Yannis Schumann
| Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-21 17:39 -0400 (Fri, 21 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4506 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-06-20 00:54:07 -0400 (Thu, 20 Jun 2024) |
| EndedAt: 2024-06-20 01:01:24 -0400 (Thu, 20 Jun 2024) |
| EllapsedTime: 436.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R version 4.4.0 (2024-04-24 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 '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 8.48 5.28 31.03
* 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-3.19-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
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")
2024-06-20 00:57:12.311922 INFO::Formatting Data.
2024-06-20 00:57:12.329207 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:12.345095 INFO::Removing potential empty rows and columns
2024-06-20 00:57:12.894838 INFO::Found 0 missing values.
2024-06-20 00:57:12.897813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:57:12.89863 INFO::Done
2024-06-20 00:57:12.899368 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:57:12.962719 INFO::Starting hierarchical adjustment
2024-06-20 00:57:12.964496 INFO::Found 3 batches.
2024-06-20 00:57:12.965768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:57:12.967699 INFO::Using default BPPARAM
2024-06-20 00:57:12.968903 INFO::Processing subtree level 1
2024-06-20 00:57:26.798693 INFO::Adjusting the last 1 batches sequentially
2024-06-20 00:57:26.800953 INFO::Done
2024-06-20 00:57:26.802235 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:57:26.805336 INFO::ASW Batch was -0.0684003351413267 prior to batch effect correction and is now -0.0684003351413267 .
2024-06-20 00:57:26.80698 INFO::Total function execution time is 14.4958138465881 s and adjustment time is 13.8367660045624 s ( 95.45 )
2024-06-20 00:57:26.827375 INFO::Formatting Data.
2024-06-20 00:57:26.828394 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:26.829455 INFO::Removing potential empty rows and columns
2024-06-20 00:57:26.830653 INFO::Found 0 missing values.
2024-06-20 00:57:26.831721 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-20 00:57:26.840558 INFO::Formatting Data.
2024-06-20 00:57:26.841529 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:26.842637 INFO::Removing potential empty rows and columns
2024-06-20 00:57:26.843809 INFO::Found 0 missing values.
2024-06-20 00:57:26.844954 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-20 00:57:26.862253 INFO::Formatting Data.
2024-06-20 00:57:26.86328 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:26.86436 INFO::Removing potential empty rows and columns
2024-06-20 00:57:26.865478 INFO::Found 0 missing values.
2024-06-20 00:57:26.866551 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-20 00:57:26.870265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:57:26.870994 INFO::Done
2024-06-20 00:57:26.871687 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:57:26.873767 INFO::Starting hierarchical adjustment
2024-06-20 00:57:26.874656 INFO::Found 2 batches.
2024-06-20 00:57:26.875447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:57:26.876249 INFO::Using default BPPARAM
2024-06-20 00:57:26.876999 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:57:26.878139 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:57:26.894905 INFO::Done
2024-06-20 00:57:26.895792 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:57:26.897902 INFO::ASW Batch was -0.00484570746356348 prior to batch effect correction and is now -0.123319136730408 .
2024-06-20 00:57:26.898908 INFO::Total function execution time is 0.0367450714111328 s and adjustment time is 0.0203440189361572 s ( 55.37 )
2024-06-20 00:57:26.901781 INFO::Formatting Data.
2024-06-20 00:57:26.902601 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:26.909771 INFO::Formatting Data.
2024-06-20 00:57:26.910611 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:26.911711 INFO::Removing potential empty rows and columns
2024-06-20 00:57:26.91282 INFO::Found 0 missing values.
2024-06-20 00:57:26.915421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:57:26.91613 INFO::Done
2024-06-20 00:57:26.916833 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:57:26.918979 INFO::Starting hierarchical adjustment
2024-06-20 00:57:26.919839 INFO::Found 2 batches.
2024-06-20 00:57:26.920613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:57:26.921384 INFO::Using default BPPARAM
2024-06-20 00:57:26.92208 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:57:26.923123 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:57:26.935314 INFO::Done
2024-06-20 00:57:26.936242 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:57:26.938436 INFO::ASW Batch was -0.008948133845907 prior to batch effect correction and is now -0.120298404274054 .
