Yannis Schumann
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 154/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-07-15 22:00:27 -0400 (Mon, 15 Jul 2024) |
| EndedAt: 2024-07-15 22:02:27 -0400 (Mon, 15 Jul 2024) |
| EllapsedTime: 119.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 7.78 0.44 15.66
* 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: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BERT' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-07-15 22:01:20.14959 INFO::Formatting Data.
2024-07-15 22:01:20.151738 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:20.16034 INFO::Removing potential empty rows and columns
2024-07-15 22:01:20.343431 INFO::Found 0 missing values.
2024-07-15 22:01:20.346447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:20.347134 INFO::Done
2024-07-15 22:01:20.34776 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:20.362966 INFO::Starting hierarchical adjustment
2024-07-15 22:01:20.364354 INFO::Found 3 batches.
2024-07-15 22:01:20.365103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:20.366592 INFO::Using default BPPARAM
2024-07-15 22:01:20.367277 INFO::Processing subtree level 1
2024-07-15 22:01:22.637419 INFO::Adjusting the last 1 batches sequentially
2024-07-15 22:01:22.639766 INFO::Done
2024-07-15 22:01:22.640908 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:22.643106 INFO::ASW Batch was 0.0260436835817549 prior to batch effect correction and is now 0.0260436835817549 .
2024-07-15 22:01:22.644266 INFO::Total function execution time is 2.49527096748352 s and adjustment time is 2.27543997764587 s ( 91.19 )
2024-07-15 22:01:22.659746 INFO::Formatting Data.
2024-07-15 22:01:22.660544 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:22.661468 INFO::Removing potential empty rows and columns
2024-07-15 22:01:22.662501 INFO::Found 0 missing values.
2024-07-15 22:01:22.663412 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-15 22:01:22.670838 INFO::Formatting Data.
2024-07-15 22:01:22.671699 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:22.672607 INFO::Removing potential empty rows and columns
2024-07-15 22:01:22.673577 INFO::Found 0 missing values.
2024-07-15 22:01:22.674474 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-15 22:01:22.688938 INFO::Formatting Data.
2024-07-15 22:01:22.689866 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:22.690751 INFO::Removing potential empty rows and columns
2024-07-15 22:01:22.691907 INFO::Found 0 missing values.
2024-07-15 22:01:22.69283 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-15 22:01:22.695983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:22.696644 INFO::Done
2024-07-15 22:01:22.697256 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:22.699143 INFO::Starting hierarchical adjustment
2024-07-15 22:01:22.699911 INFO::Found 2 batches.
2024-07-15 22:01:22.700638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:22.701352 INFO::Using default BPPARAM
2024-07-15 22:01:22.702074 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:22.703129 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:22.717982 INFO::Done
2024-07-15 22:01:22.718756 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:22.72074 INFO::ASW Batch was 0.0468484460104044 prior to batch effect correction and is now -0.131831744388262 .
2024-07-15 22:01:22.72159 INFO::Total function execution time is 0.0326659679412842 s and adjustment time is 0.0180528163909912 s ( 55.26 )
2024-07-15 22:01:22.724014 INFO::Formatting Data.
2024-07-15 22:01:22.724729 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:22.730787 INFO::Formatting Data.
2024-07-15 22:01:22.731494 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:22.732359 INFO::Removing potential empty rows and columns
2024-07-15 22:01:22.73333 INFO::Found 0 missing values.
2024-07-15 22:01:22.735548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:22.736206 INFO::Done
2024-07-15 22:01:22.736859 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:22.738638 INFO::Starting hierarchical adjustment
2024-07-15 22:01:22.739407 INFO::Found 2 batches.
2024-07-15 22:01:22.740111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:22.740813 INFO::Using default BPPARAM
2024-07-15 22:01:22.741424 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:22.742298 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:22.753212 INFO::Done
2024-07-15 22:01:22.75395 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:22.755752 INFO::ASW Batch was 0.026732493669882 prior to batch effect correction and is now -0.115895860962916 .
