Yannis Schumann
| Snapshot Date: 2024-10-27 02:55 -0400 (Sun, 27 Oct 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 2024-10-28 11:48 -0400 (Mon, 28 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4501 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4761 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4504 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4535 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4491 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 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: 2024-10-27 09:48:39 -0400 (Sun, 27 Oct 2024) |
| EndedAt: 2024-10-27 09:52:48 -0400 (Sun, 27 Oct 2024) |
| EllapsedTime: 249.4 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 8.408 0.268 5.868
* 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")
2024-10-27 09:52:41.494119 INFO::Formatting Data.
2024-10-27 09:52:41.495655 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:41.499629 INFO::Removing potential empty rows and columns
2024-10-27 09:52:41.602852 INFO::Found 0 missing values.
2024-10-27 09:52:41.603959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:41.604152 INFO::Done
2024-10-27 09:52:41.604315 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:41.609515 INFO::Starting hierarchical adjustment
2024-10-27 09:52:41.609739 INFO::Found 3 batches.
2024-10-27 09:52:41.609898 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:41.610225 INFO::Using default BPPARAM
2024-10-27 09:52:41.610368 INFO::Processing subtree level 1
2024-10-27 09:52:41.646175 INFO::Adjusting the last 1 batches sequentially
2024-10-27 09:52:41.64752 INFO::Done
2024-10-27 09:52:41.647732 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:41.649342 INFO::ASW Batch was -0.0751052619495718 prior to batch effect correction and is now -0.0751052619495718 .
2024-10-27 09:52:41.649938 INFO::Total function execution time is 0.156093120574951 s and adjustment time is 0.0378191471099854 s ( 24.23 )
2024-10-27 09:52:41.656808 INFO::Formatting Data.
2024-10-27 09:52:41.657032 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:41.657325 INFO::Removing potential empty rows and columns
2024-10-27 09:52:41.657744 INFO::Found 0 missing values.
2024-10-27 09:52:41.658032 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.
2024-10-27 09:52:41.661833 INFO::Formatting Data.
2024-10-27 09:52:41.662021 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:41.662281 INFO::Removing potential empty rows and columns
2024-10-27 09:52:41.662556 INFO::Found 0 missing values.
2024-10-27 09:52:41.66279 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.
2024-10-27 09:52:41.667533 INFO::Formatting Data.
2024-10-27 09:52:41.66772 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:41.667953 INFO::Removing potential empty rows and columns
2024-10-27 09:52:41.668237 INFO::Found 0 missing values.
2024-10-27 09:52:41.668473 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.
2024-10-27 09:52:41.669961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:41.670126 INFO::Done
2024-10-27 09:52:41.670274 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:41.671132 INFO::Starting hierarchical adjustment
2024-10-27 09:52:41.671317 INFO::Found 2 batches.
2024-10-27 09:52:41.671467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:41.671684 INFO::Using default BPPARAM
2024-10-27 09:52:41.671824 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:41.672066 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:41.682792 INFO::Done
2024-10-27 09:52:41.683005 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:41.683584 INFO::ASW Batch was -0.00221177072850568 prior to batch effect correction and is now -0.127916934001369 .
2024-10-27 09:52:41.683817 INFO::Total function execution time is 0.0162911415100098 s and adjustment time is 0.0115017890930176 s ( 70.6 )
2024-10-27 09:52:41.684676 INFO::Formatting Data.
2024-10-27 09:52:41.684828 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:41.687873 INFO::Formatting Data.
2024-10-27 09:52:41.688067 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:41.688415 INFO::Removing potential empty rows and columns
2024-10-27 09:52:41.688743 INFO::Found 0 missing values.
2024-10-27 09:52:41.689909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:41.690082 INFO::Done
2024-10-27 09:52:41.690316 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:41.691137 INFO::Starting hierarchical adjustment
2024-10-27 09:52:41.691438 INFO::Found 2 batches.
2024-10-27 09:52:41.691659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:41.691942 INFO::Using default BPPARAM
2024-10-27 09:52:41.692101 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:41.692461 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:41.696877 INFO::Done
2024-10-27 09:52:41.697035 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:41.697547 INFO::ASW Batch was -0.0473964784074654 prior to batch effect correction and is now -0.127214045296518 .
