Yannis Schumann
| Snapshot Date: 2025-02-09 13:40 -0500 (Sun, 09 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0500 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-10 11:40 -0500 (Mon, 10 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.3.6 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-02-09 22:54:17 -0500 (Sun, 09 Feb 2025) |
| EndedAt: 2025-02-09 22:56:36 -0500 (Sun, 09 Feb 2025) |
| EllapsedTime: 138.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '1.3.6'
* 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 8.93 0.52 18.36
* 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: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'BERT' ... ** this is package 'BERT' version '1.3.6' ** 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 Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
2025-02-09 22:55:23.054009 INFO::Formatting Data.
2025-02-09 22:55:23.057141 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:23.073339 INFO::Removing potential empty rows and columns
2025-02-09 22:55:23.371079 INFO::Found 0 missing values.
2025-02-09 22:55:23.376142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:23.377508 INFO::Done
2025-02-09 22:55:23.37873 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:23.397598 INFO::Starting hierarchical adjustment
2025-02-09 22:55:23.399221 INFO::Found 3 batches.
2025-02-09 22:55:23.400448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:23.402397 INFO::Using default BPPARAM
2025-02-09 22:55:23.403587 INFO::Processing subtree level 1
2025-02-09 22:55:26.525636 INFO::Adjusting the last 1 batches sequentially
2025-02-09 22:55:26.527824 INFO::Done
2025-02-09 22:55:26.529134 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:26.532313 INFO::ASW Batch was -0.10754490048208 prior to batch effect correction and is now -0.10754490048208 .
2025-02-09 22:55:26.534028 INFO::Total function execution time is 3.48070597648621 s and adjustment time is 3.12885999679565 s ( 89.89 )
2025-02-09 22:55:26.557977 INFO::Formatting Data.
2025-02-09 22:55:26.559513 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:26.561254 INFO::Removing potential empty rows and columns
2025-02-09 22:55:26.563118 INFO::Found 0 missing values.
2025-02-09 22:55:26.564844 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.
2025-02-09 22:55:26.57849 INFO::Formatting Data.
2025-02-09 22:55:26.579957 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:26.581667 INFO::Removing potential empty rows and columns
2025-02-09 22:55:26.583478 INFO::Found 0 missing values.
2025-02-09 22:55:26.585126 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.
2025-02-09 22:55:26.610812 INFO::Formatting Data.
2025-02-09 22:55:26.612411 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:26.614171 INFO::Removing potential empty rows and columns
2025-02-09 22:55:26.616102 INFO::Found 0 missing values.
2025-02-09 22:55:26.617845 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.
2025-02-09 22:55:26.62424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:26.625592 INFO::Done
2025-02-09 22:55:26.626854 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:26.630138 INFO::Starting hierarchical adjustment
2025-02-09 22:55:26.631609 INFO::Found 2 batches.
2025-02-09 22:55:26.632906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:26.634222 INFO::Using default BPPARAM
2025-02-09 22:55:26.635387 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:26.637163 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:26.664244 INFO::Done
2025-02-09 22:55:26.665696 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:26.669099 INFO::ASW Batch was 0.0339594517535317 prior to batch effect correction and is now -0.100395328355219 .
2025-02-09 22:55:26.670587 INFO::Total function execution time is 0.0598750114440918 s and adjustment time is 0.0328190326690674 s ( 54.81 )
2025-02-09 22:55:26.6746 INFO::Formatting Data.
2025-02-09 22:55:26.675777 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:26.683086 INFO::Formatting Data.
2025-02-09 22:55:26.683958 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:26.684971 INFO::Removing potential empty rows and columns
2025-02-09 22:55:26.686059 INFO::Found 0 missing values.
2025-02-09 22:55:26.688482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:26.689185 INFO::Done
2025-02-09 22:55:26.689872 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:26.691949 INFO::Starting hierarchical adjustment
2025-02-09 22:55:26.692822 INFO::Found 2 batches.
