Yannis Schumann
| Snapshot Date: 2025-02-05 13:48 -0500 (Wed, 05 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0500 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-06 11:41 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| 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 159/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.3.6 |
| 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_1.3.6.tar.gz |
| StartedAt: 2025-02-05 19:04:28 -0500 (Wed, 05 Feb 2025) |
| EndedAt: 2025-02-05 19:05:48 -0500 (Wed, 05 Feb 2025) |
| EllapsedTime: 80.4 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_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.6’
* 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 25.944 1.414 18.717
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.3.6’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-02-05 19:05:28.125333 INFO::Formatting Data.
2025-02-05 19:05:28.130015 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:28.144265 INFO::Removing potential empty rows and columns
2025-02-05 19:05:28.418856 INFO::Found 0 missing values.
2025-02-05 19:05:28.422695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:28.423668 INFO::Done
2025-02-05 19:05:28.424494 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:28.437625 INFO::Starting hierarchical adjustment
2025-02-05 19:05:28.43862 INFO::Found 3 batches.
2025-02-05 19:05:28.439205 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:28.4403 INFO::Using default BPPARAM
2025-02-05 19:05:28.440809 INFO::Processing subtree level 1
2025-02-05 19:05:28.609512 INFO::Adjusting the last 1 batches sequentially
2025-02-05 19:05:28.614498 INFO::Done
2025-02-05 19:05:28.61625 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:28.622286 INFO::ASW Batch was -0.014569011384264 prior to batch effect correction and is now -0.014569011384264 .
2025-02-05 19:05:28.62482 INFO::Total function execution time is 0.500257015228271 s and adjustment time is 0.176044940948486 s ( 35.19 )
2025-02-05 19:05:28.650641 INFO::Formatting Data.
2025-02-05 19:05:28.651822 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:28.653111 INFO::Removing potential empty rows and columns
2025-02-05 19:05:28.654369 INFO::Found 0 missing values.
2025-02-05 19:05:28.65531 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.
2025-02-05 19:05:28.669705 INFO::Formatting Data.
2025-02-05 19:05:28.6707 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:28.672024 INFO::Removing potential empty rows and columns
2025-02-05 19:05:28.672999 INFO::Found 0 missing values.
2025-02-05 19:05:28.67387 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.
2025-02-05 19:05:28.694253 INFO::Formatting Data.
2025-02-05 19:05:28.695127 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:28.696015 INFO::Removing potential empty rows and columns
2025-02-05 19:05:28.697225 INFO::Found 0 missing values.
2025-02-05 19:05:28.698116 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.
2025-02-05 19:05:28.702952 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:28.703538 INFO::Done
2025-02-05 19:05:28.704223 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:28.706606 INFO::Starting hierarchical adjustment
2025-02-05 19:05:28.707291 INFO::Found 2 batches.
2025-02-05 19:05:28.707969 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:28.708665 INFO::Using default BPPARAM
2025-02-05 19:05:28.709149 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:28.710016 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:28.736374 INFO::Done
2025-02-05 19:05:28.737185 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:28.739407 INFO::ASW Batch was 0.00970347470365766 prior to batch effect correction and is now -0.116157229758368 .
2025-02-05 19:05:28.740168 INFO::Total function execution time is 0.0459909439086914 s and adjustment time is 0.0291910171508789 s ( 63.47 )
2025-02-05 19:05:28.742961 INFO::Formatting Data.
2025-02-05 19:05:28.743688 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:28.755067 INFO::Formatting Data.
2025-02-05 19:05:28.755986 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:28.757415 INFO::Removing potential empty rows and columns
2025-02-05 19:05:28.758956 INFO::Found 0 missing values.
2025-02-05 19:05:28.796425 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:28.797206 INFO::Done
2025-02-05 19:05:28.797869 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:28.799832 INFO::Starting hierarchical adjustment
2025-02-05 19:05:28.800634 INFO::Found 2 batches.
