Yannis Schumann
| Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-15 11:44 -0400 (Mon, 15 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 154/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | 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 | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | 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: 1.1.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-07-14 22:06:55 -0400 (Sun, 14 Jul 2024) |
| EndedAt: 2024-07-14 22:09:12 -0400 (Sun, 14 Jul 2024) |
| EllapsedTime: 136.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.1.0'
* 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 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 9.07 0.5 18.83
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2024-07-14 22:07:59.538272 INFO::Formatting Data.
2024-07-14 22:07:59.541389 INFO::Replacing NaNs with NAs.
2024-07-14 22:07:59.557295 INFO::Removing potential empty rows and columns
2024-07-14 22:07:59.882986 INFO::Found 0 missing values.
2024-07-14 22:07:59.889322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:07:59.890751 INFO::Done
2024-07-14 22:07:59.892024 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:07:59.911472 INFO::Starting hierarchical adjustment
2024-07-14 22:07:59.912548 INFO::Found 3 batches.
2024-07-14 22:07:59.913297 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:07:59.914576 INFO::Using default BPPARAM
2024-07-14 22:07:59.915327 INFO::Processing subtree level 1
2024-07-14 22:08:02.633154 INFO::Adjusting the last 1 batches sequentially
2024-07-14 22:08:02.635518 INFO::Done
2024-07-14 22:08:02.636848 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:02.639972 INFO::ASW Batch was -0.136175050449096 prior to batch effect correction and is now -0.136175050449096 .
2024-07-14 22:08:02.641595 INFO::Total function execution time is 3.10408091545105 s and adjustment time is 2.72310614585876 s ( 87.73 )
2024-07-14 22:08:02.66299 INFO::Formatting Data.
2024-07-14 22:08:02.663987 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:02.665068 INFO::Removing potential empty rows and columns
2024-07-14 22:08:02.666222 INFO::Found 0 missing values.
2024-07-14 22:08:02.667309 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.
2024-07-14 22:08:02.681177 INFO::Formatting Data.
2024-07-14 22:08:02.682814 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:02.684679 INFO::Removing potential empty rows and columns
2024-07-14 22:08:02.686673 INFO::Found 0 missing values.
2024-07-14 22:08:02.688456 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.
2024-07-14 22:08:02.715944 INFO::Formatting Data.
2024-07-14 22:08:02.717575 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:02.719409 INFO::Removing potential empty rows and columns
2024-07-14 22:08:02.721431 INFO::Found 0 missing values.
2024-07-14 22:08:02.723282 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.
2024-07-14 22:08:02.730655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:02.732156 INFO::Done
2024-07-14 22:08:02.733489 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:02.736932 INFO::Starting hierarchical adjustment
2024-07-14 22:08:02.73839 INFO::Found 2 batches.
2024-07-14 22:08:02.739743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:02.741126 INFO::Using default BPPARAM
2024-07-14 22:08:02.742366 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:02.744245 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:02.771134 INFO::Done
2024-07-14 22:08:02.772573 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:02.775961 INFO::ASW Batch was 0.0103291984222401 prior to batch effect correction and is now -0.111561672838852 .
2024-07-14 22:08:02.777515 INFO::Total function execution time is 0.0616950988769531 s and adjustment time is 0.0329201221466064 s ( 53.36 )
2024-07-14 22:08:02.781764 INFO::Formatting Data.
2024-07-14 22:08:02.783183 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:02.794746 INFO::Formatting Data.
2024-07-14 22:08:02.796311 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:02.798179 INFO::Removing potential empty rows and columns
2024-07-14 22:08:02.80019 INFO::Found 0 missing values.
2024-07-14 22:08:02.804457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:02.805723 INFO::Done
2024-07-14 22:08:02.806956 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:02.810214 INFO::Starting hierarchical adjustment
2024-07-14 22:08:02.811633 INFO::Found 2 batches.
