Yannis Schumann
| Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 65b1ece |
| git_last_commit_date: 2024-02-28 02:41:28 -0500 (Wed, 28 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:38:53 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 155/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 0.99.16 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 0.99.16 |
| 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_0.99.16.tar.gz |
| StartedAt: 2024-03-02 00:33:54 -0500 (Sat, 02 Mar 2024) |
| EndedAt: 2024-03-02 00:36:31 -0500 (Sat, 02 Mar 2024) |
| EllapsedTime: 157.5 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_0.99.16.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘0.99.16’
* 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 R 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 45.195 2.919 41.62
* 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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")
2024-03-02 00:35:53.072554 INFO::Formatting Data.
2024-03-02 00:35:53.080437 INFO::Replacing NaNs with NAs.
2024-03-02 00:35:53.119928 INFO::Removing potential empty rows and columns
2024-03-02 00:35:53.965672 INFO::Found 0 missing values.
2024-03-02 00:35:53.977512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:35:53.979082 INFO::Done
2024-03-02 00:35:53.981017 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:35:54.019064 INFO::Starting hierarchical adjustment
2024-03-02 00:35:54.020992 INFO::Found 3 batches.
2024-03-02 00:35:54.022317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:35:54.025611 INFO::Using default BPPARAM
2024-03-02 00:35:54.027497 INFO::Processing subtree level 1
2024-03-02 00:35:54.307771 INFO::Adjusting the last 1 batches sequentially
2024-03-02 00:35:54.314645 INFO::Done
2024-03-02 00:35:54.316648 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:35:54.323417 INFO::ASW Batch was -0.0534438583040906 prior to batch effect correction and is now -0.0534438583040906 .
2024-03-02 00:35:54.326456 INFO::Total function execution time is 1.25510096549988 s and adjustment time is 0.294037818908691 s ( 23.43 )
2024-03-02 00:35:54.361767 INFO::Formatting Data.
2024-03-02 00:35:54.363382 INFO::Replacing NaNs with NAs.
2024-03-02 00:35:54.365481 INFO::Removing potential empty rows and columns
2024-03-02 00:35:54.368188 INFO::Found 0 missing values.
2024-03-02 00:35:54.37253 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.
2024-03-02 00:35:54.406579 INFO::Formatting Data.
2024-03-02 00:35:54.408215 INFO::Replacing NaNs with NAs.
2024-03-02 00:35:54.411437 INFO::Removing potential empty rows and columns
2024-03-02 00:35:54.41416 INFO::Found 0 missing values.
2024-03-02 00:35:54.417038 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.
2024-03-02 00:35:54.463605 INFO::Formatting Data.
2024-03-02 00:35:54.465155 INFO::Replacing NaNs with NAs.
2024-03-02 00:35:54.467095 INFO::Removing potential empty rows and columns
2024-03-02 00:35:54.47252 INFO::Found 0 missing values.
2024-03-02 00:35:54.47507 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.
2024-03-02 00:35:54.48988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:35:54.491756 INFO::Done
2024-03-02 00:35:54.493292 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:35:54.498259 INFO::Starting hierarchical adjustment
2024-03-02 00:35:54.500146 INFO::Found 2 batches.
2024-03-02 00:35:54.505384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:35:54.507209 INFO::Using default BPPARAM
2024-03-02 00:35:54.5086 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:35:54.51161 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:35:54.574892 INFO::Done
2024-03-02 00:35:54.576412 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:35:54.581231 INFO::ASW Batch was 0.0116089855560074 prior to batch effect correction and is now -0.1237946961517 .
2024-03-02 00:35:54.584446 INFO::Total function execution time is 0.120726108551025 s and adjustment time is 0.0751299858093262 s ( 62.23 )
2024-03-02 00:35:54.592151 INFO::Formatting Data.
2024-03-02 00:35:54.593847 INFO::Replacing NaNs with NAs.
2024-03-02 00:35:54.622903 INFO::Formatting Data.
2024-03-02 00:35:54.624516 INFO::Replacing NaNs with NAs.
2024-03-02 00:35:54.626688 INFO::Removing potential empty rows and columns
2024-03-02 00:35:54.631856 INFO::Found 0 missing values.
