Yannis Schumann
| Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (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 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-06-24 12:13:32 -0400 (Mon, 24 Jun 2024) |
| EndedAt: 2024-06-24 12:14:50 -0400 (Mon, 24 Jun 2024) |
| EllapsedTime: 78.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 29.098 1.13 20.526
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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")
2024-06-24 12:14:30.340131 INFO::Formatting Data.
2024-06-24 12:14:30.344487 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:30.357149 INFO::Removing potential empty rows and columns
2024-06-24 12:14:30.667075 INFO::Found 0 missing values.
2024-06-24 12:14:30.670808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:30.671459 INFO::Done
2024-06-24 12:14:30.67199 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:30.688413 INFO::Starting hierarchical adjustment
2024-06-24 12:14:30.689372 INFO::Found 3 batches.
2024-06-24 12:14:30.689916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:30.691209 INFO::Using default BPPARAM
2024-06-24 12:14:30.691701 INFO::Processing subtree level 1
2024-06-24 12:14:30.808806 INFO::Adjusting the last 1 batches sequentially
2024-06-24 12:14:30.812988 INFO::Done
2024-06-24 12:14:30.814161 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:30.820974 INFO::ASW Batch was -0.082735753375698 prior to batch effect correction and is now -0.082735753375698 .
2024-06-24 12:14:30.823377 INFO::Total function execution time is 0.484048128128052 s and adjustment time is 0.123682022094727 s ( 25.55 )
2024-06-24 12:14:30.841751 INFO::Formatting Data.
2024-06-24 12:14:30.842754 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:30.843911 INFO::Removing potential empty rows and columns
2024-06-24 12:14:30.84521 INFO::Found 0 missing values.
2024-06-24 12:14:30.846262 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.
2024-06-24 12:14:30.859432 INFO::Formatting Data.
2024-06-24 12:14:30.860256 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:30.861143 INFO::Removing potential empty rows and columns
2024-06-24 12:14:30.862683 INFO::Found 0 missing values.
2024-06-24 12:14:30.863671 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.
2024-06-24 12:14:30.882818 INFO::Formatting Data.
2024-06-24 12:14:30.883678 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:30.884562 INFO::Removing potential empty rows and columns
2024-06-24 12:14:30.885564 INFO::Found 0 missing values.
2024-06-24 12:14:30.886423 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.
2024-06-24 12:14:30.890458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:30.891029 INFO::Done
2024-06-24 12:14:30.891521 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:30.893619 INFO::Starting hierarchical adjustment
2024-06-24 12:14:30.894274 INFO::Found 2 batches.
2024-06-24 12:14:30.894771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:30.895489 INFO::Using default BPPARAM
2024-06-24 12:14:30.89594 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:30.896764 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:30.921194 INFO::Done
2024-06-24 12:14:30.921988 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:30.924044 INFO::ASW Batch was -0.0495890449523528 prior to batch effect correction and is now -0.125480827271567 .
2024-06-24 12:14:30.924814 INFO::Total function execution time is 0.0421609878540039 s and adjustment time is 0.0269858837127686 s ( 64.01 )
2024-06-24 12:14:30.927899 INFO::Formatting Data.
2024-06-24 12:14:30.928508 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:30.937713 INFO::Formatting Data.
2024-06-24 12:14:30.938484 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:30.93932 INFO::Removing potential empty rows and columns
2024-06-24 12:14:30.940298 INFO::Found 0 missing values.
2024-06-24 12:14:30.942996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:30.943569 INFO::Done
2024-06-24 12:14:30.944017 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:30.946255 INFO::Starting hierarchical adjustment
2024-06-24 12:14:30.946905 INFO::Found 2 batches.
2024-06-24 12:14:30.947346 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:30.947886 INFO::Using default BPPARAM
2024-06-24 12:14:30.948318 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:30.949078 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:30.964523 INFO::Done
2024-06-24 12:14:30.965269 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:30.967343 INFO::ASW Batch was -0.0148697362925337 prior to batch effect correction and is now -0.0782198446448627 .