2024-10-27 09:52:41.697774 INFO::Total function execution time is 0.00989913940429688 s and adjustment time is 0.00547599792480469 s ( 55.32 )
2024-10-27 09:52:41.698031 INFO::Formatting Data.
2024-10-27 09:52:41.698183 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:41.698399 INFO::Removing potential empty rows and columns
2024-10-27 09:52:41.698657 INFO::Found 0 missing values.
2024-10-27 09:52:41.699405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:41.699537 INFO::Done
2024-10-27 09:52:41.699661 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:41.7002 INFO::Starting hierarchical adjustment
2024-10-27 09:52:41.700363 INFO::Found 2 batches.
2024-10-27 09:52:41.70049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:41.700631 INFO::Using default BPPARAM
2024-10-27 09:52:41.700749 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:41.700976 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:41.704865 INFO::Done
2024-10-27 09:52:41.705027 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:41.705574 INFO::ASW Batch was -0.0473964784074654 prior to batch effect correction and is now -0.127214045296518 .
2024-10-27 09:52:41.705785 INFO::Total function execution time is 0.00773096084594727 s and adjustment time is 0.0045318603515625 s ( 58.62 )
2024-10-27 09:52:42.581075 INFO::Formatting Data.
2024-10-27 09:52:42.581332 INFO::Recognized SummarizedExperiment
2024-10-27 09:52:42.581487 INFO::Typecasting input to dataframe.
2024-10-27 09:52:42.591973 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:42.592317 INFO::Removing potential empty rows and columns
2024-10-27 09:52:42.593373 INFO::Found 0 missing values.
2024-10-27 09:52:42.595192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:42.595328 INFO::Done
2024-10-27 09:52:42.595451 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:42.596522 INFO::Starting hierarchical adjustment
2024-10-27 09:52:42.59669 INFO::Found 2 batches.
2024-10-27 09:52:42.596818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:42.597087 INFO::Using default BPPARAM
2024-10-27 09:52:42.597205 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:42.597439 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:42.612426 INFO::Done
2024-10-27 09:52:42.612604 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:42.613629 INFO::ASW Batch was 0.0081879320060742 prior to batch effect correction and is now -0.0864803364037105 .
2024-10-27 09:52:42.613843 INFO::Total function execution time is 0.0328741073608398 s and adjustment time is 0.0157678127288818 s ( 47.96 )
2024-10-27 09:52:42.61902 INFO::Formatting Data.
2024-10-27 09:52:42.61919 INFO::Recognized SummarizedExperiment
2024-10-27 09:52:42.619322 INFO::Typecasting input to dataframe.
2024-10-27 09:52:42.621749 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:42.622034 INFO::Removing potential empty rows and columns
2024-10-27 09:52:42.622965 INFO::Found 0 missing values.
2024-10-27 09:52:42.624738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:42.62487 INFO::Done
2024-10-27 09:52:42.624994 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:42.625969 INFO::Starting hierarchical adjustment
2024-10-27 09:52:42.626138 INFO::Found 2 batches.
2024-10-27 09:52:42.626267 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:42.626409 INFO::Using default BPPARAM
2024-10-27 09:52:42.626527 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:42.626762 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:42.633366 INFO::Done
2024-10-27 09:52:42.633525 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:42.634488 INFO::ASW Batch was 0.0183864108171826 prior to batch effect correction and is now 0.0183864108171826 .
2024-10-27 09:52:42.634688 INFO::Total function execution time is 0.0156610012054443 s and adjustment time is 0.00726509094238281 s ( 46.39 )
2024-10-27 09:52:42.639891 INFO::Formatting Data.
2024-10-27 09:52:42.640077 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:42.640296 INFO::Removing potential empty rows and columns
2024-10-27 09:52:42.640549 INFO::Found 0 missing values.
2024-10-27 09:52:42.641268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:42.641402 INFO::Done
2024-10-27 09:52:42.641529 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:42.642019 INFO::Starting hierarchical adjustment
2024-10-27 09:52:42.642194 INFO::Found 3 batches.
2024-10-27 09:52:42.642328 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:42.642473 INFO::Using default BPPARAM
2024-10-27 09:52:42.642589 INFO::Processing subtree level 1
2024-10-27 09:52:42.723228 INFO::Adjusting the last 1 batches sequentially
2024-10-27 09:52:42.724541 INFO::Done
2024-10-27 09:52:42.72495 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:42.726753 INFO::ASW Batch was 0.0135526827996466 prior to batch effect correction and is now -0.128518775098045 .