2025-02-09 22:55:26.693518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:26.694276 INFO::Using default BPPARAM
2025-02-09 22:55:26.694964 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:26.696004 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:26.716064 INFO::Done
2025-02-09 22:55:26.717459 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:26.720806 INFO::ASW Batch was 0.0929050577450091 prior to batch effect correction and is now -0.097150245434721 .
2025-02-09 22:55:26.722438 INFO::Total function execution time is 0.0392980575561523 s and adjustment time is 0.0232899188995361 s ( 59.26 )
2025-02-09 22:55:26.72427 INFO::Formatting Data.
2025-02-09 22:55:26.725492 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:26.727035 INFO::Removing potential empty rows and columns
2025-02-09 22:55:26.728841 INFO::Found 0 missing values.
2025-02-09 22:55:26.73303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:26.734168 INFO::Done
2025-02-09 22:55:26.735391 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:26.738647 INFO::Starting hierarchical adjustment
2025-02-09 22:55:26.740086 INFO::Found 2 batches.
2025-02-09 22:55:26.741203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:26.74244 INFO::Using default BPPARAM
2025-02-09 22:55:26.743562 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:26.745234 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:26.765376 INFO::Done
2025-02-09 22:55:26.766829 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:26.770217 INFO::ASW Batch was 0.0929050577450091 prior to batch effect correction and is now -0.097150245434721 .
2025-02-09 22:55:26.771793 INFO::Total function execution time is 0.0474750995635986 s and adjustment time is 0.0254509449005127 s ( 53.61 )
2025-02-09 22:55:29.656555 INFO::Formatting Data.
2025-02-09 22:55:29.65789 INFO::Recognized SummarizedExperiment
2025-02-09 22:55:29.659036 INFO::Typecasting input to dataframe.
2025-02-09 22:55:29.70408 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:29.70636 INFO::Removing potential empty rows and columns
2025-02-09 22:55:29.711642 INFO::Found 0 missing values.
2025-02-09 22:55:29.721348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:29.722879 INFO::Done
2025-02-09 22:55:29.724218 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:29.730501 INFO::Starting hierarchical adjustment
2025-02-09 22:55:29.732217 INFO::Found 2 batches.
2025-02-09 22:55:29.733501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:29.735537 INFO::Using default BPPARAM
2025-02-09 22:55:29.736785 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:29.738814 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:30.521274 INFO::Done
2025-02-09 22:55:30.522766 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:30.528985 INFO::ASW Batch was 0.0247872468679599 prior to batch effect correction and is now -0.0924489807482936 .
2025-02-09 22:55:30.530756 INFO::Total function execution time is 0.874572038650513 s and adjustment time is 0.789308071136475 s ( 90.25 )
2025-02-09 22:55:30.560179 INFO::Formatting Data.
2025-02-09 22:55:30.561651 INFO::Recognized SummarizedExperiment
2025-02-09 22:55:30.56296 INFO::Typecasting input to dataframe.
2025-02-09 22:55:30.576503 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:30.578742 INFO::Removing potential empty rows and columns
2025-02-09 22:55:30.583694 INFO::Found 0 missing values.
2025-02-09 22:55:30.593209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:30.594666 INFO::Done
2025-02-09 22:55:30.595952 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:30.602091 INFO::Starting hierarchical adjustment
2025-02-09 22:55:30.603656 INFO::Found 2 batches.
2025-02-09 22:55:30.60494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:30.606325 INFO::Using default BPPARAM
2025-02-09 22:55:30.607579 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:30.609609 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:30.643371 INFO::Done
2025-02-09 22:55:30.644821 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:30.651051 INFO::ASW Batch was -0.0139537915695757 prior to batch effect correction and is now -0.0139537915695757 .
2025-02-09 22:55:30.652848 INFO::Total function execution time is 0.092602014541626 s and adjustment time is 0.0399389266967773 s ( 43.13 )
2025-02-09 22:55:30.686151 INFO::Formatting Data.
2025-02-09 22:55:30.687788 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:30.689625 INFO::Removing potential empty rows and columns
2025-02-09 22:55:30.691475 INFO::Found 0 missing values.