2024-07-14 22:08:02.812863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:02.814151 INFO::Using default BPPARAM
2024-07-14 22:08:02.815331 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:02.817061 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:02.837604 INFO::Done
2024-07-14 22:08:02.839051 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:02.84254 INFO::ASW Batch was -0.00839449713198305 prior to batch effect correction and is now -0.0738498808928332 .
2024-07-14 22:08:02.844201 INFO::Total function execution time is 0.0495190620422363 s and adjustment time is 0.0261440277099609 s ( 52.8 )
2024-07-14 22:08:02.846203 INFO::Formatting Data.
2024-07-14 22:08:02.847607 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:02.849267 INFO::Removing potential empty rows and columns
2024-07-14 22:08:02.850928 INFO::Found 0 missing values.
2024-07-14 22:08:02.85353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:02.854254 INFO::Done
2024-07-14 22:08:02.854954 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:02.857042 INFO::Starting hierarchical adjustment
2024-07-14 22:08:02.857919 INFO::Found 2 batches.
2024-07-14 22:08:02.858633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:02.859415 INFO::Using default BPPARAM
2024-07-14 22:08:02.860114 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:02.861178 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:02.879974 INFO::Done
2024-07-14 22:08:02.88141 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:02.884815 INFO::ASW Batch was -0.00839449713198305 prior to batch effect correction and is now -0.0738498808928332 .
2024-07-14 22:08:02.886177 INFO::Total function execution time is 0.0400450229644775 s and adjustment time is 0.0220968723297119 s ( 55.18 )
2024-07-14 22:08:05.634239 INFO::Formatting Data.
2024-07-14 22:08:05.635776 INFO::Recognized SummarizedExperiment
2024-07-14 22:08:05.637061 INFO::Typecasting input to dataframe.
2024-07-14 22:08:05.68205 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:05.684227 INFO::Removing potential empty rows and columns
2024-07-14 22:08:05.689189 INFO::Found 0 missing values.
2024-07-14 22:08:05.698544 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:05.700016 INFO::Done
2024-07-14 22:08:05.701338 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:05.707487 INFO::Starting hierarchical adjustment
2024-07-14 22:08:05.708974 INFO::Found 2 batches.
2024-07-14 22:08:05.710189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:05.712178 INFO::Using default BPPARAM
2024-07-14 22:08:05.713406 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:05.715399 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:05.773098 INFO::Done
2024-07-14 22:08:05.77461 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:05.780766 INFO::ASW Batch was -0.018441348670128 prior to batch effect correction and is now -0.0861913241925758 .
2024-07-14 22:08:05.782311 INFO::Total function execution time is 0.148423910140991 s and adjustment time is 0.064284086227417 s ( 43.31 )
2024-07-14 22:08:05.813998 INFO::Formatting Data.
2024-07-14 22:08:05.815536 INFO::Recognized SummarizedExperiment
2024-07-14 22:08:05.816862 INFO::Typecasting input to dataframe.
2024-07-14 22:08:05.832322 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:05.834796 INFO::Removing potential empty rows and columns
2024-07-14 22:08:05.840877 INFO::Found 0 missing values.
2024-07-14 22:08:05.852288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:05.853881 INFO::Done
2024-07-14 22:08:05.855247 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:05.861903 INFO::Starting hierarchical adjustment
2024-07-14 22:08:05.863508 INFO::Found 2 batches.
2024-07-14 22:08:05.86477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:05.866107 INFO::Using default BPPARAM
2024-07-14 22:08:05.867282 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:05.869242 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:05.906312 INFO::Done
2024-07-14 22:08:05.907871 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:05.914985 INFO::ASW Batch was -0.0283313262215689 prior to batch effect correction and is now -0.0283313262215689 .
2024-07-14 22:08:05.916899 INFO::Total function execution time is 0.102832078933716 s and adjustment time is 0.0430190563201904 s ( 41.83 )
2024-07-14 22:08:05.952839 INFO::Formatting Data.
2024-07-14 22:08:05.954464 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:05.956289 INFO::Removing potential empty rows and columns
2024-07-14 22:08:05.9583 INFO::Found 0 missing values.