2024-10-27 09:52:42.727452 INFO::Total function execution time is 0.0874269008636475 s and adjustment time is 0.0823800563812256 s ( 94.23 )
2024-10-27 09:52:42.735338 INFO::Skipping initial DF formatting
2024-10-27 09:52:42.73559 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:42.737001 INFO::Starting hierarchical adjustment
2024-10-27 09:52:42.737298 INFO::Found 5 batches.
2024-10-27 09:52:42.737496 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:42.737752 INFO::Using default BPPARAM
2024-10-27 09:52:42.73804 INFO::Processing subtree level 1
2024-10-27 09:52:42.791714 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:42.793521 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:42.804451 INFO::Done
2024-10-27 09:52:42.804703 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:42.807061 INFO::ASW Batch was 0.541617650852523 prior to batch effect correction and is now 0.541617650852523 .
2024-10-27 09:52:42.807281 INFO::ASW Label was 0.355267527366284 prior to batch effect correction and is now 0.355267527366284 .
2024-10-27 09:52:42.807932 INFO::Total function execution time is 0.0724630355834961 s and adjustment time is 0.0671970844268799 s ( 92.73 )
2024-10-27 09:52:42.816314 INFO::Formatting Data.
2024-10-27 09:52:42.816665 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:42.816981 INFO::Removing potential empty rows and columns
2024-10-27 09:52:42.817373 INFO::Found 0 missing values.
2024-10-27 09:52:42.818999 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:42.819209 INFO::Done
2024-10-27 09:52:42.819395 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:42.8205 INFO::Starting hierarchical adjustment
2024-10-27 09:52:42.820737 INFO::Found 5 batches.
2024-10-27 09:52:42.820929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:42.82117 INFO::Using default BPPARAM
2024-10-27 09:52:42.821336 INFO::Processing subtree level 1
2024-10-27 09:52:42.871414 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:42.873441 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:42.884157 INFO::Done
2024-10-27 09:52:42.884519 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:42.886128 INFO::ASW Batch was 0.394224642380832 prior to batch effect correction and is now -0.0609471220079854 .
2024-10-27 09:52:42.886398 INFO::ASW Label was 0.488072922955819 prior to batch effect correction and is now 0.746386864782654 .
2024-10-27 09:52:42.88682 INFO::Total function execution time is 0.0704939365386963 s and adjustment time is 0.0634651184082031 s ( 90.03 )
2024-10-27 09:52:42.887141 INFO::Formatting Data.
2024-10-27 09:52:42.887402 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:42.887701 INFO::Removing potential empty rows and columns
2024-10-27 09:52:42.888076 INFO::Found 0 missing values.
2024-10-27 09:52:42.889437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:42.889738 INFO::Done
2024-10-27 09:52:42.889946 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:42.890991 INFO::Starting hierarchical adjustment
2024-10-27 09:52:42.891251 INFO::Found 5 batches.
2024-10-27 09:52:42.891414 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:42.891663 INFO::Using default BPPARAM
2024-10-27 09:52:42.891946 INFO::Processing subtree level 1
2024-10-27 09:52:42.938484 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:42.939796 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:42.948071 INFO::Done
2024-10-27 09:52:42.948342 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:42.949821 INFO::ASW Batch was 0.394224642380832 prior to batch effect correction and is now -0.0609471220079854 .
2024-10-27 09:52:42.950058 INFO::ASW Label was 0.488072922955819 prior to batch effect correction and is now 0.746386864782654 .
2024-10-27 09:52:42.950457 INFO::Total function execution time is 0.0632491111755371 s and adjustment time is 0.0568649768829346 s ( 89.91 )
2024-10-27 09:52:42.957989 INFO::Formatting Data.
2024-10-27 09:52:42.9583 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:42.958696 INFO::Removing potential empty rows and columns
2024-10-27 09:52:42.959166 INFO::Found 0 missing values.
2024-10-27 09:52:42.960828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:42.961018 INFO::Done
2024-10-27 09:52:42.961199 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:42.9623 INFO::Starting hierarchical adjustment
2024-10-27 09:52:42.962597 INFO::Found 5 batches.
