Yannis Schumann
| Snapshot Date: 2025-01-30 13:00 -0500 (Thu, 30 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-03 12:07 -0500 (Mon, 03 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4400 |
| 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 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2025-01-31 00:35:09 -0500 (Fri, 31 Jan 2025) |
| EndedAt: 2025-01-31 00:37:39 -0500 (Fri, 31 Jan 2025) |
| EllapsedTime: 150.1 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 44.95 2.562 36.661
* 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-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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")
2025-01-31 00:37:05.000649 INFO::Formatting Data.
2025-01-31 00:37:05.007624 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:05.041224 INFO::Removing potential empty rows and columns
2025-01-31 00:37:05.726853 INFO::Found 0 missing values.
2025-01-31 00:37:05.735509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:05.736989 INFO::Done
2025-01-31 00:37:05.738333 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:05.766408 INFO::Starting hierarchical adjustment
2025-01-31 00:37:05.768512 INFO::Found 3 batches.
2025-01-31 00:37:05.76999 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:05.772759 INFO::Using default BPPARAM
2025-01-31 00:37:05.774213 INFO::Processing subtree level 1
2025-01-31 00:37:06.061691 INFO::Adjusting the last 1 batches sequentially
2025-01-31 00:37:06.075678 INFO::Done
2025-01-31 00:37:06.077302 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:06.088396 INFO::ASW Batch was -0.118663170557397 prior to batch effect correction and is now -0.118663170557397 .
2025-01-31 00:37:06.090947 INFO::Total function execution time is 1.09152603149414 s and adjustment time is 0.30756688117981 s ( 28.18 )
2025-01-31 00:37:06.127749 INFO::Formatting Data.
2025-01-31 00:37:06.129405 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:06.131563 INFO::Removing potential empty rows and columns
2025-01-31 00:37:06.134475 INFO::Found 0 missing values.
2025-01-31 00:37:06.136943 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.
2025-01-31 00:37:06.165027 INFO::Formatting Data.
2025-01-31 00:37:06.166762 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:06.168991 INFO::Removing potential empty rows and columns
2025-01-31 00:37:06.171798 INFO::Found 0 missing values.
2025-01-31 00:37:06.174318 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.
2025-01-31 00:37:06.217248 INFO::Formatting Data.
2025-01-31 00:37:06.219028 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:06.221359 INFO::Removing potential empty rows and columns
2025-01-31 00:37:06.224774 INFO::Found 0 missing values.
2025-01-31 00:37:06.227513 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.
2025-01-31 00:37:06.241564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:06.2432 INFO::Done
2025-01-31 00:37:06.244658 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:06.250583 INFO::Starting hierarchical adjustment
2025-01-31 00:37:06.252653 INFO::Found 2 batches.
2025-01-31 00:37:06.254939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:06.256865 INFO::Using default BPPARAM
2025-01-31 00:37:06.258385 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:06.260922 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:06.320348 INFO::Done
2025-01-31 00:37:06.322053 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:06.327875 INFO::ASW Batch was 0.0138826412990126 prior to batch effect correction and is now -0.117886767065612 .
2025-01-31 00:37:06.330349 INFO::Total function execution time is 0.113077878952026 s and adjustment time is 0.0680561065673828 s ( 60.19 )
2025-01-31 00:37:06.337381 INFO::Formatting Data.
2025-01-31 00:37:06.339165 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:06.362426 INFO::Formatting Data.
2025-01-31 00:37:06.364145 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:06.366454 INFO::Removing potential empty rows and columns
2025-01-31 00:37:06.369128 INFO::Found 0 missing values.
2025-01-31 00:37:06.377573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:06.37905 INFO::Done
2025-01-31 00:37:06.380326 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:06.385056 INFO::Starting hierarchical adjustment
2025-01-31 00:37:06.386945 INFO::Found 2 batches.
2025-01-31 00:37:06.388228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:06.389858 INFO::Using default BPPARAM
2025-01-31 00:37:06.391332 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:06.393667 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:06.433318 INFO::Done
2025-01-31 00:37:06.434765 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:06.440094 INFO::ASW Batch was -0.0167295273790042 prior to batch effect correction and is now -0.134284825255953 .
