Yannis Schumann
| Snapshot Date: 2024-10-04 13:40 -0400 (Fri, 04 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-05 11:43 -0400 (Sat, 05 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| 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 158/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.1.2 |
| 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_1.1.2.tar.gz |
| StartedAt: 2024-10-04 19:35:57 -0400 (Fri, 04 Oct 2024) |
| EndedAt: 2024-10-04 19:36:26 -0400 (Fri, 04 Oct 2024) |
| EllapsedTime: 29.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* 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 9.487 0.354 6.73
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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")
2024-10-04 19:36:19.338091 INFO::Formatting Data.
2024-10-04 19:36:19.339732 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:19.344023 INFO::Removing potential empty rows and columns
2024-10-04 19:36:19.452287 INFO::Found 0 missing values.
2024-10-04 19:36:19.453534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:19.453746 INFO::Done
2024-10-04 19:36:19.453922 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:19.459647 INFO::Starting hierarchical adjustment
2024-10-04 19:36:19.459949 INFO::Found 3 batches.
2024-10-04 19:36:19.460135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:19.460539 INFO::Using default BPPARAM
2024-10-04 19:36:19.460699 INFO::Processing subtree level 1
2024-10-04 19:36:19.502978 INFO::Adjusting the last 1 batches sequentially
2024-10-04 19:36:19.504606 INFO::Done
2024-10-04 19:36:19.504982 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:19.506343 INFO::ASW Batch was -0.0706990827399764 prior to batch effect correction and is now -0.0706990827399764 .
2024-10-04 19:36:19.50692 INFO::Total function execution time is 0.169107913970947 s and adjustment time is 0.0447080135345459 s ( 26.44 )
2024-10-04 19:36:19.514508 INFO::Formatting Data.
2024-10-04 19:36:19.514776 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:19.515074 INFO::Removing potential empty rows and columns
2024-10-04 19:36:19.515474 INFO::Found 0 missing values.
2024-10-04 19:36:19.515779 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-04 19:36:19.519666 INFO::Formatting Data.
2024-10-04 19:36:19.519879 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:19.520149 INFO::Removing potential empty rows and columns
2024-10-04 19:36:19.520451 INFO::Found 0 missing values.
2024-10-04 19:36:19.52102 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-04 19:36:19.527987 INFO::Formatting Data.
2024-10-04 19:36:19.528262 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:19.528593 INFO::Removing potential empty rows and columns
2024-10-04 19:36:19.528983 INFO::Found 0 missing values.
2024-10-04 19:36:19.529295 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-04 19:36:19.530952 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:19.531166 INFO::Done
2024-10-04 19:36:19.531379 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:19.532044 INFO::Starting hierarchical adjustment
2024-10-04 19:36:19.532254 INFO::Found 2 batches.
2024-10-04 19:36:19.532427 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:19.53267 INFO::Using default BPPARAM
2024-10-04 19:36:19.532827 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:19.533099 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:19.543277 INFO::Done
2024-10-04 19:36:19.556947 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:19.558034 INFO::ASW Batch was -0.0331714356010954 prior to batch effect correction and is now -0.131764592297778 .
2024-10-04 19:36:19.55841 INFO::Total function execution time is 0.0304489135742188 s and adjustment time is 0.0110499858856201 s ( 36.29 )
2024-10-04 19:36:19.559712 INFO::Formatting Data.
2024-10-04 19:36:19.559971 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:19.563178 INFO::Formatting Data.
2024-10-04 19:36:19.563397 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:19.563679 INFO::Removing potential empty rows and columns
2024-10-04 19:36:19.564024 INFO::Found 0 missing values.
2024-10-04 19:36:19.564975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:19.565179 INFO::Done
2024-10-04 19:36:19.565373 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:19.566095 INFO::Starting hierarchical adjustment
2024-10-04 19:36:19.566358 INFO::Found 2 batches.
2024-10-04 19:36:19.566536 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:19.566763 INFO::Using default BPPARAM
2024-10-04 19:36:19.567027 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:19.567343 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:19.57258 INFO::Done
2024-10-04 19:36:19.572802 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:19.57343 INFO::ASW Batch was -0.0678530416913705 prior to batch effect correction and is now -0.11570160921899 .