2024-07-15 22:01:22.756621 INFO::Total function execution time is 0.0258212089538574 s and adjustment time is 0.0138578414916992 s ( 53.67 )
2024-07-15 22:01:22.757682 INFO::Formatting Data.
2024-07-15 22:01:22.75837 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:22.759223 INFO::Removing potential empty rows and columns
2024-07-15 22:01:22.760195 INFO::Found 0 missing values.
2024-07-15 22:01:22.762404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:22.763044 INFO::Done
2024-07-15 22:01:22.76365 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:22.76541 INFO::Starting hierarchical adjustment
2024-07-15 22:01:22.766317 INFO::Found 2 batches.
2024-07-15 22:01:22.766986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:22.767686 INFO::Using default BPPARAM
2024-07-15 22:01:22.768322 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:22.769214 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:22.779932 INFO::Done
2024-07-15 22:01:22.780638 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:22.78248 INFO::ASW Batch was 0.026732493669882 prior to batch effect correction and is now -0.115895860962916 .
2024-07-15 22:01:22.78332 INFO::Total function execution time is 0.025623083114624 s and adjustment time is 0.0138430595397949 s ( 54.03 )
2024-07-15 22:01:25.170876 INFO::Formatting Data.
2024-07-15 22:01:25.171775 INFO::Recognized SummarizedExperiment
2024-07-15 22:01:25.17244 INFO::Typecasting input to dataframe.
2024-07-15 22:01:25.197579 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:25.198837 INFO::Removing potential empty rows and columns
2024-07-15 22:01:25.201982 INFO::Found 0 missing values.
2024-07-15 22:01:25.207376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:25.20823 INFO::Done
2024-07-15 22:01:25.208892 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:25.212478 INFO::Starting hierarchical adjustment
2024-07-15 22:01:25.213321 INFO::Found 2 batches.
2024-07-15 22:01:25.213949 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:25.215076 INFO::Using default BPPARAM
2024-07-15 22:01:25.215721 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:25.21677 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:25.259278 INFO::Done
2024-07-15 22:01:25.260174 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:25.263879 INFO::ASW Batch was -0.00432368514311373 prior to batch effect correction and is now -0.0983734673803984 .
2024-07-15 22:01:25.264884 INFO::Total function execution time is 0.0942718982696533 s and adjustment time is 0.0460400581359863 s ( 48.84 )
2024-07-15 22:01:25.282932 INFO::Formatting Data.
2024-07-15 22:01:25.283739 INFO::Recognized SummarizedExperiment
2024-07-15 22:01:25.284496 INFO::Typecasting input to dataframe.
2024-07-15 22:01:25.293338 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:25.29465 INFO::Removing potential empty rows and columns
2024-07-15 22:01:25.298395 INFO::Found 0 missing values.
2024-07-15 22:01:25.305285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:25.306101 INFO::Done
2024-07-15 22:01:25.306886 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:25.311144 INFO::Starting hierarchical adjustment
2024-07-15 22:01:25.312066 INFO::Found 2 batches.
2024-07-15 22:01:25.312782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:25.313569 INFO::Using default BPPARAM
2024-07-15 22:01:25.314253 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:25.315405 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:25.338965 INFO::Done
2024-07-15 22:01:25.339945 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:25.344039 INFO::ASW Batch was 0.00493690779415648 prior to batch effect correction and is now 0.00493690779415648 .
2024-07-15 22:01:25.345111 INFO::Total function execution time is 0.0621471405029297 s and adjustment time is 0.0269629955291748 s ( 43.39 )
2024-07-15 22:01:25.368491 INFO::Formatting Data.
2024-07-15 22:01:25.36957 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:25.370711 INFO::Removing potential empty rows and columns
2024-07-15 22:01:25.371953 INFO::Found 0 missing values.
2024-07-15 22:01:25.3749 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:25.375629 INFO::Done
2024-07-15 22:01:25.376349 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:25.378664 INFO::Starting hierarchical adjustment
2024-07-15 22:01:25.379564 INFO::Found 3 batches.