2025-01-31 00:37:06.442268 INFO::Total function execution time is 0.079887866973877 s and adjustment time is 0.0467522144317627 s ( 58.52 )
2025-01-31 00:37:06.445023 INFO::Formatting Data.
2025-01-31 00:37:06.446591 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:06.448666 INFO::Removing potential empty rows and columns
2025-01-31 00:37:06.451741 INFO::Found 0 missing values.
2025-01-31 00:37:06.460651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:06.462282 INFO::Done
2025-01-31 00:37:06.463716 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:06.468898 INFO::Starting hierarchical adjustment
2025-01-31 00:37:06.470924 INFO::Found 2 batches.
2025-01-31 00:37:06.4724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:06.47399 INFO::Using default BPPARAM
2025-01-31 00:37:06.475375 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:06.47769 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:06.520014 INFO::Done
2025-01-31 00:37:06.521559 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:06.526603 INFO::ASW Batch was -0.0167295273790042 prior to batch effect correction and is now -0.134284825255953 .
2025-01-31 00:37:06.52883 INFO::Total function execution time is 0.083791971206665 s and adjustment time is 0.0495271682739258 s ( 59.11 )
2025-01-31 00:37:12.616806 INFO::Formatting Data.
2025-01-31 00:37:12.618149 INFO::Recognized SummarizedExperiment
2025-01-31 00:37:12.619214 INFO::Typecasting input to dataframe.
2025-01-31 00:37:12.682865 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:12.685215 INFO::Removing potential empty rows and columns
2025-01-31 00:37:12.694242 INFO::Found 0 missing values.
2025-01-31 00:37:12.712293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:12.713597 INFO::Done
2025-01-31 00:37:12.714751 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:12.72298 INFO::Starting hierarchical adjustment
2025-01-31 00:37:12.724679 INFO::Found 2 batches.
2025-01-31 00:37:12.725891 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:12.728057 INFO::Using default BPPARAM
2025-01-31 00:37:12.729178 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:12.731427 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:12.873786 INFO::Done
2025-01-31 00:37:12.87514 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:12.883175 INFO::ASW Batch was -0.00172805493873609 prior to batch effect correction and is now -0.089123441658436 .
2025-01-31 00:37:12.884986 INFO::Total function execution time is 0.268815994262695 s and adjustment time is 0.149479150772095 s ( 55.61 )
2025-01-31 00:37:12.929279 INFO::Formatting Data.
2025-01-31 00:37:12.930976 INFO::Recognized SummarizedExperiment
2025-01-31 00:37:12.932468 INFO::Typecasting input to dataframe.
2025-01-31 00:37:12.958658 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:12.961613 INFO::Removing potential empty rows and columns
2025-01-31 00:37:12.973097 INFO::Found 0 missing values.
2025-01-31 00:37:12.995322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:12.996868 INFO::Done
2025-01-31 00:37:12.998528 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:13.007252 INFO::Starting hierarchical adjustment
2025-01-31 00:37:13.009049 INFO::Found 2 batches.
2025-01-31 00:37:13.01031 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:13.011711 INFO::Using default BPPARAM
2025-01-31 00:37:13.012927 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:13.015265 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:13.090101 INFO::Done
2025-01-31 00:37:13.091637 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:13.101076 INFO::ASW Batch was 0.00159366951223692 prior to batch effect correction and is now 0.00159366951223692 .
2025-01-31 00:37:13.103175 INFO::Total function execution time is 0.173842906951904 s and adjustment time is 0.0813100337982178 s ( 46.77 )
2025-01-31 00:37:13.148318 INFO::Formatting Data.
2025-01-31 00:37:13.150046 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:13.15241 INFO::Removing potential empty rows and columns
2025-01-31 00:37:13.154736 INFO::Found 0 missing values.
2025-01-31 00:37:13.162768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:13.164251 INFO::Done
2025-01-31 00:37:13.165554 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:13.170386 INFO::Starting hierarchical adjustment
2025-01-31 00:37:13.172251 INFO::Found 3 batches.