2024-10-04 19:36:19.573655 INFO::Total function execution time is 0.0104911327362061 s and adjustment time is 0.00627708435058594 s ( 59.83 )
2024-10-04 19:36:19.573959 INFO::Formatting Data.
2024-10-04 19:36:19.574124 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:19.574363 INFO::Removing potential empty rows and columns
2024-10-04 19:36:19.574646 INFO::Found 0 missing values.
2024-10-04 19:36:19.575457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:19.575612 INFO::Done
2024-10-04 19:36:19.57575 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:19.576307 INFO::Starting hierarchical adjustment
2024-10-04 19:36:19.576504 INFO::Found 2 batches.
2024-10-04 19:36:19.576666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:19.57684 INFO::Using default BPPARAM
2024-10-04 19:36:19.576983 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:19.577225 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:19.581934 INFO::Done
2024-10-04 19:36:19.582131 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:19.58275 INFO::ASW Batch was -0.0678530416913705 prior to batch effect correction and is now -0.11570160921899 .
2024-10-04 19:36:19.582988 INFO::Total function execution time is 0.00902199745178223 s and adjustment time is 0.0054619312286377 s ( 60.54 )
2024-10-04 19:36:20.429279 INFO::Formatting Data.
2024-10-04 19:36:20.429527 INFO::Recognized SummarizedExperiment
2024-10-04 19:36:20.429676 INFO::Typecasting input to dataframe.
2024-10-04 19:36:20.440138 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:20.440506 INFO::Removing potential empty rows and columns
2024-10-04 19:36:20.441553 INFO::Found 0 missing values.
2024-10-04 19:36:20.44338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:20.443522 INFO::Done
2024-10-04 19:36:20.44365 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:20.444732 INFO::Starting hierarchical adjustment
2024-10-04 19:36:20.444916 INFO::Found 2 batches.
2024-10-04 19:36:20.445044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:20.44532 INFO::Using default BPPARAM
2024-10-04 19:36:20.445447 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:20.445692 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:20.460965 INFO::Done
2024-10-04 19:36:20.461156 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:20.462197 INFO::ASW Batch was 0.00407280253101662 prior to batch effect correction and is now -0.0897580296273253 .
2024-10-04 19:36:20.462424 INFO::Total function execution time is 0.0332620143890381 s and adjustment time is 0.0160810947418213 s ( 48.35 )
2024-10-04 19:36:20.468031 INFO::Formatting Data.
2024-10-04 19:36:20.468211 INFO::Recognized SummarizedExperiment
2024-10-04 19:36:20.468346 INFO::Typecasting input to dataframe.
2024-10-04 19:36:20.470906 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:20.471213 INFO::Removing potential empty rows and columns
2024-10-04 19:36:20.472177 INFO::Found 0 missing values.
2024-10-04 19:36:20.474055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:20.474202 INFO::Done
2024-10-04 19:36:20.474337 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:20.475377 INFO::Starting hierarchical adjustment
2024-10-04 19:36:20.475557 INFO::Found 2 batches.
2024-10-04 19:36:20.475691 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:20.475842 INFO::Using default BPPARAM
2024-10-04 19:36:20.475968 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:20.476214 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:20.483035 INFO::Done
2024-10-04 19:36:20.483198 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:20.4842 INFO::ASW Batch was -0.0144603325597335 prior to batch effect correction and is now -0.0144603325597335 .
2024-10-04 19:36:20.484419 INFO::Total function execution time is 0.0163810253143311 s and adjustment time is 0.00751495361328125 s ( 45.88 )
2024-10-04 19:36:20.490628 INFO::Formatting Data.
2024-10-04 19:36:20.490816 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:20.491044 INFO::Removing potential empty rows and columns
2024-10-04 19:36:20.491312 INFO::Found 0 missing values.
2024-10-04 19:36:20.492045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:20.492182 INFO::Done
2024-10-04 19:36:20.492318 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:20.492834 INFO::Starting hierarchical adjustment
2024-10-04 19:36:20.493013 INFO::Found 3 batches.
2024-10-04 19:36:20.493142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:20.493299 INFO::Using default BPPARAM
2024-10-04 19:36:20.493423 INFO::Processing subtree level 1
2024-10-04 19:36:20.558331 INFO::Adjusting the last 1 batches sequentially
2024-10-04 19:36:20.559732 INFO::Done
2024-10-04 19:36:20.560085 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:20.561593 INFO::ASW Batch was -0.127935445680815 prior to batch effect correction and is now -0.153293772887225 .
