Yannis Schumann
| Snapshot Date: 2024-07-25 14:00 -0400 (Thu, 25 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-26 11:42 -0400 (Fri, 26 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" | 4690 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4384 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4406 |
| 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 157/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-07-25 20:09:29 -0400 (Thu, 25 Jul 2024) |
| EndedAt: 2024-07-25 20:09:58 -0400 (Thu, 25 Jul 2024) |
| EllapsedTime: 29.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.527 0.347 6.7
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-07-25 20:09:51.796446 INFO::Formatting Data.
2024-07-25 20:09:51.797715 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:51.801509 INFO::Removing potential empty rows and columns
2024-07-25 20:09:51.89982 INFO::Found 0 missing values.
2024-07-25 20:09:51.901148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:51.901364 INFO::Done
2024-07-25 20:09:51.90157 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:51.906716 INFO::Starting hierarchical adjustment
2024-07-25 20:09:51.906986 INFO::Found 3 batches.
2024-07-25 20:09:51.907159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:51.907541 INFO::Using default BPPARAM
2024-07-25 20:09:51.907687 INFO::Processing subtree level 1
2024-07-25 20:09:51.948161 INFO::Adjusting the last 1 batches sequentially
2024-07-25 20:09:51.949323 INFO::Done
2024-07-25 20:09:51.94957 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:51.951166 INFO::ASW Batch was -0.0720937945675739 prior to batch effect correction and is now -0.0720937945675739 .
2024-07-25 20:09:51.95164 INFO::Total function execution time is 0.155481100082397 s and adjustment time is 0.0423920154571533 s ( 27.27 )
2024-07-25 20:09:51.958428 INFO::Formatting Data.
2024-07-25 20:09:51.958676 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:51.959095 INFO::Removing potential empty rows and columns
2024-07-25 20:09:51.959544 INFO::Found 0 missing values.
2024-07-25 20:09:51.959865 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.
2024-07-25 20:09:51.963959 INFO::Formatting Data.
2024-07-25 20:09:51.964193 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:51.964455 INFO::Removing potential empty rows and columns
2024-07-25 20:09:51.964778 INFO::Found 0 missing values.
2024-07-25 20:09:51.965069 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.
2024-07-25 20:09:51.970874 INFO::Formatting Data.
2024-07-25 20:09:51.971089 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:51.971342 INFO::Removing potential empty rows and columns
2024-07-25 20:09:51.97163 INFO::Found 0 missing values.
2024-07-25 20:09:51.971889 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.
2024-07-25 20:09:51.973128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:51.973291 INFO::Done
2024-07-25 20:09:51.973449 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:51.974083 INFO::Starting hierarchical adjustment
2024-07-25 20:09:51.974278 INFO::Found 2 batches.
2024-07-25 20:09:51.974428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:51.974659 INFO::Using default BPPARAM
2024-07-25 20:09:51.974799 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:51.975047 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:51.983933 INFO::Done
2024-07-25 20:09:51.984135 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:51.984735 INFO::ASW Batch was 0.0341218531866463 prior to batch effect correction and is now -0.107134991211917 .
2024-07-25 20:09:51.984976 INFO::Total function execution time is 0.0141150951385498 s and adjustment time is 0.00968503952026367 s ( 68.61 )
2024-07-25 20:09:51.985898 INFO::Formatting Data.
2024-07-25 20:09:51.986066 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:51.988775 INFO::Formatting Data.
2024-07-25 20:09:51.988965 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:51.989205 INFO::Removing potential empty rows and columns
2024-07-25 20:09:51.989511 INFO::Found 0 missing values.
2024-07-25 20:09:51.990317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:51.990475 INFO::Done
2024-07-25 20:09:51.99062 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:51.991202 INFO::Starting hierarchical adjustment
2024-07-25 20:09:51.99139 INFO::Found 2 batches.
2024-07-25 20:09:51.99153 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:51.991696 INFO::Using default BPPARAM
2024-07-25 20:09:51.991831 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:51.99207 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:51.996934 INFO::Done
2024-07-25 20:09:51.997143 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:51.997762 INFO::ASW Batch was -0.0172391945702726 prior to batch effect correction and is now -0.100043894065199 .