2024-06-20 00:57:26.939434 INFO::Total function execution time is 0.0296831130981445 s and adjustment time is 0.0155708789825439 s ( 52.46 )
2024-06-20 00:57:26.940645 INFO::Formatting Data.
2024-06-20 00:57:26.941508 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:26.94262 INFO::Removing potential empty rows and columns
2024-06-20 00:57:26.943713 INFO::Found 0 missing values.
2024-06-20 00:57:26.946322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:57:26.947076 INFO::Done
2024-06-20 00:57:26.947775 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:57:26.949875 INFO::Starting hierarchical adjustment
2024-06-20 00:57:26.950734 INFO::Found 2 batches.
2024-06-20 00:57:26.951433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:57:26.952247 INFO::Using default BPPARAM
2024-06-20 00:57:26.952985 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:57:26.954035 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:57:26.966183 INFO::Done
2024-06-20 00:57:26.967043 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:57:26.969194 INFO::ASW Batch was -0.008948133845907 prior to batch effect correction and is now -0.120298404274054 .
2024-06-20 00:57:26.970168 INFO::Total function execution time is 0.0295178890228271 s and adjustment time is 0.0155560970306396 s ( 52.7 )
2024-06-20 00:57:29.60928 INFO::Formatting Data.
2024-06-20 00:57:29.610218 INFO::Recognized SummarizedExperiment
2024-06-20 00:57:29.611185 INFO::Typecasting input to dataframe.
2024-06-20 00:57:29.664822 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:29.666291 INFO::Removing potential empty rows and columns
2024-06-20 00:57:29.669734 INFO::Found 0 missing values.
2024-06-20 00:57:30.403287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:57:30.404314 INFO::Done
2024-06-20 00:57:30.405096 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:57:30.408727 INFO::Starting hierarchical adjustment
2024-06-20 00:57:30.409655 INFO::Found 2 batches.
2024-06-20 00:57:30.410367 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:57:30.411611 INFO::Using default BPPARAM
2024-06-20 00:57:30.412342 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:57:30.413522 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:57:30.454214 INFO::Done
2024-06-20 00:57:30.45509 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:57:30.458759 INFO::ASW Batch was -0.00658349142529444 prior to batch effect correction and is now -0.0963309594530083 .
2024-06-20 00:57:30.459825 INFO::Total function execution time is 0.850832939147949 s and adjustment time is 0.0446739196777344 s ( 5.25 )
2024-06-20 00:57:30.478428 INFO::Formatting Data.
2024-06-20 00:57:30.479373 INFO::Recognized SummarizedExperiment
2024-06-20 00:57:30.480106 INFO::Typecasting input to dataframe.
2024-06-20 00:57:30.487897 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:30.489233 INFO::Removing potential empty rows and columns
2024-06-20 00:57:30.492144 INFO::Found 0 missing values.
2024-06-20 00:57:30.497494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:57:30.498302 INFO::Done
2024-06-20 00:57:30.499029 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:57:30.502784 INFO::Starting hierarchical adjustment
2024-06-20 00:57:30.503681 INFO::Found 2 batches.
2024-06-20 00:57:30.504385 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:57:30.505158 INFO::Using default BPPARAM
2024-06-20 00:57:30.505863 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:57:30.507028 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:57:30.526153 INFO::Done
2024-06-20 00:57:30.527079 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:57:30.530951 INFO::ASW Batch was -0.0178766581944013 prior to batch effect correction and is now -0.0178766581944013 .
2024-06-20 00:57:30.532034 INFO::Total function execution time is 0.0535781383514404 s and adjustment time is 0.0225660800933838 s ( 42.12 )
2024-06-20 00:57:30.55361 INFO::Formatting Data.
2024-06-20 00:57:30.554607 INFO::Replacing NaNs with NAs.
2024-06-20 00:57:30.555691 INFO::Removing potential empty rows and columns
2024-06-20 00:57:30.556852 INFO::Found 0 missing values.
2024-06-20 00:57:30.559596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:57:30.560352 INFO::Done
2024-06-20 00:57:30.561069 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:57:30.563194 INFO::Starting hierarchical adjustment
2024-06-20 00:57:30.564088 INFO::Found 3 batches.