2024-10-04 19:36:20.562115 INFO::Total function execution time is 0.0713307857513428 s and adjustment time is 0.0667529106140137 s ( 93.58 )
2024-10-04 19:36:20.569939 INFO::Skipping initial DF formatting
2024-10-04 19:36:20.570191 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:20.571728 INFO::Starting hierarchical adjustment
2024-10-04 19:36:20.572001 INFO::Found 5 batches.
2024-10-04 19:36:20.572187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:20.572443 INFO::Using default BPPARAM
2024-10-04 19:36:20.572637 INFO::Processing subtree level 1
2024-10-04 19:36:20.627269 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:20.628937 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:20.637169 INFO::Done
2024-10-04 19:36:20.6374 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:20.639134 INFO::ASW Batch was 0.530242145579946 prior to batch effect correction and is now 0.530242145579946 .
2024-10-04 19:36:20.639325 INFO::ASW Label was 0.372340532970127 prior to batch effect correction and is now 0.372340532970127 .
2024-10-04 19:36:20.639654 INFO::Total function execution time is 0.0697221755981445 s and adjustment time is 0.0652329921722412 s ( 93.56 )
2024-10-04 19:36:20.646605 INFO::Formatting Data.
2024-10-04 19:36:20.646832 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:20.647112 INFO::Removing potential empty rows and columns
2024-10-04 19:36:20.647443 INFO::Found 0 missing values.
2024-10-04 19:36:20.6486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:20.64876 INFO::Done
2024-10-04 19:36:20.648907 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:20.649783 INFO::Starting hierarchical adjustment
2024-10-04 19:36:20.650005 INFO::Found 5 batches.
2024-10-04 19:36:20.650163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:20.650361 INFO::Using default BPPARAM
2024-10-04 19:36:20.650513 INFO::Processing subtree level 1
2024-10-04 19:36:20.703602 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:20.705554 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:20.713574 INFO::Done
2024-10-04 19:36:20.713807 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:20.715251 INFO::ASW Batch was 0.274018594875352 prior to batch effect correction and is now -0.0777816571838508 .
2024-10-04 19:36:20.71559 INFO::ASW Label was 0.482393675679598 prior to batch effect correction and is now 0.845477278543132 .
2024-10-04 19:36:20.715903 INFO::Total function execution time is 0.0692770481109619 s and adjustment time is 0.0636038780212402 s ( 91.81 )
2024-10-04 19:36:20.716237 INFO::Formatting Data.
2024-10-04 19:36:20.716436 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:20.716735 INFO::Removing potential empty rows and columns
2024-10-04 19:36:20.717418 INFO::Found 0 missing values.
2024-10-04 19:36:20.718709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:20.718896 INFO::Done
2024-10-04 19:36:20.71906 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:20.720159 INFO::Starting hierarchical adjustment
2024-10-04 19:36:20.720446 INFO::Found 5 batches.
2024-10-04 19:36:20.720616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:20.72088 INFO::Using default BPPARAM
2024-10-04 19:36:20.721253 INFO::Processing subtree level 1
2024-10-04 19:36:20.767984 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:20.769789 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:20.785307 INFO::Done
2024-10-04 19:36:20.785574 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:20.786995 INFO::ASW Batch was 0.274018594875352 prior to batch effect correction and is now -0.0777816571838508 .
2024-10-04 19:36:20.787324 INFO::ASW Label was 0.482393675679598 prior to batch effect correction and is now 0.845477278543132 .
2024-10-04 19:36:20.787667 INFO::Total function execution time is 0.0713870525360107 s and adjustment time is 0.0647449493408203 s ( 90.7 )
2024-10-04 19:36:20.803042 INFO::Formatting Data.
2024-10-04 19:36:20.803383 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:20.80375 INFO::Removing potential empty rows and columns
2024-10-04 19:36:20.804223 INFO::Found 0 missing values.
2024-10-04 19:36:20.805793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:20.806139 INFO::Done
2024-10-04 19:36:20.806333 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:20.807566 INFO::Starting hierarchical adjustment
2024-10-04 19:36:20.80785 INFO::Found 5 batches.