2025-01-31 00:37:13.17358 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:13.175026 INFO::Using default BPPARAM
2025-01-31 00:37:13.176357 INFO::Processing subtree level 1
2025-01-31 00:37:13.547567 INFO::Adjusting the last 1 batches sequentially
2025-01-31 00:37:13.556954 INFO::Done
2025-01-31 00:37:13.559143 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:13.569664 INFO::ASW Batch was -0.0959868535650193 prior to batch effect correction and is now -0.143319414753501 .
2025-01-31 00:37:13.573556 INFO::Total function execution time is 0.425223112106323 s and adjustment time is 0.385035991668701 s ( 90.55 )
2025-01-31 00:37:13.618864 INFO::Skipping initial DF formatting
2025-01-31 00:37:13.621195 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:13.633071 INFO::Starting hierarchical adjustment
2025-01-31 00:37:13.635202 INFO::Found 5 batches.
2025-01-31 00:37:13.63683 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:13.63879 INFO::Using default BPPARAM
2025-01-31 00:37:13.640359 INFO::Processing subtree level 1
2025-01-31 00:37:13.955996 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:13.971247 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:14.050512 INFO::Done
2025-01-31 00:37:14.052104 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:14.065813 INFO::ASW Batch was 0.545663613169774 prior to batch effect correction and is now 0.545663613169774 .
2025-01-31 00:37:14.067422 INFO::ASW Label was 0.337452057357967 prior to batch effect correction and is now 0.337452057357967 .
2025-01-31 00:37:14.070588 INFO::Total function execution time is 0.451708078384399 s and adjustment time is 0.415803909301758 s ( 92.05 )
2025-01-31 00:37:14.124925 INFO::Formatting Data.
2025-01-31 00:37:14.126778 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:14.129067 INFO::Removing potential empty rows and columns
2025-01-31 00:37:14.131813 INFO::Found 0 missing values.
2025-01-31 00:37:14.143707 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:14.145233 INFO::Done
2025-01-31 00:37:14.146643 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:14.153665 INFO::Starting hierarchical adjustment
2025-01-31 00:37:14.155361 INFO::Found 5 batches.
2025-01-31 00:37:14.156548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:14.158274 INFO::Using default BPPARAM
2025-01-31 00:37:14.159469 INFO::Processing subtree level 1
2025-01-31 00:37:14.420737 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:14.433093 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:14.486731 INFO::Done
2025-01-31 00:37:14.488296 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:14.498405 INFO::ASW Batch was 0.541023606071148 prior to batch effect correction and is now -0.106272535289201 .
2025-01-31 00:37:14.499999 INFO::ASW Label was 0.201670484318853 prior to batch effect correction and is now 0.863038348112206 .
2025-01-31 00:37:14.502177 INFO::Total function execution time is 0.377275943756104 s and adjustment time is 0.331654071807861 s ( 87.91 )
2025-01-31 00:37:14.50455 INFO::Formatting Data.
2025-01-31 00:37:14.506154 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:14.508468 INFO::Removing potential empty rows and columns
2025-01-31 00:37:14.511145 INFO::Found 0 missing values.
2025-01-31 00:37:14.522561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:14.524131 INFO::Done
2025-01-31 00:37:14.525468 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:14.532697 INFO::Starting hierarchical adjustment
2025-01-31 00:37:14.535374 INFO::Found 5 batches.
2025-01-31 00:37:14.537318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:14.53898 INFO::Using default BPPARAM
2025-01-31 00:37:14.540352 INFO::Processing subtree level 1
2025-01-31 00:37:14.795253 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:14.809458 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:14.86638 INFO::Done
2025-01-31 00:37:14.867975 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:14.877553 INFO::ASW Batch was 0.541023606071148 prior to batch effect correction and is now -0.106272535289201 .
2025-01-31 00:37:14.879109 INFO::ASW Label was 0.201670484318853 prior to batch effect correction and is now 0.863038348112206 .