2024-10-27 09:52:42.96278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:42.963073 INFO::Using default BPPARAM
2024-10-27 09:52:42.963252 INFO::Processing subtree level 1
2024-10-27 09:52:43.049078 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:43.050369 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:43.059841 INFO::Done
2024-10-27 09:52:43.060124 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.061698 INFO::ASW Batch was 0.336607057696694 prior to batch effect correction and is now -0.018576111147558 .
2024-10-27 09:52:43.061957 INFO::ASW Label was 0.493312094628473 prior to batch effect correction and is now 0.735624824248149 .
2024-10-27 09:52:43.062393 INFO::Total function execution time is 0.104391098022461 s and adjustment time is 0.0972850322723389 s ( 93.19 )
2024-10-27 09:52:43.06276 INFO::Formatting Data.
2024-10-27 09:52:43.063012 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.063381 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.063846 INFO::Found 0 missing values.
2024-10-27 09:52:43.087332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.087609 INFO::Done
2024-10-27 09:52:43.087812 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.08913 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.0894 INFO::Found 5 batches.
2024-10-27 09:52:43.089679 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.090027 INFO::Using default BPPARAM
2024-10-27 09:52:43.090334 INFO::Processing subtree level 1
2024-10-27 09:52:43.154841 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:43.156238 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:43.167769 INFO::Done
2024-10-27 09:52:43.16813 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.170347 INFO::ASW Batch was 0.336607057696694 prior to batch effect correction and is now -0.018576111147558 .
2024-10-27 09:52:43.170662 INFO::ASW Label was 0.493312094628473 prior to batch effect correction and is now 0.735624824248149 .
2024-10-27 09:52:43.171153 INFO::Total function execution time is 0.108352899551392 s and adjustment time is 0.0784080028533936 s ( 72.36 )
2024-10-27 09:52:43.180443 INFO::Formatting Data.
2024-10-27 09:52:43.180852 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.181302 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.181844 INFO::Found 0 missing values.
2024-10-27 09:52:43.183127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.183331 INFO::Done
2024-10-27 09:52:43.183526 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.184982 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.185329 INFO::Found 2 batches.
2024-10-27 09:52:43.185556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.185848 INFO::Using default BPPARAM
2024-10-27 09:52:43.186051 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:43.186359 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:43.193786 INFO::Done
2024-10-27 09:52:43.194098 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.195605 INFO::ASW Batch was 0.620675732756774 prior to batch effect correction and is now -0.000478026857060232 .
2024-10-27 09:52:43.195907 INFO::ASW Label was 0.446837148716155 prior to batch effect correction and is now 0.906195805404834 .
2024-10-27 09:52:43.196315 INFO::Total function execution time is 0.0159220695495605 s and adjustment time is 0.0085291862487793 s ( 53.57 )
2024-10-27 09:52:43.196685 INFO::Formatting Data.
2024-10-27 09:52:43.196956 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.197358 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.197843 INFO::Found 0 missing values.
2024-10-27 09:52:43.199148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.199357 INFO::Done
2024-10-27 09:52:43.199624 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.201048 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.201291 INFO::Found 2 batches.
2024-10-27 09:52:43.201507 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.201765 INFO::Using default BPPARAM
2024-10-27 09:52:43.201956 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:43.202302 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:43.208567 INFO::Done
2024-10-27 09:52:43.208827 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.209984 INFO::ASW Batch was 0.620675732756774 prior to batch effect correction and is now -0.000478026857060232 .
2024-10-27 09:52:43.210206 INFO::ASW Label was 0.446837148716155 prior to batch effect correction and is now 0.906195805404834 .
2024-10-27 09:52:43.210506 INFO::Total function execution time is 0.0138180255889893 s and adjustment time is 0.00732588768005371 s ( 53.02 )
2024-10-27 09:52:43.217614 INFO::Formatting Data.
2024-10-27 09:52:43.217936 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.218467 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.218853 INFO::Found 0 missing values.
2024-10-27 09:52:43.21982 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.220066 INFO::Done
2024-10-27 09:52:43.220272 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.221082 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.221387 INFO::Found 2 batches.
2024-10-27 09:52:43.221626 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.221888 INFO::Using default BPPARAM
2024-10-27 09:52:43.222127 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:43.222478 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:43.238133 INFO::Done
2024-10-27 09:52:43.238511 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.239774 INFO::ASW Batch was -0.0657736830972682 prior to batch effect correction and is now -0.149823208431143 .