2024-10-04 19:36:20.808071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:20.80832 INFO::Using default BPPARAM
2024-10-04 19:36:20.808499 INFO::Processing subtree level 1
2024-10-04 19:36:20.902534 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:20.903642 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:20.928095 INFO::Done
2024-10-04 19:36:20.928375 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:20.929581 INFO::ASW Batch was 0.147845124885957 prior to batch effect correction and is now -0.0845024273300818 .
2024-10-04 19:36:20.92977 INFO::ASW Label was 0.579116020440558 prior to batch effect correction and is now 0.841057808217089 .
2024-10-04 19:36:20.930034 INFO::Total function execution time is 0.12703800201416 s and adjustment time is 0.120280981063843 s ( 94.68 )
2024-10-04 19:36:20.93028 INFO::Formatting Data.
2024-10-04 19:36:20.930458 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:20.930722 INFO::Removing potential empty rows and columns
2024-10-04 19:36:20.931035 INFO::Found 0 missing values.
2024-10-04 19:36:20.932292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:20.932469 INFO::Done
2024-10-04 19:36:20.932621 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:20.933594 INFO::Starting hierarchical adjustment
2024-10-04 19:36:20.933817 INFO::Found 5 batches.
2024-10-04 19:36:20.934025 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:20.934283 INFO::Using default BPPARAM
2024-10-04 19:36:20.934495 INFO::Processing subtree level 1
2024-10-04 19:36:20.987845 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:20.989708 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:21.004326 INFO::Done
2024-10-04 19:36:21.005995 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.007454 INFO::ASW Batch was 0.147845124885957 prior to batch effect correction and is now -0.0845024273300818 .
2024-10-04 19:36:21.007674 INFO::ASW Label was 0.579116020440558 prior to batch effect correction and is now 0.841057808217089 .
2024-10-04 19:36:21.007982 INFO::Total function execution time is 0.0776739120483398 s and adjustment time is 0.0705451965332031 s ( 90.82 )
2024-10-04 19:36:21.01865 INFO::Formatting Data.
2024-10-04 19:36:21.018936 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.019274 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.019659 INFO::Found 0 missing values.
2024-10-04 19:36:21.020713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.020893 INFO::Done
2024-10-04 19:36:21.021089 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.022194 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.022479 INFO::Found 2 batches.
2024-10-04 19:36:21.022684 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.022929 INFO::Using default BPPARAM
2024-10-04 19:36:21.023632 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:21.024069 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:21.034513 INFO::Done
2024-10-04 19:36:21.052167 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.053375 INFO::ASW Batch was 0.721112365926837 prior to batch effect correction and is now -0.0114585316599334 .
2024-10-04 19:36:21.053589 INFO::ASW Label was 0.322899320845539 prior to batch effect correction and is now 0.848523353978718 .
2024-10-04 19:36:21.053853 INFO::Total function execution time is 0.035250186920166 s and adjustment time is 0.0120749473571777 s ( 34.25 )
2024-10-04 19:36:21.054125 INFO::Formatting Data.
2024-10-04 19:36:21.054299 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.054558 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.054877 INFO::Found 0 missing values.
2024-10-04 19:36:21.055861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.056027 INFO::Done
2024-10-04 19:36:21.056315 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.057773 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.058073 INFO::Found 2 batches.
2024-10-04 19:36:21.058251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.058454 INFO::Using default BPPARAM
2024-10-04 19:36:21.058626 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:21.058928 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:21.064482 INFO::Done
2024-10-04 19:36:21.064731 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.065686 INFO::ASW Batch was 0.721112365926837 prior to batch effect correction and is now -0.0114585316599334 .
2024-10-04 19:36:21.065871 INFO::ASW Label was 0.322899320845539 prior to batch effect correction and is now 0.848523353978718 .
2024-10-04 19:36:21.066102 INFO::Total function execution time is 0.0119690895080566 s and adjustment time is 0.00648093223571777 s ( 54.15 )
2024-10-04 19:36:21.072305 INFO::Formatting Data.
2024-10-04 19:36:21.072534 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.072807 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.073119 INFO::Found 0 missing values.
2024-10-04 19:36:21.073778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.073939 INFO::Done
2024-10-04 19:36:21.074094 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.074781 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.075001 INFO::Found 2 batches.