2025-01-31 00:37:14.881394 INFO::Total function execution time is 0.376776933670044 s and adjustment time is 0.331984043121338 s ( 88.11 )
2025-01-31 00:37:14.921195 INFO::Formatting Data.
2025-01-31 00:37:14.922956 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:14.925413 INFO::Removing potential empty rows and columns
2025-01-31 00:37:14.927971 INFO::Found 0 missing values.
2025-01-31 00:37:14.938596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:14.939857 INFO::Done
2025-01-31 00:37:14.941146 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:14.948987 INFO::Starting hierarchical adjustment
2025-01-31 00:37:14.950983 INFO::Found 5 batches.
2025-01-31 00:37:14.952336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:14.953844 INFO::Using default BPPARAM
2025-01-31 00:37:14.955143 INFO::Processing subtree level 1
2025-01-31 00:37:15.223581 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:15.236622 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:15.287234 INFO::Done
2025-01-31 00:37:15.2895 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:15.299034 INFO::ASW Batch was 0.563529192835607 prior to batch effect correction and is now -0.0730343666217214 .
2025-01-31 00:37:15.30053 INFO::ASW Label was 0.206625807595468 prior to batch effect correction and is now 0.773516028861992 .
2025-01-31 00:37:15.302469 INFO::Total function execution time is 0.381410837173462 s and adjustment time is 0.336676836013794 s ( 88.27 )
2025-01-31 00:37:15.304365 INFO::Formatting Data.
2025-01-31 00:37:15.305733 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:15.307622 INFO::Removing potential empty rows and columns
2025-01-31 00:37:15.30975 INFO::Found 0 missing values.
2025-01-31 00:37:15.32185 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:15.323519 INFO::Done
2025-01-31 00:37:15.324941 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:15.332636 INFO::Starting hierarchical adjustment
2025-01-31 00:37:15.334652 INFO::Found 5 batches.
2025-01-31 00:37:15.336083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:15.33771 INFO::Using default BPPARAM
2025-01-31 00:37:15.339645 INFO::Processing subtree level 1
2025-01-31 00:37:15.598129 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:15.615478 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:15.67616 INFO::Done
2025-01-31 00:37:15.677918 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:15.685449 INFO::ASW Batch was 0.563529192835607 prior to batch effect correction and is now -0.0730343666217214 .
2025-01-31 00:37:15.686759 INFO::ASW Label was 0.206625807595468 prior to batch effect correction and is now 0.773516028861992 .
2025-01-31 00:37:15.688427 INFO::Total function execution time is 0.384071111679077 s and adjustment time is 0.341965913772583 s ( 89.04 )
2025-01-31 00:37:15.725968 INFO::Formatting Data.
2025-01-31 00:37:15.727701 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:15.72989 INFO::Removing potential empty rows and columns
2025-01-31 00:37:15.732476 INFO::Found 0 missing values.
2025-01-31 00:37:15.739877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:15.741345 INFO::Done
2025-01-31 00:37:15.742666 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:15.750213 INFO::Starting hierarchical adjustment
2025-01-31 00:37:15.752184 INFO::Found 2 batches.
2025-01-31 00:37:15.753499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:15.755759 INFO::Using default BPPARAM
2025-01-31 00:37:15.757098 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:15.75935 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:15.79633 INFO::Done
2025-01-31 00:37:15.797815 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:15.804556 INFO::ASW Batch was 0.638830831672273 prior to batch effect correction and is now 0.0224603354050445 .
2025-01-31 00:37:15.806053 INFO::ASW Label was 0.429433611168785 prior to batch effect correction and is now 0.886251349947097 .
2025-01-31 00:37:15.807938 INFO::Total function execution time is 0.0820858478546143 s and adjustment time is 0.0445220470428467 s ( 54.24 )
2025-01-31 00:37:15.810522 INFO::Formatting Data.
2025-01-31 00:37:15.811923 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:15.813962 INFO::Removing potential empty rows and columns
2025-01-31 00:37:15.81641 INFO::Found 0 missing values.
2025-01-31 00:37:15.823528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:15.824923 INFO::Done
2025-01-31 00:37:15.82616 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:15.832202 INFO::Starting hierarchical adjustment
2025-01-31 00:37:15.83376 INFO::Found 2 batches.