2024-06-24 12:14:30.968138 INFO::Total function execution time is 0.0304980278015137 s and adjustment time is 0.0177178382873535 s ( 58.1 )
2024-06-24 12:14:30.969113 INFO::Formatting Data.
2024-06-24 12:14:30.969626 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:30.970419 INFO::Removing potential empty rows and columns
2024-06-24 12:14:30.971402 INFO::Found 0 missing values.
2024-06-24 12:14:30.973938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:30.974527 INFO::Done
2024-06-24 12:14:30.974978 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:30.976948 INFO::Starting hierarchical adjustment
2024-06-24 12:14:30.977607 INFO::Found 2 batches.
2024-06-24 12:14:30.978075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:30.97863 INFO::Using default BPPARAM
2024-06-24 12:14:30.979068 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:30.979837 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:30.995103 INFO::Done
2024-06-24 12:14:30.995817 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:30.997812 INFO::ASW Batch was -0.0148697362925337 prior to batch effect correction and is now -0.0782198446448627 .
2024-06-24 12:14:30.99858 INFO::Total function execution time is 0.02944016456604 s and adjustment time is 0.0176069736480713 s ( 59.81 )
2024-06-24 12:14:33.631211 INFO::Formatting Data.
2024-06-24 12:14:33.632049 INFO::Recognized SummarizedExperiment
2024-06-24 12:14:33.632511 INFO::Typecasting input to dataframe.
2024-06-24 12:14:34.393151 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:34.394373 INFO::Removing potential empty rows and columns
2024-06-24 12:14:34.397436 INFO::Found 0 missing values.
2024-06-24 12:14:34.403198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:34.4038 INFO::Done
2024-06-24 12:14:34.40423 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:34.407675 INFO::Starting hierarchical adjustment
2024-06-24 12:14:34.408332 INFO::Found 2 batches.
2024-06-24 12:14:34.408732 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:34.409727 INFO::Using default BPPARAM
2024-06-24 12:14:34.410132 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:34.410955 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:34.442524 INFO::Done
2024-06-24 12:14:34.443246 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:34.44689 INFO::ASW Batch was 0.00147468135692957 prior to batch effect correction and is now -0.0953514039120283 .
2024-06-24 12:14:34.447712 INFO::Total function execution time is 0.816857099533081 s and adjustment time is 0.0342631340026855 s ( 4.19 )
2024-06-24 12:14:34.460774 INFO::Formatting Data.
2024-06-24 12:14:34.461301 INFO::Recognized SummarizedExperiment
2024-06-24 12:14:34.461517 INFO::Typecasting input to dataframe.
2024-06-24 12:14:34.466078 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:34.466899 INFO::Removing potential empty rows and columns
2024-06-24 12:14:34.468695 INFO::Found 0 missing values.
2024-06-24 12:14:34.472152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:34.472606 INFO::Done
2024-06-24 12:14:34.47283 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:34.474718 INFO::Starting hierarchical adjustment
2024-06-24 12:14:34.475173 INFO::Found 2 batches.
2024-06-24 12:14:34.475363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:34.475597 INFO::Using default BPPARAM
2024-06-24 12:14:34.475751 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:34.476211 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:34.487101 INFO::Done
2024-06-24 12:14:34.487591 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:34.489249 INFO::ASW Batch was 0.0265362469649419 prior to batch effect correction and is now 0.0265362469649419 .
2024-06-24 12:14:34.489684 INFO::Total function execution time is 0.0289831161499023 s and adjustment time is 0.0119290351867676 s ( 41.16 )
2024-06-24 12:14:34.500523 INFO::Formatting Data.
2024-06-24 12:14:34.501296 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:34.502065 INFO::Removing potential empty rows and columns
2024-06-24 12:14:34.502689 INFO::Found 0 missing values.
2024-06-24 12:14:34.504083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:34.504677 INFO::Done
2024-06-24 12:14:34.505257 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:34.507072 INFO::Starting hierarchical adjustment
2024-06-24 12:14:34.507596 INFO::Found 3 batches.