2024-07-15 22:01:25.380276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:25.381099 INFO::Using default BPPARAM
2024-07-15 22:01:25.381785 INFO::Processing subtree level 1
2024-07-15 22:01:33.534166 INFO::Adjusting the last 1 batches sequentially
2024-07-15 22:01:33.535725 INFO::Done
2024-07-15 22:01:33.536449 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:33.538421 INFO::ASW Batch was -0.0732305057051544 prior to batch effect correction and is now -0.15985247672382 .
2024-07-15 22:01:33.539286 INFO::Total function execution time is 8.17096209526062 s and adjustment time is 8.15630912780762 s ( 99.82 )
2024-07-15 22:01:33.558759 INFO::Skipping initial DF formatting
2024-07-15 22:01:33.559634 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:33.563677 INFO::Starting hierarchical adjustment
2024-07-15 22:01:33.564541 INFO::Found 5 batches.
2024-07-15 22:01:33.565181 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:33.565906 INFO::Using default BPPARAM
2024-07-15 22:01:33.566523 INFO::Processing subtree level 1
2024-07-15 22:01:36.144375 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:36.146056 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:36.159836 INFO::Done
2024-07-15 22:01:36.160608 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:36.166743 INFO::ASW Batch was 0.507514006670782 prior to batch effect correction and is now 0.507514006670782 .
2024-07-15 22:01:36.167746 INFO::ASW Label was 0.353168959781262 prior to batch effect correction and is now 0.353168959781262 .
2024-07-15 22:01:36.168906 INFO::Total function execution time is 2.61023497581482 s and adjustment time is 2.59544491767883 s ( 99.43 )
2024-07-15 22:01:36.194919 INFO::Formatting Data.
2024-07-15 22:01:36.195882 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:36.196849 INFO::Removing potential empty rows and columns
2024-07-15 22:01:36.197931 INFO::Found 0 missing values.
2024-07-15 22:01:36.201053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:36.201686 INFO::Done
2024-07-15 22:01:36.202343 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:36.205267 INFO::Starting hierarchical adjustment
2024-07-15 22:01:36.206082 INFO::Found 5 batches.
2024-07-15 22:01:36.206794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:36.207624 INFO::Using default BPPARAM
2024-07-15 22:01:36.20824 INFO::Processing subtree level 1
2024-07-15 22:01:38.764258 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:38.765883 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:38.777898 INFO::Done
2024-07-15 22:01:38.778719 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:38.781523 INFO::ASW Batch was 0.405692399066099 prior to batch effect correction and is now -0.0447959444096885 .
2024-07-15 22:01:38.78222 INFO::ASW Label was 0.287135816124097 prior to batch effect correction and is now 0.81338336337585 .
2024-07-15 22:01:38.783094 INFO::Total function execution time is 2.58834004402161 s and adjustment time is 2.57190704345703 s ( 99.37 )
2024-07-15 22:01:38.783918 INFO::Formatting Data.
2024-07-15 22:01:38.784612 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:38.785471 INFO::Removing potential empty rows and columns
2024-07-15 22:01:38.786436 INFO::Found 0 missing values.
2024-07-15 22:01:38.789571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:38.790216 INFO::Done
2024-07-15 22:01:38.790826 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:38.793354 INFO::Starting hierarchical adjustment
2024-07-15 22:01:38.794193 INFO::Found 5 batches.
2024-07-15 22:01:38.794815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:38.795508 INFO::Using default BPPARAM
2024-07-15 22:01:38.796113 INFO::Processing subtree level 1
2024-07-15 22:01:41.371904 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:41.373277 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:41.393781 INFO::Done
2024-07-15 22:01:41.394738 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:41.399629 INFO::ASW Batch was 0.405692399066099 prior to batch effect correction and is now -0.0447959444096885 .
2024-07-15 22:01:41.400757 INFO::ASW Label was 0.287135816124097 prior to batch effect correction and is now 0.81338336337585 .
2024-07-15 22:01:41.401961 INFO::Total function execution time is 2.61794495582581 s and adjustment time is 2.59966111183167 s ( 99.3 )
2024-07-15 22:01:41.435425 INFO::Formatting Data.