2024-07-14 22:08:05.963736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:05.965069 INFO::Done
2024-07-14 22:08:05.966393 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:05.969961 INFO::Starting hierarchical adjustment
2024-07-14 22:08:05.971599 INFO::Found 3 batches.
2024-07-14 22:08:05.972971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:05.974439 INFO::Using default BPPARAM
2024-07-14 22:08:05.975767 INFO::Processing subtree level 1
2024-07-14 22:08:15.870422 INFO::Adjusting the last 1 batches sequentially
2024-07-14 22:08:15.872734 INFO::Done
2024-07-14 22:08:15.874102 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:15.877598 INFO::ASW Batch was -0.0683151906010887 prior to batch effect correction and is now -0.158163439327074 .
2024-07-14 22:08:15.87924 INFO::Total function execution time is 9.92650294303894 s and adjustment time is 9.90136194229126 s ( 99.75 )
2024-07-14 22:08:15.90439 INFO::Skipping initial DF formatting
2024-07-14 22:08:15.905326 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:15.909868 INFO::Starting hierarchical adjustment
2024-07-14 22:08:15.910976 INFO::Found 5 batches.
2024-07-14 22:08:15.911809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:15.912634 INFO::Using default BPPARAM
2024-07-14 22:08:15.913404 INFO::Processing subtree level 1
2024-07-14 22:08:18.85183 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:18.853373 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:18.867505 INFO::Done
2024-07-14 22:08:18.86841 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:18.872567 INFO::ASW Batch was 0.539418211564919 prior to batch effect correction and is now 0.539418211564919 .
2024-07-14 22:08:18.87343 INFO::ASW Label was 0.372253941708446 prior to batch effect correction and is now 0.372253941708446 .
2024-07-14 22:08:18.874446 INFO::Total function execution time is 2.97020506858826 s and adjustment time is 2.95670986175537 s ( 99.55 )
2024-07-14 22:08:18.900723 INFO::Formatting Data.
2024-07-14 22:08:18.902249 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:18.903958 INFO::Removing potential empty rows and columns
2024-07-14 22:08:18.905724 INFO::Found 0 missing values.
2024-07-14 22:08:18.910996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:18.912211 INFO::Done
2024-07-14 22:08:18.913379 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:18.917853 INFO::Starting hierarchical adjustment
2024-07-14 22:08:18.919251 INFO::Found 5 batches.
2024-07-14 22:08:18.920425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:18.921687 INFO::Using default BPPARAM
2024-07-14 22:08:18.922872 INFO::Processing subtree level 1
2024-07-14 22:08:23.874931 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:23.876944 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:23.890645 INFO::Done
2024-07-14 22:08:23.892133 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:23.897114 INFO::ASW Batch was 0.144596224782471 prior to batch effect correction and is now -0.0303614560594078 .
2024-07-14 22:08:23.898424 INFO::ASW Label was 0.633645914987338 prior to batch effect correction and is now 0.827312948036613 .
2024-07-14 22:08:23.899862 INFO::Total function execution time is 4.99928402900696 s and adjustment time is 4.97153091430664 s ( 99.44 )
2024-07-14 22:08:23.901022 INFO::Formatting Data.
2024-07-14 22:08:23.90182 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:23.902892 INFO::Removing potential empty rows and columns
2024-07-14 22:08:23.904023 INFO::Found 0 missing values.
2024-07-14 22:08:23.90752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:23.908275 INFO::Done
2024-07-14 22:08:23.908973 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:23.912314 INFO::Starting hierarchical adjustment
2024-07-14 22:08:23.913532 INFO::Found 5 batches.
2024-07-14 22:08:23.914354 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:23.915254 INFO::Using default BPPARAM
2024-07-14 22:08:23.91596 INFO::Processing subtree level 1
2024-07-14 22:08:26.881229 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:26.883378 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:26.90243 INFO::Done
2024-07-14 22:08:26.903348 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:26.906286 INFO::ASW Batch was 0.144596224782471 prior to batch effect correction and is now -0.0303614560594078 .