2024-06-24 12:14:34.507813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:34.508031 INFO::Using default BPPARAM
2024-06-24 12:14:34.508208 INFO::Processing subtree level 1
2024-06-24 12:14:34.64921 INFO::Adjusting the last 1 batches sequentially
2024-06-24 12:14:34.651855 INFO::Done
2024-06-24 12:14:34.652503 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:34.656241 INFO::ASW Batch was -0.0578670190626277 prior to batch effect correction and is now -0.164065032487032 .
2024-06-24 12:14:34.657199 INFO::Total function execution time is 0.156538009643555 s and adjustment time is 0.144330024719238 s ( 92.2 )
2024-06-24 12:14:34.667373 INFO::Skipping initial DF formatting
2024-06-24 12:14:34.66787 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:34.67021 INFO::Starting hierarchical adjustment
2024-06-24 12:14:34.670727 INFO::Found 5 batches.
2024-06-24 12:14:34.670972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:34.671276 INFO::Using default BPPARAM
2024-06-24 12:14:34.671508 INFO::Processing subtree level 1
2024-06-24 12:14:34.78455 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:34.787179 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:34.809387 INFO::Done
2024-06-24 12:14:34.810011 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:34.813322 INFO::ASW Batch was 0.589352321232251 prior to batch effect correction and is now 0.589352321232251 .
2024-06-24 12:14:34.81378 INFO::ASW Label was 0.394787031882691 prior to batch effect correction and is now 0.394787031882691 .
2024-06-24 12:14:34.814498 INFO::Total function execution time is 0.147197008132935 s and adjustment time is 0.138700008392334 s ( 94.23 )
2024-06-24 12:14:34.829714 INFO::Formatting Data.
2024-06-24 12:14:34.83024 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:34.830734 INFO::Removing potential empty rows and columns
2024-06-24 12:14:34.831315 INFO::Found 0 missing values.
2024-06-24 12:14:34.833047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:34.833302 INFO::Done
2024-06-24 12:14:34.833524 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:34.834951 INFO::Starting hierarchical adjustment
2024-06-24 12:14:34.835389 INFO::Found 5 batches.
2024-06-24 12:14:34.835585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:34.83594 INFO::Using default BPPARAM
2024-06-24 12:14:34.83614 INFO::Processing subtree level 1
2024-06-24 12:14:34.941611 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:34.947612 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:34.965744 INFO::Done
2024-06-24 12:14:34.966278 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:34.969119 INFO::ASW Batch was 0.229087703308152 prior to batch effect correction and is now 0.0459481751484796 .
2024-06-24 12:14:34.969517 INFO::ASW Label was 0.413282819707543 prior to batch effect correction and is now 0.663089231963153 .
2024-06-24 12:14:34.970909 INFO::Total function execution time is 0.14099383354187 s and adjustment time is 0.130404949188232 s ( 92.49 )
2024-06-24 12:14:34.971452 INFO::Formatting Data.
2024-06-24 12:14:34.971687 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:34.972105 INFO::Removing potential empty rows and columns
2024-06-24 12:14:34.972636 INFO::Found 0 missing values.
2024-06-24 12:14:34.974622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:34.974894 INFO::Done
2024-06-24 12:14:34.975086 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:34.976314 INFO::Starting hierarchical adjustment
2024-06-24 12:14:34.976663 INFO::Found 5 batches.
2024-06-24 12:14:34.97687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:34.977192 INFO::Using default BPPARAM
2024-06-24 12:14:34.977398 INFO::Processing subtree level 1
2024-06-24 12:14:35.059214 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:35.062906 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:35.083094 INFO::Done
2024-06-24 12:14:35.083936 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:35.086315 INFO::ASW Batch was 0.229087703308152 prior to batch effect correction and is now 0.0459481751484796 .
2024-06-24 12:14:35.086943 INFO::ASW Label was 0.413282819707543 prior to batch effect correction and is now 0.663089231963153 .
2024-06-24 12:14:35.087883 INFO::Total function execution time is 0.116155862808228 s and adjustment time is 0.10644006729126 s ( 91.64 )
2024-06-24 12:14:35.100772 INFO::Formatting Data.