2024-10-04 19:36:21.075164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.075347 INFO::Using default BPPARAM
2024-10-04 19:36:21.075503 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:21.075794 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:21.087323 INFO::Done
2024-10-04 19:36:21.087651 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.088378 INFO::ASW Batch was 0.114960805101709 prior to batch effect correction and is now -0.178130880667496 .
2024-10-04 19:36:21.088663 INFO::Total function execution time is 0.0163741111755371 s and adjustment time is 0.0123510360717773 s ( 75.43 )
2024-10-04 19:36:21.094965 INFO::Formatting Data.
2024-10-04 19:36:21.095214 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.095586 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.096035 INFO::Found 0 missing values.
2024-10-04 19:36:21.096563 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-04 19:36:21.098594 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.0988 INFO::Done
2024-10-04 19:36:21.098991 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.100059 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.10039 INFO::Found 2 batches.
2024-10-04 19:36:21.100629 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.100888 INFO::Using default BPPARAM
2024-10-04 19:36:21.101037 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:21.101329 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:21.108143 INFO::Done
2024-10-04 19:36:21.108395 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.109373 INFO::ASW Batch was 0.580180050161829 prior to batch effect correction and is now 0.014569570558992 .
2024-10-04 19:36:21.109592 INFO::ASW Label was 0.475367455658635 prior to batch effect correction and is now 0.897680656092597 .
2024-10-04 19:36:21.109846 INFO::Total function execution time is 0.0148940086364746 s and adjustment time is 0.00782394409179688 s ( 52.53 )
2024-10-04 19:36:21.110095 INFO::Formatting Data.
2024-10-04 19:36:21.110294 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.110602 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.110919 INFO::Found 0 missing values.
2024-10-04 19:36:21.111222 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-04 19:36:21.112879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.113054 INFO::Done
2024-10-04 19:36:21.113211 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.114103 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.114321 INFO::Found 2 batches.
2024-10-04 19:36:21.114481 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.114671 INFO::Using default BPPARAM
2024-10-04 19:36:21.114834 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:21.11511 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:21.121495 INFO::Done
2024-10-04 19:36:21.121732 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.122661 INFO::ASW Batch was 0.580180050161829 prior to batch effect correction and is now 0.014569570558992 .
2024-10-04 19:36:21.122845 INFO::ASW Label was 0.475367455658635 prior to batch effect correction and is now 0.897680656092597 .
2024-10-04 19:36:21.123099 INFO::Total function execution time is 0.0129930973052979 s and adjustment time is 0.00720500946044922 s ( 55.45 )
2024-10-04 19:36:21.201249 INFO::Formatting Data.
2024-10-04 19:36:21.201535 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.201816 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.202143 INFO::Found 0 missing values.
2024-10-04 19:36:21.203118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.203289 INFO::Done
2024-10-04 19:36:21.203445 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.204101 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.204303 INFO::Found 3 batches.
2024-10-04 19:36:21.20445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.204634 INFO::Using default BPPARAM
2024-10-04 19:36:21.204774 INFO::Processing subtree level 1
2024-10-04 19:36:21.264422 INFO::Adjusting the last 1 batches sequentially
2024-10-04 19:36:21.266576 INFO::Done
2024-10-04 19:36:21.266837 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.268563 INFO::ASW Batch was -0.0847273340037073 prior to batch effect correction and is now -0.0847273340037073 .
2024-10-04 19:36:21.269021 INFO::Total function execution time is 0.0677900314331055 s and adjustment time is 0.0622990131378174 s ( 91.9 )
2024-10-04 19:36:21.269426 INFO::Formatting Data.
2024-10-04 19:36:21.269636 INFO::Typecasting input to dataframe.
2024-10-04 19:36:21.270029 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.270518 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.27118 INFO::Found 0 missing values.
2024-10-04 19:36:21.272382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.272596 INFO::Done
2024-10-04 19:36:21.272779 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.273698 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.273982 INFO::Found 3 batches.
2024-10-04 19:36:21.274218 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.274504 INFO::Using default BPPARAM
2024-10-04 19:36:21.274742 INFO::Processing subtree level 1
2024-10-04 19:36:21.327105 INFO::Adjusting the last 1 batches sequentially
2024-10-04 19:36:21.328868 INFO::Done
2024-10-04 19:36:21.329352 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.330999 INFO::ASW Batch was -0.0847273340037073 prior to batch effect correction and is now -0.0847273340037073 .
