Yannis Schumann
| Snapshot Date: 2025-03-20 13:00 -0400 (Thu, 20 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-24 12:08 -0400 (Mon, 24 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4521 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4448 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4414 |
| 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 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-03-20 23:45:57 -0400 (Thu, 20 Mar 2025) |
| EndedAt: 2025-03-20 23:48:20 -0400 (Thu, 20 Mar 2025) |
| EllapsedTime: 143.1 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 43.895 2.535 34.484
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
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")
2025-03-20 23:47:41.956409 INFO::Formatting Data.
2025-03-20 23:47:41.96224 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:42.002377 INFO::Removing potential empty rows and columns
2025-03-20 23:47:42.762129 INFO::Found 0 missing values.
2025-03-20 23:47:42.770095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:42.77105 INFO::Done
2025-03-20 23:47:42.771847 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:42.800708 INFO::Starting hierarchical adjustment
2025-03-20 23:47:42.802602 INFO::Found 3 batches.
2025-03-20 23:47:42.803872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:42.806353 INFO::Using default BPPARAM
2025-03-20 23:47:42.807842 INFO::Processing subtree level 1
2025-03-20 23:47:43.090116 INFO::Adjusting the last 1 batches sequentially
2025-03-20 23:47:43.095141 INFO::Done
2025-03-20 23:47:43.096622 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:43.104303 INFO::ASW Batch was -0.104818128790135 prior to batch effect correction and is now -0.104818128790135 .
2025-03-20 23:47:43.1065 INFO::Total function execution time is 1.15138387680054 s and adjustment time is 0.292896032333374 s ( 25.44 )
2025-03-20 23:47:43.139019 INFO::Formatting Data.
2025-03-20 23:47:43.140634 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:43.142711 INFO::Removing potential empty rows and columns
2025-03-20 23:47:43.145512 INFO::Found 0 missing values.
2025-03-20 23:47:43.148295 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.
2025-03-20 23:47:43.183334 INFO::Formatting Data.
2025-03-20 23:47:43.184959 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:43.18696 INFO::Removing potential empty rows and columns
2025-03-20 23:47:43.189747 INFO::Found 0 missing values.
2025-03-20 23:47:43.192116 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.
2025-03-20 23:47:43.238105 INFO::Formatting Data.
2025-03-20 23:47:43.239872 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:43.242831 INFO::Removing potential empty rows and columns
2025-03-20 23:47:43.245449 INFO::Found 0 missing values.
2025-03-20 23:47:43.249516 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.
2025-03-20 23:47:43.265417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:43.26691 INFO::Done
2025-03-20 23:47:43.268211 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:43.273646 INFO::Starting hierarchical adjustment
2025-03-20 23:47:43.275614 INFO::Found 2 batches.
2025-03-20 23:47:43.276978 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:43.278765 INFO::Using default BPPARAM
2025-03-20 23:47:43.282428 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:43.285188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:43.346915 INFO::Done
2025-03-20 23:47:43.348574 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:43.353456 INFO::ASW Batch was 0.00673061209015998 prior to batch effect correction and is now -0.121168885168946 .
2025-03-20 23:47:43.355579 INFO::Total function execution time is 0.117563009262085 s and adjustment time is 0.0716609954833984 s ( 60.96 )
2025-03-20 23:47:43.362575 INFO::Formatting Data.
2025-03-20 23:47:43.364154 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:43.387607 INFO::Formatting Data.
2025-03-20 23:47:43.389544 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:43.391594 INFO::Removing potential empty rows and columns
2025-03-20 23:47:43.394282 INFO::Found 0 missing values.
2025-03-20 23:47:43.4053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:43.40682 INFO::Done
2025-03-20 23:47:43.408086 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:43.413498 INFO::Starting hierarchical adjustment
2025-03-20 23:47:43.415382 INFO::Found 2 batches.