2024-06-24 12:14:35.101565 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:35.102444 INFO::Removing potential empty rows and columns
2024-06-24 12:14:35.103435 INFO::Found 0 missing values.
2024-06-24 12:14:35.106168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:35.106494 INFO::Done
2024-06-24 12:14:35.106716 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:35.108267 INFO::Starting hierarchical adjustment
2024-06-24 12:14:35.108642 INFO::Found 5 batches.
2024-06-24 12:14:35.108855 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:35.109151 INFO::Using default BPPARAM
2024-06-24 12:14:35.10936 INFO::Processing subtree level 1
2024-06-24 12:14:35.199836 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:35.207183 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:35.232258 INFO::Done
2024-06-24 12:14:35.233028 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:35.237864 INFO::ASW Batch was 0.34344022986479 prior to batch effect correction and is now -0.108044137643097 .
2024-06-24 12:14:35.238498 INFO::ASW Label was 0.417375147815273 prior to batch effect correction and is now 0.817566820621632 .
2024-06-24 12:14:35.240528 INFO::Total function execution time is 0.139515161514282 s and adjustment time is 0.123599052429199 s ( 88.59 )
2024-06-24 12:14:35.241418 INFO::Formatting Data.
2024-06-24 12:14:35.241959 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:35.242789 INFO::Removing potential empty rows and columns
2024-06-24 12:14:35.243716 INFO::Found 0 missing values.
2024-06-24 12:14:35.247652 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:35.248213 INFO::Done
2024-06-24 12:14:35.248695 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:35.251937 INFO::Starting hierarchical adjustment
2024-06-24 12:14:35.252651 INFO::Found 5 batches.
2024-06-24 12:14:35.253117 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:35.253704 INFO::Using default BPPARAM
2024-06-24 12:14:35.254147 INFO::Processing subtree level 1
2024-06-24 12:14:35.376991 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:35.380323 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:35.404039 INFO::Done
2024-06-24 12:14:35.40498 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:35.409232 INFO::ASW Batch was 0.34344022986479 prior to batch effect correction and is now -0.108044137643097 .
2024-06-24 12:14:35.40992 INFO::ASW Label was 0.417375147815273 prior to batch effect correction and is now 0.817566820621632 .
2024-06-24 12:14:35.411231 INFO::Total function execution time is 0.169705867767334 s and adjustment time is 0.151462078094482 s ( 89.25 )
2024-06-24 12:14:35.430172 INFO::Formatting Data.
2024-06-24 12:14:35.431038 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:35.431995 INFO::Removing potential empty rows and columns
2024-06-24 12:14:35.433115 INFO::Found 0 missing values.
2024-06-24 12:14:35.436165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:35.436857 INFO::Done
2024-06-24 12:14:35.437352 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:35.44045 INFO::Starting hierarchical adjustment
2024-06-24 12:14:35.441284 INFO::Found 2 batches.
2024-06-24 12:14:35.441831 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:35.442485 INFO::Using default BPPARAM
2024-06-24 12:14:35.442985 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:35.44386 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:35.458939 INFO::Done
2024-06-24 12:14:35.459749 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:35.46267 INFO::ASW Batch was 0.701568411253285 prior to batch effect correction and is now -0.0256630568958733 .
2024-06-24 12:14:35.463408 INFO::ASW Label was 0.311009614454255 prior to batch effect correction and is now 0.879097742145719 .
2024-06-24 12:14:35.464182 INFO::Total function execution time is 0.0341720581054688 s and adjustment time is 0.0177600383758545 s ( 51.97 )
2024-06-24 12:14:35.464903 INFO::Formatting Data.
2024-06-24 12:14:35.465526 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:35.466345 INFO::Removing potential empty rows and columns
2024-06-24 12:14:35.467185 INFO::Found 0 missing values.
2024-06-24 12:14:35.469592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:35.470127 INFO::Done
2024-06-24 12:14:35.470584 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:35.473271 INFO::Starting hierarchical adjustment
2024-06-24 12:14:35.474436 INFO::Found 2 batches.
