adjusting the last 1 batches sequentially
2024-06-05 18:57:36.941476 INFO::Done
2024-06-05 18:57:36.944926 INFO::Acquiring quality metrics after batch effect correction.
2024-06-05 18:57:36.97032 INFO::ASW Batch was 0.208651256546578 prior to batch effect correction and is now -0.142531396009883 .
2024-06-05 18:57:36.971404 INFO::ASW Label was -0.181836323355704 prior to batch effect correction and is now -0.0334009691526365 .
2024-06-05 18:57:36.974251 INFO::Total function execution time is 0.235107898712158 s and adjustment time is 0.185494899749756 s ( 78.9 )
2024-06-05 18:57:37.155223 INFO::Formatting Data.
2024-06-05 18:57:37.156104 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.157032 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.158932 INFO::Found 2 missing values.
2024-06-05 18:57:37.163049 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.163807 INFO::Done
2024-06-05 18:57:37.213285 INFO::Found NA in Reference column
2024-06-05 18:57:37.228765 INFO::Require at least two references per batch.
2024-06-05 18:57:37.260447 INFO::Formatting Data.
2024-06-05 18:57:37.261816 INFO::Recognized SummarizedExperiment
2024-06-05 18:57:37.262899 INFO::Typecasting input to dataframe.
2024-06-05 18:57:37.279067 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.281069 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.286417 INFO::Found 0 missing values.
2024-06-05 18:57:37.295602 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.296494 INFO::Done
2024-06-05 18:57:37.315206 INFO::Formatting Data.
2024-06-05 18:57:37.316323 INFO::Recognized SummarizedExperiment
2024-06-05 18:57:37.317146 INFO::Typecasting input to dataframe.
2024-06-05 18:57:37.338945 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.340893 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.346323 INFO::Found 0 missing values.
2024-06-05 18:57:37.357812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.358889 INFO::Done
2024-06-05 18:57:37.378904 INFO::Formatting Data.
2024-06-05 18:57:37.379956 INFO::Recognized SummarizedExperiment
2024-06-05 18:57:37.380754 INFO::Typecasting input to dataframe.
2024-06-05 18:57:37.406426 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.408 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.409633 INFO::Found 0 missing values.
2024-06-05 18:57:37.41105 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.
2024-06-05 18:57:37.416634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.417383 INFO::Done
2024-06-05 18:57:37.431723 INFO::Formatting Data.
2024-06-05 18:57:37.432549 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.433422 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.434325 INFO::Found 0 missing values.
2024-06-05 18:57:37.436902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.437405 INFO::Done
2024-06-05 18:57:37.453204 INFO::Formatting Data.
2024-06-05 18:57:37.454444 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.455865 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.457451 INFO::Found 0 missing values.
2024-06-05 18:57:37.462351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.463358 INFO::Done
2024-06-05 18:57:37.513274 INFO::Formatting Data.
2024-06-05 18:57:37.514545 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.516248 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.517421 INFO::Found 1 missing values.
2024-06-05 18:57:37.520192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.520694 INFO::Done
2024-06-05 18:57:37.554489 INFO::Formatting Data.
2024-06-05 18:57:37.55564 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.556959 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.558349 INFO::Found 2 missing values.
2024-06-05 18:57:37.559675 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.
2024-06-05 18:57:37.563244 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.564059 INFO::Done
2024-06-05 18:57:37.580438 INFO::Formatting Data.
2024-06-05 18:57:37.581315 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.582243 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.583167 INFO::Found 2 missing values.
2024-06-05 18:57:37.584783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.585295 INFO::Done
2024-06-05 18:57:37.601457 INFO::Formatting Data.
2024-06-05 18:57:37.602696 INFO::Typecasting input to dataframe.
2024-06-05 18:57:37.60407 INFO::Replacing NaNs with NAs.
2024-06-05 18:57:37.605544 INFO::Removing potential empty rows and columns
2024-06-05 18:57:37.606845 INFO::Found 0 missing values.
2024-06-05 18:57:37.611441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-05 18:57:37.612035 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.101 3.762 24.284
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.888 | 1.415 | 19.365 | |
| compute_asw | 0.020 | 0.001 | 0.021 | |
| count_existing | 0.011 | 0.000 | 0.011 | |
| generate_data_covariables | 0.010 | 0.001 | 0.011 | |
| generate_dataset | 0.010 | 0.001 | 0.010 | |