2025-02-05 19:05:28.801353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:28.8022 INFO::Using default BPPARAM
2025-02-05 19:05:28.802919 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:28.804203 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:28.821167 INFO::Done
2025-02-05 19:05:28.822087 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:28.824504 INFO::ASW Batch was 0.000965064680918407 prior to batch effect correction and is now -0.12064076655083 .
2025-02-05 19:05:28.82559 INFO::Total function execution time is 0.0705111026763916 s and adjustment time is 0.020676851272583 s ( 29.32 )
2025-02-05 19:05:28.827127 INFO::Formatting Data.
2025-02-05 19:05:28.828022 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:28.829254 INFO::Removing potential empty rows and columns
2025-02-05 19:05:28.830648 INFO::Found 0 missing values.
2025-02-05 19:05:28.83382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:28.834538 INFO::Done
2025-02-05 19:05:28.835178 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:28.837179 INFO::Starting hierarchical adjustment
2025-02-05 19:05:28.83781 INFO::Found 2 batches.
2025-02-05 19:05:28.838274 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:28.838805 INFO::Using default BPPARAM
2025-02-05 19:05:28.839638 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:28.840904 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:28.861828 INFO::Done
2025-02-05 19:05:28.862702 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:28.864876 INFO::ASW Batch was 0.000965064680918407 prior to batch effect correction and is now -0.12064076655083 .
2025-02-05 19:05:28.865803 INFO::Total function execution time is 0.038679838180542 s and adjustment time is 0.0240612030029297 s ( 62.21 )
2025-02-05 19:05:31.977121 INFO::Formatting Data.
2025-02-05 19:05:31.977768 INFO::Recognized SummarizedExperiment
2025-02-05 19:05:31.978334 INFO::Typecasting input to dataframe.
2025-02-05 19:05:32.012064 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:32.013132 INFO::Removing potential empty rows and columns
2025-02-05 19:05:32.016643 INFO::Found 0 missing values.
2025-02-05 19:05:32.025287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:32.026268 INFO::Done
2025-02-05 19:05:32.027048 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:32.032095 INFO::Starting hierarchical adjustment
2025-02-05 19:05:32.032882 INFO::Found 2 batches.
2025-02-05 19:05:32.033389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:32.034375 INFO::Using default BPPARAM
2025-02-05 19:05:32.034875 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:32.035772 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:32.092316 INFO::Done
2025-02-05 19:05:32.093162 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:32.097266 INFO::ASW Batch was -0.00429326025760427 prior to batch effect correction and is now -0.0863422012427231 .
2025-02-05 19:05:32.098157 INFO::Total function execution time is 0.121252059936523 s and adjustment time is 0.0595340728759766 s ( 49.1 )
2025-02-05 19:05:32.120756 INFO::Formatting Data.
2025-02-05 19:05:32.121454 INFO::Recognized SummarizedExperiment
2025-02-05 19:05:32.121963 INFO::Typecasting input to dataframe.
2025-02-05 19:05:32.13095 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:32.132477 INFO::Removing potential empty rows and columns
2025-02-05 19:05:32.136954 INFO::Found 0 missing values.
2025-02-05 19:05:32.144627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:32.145436 INFO::Done
2025-02-05 19:05:32.14617 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:32.150517 INFO::Starting hierarchical adjustment
2025-02-05 19:05:32.151656 INFO::Found 2 batches.
2025-02-05 19:05:32.152424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:32.153238 INFO::Using default BPPARAM
2025-02-05 19:05:32.153937 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:32.155357 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:32.18499 INFO::Done
2025-02-05 19:05:32.185686 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:32.188979 INFO::ASW Batch was -0.00790398746407042 prior to batch effect correction and is now -0.00790398746407042 .
2025-02-05 19:05:32.190029 INFO::Total function execution time is 0.0691380500793457 s and adjustment time is 0.0335659980773926 s ( 48.55 )
2025-02-05 19:05:32.213765 INFO::Formatting Data.
2025-02-05 19:05:32.214426 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:32.215155 INFO::Removing potential empty rows and columns
2025-02-05 19:05:32.216007 INFO::Found 0 missing values.