2025-01-31 00:37:15.83487 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:15.836146 INFO::Using default BPPARAM
2025-01-31 00:37:15.837223 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:15.839329 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:15.875986 INFO::Done
2025-01-31 00:37:15.877403 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:15.883809 INFO::ASW Batch was 0.638830831672273 prior to batch effect correction and is now 0.0224603354050445 .
2025-01-31 00:37:15.885208 INFO::ASW Label was 0.429433611168785 prior to batch effect correction and is now 0.886251349947097 .
2025-01-31 00:37:15.886986 INFO::Total function execution time is 0.0765190124511719 s and adjustment time is 0.0424799919128418 s ( 55.52 )
2025-01-31 00:37:15.916721 INFO::Formatting Data.
2025-01-31 00:37:15.918352 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:15.920436 INFO::Removing potential empty rows and columns
2025-01-31 00:37:15.922709 INFO::Found 0 missing values.
2025-01-31 00:37:15.928276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:15.929649 INFO::Done
2025-01-31 00:37:15.930973 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:15.935582 INFO::Starting hierarchical adjustment
2025-01-31 00:37:15.93739 INFO::Found 2 batches.
2025-01-31 00:37:15.938679 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:15.940154 INFO::Using default BPPARAM
2025-01-31 00:37:15.941391 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:15.943712 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:16.02854 INFO::Done
2025-01-31 00:37:16.030081 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:16.034827 INFO::ASW Batch was -0.112515626915451 prior to batch effect correction and is now -0.143942773436159 .
2025-01-31 00:37:16.036946 INFO::Total function execution time is 0.120490074157715 s and adjustment time is 0.0914499759674072 s ( 75.9 )
2025-01-31 00:37:16.072304 INFO::Formatting Data.
2025-01-31 00:37:16.074048 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:16.076329 INFO::Removing potential empty rows and columns
2025-01-31 00:37:16.079185 INFO::Found 0 missing values.
2025-01-31 00:37:16.082094 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.
2025-01-31 00:37:16.095842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:16.097304 INFO::Done
2025-01-31 00:37:16.098586 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:16.106643 INFO::Starting hierarchical adjustment
2025-01-31 00:37:16.108552 INFO::Found 2 batches.
2025-01-31 00:37:16.109998 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:16.111591 INFO::Using default BPPARAM
2025-01-31 00:37:16.112923 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:16.115345 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:16.159762 INFO::Done
2025-01-31 00:37:16.161221 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:16.168787 INFO::ASW Batch was 0.527809088151646 prior to batch effect correction and is now 0.0485309276810634 .
2025-01-31 00:37:16.170159 INFO::ASW Label was 0.462498761960154 prior to batch effect correction and is now 0.804126787002972 .
2025-01-31 00:37:16.171936 INFO::Total function execution time is 0.0997610092163086 s and adjustment time is 0.0516319274902344 s ( 51.76 )
2025-01-31 00:37:16.173895 INFO::Formatting Data.
2025-01-31 00:37:16.175422 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:16.177823 INFO::Removing potential empty rows and columns
2025-01-31 00:37:16.180191 INFO::Found 0 missing values.
2025-01-31 00:37:16.182503 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.
2025-01-31 00:37:16.195413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:16.196919 INFO::Done
2025-01-31 00:37:16.198306 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:16.205413 INFO::Starting hierarchical adjustment
2025-01-31 00:37:16.207314 INFO::Found 2 batches.
2025-01-31 00:37:16.208819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:16.210511 INFO::Using default BPPARAM
2025-01-31 00:37:16.211861 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:16.214142 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:16.255933 INFO::Done
2025-01-31 00:37:16.257323 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:16.263646 INFO::ASW Batch was 0.527809088151646 prior to batch effect correction and is now 0.0485309276810634 .
2025-01-31 00:37:16.265036 INFO::ASW Label was 0.462498761960154 prior to batch effect correction and is now 0.804126787002972 .