2025-03-20 23:47:43.416655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:43.418283 INFO::Using default BPPARAM
2025-03-20 23:47:43.419718 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:43.423377 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:43.46577 INFO::Done
2025-03-20 23:47:43.467256 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:43.47194 INFO::ASW Batch was -0.018617357275252 prior to batch effect correction and is now -0.121112059360938 .
2025-03-20 23:47:43.473847 INFO::Total function execution time is 0.0863780975341797 s and adjustment time is 0.0508010387420654 s ( 58.81 )
2025-03-20 23:47:43.477141 INFO::Formatting Data.
2025-03-20 23:47:43.478648 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:43.48064 INFO::Removing potential empty rows and columns
2025-03-20 23:47:43.483164 INFO::Found 0 missing values.
2025-03-20 23:47:43.490727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:43.492119 INFO::Done
2025-03-20 23:47:43.493316 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:43.498162 INFO::Starting hierarchical adjustment
2025-03-20 23:47:43.499919 INFO::Found 2 batches.
2025-03-20 23:47:43.501179 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:43.502654 INFO::Using default BPPARAM
2025-03-20 23:47:43.503875 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:43.506014 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:43.54735 INFO::Done
2025-03-20 23:47:43.548798 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:43.554289 INFO::ASW Batch was -0.018617357275252 prior to batch effect correction and is now -0.121112059360938 .
2025-03-20 23:47:43.556124 INFO::Total function execution time is 0.0796990394592285 s and adjustment time is 0.0477731227874756 s ( 59.94 )
2025-03-20 23:47:50.121497 INFO::Formatting Data.
2025-03-20 23:47:50.124024 INFO::Recognized SummarizedExperiment
2025-03-20 23:47:50.125352 INFO::Typecasting input to dataframe.
2025-03-20 23:47:50.204777 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:50.207752 INFO::Removing potential empty rows and columns
2025-03-20 23:47:50.222291 INFO::Found 0 missing values.
2025-03-20 23:47:50.244817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:50.246217 INFO::Done
2025-03-20 23:47:50.247526 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:50.258331 INFO::Starting hierarchical adjustment
2025-03-20 23:47:50.260171 INFO::Found 2 batches.
2025-03-20 23:47:50.261614 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:50.264136 INFO::Using default BPPARAM
2025-03-20 23:47:50.266562 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:50.269045 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:50.415154 INFO::Done
2025-03-20 23:47:50.416498 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:50.424621 INFO::ASW Batch was -0.00974924661069978 prior to batch effect correction and is now -0.0933028682672689 .
2025-03-20 23:47:50.426508 INFO::Total function execution time is 0.30579686164856 s and adjustment time is 0.154077053070068 s ( 50.39 )
2025-03-20 23:47:50.475777 INFO::Formatting Data.
2025-03-20 23:47:50.477267 INFO::Recognized SummarizedExperiment
2025-03-20 23:47:50.47851 INFO::Typecasting input to dataframe.
2025-03-20 23:47:50.505008 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:50.507615 INFO::Removing potential empty rows and columns
2025-03-20 23:47:50.51931 INFO::Found 0 missing values.
2025-03-20 23:47:50.545201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:50.546563 INFO::Done
2025-03-20 23:47:50.548297 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:50.557835 INFO::Starting hierarchical adjustment
2025-03-20 23:47:50.559703 INFO::Found 2 batches.
2025-03-20 23:47:50.561019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:50.562501 INFO::Using default BPPARAM
2025-03-20 23:47:50.563788 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:50.566199 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:50.649747 INFO::Done
2025-03-20 23:47:50.651255 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:50.660516 INFO::ASW Batch was 0.0249650501171398 prior to batch effect correction and is now 0.0249650501171398 .
2025-03-20 23:47:50.662587 INFO::Total function execution time is 0.186718940734863 s and adjustment time is 0.0903918743133545 s ( 48.41 )
2025-03-20 23:47:50.718191 INFO::Formatting Data.
2025-03-20 23:47:50.719822 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:50.721905 INFO::Removing potential empty rows and columns
2025-03-20 23:47:50.724507 INFO::Found 0 missing values.
