Yannis Schumann
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:06 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-12-31 11:52:40 -0500 (Tue, 31 Dec 2024) |
| EndedAt: 2024-12-31 11:53:46 -0500 (Tue, 31 Dec 2024) |
| EllapsedTime: 65.7 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 28.761 1.185 20.513
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-12-31 11:53:34.427772 INFO::Formatting Data.
2024-12-31 11:53:34.432874 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:34.441784 INFO::Removing potential empty rows and columns
2024-12-31 11:53:34.617814 INFO::Found 0 missing values.
2024-12-31 11:53:34.620743 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:34.621348 INFO::Done
2024-12-31 11:53:34.621844 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:34.630991 INFO::Starting hierarchical adjustment
2024-12-31 11:53:34.631344 INFO::Found 3 batches.
2024-12-31 11:53:34.631545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:34.631971 INFO::Using default BPPARAM
2024-12-31 11:53:34.632146 INFO::Processing subtree level 1
2024-12-31 11:53:34.677316 INFO::Adjusting the last 1 batches sequentially
2024-12-31 11:53:34.681289 INFO::Done
2024-12-31 11:53:34.682125 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:34.684483 INFO::ASW Batch was -0.067147062512161 prior to batch effect correction and is now -0.067147062512161 .
2024-12-31 11:53:34.685228 INFO::Total function execution time is 0.26145601272583 s and adjustment time is 0.0498840808868408 s ( 19.08 )
2024-12-31 11:53:34.692466 INFO::Formatting Data.
2024-12-31 11:53:34.692827 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:34.693252 INFO::Removing potential empty rows and columns
2024-12-31 11:53:34.693736 INFO::Found 0 missing values.
2024-12-31 11:53:34.694063 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.
2024-12-31 11:53:34.698598 INFO::Formatting Data.
2024-12-31 11:53:34.69889 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:34.699203 INFO::Removing potential empty rows and columns
2024-12-31 11:53:34.699573 INFO::Found 0 missing values.
2024-12-31 11:53:34.699893 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.
2024-12-31 11:53:34.706602 INFO::Formatting Data.
2024-12-31 11:53:34.706909 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:34.707263 INFO::Removing potential empty rows and columns
2024-12-31 11:53:34.707753 INFO::Found 0 missing values.
2024-12-31 11:53:34.708086 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.
2024-12-31 11:53:34.709819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:34.710053 INFO::Done
2024-12-31 11:53:34.710236 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:34.710962 INFO::Starting hierarchical adjustment
2024-12-31 11:53:34.711216 INFO::Found 2 batches.
2024-12-31 11:53:34.711387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:34.711613 INFO::Using default BPPARAM
2024-12-31 11:53:34.711789 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:34.712088 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:34.721167 INFO::Done
2024-12-31 11:53:34.72144 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:34.722187 INFO::ASW Batch was -0.0283750727944746 prior to batch effect correction and is now -0.11778423167847 .
2024-12-31 11:53:34.722514 INFO::Total function execution time is 0.0159451961517334 s and adjustment time is 0.0099790096282959 s ( 62.58 )
2024-12-31 11:53:34.723681 INFO::Formatting Data.
2024-12-31 11:53:34.723942 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:34.727245 INFO::Formatting Data.
2024-12-31 11:53:34.727504 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:34.727821 INFO::Removing potential empty rows and columns
2024-12-31 11:53:34.72816 INFO::Found 0 missing values.
2024-12-31 11:53:34.729117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:34.729315 INFO::Done
2024-12-31 11:53:34.729478 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:34.730215 INFO::Starting hierarchical adjustment
2024-12-31 11:53:34.730467 INFO::Found 2 batches.
2024-12-31 11:53:34.73063 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:34.73082 INFO::Using default BPPARAM
2024-12-31 11:53:34.731065 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:34.731398 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:34.736324 INFO::Done
2024-12-31 11:53:34.736547 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:34.737217 INFO::ASW Batch was -0.0307173849743932 prior to batch effect correction and is now -0.123306237091196 .
2024-12-31 11:53:34.737473 INFO::Total function execution time is 0.0102620124816895 s and adjustment time is 0.00590109825134277 s ( 57.5 )
2024-12-31 11:53:34.737799 INFO::Formatting Data.