2025-02-05 19:05:32.218914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:32.219426 INFO::Done
2025-02-05 19:05:32.219888 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:32.221629 INFO::Starting hierarchical adjustment
2025-02-05 19:05:32.2227 INFO::Found 3 batches.
2025-02-05 19:05:32.223646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:32.224485 INFO::Using default BPPARAM
2025-02-05 19:05:32.225148 INFO::Processing subtree level 1
2025-02-05 19:05:32.427214 INFO::Adjusting the last 1 batches sequentially
2025-02-05 19:05:32.43663 INFO::Done
2025-02-05 19:05:32.438746 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:32.445685 INFO::ASW Batch was -0.110153551686256 prior to batch effect correction and is now -0.165906169417429 .
2025-02-05 19:05:32.447713 INFO::Total function execution time is 0.233727216720581 s and adjustment time is 0.21403694152832 s ( 91.58 )
2025-02-05 19:05:32.472249 INFO::Skipping initial DF formatting
2025-02-05 19:05:32.473284 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:32.477997 INFO::Starting hierarchical adjustment
2025-02-05 19:05:32.47894 INFO::Found 5 batches.
2025-02-05 19:05:32.479511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:32.480792 INFO::Using default BPPARAM
2025-02-05 19:05:32.481592 INFO::Processing subtree level 1
2025-02-05 19:05:32.635355 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:32.646099 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:32.681835 INFO::Done
2025-02-05 19:05:32.683332 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:32.692047 INFO::ASW Batch was 0.509737433672258 prior to batch effect correction and is now 0.509737433672258 .
2025-02-05 19:05:32.693176 INFO::ASW Label was 0.388280048046506 prior to batch effect correction and is now 0.388280048046506 .
2025-02-05 19:05:32.695237 INFO::Total function execution time is 0.222922086715698 s and adjustment time is 0.202955961227417 s ( 91.04 )
2025-02-05 19:05:32.722788 INFO::Formatting Data.
2025-02-05 19:05:32.724594 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:32.726617 INFO::Removing potential empty rows and columns
2025-02-05 19:05:32.727963 INFO::Found 0 missing values.
2025-02-05 19:05:32.732909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:32.733607 INFO::Done
2025-02-05 19:05:32.734139 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:32.737403 INFO::Starting hierarchical adjustment
2025-02-05 19:05:32.738471 INFO::Found 5 batches.
2025-02-05 19:05:32.739238 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:32.740137 INFO::Using default BPPARAM
2025-02-05 19:05:32.741045 INFO::Processing subtree level 1
2025-02-05 19:05:32.868856 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:32.886697 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:32.923892 INFO::Done
2025-02-05 19:05:32.925459 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:32.93234 INFO::ASW Batch was 0.543686143754018 prior to batch effect correction and is now -0.0330968943168844 .
2025-02-05 19:05:32.933389 INFO::ASW Label was 0.252787313868746 prior to batch effect correction and is now 0.726947208186311 .
2025-02-05 19:05:32.93505 INFO::Total function execution time is 0.212306022644043 s and adjustment time is 0.185567140579224 s ( 87.41 )
2025-02-05 19:05:32.936232 INFO::Formatting Data.
2025-02-05 19:05:32.937327 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:32.938672 INFO::Removing potential empty rows and columns
2025-02-05 19:05:32.940087 INFO::Found 0 missing values.
2025-02-05 19:05:32.944903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:32.945726 INFO::Done
2025-02-05 19:05:32.946504 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:32.95066 INFO::Starting hierarchical adjustment
2025-02-05 19:05:32.951894 INFO::Found 5 batches.
2025-02-05 19:05:32.952886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:32.953506 INFO::Using default BPPARAM
2025-02-05 19:05:32.954016 INFO::Processing subtree level 1
2025-02-05 19:05:33.08614 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:33.089351 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:33.115025 INFO::Done
2025-02-05 19:05:33.116177 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:33.121548 INFO::ASW Batch was 0.543686143754018 prior to batch effect correction and is now -0.0330968943168844 .
2025-02-05 19:05:33.122514 INFO::ASW Label was 0.252787313868746 prior to batch effect correction and is now 0.726947208186311 .