2025-03-20 23:47:50.733121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:50.734626 INFO::Done
2025-03-20 23:47:50.736351 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:50.74155 INFO::Starting hierarchical adjustment
2025-03-20 23:47:50.743536 INFO::Found 3 batches.
2025-03-20 23:47:50.746002 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:50.748002 INFO::Using default BPPARAM
2025-03-20 23:47:50.749329 INFO::Processing subtree level 1
2025-03-20 23:47:51.120938 INFO::Adjusting the last 1 batches sequentially
2025-03-20 23:47:51.13035 INFO::Done
2025-03-20 23:47:51.13268 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:51.144376 INFO::ASW Batch was -0.131850916221415 prior to batch effect correction and is now -0.173834091939434 .
2025-03-20 23:47:51.147823 INFO::Total function execution time is 0.429191112518311 s and adjustment time is 0.387224912643433 s ( 90.22 )
2025-03-20 23:47:51.191062 INFO::Skipping initial DF formatting
2025-03-20 23:47:51.192545 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:51.202849 INFO::Starting hierarchical adjustment
2025-03-20 23:47:51.205812 INFO::Found 5 batches.
2025-03-20 23:47:51.20797 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:51.210474 INFO::Using default BPPARAM
2025-03-20 23:47:51.212008 INFO::Processing subtree level 1
2025-03-20 23:47:51.517145 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:51.528601 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:51.600088 INFO::Done
2025-03-20 23:47:51.602457 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:51.618754 INFO::ASW Batch was 0.539828700434406 prior to batch effect correction and is now 0.539828700434406 .
2025-03-20 23:47:51.620792 INFO::ASW Label was 0.33935670944448 prior to batch effect correction and is now 0.33935670944448 .
2025-03-20 23:47:51.625328 INFO::Total function execution time is 0.433634996414185 s and adjustment time is 0.39541482925415 s ( 91.19 )
2025-03-20 23:47:51.682118 INFO::Formatting Data.
2025-03-20 23:47:51.683964 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:51.686374 INFO::Removing potential empty rows and columns
2025-03-20 23:47:51.690191 INFO::Found 0 missing values.
2025-03-20 23:47:51.703404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:51.704847 INFO::Done
2025-03-20 23:47:51.70608 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:51.714957 INFO::Starting hierarchical adjustment
2025-03-20 23:47:51.716941 INFO::Found 5 batches.
2025-03-20 23:47:51.718322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:51.719891 INFO::Using default BPPARAM
2025-03-20 23:47:51.721882 INFO::Processing subtree level 1
2025-03-20 23:47:51.979513 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:51.991535 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:52.048571 INFO::Done
2025-03-20 23:47:52.051193 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:52.059454 INFO::ASW Batch was 0.590915844980338 prior to batch effect correction and is now -0.0130582616939231 .
2025-03-20 23:47:52.061687 INFO::ASW Label was 0.123316394874578 prior to batch effect correction and is now 0.6048878341768 .
2025-03-20 23:47:52.064819 INFO::Total function execution time is 0.382766008377075 s and adjustment time is 0.332041025161743 s ( 86.75 )
2025-03-20 23:47:52.067125 INFO::Formatting Data.
2025-03-20 23:47:52.070557 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:52.073129 INFO::Removing potential empty rows and columns
2025-03-20 23:47:52.075976 INFO::Found 0 missing values.
2025-03-20 23:47:52.089559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:52.091431 INFO::Done
2025-03-20 23:47:52.092862 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:52.100999 INFO::Starting hierarchical adjustment
2025-03-20 23:47:52.103063 INFO::Found 5 batches.
2025-03-20 23:47:52.104545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:52.106219 INFO::Using default BPPARAM
2025-03-20 23:47:52.107591 INFO::Processing subtree level 1
2025-03-20 23:47:52.368333 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:52.378631 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:52.43555 INFO::Done
2025-03-20 23:47:52.437728 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:52.446626 INFO::ASW Batch was 0.590915844980338 prior to batch effect correction and is now -0.0130582616939231 .