2024-07-25 20:09:51.998003 INFO::Total function execution time is 0.00921988487243652 s and adjustment time is 0.00557494163513184 s ( 60.47 )
2024-07-25 20:09:51.998318 INFO::Formatting Data.
2024-07-25 20:09:51.998485 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:51.998743 INFO::Removing potential empty rows and columns
2024-07-25 20:09:51.999051 INFO::Found 0 missing values.
2024-07-25 20:09:51.999886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:52.000045 INFO::Done
2024-07-25 20:09:52.000194 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:52.000774 INFO::Starting hierarchical adjustment
2024-07-25 20:09:52.000976 INFO::Found 2 batches.
2024-07-25 20:09:52.00112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:52.001292 INFO::Using default BPPARAM
2024-07-25 20:09:52.001435 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:52.001676 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:52.006732 INFO::Done
2024-07-25 20:09:52.006956 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:52.007561 INFO::ASW Batch was -0.0172391945702726 prior to batch effect correction and is now -0.100043894065199 .
2024-07-25 20:09:52.00779 INFO::Total function execution time is 0.00946402549743652 s and adjustment time is 0.00578689575195312 s ( 61.15 )
2024-07-25 20:09:52.899454 INFO::Formatting Data.
2024-07-25 20:09:52.8997 INFO::Recognized SummarizedExperiment
2024-07-25 20:09:52.899846 INFO::Typecasting input to dataframe.
2024-07-25 20:09:53.219315 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.21978 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.22087 INFO::Found 0 missing values.
2024-07-25 20:09:53.222772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.222928 INFO::Done
2024-07-25 20:09:53.223064 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.224208 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.224398 INFO::Found 2 batches.
2024-07-25 20:09:53.224526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.224824 INFO::Using default BPPARAM
2024-07-25 20:09:53.224953 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.225219 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.241487 INFO::Done
2024-07-25 20:09:53.241701 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.242834 INFO::ASW Batch was -0.000237574641041311 prior to batch effect correction and is now -0.0920612987611742 .
2024-07-25 20:09:53.243082 INFO::Total function execution time is 0.343739986419678 s and adjustment time is 0.0171198844909668 s ( 4.98 )
2024-07-25 20:09:53.24895 INFO::Formatting Data.
2024-07-25 20:09:53.249154 INFO::Recognized SummarizedExperiment
2024-07-25 20:09:53.249302 INFO::Typecasting input to dataframe.
2024-07-25 20:09:53.252051 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.252377 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.253409 INFO::Found 0 missing values.
2024-07-25 20:09:53.255337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.255486 INFO::Done
2024-07-25 20:09:53.255624 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.256743 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.256928 INFO::Found 2 batches.
2024-07-25 20:09:53.257056 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.257215 INFO::Using default BPPARAM
2024-07-25 20:09:53.257341 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.257592 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.26501 INFO::Done
2024-07-25 20:09:53.265211 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.266311 INFO::ASW Batch was 0.00680611804677017 prior to batch effect correction and is now 0.00680611804677017 .
2024-07-25 20:09:53.266549 INFO::Total function execution time is 0.0175960063934326 s and adjustment time is 0.00811290740966797 s ( 46.11 )
2024-07-25 20:09:53.272618 INFO::Formatting Data.
2024-07-25 20:09:53.272816 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.273054 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.273336 INFO::Found 0 missing values.
2024-07-25 20:09:53.27411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.274244 INFO::Done
2024-07-25 20:09:53.274374 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.274964 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.27515 INFO::Found 3 batches.
2024-07-25 20:09:53.275279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.275435 INFO::Using default BPPARAM
2024-07-25 20:09:53.275557 INFO::Processing subtree level 1
2024-07-25 20:09:53.345535 INFO::Adjusting the last 1 batches sequentially
2024-07-25 20:09:53.346953 INFO::Done
2024-07-25 20:09:53.347176 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.348769 INFO::ASW Batch was -0.062107395399655 prior to batch effect correction and is now -0.168759207904194 .