2024-06-20 00:57:30.564809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:57:30.565596 INFO::Using default BPPARAM
2024-06-20 00:57:30.56632 INFO::Processing subtree level 1
2024-06-20 00:57:54.298605 INFO::Adjusting the last 1 batches sequentially
2024-06-20 00:57:54.300852 INFO::Done
2024-06-20 00:57:54.301968 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:57:54.30463 INFO::ASW Batch was -0.0658248790539238 prior to batch effect correction and is now -0.173440717229229 .
2024-06-20 00:57:54.305625 INFO::Total function execution time is 23.7521090507507 s and adjustment time is 23.7368440628052 s ( 99.94 )
2024-06-20 00:57:54.323354 INFO::Skipping initial DF formatting
2024-06-20 00:57:54.324783 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:57:54.331254 INFO::Starting hierarchical adjustment
2024-06-20 00:57:54.332585 INFO::Found 5 batches.
2024-06-20 00:57:54.333793 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:57:54.335052 INFO::Using default BPPARAM
2024-06-20 00:57:54.335939 INFO::Processing subtree level 1
2024-06-20 00:58:08.201835 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:58:08.204057 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:58:08.229368 INFO::Done
2024-06-20 00:58:08.230907 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:58:08.237847 INFO::ASW Batch was 0.582540955729142 prior to batch effect correction and is now 0.582540955729142 .
2024-06-20 00:58:08.239179 INFO::ASW Label was 0.353409409083094 prior to batch effect correction and is now 0.353409409083094 .
2024-06-20 00:58:08.240849 INFO::Total function execution time is 13.9175908565521 s and adjustment time is 13.8970119953156 s ( 99.85 )
2024-06-20 00:58:08.264269 INFO::Formatting Data.
2024-06-20 00:58:08.265287 INFO::Replacing NaNs with NAs.
2024-06-20 00:58:08.266385 INFO::Removing potential empty rows and columns
2024-06-20 00:58:08.267516 INFO::Found 0 missing values.
2024-06-20 00:58:08.27128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:58:08.272131 INFO::Done
2024-06-20 00:58:08.272914 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:58:08.27612 INFO::Starting hierarchical adjustment
2024-06-20 00:58:08.277049 INFO::Found 5 batches.
2024-06-20 00:58:08.27778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:58:08.278576 INFO::Using default BPPARAM
2024-06-20 00:58:08.279284 INFO::Processing subtree level 1
2024-06-20 00:58:22.536163 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:58:22.538203 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:58:22.557998 INFO::Done
2024-06-20 00:58:22.559314 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:58:22.564051 INFO::ASW Batch was 0.58397548329074 prior to batch effect correction and is now -0.0871090427423344 .
2024-06-20 00:58:22.565581 INFO::ASW Label was 0.129931789637545 prior to batch effect correction and is now 0.67975734224303 .
2024-06-20 00:58:22.567073 INFO::Total function execution time is 14.3028130531311 s and adjustment time is 14.281005859375 s ( 99.85 )
2024-06-20 00:58:22.56856 INFO::Formatting Data.
2024-06-20 00:58:22.569794 INFO::Replacing NaNs with NAs.
2024-06-20 00:58:22.571381 INFO::Removing potential empty rows and columns
2024-06-20 00:58:22.573267 INFO::Found 0 missing values.
2024-06-20 00:58:22.578973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:58:22.580129 INFO::Done
2024-06-20 00:58:22.581412 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:58:22.586048 INFO::Starting hierarchical adjustment
2024-06-20 00:58:22.587423 INFO::Found 5 batches.
2024-06-20 00:58:22.588526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:58:22.589726 INFO::Using default BPPARAM
2024-06-20 00:58:22.590825 INFO::Processing subtree level 1
2024-06-20 00:58:36.954691 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:58:36.9568 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:58:36.975493 INFO::Done
2024-06-20 00:58:36.976712 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:58:36.981039 INFO::ASW Batch was 0.58397548329074 prior to batch effect correction and is now -0.0871090427423344 .
2024-06-20 00:58:36.982179 INFO::ASW Label was 0.129931789637545 prior to batch effect correction and is now 0.67975734224303 .