2024-10-27 09:52:43.240096 INFO::Total function execution time is 0.0225419998168945 s and adjustment time is 0.0168180465698242 s ( 74.61 )
2024-10-27 09:52:43.246075 INFO::Formatting Data.
2024-10-27 09:52:43.246361 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.24674 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.24716 INFO::Found 0 missing values.
2024-10-27 09:52:43.24775 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.
2024-10-27 09:52:43.24995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.250183 INFO::Done
2024-10-27 09:52:43.250373 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.252022 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.252378 INFO::Found 2 batches.
2024-10-27 09:52:43.252605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.253034 INFO::Using default BPPARAM
2024-10-27 09:52:43.253277 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:43.253844 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:43.263488 INFO::Done
2024-10-27 09:52:43.263807 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.265444 INFO::ASW Batch was 0.679356998185151 prior to batch effect correction and is now 0.212490656551015 .
2024-10-27 09:52:43.265862 INFO::ASW Label was 0.513055629930474 prior to batch effect correction and is now 0.851659649833486 .
2024-10-27 09:52:43.266328 INFO::Total function execution time is 0.0202181339263916 s and adjustment time is 0.0111629962921143 s ( 55.21 )
2024-10-27 09:52:43.266614 INFO::Formatting Data.
2024-10-27 09:52:43.266808 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.267119 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.267462 INFO::Found 0 missing values.
2024-10-27 09:52:43.267754 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.
2024-10-27 09:52:43.269331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.269507 INFO::Done
2024-10-27 09:52:43.269689 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.270628 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.270856 INFO::Found 2 batches.
2024-10-27 09:52:43.271031 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.271242 INFO::Using default BPPARAM
2024-10-27 09:52:43.271416 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:43.271717 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:43.277963 INFO::Done
2024-10-27 09:52:43.278171 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.279128 INFO::ASW Batch was 0.679356998185151 prior to batch effect correction and is now 0.212490656551015 .
2024-10-27 09:52:43.279348 INFO::ASW Label was 0.513055629930474 prior to batch effect correction and is now 0.851659649833486 .
2024-10-27 09:52:43.279606 INFO::Total function execution time is 0.012984037399292 s and adjustment time is 0.00714683532714844 s ( 55.04 )
2024-10-27 09:52:43.361329 INFO::Formatting Data.
2024-10-27 09:52:43.361653 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.361985 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.362348 INFO::Found 0 missing values.
2024-10-27 09:52:43.363452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.363661 INFO::Done
2024-10-27 09:52:43.363817 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.364641 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.364898 INFO::Found 3 batches.
2024-10-27 09:52:43.365048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.365262 INFO::Using default BPPARAM
2024-10-27 09:52:43.365446 INFO::Processing subtree level 1
2024-10-27 09:52:43.444231 INFO::Adjusting the last 1 batches sequentially
2024-10-27 09:52:43.447251 INFO::Done
2024-10-27 09:52:43.447615 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.449277 INFO::ASW Batch was -0.153622720039956 prior to batch effect correction and is now -0.153622720039956 .
2024-10-27 09:52:43.449818 INFO::Total function execution time is 0.088482141494751 s and adjustment time is 0.082360029220581 s ( 93.08 )
2024-10-27 09:52:43.450243 INFO::Formatting Data.
2024-10-27 09:52:43.450481 INFO::Typecasting input to dataframe.
2024-10-27 09:52:43.450904 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.451296 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.451738 INFO::Found 0 missing values.
2024-10-27 09:52:43.452966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.453163 INFO::Done
2024-10-27 09:52:43.453346 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.454172 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.45441 INFO::Found 3 batches.
2024-10-27 09:52:43.454601 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.454974 INFO::Using default BPPARAM
2024-10-27 09:52:43.45525 INFO::Processing subtree level 1
2024-10-27 09:52:43.536058 INFO::Adjusting the last 1 batches sequentially
2024-10-27 09:52:43.538595 INFO::Done
2024-10-27 09:52:43.53906 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.540858 INFO::ASW Batch was -0.153622720039956 prior to batch effect correction and is now -0.153622720039956 .
2024-10-27 09:52:43.541535 INFO::Total function execution time is 0.0910952091217041 s and adjustment time is 0.0842499732971191 s ( 92.49 )
2024-10-27 09:52:43.547975 INFO::Formatting Data.