2024-07-25 20:09:53.349608 INFO::Total function execution time is 0.0769329071044922 s and adjustment time is 0.0718309879302979 s ( 93.37 )
2024-07-25 20:09:53.356689 INFO::Skipping initial DF formatting
2024-07-25 20:09:53.35693 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.35866 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.358966 INFO::Found 5 batches.
2024-07-25 20:09:53.359164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.359425 INFO::Using default BPPARAM
2024-07-25 20:09:53.359695 INFO::Processing subtree level 1
2024-07-25 20:09:53.406632 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.408313 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.417696 INFO::Done
2024-07-25 20:09:53.417926 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.419457 INFO::ASW Batch was 0.428709641028807 prior to batch effect correction and is now 0.428709641028807 .
2024-07-25 20:09:53.419645 INFO::ASW Label was 0.454615098219585 prior to batch effect correction and is now 0.454615098219585 .
2024-07-25 20:09:53.42011 INFO::Total function execution time is 0.0634489059448242 s and adjustment time is 0.0587949752807617 s ( 92.67 )
2024-07-25 20:09:53.426562 INFO::Formatting Data.
2024-07-25 20:09:53.426779 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.427057 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.427479 INFO::Found 0 missing values.
2024-07-25 20:09:53.428593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.428748 INFO::Done
2024-07-25 20:09:53.428894 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.429749 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.429956 INFO::Found 5 batches.
2024-07-25 20:09:53.430107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.4303 INFO::Using default BPPARAM
2024-07-25 20:09:53.43044 INFO::Processing subtree level 1
2024-07-25 20:09:53.468451 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.469627 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.478139 INFO::Done
2024-07-25 20:09:53.478619 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.479737 INFO::ASW Batch was 0.528300509066346 prior to batch effect correction and is now -0.047398222017532 .
2024-07-25 20:09:53.479933 INFO::ASW Label was 0.276251920222272 prior to batch effect correction and is now 0.718494670512908 .
2024-07-25 20:09:53.48044 INFO::Total function execution time is 0.0538718700408936 s and adjustment time is 0.0482211112976074 s ( 89.51 )
2024-07-25 20:09:53.480759 INFO::Formatting Data.
2024-07-25 20:09:53.480935 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.481203 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.481518 INFO::Found 0 missing values.
2024-07-25 20:09:53.482663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.482822 INFO::Done
2024-07-25 20:09:53.482967 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.483812 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.484058 INFO::Found 5 batches.
2024-07-25 20:09:53.484214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.484423 INFO::Using default BPPARAM
2024-07-25 20:09:53.484574 INFO::Processing subtree level 1
2024-07-25 20:09:53.520847 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.522264 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.530501 INFO::Done
2024-07-25 20:09:53.530726 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.531884 INFO::ASW Batch was 0.528300509066346 prior to batch effect correction and is now -0.047398222017532 .
2024-07-25 20:09:53.532066 INFO::ASW Label was 0.276251920222272 prior to batch effect correction and is now 0.718494670512908 .
2024-07-25 20:09:53.532583 INFO::Total function execution time is 0.0518109798431396 s and adjustment time is 0.046504020690918 s ( 89.76 )
2024-07-25 20:09:53.538408 INFO::Formatting Data.
2024-07-25 20:09:53.538638 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.538923 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.539265 INFO::Found 0 missing values.
2024-07-25 20:09:53.54044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.540606 INFO::Done
2024-07-25 20:09:53.540754 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.541613 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.541827 INFO::Found 5 batches.
2024-07-25 20:09:53.541985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.542201 INFO::Using default BPPARAM
2024-07-25 20:09:53.542349 INFO::Processing subtree level 1
2024-07-25 20:09:53.583622 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.585019 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.59346 INFO::Done
2024-07-25 20:09:53.5937 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.595039 INFO::ASW Batch was 0.323921827499875 prior to batch effect correction and is now -0.0743391223325176 .
2024-07-25 20:09:53.595232 INFO::ASW Label was 0.291395839854036 prior to batch effect correction and is now 0.786825974050952 .
2024-07-25 20:09:53.595824 INFO::Total function execution time is 0.0573999881744385 s and adjustment time is 0.0516729354858398 s ( 90.02 )
2024-07-25 20:09:53.596125 INFO::Formatting Data.