2025-02-09 22:55:30.696115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:30.697368 INFO::Done
2025-02-09 22:55:30.698587 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:30.701968 INFO::Starting hierarchical adjustment
2025-02-09 22:55:30.703419 INFO::Found 3 batches.
2025-02-09 22:55:30.704555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:30.705801 INFO::Using default BPPARAM
2025-02-09 22:55:30.706966 INFO::Processing subtree level 1
2025-02-09 22:55:41.481567 INFO::Adjusting the last 1 batches sequentially
2025-02-09 22:55:41.483793 INFO::Done
2025-02-09 22:55:41.485011 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:41.488106 INFO::ASW Batch was 0.0108636971780923 prior to batch effect correction and is now -0.165533898319822 .
2025-02-09 22:55:41.489671 INFO::Total function execution time is 10.8036398887634 s and adjustment time is 10.7805759906769 s ( 99.79 )
2025-02-09 22:55:41.514877 INFO::Skipping initial DF formatting
2025-02-09 22:55:41.516241 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:41.522955 INFO::Starting hierarchical adjustment
2025-02-09 22:55:41.524534 INFO::Found 5 batches.
2025-02-09 22:55:41.525792 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:41.52711 INFO::Using default BPPARAM
2025-02-09 22:55:41.528319 INFO::Processing subtree level 1
2025-02-09 22:55:44.460814 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:44.463007 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:44.482944 INFO::Done
2025-02-09 22:55:44.484158 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:44.490804 INFO::ASW Batch was 0.47828732103262 prior to batch effect correction and is now 0.47828732103262 .
2025-02-09 22:55:44.492206 INFO::ASW Label was 0.382353036060086 prior to batch effect correction and is now 0.382353036060086 .
2025-02-09 22:55:44.49381 INFO::Total function execution time is 2.97902798652649 s and adjustment time is 2.9586009979248 s ( 99.31 )
2025-02-09 22:55:44.521831 INFO::Formatting Data.
2025-02-09 22:55:44.523338 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:44.525044 INFO::Removing potential empty rows and columns
2025-02-09 22:55:44.526947 INFO::Found 0 missing values.
2025-02-09 22:55:44.53055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:44.531619 INFO::Done
2025-02-09 22:55:44.532527 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:44.535697 INFO::Starting hierarchical adjustment
2025-02-09 22:55:44.53668 INFO::Found 5 batches.
2025-02-09 22:55:44.537488 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:44.53839 INFO::Using default BPPARAM
2025-02-09 22:55:44.539229 INFO::Processing subtree level 1
2025-02-09 22:55:47.46181 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:47.463584 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:47.475723 INFO::Done
2025-02-09 22:55:47.476657 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:47.480788 INFO::ASW Batch was 0.274074597898137 prior to batch effect correction and is now -0.0401010792347934 .
2025-02-09 22:55:47.482238 INFO::ASW Label was 0.491700018327937 prior to batch effect correction and is now 0.822318322526968 .
2025-02-09 22:55:47.483951 INFO::Total function execution time is 2.96218109130859 s and adjustment time is 2.93917608261108 s ( 99.22 )
2025-02-09 22:55:47.48561 INFO::Formatting Data.
2025-02-09 22:55:47.487007 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:47.488782 INFO::Removing potential empty rows and columns
2025-02-09 22:55:47.490713 INFO::Found 0 missing values.
2025-02-09 22:55:47.497056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:47.49846 INFO::Done
2025-02-09 22:55:47.499824 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:47.504933 INFO::Starting hierarchical adjustment
2025-02-09 22:55:47.506522 INFO::Found 5 batches.
2025-02-09 22:55:47.507791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:47.509152 INFO::Using default BPPARAM
2025-02-09 22:55:47.510437 INFO::Processing subtree level 1
2025-02-09 22:55:50.573371 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:50.575541 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:50.595404 INFO::Done
2025-02-09 22:55:50.596815 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:50.601614 INFO::ASW Batch was 0.274074597898137 prior to batch effect correction and is now -0.0401010792347934 .