2024-10-27 09:52:43.548217 INFO::Typecasting input to dataframe.
2024-10-27 09:52:43.548482 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.54889 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.549339 INFO::Found 0 missing values.
2024-10-27 09:52:43.55999 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.560292 INFO::Done
2024-10-27 09:52:43.560528 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.561519 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.561837 INFO::Found 3 batches.
2024-10-27 09:52:43.562078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.562339 INFO::Using default BPPARAM
2024-10-27 09:52:43.562563 INFO::Processing subtree level 1
2024-10-27 09:52:43.62509 INFO::Adjusting the last 1 batches sequentially
2024-10-27 09:52:43.626554 INFO::Done
2024-10-27 09:52:43.626905 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.628636 INFO::ASW Batch was -0.0948764770058645 prior to batch effect correction and is now -0.0948764770058645 .
2024-10-27 09:52:43.629183 INFO::Total function execution time is 0.0811450481414795 s and adjustment time is 0.0648040771484375 s ( 79.86 )
2024-10-27 09:52:43.714551 INFO::Formatting Data.
2024-10-27 09:52:43.714813 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.715245 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.716486 INFO::Found 1000 missing values.
2024-10-27 09:52:43.724458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.724775 INFO::Done
2024-10-27 09:52:43.724957 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.727028 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.727312 INFO::Found 10 batches.
2024-10-27 09:52:43.727478 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:43.727711 INFO::Using default BPPARAM
2024-10-27 09:52:43.727872 INFO::Processing subtree level 1
2024-10-27 09:52:43.805722 INFO::Processing subtree level 2
2024-10-27 09:52:43.893391 INFO::Adjusting the last 1 batches sequentially
2024-10-27 09:52:43.894848 INFO::Done
2024-10-27 09:52:43.895167 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:43.898389 INFO::ASW Batch was 0.448543479740452 prior to batch effect correction and is now 0.448543479740452 .
2024-10-27 09:52:43.898717 INFO::ASW Label was 0.376133869508704 prior to batch effect correction and is now 0.376133869508704 .
2024-10-27 09:52:43.89918 INFO::Total function execution time is 0.184612035751343 s and adjustment time is 0.167585849761963 s ( 90.78 )
2024-10-27 09:52:43.899556 INFO::Formatting Data.
2024-10-27 09:52:43.899781 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:43.900399 INFO::Removing potential empty rows and columns
2024-10-27 09:52:43.90196 INFO::Found 1000 missing values.
2024-10-27 09:52:43.910911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:43.911194 INFO::Done
2024-10-27 09:52:43.911404 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:43.914008 INFO::Starting hierarchical adjustment
2024-10-27 09:52:43.914403 INFO::Found 10 batches.
2024-10-27 09:52:44.327492 INFO::Set up parallel execution backend with 2 workers
2024-10-27 09:52:44.327728 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-27 09:52:44.74693 INFO::Adjusting the last 2 batches sequentially
2024-10-27 09:52:44.74748 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-27 09:52:44.752829 INFO::Done
2024-10-27 09:52:44.753009 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:44.755004 INFO::ASW Batch was 0.448543479740452 prior to batch effect correction and is now 0.448543479740452 .
2024-10-27 09:52:44.755178 INFO::ASW Label was 0.376133869508704 prior to batch effect correction and is now 0.376133869508704 .
2024-10-27 09:52:44.755391 INFO::Total function execution time is 0.855849027633667 s and adjustment time is 0.838520050048828 s ( 97.98 )
2024-10-27 09:52:44.807004 INFO::Formatting Data.
2024-10-27 09:52:44.807229 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.807512 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.807951 INFO::Found 0 missing values.
2024-10-27 09:52:44.809068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.809222 INFO::Done
2024-10-27 09:52:44.809377 INFO::Acquiring quality metrics before batch effect correction.
2024-10-27 09:52:44.81017 INFO::Starting hierarchical adjustment
2024-10-27 09:52:44.810366 INFO::Found 3 batches.
2024-10-27 09:52:44.8105 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-27 09:52:44.810675 INFO::Using default BPPARAM
2024-10-27 09:52:44.810812 INFO::Processing subtree level 1
2024-10-27 09:52:44.851295 INFO::Adjusting the last 1 batches sequentially
2024-10-27 09:52:44.852556 INFO::Done
2024-10-27 09:52:44.852736 INFO::Acquiring quality metrics after batch effect correction.