2024-07-15 22:01:41.449609 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:41.451561 INFO::Removing potential empty rows and columns
2024-07-15 22:01:41.452843 INFO::Found 0 missing values.
2024-07-15 22:01:41.456078 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:41.456767 INFO::Done
2024-07-15 22:01:41.457398 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:41.460412 INFO::Starting hierarchical adjustment
2024-07-15 22:01:41.461329 INFO::Found 5 batches.
2024-07-15 22:01:41.462078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:41.46304 INFO::Using default BPPARAM
2024-07-15 22:01:41.463772 INFO::Processing subtree level 1
2024-07-15 22:01:46.863481 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:46.864943 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:46.876889 INFO::Done
2024-07-15 22:01:46.877751 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:46.880558 INFO::ASW Batch was 0.433474736404685 prior to batch effect correction and is now -0.0964283966468997 .
2024-07-15 22:01:46.881245 INFO::ASW Label was 0.292457258603402 prior to batch effect correction and is now 0.876598507424121 .
2024-07-15 22:01:46.882111 INFO::Total function execution time is 5.44695806503296 s and adjustment time is 5.41565799713135 s ( 99.43 )
2024-07-15 22:01:46.882919 INFO::Formatting Data.
2024-07-15 22:01:46.883582 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:46.884427 INFO::Removing potential empty rows and columns
2024-07-15 22:01:46.885378 INFO::Found 0 missing values.
2024-07-15 22:01:46.888297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:46.888957 INFO::Done
2024-07-15 22:01:46.889639 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:46.892121 INFO::Starting hierarchical adjustment
2024-07-15 22:01:46.892927 INFO::Found 5 batches.
2024-07-15 22:01:46.893542 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:46.894275 INFO::Using default BPPARAM
2024-07-15 22:01:46.894891 INFO::Processing subtree level 1
2024-07-15 22:01:49.455736 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:49.457112 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:49.467974 INFO::Done
2024-07-15 22:01:49.468784 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:49.4715 INFO::ASW Batch was 0.433474736404685 prior to batch effect correction and is now -0.0964283966468997 .
2024-07-15 22:01:49.472185 INFO::ASW Label was 0.292457258603402 prior to batch effect correction and is now 0.876598507424121 .
2024-07-15 22:01:49.473022 INFO::Total function execution time is 2.59008502960205 s and adjustment time is 2.57515001296997 s ( 99.42 )
2024-07-15 22:01:49.48773 INFO::Formatting Data.
2024-07-15 22:01:49.488516 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:49.489438 INFO::Removing potential empty rows and columns
2024-07-15 22:01:49.490424 INFO::Found 0 missing values.
2024-07-15 22:01:49.492505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:49.493153 INFO::Done
2024-07-15 22:01:49.493885 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:49.496557 INFO::Starting hierarchical adjustment
2024-07-15 22:01:49.497359 INFO::Found 2 batches.
2024-07-15 22:01:49.497974 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:49.498649 INFO::Using default BPPARAM
2024-07-15 22:01:49.49929 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:49.500253 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:49.511251 INFO::Done
2024-07-15 22:01:49.512067 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:49.514801 INFO::ASW Batch was 0.415588824604744 prior to batch effect correction and is now 0.128147991914466 .
2024-07-15 22:01:49.51548 INFO::ASW Label was 0.693345992671774 prior to batch effect correction and is now 0.845503150634394 .
2024-07-15 22:01:49.516298 INFO::Total function execution time is 0.0286390781402588 s and adjustment time is 0.0139830112457275 s ( 48.82 )
2024-07-15 22:01:49.517116 INFO::Formatting Data.
2024-07-15 22:01:49.517797 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:49.518706 INFO::Removing potential empty rows and columns
2024-07-15 22:01:49.51966 INFO::Found 0 missing values.
2024-07-15 22:01:49.521783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:49.522413 INFO::Done
2024-07-15 22:01:49.523041 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:49.525882 INFO::Starting hierarchical adjustment
2024-07-15 22:01:49.526715 INFO::Found 2 batches.