2025-02-05 19:05:33.123945 INFO::Total function execution time is 0.187544107437134 s and adjustment time is 0.163404941558838 s ( 87.13 )
2025-02-05 19:05:33.148676 INFO::Formatting Data.
2025-02-05 19:05:33.149516 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:33.150835 INFO::Removing potential empty rows and columns
2025-02-05 19:05:33.152964 INFO::Found 0 missing values.
2025-02-05 19:05:33.158872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:33.159515 INFO::Done
2025-02-05 19:05:33.160066 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:33.164475 INFO::Starting hierarchical adjustment
2025-02-05 19:05:33.165659 INFO::Found 5 batches.
2025-02-05 19:05:33.166535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:33.167549 INFO::Using default BPPARAM
2025-02-05 19:05:33.168269 INFO::Processing subtree level 1
2025-02-05 19:05:33.286908 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:33.291943 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:33.313348 INFO::Done
2025-02-05 19:05:33.314129 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:33.319042 INFO::ASW Batch was 0.551486618088806 prior to batch effect correction and is now -0.0583279216041444 .
2025-02-05 19:05:33.320143 INFO::ASW Label was 0.157448307550938 prior to batch effect correction and is now 0.769618605601265 .
2025-02-05 19:05:33.321246 INFO::Total function execution time is 0.17249608039856 s and adjustment time is 0.147923946380615 s ( 85.75 )
2025-02-05 19:05:33.322523 INFO::Formatting Data.
2025-02-05 19:05:33.323294 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:33.325216 INFO::Removing potential empty rows and columns
2025-02-05 19:05:33.326567 INFO::Found 0 missing values.
2025-02-05 19:05:33.330974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:33.332066 INFO::Done
2025-02-05 19:05:33.333197 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:33.337758 INFO::Starting hierarchical adjustment
2025-02-05 19:05:33.338724 INFO::Found 5 batches.
2025-02-05 19:05:33.339451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:33.340411 INFO::Using default BPPARAM
2025-02-05 19:05:33.341145 INFO::Processing subtree level 1
2025-02-05 19:05:33.461868 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:33.467914 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:33.486463 INFO::Done
2025-02-05 19:05:33.487402 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:33.491529 INFO::ASW Batch was 0.551486618088806 prior to batch effect correction and is now -0.0583279216041444 .
2025-02-05 19:05:33.49213 INFO::ASW Label was 0.157448307550938 prior to batch effect correction and is now 0.769618605601265 .
2025-02-05 19:05:33.492941 INFO::Total function execution time is 0.170437097549438 s and adjustment time is 0.147953033447266 s ( 86.81 )
2025-02-05 19:05:33.510947 INFO::Formatting Data.
2025-02-05 19:05:33.512111 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:33.513478 INFO::Removing potential empty rows and columns
2025-02-05 19:05:33.514977 INFO::Found 0 missing values.
2025-02-05 19:05:33.518528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:33.519583 INFO::Done
2025-02-05 19:05:33.520171 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:33.524057 INFO::Starting hierarchical adjustment
2025-02-05 19:05:33.525183 INFO::Found 2 batches.
2025-02-05 19:05:33.52598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:33.526871 INFO::Using default BPPARAM
2025-02-05 19:05:33.527629 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:33.528855 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:33.547809 INFO::Done
2025-02-05 19:05:33.54852 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:33.552425 INFO::ASW Batch was 0.647450952994578 prior to batch effect correction and is now 0.0535392288153902 .
2025-02-05 19:05:33.553451 INFO::ASW Label was 0.427001135286347 prior to batch effect correction and is now 0.809384804296404 .
2025-02-05 19:05:33.68154 INFO::Total function execution time is 0.170531988143921 s and adjustment time is 0.0228509902954102 s ( 13.4 )
2025-02-05 19:05:33.682579 INFO::Formatting Data.
2025-02-05 19:05:33.683216 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:33.684284 INFO::Removing potential empty rows and columns
2025-02-05 19:05:33.685622 INFO::Found 0 missing values.