2024-06-24 12:14:35.474902 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:35.47546 INFO::Using default BPPARAM
2024-06-24 12:14:35.475902 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:35.476738 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:35.493349 INFO::Done
2024-06-24 12:14:35.494207 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:35.497339 INFO::ASW Batch was 0.701568411253285 prior to batch effect correction and is now -0.0256630568958733 .
2024-06-24 12:14:35.497946 INFO::ASW Label was 0.311009614454255 prior to batch effect correction and is now 0.879097742145719 .
2024-06-24 12:14:35.498698 INFO::Total function execution time is 0.0337550640106201 s and adjustment time is 0.019010066986084 s ( 56.32 )
2024-06-24 12:14:35.512009 INFO::Formatting Data.
2024-06-24 12:14:35.512804 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:35.513631 INFO::Removing potential empty rows and columns
2024-06-24 12:14:35.51447 INFO::Found 0 missing values.
2024-06-24 12:14:35.516388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:35.51689 INFO::Done
2024-06-24 12:14:35.517349 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:35.51928 INFO::Starting hierarchical adjustment
2024-06-24 12:14:35.519914 INFO::Found 2 batches.
2024-06-24 12:14:35.520362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:35.520884 INFO::Using default BPPARAM
2024-06-24 12:14:35.521308 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:35.522052 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:35.558129 INFO::Done
2024-06-24 12:14:35.558944 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:35.561048 INFO::ASW Batch was 0.00310870611972771 prior to batch effect correction and is now -0.156643990227963 .
2024-06-24 12:14:35.561858 INFO::Total function execution time is 0.0499958992004395 s and adjustment time is 0.0382890701293945 s ( 76.58 )
2024-06-24 12:14:35.57706 INFO::Formatting Data.
2024-06-24 12:14:35.577926 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:35.579009 INFO::Removing potential empty rows and columns
2024-06-24 12:14:35.580007 INFO::Found 0 missing values.
2024-06-24 12:14:35.581388 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.
2024-06-24 12:14:35.586127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:35.586813 INFO::Done
2024-06-24 12:14:35.587328 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:35.590552 INFO::Starting hierarchical adjustment
2024-06-24 12:14:35.591293 INFO::Found 2 batches.
2024-06-24 12:14:35.591799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:35.592363 INFO::Using default BPPARAM
2024-06-24 12:14:35.592838 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:35.59373 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:35.610578 INFO::Done
2024-06-24 12:14:35.611418 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:35.614574 INFO::ASW Batch was 0.41915477660232 prior to batch effect correction and is now -0.0375252084559879 .
2024-06-24 12:14:35.615187 INFO::ASW Label was 0.658943229928883 prior to batch effect correction and is now 0.958106595188736 .
2024-06-24 12:14:35.615982 INFO::Total function execution time is 0.0390658378601074 s and adjustment time is 0.0193760395050049 s ( 49.6 )
2024-06-24 12:14:35.61685 INFO::Formatting Data.
2024-06-24 12:14:35.617401 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:35.618263 INFO::Removing potential empty rows and columns
2024-06-24 12:14:35.61951 INFO::Found 0 missing values.
2024-06-24 12:14:35.620355 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.
2024-06-24 12:14:35.624788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:35.625445 INFO::Done
2024-06-24 12:14:35.625944 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:35.628733 INFO::Starting hierarchical adjustment
2024-06-24 12:14:35.629411 INFO::Found 2 batches.
2024-06-24 12:14:35.629867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:35.630435 INFO::Using default BPPARAM
2024-06-24 12:14:35.630865 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:35.63169 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:35.648466 INFO::Done
2024-06-24 12:14:35.649245 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:35.652242 INFO::ASW Batch was 0.41915477660232 prior to batch effect correction and is now -0.0375252084559879 .
2024-06-24 12:14:35.652877 INFO::ASW Label was 0.658943229928883 prior to batch effect correction and is now 0.958106595188736 .