2024-06-20 00:58:36.983534 INFO::Total function execution time is 14.4149940013885 s and adjustment time is 14.3882489204407 s ( 99.81 )
2024-06-20 00:58:37.007611 INFO::Formatting Data.
2024-06-20 00:58:37.009079 INFO::Replacing NaNs with NAs.
2024-06-20 00:58:37.010651 INFO::Removing potential empty rows and columns
2024-06-20 00:58:37.012246 INFO::Found 0 missing values.
2024-06-20 00:58:37.017745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:58:37.01882 INFO::Done
2024-06-20 00:58:37.019912 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:58:37.024182 INFO::Starting hierarchical adjustment
2024-06-20 00:58:37.02546 INFO::Found 5 batches.
2024-06-20 00:58:37.026532 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:58:37.027679 INFO::Using default BPPARAM
2024-06-20 00:58:37.028715 INFO::Processing subtree level 1
2024-06-20 00:58:50.671272 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:58:50.6732 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:58:50.690647 INFO::Done
2024-06-20 00:58:50.691867 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:58:50.69613 INFO::ASW Batch was 0.324095008608112 prior to batch effect correction and is now -0.109781110858209 .
2024-06-20 00:58:50.697265 INFO::ASW Label was 0.367306401901229 prior to batch effect correction and is now 0.879067038056108 .
2024-06-20 00:58:50.698608 INFO::Total function execution time is 13.691153049469 s and adjustment time is 13.6653640270233 s ( 99.81 )
2024-06-20 00:58:50.699941 INFO::Formatting Data.
2024-06-20 00:58:50.701044 INFO::Replacing NaNs with NAs.
2024-06-20 00:58:50.70258 INFO::Removing potential empty rows and columns
2024-06-20 00:58:50.704099 INFO::Found 0 missing values.
2024-06-20 00:58:50.709182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:58:50.710197 INFO::Done
2024-06-20 00:58:50.711189 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:58:50.715274 INFO::Starting hierarchical adjustment
2024-06-20 00:58:50.716486 INFO::Found 5 batches.
2024-06-20 00:58:50.717477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:58:50.718557 INFO::Using default BPPARAM
2024-06-20 00:58:50.71955 INFO::Processing subtree level 1
2024-06-20 00:59:05.00918 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:59:05.012498 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:59:05.031642 INFO::Done
2024-06-20 00:59:05.033025 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:05.037874 INFO::ASW Batch was 0.324095008608112 prior to batch effect correction and is now -0.109781110858209 .
2024-06-20 00:59:05.039169 INFO::ASW Label was 0.367306401901229 prior to batch effect correction and is now 0.879067038056108 .
2024-06-20 00:59:05.040751 INFO::Total function execution time is 14.3407819271088 s and adjustment time is 14.3152770996094 s ( 99.82 )
2024-06-20 00:59:05.062777 INFO::Formatting Data.
2024-06-20 00:59:05.064219 INFO::Replacing NaNs with NAs.
2024-06-20 00:59:05.066155 INFO::Removing potential empty rows and columns
2024-06-20 00:59:05.067737 INFO::Found 0 missing values.
2024-06-20 00:59:05.07067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:59:05.071643 INFO::Done
2024-06-20 00:59:05.072451 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:59:05.075453 INFO::Starting hierarchical adjustment
2024-06-20 00:59:05.076333 INFO::Found 2 batches.
2024-06-20 00:59:05.077031 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:59:05.077801 INFO::Using default BPPARAM
2024-06-20 00:59:05.07855 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:59:05.079627 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:59:05.091564 INFO::Done
2024-06-20 00:59:05.092519 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:05.095559 INFO::ASW Batch was 0.645362174727792 prior to batch effect correction and is now 0.0501419913702174 .
2024-06-20 00:59:05.096334 INFO::ASW Label was 0.451702885692222 prior to batch effect correction and is now 0.866374542555921 .
2024-06-20 00:59:05.097271 INFO::Total function execution time is 0.0346879959106445 s and adjustment time is 0.0153348445892334 s ( 44.21 )
2024-06-20 00:59:05.098181 INFO::Formatting Data.