2025-03-20 23:47:52.448313 INFO::ASW Label was 0.123316394874578 prior to batch effect correction and is now 0.6048878341768 .
2025-03-20 23:47:52.451717 INFO::Total function execution time is 0.384571075439453 s and adjustment time is 0.332866907119751 s ( 86.56 )
2025-03-20 23:47:52.493133 INFO::Formatting Data.
2025-03-20 23:47:52.496227 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:52.498531 INFO::Removing potential empty rows and columns
2025-03-20 23:47:52.50169 INFO::Found 0 missing values.
2025-03-20 23:47:52.512674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:52.514225 INFO::Done
2025-03-20 23:47:52.515613 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:52.522888 INFO::Starting hierarchical adjustment
2025-03-20 23:47:52.524824 INFO::Found 5 batches.
2025-03-20 23:47:52.527772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:52.530247 INFO::Using default BPPARAM
2025-03-20 23:47:52.531818 INFO::Processing subtree level 1
2025-03-20 23:47:52.791222 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:52.801455 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:52.861346 INFO::Done
2025-03-20 23:47:52.864179 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:52.872621 INFO::ASW Batch was 0.40763722535022 prior to batch effect correction and is now -0.0936145790621835 .
2025-03-20 23:47:52.874299 INFO::ASW Label was 0.298957989866439 prior to batch effect correction and is now 0.837311642896046 .
2025-03-20 23:47:52.877629 INFO::Total function execution time is 0.384459018707275 s and adjustment time is 0.336905002593994 s ( 87.63 )
2025-03-20 23:47:52.88005 INFO::Formatting Data.
2025-03-20 23:47:52.882159 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:52.885132 INFO::Removing potential empty rows and columns
2025-03-20 23:47:52.888016 INFO::Found 0 missing values.
2025-03-20 23:47:52.89974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:52.901283 INFO::Done
2025-03-20 23:47:52.903607 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:52.911417 INFO::Starting hierarchical adjustment
2025-03-20 23:47:52.914257 INFO::Found 5 batches.
2025-03-20 23:47:52.915791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:52.917218 INFO::Using default BPPARAM
2025-03-20 23:47:52.918535 INFO::Processing subtree level 1
2025-03-20 23:47:53.181272 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:53.193914 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:53.256945 INFO::Done
2025-03-20 23:47:53.25873 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:53.267212 INFO::ASW Batch was 0.40763722535022 prior to batch effect correction and is now -0.0936145790621835 .
2025-03-20 23:47:53.269234 INFO::ASW Label was 0.298957989866439 prior to batch effect correction and is now 0.837311642896046 .
2025-03-20 23:47:53.273513 INFO::Total function execution time is 0.393466949462891 s and adjustment time is 0.343916893005371 s ( 87.41 )
2025-03-20 23:47:53.320995 INFO::Formatting Data.
2025-03-20 23:47:53.322821 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:53.325108 INFO::Removing potential empty rows and columns
2025-03-20 23:47:53.327816 INFO::Found 0 missing values.
2025-03-20 23:47:53.337428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:53.338907 INFO::Done
2025-03-20 23:47:53.340051 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:53.348363 INFO::Starting hierarchical adjustment
2025-03-20 23:47:53.350353 INFO::Found 2 batches.
2025-03-20 23:47:53.351844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:53.353426 INFO::Using default BPPARAM
2025-03-20 23:47:53.354724 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:53.356971 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:53.39551 INFO::Done
2025-03-20 23:47:53.397318 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:53.404585 INFO::ASW Batch was 0.728686719581576 prior to batch effect correction and is now 0.0234775524568955 .
2025-03-20 23:47:53.406167 INFO::ASW Label was 0.353952949167967 prior to batch effect correction and is now 0.880887755500689 .
2025-03-20 23:47:53.408065 INFO::Total function execution time is 0.0872189998626709 s and adjustment time is 0.045536994934082 s ( 52.21 )
2025-03-20 23:47:53.410817 INFO::Formatting Data.