2024-06-24 12:14:35.653643 INFO::Total function execution time is 0.0367841720581055 s and adjustment time is 0.0191080570220947 s ( 51.95 )
2024-06-24 12:14:35.877489 INFO::Formatting Data.
2024-06-24 12:14:35.878317 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:35.879189 INFO::Removing potential empty rows and columns
2024-06-24 12:14:35.880147 INFO::Found 0 missing values.
2024-06-24 12:14:35.882801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:35.883318 INFO::Done
2024-06-24 12:14:35.883793 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:35.885804 INFO::Starting hierarchical adjustment
2024-06-24 12:14:35.886497 INFO::Found 3 batches.
2024-06-24 12:14:35.887031 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:35.887584 INFO::Using default BPPARAM
2024-06-24 12:14:35.888017 INFO::Processing subtree level 1
2024-06-24 12:14:35.995882 INFO::Adjusting the last 1 batches sequentially
2024-06-24 12:14:36.000018 INFO::Done
2024-06-24 12:14:36.000991 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:36.008441 INFO::ASW Batch was -0.019976757375728 prior to batch effect correction and is now -0.019976757375728 .
2024-06-24 12:14:36.011059 INFO::Total function execution time is 0.133299112319946 s and adjustment time is 0.113646984100342 s ( 85.26 )
2024-06-24 12:14:36.012177 INFO::Formatting Data.
2024-06-24 12:14:36.012781 INFO::Typecasting input to dataframe.
2024-06-24 12:14:36.013472 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:36.014389 INFO::Removing potential empty rows and columns
2024-06-24 12:14:36.015475 INFO::Found 0 missing values.
2024-06-24 12:14:36.018223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:36.019154 INFO::Done
2024-06-24 12:14:36.019655 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:36.02164 INFO::Starting hierarchical adjustment
2024-06-24 12:14:36.022299 INFO::Found 3 batches.
2024-06-24 12:14:36.022732 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:36.023401 INFO::Using default BPPARAM
2024-06-24 12:14:36.023857 INFO::Processing subtree level 1
2024-06-24 12:14:36.130833 INFO::Adjusting the last 1 batches sequentially
2024-06-24 12:14:36.134433 INFO::Done
2024-06-24 12:14:36.135491 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:36.142162 INFO::ASW Batch was -0.019976757375728 prior to batch effect correction and is now -0.019976757375728 .
2024-06-24 12:14:36.144366 INFO::Total function execution time is 0.132111072540283 s and adjustment time is 0.112246990203857 s ( 84.96 )
2024-06-24 12:14:36.160802 INFO::Formatting Data.
2024-06-24 12:14:36.161604 INFO::Typecasting input to dataframe.
2024-06-24 12:14:36.162375 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:36.163263 INFO::Removing potential empty rows and columns
2024-06-24 12:14:36.164652 INFO::Found 0 missing values.
2024-06-24 12:14:36.167394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:36.167969 INFO::Done
2024-06-24 12:14:36.168451 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:36.170399 INFO::Starting hierarchical adjustment
2024-06-24 12:14:36.171035 INFO::Found 3 batches.
2024-06-24 12:14:36.171491 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:36.172087 INFO::Using default BPPARAM
2024-06-24 12:14:36.17254 INFO::Processing subtree level 1
2024-06-24 12:14:36.271153 INFO::Adjusting the last 1 batches sequentially
2024-06-24 12:14:36.2744 INFO::Done
2024-06-24 12:14:36.274937 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:36.282358 INFO::ASW Batch was -0.123904352981755 prior to batch effect correction and is now -0.123904352981755 .
2024-06-24 12:14:36.285913 INFO::Total function execution time is 0.124470949172974 s and adjustment time is 0.103485822677612 s ( 83.14 )
2024-06-24 12:14:36.45876 INFO::Formatting Data.
2024-06-24 12:14:36.459684 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:36.460775 INFO::Removing potential empty rows and columns
2024-06-24 12:14:36.484787 INFO::Found 1000 missing values.