2025-02-05 19:05:33.689071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:33.689786 INFO::Done
2025-02-05 19:05:33.690817 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:33.695944 INFO::Starting hierarchical adjustment
2025-02-05 19:05:33.697413 INFO::Found 2 batches.
2025-02-05 19:05:33.698399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:33.69949 INFO::Using default BPPARAM
2025-02-05 19:05:33.700419 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:33.702003 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:33.728407 INFO::Done
2025-02-05 19:05:33.729859 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:33.734482 INFO::ASW Batch was 0.647450952994578 prior to batch effect correction and is now 0.0535392288153902 .
2025-02-05 19:05:33.735526 INFO::ASW Label was 0.427001135286347 prior to batch effect correction and is now 0.809384804296404 .
2025-02-05 19:05:33.736827 INFO::Total function execution time is 0.0541820526123047 s and adjustment time is 0.0312581062316895 s ( 57.69 )
2025-02-05 19:05:33.757392 INFO::Formatting Data.
2025-02-05 19:05:33.75865 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:33.760077 INFO::Removing potential empty rows and columns
2025-02-05 19:05:33.761532 INFO::Found 0 missing values.
2025-02-05 19:05:33.764789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:33.766136 INFO::Done
2025-02-05 19:05:33.767032 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:33.76942 INFO::Starting hierarchical adjustment
2025-02-05 19:05:33.770214 INFO::Found 2 batches.
2025-02-05 19:05:33.770979 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:33.771619 INFO::Using default BPPARAM
2025-02-05 19:05:33.772179 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:33.773172 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:33.818924 INFO::Done
2025-02-05 19:05:33.819728 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:33.822125 INFO::ASW Batch was 0.118880160002016 prior to batch effect correction and is now -0.199838247380865 .
2025-02-05 19:05:33.823087 INFO::Total function execution time is 0.0658590793609619 s and adjustment time is 0.0488369464874268 s ( 74.15 )
2025-02-05 19:05:33.84175 INFO::Formatting Data.
2025-02-05 19:05:33.842999 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:33.84456 INFO::Removing potential empty rows and columns
2025-02-05 19:05:33.845806 INFO::Found 0 missing values.
2025-02-05 19:05:33.847145 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.
2025-02-05 19:05:33.854332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:33.855392 INFO::Done
2025-02-05 19:05:33.856553 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:33.863168 INFO::Starting hierarchical adjustment
2025-02-05 19:05:33.864539 INFO::Found 2 batches.
2025-02-05 19:05:33.865573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:33.866601 INFO::Using default BPPARAM
2025-02-05 19:05:33.867321 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:33.868476 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:33.891215 INFO::Done
2025-02-05 19:05:33.892088 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:33.89606 INFO::ASW Batch was 0.736120843068566 prior to batch effect correction and is now 0.0784671175722081 .
2025-02-05 19:05:33.896956 INFO::ASW Label was 0.353789040847804 prior to batch effect correction and is now 0.857489932404966 .
2025-02-05 19:05:33.89795 INFO::Total function execution time is 0.0563898086547852 s and adjustment time is 0.0269279479980469 s ( 47.75 )
2025-02-05 19:05:33.899065 INFO::Formatting Data.
2025-02-05 19:05:33.89986 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:33.900937 INFO::Removing potential empty rows and columns
2025-02-05 19:05:33.902037 INFO::Found 0 missing values.
2025-02-05 19:05:33.903296 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.
2025-02-05 19:05:33.90994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:33.910997 INFO::Done
2025-02-05 19:05:33.911915 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:33.916265 INFO::Starting hierarchical adjustment
2025-02-05 19:05:33.917349 INFO::Found 2 batches.
2025-02-05 19:05:33.918303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:33.919137 INFO::Using default BPPARAM
2025-02-05 19:05:33.920082 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:33.921663 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:33.947518 INFO::Done
2025-02-05 19:05:33.948396 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:33.952437 INFO::ASW Batch was 0.736120843068566 prior to batch effect correction and is now 0.0784671175722081 .
2025-02-05 19:05:33.953319 INFO::ASW Label was 0.353789040847804 prior to batch effect correction and is now 0.857489932404966 .