2024-03-02 00:35:54.641916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:35:54.645396 INFO::Done
2024-03-02 00:35:54.646835 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:35:54.651655 INFO::Starting hierarchical adjustment
2024-03-02 00:35:54.653533 INFO::Found 2 batches.
2024-03-02 00:35:54.658102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:35:54.659917 INFO::Using default BPPARAM
2024-03-02 00:35:54.661964 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:35:54.664596 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:35:54.707684 INFO::Done
2024-03-02 00:35:54.709052 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:35:54.714724 INFO::ASW Batch was -0.0360446760234023 prior to batch effect correction and is now -0.122308587969692 .
2024-03-02 00:35:54.718831 INFO::Total function execution time is 0.0959300994873047 s and adjustment time is 0.0545520782470703 s ( 56.87 )
2024-03-02 00:35:54.721688 INFO::Formatting Data.
2024-03-02 00:35:54.723307 INFO::Replacing NaNs with NAs.
2024-03-02 00:35:54.726262 INFO::Removing potential empty rows and columns
2024-03-02 00:35:54.731286 INFO::Found 0 missing values.
2024-03-02 00:35:54.739835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:35:54.743062 INFO::Done
2024-03-02 00:35:54.744568 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:35:54.749376 INFO::Starting hierarchical adjustment
2024-03-02 00:35:54.751247 INFO::Found 2 batches.
2024-03-02 00:35:54.753369 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:35:54.755011 INFO::Using default BPPARAM
2024-03-02 00:35:54.756372 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:35:54.758554 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:35:54.807866 INFO::Done
2024-03-02 00:35:54.809339 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:35:54.814855 INFO::ASW Batch was -0.0360446760234023 prior to batch effect correction and is now -0.122308587969692 .
2024-03-02 00:35:54.816907 INFO::Total function execution time is 0.0952260494232178 s and adjustment time is 0.0570068359375 s ( 59.86 )
2024-03-02 00:36:01.041769 INFO::Formatting Data.
2024-03-02 00:36:01.04312 INFO::Recognized SummarizedExperiment
2024-03-02 00:36:01.044217 INFO::Typecasting input to dataframe.
2024-03-02 00:36:02.281047 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:02.286284 INFO::Removing potential empty rows and columns
2024-03-02 00:36:02.296728 INFO::Found 0 missing values.
2024-03-02 00:36:02.317448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:02.318771 INFO::Done
2024-03-02 00:36:02.323477 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:02.330188 INFO::Starting hierarchical adjustment
2024-03-02 00:36:02.331665 INFO::Found 2 batches.
2024-03-02 00:36:02.334221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:02.336754 INFO::Using default BPPARAM
2024-03-02 00:36:02.337967 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:02.339831 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:02.488767 INFO::Done
2024-03-02 00:36:02.489969 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:02.499862 INFO::ASW Batch was 0.038862089177181 prior to batch effect correction and is now -0.0955506524591502 .
2024-03-02 00:36:02.501709 INFO::Total function execution time is 1.46064305305481 s and adjustment time is 0.157388925552368 s ( 10.78 )
2024-03-02 00:36:02.549386 INFO::Formatting Data.
2024-03-02 00:36:02.5507 INFO::Recognized SummarizedExperiment
2024-03-02 00:36:02.551815 INFO::Typecasting input to dataframe.
2024-03-02 00:36:02.575143 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:02.577307 INFO::Removing potential empty rows and columns
2024-03-02 00:36:02.587661 INFO::Found 0 missing values.
2024-03-02 00:36:02.60783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:02.609046 INFO::Done
2024-03-02 00:36:02.610131 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:02.619264 INFO::Starting hierarchical adjustment
2024-03-02 00:36:02.620842 INFO::Found 2 batches.
2024-03-02 00:36:02.621926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:02.623074 INFO::Using default BPPARAM
2024-03-02 00:36:02.624668 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:02.630528 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:02.70331 INFO::Done
2024-03-02 00:36:02.704547 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:02.712476 INFO::ASW Batch was -0.00177137706216201 prior to batch effect correction and is now -0.00177137706216201 .
2024-03-02 00:36:02.716532 INFO::Total function execution time is 0.16703200340271 s and adjustment time is 0.0827620029449463 s ( 49.55 )
2024-03-02 00:36:02.765266 INFO::Formatting Data.
2024-03-02 00:36:02.76701 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:02.768904 INFO::Removing potential empty rows and columns
2024-03-02 00:36:02.771161 INFO::Found 0 missing values.
2024-03-02 00:36:02.779567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:02.781441 INFO::Done
2024-03-02 00:36:02.783184 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:02.789486 INFO::Starting hierarchical adjustment
2024-03-02 00:36:02.791155 INFO::Found 3 batches.
2024-03-02 00:36:02.792423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:02.793744 INFO::Using default BPPARAM
2024-03-02 00:36:02.7949 INFO::Processing subtree level 1
2024-03-02 00:36:03.255856 INFO::Adjusting the last 1 batches sequentially
2024-03-02 00:36:03.266435 INFO::Done
2024-03-02 00:36:03.27021 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:03.282226 INFO::ASW Batch was -0.0425695883684412 prior to batch effect correction and is now -0.155487692397541 .
2024-03-02 00:36:03.286352 INFO::Total function execution time is 0.520944118499756 s and adjustment time is 0.475590944290161 s ( 91.29 )
2024-03-02 00:36:03.325398 INFO::Skipping initial DF formatting
2024-03-02 00:36:03.326947 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:03.336668 INFO::Starting hierarchical adjustment
2024-03-02 00:36:03.338498 INFO::Found 5 batches.
2024-03-02 00:36:03.341131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:03.343633 INFO::Using default BPPARAM
2024-03-02 00:36:03.345074 INFO::Processing subtree level 1
2024-03-02 00:36:03.664907 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:03.670769 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:03.749903 INFO::Done
2024-03-02 00:36:03.751579 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:03.764174 INFO::ASW Batch was 0.530864012467273 prior to batch effect correction and is now 0.530864012467273 .
2024-03-02 00:36:03.766154 INFO::ASW Label was 0.343887144989775 prior to batch effect correction and is now 0.343887144989775 .
2024-03-02 00:36:03.769035 INFO::Total function execution time is 0.44369912147522 s and adjustment time is 0.411732912063599 s ( 92.8 )
2024-03-02 00:36:03.835984 INFO::Formatting Data.
2024-03-02 00:36:03.837999 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:03.840829 INFO::Removing potential empty rows and columns
2024-03-02 00:36:03.843885 INFO::Found 0 missing values.
2024-03-02 00:36:03.857408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:03.858929 INFO::Done
2024-03-02 00:36:03.860396 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:03.86881 INFO::Starting hierarchical adjustment
2024-03-02 00:36:03.870857 INFO::Found 5 batches.
2024-03-02 00:36:03.872609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:03.874511 INFO::Using default BPPARAM
2024-03-02 00:36:03.877971 INFO::Processing subtree level 1
2024-03-02 00:36:04.11758 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:04.121646 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:04.168443 INFO::Done
2024-03-02 00:36:04.170071 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:04.178019 INFO::ASW Batch was 0.346545295620875 prior to batch effect correction and is now -0.0926932700511909 .
2024-03-02 00:36:04.179633 INFO::ASW Label was 0.392890487690967 prior to batch effect correction and is now 0.904975790000801 .
2024-03-02 00:36:04.18175 INFO::Total function execution time is 0.345845937728882 s and adjustment time is 0.297998905181885 s ( 86.17 )
2024-03-02 00:36:04.184016 INFO::Formatting Data.
2024-03-02 00:36:04.185703 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:04.188017 INFO::Removing potential empty rows and columns
2024-03-02 00:36:04.190737 INFO::Found 0 missing values.
2024-03-02 00:36:04.201926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:04.2033 INFO::Done
2024-03-02 00:36:04.20455 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:04.211036 INFO::Starting hierarchical adjustment
2024-03-02 00:36:04.212922 INFO::Found 5 batches.
2024-03-02 00:36:04.214273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:04.21583 INFO::Using default BPPARAM
2024-03-02 00:36:04.217137 INFO::Processing subtree level 1
2024-03-02 00:36:04.449018 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:04.453522 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:04.497844 INFO::Done
2024-03-02 00:36:04.49935 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:04.506764 INFO::ASW Batch was 0.346545295620875 prior to batch effect correction and is now -0.0926932700511909 .
2024-03-02 00:36:04.508219 INFO::ASW Label was 0.392890487690967 prior to batch effect correction and is now 0.904975790000801 .
2024-03-02 00:36:04.510184 INFO::Total function execution time is 0.326198816299438 s and adjustment time is 0.285252094268799 s ( 87.45 )
2024-03-02 00:36:04.55056 INFO::Formatting Data.
2024-03-02 00:36:04.552626 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:04.556256 INFO::Removing potential empty rows and columns
2024-03-02 00:36:04.559047 INFO::Found 0 missing values.
2024-03-02 00:36:04.570809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:04.572201 INFO::Done
2024-03-02 00:36:04.573514 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:04.582142 INFO::Starting hierarchical adjustment
2024-03-02 00:36:04.586025 INFO::Found 5 batches.
2024-03-02 00:36:04.587976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:04.589676 INFO::Using default BPPARAM
2024-03-02 00:36:04.592016 INFO::Processing subtree level 1
2024-03-02 00:36:04.89154 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:04.904554 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:04.960293 INFO::Done
2024-03-02 00:36:04.963136 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:04.971315 INFO::ASW Batch was 0.492826356038422 prior to batch effect correction and is now -0.089033713976249 .
2024-03-02 00:36:04.972916 INFO::ASW Label was 0.253538185362393 prior to batch effect correction and is now 0.828723813108112 .
2024-03-02 00:36:04.976367 INFO::Total function execution time is 0.42598819732666 s and adjustment time is 0.37468695640564 s ( 87.96 )
2024-03-02 00:36:04.978544 INFO::Formatting Data.
2024-03-02 00:36:04.980075 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:04.982084 INFO::Removing potential empty rows and columns
2024-03-02 00:36:04.984694 INFO::Found 0 missing values.
2024-03-02 00:36:04.997046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:04.998504 INFO::Done
2024-03-02 00:36:04.999817 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:05.008291 INFO::Starting hierarchical adjustment
2024-03-02 00:36:05.010075 INFO::Found 5 batches.
2024-03-02 00:36:05.011489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:05.013046 INFO::Using default BPPARAM
2024-03-02 00:36:05.014354 INFO::Processing subtree level 1
2024-03-02 00:36:05.28052 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:05.297315 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:05.353771 INFO::Done
2024-03-02 00:36:05.355218 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:05.364331 INFO::ASW Batch was 0.492826356038422 prior to batch effect correction and is now -0.089033713976249 .
2024-03-02 00:36:05.365892 INFO::ASW Label was 0.253538185362393 prior to batch effect correction and is now 0.828723813108112 .
2024-03-02 00:36:05.368928 INFO::Total function execution time is 0.39030385017395 s and adjustment time is 0.344010829925537 s ( 88.14 )
2024-03-02 00:36:05.408153 INFO::Formatting Data.
2024-03-02 00:36:05.40992 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:05.414158 INFO::Removing potential empty rows and columns
2024-03-02 00:36:05.41747 INFO::Found 0 missing values.
2024-03-02 00:36:05.425151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:05.426797 INFO::Done
2024-03-02 00:36:05.428225 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:05.437403 INFO::Starting hierarchical adjustment
2024-03-02 00:36:05.439765 INFO::Found 2 batches.
2024-03-02 00:36:05.441322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:05.443776 INFO::Using default BPPARAM
2024-03-02 00:36:05.445448 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:05.448171 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:05.48855 INFO::Done
2024-03-02 00:36:05.490645 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:05.499301 INFO::ASW Batch was 0.625732906093713 prior to batch effect correction and is now 0.139470302677847 .
2024-03-02 00:36:05.501247 INFO::ASW Label was 0.534373882709661 prior to batch effect correction and is now 0.844928856314267 .
2024-03-02 00:36:05.503474 INFO::Total function execution time is 0.0953519344329834 s and adjustment time is 0.0494790077209473 s ( 51.89 )
2024-03-02 00:36:05.506169 INFO::Formatting Data.
2024-03-02 00:36:05.507787 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:05.510727 INFO::Removing potential empty rows and columns
2024-03-02 00:36:05.513541 INFO::Found 0 missing values.
2024-03-02 00:36:05.523952 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:05.525706 INFO::Done
2024-03-02 00:36:05.52722 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:05.536283 INFO::Starting hierarchical adjustment
2024-03-02 00:36:05.538632 INFO::Found 2 batches.
2024-03-02 00:36:05.539902 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:05.541293 INFO::Using default BPPARAM
2024-03-02 00:36:05.542518 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:05.545375 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:05.59092 INFO::Done
2024-03-02 00:36:05.592587 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:05.602988 INFO::ASW Batch was 0.625732906093713 prior to batch effect correction and is now 0.139470302677847 .
2024-03-02 00:36:05.604698 INFO::ASW Label was 0.534373882709661 prior to batch effect correction and is now 0.844928856314267 .
2024-03-02 00:36:05.606665 INFO::Total function execution time is 0.101181983947754 s and adjustment time is 0.0530910491943359 s ( 52.47 )
2024-03-02 00:36:05.642451 INFO::Formatting Data.
2024-03-02 00:36:05.644446 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:05.648423 INFO::Removing potential empty rows and columns
2024-03-02 00:36:05.650948 INFO::Found 0 missing values.
2024-03-02 00:36:05.657312 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:05.661503 INFO::Done
2024-03-02 00:36:05.663045 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:05.669814 INFO::Starting hierarchical adjustment
2024-03-02 00:36:05.674328 INFO::Found 2 batches.
2024-03-02 00:36:05.675915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:05.677606 INFO::Using default BPPARAM
2024-03-02 00:36:05.679097 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:05.681543 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:05.782013 INFO::Done
2024-03-02 00:36:05.783522 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:05.788047 INFO::ASW Batch was -0.0940322534260023 prior to batch effect correction and is now -0.164382336081567 .
2024-03-02 00:36:05.793851 INFO::Total function execution time is 0.15156102180481 s and adjustment time is 0.109953880310059 s ( 72.55 )
2024-03-02 00:36:05.828751 INFO::Formatting Data.
2024-03-02 00:36:05.830252 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:05.832245 INFO::Removing potential empty rows and columns
2024-03-02 00:36:05.834784 INFO::Found 0 missing values.
2024-03-02 00:36:05.839152 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.
2024-03-02 00:36:05.853071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:05.85453 INFO::Done
2024-03-02 00:36:05.855834 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:05.864072 INFO::Starting hierarchical adjustment
2024-03-02 00:36:05.865969 INFO::Found 2 batches.
2024-03-02 00:36:05.86722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:05.868545 INFO::Using default BPPARAM
2024-03-02 00:36:05.871061 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:05.873512 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:05.923832 INFO::Done
2024-03-02 00:36:05.925276 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:05.934326 INFO::ASW Batch was 0.623933721064662 prior to batch effect correction and is now 0.046232675877034 .
2024-03-02 00:36:05.935784 INFO::ASW Label was 0.481827915577952 prior to batch effect correction and is now 0.894073563092682 .
2024-03-02 00:36:05.937453 INFO::Total function execution time is 0.108804941177368 s and adjustment time is 0.0582728385925293 s ( 53.56 )
2024-03-02 00:36:05.939187 INFO::Formatting Data.
2024-03-02 00:36:05.941405 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:05.943789 INFO::Removing potential empty rows and columns
2024-03-02 00:36:05.947109 INFO::Found 0 missing values.
2024-03-02 00:36:05.949588 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.
2024-03-02 00:36:05.966959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:05.968375 INFO::Done
2024-03-02 00:36:05.96965 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:05.979688 INFO::Starting hierarchical adjustment
2024-03-02 00:36:05.982248 INFO::Found 2 batches.
2024-03-02 00:36:05.98365 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:05.985177 INFO::Using default BPPARAM
2024-03-02 00:36:05.986486 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:05.988862 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:06.039009 INFO::Done
2024-03-02 00:36:06.040403 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:06.047791 INFO::ASW Batch was 0.623933721064662 prior to batch effect correction and is now 0.046232675877034 .
2024-03-02 00:36:06.050383 INFO::ASW Label was 0.481827915577952 prior to batch effect correction and is now 0.894073563092682 .
2024-03-02 00:36:06.052212 INFO::Total function execution time is 0.113047122955322 s and adjustment time is 0.0578770637512207 s ( 51.2 )
2024-03-02 00:36:06.7506 INFO::Formatting Data.
2024-03-02 00:36:06.752684 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:06.755833 INFO::Removing potential empty rows and columns
2024-03-02 00:36:06.758625 INFO::Found 0 missing values.
2024-03-02 00:36:06.768237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:06.76974 INFO::Done
2024-03-02 00:36:06.771127 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:06.776627 INFO::Starting hierarchical adjustment
2024-03-02 00:36:06.778511 INFO::Found 3 batches.
2024-03-02 00:36:06.780075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:06.781946 INFO::Using default BPPARAM
2024-03-02 00:36:06.783243 INFO::Processing subtree level 1
2024-03-02 00:36:07.02341 INFO::Adjusting the last 1 batches sequentially
2024-03-02 00:36:07.034358 INFO::Done
2024-03-02 00:36:07.037678 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:07.050385 INFO::ASW Batch was -0.0255625082430665 prior to batch effect correction and is now -0.0255625082430665 .
2024-03-02 00:36:07.054716 INFO::Total function execution time is 0.303471803665161 s and adjustment time is 0.256196022033691 s ( 84.42 )
2024-03-02 00:36:07.060982 INFO::Formatting Data.
2024-03-02 00:36:07.063324 INFO::Typecasting input to dataframe.
2024-03-02 00:36:07.066055 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:07.068354 INFO::Removing potential empty rows and columns
2024-03-02 00:36:07.071993 INFO::Found 0 missing values.
2024-03-02 00:36:07.080007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:07.081561 INFO::Done
2024-03-02 00:36:07.082934 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:07.087566 INFO::Starting hierarchical adjustment
2024-03-02 00:36:07.089421 INFO::Found 3 batches.
2024-03-02 00:36:07.0915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:07.093183 INFO::Using default BPPARAM
2024-03-02 00:36:07.094661 INFO::Processing subtree level 1
2024-03-02 00:36:07.343048 INFO::Adjusting the last 1 batches sequentially
2024-03-02 00:36:07.353973 INFO::Done
2024-03-02 00:36:07.357134 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:07.368022 INFO::ASW Batch was -0.0255625082430665 prior to batch effect correction and is now -0.0255625082430665 .
2024-03-02 00:36:07.374736 INFO::Total function execution time is 0.312741994857788 s and adjustment time is 0.264924049377441 s ( 84.71 )
2024-03-02 00:36:07.421696 INFO::Formatting Data.
2024-03-02 00:36:07.423477 INFO::Typecasting input to dataframe.
2024-03-02 00:36:07.426487 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:07.430044 INFO::Removing potential empty rows and columns
2024-03-02 00:36:07.436577 INFO::Found 0 missing values.
2024-03-02 00:36:07.444477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:07.445908 INFO::Done
2024-03-02 00:36:07.447151 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:07.451799 INFO::Starting hierarchical adjustment
2024-03-02 00:36:07.453629 INFO::Found 3 batches.
2024-03-02 00:36:07.45494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:07.456488 INFO::Using default BPPARAM
2024-03-02 00:36:07.458687 INFO::Processing subtree level 1
2024-03-02 00:36:07.762395 INFO::Adjusting the last 1 batches sequentially
2024-03-02 00:36:07.782053 INFO::Done
2024-03-02 00:36:07.786878 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:07.807381 INFO::ASW Batch was -0.0410094808466361 prior to batch effect correction and is now -0.0410094808466361 .
2024-03-02 00:36:07.813038 INFO::Total function execution time is 0.393960952758789 s and adjustment time is 0.328764915466309 s ( 83.45 )
2024-03-02 00:36:08.233185 INFO::Formatting Data.
2024-03-02 00:36:08.234848 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:08.23732 INFO::Removing potential empty rows and columns
2024-03-02 00:36:08.244775 INFO::Found 1000 missing values.
2024-03-02 00:36:08.320435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:08.321945 INFO::Done
2024-03-02 00:36:08.323237 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:08.334645 INFO::Starting hierarchical adjustment
2024-03-02 00:36:08.336346 INFO::Found 10 batches.
2024-03-02 00:36:08.337561 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:08.338965 INFO::Using default BPPARAM
2024-03-02 00:36:08.340822 INFO::Processing subtree level 1
2024-03-02 00:36:08.667379 INFO::Processing subtree level 2
2024-03-02 00:36:09.088774 INFO::Adjusting the last 1 batches sequentially
2024-03-02 00:36:09.102413 INFO::Done
2024-03-02 00:36:09.105741 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:09.127015 INFO::ASW Batch was 0.474314687485831 prior to batch effect correction and is now 0.474314687485831 .
2024-03-02 00:36:09.129642 INFO::ASW Label was 0.345323609597532 prior to batch effect correction and is now 0.345323609597532 .
2024-03-02 00:36:09.133465 INFO::Total function execution time is 0.8994460105896 s and adjustment time is 0.766366004943848 s ( 85.2 )
2024-03-02 00:36:09.136555 INFO::Formatting Data.
2024-03-02 00:36:09.138118 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:09.142151 INFO::Removing potential empty rows and columns
2024-03-02 00:36:09.150059 INFO::Found 1000 missing values.
2024-03-02 00:36:09.212274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:09.213689 INFO::Done
2024-03-02 00:36:09.21603 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:09.229633 INFO::Starting hierarchical adjustment
2024-03-02 00:36:09.235126 INFO::Found 10 batches.
2024-03-02 00:36:10.788656 INFO::Set up parallel execution backend with 2 workers
2024-03-02 00:36:10.789894 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-03-02 00:36:12.829798 INFO::Adjusting the last 2 batches sequentially
2024-03-02 00:36:12.832096 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-02 00:36:12.892281 INFO::Done
2024-03-02 00:36:12.893531 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:12.905256 INFO::ASW Batch was 0.474314687485831 prior to batch effect correction and is now 0.474314687485831 .
2024-03-02 00:36:12.906573 INFO::ASW Label was 0.345323609597532 prior to batch effect correction and is now 0.345323609597532 .
2024-03-02 00:36:12.908476 INFO::Total function execution time is 3.77207612991333 s and adjustment time is 3.65767502784729 s ( 96.97 )
2024-03-02 00:36:13.340412 INFO::Formatting Data.
2024-03-02 00:36:13.343429 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:13.345695 INFO::Removing potential empty rows and columns
2024-03-02 00:36:13.349097 INFO::Found 0 missing values.
2024-03-02 00:36:13.359889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:13.361242 INFO::Done
2024-03-02 00:36:13.362496 INFO::Acquiring quality metrics before batch effect correction.
2024-03-02 00:36:13.369768 INFO::Starting hierarchical adjustment
2024-03-02 00:36:13.371811 INFO::Found 3 batches.
2024-03-02 00:36:13.374093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-02 00:36:13.37553 INFO::Using default BPPARAM
2024-03-02 00:36:13.377331 INFO::Processing subtree level 1
2024-03-02 00:36:13.69479 INFO::Adjusting the last 1 batches sequentially
2024-03-02 00:36:13.706762 INFO::Done
2024-03-02 00:36:13.709078 INFO::Acquiring quality metrics after batch effect correction.
2024-03-02 00:36:13.725507 INFO::ASW Batch was 0.214848375636839 prior to batch effect correction and is now -0.128970109202123 .
2024-03-02 00:36:13.72876 INFO::ASW Label was -0.175672320549695 prior to batch effect correction and is now 0.0735130159085898 .
2024-03-02 00:36:13.732707 INFO::Total function execution time is 0.391209125518799 s and adjustment time is 0.335390090942383 s ( 85.73 )
2024-03-02 00:36:14.116651 INFO::Formatting Data.
2024-03-02 00:36:14.118672 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:14.123106 INFO::Removing potential empty rows and columns
2024-03-02 00:36:14.126422 INFO::Found 2 missing values.
2024-03-02 00:36:14.135734 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:14.137185 INFO::Done
2024-03-02 00:36:14.237247 INFO::Found NA in Reference column
2024-03-02 00:36:14.272762 INFO::Require at least two references per batch.
2024-03-02 00:36:14.333753 INFO::Formatting Data.
2024-03-02 00:36:14.335429 INFO::Recognized SummarizedExperiment
2024-03-02 00:36:14.338196 INFO::Typecasting input to dataframe.
2024-03-02 00:36:14.367879 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:14.371916 INFO::Removing potential empty rows and columns
2024-03-02 00:36:14.384976 INFO::Found 0 missing values.
2024-03-02 00:36:14.410898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:14.412331 INFO::Done
2024-03-02 00:36:14.459171 INFO::Formatting Data.
2024-03-02 00:36:14.461098 INFO::Recognized SummarizedExperiment
2024-03-02 00:36:14.462455 INFO::Typecasting input to dataframe.
2024-03-02 00:36:14.516249 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:14.518787 INFO::Removing potential empty rows and columns
2024-03-02 00:36:14.534582 INFO::Found 0 missing values.
2024-03-02 00:36:14.578312 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:14.582214 INFO::Done
2024-03-02 00:36:14.628929 INFO::Formatting Data.
2024-03-02 00:36:14.630515 INFO::Recognized SummarizedExperiment
2024-03-02 00:36:14.631757 INFO::Typecasting input to dataframe.
2024-03-02 00:36:14.687398 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:14.690745 INFO::Removing potential empty rows and columns
2024-03-02 00:36:14.693733 INFO::Found 0 missing values.
2024-03-02 00:36:14.696086 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.
2024-03-02 00:36:14.711797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:14.713198 INFO::Done
2024-03-02 00:36:14.744205 INFO::Formatting Data.
2024-03-02 00:36:14.745955 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:14.74795 INFO::Removing potential empty rows and columns
2024-03-02 00:36:14.75021 INFO::Found 0 missing values.
2024-03-02 00:36:14.762171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:14.763533 INFO::Done
2024-03-02 00:36:14.800227 INFO::Formatting Data.
2024-03-02 00:36:14.801934 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:14.803911 INFO::Removing potential empty rows and columns
2024-03-02 00:36:14.806417 INFO::Found 0 missing values.
2024-03-02 00:36:14.815924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:14.818245 INFO::Done
2024-03-02 00:36:14.915315 INFO::Formatting Data.
2024-03-02 00:36:14.916825 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:14.919551 INFO::Removing potential empty rows and columns
2024-03-02 00:36:14.924527 INFO::Found 1 missing values.
2024-03-02 00:36:14.935087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:14.936778 INFO::Done
2024-03-02 00:36:14.996101 INFO::Formatting Data.
2024-03-02 00:36:14.998805 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:15.000883 INFO::Removing potential empty rows and columns
2024-03-02 00:36:15.005478 INFO::Found 2 missing values.
2024-03-02 00:36:15.008696 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.
2024-03-02 00:36:15.014709 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:15.016118 INFO::Done
2024-03-02 00:36:15.045603 INFO::Formatting Data.
2024-03-02 00:36:15.047143 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:15.04901 INFO::Removing potential empty rows and columns
2024-03-02 00:36:15.052645 INFO::Found 2 missing values.
2024-03-02 00:36:15.056928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:15.058352 INFO::Done
2024-03-02 00:36:15.088949 INFO::Formatting Data.
2024-03-02 00:36:15.0906 INFO::Typecasting input to dataframe.
2024-03-02 00:36:15.092741 INFO::Replacing NaNs with NAs.
2024-03-02 00:36:15.097986 INFO::Removing potential empty rows and columns
2024-03-02 00:36:15.100948 INFO::Found 0 missing values.
2024-03-02 00:36:15.112647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-02 00:36:15.113969 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.335 6.521 49.770
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 45.195 | 2.919 | 41.620 | |
| compute_asw | 0.058 | 0.003 | 0.073 | |
| count_existing | 0.028 | 0.001 | 0.036 | |
| generate_data_covariables | 0.026 | 0.002 | 0.036 | |
| generate_dataset | 0.026 | 0.003 | 0.037 | |