2025-02-09 22:55:50.602907 INFO::ASW Label was 0.491700018327937 prior to batch effect correction and is now 0.822318322526968 .
2025-02-09 22:55:50.604419 INFO::Total function execution time is 3.11884498596191 s and adjustment time is 3.08908200263977 s ( 99.05 )
2025-02-09 22:55:50.627959 INFO::Formatting Data.
2025-02-09 22:55:50.629517 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:50.631268 INFO::Removing potential empty rows and columns
2025-02-09 22:55:50.63303 INFO::Found 0 missing values.
2025-02-09 22:55:50.638808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:50.640112 INFO::Done
2025-02-09 22:55:50.641372 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:50.646036 INFO::Starting hierarchical adjustment
2025-02-09 22:55:50.647586 INFO::Found 5 batches.
2025-02-09 22:55:50.648781 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:50.650097 INFO::Using default BPPARAM
2025-02-09 22:55:50.651283 INFO::Processing subtree level 1
2025-02-09 22:55:53.586452 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:53.587981 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:53.599432 INFO::Done
2025-02-09 22:55:53.600302 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:53.603227 INFO::ASW Batch was 0.446715238285257 prior to batch effect correction and is now -0.10404780455848 .
2025-02-09 22:55:53.604032 INFO::ASW Label was 0.228384286630476 prior to batch effect correction and is now 0.85495234843847 .
2025-02-09 22:55:53.605004 INFO::Total function execution time is 2.97717189788818 s and adjustment time is 2.95207810401917 s ( 99.16 )
2025-02-09 22:55:53.605958 INFO::Formatting Data.
2025-02-09 22:55:53.606745 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:53.607741 INFO::Removing potential empty rows and columns
2025-02-09 22:55:53.608778 INFO::Found 0 missing values.
2025-02-09 22:55:53.61218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:53.612876 INFO::Done
2025-02-09 22:55:53.613548 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:53.616358 INFO::Starting hierarchical adjustment
2025-02-09 22:55:53.617208 INFO::Found 5 batches.
2025-02-09 22:55:53.617882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:53.618622 INFO::Using default BPPARAM
2025-02-09 22:55:53.6193 INFO::Processing subtree level 1
2025-02-09 22:55:56.62323 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:56.625403 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:56.644274 INFO::Done
2025-02-09 22:55:56.64519 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:56.648156 INFO::ASW Batch was 0.446715238285257 prior to batch effect correction and is now -0.10404780455848 .
2025-02-09 22:55:56.648927 INFO::ASW Label was 0.228384286630476 prior to batch effect correction and is now 0.85495234843847 .
2025-02-09 22:55:56.649906 INFO::Total function execution time is 3.04395198822021 s and adjustment time is 3.02715301513672 s ( 99.45 )
2025-02-09 22:55:56.672932 INFO::Formatting Data.
2025-02-09 22:55:56.673899 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:56.674991 INFO::Removing potential empty rows and columns
2025-02-09 22:55:56.676091 INFO::Found 0 missing values.
2025-02-09 22:55:56.67842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:56.679148 INFO::Done
2025-02-09 22:55:56.679839 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:56.682708 INFO::Starting hierarchical adjustment
2025-02-09 22:55:56.683583 INFO::Found 2 batches.
2025-02-09 22:55:56.684674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:56.685983 INFO::Using default BPPARAM
2025-02-09 22:55:56.68719 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:56.688979 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:56.703727 INFO::Done
2025-02-09 22:55:56.704637 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:56.707632 INFO::ASW Batch was 0.54657496191568 prior to batch effect correction and is now -0.0245744220274277 .
2025-02-09 22:55:56.708436 INFO::ASW Label was 0.547011052602739 prior to batch effect correction and is now 0.935627212851777 .
2025-02-09 22:55:56.709435 INFO::Total function execution time is 0.0365321636199951 s and adjustment time is 0.020237922668457 s ( 55.4 )
2025-02-09 22:55:56.7109 INFO::Formatting Data.