2024-07-14 22:08:26.907057 INFO::ASW Label was 0.633645914987338 prior to batch effect correction and is now 0.827312948036613 .
2024-07-14 22:08:26.907981 INFO::Total function execution time is 3.00698304176331 s and adjustment time is 2.98902297019958 s ( 99.4 )
2024-07-14 22:08:26.9263 INFO::Formatting Data.
2024-07-14 22:08:26.92743 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:26.928563 INFO::Removing potential empty rows and columns
2024-07-14 22:08:26.929649 INFO::Found 0 missing values.
2024-07-14 22:08:26.933388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:26.934138 INFO::Done
2024-07-14 22:08:26.934836 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:26.937785 INFO::Starting hierarchical adjustment
2024-07-14 22:08:26.938678 INFO::Found 5 batches.
2024-07-14 22:08:26.939451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:26.940307 INFO::Using default BPPARAM
2024-07-14 22:08:26.941031 INFO::Processing subtree level 1
2024-07-14 22:08:30.153954 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:30.155993 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:30.172899 INFO::Done
2024-07-14 22:08:30.174171 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:30.178422 INFO::ASW Batch was 0.384032683982196 prior to batch effect correction and is now -0.0957146931713199 .
2024-07-14 22:08:30.179664 INFO::ASW Label was 0.314760518315855 prior to batch effect correction and is now 0.887251326060377 .
2024-07-14 22:08:30.180768 INFO::Total function execution time is 3.25463819503784 s and adjustment time is 3.23429203033447 s ( 99.37 )
2024-07-14 22:08:30.181811 INFO::Formatting Data.
2024-07-14 22:08:30.182687 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:30.18379 INFO::Removing potential empty rows and columns
2024-07-14 22:08:30.18487 INFO::Found 0 missing values.
2024-07-14 22:08:30.188387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:30.189144 INFO::Done
2024-07-14 22:08:30.190345 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:30.194735 INFO::Starting hierarchical adjustment
2024-07-14 22:08:30.196023 INFO::Found 5 batches.
2024-07-14 22:08:30.197067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:30.198196 INFO::Using default BPPARAM
2024-07-14 22:08:30.199234 INFO::Processing subtree level 1
2024-07-14 22:08:33.346132 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:33.348251 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:33.366331 INFO::Done
2024-07-14 22:08:33.367717 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:33.372392 INFO::ASW Batch was 0.384032683982196 prior to batch effect correction and is now -0.0957146931713199 .
2024-07-14 22:08:33.37372 INFO::ASW Label was 0.314760518315855 prior to batch effect correction and is now 0.887251326060377 .
2024-07-14 22:08:33.375303 INFO::Total function execution time is 3.19343709945679 s and adjustment time is 3.17045187950134 s ( 99.28 )
2024-07-14 22:08:33.396795 INFO::Formatting Data.
2024-07-14 22:08:33.39777 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:33.398843 INFO::Removing potential empty rows and columns
2024-07-14 22:08:33.399937 INFO::Found 0 missing values.
2024-07-14 22:08:33.402314 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:33.403075 INFO::Done
2024-07-14 22:08:33.403779 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:33.406713 INFO::Starting hierarchical adjustment
2024-07-14 22:08:33.407596 INFO::Found 2 batches.
2024-07-14 22:08:33.408301 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:33.409068 INFO::Using default BPPARAM
2024-07-14 22:08:33.409762 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:33.410833 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:33.422494 INFO::Done
2024-07-14 22:08:33.423364 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:33.426329 INFO::ASW Batch was 0.321963394708402 prior to batch effect correction and is now 0.0868654922456865 .
2024-07-14 22:08:33.427115 INFO::ASW Label was 0.724440345018136 prior to batch effect correction and is now 0.854704168119144 .
2024-07-14 22:08:33.428056 INFO::Total function execution time is 0.0313599109649658 s and adjustment time is 0.0150179862976074 s ( 47.89 )
2024-07-14 22:08:33.42898 INFO::Formatting Data.