2025-03-20 23:47:53.412602 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:53.414935 INFO::Removing potential empty rows and columns
2025-03-20 23:47:53.417796 INFO::Found 0 missing values.
2025-03-20 23:47:53.427346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:53.428848 INFO::Done
2025-03-20 23:47:53.430112 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:53.438637 INFO::Starting hierarchical adjustment
2025-03-20 23:47:53.440661 INFO::Found 2 batches.
2025-03-20 23:47:53.442042 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:53.444549 INFO::Using default BPPARAM
2025-03-20 23:47:53.446549 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:53.449112 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:53.490528 INFO::Done
2025-03-20 23:47:53.493704 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:53.500902 INFO::ASW Batch was 0.728686719581576 prior to batch effect correction and is now 0.0234775524568955 .
2025-03-20 23:47:53.502487 INFO::ASW Label was 0.353952949167967 prior to batch effect correction and is now 0.880887755500689 .
2025-03-20 23:47:53.506313 INFO::Total function execution time is 0.0957059860229492 s and adjustment time is 0.0502970218658447 s ( 52.55 )
2025-03-20 23:47:53.536756 INFO::Formatting Data.
2025-03-20 23:47:53.538739 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:53.541019 INFO::Removing potential empty rows and columns
2025-03-20 23:47:53.543325 INFO::Found 0 missing values.
2025-03-20 23:47:53.550657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:53.552222 INFO::Done
2025-03-20 23:47:53.553541 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:53.558362 INFO::Starting hierarchical adjustment
2025-03-20 23:47:53.560221 INFO::Found 2 batches.
2025-03-20 23:47:53.561584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:53.563682 INFO::Using default BPPARAM
2025-03-20 23:47:53.5656 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:53.568205 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:53.663088 INFO::Done
2025-03-20 23:47:53.664574 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:53.66957 INFO::ASW Batch was 0.223424770254674 prior to batch effect correction and is now -0.102630873470485 .
2025-03-20 23:47:53.671604 INFO::Total function execution time is 0.13493013381958 s and adjustment time is 0.103216171264648 s ( 76.5 )
2025-03-20 23:47:53.703788 INFO::Formatting Data.
2025-03-20 23:47:53.705484 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:53.70762 INFO::Removing potential empty rows and columns
2025-03-20 23:47:53.711024 INFO::Found 0 missing values.
2025-03-20 23:47:53.714242 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.
2025-03-20 23:47:53.727642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:53.729071 INFO::Done
2025-03-20 23:47:53.731068 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:53.74121 INFO::Starting hierarchical adjustment
2025-03-20 23:47:53.743061 INFO::Found 2 batches.
2025-03-20 23:47:53.744419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:53.747566 INFO::Using default BPPARAM
2025-03-20 23:47:53.748908 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:53.751232 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:53.797688 INFO::Done
2025-03-20 23:47:53.79925 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:53.806522 INFO::ASW Batch was 0.55020775241358 prior to batch effect correction and is now -0.0273110327548212 .
2025-03-20 23:47:53.808052 INFO::ASW Label was 0.46613835920373 prior to batch effect correction and is now 0.938286625362276 .
2025-03-20 23:47:53.811073 INFO::Total function execution time is 0.106348991394043 s and adjustment time is 0.0549709796905518 s ( 51.69 )
2025-03-20 23:47:53.81331 INFO::Formatting Data.
2025-03-20 23:47:53.815055 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:53.817403 INFO::Removing potential empty rows and columns
2025-03-20 23:47:53.819929 INFO::Found 0 missing values.
2025-03-20 23:47:53.822408 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.
2025-03-20 23:47:53.835827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:53.837255 INFO::Done
2025-03-20 23:47:53.838512 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:53.847067 INFO::Starting hierarchical adjustment
2025-03-20 23:47:53.849045 INFO::Found 2 batches.
2025-03-20 23:47:53.850627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:53.852422 INFO::Using default BPPARAM
2025-03-20 23:47:53.855994 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:47:53.858576 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:47:53.91009 INFO::Done
2025-03-20 23:47:53.912798 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:53.919976 INFO::ASW Batch was 0.55020775241358 prior to batch effect correction and is now -0.0273110327548212 .