2025-02-09 22:55:56.711734 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:56.712754 INFO::Removing potential empty rows and columns
2025-02-09 22:55:56.713834 INFO::Found 0 missing values.
2025-02-09 22:55:56.71621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:56.716932 INFO::Done
2025-02-09 22:55:56.717636 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:56.720502 INFO::Starting hierarchical adjustment
2025-02-09 22:55:56.72139 INFO::Found 2 batches.
2025-02-09 22:55:56.72249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:56.723795 INFO::Using default BPPARAM
2025-02-09 22:55:56.725051 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:56.726823 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:56.745693 INFO::Done
2025-02-09 22:55:56.747099 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:56.751871 INFO::ASW Batch was 0.54657496191568 prior to batch effect correction and is now -0.0245744220274277 .
2025-02-09 22:55:56.753198 INFO::ASW Label was 0.547011052602739 prior to batch effect correction and is now 0.935627212851777 .
2025-02-09 22:55:56.754793 INFO::Total function execution time is 0.0438530445098877 s and adjustment time is 0.0243518352508545 s ( 55.53 )
2025-02-09 22:55:56.776971 INFO::Formatting Data.
2025-02-09 22:55:56.778461 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:56.780177 INFO::Removing potential empty rows and columns
2025-02-09 22:55:56.781852 INFO::Found 0 missing values.
2025-02-09 22:55:56.784955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:56.786122 INFO::Done
2025-02-09 22:55:56.787345 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:56.790392 INFO::Starting hierarchical adjustment
2025-02-09 22:55:56.791826 INFO::Found 2 batches.
2025-02-09 22:55:56.793 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:56.794295 INFO::Using default BPPARAM
2025-02-09 22:55:56.795495 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:56.797192 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:56.837351 INFO::Done
2025-02-09 22:55:56.838736 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:56.841885 INFO::ASW Batch was -0.0921252994290892 prior to batch effect correction and is now -0.148690169796443 .
2025-02-09 22:55:56.843432 INFO::Total function execution time is 0.0665509700775146 s and adjustment time is 0.0457348823547363 s ( 68.72 )
2025-02-09 22:55:56.866279 INFO::Formatting Data.
2025-02-09 22:55:56.867869 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:56.869611 INFO::Removing potential empty rows and columns
2025-02-09 22:55:56.871405 INFO::Found 0 missing values.
2025-02-09 22:55:56.873419 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.
2025-02-09 22:55:56.880046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:56.881368 INFO::Done
2025-02-09 22:55:56.882568 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:56.887264 INFO::Starting hierarchical adjustment
2025-02-09 22:55:56.888799 INFO::Found 2 batches.
2025-02-09 22:55:56.890034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:56.891395 INFO::Using default BPPARAM
2025-02-09 22:55:56.892594 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:56.894422 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:56.916893 INFO::Done
2025-02-09 22:55:56.918323 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:56.923246 INFO::ASW Batch was 0.450913668834588 prior to batch effect correction and is now -0.020337491837569 .
2025-02-09 22:55:56.924689 INFO::ASW Label was 0.538256010460524 prior to batch effect correction and is now 0.922646352602913 .
2025-02-09 22:55:56.926379 INFO::Total function execution time is 0.0601987838745117 s and adjustment time is 0.0282540321350098 s ( 46.93 )
2025-02-09 22:55:56.927961 INFO::Formatting Data.
2025-02-09 22:55:56.929304 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:56.931107 INFO::Removing potential empty rows and columns
2025-02-09 22:55:56.932923 INFO::Found 0 missing values.
2025-02-09 22:55:56.934682 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.
2025-02-09 22:55:56.94168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:56.943067 INFO::Done
2025-02-09 22:55:56.944365 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:56.949053 INFO::Starting hierarchical adjustment
2025-02-09 22:55:56.950622 INFO::Found 2 batches.