2024-07-14 22:08:33.429764 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:33.430777 INFO::Removing potential empty rows and columns
2024-07-14 22:08:33.431865 INFO::Found 0 missing values.
2024-07-14 22:08:33.434248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:33.434981 INFO::Done
2024-07-14 22:08:33.435686 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:33.438793 INFO::Starting hierarchical adjustment
2024-07-14 22:08:33.439694 INFO::Found 2 batches.
2024-07-14 22:08:33.440402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:33.441168 INFO::Using default BPPARAM
2024-07-14 22:08:33.441868 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:33.442938 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:33.454773 INFO::Done
2024-07-14 22:08:33.455659 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:33.458656 INFO::ASW Batch was 0.321963394708402 prior to batch effect correction and is now 0.0868654922456865 .
2024-07-14 22:08:33.459444 INFO::ASW Label was 0.724440345018136 prior to batch effect correction and is now 0.854704168119144 .
2024-07-14 22:08:33.460408 INFO::Total function execution time is 0.0314340591430664 s and adjustment time is 0.0151760578155518 s ( 48.28 )
2024-07-14 22:08:33.475296 INFO::Formatting Data.
2024-07-14 22:08:33.476262 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:33.477361 INFO::Removing potential empty rows and columns
2024-07-14 22:08:33.478402 INFO::Found 0 missing values.
2024-07-14 22:08:33.480383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:33.481136 INFO::Done
2024-07-14 22:08:33.481849 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:33.483812 INFO::Starting hierarchical adjustment
2024-07-14 22:08:33.484681 INFO::Found 2 batches.
2024-07-14 22:08:33.485404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:33.486188 INFO::Using default BPPARAM
2024-07-14 22:08:33.486894 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:33.487982 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:33.514927 INFO::Done
2024-07-14 22:08:33.51582 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:33.51802 INFO::ASW Batch was -0.0195459748891392 prior to batch effect correction and is now -0.157669056256432 .
2024-07-14 22:08:33.519036 INFO::Total function execution time is 0.043828010559082 s and adjustment time is 0.0303268432617188 s ( 69.2 )
2024-07-14 22:08:33.535296 INFO::Formatting Data.
2024-07-14 22:08:33.536282 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:33.537337 INFO::Removing potential empty rows and columns
2024-07-14 22:08:33.538495 INFO::Found 0 missing values.
2024-07-14 22:08:33.539838 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.
2024-07-14 22:08:33.544847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:33.546112 INFO::Done
2024-07-14 22:08:33.547351 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:33.551993 INFO::Starting hierarchical adjustment
2024-07-14 22:08:33.553044 INFO::Found 2 batches.
2024-07-14 22:08:33.553829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:33.554607 INFO::Using default BPPARAM
2024-07-14 22:08:33.555321 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:33.556413 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:33.571071 INFO::Done
2024-07-14 22:08:33.572574 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:33.577473 INFO::ASW Batch was 0.268762706552449 prior to batch effect correction and is now 0.138959279813974 .
2024-07-14 22:08:33.578871 INFO::ASW Label was 0.776304272166019 prior to batch effect correction and is now 0.844218569923248 .
2024-07-14 22:08:33.580501 INFO::Total function execution time is 0.0452051162719727 s and adjustment time is 0.0181059837341309 s ( 40.05 )
2024-07-14 22:08:33.582079 INFO::Formatting Data.
2024-07-14 22:08:33.583277 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:33.584369 INFO::Removing potential empty rows and columns
2024-07-14 22:08:33.585514 INFO::Found 0 missing values.
2024-07-14 22:08:33.586624 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.
2024-07-14 22:08:33.590822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:33.591658 INFO::Done
2024-07-14 22:08:33.592377 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:33.595597 INFO::Starting hierarchical adjustment
2024-07-14 22:08:33.596544 INFO::Found 2 batches.