2024-10-04 19:36:21.331531 INFO::Total function execution time is 0.0619769096374512 s and adjustment time is 0.0549509525299072 s ( 88.66 )
2024-10-04 19:36:21.339228 INFO::Formatting Data.
2024-10-04 19:36:21.339516 INFO::Typecasting input to dataframe.
2024-10-04 19:36:21.339877 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.340265 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.340771 INFO::Found 0 missing values.
2024-10-04 19:36:21.342257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.342452 INFO::Done
2024-10-04 19:36:21.342773 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.34354 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.34378 INFO::Found 3 batches.
2024-10-04 19:36:21.343964 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.344208 INFO::Using default BPPARAM
2024-10-04 19:36:21.344405 INFO::Processing subtree level 1
2024-10-04 19:36:21.396308 INFO::Adjusting the last 1 batches sequentially
2024-10-04 19:36:21.398274 INFO::Done
2024-10-04 19:36:21.398667 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.400449 INFO::ASW Batch was 0.0829607397571273 prior to batch effect correction and is now 0.0829607397571273 .
2024-10-04 19:36:21.401216 INFO::Total function execution time is 0.0619769096374512 s and adjustment time is 0.0545389652252197 s ( 88 )
2024-10-04 19:36:21.497749 INFO::Formatting Data.
2024-10-04 19:36:21.498055 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.498495 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.499767 INFO::Found 1000 missing values.
2024-10-04 19:36:21.50953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.509968 INFO::Done
2024-10-04 19:36:21.510284 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.513156 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.513471 INFO::Found 10 batches.
2024-10-04 19:36:21.513709 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:21.514074 INFO::Using default BPPARAM
2024-10-04 19:36:21.51431 INFO::Processing subtree level 1
2024-10-04 19:36:21.596661 INFO::Processing subtree level 2
2024-10-04 19:36:21.677274 INFO::Adjusting the last 1 batches sequentially
2024-10-04 19:36:21.67894 INFO::Done
2024-10-04 19:36:21.6795 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:21.683121 INFO::ASW Batch was 0.50550159030874 prior to batch effect correction and is now 0.50550159030874 .
2024-10-04 19:36:21.683489 INFO::ASW Label was 0.352222732547383 prior to batch effect correction and is now 0.352222732547383 .
2024-10-04 19:36:21.684086 INFO::Total function execution time is 0.186308145523071 s and adjustment time is 0.165512084960938 s ( 88.84 )
2024-10-04 19:36:21.684744 INFO::Formatting Data.
2024-10-04 19:36:21.685115 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:21.685968 INFO::Removing potential empty rows and columns
2024-10-04 19:36:21.696081 INFO::Found 1000 missing values.
2024-10-04 19:36:21.704043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:21.704334 INFO::Done
2024-10-04 19:36:21.704522 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:21.706725 INFO::Starting hierarchical adjustment
2024-10-04 19:36:21.707017 INFO::Found 10 batches.
2024-10-04 19:36:22.095066 INFO::Set up parallel execution backend with 2 workers
2024-10-04 19:36:22.095305 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-04 19:36:22.527409 INFO::Adjusting the last 2 batches sequentially
2024-10-04 19:36:22.527911 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-04 19:36:22.533271 INFO::Done
2024-10-04 19:36:22.533469 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:22.535188 INFO::ASW Batch was 0.50550159030874 prior to batch effect correction and is now 0.50550159030874 .
2024-10-04 19:36:22.535352 INFO::ASW Label was 0.352222732547383 prior to batch effect correction and is now 0.352222732547383 .
2024-10-04 19:36:22.535566 INFO::Total function execution time is 0.850903987884521 s and adjustment time is 0.826312065124512 s ( 97.11 )
2024-10-04 19:36:22.596508 INFO::Formatting Data.
2024-10-04 19:36:22.596797 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.597096 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.597522 INFO::Found 0 missing values.
2024-10-04 19:36:22.598847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.599053 INFO::Done
2024-10-04 19:36:22.599205 INFO::Acquiring quality metrics before batch effect correction.
2024-10-04 19:36:22.600139 INFO::Starting hierarchical adjustment
2024-10-04 19:36:22.600383 INFO::Found 3 batches.