2024-06-24 12:14:36.503104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:36.504345 INFO::Done
2024-06-24 12:14:36.504855 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:36.510973 INFO::Starting hierarchical adjustment
2024-06-24 12:14:36.511812 INFO::Found 10 batches.
2024-06-24 12:14:36.512977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:36.514583 INFO::Using default BPPARAM
2024-06-24 12:14:36.515295 INFO::Processing subtree level 1
2024-06-24 12:14:36.650839 INFO::Processing subtree level 2
2024-06-24 12:14:36.801275 INFO::Adjusting the last 1 batches sequentially
2024-06-24 12:14:36.804509 INFO::Done
2024-06-24 12:14:36.805228 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:36.812837 INFO::ASW Batch was 0.512710184831786 prior to batch effect correction and is now 0.512710184831786 .
2024-06-24 12:14:36.813598 INFO::ASW Label was 0.325363778268668 prior to batch effect correction and is now 0.325363778268668 .
2024-06-24 12:14:36.814884 INFO::Total function execution time is 0.35616397857666 s and adjustment time is 0.292840957641602 s ( 82.22 )
2024-06-24 12:14:36.815783 INFO::Formatting Data.
2024-06-24 12:14:36.81635 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:36.8176 INFO::Removing potential empty rows and columns
2024-06-24 12:14:36.820441 INFO::Found 1000 missing values.
2024-06-24 12:14:36.838014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:36.838873 INFO::Done
2024-06-24 12:14:36.839399 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:36.845855 INFO::Starting hierarchical adjustment
2024-06-24 12:14:36.846916 INFO::Found 10 batches.
2024-06-24 12:14:38.133848 INFO::Set up parallel execution backend with 2 workers
2024-06-24 12:14:38.134781 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-24 12:14:39.273944 INFO::Adjusting the last 2 batches sequentially
2024-06-24 12:14:39.275704 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 12:14:39.293131 INFO::Done
2024-06-24 12:14:39.293957 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:39.299768 INFO::ASW Batch was 0.512710184831786 prior to batch effect correction and is now 0.512710184831786 .
2024-06-24 12:14:39.300386 INFO::ASW Label was 0.325363778268668 prior to batch effect correction and is now 0.325363778268668 .
2024-06-24 12:14:39.301132 INFO::Total function execution time is 2.485347032547 s and adjustment time is 2.44637393951416 s ( 98.43 )
2024-06-24 12:14:39.4973 INFO::Formatting Data.
2024-06-24 12:14:39.498348 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:39.499425 INFO::Removing potential empty rows and columns
2024-06-24 12:14:39.500876 INFO::Found 0 missing values.
2024-06-24 12:14:39.505096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:39.505821 INFO::Done
2024-06-24 12:14:39.506414 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 12:14:39.509566 INFO::Starting hierarchical adjustment
2024-06-24 12:14:39.510424 INFO::Found 3 batches.
2024-06-24 12:14:39.510928 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 12:14:39.51171 INFO::Using default BPPARAM
2024-06-24 12:14:39.512251 INFO::Processing subtree level 1
2024-06-24 12:14:39.670943 INFO::Adjusting the last 1 batches sequentially
2024-06-24 12:14:39.674781 INFO::Done
2024-06-24 12:14:39.676055 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 12:14:39.684495 INFO::ASW Batch was 0.168654340211262 prior to batch effect correction and is now -0.110806909787685 .
2024-06-24 12:14:39.685353 INFO::ASW Label was -0.204861625565911 prior to batch effect correction and is now -0.152810257529811 .
2024-06-24 12:14:39.687364 INFO::Total function execution time is 0.190138101577759 s and adjustment time is 0.164490222930908 s ( 86.51 )
2024-06-24 12:14:39.847537 INFO::Formatting Data.
2024-06-24 12:14:39.849244 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:39.850433 INFO::Removing potential empty rows and columns
2024-06-24 12:14:39.851827 INFO::Found 2 missing values.
2024-06-24 12:14:39.855072 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:39.855776 INFO::Done
2024-06-24 12:14:39.891725 INFO::Found NA in Reference column
2024-06-24 12:14:39.905416 INFO::Require at least two references per batch.