2025-03-20 23:47:53.92159 INFO::ASW Label was 0.46613835920373 prior to batch effect correction and is now 0.938286625362276 .
2025-03-20 23:47:53.923946 INFO::Total function execution time is 0.11070704460144 s and adjustment time is 0.0614669322967529 s ( 55.52 )
2025-03-20 23:47:54.548837 INFO::Formatting Data.
2025-03-20 23:47:54.55121 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:54.554177 INFO::Removing potential empty rows and columns
2025-03-20 23:47:54.558087 INFO::Found 0 missing values.
2025-03-20 23:47:54.56968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:54.571329 INFO::Done
2025-03-20 23:47:54.572944 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:54.578245 INFO::Starting hierarchical adjustment
2025-03-20 23:47:54.58135 INFO::Found 3 batches.
2025-03-20 23:47:54.582869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:54.584563 INFO::Using default BPPARAM
2025-03-20 23:47:54.58621 INFO::Processing subtree level 1
2025-03-20 23:47:54.828164 INFO::Adjusting the last 1 batches sequentially
2025-03-20 23:47:54.838645 INFO::Done
2025-03-20 23:47:54.841678 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:54.853189 INFO::ASW Batch was -0.0525562705571138 prior to batch effect correction and is now -0.0525562705571138 .
2025-03-20 23:47:54.858668 INFO::Total function execution time is 0.308633804321289 s and adjustment time is 0.258356094360352 s ( 83.71 )
2025-03-20 23:47:54.861959 INFO::Formatting Data.
2025-03-20 23:47:54.863746 INFO::Typecasting input to dataframe.
2025-03-20 23:47:54.867116 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:54.870029 INFO::Removing potential empty rows and columns
2025-03-20 23:47:54.874561 INFO::Found 0 missing values.
2025-03-20 23:47:54.883017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:54.884478 INFO::Done
2025-03-20 23:47:54.885774 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:54.890517 INFO::Starting hierarchical adjustment
2025-03-20 23:47:54.892887 INFO::Found 3 batches.
2025-03-20 23:47:54.894252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:54.895874 INFO::Using default BPPARAM
2025-03-20 23:47:54.898203 INFO::Processing subtree level 1
2025-03-20 23:47:55.1416 INFO::Adjusting the last 1 batches sequentially
2025-03-20 23:47:55.150863 INFO::Done
2025-03-20 23:47:55.153528 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:55.16357 INFO::ASW Batch was -0.0525562705571138 prior to batch effect correction and is now -0.0525562705571138 .
2025-03-20 23:47:55.168092 INFO::Total function execution time is 0.305499076843262 s and adjustment time is 0.258323192596436 s ( 84.56 )
2025-03-20 23:47:55.218156 INFO::Formatting Data.
2025-03-20 23:47:55.22087 INFO::Typecasting input to dataframe.
2025-03-20 23:47:55.223937 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:55.228227 INFO::Removing potential empty rows and columns
2025-03-20 23:47:55.232495 INFO::Found 0 missing values.
2025-03-20 23:47:55.241966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:55.243441 INFO::Done
2025-03-20 23:47:55.244797 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:55.24959 INFO::Starting hierarchical adjustment
2025-03-20 23:47:55.251471 INFO::Found 3 batches.
2025-03-20 23:47:55.252802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:55.254421 INFO::Using default BPPARAM
2025-03-20 23:47:55.256452 INFO::Processing subtree level 1
2025-03-20 23:47:55.743854 INFO::Adjusting the last 1 batches sequentially
2025-03-20 23:47:55.749912 INFO::Done
2025-03-20 23:47:55.751669 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:55.788923 INFO::ASW Batch was -0.0852256428615144 prior to batch effect correction and is now -0.0852256428615144 .
2025-03-20 23:47:55.80052 INFO::Total function execution time is 0.580818176269531 s and adjustment time is 0.498755931854248 s ( 85.87 )
2025-03-20 23:47:56.435866 INFO::Formatting Data.