2025-01-31 00:37:16.266743 INFO::Total function execution time is 0.0929610729217529 s and adjustment time is 0.0490179061889648 s ( 52.73 )
2025-01-31 00:37:16.814494 INFO::Formatting Data.
2025-01-31 00:37:16.816508 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:16.818736 INFO::Removing potential empty rows and columns
2025-01-31 00:37:16.821453 INFO::Found 0 missing values.
2025-01-31 00:37:16.829878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:16.831391 INFO::Done
2025-01-31 00:37:16.832778 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:16.837815 INFO::Starting hierarchical adjustment
2025-01-31 00:37:16.839821 INFO::Found 3 batches.
2025-01-31 00:37:16.8413 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:16.842876 INFO::Using default BPPARAM
2025-01-31 00:37:16.844283 INFO::Processing subtree level 1
2025-01-31 00:37:17.095582 INFO::Adjusting the last 1 batches sequentially
2025-01-31 00:37:17.102871 INFO::Done
2025-01-31 00:37:17.106249 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:17.116062 INFO::ASW Batch was -0.0272811554529915 prior to batch effect correction and is now -0.0272811554529915 .
2025-01-31 00:37:17.12001 INFO::Total function execution time is 0.305405855178833 s and adjustment time is 0.263458967208862 s ( 86.27 )
2025-01-31 00:37:17.122956 INFO::Formatting Data.
2025-01-31 00:37:17.124873 INFO::Typecasting input to dataframe.
2025-01-31 00:37:17.126951 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:17.129347 INFO::Removing potential empty rows and columns
2025-01-31 00:37:17.132813 INFO::Found 0 missing values.
2025-01-31 00:37:17.141651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:17.146073 INFO::Done
2025-01-31 00:37:17.148652 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:17.153455 INFO::Starting hierarchical adjustment
2025-01-31 00:37:17.155754 INFO::Found 3 batches.
2025-01-31 00:37:17.157451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:17.159351 INFO::Using default BPPARAM
2025-01-31 00:37:17.160889 INFO::Processing subtree level 1
2025-01-31 00:37:17.410342 INFO::Adjusting the last 1 batches sequentially
2025-01-31 00:37:17.420221 INFO::Done
2025-01-31 00:37:17.42294 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:17.440084 INFO::ASW Batch was -0.0272811554529915 prior to batch effect correction and is now -0.0272811554529915 .
2025-01-31 00:37:17.447358 INFO::Total function execution time is 0.324321985244751 s and adjustment time is 0.264888048171997 s ( 81.67 )
2025-01-31 00:37:17.516101 INFO::Formatting Data.
2025-01-31 00:37:17.517531 INFO::Typecasting input to dataframe.
2025-01-31 00:37:17.519975 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:17.522342 INFO::Removing potential empty rows and columns
2025-01-31 00:37:17.525102 INFO::Found 0 missing values.
2025-01-31 00:37:17.534505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:17.536043 INFO::Done
2025-01-31 00:37:17.537422 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:17.542559 INFO::Starting hierarchical adjustment
2025-01-31 00:37:17.545048 INFO::Found 3 batches.
2025-01-31 00:37:17.546544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:17.54871 INFO::Using default BPPARAM
2025-01-31 00:37:17.550136 INFO::Processing subtree level 1
2025-01-31 00:37:18.019928 INFO::Adjusting the last 1 batches sequentially
2025-01-31 00:37:18.034765 INFO::Done
2025-01-31 00:37:18.04097 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:18.072619 INFO::ASW Batch was -0.0807312167625712 prior to batch effect correction and is now -0.0807312167625712 .
2025-01-31 00:37:18.079032 INFO::Total function execution time is 0.562259912490845 s and adjustment time is 0.490543842315674 s ( 87.25 )
2025-01-31 00:37:18.688213 INFO::Formatting Data.
2025-01-31 00:37:18.689969 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:18.692721 INFO::Removing potential empty rows and columns
2025-01-31 00:37:18.701495 INFO::Found 1000 missing values.
2025-01-31 00:37:18.80642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:18.809435 INFO::Done
2025-01-31 00:37:18.810802 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:18.82755 INFO::Starting hierarchical adjustment
2025-01-31 00:37:18.830196 INFO::Found 10 batches.