2024-06-24 12:14:39.932286 INFO::Formatting Data.
2024-06-24 12:14:39.9333 INFO::Recognized SummarizedExperiment
2024-06-24 12:14:39.933853 INFO::Typecasting input to dataframe.
2024-06-24 12:14:39.948555 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:39.950243 INFO::Removing potential empty rows and columns
2024-06-24 12:14:39.955008 INFO::Found 0 missing values.
2024-06-24 12:14:39.964327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:39.965218 INFO::Done
2024-06-24 12:14:39.984476 INFO::Formatting Data.
2024-06-24 12:14:39.98546 INFO::Recognized SummarizedExperiment
2024-06-24 12:14:39.986039 INFO::Typecasting input to dataframe.
2024-06-24 12:14:40.005122 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:40.006713 INFO::Removing potential empty rows and columns
2024-06-24 12:14:40.010773 INFO::Found 0 missing values.
2024-06-24 12:14:40.024332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:40.025666 INFO::Done
2024-06-24 12:14:40.047021 INFO::Formatting Data.
2024-06-24 12:14:40.048276 INFO::Recognized SummarizedExperiment
2024-06-24 12:14:40.049079 INFO::Typecasting input to dataframe.
2024-06-24 12:14:40.072307 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:40.073918 INFO::Removing potential empty rows and columns
2024-06-24 12:14:40.075476 INFO::Found 0 missing values.
2024-06-24 12:14:40.076889 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.
2024-06-24 12:14:40.0827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:40.083742 INFO::Done
2024-06-24 12:14:40.096821 INFO::Formatting Data.
2024-06-24 12:14:40.097763 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:40.098661 INFO::Removing potential empty rows and columns
2024-06-24 12:14:40.099694 INFO::Found 0 missing values.
2024-06-24 12:14:40.102446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:40.103036 INFO::Done
2024-06-24 12:14:40.116547 INFO::Formatting Data.
2024-06-24 12:14:40.117457 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:40.118393 INFO::Removing potential empty rows and columns
2024-06-24 12:14:40.119569 INFO::Found 0 missing values.
2024-06-24 12:14:40.122727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:40.123463 INFO::Done
2024-06-24 12:14:40.15894 INFO::Formatting Data.
2024-06-24 12:14:40.159885 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:40.16092 INFO::Removing potential empty rows and columns
2024-06-24 12:14:40.162096 INFO::Found 1 missing values.
2024-06-24 12:14:40.16536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:40.16602 INFO::Done
2024-06-24 12:14:40.188497 INFO::Formatting Data.
2024-06-24 12:14:40.189378 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:40.190276 INFO::Removing potential empty rows and columns
2024-06-24 12:14:40.191285 INFO::Found 2 missing values.
2024-06-24 12:14:40.192176 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.
2024-06-24 12:14:40.194382 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:40.194955 INFO::Done
2024-06-24 12:14:40.206882 INFO::Formatting Data.
2024-06-24 12:14:40.207774 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:40.20863 INFO::Removing potential empty rows and columns
2024-06-24 12:14:40.209568 INFO::Found 2 missing values.
2024-06-24 12:14:40.211215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:40.211839 INFO::Done
2024-06-24 12:14:40.225405 INFO::Formatting Data.
2024-06-24 12:14:40.226289 INFO::Typecasting input to dataframe.
2024-06-24 12:14:40.227106 INFO::Replacing NaNs with NAs.
2024-06-24 12:14:40.228132 INFO::Removing potential empty rows and columns
2024-06-24 12:14:40.229193 INFO::Found 0 missing values.
2024-06-24 12:14:40.232538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 12:14:40.233127 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.864 3.575 24.027
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.098 | 1.130 | 20.526 | |
| compute_asw | 0.030 | 0.001 | 0.032 | |
| count_existing | 0.016 | 0.001 | 0.017 | |
| generate_data_covariables | 0.014 | 0.002 | 0.016 | |
| generate_dataset | 0.013 | 0.002 | 0.016 | |