2024-10-04 19:36:22.600535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-04 19:36:22.60074 INFO::Using default BPPARAM
2024-10-04 19:36:22.600903 INFO::Processing subtree level 1
2024-10-04 19:36:22.654083 INFO::Adjusting the last 1 batches sequentially
2024-10-04 19:36:22.656348 INFO::Done
2024-10-04 19:36:22.65657 INFO::Acquiring quality metrics after batch effect correction.
2024-10-04 19:36:22.658438 INFO::ASW Batch was 0.153055606560066 prior to batch effect correction and is now -0.129473368611097 .
2024-10-04 19:36:22.658665 INFO::ASW Label was -0.200849007325722 prior to batch effect correction and is now -0.0788034111639326 .
2024-10-04 19:36:22.659159 INFO::Total function execution time is 0.062628984451294 s and adjustment time is 0.0559990406036377 s ( 89.41 )
2024-10-04 19:36:22.709609 INFO::Formatting Data.
2024-10-04 19:36:22.709922 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.710229 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.710615 INFO::Found 2 missing values.
2024-10-04 19:36:22.711556 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.711724 INFO::Done
2024-10-04 19:36:22.723004 INFO::Found NA in Reference column
2024-10-04 19:36:22.72679 INFO::Require at least two references per batch.
2024-10-04 19:36:22.735942 INFO::Formatting Data.
2024-10-04 19:36:22.736209 INFO::Recognized SummarizedExperiment
2024-10-04 19:36:22.736399 INFO::Typecasting input to dataframe.
2024-10-04 19:36:22.741288 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.74173 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.743288 INFO::Found 0 missing values.
2024-10-04 19:36:22.746247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.746476 INFO::Done
2024-10-04 19:36:22.752485 INFO::Formatting Data.
2024-10-04 19:36:22.752721 INFO::Recognized SummarizedExperiment
2024-10-04 19:36:22.752877 INFO::Typecasting input to dataframe.
2024-10-04 19:36:22.758846 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.759289 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.760724 INFO::Found 0 missing values.
2024-10-04 19:36:22.765328 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.765545 INFO::Done
2024-10-04 19:36:22.771969 INFO::Formatting Data.
2024-10-04 19:36:22.772223 INFO::Recognized SummarizedExperiment
2024-10-04 19:36:22.7724 INFO::Typecasting input to dataframe.
2024-10-04 19:36:22.77843 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.778821 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.779234 INFO::Found 0 missing values.
2024-10-04 19:36:22.779576 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-04 19:36:22.781498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.781874 INFO::Done
2024-10-04 19:36:22.78658 INFO::Formatting Data.
2024-10-04 19:36:22.786888 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.787217 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.787621 INFO::Found 0 missing values.
2024-10-04 19:36:22.789118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.78932 INFO::Done
2024-10-04 19:36:22.794166 INFO::Formatting Data.
2024-10-04 19:36:22.794379 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.794632 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.794921 INFO::Found 0 missing values.
2024-10-04 19:36:22.795813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.795962 INFO::Done
2024-10-04 19:36:22.806719 INFO::Formatting Data.
2024-10-04 19:36:22.806963 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.807274 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.807616 INFO::Found 1 missing values.
2024-10-04 19:36:22.80846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.808634 INFO::Done
2024-10-04 19:36:22.815373 INFO::Formatting Data.
2024-10-04 19:36:22.815595 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.815902 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.816165 INFO::Found 2 missing values.
2024-10-04 19:36:22.816424 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-04 19:36:22.817124 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.817269 INFO::Done
2024-10-04 19:36:22.820727 INFO::Formatting Data.
2024-10-04 19:36:22.820935 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.821205 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.821514 INFO::Found 2 missing values.
2024-10-04 19:36:22.822024 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.822198 INFO::Done
2024-10-04 19:36:22.826092 INFO::Formatting Data.
2024-10-04 19:36:22.826322 INFO::Typecasting input to dataframe.
2024-10-04 19:36:22.82658 INFO::Replacing NaNs with NAs.
2024-10-04 19:36:22.82684 INFO::Removing potential empty rows and columns
2024-10-04 19:36:22.827124 INFO::Found 0 missing values.
2024-10-04 19:36:22.827958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-04 19:36:22.828116 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.296 1.568 8.130
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.487 | 0.354 | 6.730 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.005 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |