Yannis Schumann
| Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-24 11:41 -0400 (Wed, 24 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" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 157/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-07-23 20:06:22 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 20:06:52 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 29.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.525 0.333 6.658
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-07-23 20:06:44.868202 INFO::Formatting Data.
2024-07-23 20:06:44.869613 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:44.873517 INFO::Removing potential empty rows and columns
2024-07-23 20:06:44.973481 INFO::Found 0 missing values.
2024-07-23 20:06:44.974937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:44.97517 INFO::Done
2024-07-23 20:06:44.975383 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:44.981116 INFO::Starting hierarchical adjustment
2024-07-23 20:06:44.98139 INFO::Found 3 batches.
2024-07-23 20:06:44.981559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:44.981947 INFO::Using default BPPARAM
2024-07-23 20:06:44.982091 INFO::Processing subtree level 1
2024-07-23 20:06:45.037637 INFO::Adjusting the last 1 batches sequentially
2024-07-23 20:06:45.038754 INFO::Done
2024-07-23 20:06:45.038988 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:45.040801 INFO::ASW Batch was -0.0444600500989638 prior to batch effect correction and is now -0.0444600500989638 .
2024-07-23 20:06:45.041275 INFO::Total function execution time is 0.17339301109314 s and adjustment time is 0.057420015335083 s ( 33.12 )
2024-07-23 20:06:45.048709 INFO::Formatting Data.
2024-07-23 20:06:45.048969 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:45.049515 INFO::Removing potential empty rows and columns
2024-07-23 20:06:45.050021 INFO::Found 0 missing values.
2024-07-23 20:06:45.050573 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.
2024-07-23 20:06:45.05481 INFO::Formatting Data.
2024-07-23 20:06:45.055032 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:45.055296 INFO::Removing potential empty rows and columns
2024-07-23 20:06:45.055641 INFO::Found 0 missing values.
2024-07-23 20:06:45.055947 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.
2024-07-23 20:06:45.061943 INFO::Formatting Data.
2024-07-23 20:06:45.062148 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:45.062391 INFO::Removing potential empty rows and columns
2024-07-23 20:06:45.062679 INFO::Found 0 missing values.
2024-07-23 20:06:45.062931 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.
2024-07-23 20:06:45.064162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:45.064318 INFO::Done
2024-07-23 20:06:45.064471 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:45.065106 INFO::Starting hierarchical adjustment
2024-07-23 20:06:45.065303 INFO::Found 2 batches.
2024-07-23 20:06:45.065448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:45.0657 INFO::Using default BPPARAM
2024-07-23 20:06:45.065838 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:45.066085 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:45.074328 INFO::Done
2024-07-23 20:06:45.07453 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:45.075132 INFO::ASW Batch was 0.0391771089291765 prior to batch effect correction and is now -0.0901954447125437 .
2024-07-23 20:06:45.075361 INFO::Total function execution time is 0.0134248733520508 s and adjustment time is 0.00905585289001465 s ( 67.46 )
2024-07-23 20:06:45.076228 INFO::Formatting Data.
2024-07-23 20:06:45.076403 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:45.07906 INFO::Formatting Data.
2024-07-23 20:06:45.079242 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:45.079482 INFO::Removing potential empty rows and columns
2024-07-23 20:06:45.079765 INFO::Found 0 missing values.
2024-07-23 20:06:45.08055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:45.080699 INFO::Done
2024-07-23 20:06:45.080841 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:45.081407 INFO::Starting hierarchical adjustment
2024-07-23 20:06:45.081592 INFO::Found 2 batches.
2024-07-23 20:06:45.081728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:45.081893 INFO::Using default BPPARAM
2024-07-23 20:06:45.082028 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:45.082257 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:45.086688 INFO::Done
2024-07-23 20:06:45.08687 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:45.087423 INFO::ASW Batch was -0.00897931765505196 prior to batch effect correction and is now -0.107537451915861 .
2024-07-23 20:06:45.087651 INFO::Total function execution time is 0.0085909366607666 s and adjustment time is 0.00513219833374023 s ( 59.74 )
2024-07-23 20:06:45.087931 INFO::Formatting Data.
2024-07-23 20:06:45.088089 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:45.08831 INFO::Removing potential empty rows and columns
2024-07-23 20:06:45.088597 INFO::Found 0 missing values.
2024-07-23 20:06:45.089395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:45.089544 INFO::Done
2024-07-23 20:06:45.089683 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:45.090246 INFO::Starting hierarchical adjustment
2024-07-23 20:06:45.090448 INFO::Found 2 batches.
2024-07-23 20:06:45.090597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:45.090766 INFO::Using default BPPARAM
2024-07-23 20:06:45.090904 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:45.091145 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:45.095663 INFO::Done
2024-07-23 20:06:45.095854 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:45.096448 INFO::ASW Batch was -0.00897931765505196 prior to batch effect correction and is now -0.107537451915861 .
2024-07-23 20:06:45.096678 INFO::Total function execution time is 0.00873398780822754 s and adjustment time is 0.00524497032165527 s ( 60.05 )
2024-07-23 20:06:45.963088 INFO::Formatting Data.
2024-07-23 20:06:45.963357 INFO::Recognized SummarizedExperiment
2024-07-23 20:06:45.963516 INFO::Typecasting input to dataframe.
2024-07-23 20:06:46.278879 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.279341 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.280419 INFO::Found 0 missing values.
2024-07-23 20:06:46.282328 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.282481 INFO::Done
2024-07-23 20:06:46.282611 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.283755 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.283938 INFO::Found 2 batches.
2024-07-23 20:06:46.284061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.284383 INFO::Using default BPPARAM
2024-07-23 20:06:46.284508 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.284756 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.301283 INFO::Done
2024-07-23 20:06:46.301541 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.302706 INFO::ASW Batch was -0.0274167506107978 prior to batch effect correction and is now -0.087268073701933 .
2024-07-23 20:06:46.302969 INFO::Total function execution time is 0.339992046356201 s and adjustment time is 0.0173599720001221 s ( 5.11 )
2024-07-23 20:06:46.309038 INFO::Formatting Data.
2024-07-23 20:06:46.309294 INFO::Recognized SummarizedExperiment
2024-07-23 20:06:46.309435 INFO::Typecasting input to dataframe.
2024-07-23 20:06:46.311878 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.312176 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.313105 INFO::Found 0 missing values.
2024-07-23 20:06:46.314849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.314986 INFO::Done
2024-07-23 20:06:46.31511 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.316119 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.316291 INFO::Found 2 batches.
2024-07-23 20:06:46.316413 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.316559 INFO::Using default BPPARAM
2024-07-23 20:06:46.316677 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.316905 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.323494 INFO::Done
2024-07-23 20:06:46.323658 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.324614 INFO::ASW Batch was -0.00833349103262922 prior to batch effect correction and is now -0.00833349103262922 .
2024-07-23 20:06:46.32483 INFO::Total function execution time is 0.0158119201660156 s and adjustment time is 0.00723981857299805 s ( 45.79 )
2024-07-23 20:06:46.330296 INFO::Formatting Data.
2024-07-23 20:06:46.330471 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.330683 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.330936 INFO::Found 0 missing values.
2024-07-23 20:06:46.331641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.331767 INFO::Done
2024-07-23 20:06:46.331885 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.332365 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.332526 INFO::Found 3 batches.
2024-07-23 20:06:46.332645 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.332787 INFO::Using default BPPARAM
2024-07-23 20:06:46.332902 INFO::Processing subtree level 1
2024-07-23 20:06:46.40232 INFO::Adjusting the last 1 batches sequentially
2024-07-23 20:06:46.403344 INFO::Done
2024-07-23 20:06:46.403838 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.405015 INFO::ASW Batch was -0.132293061670686 prior to batch effect correction and is now -0.177621492542425 .
2024-07-23 20:06:46.405725 INFO::Total function execution time is 0.0753998756408691 s and adjustment time is 0.0708439350128174 s ( 93.96 )
2024-07-23 20:06:46.413396 INFO::Skipping initial DF formatting
2024-07-23 20:06:46.413635 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.415128 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.415499 INFO::Found 5 batches.
2024-07-23 20:06:46.41568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.415925 INFO::Using default BPPARAM
2024-07-23 20:06:46.416175 INFO::Processing subtree level 1
2024-07-23 20:06:46.472483 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.473847 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.483968 INFO::Done
2024-07-23 20:06:46.484251 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.486225 INFO::ASW Batch was 0.516069978114016 prior to batch effect correction and is now 0.516069978114016 .
2024-07-23 20:06:46.486422 INFO::ASW Label was 0.374417326597133 prior to batch effect correction and is now 0.374417326597133 .
2024-07-23 20:06:46.486784 INFO::Total function execution time is 0.0733909606933594 s and adjustment time is 0.0685160160064697 s ( 93.36 )
2024-07-23 20:06:46.493989 INFO::Formatting Data.
2024-07-23 20:06:46.494232 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.494512 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.494968 INFO::Found 0 missing values.
2024-07-23 20:06:46.496123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.496283 INFO::Done
2024-07-23 20:06:46.49643 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.497351 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.497572 INFO::Found 5 batches.
2024-07-23 20:06:46.497728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.497963 INFO::Using default BPPARAM
2024-07-23 20:06:46.498114 INFO::Processing subtree level 1
2024-07-23 20:06:46.540708 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.542581 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.551906 INFO::Done
2024-07-23 20:06:46.552195 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.554169 INFO::ASW Batch was 0.420601618689995 prior to batch effect correction and is now -0.0784426024080492 .
2024-07-23 20:06:46.554405 INFO::ASW Label was 0.332286666569943 prior to batch effect correction and is now 0.775608825571781 .
2024-07-23 20:06:46.555306 INFO::Total function execution time is 0.0611600875854492 s and adjustment time is 0.054358959197998 s ( 88.88 )
2024-07-23 20:06:46.555668 INFO::Formatting Data.
2024-07-23 20:06:46.555856 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.556167 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.556523 INFO::Found 0 missing values.
2024-07-23 20:06:46.557739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.557911 INFO::Done
2024-07-23 20:06:46.558072 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.558994 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.559251 INFO::Found 5 batches.
2024-07-23 20:06:46.55941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.559666 INFO::Using default BPPARAM
2024-07-23 20:06:46.559828 INFO::Processing subtree level 1
2024-07-23 20:06:46.600914 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.602897 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.611737 INFO::Done
2024-07-23 20:06:46.612052 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.613731 INFO::ASW Batch was 0.420601618689995 prior to batch effect correction and is now -0.0784426024080492 .
2024-07-23 20:06:46.614118 INFO::ASW Label was 0.332286666569943 prior to batch effect correction and is now 0.775608825571781 .
2024-07-23 20:06:46.615103 INFO::Total function execution time is 0.059237003326416 s and adjustment time is 0.0525140762329102 s ( 88.65 )
2024-07-23 20:06:46.621673 INFO::Formatting Data.
2024-07-23 20:06:46.621922 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.622214 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.622541 INFO::Found 0 missing values.
2024-07-23 20:06:46.623764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.62393 INFO::Done
2024-07-23 20:06:46.624082 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.624999 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.62521 INFO::Found 5 batches.
2024-07-23 20:06:46.625357 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.625558 INFO::Using default BPPARAM
2024-07-23 20:06:46.625702 INFO::Processing subtree level 1
2024-07-23 20:06:46.664665 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.666196 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.673902 INFO::Done
2024-07-23 20:06:46.674148 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.67546 INFO::ASW Batch was 0.371431001659905 prior to batch effect correction and is now -0.0357646172403977 .
2024-07-23 20:06:46.67565 INFO::ASW Label was 0.305342354247982 prior to batch effect correction and is now 0.737747698612009 .
2024-07-23 20:06:46.676407 INFO::Total function execution time is 0.0545608997344971 s and adjustment time is 0.0487308502197266 s ( 89.31 )
2024-07-23 20:06:46.676687 INFO::Formatting Data.
2024-07-23 20:06:46.67692 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.677178 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.677612 INFO::Found 0 missing values.
2024-07-23 20:06:46.678764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.678937 INFO::Done
2024-07-23 20:06:46.679083 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.679929 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.680141 INFO::Found 5 batches.
2024-07-23 20:06:46.680289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.680481 INFO::Using default BPPARAM
2024-07-23 20:06:46.680634 INFO::Processing subtree level 1
2024-07-23 20:06:46.719987 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.722093 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.729609 INFO::Done
2024-07-23 20:06:46.729843 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.731163 INFO::ASW Batch was 0.371431001659905 prior to batch effect correction and is now -0.0357646172403977 .
2024-07-23 20:06:46.731346 INFO::ASW Label was 0.305342354247982 prior to batch effect correction and is now 0.737747698612009 .
2024-07-23 20:06:46.732059 INFO::Total function execution time is 0.055164098739624 s and adjustment time is 0.0495059490203857 s ( 89.74 )
2024-07-23 20:06:46.738484 INFO::Formatting Data.
2024-07-23 20:06:46.738716 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.73899 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.739322 INFO::Found 0 missing values.
2024-07-23 20:06:46.740133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.740294 INFO::Done
2024-07-23 20:06:46.740447 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.741345 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.741563 INFO::Found 2 batches.
2024-07-23 20:06:46.741718 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.741921 INFO::Using default BPPARAM
2024-07-23 20:06:46.742067 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.742321 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.746919 INFO::Done
2024-07-23 20:06:46.747123 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.74798 INFO::ASW Batch was 0.634414487093525 prior to batch effect correction and is now -0.00626081786744075 .
2024-07-23 20:06:46.748153 INFO::ASW Label was 0.41115461690039 prior to batch effect correction and is now 0.896654634798914 .
2024-07-23 20:06:46.748389 INFO::Total function execution time is 0.00992512702941895 s and adjustment time is 0.00539922714233398 s ( 54.4 )
2024-07-23 20:06:46.748607 INFO::Formatting Data.
2024-07-23 20:06:46.748772 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.749004 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.74928 INFO::Found 0 missing values.
2024-07-23 20:06:46.75001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.750162 INFO::Done
2024-07-23 20:06:46.750305 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.751107 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.751312 INFO::Found 2 batches.
2024-07-23 20:06:46.751479 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.751654 INFO::Using default BPPARAM
2024-07-23 20:06:46.751792 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.752033 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.756374 INFO::Done
2024-07-23 20:06:46.756559 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.757393 INFO::ASW Batch was 0.634414487093525 prior to batch effect correction and is now -0.00626081786744075 .
2024-07-23 20:06:46.757563 INFO::ASW Label was 0.41115461690039 prior to batch effect correction and is now 0.896654634798914 .
2024-07-23 20:06:46.757789 INFO::Total function execution time is 0.00917601585388184 s and adjustment time is 0.00510001182556152 s ( 55.58 )
2024-07-23 20:06:46.763236 INFO::Formatting Data.
2024-07-23 20:06:46.763447 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.763698 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.763956 INFO::Found 0 missing values.
2024-07-23 20:06:46.764571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.764734 INFO::Done
2024-07-23 20:06:46.76489 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.76542 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.765611 INFO::Found 2 batches.
2024-07-23 20:06:46.765755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.765927 INFO::Using default BPPARAM
2024-07-23 20:06:46.766071 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.766308 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.776637 INFO::Done
2024-07-23 20:06:46.776852 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.777431 INFO::ASW Batch was -0.0339394392091776 prior to batch effect correction and is now -0.148008135299508 .
2024-07-23 20:06:46.777681 INFO::Total function execution time is 0.0144510269165039 s and adjustment time is 0.0110588073730469 s ( 76.53 )
2024-07-23 20:06:46.782316 INFO::Formatting Data.
2024-07-23 20:06:46.782551 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.782811 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.783104 INFO::Found 0 missing values.
2024-07-23 20:06:46.783496 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.
2024-07-23 20:06:46.784822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.784991 INFO::Done
2024-07-23 20:06:46.785146 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.785997 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.786202 INFO::Found 2 batches.
2024-07-23 20:06:46.786352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.786517 INFO::Using default BPPARAM
2024-07-23 20:06:46.786657 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.786968 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.79204 INFO::Done
2024-07-23 20:06:46.792232 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.793074 INFO::ASW Batch was 0.4532523245455 prior to batch effect correction and is now 0.046048215405753 .
2024-07-23 20:06:46.793246 INFO::ASW Label was 0.670859011842275 prior to batch effect correction and is now 0.929487003608404 .
2024-07-23 20:06:46.793473 INFO::Total function execution time is 0.0111770629882812 s and adjustment time is 0.0058741569519043 s ( 52.56 )
2024-07-23 20:06:46.793695 INFO::Formatting Data.
2024-07-23 20:06:46.793878 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.794136 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.794407 INFO::Found 0 missing values.
2024-07-23 20:06:46.794654 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.
2024-07-23 20:06:46.79592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.796216 INFO::Done
2024-07-23 20:06:46.79637 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.797197 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.797395 INFO::Found 2 batches.
2024-07-23 20:06:46.79754 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.79771 INFO::Using default BPPARAM
2024-07-23 20:06:46.79785 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:46.798095 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:46.803097 INFO::Done
2024-07-23 20:06:46.803302 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.804133 INFO::ASW Batch was 0.4532523245455 prior to batch effect correction and is now 0.046048215405753 .
2024-07-23 20:06:46.804302 INFO::ASW Label was 0.670859011842275 prior to batch effect correction and is now 0.929487003608404 .
2024-07-23 20:06:46.804544 INFO::Total function execution time is 0.010847806930542 s and adjustment time is 0.00573492050170898 s ( 52.87 )
2024-07-23 20:06:46.86947 INFO::Formatting Data.
2024-07-23 20:06:46.869747 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.870026 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.87034 INFO::Found 0 missing values.
2024-07-23 20:06:46.871232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.871397 INFO::Done
2024-07-23 20:06:46.871543 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.872179 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.872386 INFO::Found 3 batches.
2024-07-23 20:06:46.872532 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.872706 INFO::Using default BPPARAM
2024-07-23 20:06:46.872846 INFO::Processing subtree level 1
2024-07-23 20:06:46.910002 INFO::Adjusting the last 1 batches sequentially
2024-07-23 20:06:46.911109 INFO::Done
2024-07-23 20:06:46.911309 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.913028 INFO::ASW Batch was -0.100811956498918 prior to batch effect correction and is now -0.100811956498918 .
2024-07-23 20:06:46.913665 INFO::Total function execution time is 0.0441989898681641 s and adjustment time is 0.0387668609619141 s ( 87.71 )
2024-07-23 20:06:46.914222 INFO::Formatting Data.
2024-07-23 20:06:46.914411 INFO::Typecasting input to dataframe.
2024-07-23 20:06:46.914622 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.914928 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.915466 INFO::Found 0 missing values.
2024-07-23 20:06:46.916427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.916599 INFO::Done
2024-07-23 20:06:46.916753 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.917391 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.917622 INFO::Found 3 batches.
2024-07-23 20:06:46.917779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.918013 INFO::Using default BPPARAM
2024-07-23 20:06:46.918157 INFO::Processing subtree level 1
2024-07-23 20:06:46.960334 INFO::Adjusting the last 1 batches sequentially
2024-07-23 20:06:46.961402 INFO::Done
2024-07-23 20:06:46.961608 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:46.963155 INFO::ASW Batch was -0.100811956498918 prior to batch effect correction and is now -0.100811956498918 .
2024-07-23 20:06:46.96356 INFO::Total function execution time is 0.0493199825286865 s and adjustment time is 0.043828010559082 s ( 88.86 )
2024-07-23 20:06:46.970328 INFO::Formatting Data.
2024-07-23 20:06:46.970567 INFO::Typecasting input to dataframe.
2024-07-23 20:06:46.970839 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:46.971135 INFO::Removing potential empty rows and columns
2024-07-23 20:06:46.971709 INFO::Found 0 missing values.