2024-12-31 11:53:34.737978 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:34.738248 INFO::Removing potential empty rows and columns
2024-12-31 11:53:34.738568 INFO::Found 0 missing values.
2024-12-31 11:53:34.739434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:34.739613 INFO::Done
2024-12-31 11:53:34.739773 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:34.740424 INFO::Starting hierarchical adjustment
2024-12-31 11:53:34.740643 INFO::Found 2 batches.
2024-12-31 11:53:34.740794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:34.740973 INFO::Using default BPPARAM
2024-12-31 11:53:34.741121 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:34.741372 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:34.74642 INFO::Done
2024-12-31 11:53:34.746672 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:34.74743 INFO::ASW Batch was -0.0307173849743932 prior to batch effect correction and is now -0.123306237091196 .
2024-12-31 11:53:34.747733 INFO::Total function execution time is 0.00991511344909668 s and adjustment time is 0.00580787658691406 s ( 58.58 )
2024-12-31 11:53:36.813359 INFO::Formatting Data.
2024-12-31 11:53:36.81399 INFO::Recognized SummarizedExperiment
2024-12-31 11:53:36.814413 INFO::Typecasting input to dataframe.
2024-12-31 11:53:36.843038 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:36.844022 INFO::Removing potential empty rows and columns
2024-12-31 11:53:36.846875 INFO::Found 0 missing values.
2024-12-31 11:53:36.852533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:36.853023 INFO::Done
2024-12-31 11:53:36.853414 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:36.856502 INFO::Starting hierarchical adjustment
2024-12-31 11:53:36.857106 INFO::Found 2 batches.
2024-12-31 11:53:36.857515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:36.85834 INFO::Using default BPPARAM
2024-12-31 11:53:36.858729 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:36.859492 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:36.903025 INFO::Done
2024-12-31 11:53:36.903569 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:36.906648 INFO::ASW Batch was -0.0143986882829821 prior to batch effect correction and is now -0.0874013849669069 .
2024-12-31 11:53:36.907332 INFO::Total function execution time is 0.0942192077636719 s and adjustment time is 0.046018123626709 s ( 48.84 )
2024-12-31 11:53:36.922699 INFO::Formatting Data.
2024-12-31 11:53:36.923332 INFO::Recognized SummarizedExperiment
2024-12-31 11:53:36.923784 INFO::Typecasting input to dataframe.
2024-12-31 11:53:36.93225 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:36.933344 INFO::Removing potential empty rows and columns
2024-12-31 11:53:36.936585 INFO::Found 0 missing values.
2024-12-31 11:53:36.943012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:36.943565 INFO::Done
2024-12-31 11:53:36.944007 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:36.947445 INFO::Starting hierarchical adjustment
2024-12-31 11:53:36.948112 INFO::Found 2 batches.
2024-12-31 11:53:36.948554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:36.949053 INFO::Using default BPPARAM
2024-12-31 11:53:36.949479 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:36.950324 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:36.960376 INFO::Done
2024-12-31 11:53:36.960668 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:36.961905 INFO::ASW Batch was -0.0203718829322237 prior to batch effect correction and is now -0.0203718829322237 .
2024-12-31 11:53:36.962191 INFO::Total function execution time is 0.0395619869232178 s and adjustment time is 0.0124368667602539 s ( 31.44 )
2024-12-31 11:53:36.968553 INFO::Formatting Data.
2024-12-31 11:53:36.968801 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:36.969078 INFO::Removing potential empty rows and columns
2024-12-31 11:53:36.969389 INFO::Found 0 missing values.
2024-12-31 11:53:36.970254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:36.970424 INFO::Done
2024-12-31 11:53:36.970577 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:36.971219 INFO::Starting hierarchical adjustment
2024-12-31 11:53:36.971428 INFO::Found 3 batches.
2024-12-31 11:53:36.971577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:36.971751 INFO::Using default BPPARAM
2024-12-31 11:53:36.971892 INFO::Processing subtree level 1
2024-12-31 11:53:37.076719 INFO::Adjusting the last 1 batches sequentially
2024-12-31 11:53:37.078202 INFO::Done
2024-12-31 11:53:37.078417 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.080298 INFO::ASW Batch was -0.0206423626606069 prior to batch effect correction and is now -0.161918422029498 .