2025-02-05 19:05:33.954575 INFO::Total function execution time is 0.0554509162902832 s and adjustment time is 0.0304059982299805 s ( 54.83 )
2025-02-05 19:05:34.303242 INFO::Formatting Data.
2025-02-05 19:05:34.304819 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:34.306513 INFO::Removing potential empty rows and columns
2025-02-05 19:05:34.309467 INFO::Found 0 missing values.
2025-02-05 19:05:34.314583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:34.315486 INFO::Done
2025-02-05 19:05:34.317151 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:34.319951 INFO::Starting hierarchical adjustment
2025-02-05 19:05:34.320676 INFO::Found 3 batches.
2025-02-05 19:05:34.321611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:34.323297 INFO::Using default BPPARAM
2025-02-05 19:05:34.323909 INFO::Processing subtree level 1
2025-02-05 19:05:34.515732 INFO::Adjusting the last 1 batches sequentially
2025-02-05 19:05:34.524458 INFO::Done
2025-02-05 19:05:34.526021 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:34.533177 INFO::ASW Batch was -0.00729010636468158 prior to batch effect correction and is now -0.00729010636468158 .
2025-02-05 19:05:34.535109 INFO::Total function execution time is 0.231649875640869 s and adjustment time is 0.203825950622559 s ( 87.99 )
2025-02-05 19:05:34.539866 INFO::Formatting Data.
2025-02-05 19:05:34.540657 INFO::Typecasting input to dataframe.
2025-02-05 19:05:34.541743 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:34.543061 INFO::Removing potential empty rows and columns
2025-02-05 19:05:34.545059 INFO::Found 0 missing values.
2025-02-05 19:05:34.549965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:34.551072 INFO::Done
2025-02-05 19:05:34.552032 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:34.555789 INFO::Starting hierarchical adjustment
2025-02-05 19:05:34.556851 INFO::Found 3 batches.
2025-02-05 19:05:34.557636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:34.558523 INFO::Using default BPPARAM
2025-02-05 19:05:34.559261 INFO::Processing subtree level 1
2025-02-05 19:05:34.70403 INFO::Adjusting the last 1 batches sequentially
2025-02-05 19:05:34.707531 INFO::Done
2025-02-05 19:05:34.708877 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:34.713673 INFO::ASW Batch was -0.00729010636468158 prior to batch effect correction and is now -0.00729010636468158 .
2025-02-05 19:05:34.715137 INFO::Total function execution time is 0.175873041152954 s and adjustment time is 0.150843143463135 s ( 85.77 )
2025-02-05 19:05:34.741434 INFO::Formatting Data.
2025-02-05 19:05:34.743033 INFO::Typecasting input to dataframe.
2025-02-05 19:05:34.744675 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:34.746494 INFO::Removing potential empty rows and columns
2025-02-05 19:05:34.748777 INFO::Found 0 missing values.
2025-02-05 19:05:34.754015 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:34.754819 INFO::Done
2025-02-05 19:05:34.755547 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:34.758338 INFO::Starting hierarchical adjustment
2025-02-05 19:05:34.75957 INFO::Found 3 batches.
2025-02-05 19:05:34.7605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:34.761594 INFO::Using default BPPARAM
2025-02-05 19:05:34.762742 INFO::Processing subtree level 1
2025-02-05 19:05:34.892815 INFO::Adjusting the last 1 batches sequentially
2025-02-05 19:05:34.898378 INFO::Done
2025-02-05 19:05:34.899274 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:34.902848 INFO::ASW Batch was -0.0814876555230727 prior to batch effect correction and is now -0.0814876555230727 .
2025-02-05 19:05:34.904548 INFO::Total function execution time is 0.163223028182983 s and adjustment time is 0.139076948165894 s ( 85.21 )
2025-02-05 19:05:35.129491 INFO::Formatting Data.
2025-02-05 19:05:35.130733 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:35.132403 INFO::Removing potential empty rows and columns
2025-02-05 19:05:35.13623 INFO::Found 1000 missing values.