2025-02-09 22:55:56.951881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:56.953226 INFO::Using default BPPARAM
2025-02-09 22:55:56.954423 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:55:56.956263 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:55:56.978973 INFO::Done
2025-02-09 22:55:56.980429 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:55:56.985518 INFO::ASW Batch was 0.450913668834588 prior to batch effect correction and is now -0.020337491837569 .
2025-02-09 22:55:56.986883 INFO::ASW Label was 0.538256010460524 prior to batch effect correction and is now 0.922646352602913 .
2025-02-09 22:55:56.98855 INFO::Total function execution time is 0.0605950355529785 s and adjustment time is 0.0285539627075195 s ( 47.12 )
2025-02-09 22:55:57.268508 INFO::Formatting Data.
2025-02-09 22:55:57.270224 INFO::Replacing NaNs with NAs.
2025-02-09 22:55:57.272052 INFO::Removing potential empty rows and columns
2025-02-09 22:55:57.274148 INFO::Found 0 missing values.
2025-02-09 22:55:57.279298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:55:57.280788 INFO::Done
2025-02-09 22:55:57.282095 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:55:57.28578 INFO::Starting hierarchical adjustment
2025-02-09 22:55:57.28738 INFO::Found 3 batches.
2025-02-09 22:55:57.288724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:55:57.290172 INFO::Using default BPPARAM
2025-02-09 22:55:57.291434 INFO::Processing subtree level 1
2025-02-09 22:56:00.159211 INFO::Adjusting the last 1 batches sequentially
2025-02-09 22:56:00.161348 INFO::Done
2025-02-09 22:56:00.162673 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:56:00.165903 INFO::ASW Batch was 0.0453167604096783 prior to batch effect correction and is now 0.0453167604096783 .
2025-02-09 22:56:00.167347 INFO::Total function execution time is 2.89899802207947 s and adjustment time is 2.87419390678406 s ( 99.14 )
2025-02-09 22:56:00.169136 INFO::Formatting Data.
2025-02-09 22:56:00.170497 INFO::Typecasting input to dataframe.
2025-02-09 22:56:00.171962 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:00.173582 INFO::Removing potential empty rows and columns
2025-02-09 22:56:00.175309 INFO::Found 0 missing values.
2025-02-09 22:56:00.179588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:00.180774 INFO::Done
2025-02-09 22:56:00.182075 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:56:00.18568 INFO::Starting hierarchical adjustment
2025-02-09 22:56:00.187042 INFO::Found 3 batches.
2025-02-09 22:56:00.188166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:56:00.189335 INFO::Using default BPPARAM
2025-02-09 22:56:00.190563 INFO::Processing subtree level 1
2025-02-09 22:56:02.979427 INFO::Adjusting the last 1 batches sequentially
2025-02-09 22:56:02.98155 INFO::Done
2025-02-09 22:56:02.982817 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:56:02.986131 INFO::ASW Batch was 0.0453167604096783 prior to batch effect correction and is now 0.0453167604096783 .
2025-02-09 22:56:02.987661 INFO::Total function execution time is 2.81855511665344 s and adjustment time is 2.79469513893127 s ( 99.15 )
2025-02-09 22:56:03.00933 INFO::Formatting Data.
2025-02-09 22:56:03.010816 INFO::Typecasting input to dataframe.
2025-02-09 22:56:03.012368 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:03.013984 INFO::Removing potential empty rows and columns
2025-02-09 22:56:03.015233 INFO::Found 0 missing values.
2025-02-09 22:56:03.017786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:03.018582 INFO::Done
2025-02-09 22:56:03.019309 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:56:03.021332 INFO::Starting hierarchical adjustment
2025-02-09 22:56:03.022252 INFO::Found 3 batches.
2025-02-09 22:56:03.022959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:56:03.023725 INFO::Using default BPPARAM
2025-02-09 22:56:03.024419 INFO::Processing subtree level 1
2025-02-09 22:56:05.852655 INFO::Adjusting the last 1 batches sequentially
2025-02-09 22:56:05.855107 INFO::Done
2025-02-09 22:56:05.856521 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:56:05.859948 INFO::ASW Batch was -0.078957070002779 prior to batch effect correction and is now -0.078957070002779 .