2024-12-31 11:53:37.080817 INFO::Total function execution time is 0.112262964248657 s and adjustment time is 0.10680890083313 s ( 95.14 )
2024-12-31 11:53:37.086801 INFO::Skipping initial DF formatting
2024-12-31 11:53:37.087071 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.088524 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.0888 INFO::Found 5 batches.
2024-12-31 11:53:37.088974 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.089317 INFO::Using default BPPARAM
2024-12-31 11:53:37.089477 INFO::Processing subtree level 1
2024-12-31 11:53:37.1355 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.13768 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.147793 INFO::Done
2024-12-31 11:53:37.148106 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.15025 INFO::ASW Batch was 0.572947833624492 prior to batch effect correction and is now 0.572947833624492 .
2024-12-31 11:53:37.15055 INFO::ASW Label was 0.374664858507091 prior to batch effect correction and is now 0.374664858507091 .
2024-12-31 11:53:37.150927 INFO::Total function execution time is 0.0641140937805176 s and adjustment time is 0.059027910232544 s ( 92.07 )
2024-12-31 11:53:37.158755 INFO::Formatting Data.
2024-12-31 11:53:37.159081 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.159434 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.159822 INFO::Found 0 missing values.
2024-12-31 11:53:37.16106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.16132 INFO::Done
2024-12-31 11:53:37.161487 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.162777 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.163128 INFO::Found 5 batches.
2024-12-31 11:53:37.163329 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.163568 INFO::Using default BPPARAM
2024-12-31 11:53:37.163734 INFO::Processing subtree level 1
2024-12-31 11:53:37.221748 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.224154 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.234598 INFO::Done
2024-12-31 11:53:37.234899 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.236428 INFO::ASW Batch was 0.484244109544602 prior to batch effect correction and is now -0.072272286661449 .
2024-12-31 11:53:37.236644 INFO::ASW Label was 0.202524101289199 prior to batch effect correction and is now 0.805372761107967 .
2024-12-31 11:53:37.23707 INFO::Total function execution time is 0.0783329010009766 s and adjustment time is 0.0715301036834717 s ( 91.32 )
2024-12-31 11:53:37.237381 INFO::Formatting Data.
2024-12-31 11:53:37.237576 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.237868 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.238249 INFO::Found 0 missing values.
2024-12-31 11:53:37.239735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.23997 INFO::Done
2024-12-31 11:53:37.240144 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.241165 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.241459 INFO::Found 5 batches.
2024-12-31 11:53:37.241633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.241845 INFO::Using default BPPARAM
2024-12-31 11:53:37.242013 INFO::Processing subtree level 1
2024-12-31 11:53:37.324433 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.326083 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.3343 INFO::Done
2024-12-31 11:53:37.334675 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.336023 INFO::ASW Batch was 0.484244109544602 prior to batch effect correction and is now -0.072272286661449 .
2024-12-31 11:53:37.336249 INFO::ASW Label was 0.202524101289199 prior to batch effect correction and is now 0.805372761107967 .
2024-12-31 11:53:37.336549 INFO::Total function execution time is 0.0991408824920654 s and adjustment time is 0.0929181575775146 s ( 93.72 )
2024-12-31 11:53:37.342396 INFO::Formatting Data.
2024-12-31 11:53:37.342675 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.342978 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.343343 INFO::Found 0 missing values.
2024-12-31 11:53:37.344671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.344976 INFO::Done
2024-12-31 11:53:37.345189 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.346288 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.346562 INFO::Found 5 batches.
2024-12-31 11:53:37.346737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.346946 INFO::Using default BPPARAM
2024-12-31 11:53:37.347104 INFO::Processing subtree level 1
2024-12-31 11:53:37.42339 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.425169 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.432969 INFO::Done
2024-12-31 11:53:37.434048 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.437355 INFO::ASW Batch was 0.259298732613148 prior to batch effect correction and is now -0.0968924734196133 .
2024-12-31 11:53:37.438138 INFO::ASW Label was 0.363205647846828 prior to batch effect correction and is now 0.911696116066052 .
2024-12-31 11:53:37.43926 INFO::Total function execution time is 0.0967559814453125 s and adjustment time is 0.0864570140838623 s ( 89.36 )
2024-12-31 11:53:37.440055 INFO::Formatting Data.
2024-12-31 11:53:37.440694 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.441531 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.44243 INFO::Found 0 missing values.
2024-12-31 11:53:37.445954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.446478 INFO::Done
2024-12-31 11:53:37.446933 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.449517 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.450139 INFO::Found 5 batches.
2024-12-31 11:53:37.450555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.451083 INFO::Using default BPPARAM
2024-12-31 11:53:37.451513 INFO::Processing subtree level 1
2024-12-31 11:53:37.522693 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.524402 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.531989 INFO::Done
2024-12-31 11:53:37.532283 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.533455 INFO::ASW Batch was 0.259298732613148 prior to batch effect correction and is now -0.0968924734196133 .
2024-12-31 11:53:37.533664 INFO::ASW Label was 0.363205647846828 prior to batch effect correction and is now 0.911696116066052 .
2024-12-31 11:53:37.533976 INFO::Total function execution time is 0.0939731597900391 s and adjustment time is 0.0820059776306152 s ( 87.27 )
2024-12-31 11:53:37.540143 INFO::Formatting Data.
2024-12-31 11:53:37.540428 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.540759 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.541125 INFO::Found 0 missing values.
2024-12-31 11:53:37.54201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.542215 INFO::Done
2024-12-31 11:53:37.542381 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.543436 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.543707 INFO::Found 2 batches.
2024-12-31 11:53:37.543874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.544098 INFO::Using default BPPARAM
2024-12-31 11:53:37.544259 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.544537 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.549487 INFO::Done
2024-12-31 11:53:37.549731 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.550708 INFO::ASW Batch was 0.699050646355391 prior to batch effect correction and is now 0.164370946103638 .
2024-12-31 11:53:37.55096 INFO::ASW Label was 0.457071089722632 prior to batch effect correction and is now 0.781526493371437 .
2024-12-31 11:53:37.551259 INFO::Total function execution time is 0.0111558437347412 s and adjustment time is 0.00582003593444824 s ( 52.17 )
2024-12-31 11:53:37.551511 INFO::Formatting Data.
2024-12-31 11:53:37.551692 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.551994 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.552385 INFO::Found 0 missing values.
2024-12-31 11:53:37.553309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.553562 INFO::Done
2024-12-31 11:53:37.55373 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.554678 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.554931 INFO::Found 2 batches.
2024-12-31 11:53:37.555096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.555282 INFO::Using default BPPARAM
2024-12-31 11:53:37.55543 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.555723 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.5611 INFO::Done
2024-12-31 11:53:37.561407 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.562484 INFO::ASW Batch was 0.699050646355391 prior to batch effect correction and is now 0.164370946103638 .
2024-12-31 11:53:37.562681 INFO::ASW Label was 0.457071089722632 prior to batch effect correction and is now 0.781526493371437 .
2024-12-31 11:53:37.562934 INFO::Total function execution time is 0.0114169120788574 s and adjustment time is 0.00620007514953613 s ( 54.31 )
2024-12-31 11:53:37.567364 INFO::Formatting Data.
2024-12-31 11:53:37.567631 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.567917 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.568219 INFO::Found 0 missing values.
2024-12-31 11:53:37.568966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.569181 INFO::Done
2024-12-31 11:53:37.569348 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.570096 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.570401 INFO::Found 2 batches.
2024-12-31 11:53:37.570573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.570761 INFO::Using default BPPARAM
2024-12-31 11:53:37.570917 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.571258 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.582947 INFO::Done
2024-12-31 11:53:37.583204 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.583879 INFO::ASW Batch was -0.135670438427222 prior to batch effect correction and is now -0.145091163430084 .
2024-12-31 11:53:37.584149 INFO::Total function execution time is 0.0168211460113525 s and adjustment time is 0.0125911235809326 s ( 74.85 )
2024-12-31 11:53:37.589058 INFO::Formatting Data.
2024-12-31 11:53:37.589343 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.589641 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.589977 INFO::Found 0 missing values.
2024-12-31 11:53:37.590437 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.
2024-12-31 11:53:37.591883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.592088 INFO::Done
2024-12-31 11:53:37.592263 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.593241 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.593472 INFO::Found 2 batches.
2024-12-31 11:53:37.593623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.593807 INFO::Using default BPPARAM
2024-12-31 11:53:37.593972 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.594278 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.599886 INFO::Done
2024-12-31 11:53:37.600138 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.601103 INFO::ASW Batch was 0.701806986744722 prior to batch effect correction and is now 0.0137114458435482 .
2024-12-31 11:53:37.601302 INFO::ASW Label was 0.314921110786237 prior to batch effect correction and is now 0.896476400396552 .
2024-12-31 11:53:37.601545 INFO::Total function execution time is 0.0125370025634766 s and adjustment time is 0.00644683837890625 s ( 51.42 )
2024-12-31 11:53:37.601789 INFO::Formatting Data.
2024-12-31 11:53:37.601957 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.60225 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.602563 INFO::Found 0 missing values.
2024-12-31 11:53:37.602833 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.
2024-12-31 11:53:37.604243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.604477 INFO::Done
2024-12-31 11:53:37.604729 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.605744 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.60601 INFO::Found 2 batches.
2024-12-31 11:53:37.606172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.606363 INFO::Using default BPPARAM
2024-12-31 11:53:37.606515 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:37.606813 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:37.612379 INFO::Done
2024-12-31 11:53:37.612624 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.613547 INFO::ASW Batch was 0.701806986744722 prior to batch effect correction and is now 0.0137114458435482 .
2024-12-31 11:53:37.61374 INFO::ASW Label was 0.314921110786237 prior to batch effect correction and is now 0.896476400396552 .
2024-12-31 11:53:37.613984 INFO::Total function execution time is 0.0121951103210449 s and adjustment time is 0.0063939094543457 s ( 52.43 )
2024-12-31 11:53:37.754819 INFO::Formatting Data.
2024-12-31 11:53:37.755522 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.756314 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.757224 INFO::Found 0 missing values.
2024-12-31 11:53:37.759794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.760309 INFO::Done
2024-12-31 11:53:37.760756 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.76245 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.763022 INFO::Found 3 batches.
2024-12-31 11:53:37.763437 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.763937 INFO::Using default BPPARAM
2024-12-31 11:53:37.764351 INFO::Processing subtree level 1
2024-12-31 11:53:37.840389 INFO::Adjusting the last 1 batches sequentially
2024-12-31 11:53:37.841909 INFO::Done
2024-12-31 11:53:37.842241 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.843809 INFO::ASW Batch was -0.10831911177913 prior to batch effect correction and is now -0.10831911177913 .
2024-12-31 11:53:37.844479 INFO::Total function execution time is 0.0897941589355469 s and adjustment time is 0.0790400505065918 s ( 88.02 )
2024-12-31 11:53:37.845017 INFO::Formatting Data.
2024-12-31 11:53:37.845235 INFO::Typecasting input to dataframe.
2024-12-31 11:53:37.845475 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.84695 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.848171 INFO::Found 0 missing values.
2024-12-31 11:53:37.851304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.852171 INFO::Done
2024-12-31 11:53:37.852713 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.854574 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.855215 INFO::Found 3 batches.
2024-12-31 11:53:37.855661 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.856196 INFO::Using default BPPARAM
2024-12-31 11:53:37.856625 INFO::Processing subtree level 1
2024-12-31 11:53:37.898713 INFO::Adjusting the last 1 batches sequentially
2024-12-31 11:53:37.901112 INFO::Done
2024-12-31 11:53:37.901371 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:37.903833 INFO::ASW Batch was -0.10831911177913 prior to batch effect correction and is now -0.10831911177913 .
2024-12-31 11:53:37.904728 INFO::Total function execution time is 0.0596909523010254 s and adjustment time is 0.046051025390625 s ( 77.15 )
2024-12-31 11:53:37.912077 INFO::Formatting Data.
2024-12-31 11:53:37.912394 INFO::Typecasting input to dataframe.
2024-12-31 11:53:37.912689 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:37.913023 INFO::Removing potential empty rows and columns
2024-12-31 11:53:37.91356 INFO::Found 0 missing values.
2024-12-31 11:53:37.914571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:37.914802 INFO::Done
2024-12-31 11:53:37.914968 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:37.915747 INFO::Starting hierarchical adjustment
2024-12-31 11:53:37.916141 INFO::Found 3 batches.