2024-07-25 20:09:53.596311 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.596583 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.597018 INFO::Found 0 missing values.
2024-07-25 20:09:53.598174 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.598344 INFO::Done
2024-07-25 20:09:53.598504 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.599358 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.599593 INFO::Found 5 batches.
2024-07-25 20:09:53.599748 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.599976 INFO::Using default BPPARAM
2024-07-25 20:09:53.600124 INFO::Processing subtree level 1
2024-07-25 20:09:53.641173 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.643073 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.650494 INFO::Done
2024-07-25 20:09:53.650832 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.651928 INFO::ASW Batch was 0.323921827499875 prior to batch effect correction and is now -0.0743391223325176 .
2024-07-25 20:09:53.652108 INFO::ASW Label was 0.291395839854036 prior to batch effect correction and is now 0.786825974050952 .
2024-07-25 20:09:53.652643 INFO::Total function execution time is 0.056494951248169 s and adjustment time is 0.0509369373321533 s ( 90.16 )
2024-07-25 20:09:53.658311 INFO::Formatting Data.
2024-07-25 20:09:53.658543 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.659007 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.659345 INFO::Found 0 missing values.
2024-07-25 20:09:53.660148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.660315 INFO::Done
2024-07-25 20:09:53.660464 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.661347 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.661558 INFO::Found 2 batches.
2024-07-25 20:09:53.661713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.661936 INFO::Using default BPPARAM
2024-07-25 20:09:53.662081 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.662323 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.666941 INFO::Done
2024-07-25 20:09:53.667133 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.667978 INFO::ASW Batch was 0.332998765241144 prior to batch effect correction and is now -0.0273381911673268 .
2024-07-25 20:09:53.668148 INFO::ASW Label was 0.690285869098817 prior to batch effect correction and is now 0.914695478487493 .
2024-07-25 20:09:53.668389 INFO::Total function execution time is 0.0101039409637451 s and adjustment time is 0.00542593002319336 s ( 53.7 )
2024-07-25 20:09:53.668603 INFO::Formatting Data.
2024-07-25 20:09:53.668773 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.669013 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.669283 INFO::Found 0 missing values.
2024-07-25 20:09:53.670024 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.670177 INFO::Done
2024-07-25 20:09:53.670325 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.671147 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.671351 INFO::Found 2 batches.
2024-07-25 20:09:53.671494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.671667 INFO::Using default BPPARAM
2024-07-25 20:09:53.671804 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.672045 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.676376 INFO::Done
2024-07-25 20:09:53.676572 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.677406 INFO::ASW Batch was 0.332998765241144 prior to batch effect correction and is now -0.0273381911673268 .
2024-07-25 20:09:53.677566 INFO::ASW Label was 0.690285869098817 prior to batch effect correction and is now 0.914695478487493 .
2024-07-25 20:09:53.677791 INFO::Total function execution time is 0.00917601585388184 s and adjustment time is 0.00506091117858887 s ( 55.15 )
2024-07-25 20:09:53.68202 INFO::Formatting Data.
2024-07-25 20:09:53.682236 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.682484 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.682748 INFO::Found 0 missing values.
2024-07-25 20:09:53.683361 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.683508 INFO::Done
2024-07-25 20:09:53.683655 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.684226 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.68442 INFO::Found 2 batches.
2024-07-25 20:09:53.684567 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.684741 INFO::Using default BPPARAM
2024-07-25 20:09:53.684882 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.685132 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.695788 INFO::Done
2024-07-25 20:09:53.696045 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.696729 INFO::ASW Batch was -0.0347305965623097 prior to batch effect correction and is now -0.143021967870644 .
2024-07-25 20:09:53.696992 INFO::Total function execution time is 0.0149879455566406 s and adjustment time is 0.0113868713378906 s ( 75.97 )
2024-07-25 20:09:53.701824 INFO::Formatting Data.
2024-07-25 20:09:53.702086 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.702364 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.702683 INFO::Found 0 missing values.
2024-07-25 20:09:53.703112 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.