2025-02-05 19:05:35.166284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:35.167627 INFO::Done
2025-02-05 19:05:35.168846 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:35.176807 INFO::Starting hierarchical adjustment
2025-02-05 19:05:35.177989 INFO::Found 10 batches.
2025-02-05 19:05:35.178711 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:35.179743 INFO::Using default BPPARAM
2025-02-05 19:05:35.180748 INFO::Processing subtree level 1
2025-02-05 19:05:35.384836 INFO::Processing subtree level 2
2025-02-05 19:05:35.60324 INFO::Adjusting the last 1 batches sequentially
2025-02-05 19:05:35.609691 INFO::Done
2025-02-05 19:05:35.610667 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:35.621955 INFO::ASW Batch was 0.49145169740022 prior to batch effect correction and is now 0.49145169740022 .
2025-02-05 19:05:35.623204 INFO::ASW Label was 0.385408680633026 prior to batch effect correction and is now 0.385408680633026 .
2025-02-05 19:05:35.624813 INFO::Total function execution time is 0.495308876037598 s and adjustment time is 0.431924104690552 s ( 87.2 )
2025-02-05 19:05:35.626319 INFO::Formatting Data.
2025-02-05 19:05:35.627133 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:35.628872 INFO::Removing potential empty rows and columns
2025-02-05 19:05:35.633127 INFO::Found 1000 missing values.
2025-02-05 19:05:35.666828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:35.668068 INFO::Done
2025-02-05 19:05:35.669175 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:35.678538 INFO::Starting hierarchical adjustment
2025-02-05 19:05:35.679889 INFO::Found 10 batches.
2025-02-05 19:05:36.858241 INFO::Set up parallel execution backend with 2 workers
2025-02-05 19:05:36.858888 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-05 19:05:38.107629 INFO::Adjusting the last 2 batches sequentially
2025-02-05 19:05:38.108912 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 19:05:38.127748 INFO::Done
2025-02-05 19:05:38.128728 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:38.135418 INFO::ASW Batch was 0.49145169740022 prior to batch effect correction and is now 0.49145169740022 .
2025-02-05 19:05:38.136078 INFO::ASW Label was 0.385408680633026 prior to batch effect correction and is now 0.385408680633026 .
2025-02-05 19:05:38.136796 INFO::Total function execution time is 2.51060390472412 s and adjustment time is 2.44821000099182 s ( 97.51 )
2025-02-05 19:05:38.365455 INFO::Formatting Data.
2025-02-05 19:05:38.366712 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:38.368729 INFO::Removing potential empty rows and columns
2025-02-05 19:05:38.370063 INFO::Found 0 missing values.
2025-02-05 19:05:38.373626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:38.374244 INFO::Done
2025-02-05 19:05:38.374745 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 19:05:38.378349 INFO::Starting hierarchical adjustment
2025-02-05 19:05:38.379899 INFO::Found 3 batches.
2025-02-05 19:05:38.3807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 19:05:38.381638 INFO::Using default BPPARAM
2025-02-05 19:05:38.38241 INFO::Processing subtree level 1
2025-02-05 19:05:38.533237 INFO::Adjusting the last 1 batches sequentially
2025-02-05 19:05:38.556597 INFO::Done
2025-02-05 19:05:38.560719 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 19:05:38.574582 INFO::ASW Batch was 0.217594599609127 prior to batch effect correction and is now -0.201639252378112 .
2025-02-05 19:05:38.575971 INFO::ASW Label was -0.166080344600554 prior to batch effect correction and is now 0.0440775433978642 .
2025-02-05 19:05:38.578567 INFO::Total function execution time is 0.212970972061157 s and adjustment time is 0.176524877548218 s ( 82.89 )
2025-02-05 19:05:38.751751 INFO::Formatting Data.
2025-02-05 19:05:38.752596 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:38.753536 INFO::Removing potential empty rows and columns
2025-02-05 19:05:38.754538 INFO::Found 2 missing values.
2025-02-05 19:05:38.757098 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:38.757605 INFO::Done
2025-02-05 19:05:38.801277 INFO::Found NA in Reference column
2025-02-05 19:05:38.816483 INFO::Require at least two references per batch.