2025-02-09 22:56:05.861632 INFO::Total function execution time is 2.85239195823669 s and adjustment time is 2.83291888237 s ( 99.32 )
2025-02-09 22:56:08.718867 INFO::Formatting Data.
2025-02-09 22:56:08.720248 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:08.722119 INFO::Removing potential empty rows and columns
2025-02-09 22:56:08.72548 INFO::Found 1000 missing values.
2025-02-09 22:56:08.748061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:08.7495 INFO::Done
2025-02-09 22:56:08.75082 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:56:08.760691 INFO::Starting hierarchical adjustment
2025-02-09 22:56:08.762445 INFO::Found 10 batches.
2025-02-09 22:56:08.763781 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:56:08.765198 INFO::Using default BPPARAM
2025-02-09 22:56:08.766444 INFO::Processing subtree level 1
2025-02-09 22:56:11.905305 INFO::Processing subtree level 2
2025-02-09 22:56:14.64869 INFO::Adjusting the last 1 batches sequentially
2025-02-09 22:56:14.65103 INFO::Done
2025-02-09 22:56:14.652243 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:56:14.66078 INFO::ASW Batch was 0.472350349458272 prior to batch effect correction and is now 0.472350349458272 .
2025-02-09 22:56:14.662019 INFO::ASW Label was 0.353736927862335 prior to batch effect correction and is now 0.353736927862335 .
2025-02-09 22:56:14.663569 INFO::Total function execution time is 5.94482398033142 s and adjustment time is 5.88891506195068 s ( 99.06 )
2025-02-09 22:56:14.664921 INFO::Formatting Data.
2025-02-09 22:56:14.666086 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:14.667804 INFO::Removing potential empty rows and columns
2025-02-09 22:56:14.671245 INFO::Found 1000 missing values.
2025-02-09 22:56:14.693451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:14.694993 INFO::Done
2025-02-09 22:56:14.69619 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:56:14.704997 INFO::Starting hierarchical adjustment
2025-02-09 22:56:14.706407 INFO::Found 10 batches.
2025-02-09 22:56:15.502736 INFO::Set up parallel execution backend with 2 workers
2025-02-09 22:56:15.504259 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-09 22:56:18.372756 INFO::Adjusting the last 2 batches sequentially
2025-02-09 22:56:18.374187 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-09 22:56:18.388016 INFO::Done
2025-02-09 22:56:18.388899 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:56:18.395599 INFO::ASW Batch was 0.472350349458272 prior to batch effect correction and is now 0.472350349458272 .
2025-02-09 22:56:18.396455 INFO::ASW Label was 0.353736927862335 prior to batch effect correction and is now 0.353736927862335 .
2025-02-09 22:56:18.397407 INFO::Total function execution time is 3.73256492614746 s and adjustment time is 3.68182897567749 s ( 98.64 )
2025-02-09 22:56:21.398342 INFO::Formatting Data.
2025-02-09 22:56:21.399872 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:21.40156 INFO::Removing potential empty rows and columns
2025-02-09 22:56:21.403395 INFO::Found 0 missing values.
2025-02-09 22:56:21.408688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:21.409881 INFO::Done
2025-02-09 22:56:21.411077 INFO::Acquiring quality metrics before batch effect correction.
2025-02-09 22:56:21.415348 INFO::Starting hierarchical adjustment
2025-02-09 22:56:21.416801 INFO::Found 3 batches.
2025-02-09 22:56:21.417913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-09 22:56:21.419082 INFO::Using default BPPARAM
2025-02-09 22:56:21.420162 INFO::Processing subtree level 1
2025-02-09 22:56:24.792124 INFO::Adjusting the last 1 batches sequentially
2025-02-09 22:56:24.794222 INFO::Done
2025-02-09 22:56:24.795428 INFO::Acquiring quality metrics after batch effect correction.
2025-02-09 22:56:24.799265 INFO::ASW Batch was 0.190601171998854 prior to batch effect correction and is now -0.141099677878484 .