2025-03-20 23:47:56.438544 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:56.441652 INFO::Removing potential empty rows and columns
2025-03-20 23:47:56.448839 INFO::Found 1000 missing values.
2025-03-20 23:47:56.524651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:56.526773 INFO::Done
2025-03-20 23:47:56.528146 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:56.543402 INFO::Starting hierarchical adjustment
2025-03-20 23:47:56.545532 INFO::Found 10 batches.
2025-03-20 23:47:56.547151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:47:56.550639 INFO::Using default BPPARAM
2025-03-20 23:47:56.55211 INFO::Processing subtree level 1
2025-03-20 23:47:56.971932 INFO::Processing subtree level 2
2025-03-20 23:47:57.5664 INFO::Adjusting the last 1 batches sequentially
2025-03-20 23:47:57.579197 INFO::Done
2025-03-20 23:47:57.582875 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:47:57.603577 INFO::ASW Batch was 0.509020036521719 prior to batch effect correction and is now 0.509020036521719 .
2025-03-20 23:47:57.605215 INFO::ASW Label was 0.332073127266776 prior to batch effect correction and is now 0.332073127266776 .
2025-03-20 23:47:57.609673 INFO::Total function execution time is 1.17381906509399 s and adjustment time is 1.0340781211853 s ( 88.1 )
2025-03-20 23:47:57.613914 INFO::Formatting Data.
2025-03-20 23:47:57.616537 INFO::Replacing NaNs with NAs.
2025-03-20 23:47:57.619855 INFO::Removing potential empty rows and columns
2025-03-20 23:47:57.628795 INFO::Found 1000 missing values.
2025-03-20 23:47:57.699796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:47:57.701355 INFO::Done
2025-03-20 23:47:57.702661 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:47:57.715585 INFO::Starting hierarchical adjustment
2025-03-20 23:47:57.717702 INFO::Found 10 batches.
2025-03-20 23:47:59.106534 INFO::Set up parallel execution backend with 2 workers
2025-03-20 23:47:59.107852 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-20 23:48:01.627987 INFO::Adjusting the last 2 batches sequentially
2025-03-20 23:48:01.631048 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-20 23:48:01.684028 INFO::Done
2025-03-20 23:48:01.685304 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:48:01.700565 INFO::ASW Batch was 0.509020036521719 prior to batch effect correction and is now 0.509020036521719 .
2025-03-20 23:48:01.701992 INFO::ASW Label was 0.332073127266776 prior to batch effect correction and is now 0.332073127266776 .
2025-03-20 23:48:01.703788 INFO::Total function execution time is 4.09024000167847 s and adjustment time is 3.96683192253113 s ( 96.98 )
2025-03-20 23:48:02.12286 INFO::Formatting Data.
2025-03-20 23:48:02.126188 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:02.128503 INFO::Removing potential empty rows and columns
2025-03-20 23:48:02.131261 INFO::Found 0 missing values.
2025-03-20 23:48:02.142708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:02.144195 INFO::Done
2025-03-20 23:48:02.145428 INFO::Acquiring quality metrics before batch effect correction.
2025-03-20 23:48:02.151922 INFO::Starting hierarchical adjustment
2025-03-20 23:48:02.153773 INFO::Found 3 batches.
2025-03-20 23:48:02.155074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-20 23:48:02.156631 INFO::Using default BPPARAM
2025-03-20 23:48:02.158024 INFO::Processing subtree level 1
2025-03-20 23:48:02.474929 INFO::Adjusting the last 1 batches sequentially
2025-03-20 23:48:02.486612 INFO::Done
2025-03-20 23:48:02.488756 INFO::Acquiring quality metrics after batch effect correction.
2025-03-20 23:48:02.502061 INFO::ASW Batch was 0.173535152634962 prior to batch effect correction and is now -0.170289992756901 .
2025-03-20 23:48:02.504342 INFO::ASW Label was -0.195674104126924 prior to batch effect correction and is now -0.0191249140490355 .