2025-02-05 19:05:38.844478 INFO::Formatting Data.
2025-02-05 19:05:38.84558 INFO::Recognized SummarizedExperiment
2025-02-05 19:05:38.846442 INFO::Typecasting input to dataframe.
2025-02-05 19:05:38.860993 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:38.862747 INFO::Removing potential empty rows and columns
2025-02-05 19:05:38.867923 INFO::Found 0 missing values.
2025-02-05 19:05:38.876478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:38.877546 INFO::Done
2025-02-05 19:05:38.896751 INFO::Formatting Data.
2025-02-05 19:05:38.897576 INFO::Recognized SummarizedExperiment
2025-02-05 19:05:38.898114 INFO::Typecasting input to dataframe.
2025-02-05 19:05:38.919551 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:38.921424 INFO::Removing potential empty rows and columns
2025-02-05 19:05:38.926941 INFO::Found 0 missing values.
2025-02-05 19:05:38.941039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:38.941885 INFO::Done
2025-02-05 19:05:38.962551 INFO::Formatting Data.
2025-02-05 19:05:38.964018 INFO::Recognized SummarizedExperiment
2025-02-05 19:05:38.965196 INFO::Typecasting input to dataframe.
2025-02-05 19:05:38.988113 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:38.989297 INFO::Removing potential empty rows and columns
2025-02-05 19:05:38.990563 INFO::Found 0 missing values.
2025-02-05 19:05:38.991619 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.
2025-02-05 19:05:38.996292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:38.99689 INFO::Done
2025-02-05 19:05:39.011467 INFO::Formatting Data.
2025-02-05 19:05:39.012343 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:39.013229 INFO::Removing potential empty rows and columns
2025-02-05 19:05:39.014158 INFO::Found 0 missing values.
2025-02-05 19:05:39.016968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:39.017696 INFO::Done
2025-02-05 19:05:39.034851 INFO::Formatting Data.
2025-02-05 19:05:39.035957 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:39.036841 INFO::Removing potential empty rows and columns
2025-02-05 19:05:39.038114 INFO::Found 0 missing values.
2025-02-05 19:05:39.042003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:39.042617 INFO::Done
2025-02-05 19:05:39.09073 INFO::Formatting Data.
2025-02-05 19:05:39.091743 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:39.092945 INFO::Removing potential empty rows and columns
2025-02-05 19:05:39.094082 INFO::Found 1 missing values.
2025-02-05 19:05:39.098082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:39.09915 INFO::Done
2025-02-05 19:05:39.12803 INFO::Formatting Data.
2025-02-05 19:05:39.129151 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:39.130453 INFO::Removing potential empty rows and columns
2025-02-05 19:05:39.131926 INFO::Found 2 missing values.
2025-02-05 19:05:39.133206 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.
2025-02-05 19:05:39.136398 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:39.137083 INFO::Done
2025-02-05 19:05:39.154186 INFO::Formatting Data.
2025-02-05 19:05:39.155002 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:39.156071 INFO::Removing potential empty rows and columns
2025-02-05 19:05:39.156986 INFO::Found 2 missing values.
2025-02-05 19:05:39.158799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:39.159292 INFO::Done
2025-02-05 19:05:39.174281 INFO::Formatting Data.
2025-02-05 19:05:39.17543 INFO::Typecasting input to dataframe.
2025-02-05 19:05:39.176704 INFO::Replacing NaNs with NAs.
2025-02-05 19:05:39.17796 INFO::Removing potential empty rows and columns
2025-02-05 19:05:39.179342 INFO::Found 0 missing values.
2025-02-05 19:05:39.183448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 19:05:39.184236 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.520 3.940 23.816
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.944 | 1.414 | 18.717 | |
| compute_asw | 0.028 | 0.002 | 0.030 | |
| count_existing | 0.016 | 0.001 | 0.016 | |
| generate_data_covariables | 0.013 | 0.001 | 0.015 | |
| generate_dataset | 0.014 | 0.001 | 0.015 | |