2024-06-20 00:59:05.098953 INFO::Replacing NaNs with NAs.
2024-06-20 00:59:05.099961 INFO::Removing potential empty rows and columns
2024-06-20 00:59:05.10103 INFO::Found 0 missing values.
2024-06-20 00:59:05.103581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:59:05.104302 INFO::Done
2024-06-20 00:59:05.105087 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:59:05.108196 INFO::Starting hierarchical adjustment
2024-06-20 00:59:05.109067 INFO::Found 2 batches.
2024-06-20 00:59:05.109766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:59:05.110522 INFO::Using default BPPARAM
2024-06-20 00:59:05.111272 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:59:05.112339 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:59:05.124844 INFO::Done
2024-06-20 00:59:05.125688 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:05.128633 INFO::ASW Batch was 0.645362174727792 prior to batch effect correction and is now 0.0501419913702174 .
2024-06-20 00:59:05.129404 INFO::ASW Label was 0.451702885692222 prior to batch effect correction and is now 0.866374542555921 .
2024-06-20 00:59:05.130347 INFO::Total function execution time is 0.0321660041809082 s and adjustment time is 0.0158779621124268 s ( 49.36 )
2024-06-20 00:59:05.146442 INFO::Formatting Data.
2024-06-20 00:59:05.147407 INFO::Replacing NaNs with NAs.
2024-06-20 00:59:05.148451 INFO::Removing potential empty rows and columns
2024-06-20 00:59:05.149474 INFO::Found 0 missing values.
2024-06-20 00:59:05.151459 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:59:05.15217 INFO::Done
2024-06-20 00:59:05.152856 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:59:05.154941 INFO::Starting hierarchical adjustment
2024-06-20 00:59:05.155809 INFO::Found 2 batches.
2024-06-20 00:59:05.156508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:59:05.157268 INFO::Using default BPPARAM
2024-06-20 00:59:05.157988 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:59:05.159061 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:59:05.184072 INFO::Done
2024-06-20 00:59:05.185065 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:05.187203 INFO::ASW Batch was -0.136729698771121 prior to batch effect correction and is now -0.160707047253783 .
2024-06-20 00:59:05.188184 INFO::Total function execution time is 0.0418441295623779 s and adjustment time is 0.0283570289611816 s ( 67.77 )
2024-06-20 00:59:05.205103 INFO::Formatting Data.
2024-06-20 00:59:05.206149 INFO::Replacing NaNs with NAs.
2024-06-20 00:59:05.20735 INFO::Removing potential empty rows and columns
2024-06-20 00:59:05.209623 INFO::Found 0 missing values.
2024-06-20 00:59:05.211006 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-20 00:59:05.215115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:59:05.215887 INFO::Done
2024-06-20 00:59:05.216717 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:59:05.219695 INFO::Starting hierarchical adjustment
2024-06-20 00:59:05.220655 INFO::Found 2 batches.
2024-06-20 00:59:05.221396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:59:05.222193 INFO::Using default BPPARAM
2024-06-20 00:59:05.222909 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:59:05.223992 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:59:05.239652 INFO::Done
2024-06-20 00:59:05.240537 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:05.24364 INFO::ASW Batch was 0.278229227498224 prior to batch effect correction and is now -0.0280239689119315 .
2024-06-20 00:59:05.244436 INFO::ASW Label was 0.762129907522875 prior to batch effect correction and is now 0.952621660110316 .
2024-06-20 00:59:05.245515 INFO::Total function execution time is 0.0404951572418213 s and adjustment time is 0.0191149711608887 s ( 47.2 )
2024-06-20 00:59:05.246538 INFO::Formatting Data.
2024-06-20 00:59:05.247357 INFO::Replacing NaNs with NAs.
2024-06-20 00:59:05.248566 INFO::Removing potential empty rows and columns
2024-06-20 00:59:05.250248 INFO::Found 0 missing values.
2024-06-20 00:59:05.251652 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-20 00:59:05.256377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:59:05.257129 INFO::Done
2024-06-20 00:59:05.257845 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:59:05.260875 INFO::Starting hierarchical adjustment
2024-06-20 00:59:05.261777 INFO::Found 2 batches.