2024-07-15 22:01:49.527352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:49.528038 INFO::Using default BPPARAM
2024-07-15 22:01:49.528823 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:49.529797 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:49.540903 INFO::Done
2024-07-15 22:01:49.541704 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:49.544348 INFO::ASW Batch was 0.415588824604744 prior to batch effect correction and is now 0.128147991914466 .
2024-07-15 22:01:49.545035 INFO::ASW Label was 0.693345992671774 prior to batch effect correction and is now 0.845503150634394 .
2024-07-15 22:01:49.545848 INFO::Total function execution time is 0.0287129878997803 s and adjustment time is 0.0143208503723145 s ( 49.88 )
2024-07-15 22:01:49.561845 INFO::Formatting Data.
2024-07-15 22:01:49.562799 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:49.563787 INFO::Removing potential empty rows and columns
2024-07-15 22:01:49.564817 INFO::Found 0 missing values.
2024-07-15 22:01:49.569329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:49.57037 INFO::Done
2024-07-15 22:01:49.571084 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:49.573119 INFO::Starting hierarchical adjustment
2024-07-15 22:01:49.574059 INFO::Found 2 batches.
2024-07-15 22:01:49.574707 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:49.575426 INFO::Using default BPPARAM
2024-07-15 22:01:49.576092 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:49.577085 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:49.599087 INFO::Done
2024-07-15 22:01:49.599803 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:49.601571 INFO::ASW Batch was -7.03332012433123e-05 prior to batch effect correction and is now -0.116834266801306 .
2024-07-15 22:01:49.602433 INFO::Total function execution time is 0.0407509803771973 s and adjustment time is 0.0251460075378418 s ( 61.71 )
2024-07-15 22:01:49.617105 INFO::Formatting Data.
2024-07-15 22:01:49.61784 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:49.618721 INFO::Removing potential empty rows and columns
2024-07-15 22:01:49.619711 INFO::Found 0 missing values.
2024-07-15 22:01:49.620853 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-15 22:01:49.624303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:49.624968 INFO::Done
2024-07-15 22:01:49.625584 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:49.628214 INFO::Starting hierarchical adjustment
2024-07-15 22:01:49.629018 INFO::Found 2 batches.
2024-07-15 22:01:49.629673 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:49.630372 INFO::Using default BPPARAM
2024-07-15 22:01:49.630976 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:49.631862 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:49.643863 INFO::Done
2024-07-15 22:01:49.644635 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:49.647294 INFO::ASW Batch was 0.386257008695583 prior to batch effect correction and is now 0.0712985361136641 .
2024-07-15 22:01:49.648002 INFO::ASW Label was 0.696667587776279 prior to batch effect correction and is now 0.881293717724234 .
2024-07-15 22:01:49.648837 INFO::Total function execution time is 0.0317418575286865 s and adjustment time is 0.0149531364440918 s ( 47.11 )
2024-07-15 22:01:49.649715 INFO::Formatting Data.
2024-07-15 22:01:49.650392 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:49.651274 INFO::Removing potential empty rows and columns
2024-07-15 22:01:49.65262 INFO::Found 0 missing values.
2024-07-15 22:01:49.653526 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-15 22:01:49.656787 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:49.657425 INFO::Done
2024-07-15 22:01:49.658032 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:49.660533 INFO::Starting hierarchical adjustment
2024-07-15 22:01:49.661333 INFO::Found 2 batches.
2024-07-15 22:01:49.661981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:49.662674 INFO::Using default BPPARAM
2024-07-15 22:01:49.66328 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:01:49.664161 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:01:49.675995 INFO::Done
2024-07-15 22:01:49.676659 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:49.67917 INFO::ASW Batch was 0.386257008695583 prior to batch effect correction and is now 0.0712985361136641 .
2024-07-15 22:01:49.679837 INFO::ASW Label was 0.696667587776279 prior to batch effect correction and is now 0.881293717724234 .
2024-07-15 22:01:49.680649 INFO::Total function execution time is 0.0309300422668457 s and adjustment time is 0.0147740840911865 s ( 47.77 )
2024-07-15 22:01:50.112178 INFO::Formatting Data.