2025-03-20 23:48:02.510424 INFO::Total function execution time is 0.387537002563477 s and adjustment time is 0.333191871643066 s ( 85.98 )
2025-03-20 23:48:02.89243 INFO::Formatting Data.
2025-03-20 23:48:02.896784 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:02.899059 INFO::Removing potential empty rows and columns
2025-03-20 23:48:02.901835 INFO::Found 2 missing values.
2025-03-20 23:48:02.910812 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:02.912564 INFO::Done
2025-03-20 23:48:03.003404 INFO::Found NA in Reference column
2025-03-20 23:48:03.034182 INFO::Require at least two references per batch.
2025-03-20 23:48:03.101221 INFO::Formatting Data.
2025-03-20 23:48:03.103334 INFO::Recognized SummarizedExperiment
2025-03-20 23:48:03.104745 INFO::Typecasting input to dataframe.
2025-03-20 23:48:03.133543 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.137431 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.150723 INFO::Found 0 missing values.
2025-03-20 23:48:03.179329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.18086 INFO::Done
2025-03-20 23:48:03.224596 INFO::Formatting Data.
2025-03-20 23:48:03.226924 INFO::Recognized SummarizedExperiment
2025-03-20 23:48:03.228462 INFO::Typecasting input to dataframe.
2025-03-20 23:48:03.283335 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.286162 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.301208 INFO::Found 0 missing values.
2025-03-20 23:48:03.348713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.350801 INFO::Done
2025-03-20 23:48:03.400553 INFO::Formatting Data.
2025-03-20 23:48:03.402213 INFO::Recognized SummarizedExperiment
2025-03-20 23:48:03.403442 INFO::Typecasting input to dataframe.
2025-03-20 23:48:03.459124 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.461526 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.467282 INFO::Found 0 missing values.
2025-03-20 23:48:03.470149 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.
2025-03-20 23:48:03.483977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.485598 INFO::Done
2025-03-20 23:48:03.521061 INFO::Formatting Data.
2025-03-20 23:48:03.522934 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.525144 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.527804 INFO::Found 0 missing values.
2025-03-20 23:48:03.536419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.537987 INFO::Done
2025-03-20 23:48:03.578012 INFO::Formatting Data.
2025-03-20 23:48:03.580348 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.582458 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.584902 INFO::Found 0 missing values.
2025-03-20 23:48:03.594297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.595809 INFO::Done
2025-03-20 23:48:03.688419 INFO::Formatting Data.
2025-03-20 23:48:03.691165 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.694104 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.697487 INFO::Found 1 missing values.
2025-03-20 23:48:03.706888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.708449 INFO::Done
2025-03-20 23:48:03.772403 INFO::Formatting Data.
2025-03-20 23:48:03.774321 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.776901 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.779686 INFO::Found 2 missing values.
2025-03-20 23:48:03.782161 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.
2025-03-20 23:48:03.789853 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.791472 INFO::Done
2025-03-20 23:48:03.821618 INFO::Formatting Data.
2025-03-20 23:48:03.823952 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.826569 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.830529 INFO::Found 2 missing values.
2025-03-20 23:48:03.835019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.836477 INFO::Done
2025-03-20 23:48:03.874114 INFO::Formatting Data.
2025-03-20 23:48:03.875999 INFO::Typecasting input to dataframe.
2025-03-20 23:48:03.878104 INFO::Replacing NaNs with NAs.
2025-03-20 23:48:03.880973 INFO::Removing potential empty rows and columns
2025-03-20 23:48:03.885585 INFO::Found 0 missing values.
2025-03-20 23:48:03.899805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-20 23:48:03.901494 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.210 7.193 44.711
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.895 | 2.535 | 34.484 | |
| compute_asw | 0.058 | 0.002 | 0.063 | |
| count_existing | 0.028 | 0.001 | 0.034 | |
| generate_data_covariables | 0.024 | 0.001 | 0.032 | |
| generate_dataset | 0.025 | 0.002 | 0.034 | |