2024-07-14 22:08:33.597259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:33.598102 INFO::Using default BPPARAM
2024-07-14 22:08:33.598892 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:33.600071 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:33.620968 INFO::Done
2024-07-14 22:08:33.621991 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:33.625107 INFO::ASW Batch was 0.268762706552449 prior to batch effect correction and is now 0.138959279813974 .
2024-07-14 22:08:33.625926 INFO::ASW Label was 0.776304272166019 prior to batch effect correction and is now 0.844218569923248 .
2024-07-14 22:08:33.626897 INFO::Total function execution time is 0.0449559688568115 s and adjustment time is 0.0245208740234375 s ( 54.54 )
2024-07-14 22:08:33.846557 INFO::Formatting Data.
2024-07-14 22:08:33.848231 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:33.85015 INFO::Removing potential empty rows and columns
2024-07-14 22:08:33.85218 INFO::Found 0 missing values.
2024-07-14 22:08:33.857209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:33.858402 INFO::Done
2024-07-14 22:08:33.859607 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:33.863005 INFO::Starting hierarchical adjustment
2024-07-14 22:08:33.864414 INFO::Found 3 batches.
2024-07-14 22:08:33.865582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:33.866878 INFO::Using default BPPARAM
2024-07-14 22:08:33.868055 INFO::Processing subtree level 1
2024-07-14 22:08:36.683068 INFO::Adjusting the last 1 batches sequentially
2024-07-14 22:08:36.685349 INFO::Done
2024-07-14 22:08:36.686636 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:36.689677 INFO::ASW Batch was -0.063608125874768 prior to batch effect correction and is now -0.063608125874768 .
2024-07-14 22:08:36.691183 INFO::Total function execution time is 2.84475612640381 s and adjustment time is 2.82113313674927 s ( 99.17 )
2024-07-14 22:08:36.692793 INFO::Formatting Data.
2024-07-14 22:08:36.694013 INFO::Typecasting input to dataframe.
2024-07-14 22:08:36.695428 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:36.696996 INFO::Removing potential empty rows and columns
2024-07-14 22:08:36.698675 INFO::Found 0 missing values.
2024-07-14 22:08:36.702704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:36.703903 INFO::Done
2024-07-14 22:08:36.705063 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:36.708204 INFO::Starting hierarchical adjustment
2024-07-14 22:08:36.709616 INFO::Found 3 batches.
2024-07-14 22:08:36.710796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:36.712031 INFO::Using default BPPARAM
2024-07-14 22:08:36.713152 INFO::Processing subtree level 1
2024-07-14 22:08:39.992748 INFO::Adjusting the last 1 batches sequentially
2024-07-14 22:08:39.995059 INFO::Done
2024-07-14 22:08:39.996532 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:39.999887 INFO::ASW Batch was -0.063608125874768 prior to batch effect correction and is now -0.063608125874768 .
2024-07-14 22:08:40.001572 INFO::Total function execution time is 3.30875301361084 s and adjustment time is 3.28562808036804 s ( 99.3 )
2024-07-14 22:08:40.024515 INFO::Formatting Data.
2024-07-14 22:08:40.026153 INFO::Typecasting input to dataframe.
2024-07-14 22:08:40.027868 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:40.029661 INFO::Removing potential empty rows and columns
2024-07-14 22:08:40.031613 INFO::Found 0 missing values.
2024-07-14 22:08:40.036126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:40.037449 INFO::Done
2024-07-14 22:08:40.038736 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:40.042079 INFO::Starting hierarchical adjustment
2024-07-14 22:08:40.043494 INFO::Found 3 batches.
2024-07-14 22:08:40.044685 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:40.045988 INFO::Using default BPPARAM
2024-07-14 22:08:40.047189 INFO::Processing subtree level 1
2024-07-14 22:08:43.247457 INFO::Adjusting the last 1 batches sequentially
2024-07-14 22:08:43.249799 INFO::Done
2024-07-14 22:08:43.251169 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:43.254763 INFO::ASW Batch was -0.0993385222298221 prior to batch effect correction and is now -0.0993385222298221 .