2024-07-15 22:01:50.113437 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:50.114766 INFO::Removing potential empty rows and columns
2024-07-15 22:01:50.116224 INFO::Found 0 missing values.
2024-07-15 22:01:50.119525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:50.120363 INFO::Done
2024-07-15 22:01:50.121105 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:50.123541 INFO::Starting hierarchical adjustment
2024-07-15 22:01:50.124458 INFO::Found 3 batches.
2024-07-15 22:01:50.125194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:50.125977 INFO::Using default BPPARAM
2024-07-15 22:01:50.126673 INFO::Processing subtree level 1
2024-07-15 22:01:52.932514 INFO::Adjusting the last 1 batches sequentially
2024-07-15 22:01:52.934129 INFO::Done
2024-07-15 22:01:52.934851 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:52.936817 INFO::ASW Batch was -0.136006378042292 prior to batch effect correction and is now -0.136006378042292 .
2024-07-15 22:01:52.937683 INFO::Total function execution time is 2.82570385932922 s and adjustment time is 2.80981588363647 s ( 99.44 )
2024-07-15 22:01:52.938608 INFO::Formatting Data.
2024-07-15 22:01:52.939321 INFO::Typecasting input to dataframe.
2024-07-15 22:01:52.940098 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:52.940981 INFO::Removing potential empty rows and columns
2024-07-15 22:01:52.94196 INFO::Found 0 missing values.
2024-07-15 22:01:52.944261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:52.944929 INFO::Done
2024-07-15 22:01:52.945538 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:52.947312 INFO::Starting hierarchical adjustment
2024-07-15 22:01:52.948139 INFO::Found 3 batches.
2024-07-15 22:01:52.948984 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:52.949729 INFO::Using default BPPARAM
2024-07-15 22:01:52.95035 INFO::Processing subtree level 1
2024-07-15 22:01:55.349752 INFO::Adjusting the last 1 batches sequentially
2024-07-15 22:01:55.351222 INFO::Done
2024-07-15 22:01:55.351892 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:55.353848 INFO::ASW Batch was -0.136006378042292 prior to batch effect correction and is now -0.136006378042292 .
2024-07-15 22:01:55.354727 INFO::Total function execution time is 2.41610598564148 s and adjustment time is 2.40324592590332 s ( 99.47 )
2024-07-15 22:01:55.379355 INFO::Formatting Data.
2024-07-15 22:01:55.380487 INFO::Typecasting input to dataframe.
2024-07-15 22:01:55.381636 INFO::Replacing NaNs with NAs.
2024-07-15 22:01:55.382932 INFO::Removing potential empty rows and columns
2024-07-15 22:01:55.384153 INFO::Found 0 missing values.
2024-07-15 22:01:55.386492 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:01:55.387137 INFO::Done
2024-07-15 22:01:55.387754 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:01:55.389814 INFO::Starting hierarchical adjustment
2024-07-15 22:01:55.390608 INFO::Found 3 batches.
2024-07-15 22:01:55.391242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:01:55.391926 INFO::Using default BPPARAM
2024-07-15 22:01:55.392531 INFO::Processing subtree level 1
2024-07-15 22:01:58.793188 INFO::Adjusting the last 1 batches sequentially
2024-07-15 22:01:58.795107 INFO::Done
2024-07-15 22:01:58.796242 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:01:58.798654 INFO::ASW Batch was -0.118365790345764 prior to batch effect correction and is now -0.118365790345764 .
2024-07-15 22:01:58.799797 INFO::Total function execution time is 3.42055201530457 s and adjustment time is 3.40447902679443 s ( 99.53 )
2024-07-15 22:02:01.277395 INFO::Formatting Data.
2024-07-15 22:02:01.278393 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:01.279474 INFO::Removing potential empty rows and columns
2024-07-15 22:02:01.281609 INFO::Found 1000 missing values.
2024-07-15 22:02:01.294532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:01.295427 INFO::Done
2024-07-15 22:02:01.296063 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:02:01.301882 INFO::Starting hierarchical adjustment
2024-07-15 22:02:01.30275 INFO::Found 10 batches.