2024-12-31 11:53:37.916314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:37.91665 INFO::Using default BPPARAM
2024-12-31 11:53:37.916894 INFO::Processing subtree level 1
2024-12-31 11:53:38.025028 INFO::Adjusting the last 1 batches sequentially
2024-12-31 11:53:38.027719 INFO::Done
2024-12-31 11:53:38.027929 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:38.030292 INFO::ASW Batch was -0.0505498432076253 prior to batch effect correction and is now -0.0505498432076253 .
2024-12-31 11:53:38.031191 INFO::Total function execution time is 0.119047164916992 s and adjustment time is 0.111745834350586 s ( 93.87 )
2024-12-31 11:53:38.162627 INFO::Formatting Data.
2024-12-31 11:53:38.163002 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:38.16344 INFO::Removing potential empty rows and columns
2024-12-31 11:53:38.164822 INFO::Found 1000 missing values.
2024-12-31 11:53:38.174028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:38.174368 INFO::Done
2024-12-31 11:53:38.174802 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:38.178984 INFO::Starting hierarchical adjustment
2024-12-31 11:53:38.179322 INFO::Found 10 batches.
2024-12-31 11:53:38.179524 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:38.179751 INFO::Using default BPPARAM
2024-12-31 11:53:38.179937 INFO::Processing subtree level 1
2024-12-31 11:53:38.290867 INFO::Processing subtree level 2
2024-12-31 11:53:38.429725 INFO::Adjusting the last 1 batches sequentially
2024-12-31 11:53:38.432037 INFO::Done
2024-12-31 11:53:38.432341 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:38.436269 INFO::ASW Batch was 0.500664621122176 prior to batch effect correction and is now 0.500664621122176 .
2024-12-31 11:53:38.436623 INFO::ASW Label was 0.330384912371837 prior to batch effect correction and is now 0.330384912371837 .
2024-12-31 11:53:38.437365 INFO::Total function execution time is 0.274724006652832 s and adjustment time is 0.252755165100098 s ( 92 )
2024-12-31 11:53:38.437863 INFO::Formatting Data.
2024-12-31 11:53:38.438147 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:38.438816 INFO::Removing potential empty rows and columns
2024-12-31 11:53:38.4401 INFO::Found 1000 missing values.
2024-12-31 11:53:38.447115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:38.447427 INFO::Done
2024-12-31 11:53:38.447614 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:38.449786 INFO::Starting hierarchical adjustment
2024-12-31 11:53:38.450098 INFO::Found 10 batches.
2024-12-31 11:53:38.934568 INFO::Set up parallel execution backend with 2 workers
2024-12-31 11:53:38.935259 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-12-31 11:53:39.472411 INFO::Adjusting the last 2 batches sequentially
2024-12-31 11:53:39.473029 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-31 11:53:39.480988 INFO::Done
2024-12-31 11:53:39.481302 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:39.483429 INFO::ASW Batch was 0.500664621122176 prior to batch effect correction and is now 0.500664621122176 .
2024-12-31 11:53:39.483674 INFO::ASW Label was 0.330384912371837 prior to batch effect correction and is now 0.330384912371837 .
2024-12-31 11:53:39.483917 INFO::Total function execution time is 1.04608201980591 s and adjustment time is 1.03091883659363 s ( 98.55 )
2024-12-31 11:53:39.544563 INFO::Formatting Data.
2024-12-31 11:53:39.544854 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.545323 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.545737 INFO::Found 0 missing values.
2024-12-31 11:53:39.546949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.547149 INFO::Done
2024-12-31 11:53:39.547317 INFO::Acquiring quality metrics before batch effect correction.
2024-12-31 11:53:39.548305 INFO::Starting hierarchical adjustment
2024-12-31 11:53:39.548608 INFO::Found 3 batches.
2024-12-31 11:53:39.5488 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-31 11:53:39.549032 INFO::Using default BPPARAM
2024-12-31 11:53:39.549208 INFO::Processing subtree level 1
2024-12-31 11:53:39.592239 INFO::Adjusting the last 1 batches sequentially
2024-12-31 11:53:39.596441 INFO::Done
2024-12-31 11:53:39.596805 INFO::Acquiring quality metrics after batch effect correction.