2024-07-25 20:09:53.704505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.704676 INFO::Done
2024-07-25 20:09:53.704831 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.705793 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.705995 INFO::Found 2 batches.
2024-07-25 20:09:53.706144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.706344 INFO::Using default BPPARAM
2024-07-25 20:09:53.706493 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.706779 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.712927 INFO::Done
2024-07-25 20:09:53.713169 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.714145 INFO::ASW Batch was 0.662633891348027 prior to batch effect correction and is now 0.0712136162804832 .
2024-07-25 20:09:53.714337 INFO::ASW Label was 0.36692638736679 prior to batch effect correction and is now 0.80161812158842 .
2024-07-25 20:09:53.714596 INFO::Total function execution time is 0.0128090381622314 s and adjustment time is 0.00695490837097168 s ( 54.3 )
2024-07-25 20:09:53.714826 INFO::Formatting Data.
2024-07-25 20:09:53.715009 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.715283 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.715582 INFO::Found 0 missing values.
2024-07-25 20:09:53.715853 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.
2024-07-25 20:09:53.71726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.71744 INFO::Done
2024-07-25 20:09:53.717597 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.718541 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.718744 INFO::Found 2 batches.
2024-07-25 20:09:53.71889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.719061 INFO::Using default BPPARAM
2024-07-25 20:09:53.719205 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:53.719463 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:53.724592 INFO::Done
2024-07-25 20:09:53.724773 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.725588 INFO::ASW Batch was 0.662633891348027 prior to batch effect correction and is now 0.0712136162804832 .
2024-07-25 20:09:53.725754 INFO::ASW Label was 0.36692638736679 prior to batch effect correction and is now 0.80161812158842 .
2024-07-25 20:09:53.725984 INFO::Total function execution time is 0.0111517906188965 s and adjustment time is 0.00588202476501465 s ( 52.75 )
2024-07-25 20:09:53.789473 INFO::Formatting Data.
2024-07-25 20:09:53.789765 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.790053 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.790384 INFO::Found 0 missing values.
2024-07-25 20:09:53.791288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.791459 INFO::Done
2024-07-25 20:09:53.791606 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.792295 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.7925 INFO::Found 3 batches.
2024-07-25 20:09:53.792647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.792836 INFO::Using default BPPARAM
2024-07-25 20:09:53.792977 INFO::Processing subtree level 1
2024-07-25 20:09:53.828407 INFO::Adjusting the last 1 batches sequentially
2024-07-25 20:09:53.82937 INFO::Done
2024-07-25 20:09:53.829566 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.831021 INFO::ASW Batch was -0.0380096953040315 prior to batch effect correction and is now -0.0380096953040315 .
2024-07-25 20:09:53.831533 INFO::Total function execution time is 0.0420880317687988 s and adjustment time is 0.0369150638580322 s ( 87.71 )
2024-07-25 20:09:53.831926 INFO::Formatting Data.
2024-07-25 20:09:53.832118 INFO::Typecasting input to dataframe.
2024-07-25 20:09:53.832343 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.832643 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.833151 INFO::Found 0 missing values.
2024-07-25 20:09:53.834075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.83425 INFO::Done
2024-07-25 20:09:53.834401 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.835014 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.83521 INFO::Found 3 batches.
2024-07-25 20:09:53.835359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.835551 INFO::Using default BPPARAM
2024-07-25 20:09:53.835691 INFO::Processing subtree level 1
2024-07-25 20:09:53.872868 INFO::Adjusting the last 1 batches sequentially
2024-07-25 20:09:53.873851 INFO::Done
2024-07-25 20:09:53.874041 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.875498 INFO::ASW Batch was -0.0380096953040315 prior to batch effect correction and is now -0.0380096953040315 .
2024-07-25 20:09:53.875966 INFO::Total function execution time is 0.0440299510955811 s and adjustment time is 0.0386850833892822 s ( 87.86 )
2024-07-25 20:09:53.881645 INFO::Formatting Data.
2024-07-25 20:09:53.881871 INFO::Typecasting input to dataframe.
2024-07-25 20:09:53.882124 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.8824 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.882882 INFO::Found 0 missing values.