2024-07-15 22:02:01.303372 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:02:01.304063 INFO::Using default BPPARAM
2024-07-15 22:02:01.304668 INFO::Processing subtree level 1
2024-07-15 22:02:03.804643 INFO::Processing subtree level 2
2024-07-15 22:02:08.874518 INFO::Adjusting the last 1 batches sequentially
2024-07-15 22:02:08.876901 INFO::Done
2024-07-15 22:02:08.878014 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:02:08.883981 INFO::ASW Batch was 0.527596848523833 prior to batch effect correction and is now 0.527596848523833 .
2024-07-15 22:02:08.88472 INFO::ASW Label was 0.306876534716227 prior to batch effect correction and is now 0.306876534716227 .
2024-07-15 22:02:08.885894 INFO::Total function execution time is 7.60864686965942 s and adjustment time is 7.57415199279785 s ( 99.55 )
2024-07-15 22:02:08.88679 INFO::Formatting Data.
2024-07-15 22:02:08.887495 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:08.888523 INFO::Removing potential empty rows and columns
2024-07-15 22:02:08.891074 INFO::Found 1000 missing values.
2024-07-15 22:02:08.90344 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:08.904295 INFO::Done
2024-07-15 22:02:08.90493 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:02:08.910756 INFO::Starting hierarchical adjustment
2024-07-15 22:02:08.911594 INFO::Found 10 batches.
2024-07-15 22:02:09.642527 INFO::Set up parallel execution backend with 2 workers
2024-07-15 22:02:09.643836 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-15 22:02:12.751093 INFO::Adjusting the last 2 batches sequentially
2024-07-15 22:02:12.752708 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-15 22:02:12.766482 INFO::Done
2024-07-15 22:02:12.767239 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:02:12.7727 INFO::ASW Batch was 0.527596848523833 prior to batch effect correction and is now 0.527596848523833 .
2024-07-15 22:02:12.773397 INFO::ASW Label was 0.306876534716227 prior to batch effect correction and is now 0.306876534716227 .
2024-07-15 22:02:12.774253 INFO::Total function execution time is 3.88745403289795 s and adjustment time is 3.85499501228333 s ( 99.17 )
2024-07-15 22:02:15.207254 INFO::Formatting Data.
2024-07-15 22:02:15.208175 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:15.209147 INFO::Removing potential empty rows and columns
2024-07-15 22:02:15.210171 INFO::Found 0 missing values.
2024-07-15 22:02:15.212912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:15.213566 INFO::Done
2024-07-15 22:02:15.214178 INFO::Acquiring quality metrics before batch effect correction.
2024-07-15 22:02:15.216629 INFO::Starting hierarchical adjustment
2024-07-15 22:02:15.217446 INFO::Found 3 batches.
2024-07-15 22:02:15.218069 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-15 22:02:15.218761 INFO::Using default BPPARAM
2024-07-15 22:02:15.219402 INFO::Processing subtree level 1
2024-07-15 22:02:18.580291 INFO::Adjusting the last 1 batches sequentially
2024-07-15 22:02:18.583445 INFO::Done
2024-07-15 22:02:18.584537 INFO::Acquiring quality metrics after batch effect correction.
2024-07-15 22:02:18.587215 INFO::ASW Batch was 0.264113081906454 prior to batch effect correction and is now -0.143742268547556 .
2024-07-15 22:02:18.587906 INFO::ASW Label was -0.199494856660078 prior to batch effect correction and is now 0.0339246735014943 .
2024-07-15 22:02:18.588782 INFO::Total function execution time is 3.38167500495911 s and adjustment time is 3.36483788490295 s ( 99.5 )
2024-07-15 22:02:18.72993 INFO::Formatting Data.
2024-07-15 22:02:18.730944 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:18.731969 INFO::Removing potential empty rows and columns
2024-07-15 22:02:18.733034 INFO::Found 2 missing values.