2024-07-23 20:06:46.972628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:46.9728 INFO::Done
2024-07-23 20:06:46.972959 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:46.973611 INFO::Starting hierarchical adjustment
2024-07-23 20:06:46.973819 INFO::Found 3 batches.
2024-07-23 20:06:46.973974 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:46.974178 INFO::Using default BPPARAM
2024-07-23 20:06:46.974328 INFO::Processing subtree level 1
2024-07-23 20:06:47.012785 INFO::Adjusting the last 1 batches sequentially
2024-07-23 20:06:47.013905 INFO::Done
2024-07-23 20:06:47.014104 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:47.015688 INFO::ASW Batch was -0.0610746228678352 prior to batch effect correction and is now -0.0610746228678352 .
2024-07-23 20:06:47.016077 INFO::Total function execution time is 0.0457510948181152 s and adjustment time is 0.0401289463043213 s ( 87.71 )
2024-07-23 20:06:47.080896 INFO::Formatting Data.
2024-07-23 20:06:47.081201 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:47.081569 INFO::Removing potential empty rows and columns
2024-07-23 20:06:47.082617 INFO::Found 1000 missing values.
2024-07-23 20:06:47.088234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:47.088448 INFO::Done
2024-07-23 20:06:47.088626 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:47.090514 INFO::Starting hierarchical adjustment
2024-07-23 20:06:47.090753 INFO::Found 10 batches.
2024-07-23 20:06:47.090918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:47.091147 INFO::Using default BPPARAM
2024-07-23 20:06:47.091308 INFO::Processing subtree level 1
2024-07-23 20:06:47.135437 INFO::Processing subtree level 2
2024-07-23 20:06:47.187807 INFO::Adjusting the last 1 batches sequentially
2024-07-23 20:06:47.189109 INFO::Done
2024-07-23 20:06:47.189424 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:47.192069 INFO::ASW Batch was 0.499350721803009 prior to batch effect correction and is now 0.499350721803009 .
2024-07-23 20:06:47.192374 INFO::ASW Label was 0.341457294190996 prior to batch effect correction and is now 0.341457294190996 .
2024-07-23 20:06:47.192744 INFO::Total function execution time is 0.11185097694397 s and adjustment time is 0.0984010696411133 s ( 87.98 )
2024-07-23 20:06:47.193036 INFO::Formatting Data.
2024-07-23 20:06:47.193235 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:47.193632 INFO::Removing potential empty rows and columns
2024-07-23 20:06:47.194733 INFO::Found 1000 missing values.
2024-07-23 20:06:47.200593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:47.20079 INFO::Done
2024-07-23 20:06:47.200951 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:47.202803 INFO::Starting hierarchical adjustment
2024-07-23 20:06:47.203039 INFO::Found 10 batches.
2024-07-23 20:06:47.618566 INFO::Set up parallel execution backend with 2 workers
2024-07-23 20:06:47.618846 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-23 20:06:48.164112 INFO::Adjusting the last 2 batches sequentially
2024-07-23 20:06:48.164729 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 20:06:48.170698 INFO::Done
2024-07-23 20:06:48.170961 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:48.172883 INFO::ASW Batch was 0.499350721803009 prior to batch effect correction and is now 0.499350721803009 .
2024-07-23 20:06:48.173064 INFO::ASW Label was 0.341457294190996 prior to batch effect correction and is now 0.341457294190996 .
2024-07-23 20:06:48.173303 INFO::Total function execution time is 0.980269908905029 s and adjustment time is 0.967689990997314 s ( 98.72 )
2024-07-23 20:06:48.233439 INFO::Formatting Data.
2024-07-23 20:06:48.233695 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.234017 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.234416 INFO::Found 0 missing values.
2024-07-23 20:06:48.235629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.235801 INFO::Done
2024-07-23 20:06:48.235968 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 20:06:48.236846 INFO::Starting hierarchical adjustment
2024-07-23 20:06:48.237232 INFO::Found 3 batches.