2025-02-09 22:56:24.800391 INFO::ASW Label was -0.213993449202509 prior to batch effect correction and is now -0.0335581972209814 .
2025-02-09 22:56:24.801741 INFO::Total function execution time is 3.40348696708679 s and adjustment time is 3.37762999534607 s ( 99.24 )
2025-02-09 22:56:25.008769 INFO::Formatting Data.
2025-02-09 22:56:25.010413 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.012266 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.014187 INFO::Found 2 missing values.
2025-02-09 22:56:25.018304 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.019471 INFO::Done
2025-02-09 22:56:25.077732 INFO::Found NA in Reference column
2025-02-09 22:56:25.098364 INFO::Require at least two references per batch.
2025-02-09 22:56:25.131269 INFO::Formatting Data.
2025-02-09 22:56:25.132721 INFO::Recognized SummarizedExperiment
2025-02-09 22:56:25.133979 INFO::Typecasting input to dataframe.
2025-02-09 22:56:25.146801 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.149029 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.153737 INFO::Found 0 missing values.
2025-02-09 22:56:25.158835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.159677 INFO::Done
2025-02-09 22:56:25.18223 INFO::Formatting Data.
2025-02-09 22:56:25.183738 INFO::Recognized SummarizedExperiment
2025-02-09 22:56:25.185097 INFO::Typecasting input to dataframe.
2025-02-09 22:56:25.210371 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.212657 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.217875 INFO::Found 0 missing values.
2025-02-09 22:56:25.232505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.23402 INFO::Done
2025-02-09 22:56:25.256224 INFO::Formatting Data.
2025-02-09 22:56:25.257669 INFO::Recognized SummarizedExperiment
2025-02-09 22:56:25.258906 INFO::Typecasting input to dataframe.
2025-02-09 22:56:25.282408 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.284407 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.286541 INFO::Found 0 missing values.
2025-02-09 22:56:25.288324 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.
2025-02-09 22:56:25.295081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.296351 INFO::Done
2025-02-09 22:56:25.319625 INFO::Formatting Data.
2025-02-09 22:56:25.32125 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.323227 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.325231 INFO::Found 0 missing values.
2025-02-09 22:56:25.329812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.331112 INFO::Done
2025-02-09 22:56:25.35491 INFO::Formatting Data.
2025-02-09 22:56:25.356505 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.358182 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.360027 INFO::Found 0 missing values.
2025-02-09 22:56:25.364595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.365775 INFO::Done
2025-02-09 22:56:25.427596 INFO::Formatting Data.
2025-02-09 22:56:25.429226 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.431206 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.433287 INFO::Found 1 missing values.
2025-02-09 22:56:25.437131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.438302 INFO::Done
2025-02-09 22:56:25.478199 INFO::Formatting Data.
2025-02-09 22:56:25.479775 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.481556 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.483261 INFO::Found 2 missing values.
2025-02-09 22:56:25.48492 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.
2025-02-09 22:56:25.488141 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.48925 INFO::Done
2025-02-09 22:56:25.50372 INFO::Formatting Data.
2025-02-09 22:56:25.504707 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.505758 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.506865 INFO::Found 2 missing values.
2025-02-09 22:56:25.508506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.50924 INFO::Done
2025-02-09 22:56:25.525722 INFO::Formatting Data.
2025-02-09 22:56:25.526734 INFO::Typecasting input to dataframe.
2025-02-09 22:56:25.52771 INFO::Replacing NaNs with NAs.
2025-02-09 22:56:25.528734 INFO::Removing potential empty rows and columns
2025-02-09 22:56:25.529835 INFO::Found 0 missing values.
2025-02-09 22:56:25.532346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-09 22:56:25.533063 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
31.57 1.18 78.61
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.93 | 0.52 | 18.36 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.02 | 0.00 | 0.02 | |
| generate_data_covariables | 0.01 | 0.00 | 0.02 | |
| generate_dataset | 0.02 | 0.00 | 0.01 | |