2024-07-15 22:02:18.735386 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:18.736048 INFO::Done
2024-07-15 22:02:18.772316 INFO::Found NA in Reference column
2024-07-15 22:02:18.785603 INFO::Require at least two references per batch.
2024-07-15 22:02:18.806681 INFO::Formatting Data.
2024-07-15 22:02:18.807647 INFO::Recognized SummarizedExperiment
2024-07-15 22:02:18.808394 INFO::Typecasting input to dataframe.
2024-07-15 22:02:18.815799 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:18.817101 INFO::Removing potential empty rows and columns
2024-07-15 22:02:18.819806 INFO::Found 0 missing values.
2024-07-15 22:02:18.824749 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:18.825461 INFO::Done
2024-07-15 22:02:18.839479 INFO::Formatting Data.
2024-07-15 22:02:18.840238 INFO::Recognized SummarizedExperiment
2024-07-15 22:02:18.840883 INFO::Typecasting input to dataframe.
2024-07-15 22:02:18.854434 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:18.855664 INFO::Removing potential empty rows and columns
2024-07-15 22:02:18.858549 INFO::Found 0 missing values.
2024-07-15 22:02:18.866533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:18.867243 INFO::Done
2024-07-15 22:02:18.881838 INFO::Formatting Data.
2024-07-15 22:02:18.882681 INFO::Recognized SummarizedExperiment
2024-07-15 22:02:18.883385 INFO::Typecasting input to dataframe.
2024-07-15 22:02:18.896577 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:18.897695 INFO::Removing potential empty rows and columns
2024-07-15 22:02:18.898861 INFO::Found 0 missing values.
2024-07-15 22:02:18.8999 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-15 22:02:18.903577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:18.904274 INFO::Done
2024-07-15 22:02:18.919065 INFO::Formatting Data.
2024-07-15 22:02:18.920027 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:18.921085 INFO::Removing potential empty rows and columns
2024-07-15 22:02:18.922207 INFO::Found 0 missing values.
2024-07-15 22:02:18.924722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:18.925444 INFO::Done
2024-07-15 22:02:18.943075 INFO::Formatting Data.
2024-07-15 22:02:18.944092 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:18.945042 INFO::Removing potential empty rows and columns
2024-07-15 22:02:18.946094 INFO::Found 0 missing values.
2024-07-15 22:02:18.948511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:18.949158 INFO::Done
2024-07-15 22:02:18.992362 INFO::Formatting Data.
2024-07-15 22:02:18.993413 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:18.994552 INFO::Removing potential empty rows and columns
2024-07-15 22:02:18.995748 INFO::Found 1 missing values.
2024-07-15 22:02:18.99791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:18.998662 INFO::Done
2024-07-15 22:02:19.022225 INFO::Formatting Data.
2024-07-15 22:02:19.02302 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:19.023891 INFO::Removing potential empty rows and columns
2024-07-15 22:02:19.024828 INFO::Found 2 missing values.
2024-07-15 22:02:19.025758 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-15 22:02:19.027598 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:19.028258 INFO::Done
2024-07-15 22:02:19.043637 INFO::Formatting Data.
2024-07-15 22:02:19.044794 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:19.04588 INFO::Removing potential empty rows and columns
2024-07-15 22:02:19.046939 INFO::Found 2 missing values.
2024-07-15 22:02:19.048525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:19.049178 INFO::Done
2024-07-15 22:02:19.063838 INFO::Formatting Data.
2024-07-15 22:02:19.064791 INFO::Typecasting input to dataframe.
2024-07-15 22:02:19.065705 INFO::Replacing NaNs with NAs.
2024-07-15 22:02:19.066662 INFO::Removing potential empty rows and columns
2024-07-15 22:02:19.067713 INFO::Found 0 missing values.
2024-07-15 22:02:19.070115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-15 22:02:19.070782 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
29.40 1.79 71.85
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 7.78 | 0.44 | 15.66 | |
| compute_asw | 0.02 | 0.00 | 0.02 | |
| count_existing | 0.02 | 0.00 | 0.02 | |
| generate_data_covariables | 0 | 0 | 0 | |
| generate_dataset | 0 | 0 | 0 | |