2024-06-20 00:59:05.262497 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:59:05.263284 INFO::Using default BPPARAM
2024-06-20 00:59:05.264008 INFO::Adjusting the last 2 batches sequentially
2024-06-20 00:59:05.265317 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 00:59:05.282741 INFO::Done
2024-06-20 00:59:05.283691 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:05.286889 INFO::ASW Batch was 0.278229227498224 prior to batch effect correction and is now -0.0280239689119315 .
2024-06-20 00:59:05.287689 INFO::ASW Label was 0.762129907522875 prior to batch effect correction and is now 0.952621660110316 .
2024-06-20 00:59:05.288689 INFO::Total function execution time is 0.0421550273895264 s and adjustment time is 0.0210630893707275 s ( 49.97 )
2024-06-20 00:59:05.512136 INFO::Formatting Data.
2024-06-20 00:59:05.513204 INFO::Replacing NaNs with NAs.
2024-06-20 00:59:05.514412 INFO::Removing potential empty rows and columns
2024-06-20 00:59:05.515733 INFO::Found 0 missing values.
2024-06-20 00:59:05.519103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:59:05.520011 INFO::Done
2024-06-20 00:59:05.520971 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:59:05.523417 INFO::Starting hierarchical adjustment
2024-06-20 00:59:05.524437 INFO::Found 3 batches.
2024-06-20 00:59:05.525251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:59:05.526146 INFO::Using default BPPARAM
2024-06-20 00:59:05.526937 INFO::Processing subtree level 1
2024-06-20 00:59:18.979657 INFO::Adjusting the last 1 batches sequentially
2024-06-20 00:59:18.981765 INFO::Done
2024-06-20 00:59:18.983052 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:18.986174 INFO::ASW Batch was -0.0367324839864798 prior to batch effect correction and is now -0.0367324839864798 .
2024-06-20 00:59:18.987751 INFO::Total function execution time is 13.4756460189819 s and adjustment time is 13.4574718475342 s ( 99.87 )
2024-06-20 00:59:18.989465 INFO::Formatting Data.
2024-06-20 00:59:18.990733 INFO::Typecasting input to dataframe.
2024-06-20 00:59:18.992128 INFO::Replacing NaNs with NAs.
2024-06-20 00:59:18.993719 INFO::Removing potential empty rows and columns
2024-06-20 00:59:18.995459 INFO::Found 0 missing values.
2024-06-20 00:59:18.999608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:59:19.000775 INFO::Done
2024-06-20 00:59:19.001964 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:59:19.005146 INFO::Starting hierarchical adjustment
2024-06-20 00:59:19.006504 INFO::Found 3 batches.
2024-06-20 00:59:19.007668 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:59:19.008922 INFO::Using default BPPARAM
2024-06-20 00:59:19.010038 INFO::Processing subtree level 1
2024-06-20 00:59:32.35636 INFO::Adjusting the last 1 batches sequentially
2024-06-20 00:59:32.358763 INFO::Done
2024-06-20 00:59:32.36004 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:32.363128 INFO::ASW Batch was -0.0367324839864798 prior to batch effect correction and is now -0.0367324839864798 .
2024-06-20 00:59:32.364675 INFO::Total function execution time is 13.3752059936523 s and adjustment time is 13.3524510860443 s ( 99.83 )
2024-06-20 00:59:32.385394 INFO::Formatting Data.
2024-06-20 00:59:32.386609 INFO::Typecasting input to dataframe.
2024-06-20 00:59:32.387896 INFO::Replacing NaNs with NAs.
2024-06-20 00:59:32.389213 INFO::Removing potential empty rows and columns
2024-06-20 00:59:32.39076 INFO::Found 0 missing values.
2024-06-20 00:59:32.393513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 00:59:32.394359 INFO::Done
2024-06-20 00:59:32.395206 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 00:59:32.397332 INFO::Starting hierarchical adjustment
2024-06-20 00:59:32.398289 INFO::Found 3 batches.