2025-01-31 00:37:18.832064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:18.833742 INFO::Using default BPPARAM
2025-01-31 00:37:18.835095 INFO::Processing subtree level 1
2025-01-31 00:37:19.265631 INFO::Processing subtree level 2
2025-01-31 00:37:19.816097 INFO::Adjusting the last 1 batches sequentially
2025-01-31 00:37:19.832729 INFO::Done
2025-01-31 00:37:19.835578 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:19.858802 INFO::ASW Batch was 0.526188639930494 prior to batch effect correction and is now 0.526188639930494 .
2025-01-31 00:37:19.860782 INFO::ASW Label was 0.29721935011817 prior to batch effect correction and is now 0.29721935011817 .
2025-01-31 00:37:19.862897 INFO::Total function execution time is 1.17477703094482 s and adjustment time is 1.00291609764099 s ( 85.37 )
2025-01-31 00:37:19.865017 INFO::Formatting Data.
2025-01-31 00:37:19.866952 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:19.869508 INFO::Removing potential empty rows and columns
2025-01-31 00:37:19.879775 INFO::Found 1000 missing values.
2025-01-31 00:37:19.957447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:19.95902 INFO::Done
2025-01-31 00:37:19.960401 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:19.973601 INFO::Starting hierarchical adjustment
2025-01-31 00:37:19.976952 INFO::Found 10 batches.
2025-01-31 00:37:21.336166 INFO::Set up parallel execution backend with 2 workers
2025-01-31 00:37:21.337815 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-31 00:37:23.190917 INFO::Adjusting the last 2 batches sequentially
2025-01-31 00:37:23.193235 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-31 00:37:23.237602 INFO::Done
2025-01-31 00:37:23.238876 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:23.24965 INFO::ASW Batch was 0.526188639930494 prior to batch effect correction and is now 0.526188639930494 .
2025-01-31 00:37:23.251015 INFO::ASW Label was 0.29721935011817 prior to batch effect correction and is now 0.29721935011817 .
2025-01-31 00:37:23.252665 INFO::Total function execution time is 3.38775396347046 s and adjustment time is 3.2616970539093 s ( 96.28 )
2025-01-31 00:37:23.663612 INFO::Formatting Data.
2025-01-31 00:37:23.666993 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:23.6695 INFO::Removing potential empty rows and columns
2025-01-31 00:37:23.672441 INFO::Found 0 missing values.
2025-01-31 00:37:23.683509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:23.685242 INFO::Done
2025-01-31 00:37:23.68646 INFO::Acquiring quality metrics before batch effect correction.
2025-01-31 00:37:23.692862 INFO::Starting hierarchical adjustment
2025-01-31 00:37:23.694609 INFO::Found 3 batches.
2025-01-31 00:37:23.69584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-31 00:37:23.697283 INFO::Using default BPPARAM
2025-01-31 00:37:23.698499 INFO::Processing subtree level 1
2025-01-31 00:37:24.000718 INFO::Adjusting the last 1 batches sequentially
2025-01-31 00:37:24.013167 INFO::Done
2025-01-31 00:37:24.015653 INFO::Acquiring quality metrics after batch effect correction.
2025-01-31 00:37:24.033234 INFO::ASW Batch was 0.171111802112684 prior to batch effect correction and is now -0.145686108586413 .
2025-01-31 00:37:24.037024 INFO::ASW Label was -0.136449312558896 prior to batch effect correction and is now 0.0666445841176344 .
2025-01-31 00:37:24.04082 INFO::Total function execution time is 0.376670122146606 s and adjustment time is 0.318846940994263 s ( 84.65 )
2025-01-31 00:37:24.37982 INFO::Formatting Data.
2025-01-31 00:37:24.381798 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:24.384232 INFO::Removing potential empty rows and columns
2025-01-31 00:37:24.387046 INFO::Found 2 missing values.
2025-01-31 00:37:24.396246 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:24.397697 INFO::Done
2025-01-31 00:37:24.476809 INFO::Found NA in Reference column
2025-01-31 00:37:24.504149 INFO::Require at least two references per batch.