2024-07-25 20:09:53.883758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.883929 INFO::Done
2024-07-25 20:09:53.884084 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.884679 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.884902 INFO::Found 3 batches.
2024-07-25 20:09:53.885047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.885236 INFO::Using default BPPARAM
2024-07-25 20:09:53.885372 INFO::Processing subtree level 1
2024-07-25 20:09:53.922649 INFO::Adjusting the last 1 batches sequentially
2024-07-25 20:09:53.923906 INFO::Done
2024-07-25 20:09:53.924086 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:53.925948 INFO::ASW Batch was -0.0470601992304038 prior to batch effect correction and is now -0.0470601992304038 .
2024-07-25 20:09:53.9265 INFO::Total function execution time is 0.0448398590087891 s and adjustment time is 0.0390479564666748 s ( 87.08 )
2024-07-25 20:09:53.989335 INFO::Formatting Data.
2024-07-25 20:09:53.989575 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:53.989932 INFO::Removing potential empty rows and columns
2024-07-25 20:09:53.990963 INFO::Found 1000 missing values.
2024-07-25 20:09:53.996484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:53.99671 INFO::Done
2024-07-25 20:09:53.996886 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:53.998708 INFO::Starting hierarchical adjustment
2024-07-25 20:09:53.998952 INFO::Found 10 batches.
2024-07-25 20:09:53.999101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:53.999321 INFO::Using default BPPARAM
2024-07-25 20:09:53.999476 INFO::Processing subtree level 1
2024-07-25 20:09:54.047787 INFO::Processing subtree level 2
2024-07-25 20:09:54.105453 INFO::Adjusting the last 1 batches sequentially
2024-07-25 20:09:54.106841 INFO::Done
2024-07-25 20:09:54.107262 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:54.110001 INFO::ASW Batch was 0.564479605899041 prior to batch effect correction and is now 0.564479605899041 .
2024-07-25 20:09:54.110215 INFO::ASW Label was 0.268671266452957 prior to batch effect correction and is now 0.268671266452957 .
2024-07-25 20:09:54.110719 INFO::Total function execution time is 0.121387004852295 s and adjustment time is 0.107933044433594 s ( 88.92 )
2024-07-25 20:09:54.111012 INFO::Formatting Data.
2024-07-25 20:09:54.1112 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:54.111581 INFO::Removing potential empty rows and columns
2024-07-25 20:09:54.112651 INFO::Found 1000 missing values.
2024-07-25 20:09:54.118279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:54.118508 INFO::Done
2024-07-25 20:09:54.118669 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:54.120562 INFO::Starting hierarchical adjustment
2024-07-25 20:09:54.120803 INFO::Found 10 batches.
2024-07-25 20:09:54.543137 INFO::Set up parallel execution backend with 2 workers
2024-07-25 20:09:54.543404 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-25 20:09:55.103383 INFO::Adjusting the last 2 batches sequentially
2024-07-25 20:09:55.103966 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 20:09:55.109291 INFO::Done
2024-07-25 20:09:55.109484 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:55.111213 INFO::ASW Batch was 0.564479605899041 prior to batch effect correction and is now 0.564479605899041 .
2024-07-25 20:09:55.11138 INFO::ASW Label was 0.268671266452957 prior to batch effect correction and is now 0.268671266452957 .
2024-07-25 20:09:55.11164 INFO::Total function execution time is 1.00063490867615 s and adjustment time is 0.98854398727417 s ( 98.79 )
2024-07-25 20:09:55.175238 INFO::Formatting Data.
2024-07-25 20:09:55.175523 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.175902 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.176595 INFO::Found 0 missing values.
2024-07-25 20:09:55.177974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.178168 INFO::Done
2024-07-25 20:09:55.178362 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 20:09:55.179396 INFO::Starting hierarchical adjustment
2024-07-25 20:09:55.179652 INFO::Found 3 batches.
2024-07-25 20:09:55.179841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 20:09:55.180097 INFO::Using default BPPARAM
2024-07-25 20:09:55.180272 INFO::Processing subtree level 1
2024-07-25 20:09:55.22873 INFO::Adjusting the last 1 batches sequentially
2024-07-25 20:09:55.229639 INFO::Done
2024-07-25 20:09:55.229919 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 20:09:55.231579 INFO::ASW Batch was 0.128207857150331 prior to batch effect correction and is now -0.138036706370255 .