2024-07-14 22:08:43.256534 INFO::Total function execution time is 3.23210501670837 s and adjustment time is 3.20647406578064 s ( 99.21 )
2024-07-14 22:08:46.349605 INFO::Formatting Data.
2024-07-14 22:08:46.350765 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:46.352084 INFO::Removing potential empty rows and columns
2024-07-14 22:08:46.354505 INFO::Found 1000 missing values.
2024-07-14 22:08:46.368085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:46.369009 INFO::Done
2024-07-14 22:08:46.36977 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:46.375949 INFO::Starting hierarchical adjustment
2024-07-14 22:08:46.376948 INFO::Found 10 batches.
2024-07-14 22:08:46.377676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:46.378452 INFO::Using default BPPARAM
2024-07-14 22:08:46.379155 INFO::Processing subtree level 1
2024-07-14 22:08:49.397823 INFO::Processing subtree level 2
2024-07-14 22:08:52.216534 INFO::Adjusting the last 1 batches sequentially
2024-07-14 22:08:52.218937 INFO::Done
2024-07-14 22:08:52.220303 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:52.22959 INFO::ASW Batch was 0.462408047449575 prior to batch effect correction and is now 0.462408047449575 .
2024-07-14 22:08:52.230998 INFO::ASW Label was 0.404950368349473 prior to batch effect correction and is now 0.404950368349473 .
2024-07-14 22:08:52.232667 INFO::Total function execution time is 5.88309502601624 s and adjustment time is 5.84209084510803 s ( 99.3 )
2024-07-14 22:08:52.23418 INFO::Formatting Data.
2024-07-14 22:08:52.23549 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:52.237366 INFO::Removing potential empty rows and columns
2024-07-14 22:08:52.240915 INFO::Found 1000 missing values.
2024-07-14 22:08:52.261967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:52.262898 INFO::Done
2024-07-14 22:08:52.263644 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:52.270839 INFO::Starting hierarchical adjustment
2024-07-14 22:08:52.271863 INFO::Found 10 batches.
2024-07-14 22:08:52.984749 INFO::Set up parallel execution backend with 2 workers
2024-07-14 22:08:52.986264 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-14 22:08:55.89779 INFO::Adjusting the last 2 batches sequentially
2024-07-14 22:08:55.900074 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 22:08:55.925249 INFO::Done
2024-07-14 22:08:55.926721 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:08:55.93641 INFO::ASW Batch was 0.462408047449575 prior to batch effect correction and is now 0.462408047449575 .
2024-07-14 22:08:55.937891 INFO::ASW Label was 0.404950368349473 prior to batch effect correction and is now 0.404950368349473 .
2024-07-14 22:08:55.939572 INFO::Total function execution time is 3.70538592338562 s and adjustment time is 3.65343880653381 s ( 98.6 )
2024-07-14 22:08:58.904652 INFO::Formatting Data.
2024-07-14 22:08:58.905701 INFO::Replacing NaNs with NAs.
2024-07-14 22:08:58.906829 INFO::Removing potential empty rows and columns
2024-07-14 22:08:58.907983 INFO::Found 0 missing values.
2024-07-14 22:08:58.911483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:08:58.912295 INFO::Done
2024-07-14 22:08:58.913062 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 22:08:58.916118 INFO::Starting hierarchical adjustment
2024-07-14 22:08:58.917105 INFO::Found 3 batches.
2024-07-14 22:08:58.917825 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 22:08:58.918595 INFO::Using default BPPARAM
2024-07-14 22:08:58.919299 INFO::Processing subtree level 1
2024-07-14 22:09:01.870025 INFO::Adjusting the last 1 batches sequentially
2024-07-14 22:09:01.872208 INFO::Done
2024-07-14 22:09:01.873507 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 22:09:01.877689 INFO::ASW Batch was 0.28622493736047 prior to batch effect correction and is now -0.14120825268928 .