2024-06-20 00:59:32.39901 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 00:59:32.399913 INFO::Using default BPPARAM
2024-06-20 00:59:32.400681 INFO::Processing subtree level 1
2024-06-20 00:59:46.494949 INFO::Adjusting the last 1 batches sequentially
2024-06-20 00:59:46.4974 INFO::Done
2024-06-20 00:59:46.498833 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 00:59:46.502259 INFO::ASW Batch was -0.0299058843536478 prior to batch effect correction and is now -0.0299058843536478 .
2024-06-20 00:59:46.503986 INFO::Total function execution time is 14.1186108589172 s and adjustment time is 14.0992040634155 s ( 99.86 )
2024-06-20 01:00:00.767886 INFO::Formatting Data.
2024-06-20 01:00:00.769281 INFO::Replacing NaNs with NAs.
2024-06-20 01:00:00.771117 INFO::Removing potential empty rows and columns
2024-06-20 01:00:00.774636 INFO::Found 1000 missing values.
2024-06-20 01:00:00.796638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:00:00.797909 INFO::Done
2024-06-20 01:00:00.799017 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 01:00:00.808135 INFO::Starting hierarchical adjustment
2024-06-20 01:00:00.809607 INFO::Found 10 batches.
2024-06-20 01:00:00.810779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 01:00:00.811946 INFO::Using default BPPARAM
2024-06-20 01:00:00.81299 INFO::Processing subtree level 1
2024-06-20 01:00:15.118245 INFO::Processing subtree level 2
2024-06-20 01:00:29.100387 INFO::Adjusting the last 1 batches sequentially
2024-06-20 01:00:29.10296 INFO::Done
2024-06-20 01:00:29.104323 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 01:00:29.114105 INFO::ASW Batch was 0.487597677548148 prior to batch effect correction and is now 0.487597677548148 .
2024-06-20 01:00:29.115581 INFO::ASW Label was 0.332368151777736 prior to batch effect correction and is now 0.332368151777736 .
2024-06-20 01:00:29.1174 INFO::Total function execution time is 28.3495869636536 s and adjustment time is 28.2935729026794 s ( 99.8 )
2024-06-20 01:00:29.118979 INFO::Formatting Data.
2024-06-20 01:00:29.12032 INFO::Replacing NaNs with NAs.
2024-06-20 01:00:29.122355 INFO::Removing potential empty rows and columns
2024-06-20 01:00:29.126157 INFO::Found 1000 missing values.
2024-06-20 01:00:29.148084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:00:29.149486 INFO::Done
2024-06-20 01:00:29.150809 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 01:00:29.159675 INFO::Starting hierarchical adjustment
2024-06-20 01:00:29.161099 INFO::Found 10 batches.
2024-06-20 01:00:29.929585 INFO::Set up parallel execution backend with 2 workers
2024-06-20 01:00:29.931146 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-20 01:00:39.009116 INFO::Adjusting the last 2 batches sequentially
2024-06-20 01:00:39.010751 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-20 01:00:39.025449 INFO::Done
2024-06-20 01:00:39.026341 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 01:00:39.032438 INFO::ASW Batch was 0.487597677548148 prior to batch effect correction and is now 0.487597677548148 .
2024-06-20 01:00:39.033404 INFO::ASW Label was 0.332368151777736 prior to batch effect correction and is now 0.332368151777736 .
2024-06-20 01:00:39.034376 INFO::Total function execution time is 9.91550183296204 s and adjustment time is 9.86457514762878 s ( 99.49 )
2024-06-20 01:00:52.825678 INFO::Formatting Data.
2024-06-20 01:00:52.8273 INFO::Replacing NaNs with NAs.
2024-06-20 01:00:52.82878 INFO::Removing potential empty rows and columns
2024-06-20 01:00:52.829951 INFO::Found 0 missing values.
2024-06-20 01:00:52.833278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:00:52.834037 INFO::Done
2024-06-20 01:00:52.834741 INFO::Acquiring quality metrics before batch effect correction.
2024-06-20 01:00:52.83748 INFO::Starting hierarchical adjustment
2024-06-20 01:00:52.838348 INFO::Found 3 batches.
2024-06-20 01:00:52.839054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-20 01:00:52.839834 INFO::Using default BPPARAM
2024-06-20 01:00:52.840594 INFO::Processing subtree level 1
2024-06-20 01:01:07.327913 INFO::Adjusting the last 1 batches sequentially
2024-06-20 01:01:07.33009 INFO::Done
2024-06-20 01:01:07.331342 INFO::Acquiring quality metrics after batch effect correction.