2024-07-25 20:09:55.23177 INFO::ASW Label was -0.199601879123831 prior to batch effect correction and is now -0.0303460511037257 .
2024-07-25 20:09:55.232414 INFO::Total function execution time is 0.057183027267456 s and adjustment time is 0.0500400066375732 s ( 87.51 )
2024-07-25 20:09:55.274147 INFO::Formatting Data.
2024-07-25 20:09:55.27444 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.274724 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.27507 INFO::Found 2 missing values.
2024-07-25 20:09:55.275975 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.276134 INFO::Done
2024-07-25 20:09:55.285475 INFO::Found NA in Reference column
2024-07-25 20:09:55.288781 INFO::Require at least two references per batch.
2024-07-25 20:09:55.296135 INFO::Formatting Data.
2024-07-25 20:09:55.296355 INFO::Recognized SummarizedExperiment
2024-07-25 20:09:55.296524 INFO::Typecasting input to dataframe.
2024-07-25 20:09:55.300702 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.301134 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.302613 INFO::Found 0 missing values.
2024-07-25 20:09:55.305045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.305219 INFO::Done
2024-07-25 20:09:55.310701 INFO::Formatting Data.
2024-07-25 20:09:55.310907 INFO::Recognized SummarizedExperiment
2024-07-25 20:09:55.311057 INFO::Typecasting input to dataframe.
2024-07-25 20:09:55.316408 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.316813 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.318048 INFO::Found 0 missing values.
2024-07-25 20:09:55.321894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.322086 INFO::Done
2024-07-25 20:09:55.327389 INFO::Formatting Data.
2024-07-25 20:09:55.327604 INFO::Recognized SummarizedExperiment
2024-07-25 20:09:55.327782 INFO::Typecasting input to dataframe.
2024-07-25 20:09:55.333496 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.333809 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.334154 INFO::Found 0 missing values.
2024-07-25 20:09:55.334434 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.
2024-07-25 20:09:55.335879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.336052 INFO::Done
2024-07-25 20:09:55.340159 INFO::Formatting Data.
2024-07-25 20:09:55.340391 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.340658 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.34097 INFO::Found 0 missing values.
2024-07-25 20:09:55.341827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.341992 INFO::Done
2024-07-25 20:09:55.368345 INFO::Formatting Data.
2024-07-25 20:09:55.368704 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.369011 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.369348 INFO::Found 0 missing values.
2024-07-25 20:09:55.3703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.370468 INFO::Done
2024-07-25 20:09:55.382052 INFO::Formatting Data.
2024-07-25 20:09:55.38234 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.382678 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.383669 INFO::Found 1 missing values.
2024-07-25 20:09:55.384773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.393659 INFO::Done
2024-07-25 20:09:55.408092 INFO::Formatting Data.
2024-07-25 20:09:55.408418 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.408979 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.40935 INFO::Found 2 missing values.
2024-07-25 20:09:55.409695 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.
2024-07-25 20:09:55.410525 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.410707 INFO::Done
2024-07-25 20:09:55.41496 INFO::Formatting Data.
2024-07-25 20:09:55.415204 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.415481 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.415803 INFO::Found 2 missing values.
2024-07-25 20:09:55.416365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.416525 INFO::Done
2024-07-25 20:09:55.420834 INFO::Formatting Data.
2024-07-25 20:09:55.421112 INFO::Typecasting input to dataframe.
2024-07-25 20:09:55.42145 INFO::Replacing NaNs with NAs.
2024-07-25 20:09:55.421777 INFO::Removing potential empty rows and columns
2024-07-25 20:09:55.42235 INFO::Found 0 missing values.
2024-07-25 20:09:55.423543 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 20:09:55.423733 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.726 1.288 8.280
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.527 | 0.347 | 6.700 | |
| compute_asw | 0.009 | 0.000 | 0.010 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.003 | 0.000 | 0.004 | |