2024-12-31 11:53:39.599808 INFO::ASW Batch was 0.187632000899964 prior to batch effect correction and is now -0.11348982267845 .
2024-12-31 11:53:39.600065 INFO::ASW Label was -0.225815061210659 prior to batch effect correction and is now -0.0920665406940366 .
2024-12-31 11:53:39.601222 INFO::Total function execution time is 0.0562288761138916 s and adjustment time is 0.0478711128234863 s ( 85.14 )
2024-12-31 11:53:39.650058 INFO::Formatting Data.
2024-12-31 11:53:39.650396 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.650842 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.65126 INFO::Found 2 missing values.
2024-12-31 11:53:39.652217 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.65241 INFO::Done
2024-12-31 11:53:39.663763 INFO::Found NA in Reference column
2024-12-31 11:53:39.667623 INFO::Require at least two references per batch.
2024-12-31 11:53:39.675422 INFO::Formatting Data.
2024-12-31 11:53:39.675749 INFO::Recognized SummarizedExperiment
2024-12-31 11:53:39.675928 INFO::Typecasting input to dataframe.
2024-12-31 11:53:39.679973 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.680444 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.681785 INFO::Found 0 missing values.
2024-12-31 11:53:39.68436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.68459 INFO::Done
2024-12-31 11:53:39.690117 INFO::Formatting Data.
2024-12-31 11:53:39.690399 INFO::Recognized SummarizedExperiment
2024-12-31 11:53:39.690569 INFO::Typecasting input to dataframe.
2024-12-31 11:53:39.697856 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.698349 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.701259 INFO::Found 0 missing values.
2024-12-31 11:53:39.712556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.713316 INFO::Done
2024-12-31 11:53:39.727864 INFO::Formatting Data.
2024-12-31 11:53:39.728549 INFO::Recognized SummarizedExperiment
2024-12-31 11:53:39.729055 INFO::Typecasting input to dataframe.
2024-12-31 11:53:39.745029 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.746132 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.747265 INFO::Found 0 missing values.
2024-12-31 11:53:39.748083 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.
2024-12-31 11:53:39.750581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.750887 INFO::Done
2024-12-31 11:53:39.755659 INFO::Formatting Data.
2024-12-31 11:53:39.756017 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.75635 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.756729 INFO::Found 0 missing values.
2024-12-31 11:53:39.757786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.758048 INFO::Done
2024-12-31 11:53:39.762526 INFO::Formatting Data.
2024-12-31 11:53:39.762809 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.763113 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.763443 INFO::Found 0 missing values.
2024-12-31 11:53:39.764376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.764555 INFO::Done
2024-12-31 11:53:39.775453 INFO::Formatting Data.
2024-12-31 11:53:39.77575 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.776107 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.776483 INFO::Found 1 missing values.
2024-12-31 11:53:39.777313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.777493 INFO::Done
2024-12-31 11:53:39.784164 INFO::Formatting Data.
2024-12-31 11:53:39.784448 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.784727 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.785026 INFO::Found 2 missing values.
2024-12-31 11:53:39.785316 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.
2024-12-31 11:53:39.78606 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.786244 INFO::Done
2024-12-31 11:53:39.790146 INFO::Formatting Data.
2024-12-31 11:53:39.790439 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.790725 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.791041 INFO::Found 2 missing values.
2024-12-31 11:53:39.791656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.791893 INFO::Done
2024-12-31 11:53:39.796087 INFO::Formatting Data.
2024-12-31 11:53:39.79638 INFO::Typecasting input to dataframe.
2024-12-31 11:53:39.796643 INFO::Replacing NaNs with NAs.
2024-12-31 11:53:39.79693 INFO::Removing potential empty rows and columns
2024-12-31 11:53:39.797274 INFO::Found 0 missing values.
2024-12-31 11:53:39.798232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-31 11:53:39.798441 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
11.109 1.673 14.000
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.761 | 1.185 | 20.513 | |
| compute_asw | 0.030 | 0.002 | 0.032 | |
| count_existing | 0.017 | 0.002 | 0.019 | |
| generate_data_covariables | 0.014 | 0.002 | 0.016 | |
| generate_dataset | 0.013 | 0.002 | 0.015 | |