2024-06-20 01:01:07.336125 INFO::ASW Batch was 0.111346188290893 prior to batch effect correction and is now -0.135026716901256 .
2024-06-20 01:01:07.337396 INFO::ASW Label was -0.176735127872082 prior to batch effect correction and is now 0.0893034603674371 .
2024-06-20 01:01:07.338867 INFO::Total function execution time is 14.5133128166199 s and adjustment time is 14.4918169975281 s ( 99.85 )
2024-06-20 01:01:07.546284 INFO::Formatting Data.
2024-06-20 01:01:07.5478 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.549506 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.551341 INFO::Found 2 missing values.
2024-06-20 01:01:07.555634 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.556889 INFO::Done
2024-06-20 01:01:07.605731 INFO::Found NA in Reference column
2024-06-20 01:01:07.620157 INFO::Require at least two references per batch.
2024-06-20 01:01:07.643021 INFO::Formatting Data.
2024-06-20 01:01:07.644017 INFO::Recognized SummarizedExperiment
2024-06-20 01:01:07.644881 INFO::Typecasting input to dataframe.
2024-06-20 01:01:07.653122 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.654514 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.657772 INFO::Found 0 missing values.
2024-06-20 01:01:07.666458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.66782 INFO::Done
2024-06-20 01:01:07.687538 INFO::Formatting Data.
2024-06-20 01:01:07.688499 INFO::Recognized SummarizedExperiment
2024-06-20 01:01:07.689247 INFO::Typecasting input to dataframe.
2024-06-20 01:01:07.708396 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.709853 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.71285 INFO::Found 0 missing values.
2024-06-20 01:01:07.720984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.721912 INFO::Done
2024-06-20 01:01:07.737184 INFO::Formatting Data.
2024-06-20 01:01:07.738144 INFO::Recognized SummarizedExperiment
2024-06-20 01:01:07.738895 INFO::Typecasting input to dataframe.
2024-06-20 01:01:07.753058 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.754289 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.755579 INFO::Found 0 missing values.
2024-06-20 01:01:07.756686 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-20 01:01:07.760583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.761315 INFO::Done
2024-06-20 01:01:07.77592 INFO::Formatting Data.
2024-06-20 01:01:07.776989 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.778106 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.779299 INFO::Found 0 missing values.
2024-06-20 01:01:07.782052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.782772 INFO::Done
2024-06-20 01:01:07.801008 INFO::Formatting Data.
2024-06-20 01:01:07.802363 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.803897 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.805519 INFO::Found 0 missing values.
2024-06-20 01:01:07.809483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.810596 INFO::Done
2024-06-20 01:01:07.860213 INFO::Formatting Data.
2024-06-20 01:01:07.861739 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.863638 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.865658 INFO::Found 1 missing values.
2024-06-20 01:01:07.869577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.870777 INFO::Done
2024-06-20 01:01:07.904408 INFO::Formatting Data.
2024-06-20 01:01:07.905785 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.9073 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.908831 INFO::Found 2 missing values.
2024-06-20 01:01:07.910317 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-20 01:01:07.913517 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.914586 INFO::Done
2024-06-20 01:01:07.934365 INFO::Formatting Data.
2024-06-20 01:01:07.935875 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.937402 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.938918 INFO::Found 2 missing values.
2024-06-20 01:01:07.941289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.942458 INFO::Done
2024-06-20 01:01:07.962703 INFO::Formatting Data.
2024-06-20 01:01:07.964037 INFO::Typecasting input to dataframe.
2024-06-20 01:01:07.965512 INFO::Replacing NaNs with NAs.
2024-06-20 01:01:07.96738 INFO::Removing potential empty rows and columns
2024-06-20 01:01:07.969147 INFO::Found 0 missing values.
2024-06-20 01:01:07.973234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-20 01:01:07.974298 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
28.09 12.10 272.73
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.48 | 5.28 | 31.03 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.03 | 0.00 | 0.03 | |
| generate_dataset | 0.02 | 0.00 | 0.02 | |