2025-01-31 00:37:24.56027 INFO::Formatting Data.
2025-01-31 00:37:24.561801 INFO::Recognized SummarizedExperiment
2025-01-31 00:37:24.563029 INFO::Typecasting input to dataframe.
2025-01-31 00:37:24.590262 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:24.593135 INFO::Removing potential empty rows and columns
2025-01-31 00:37:24.604824 INFO::Found 0 missing values.
2025-01-31 00:37:24.626959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:24.628375 INFO::Done
2025-01-31 00:37:24.669635 INFO::Formatting Data.
2025-01-31 00:37:24.67128 INFO::Recognized SummarizedExperiment
2025-01-31 00:37:24.672686 INFO::Typecasting input to dataframe.
2025-01-31 00:37:24.722989 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:24.725866 INFO::Removing potential empty rows and columns
2025-01-31 00:37:24.737906 INFO::Found 0 missing values.
2025-01-31 00:37:24.777068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:24.778693 INFO::Done
2025-01-31 00:37:24.819789 INFO::Formatting Data.
2025-01-31 00:37:24.821486 INFO::Recognized SummarizedExperiment
2025-01-31 00:37:24.822777 INFO::Typecasting input to dataframe.
2025-01-31 00:37:24.868936 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:24.871275 INFO::Removing potential empty rows and columns
2025-01-31 00:37:24.874125 INFO::Found 0 missing values.
2025-01-31 00:37:24.876517 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.
2025-01-31 00:37:24.889999 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:24.891458 INFO::Done
2025-01-31 00:37:24.917937 INFO::Formatting Data.
2025-01-31 00:37:24.919761 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:24.922023 INFO::Removing potential empty rows and columns
2025-01-31 00:37:24.924861 INFO::Found 0 missing values.
2025-01-31 00:37:24.933402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:24.934881 INFO::Done
2025-01-31 00:37:24.964159 INFO::Formatting Data.
2025-01-31 00:37:24.965944 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:24.968233 INFO::Removing potential empty rows and columns
2025-01-31 00:37:24.970921 INFO::Found 0 missing values.
2025-01-31 00:37:24.979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:24.980414 INFO::Done
2025-01-31 00:37:25.060529 INFO::Formatting Data.
2025-01-31 00:37:25.062187 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:25.064652 INFO::Removing potential empty rows and columns
2025-01-31 00:37:25.067781 INFO::Found 1 missing values.
2025-01-31 00:37:25.074975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:25.076424 INFO::Done
2025-01-31 00:37:25.12824 INFO::Formatting Data.
2025-01-31 00:37:25.129996 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:25.132068 INFO::Removing potential empty rows and columns
2025-01-31 00:37:25.134573 INFO::Found 2 missing values.
2025-01-31 00:37:25.136948 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.
2025-01-31 00:37:25.143223 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:25.144734 INFO::Done
2025-01-31 00:37:25.173337 INFO::Formatting Data.
2025-01-31 00:37:25.175203 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:25.177341 INFO::Removing potential empty rows and columns
2025-01-31 00:37:25.179797 INFO::Found 2 missing values.
2025-01-31 00:37:25.184341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:25.185795 INFO::Done
2025-01-31 00:37:25.216461 INFO::Formatting Data.
2025-01-31 00:37:25.218199 INFO::Typecasting input to dataframe.
2025-01-31 00:37:25.220259 INFO::Replacing NaNs with NAs.
2025-01-31 00:37:25.222534 INFO::Removing potential empty rows and columns
2025-01-31 00:37:25.22532 INFO::Found 0 missing values.
2025-01-31 00:37:25.233686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-31 00:37:25.235124 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.727 6.636 44.971
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 44.950 | 2.562 | 36.661 | |
| compute_asw | 0.053 | 0.003 | 0.066 | |
| count_existing | 0.029 | 0.002 | 0.034 | |
| generate_data_covariables | 0.027 | 0.002 | 0.032 | |
| generate_dataset | 0.026 | 0.003 | 0.033 | |