2024-07-14 22:09:01.878913 INFO::ASW Label was -0.214598850172651 prior to batch effect correction and is now -0.0492361544712211 .
2024-07-14 22:09:01.880415 INFO::Total function execution time is 2.97581791877747 s and adjustment time is 2.95521306991577 s ( 99.31 )
2024-07-14 22:09:02.05644 INFO::Formatting Data.
2024-07-14 22:09:02.057461 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.058619 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.059744 INFO::Found 2 missing values.
2024-07-14 22:09:02.062244 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.062973 INFO::Done
2024-07-14 22:09:02.101463 INFO::Found NA in Reference column
2024-07-14 22:09:02.114862 INFO::Require at least two references per batch.
2024-07-14 22:09:02.135812 INFO::Formatting Data.
2024-07-14 22:09:02.136786 INFO::Recognized SummarizedExperiment
2024-07-14 22:09:02.137525 INFO::Typecasting input to dataframe.
2024-07-14 22:09:02.145395 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.146746 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.149437 INFO::Found 0 missing values.
2024-07-14 22:09:02.154412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.155209 INFO::Done
2024-07-14 22:09:02.169479 INFO::Formatting Data.
2024-07-14 22:09:02.170432 INFO::Recognized SummarizedExperiment
2024-07-14 22:09:02.171179 INFO::Typecasting input to dataframe.
2024-07-14 22:09:02.186204 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.187645 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.190596 INFO::Found 0 missing values.
2024-07-14 22:09:02.198426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.199324 INFO::Done
2024-07-14 22:09:02.213794 INFO::Formatting Data.
2024-07-14 22:09:02.214811 INFO::Recognized SummarizedExperiment
2024-07-14 22:09:02.215618 INFO::Typecasting input to dataframe.
2024-07-14 22:09:02.230115 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.231359 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.232557 INFO::Found 0 missing values.
2024-07-14 22:09:02.234247 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.
2024-07-14 22:09:02.238338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.239118 INFO::Done
2024-07-14 22:09:02.253571 INFO::Formatting Data.
2024-07-14 22:09:02.254595 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.255756 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.257028 INFO::Found 0 missing values.
2024-07-14 22:09:02.2598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.260588 INFO::Done
2024-07-14 22:09:02.27636 INFO::Formatting Data.
2024-07-14 22:09:02.277371 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.278489 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.279714 INFO::Found 0 missing values.
2024-07-14 22:09:02.282661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.283415 INFO::Done
2024-07-14 22:09:02.323511 INFO::Formatting Data.
2024-07-14 22:09:02.324536 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.32575 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.327047 INFO::Found 1 missing values.
2024-07-14 22:09:02.329479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.330232 INFO::Done
2024-07-14 22:09:02.355308 INFO::Formatting Data.
2024-07-14 22:09:02.356333 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.357403 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.358521 INFO::Found 2 missing values.
2024-07-14 22:09:02.359603 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.
2024-07-14 22:09:02.361758 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.362496 INFO::Done
2024-07-14 22:09:02.376562 INFO::Formatting Data.
2024-07-14 22:09:02.377573 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.378682 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.379754 INFO::Found 2 missing values.
2024-07-14 22:09:02.381452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.382179 INFO::Done
2024-07-14 22:09:02.396594 INFO::Formatting Data.
2024-07-14 22:09:02.39762 INFO::Typecasting input to dataframe.
2024-07-14 22:09:02.398638 INFO::Replacing NaNs with NAs.
2024-07-14 22:09:02.399699 INFO::Removing potential empty rows and columns
2024-07-14 22:09:02.400828 INFO::Found 0 missing values.
2024-07-14 22:09:02.403417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 22:09:02.404163 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
29.07 1.70 77.81
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.07 | 0.50 | 18.83 | |
| compute_asw | 0.04 | 0.00 | 0.05 | |
| count_existing | 0.04 | 0.00 | 0.03 | |
| generate_data_covariables | 0.01 | 0.00 | 0.01 | |
| generate_dataset | 0.03 | 0.00 | 0.03 | |