2024-10-27 09:52:44.854425 INFO::ASW Batch was 0.181796955100836 prior to batch effect correction and is now -0.149781196795243 .
2024-10-27 09:52:44.854617 INFO::ASW Label was -0.184227843056532 prior to batch effect correction and is now -0.168766999984287 .
2024-10-27 09:52:44.855104 INFO::Total function execution time is 0.0480217933654785 s and adjustment time is 0.0422289371490479 s ( 87.94 )
2024-10-27 09:52:44.895214 INFO::Formatting Data.
2024-10-27 09:52:44.895482 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.895744 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.896074 INFO::Found 2 missing values.
2024-10-27 09:52:44.896914 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.897187 INFO::Done
2024-10-27 09:52:44.905827 INFO::Found NA in Reference column
2024-10-27 09:52:44.909012 INFO::Require at least two references per batch.
2024-10-27 09:52:44.916006 INFO::Formatting Data.
2024-10-27 09:52:44.916209 INFO::Recognized SummarizedExperiment
2024-10-27 09:52:44.916359 INFO::Typecasting input to dataframe.
2024-10-27 09:52:44.91984 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.920193 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.921379 INFO::Found 0 missing values.
2024-10-27 09:52:44.923617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.923775 INFO::Done
2024-10-27 09:52:44.928528 INFO::Formatting Data.
2024-10-27 09:52:44.928723 INFO::Recognized SummarizedExperiment
2024-10-27 09:52:44.928889 INFO::Typecasting input to dataframe.
2024-10-27 09:52:44.934132 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.934497 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.935652 INFO::Found 0 missing values.
2024-10-27 09:52:44.939447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.939625 INFO::Done
2024-10-27 09:52:44.944596 INFO::Formatting Data.
2024-10-27 09:52:44.944823 INFO::Recognized SummarizedExperiment
2024-10-27 09:52:44.945012 INFO::Typecasting input to dataframe.
2024-10-27 09:52:44.949989 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.950274 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.950599 INFO::Found 0 missing values.
2024-10-27 09:52:44.950869 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.
2024-10-27 09:52:44.952263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.952428 INFO::Done
2024-10-27 09:52:44.955812 INFO::Formatting Data.
2024-10-27 09:52:44.956013 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.956246 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.956527 INFO::Found 0 missing values.
2024-10-27 09:52:44.957792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.957963 INFO::Done
2024-10-27 09:52:44.961859 INFO::Formatting Data.
2024-10-27 09:52:44.962071 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.962311 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.962594 INFO::Found 0 missing values.
2024-10-27 09:52:44.963438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.963608 INFO::Done
2024-10-27 09:52:44.973486 INFO::Formatting Data.
2024-10-27 09:52:44.973702 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.973986 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.974321 INFO::Found 1 missing values.
2024-10-27 09:52:44.975159 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.975306 INFO::Done
2024-10-27 09:52:44.981333 INFO::Formatting Data.
2024-10-27 09:52:44.981565 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.981809 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.982073 INFO::Found 2 missing values.
2024-10-27 09:52:44.982339 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.
2024-10-27 09:52:44.983059 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.983217 INFO::Done
2024-10-27 09:52:44.986679 INFO::Formatting Data.
2024-10-27 09:52:44.986888 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.987145 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.987422 INFO::Found 2 missing values.
2024-10-27 09:52:44.987939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.988091 INFO::Done
2024-10-27 09:52:44.991832 INFO::Formatting Data.
2024-10-27 09:52:44.992045 INFO::Typecasting input to dataframe.
2024-10-27 09:52:44.992301 INFO::Replacing NaNs with NAs.
2024-10-27 09:52:44.992543 INFO::Removing potential empty rows and columns
2024-10-27 09:52:44.99287 INFO::Found 0 missing values.
2024-10-27 09:52:44.993754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-27 09:52:44.993936 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
5.923 1.746 7.658
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.408 | 0.268 | 5.868 | |
| compute_asw | 0.008 | 0.000 | 0.008 | |
| count_existing | 0.004 | 0.001 | 0.004 | |
| generate_data_covariables | 0.003 | 0.000 | 0.004 | |
| generate_dataset | 0.003 | 0.000 | 0.004 | |