2024-07-23 20:06:48.237392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 20:06:48.237592 INFO::Using default BPPARAM
2024-07-23 20:06:48.237753 INFO::Processing subtree level 1
2024-07-23 20:06:48.282461 INFO::Adjusting the last 1 batches sequentially
2024-07-23 20:06:48.283698 INFO::Done
2024-07-23 20:06:48.283912 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 20:06:48.286075 INFO::ASW Batch was 0.144572316633418 prior to batch effect correction and is now -0.164485439229311 .
2024-07-23 20:06:48.286301 INFO::ASW Label was -0.173219633030822 prior to batch effect correction and is now -0.0613229989813075 .
2024-07-23 20:06:48.28701 INFO::Total function execution time is 0.0535640716552734 s and adjustment time is 0.0465018749237061 s ( 86.82 )
2024-07-23 20:06:48.334232 INFO::Formatting Data.
2024-07-23 20:06:48.334585 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.334924 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.335341 INFO::Found 2 missing values.
2024-07-23 20:06:48.336355 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.336541 INFO::Done
2024-07-23 20:06:48.347216 INFO::Found NA in Reference column
2024-07-23 20:06:48.350921 INFO::Require at least two references per batch.
2024-07-23 20:06:48.359135 INFO::Formatting Data.
2024-07-23 20:06:48.359398 INFO::Recognized SummarizedExperiment
2024-07-23 20:06:48.359585 INFO::Typecasting input to dataframe.
2024-07-23 20:06:48.364053 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.364521 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.365958 INFO::Found 0 missing values.
2024-07-23 20:06:48.368693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.368907 INFO::Done
2024-07-23 20:06:48.374675 INFO::Formatting Data.
2024-07-23 20:06:48.374926 INFO::Recognized SummarizedExperiment
2024-07-23 20:06:48.375118 INFO::Typecasting input to dataframe.
2024-07-23 20:06:48.381832 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.382293 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.383479 INFO::Found 0 missing values.
2024-07-23 20:06:48.387194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.387396 INFO::Done
2024-07-23 20:06:48.392453 INFO::Formatting Data.
2024-07-23 20:06:48.392672 INFO::Recognized SummarizedExperiment
2024-07-23 20:06:48.39298 INFO::Typecasting input to dataframe.
2024-07-23 20:06:48.398062 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.398408 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.398769 INFO::Found 0 missing values.
2024-07-23 20:06:48.399054 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.
2024-07-23 20:06:48.400417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.400595 INFO::Done
2024-07-23 20:06:48.404577 INFO::Formatting Data.
2024-07-23 20:06:48.404821 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.405092 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.405402 INFO::Found 0 missing values.
2024-07-23 20:06:48.406303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.406473 INFO::Done
2024-07-23 20:06:48.410481 INFO::Formatting Data.
2024-07-23 20:06:48.410713 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.410973 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.411274 INFO::Found 0 missing values.
2024-07-23 20:06:48.412183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.41234 INFO::Done
2024-07-23 20:06:48.422788 INFO::Formatting Data.
2024-07-23 20:06:48.423071 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.423407 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.423816 INFO::Found 1 missing values.
2024-07-23 20:06:48.424969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.425195 INFO::Done
2024-07-23 20:06:48.432045 INFO::Formatting Data.
2024-07-23 20:06:48.432334 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.432639 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.43298 INFO::Found 2 missing values.
2024-07-23 20:06:48.433312 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.
2024-07-23 20:06:48.434247 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.434463 INFO::Done
2024-07-23 20:06:48.438251 INFO::Formatting Data.
2024-07-23 20:06:48.438477 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.43873 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.439019 INFO::Found 2 missing values.
2024-07-23 20:06:48.439499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.43965 INFO::Done
2024-07-23 20:06:48.443215 INFO::Formatting Data.
2024-07-23 20:06:48.443448 INFO::Typecasting input to dataframe.
2024-07-23 20:06:48.44372 INFO::Replacing NaNs with NAs.
2024-07-23 20:06:48.443988 INFO::Removing potential empty rows and columns
2024-07-23 20:06:48.444406 INFO::Found 0 missing values.
2024-07-23 20:06:48.445315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 20:06:48.445485 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.801 1.294 8.250
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.525 | 0.333 | 6.658 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.005 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |