Yannis Schumann
| Snapshot Date: 2025-02-14 13:40 -0500 (Fri, 14 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 2025-02-15 11:42 -0500 (Sat, 15 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" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| 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: 2025-02-14 18:57:21 -0500 (Fri, 14 Feb 2025) |
| EndedAt: 2025-02-14 18:58:44 -0500 (Fri, 14 Feb 2025) |
| EllapsedTime: 82.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.6.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 25.587 1.416 18.514
* 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")
2025-02-14 18:58:22.426017 INFO::Formatting Data.
2025-02-14 18:58:22.430396 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:22.446988 INFO::Removing potential empty rows and columns
2025-02-14 18:58:22.782928 INFO::Found 0 missing values.
2025-02-14 18:58:22.787962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:22.788922 INFO::Done
2025-02-14 18:58:22.789712 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:22.807431 INFO::Starting hierarchical adjustment
2025-02-14 18:58:22.808868 INFO::Found 3 batches.
2025-02-14 18:58:22.809819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:22.811532 INFO::Using default BPPARAM
2025-02-14 18:58:22.812411 INFO::Processing subtree level 1
2025-02-14 18:58:22.993804 INFO::Adjusting the last 1 batches sequentially
2025-02-14 18:58:23.002241 INFO::Done
2025-02-14 18:58:23.004047 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:23.010121 INFO::ASW Batch was -0.0763744420610023 prior to batch effect correction and is now -0.0763744420610023 .
2025-02-14 18:58:23.012182 INFO::Total function execution time is 0.586484909057617 s and adjustment time is 0.193711996078491 s ( 33.03 )
2025-02-14 18:58:23.038115 INFO::Formatting Data.
2025-02-14 18:58:23.039342 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:23.040922 INFO::Removing potential empty rows and columns
2025-02-14 18:58:23.042661 INFO::Found 0 missing values.
2025-02-14 18:58:23.04414 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.
2025-02-14 18:58:23.059804 INFO::Formatting Data.
2025-02-14 18:58:23.061425 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:23.062847 INFO::Removing potential empty rows and columns
2025-02-14 18:58:23.064792 INFO::Found 0 missing values.
2025-02-14 18:58:23.066382 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.
2025-02-14 18:58:23.090613 INFO::Formatting Data.
2025-02-14 18:58:23.091776 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:23.093501 INFO::Removing potential empty rows and columns
2025-02-14 18:58:23.095083 INFO::Found 0 missing values.
2025-02-14 18:58:23.096697 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.
2025-02-14 18:58:23.101813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:23.102788 INFO::Done
2025-02-14 18:58:23.103765 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:23.106392 INFO::Starting hierarchical adjustment
2025-02-14 18:58:23.107546 INFO::Found 2 batches.
2025-02-14 18:58:23.108404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:23.109429 INFO::Using default BPPARAM
2025-02-14 18:58:23.110509 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:23.112085 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:23.1459 INFO::Done
2025-02-14 18:58:23.147089 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:23.149314 INFO::ASW Batch was -0.0124419296033673 prior to batch effect correction and is now -0.120103070846692 .
2025-02-14 18:58:23.150553 INFO::Total function execution time is 0.0600957870483398 s and adjustment time is 0.0385880470275879 s ( 64.21 )
2025-02-14 18:58:23.153567 INFO::Formatting Data.
2025-02-14 18:58:23.154225 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:23.165571 INFO::Formatting Data.
2025-02-14 18:58:23.166796 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:23.168121 INFO::Removing potential empty rows and columns
2025-02-14 18:58:23.169627 INFO::Found 0 missing values.
2025-02-14 18:58:23.207108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:23.20806 INFO::Done
2025-02-14 18:58:23.208566 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:23.210589 INFO::Starting hierarchical adjustment
2025-02-14 18:58:23.211253 INFO::Found 2 batches.
2025-02-14 18:58:23.211725 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:23.212518 INFO::Using default BPPARAM
2025-02-14 18:58:23.213105 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:23.21393 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:23.233726 INFO::Done
2025-02-14 18:58:23.234735 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:23.237917 INFO::ASW Batch was -0.00562873781823779 prior to batch effect correction and is now -0.108238718664964 .
2025-02-14 18:58:23.238866 INFO::Total function execution time is 0.073422908782959 s and adjustment time is 0.0224628448486328 s ( 30.59 )
2025-02-14 18:58:23.240068 INFO::Formatting Data.
2025-02-14 18:58:23.240865 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:23.24192 INFO::Removing potential empty rows and columns
2025-02-14 18:58:23.243349 INFO::Found 0 missing values.
2025-02-14 18:58:23.247557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:23.248127 INFO::Done
2025-02-14 18:58:23.248918 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:23.251002 INFO::Starting hierarchical adjustment
2025-02-14 18:58:23.251725 INFO::Found 2 batches.
2025-02-14 18:58:23.252477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:23.253293 INFO::Using default BPPARAM
2025-02-14 18:58:23.254016 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:23.255298 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:23.275818 INFO::Done
2025-02-14 18:58:23.276798 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:23.279559 INFO::ASW Batch was -0.00562873781823779 prior to batch effect correction and is now -0.108238718664964 .
2025-02-14 18:58:23.280661 INFO::Total function execution time is 0.0405640602111816 s and adjustment time is 0.0242300033569336 s ( 59.73 )
2025-02-14 18:58:26.568038 INFO::Formatting Data.
2025-02-14 18:58:26.568694 INFO::Recognized SummarizedExperiment
2025-02-14 18:58:26.569153 INFO::Typecasting input to dataframe.
2025-02-14 18:58:26.600875 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:26.602536 INFO::Removing potential empty rows and columns
2025-02-14 18:58:26.606971 INFO::Found 0 missing values.
2025-02-14 18:58:26.613607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:26.614262 INFO::Done
2025-02-14 18:58:26.614945 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:26.61888 INFO::Starting hierarchical adjustment
2025-02-14 18:58:26.619584 INFO::Found 2 batches.
2025-02-14 18:58:26.620163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:26.621766 INFO::Using default BPPARAM
2025-02-14 18:58:26.622439 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:26.62376 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:26.689712 INFO::Done
2025-02-14 18:58:26.690707 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:26.696008 INFO::ASW Batch was -0.019211056103666 prior to batch effect correction and is now -0.0930416727269034 .
2025-02-14 18:58:26.697285 INFO::Total function execution time is 0.129394054412842 s and adjustment time is 0.0702121257781982 s ( 54.26 )
2025-02-14 18:58:26.722132 INFO::Formatting Data.
2025-02-14 18:58:26.722857 INFO::Recognized SummarizedExperiment
2025-02-14 18:58:26.72349 INFO::Typecasting input to dataframe.
2025-02-14 18:58:26.732866 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:26.734144 INFO::Removing potential empty rows and columns
2025-02-14 18:58:26.738127 INFO::Found 0 missing values.
2025-02-14 18:58:26.745347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:26.746027 INFO::Done
2025-02-14 18:58:26.746547 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:26.749728 INFO::Starting hierarchical adjustment
2025-02-14 18:58:26.750417 INFO::Found 2 batches.
2025-02-14 18:58:26.750893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:26.751416 INFO::Using default BPPARAM
2025-02-14 18:58:26.751903 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:26.753223 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:26.781614 INFO::Done
2025-02-14 18:58:26.782277 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:26.785592 INFO::ASW Batch was -0.00871088244748032 prior to batch effect correction and is now -0.00871088244748032 .
2025-02-14 18:58:26.786848 INFO::Total function execution time is 0.0645999908447266 s and adjustment time is 0.0312907695770264 s ( 48.44 )
2025-02-14 18:58:26.812221 INFO::Formatting Data.
2025-02-14 18:58:26.812966 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:26.813982 INFO::Removing potential empty rows and columns
2025-02-14 18:58:26.81524 INFO::Found 0 missing values.
2025-02-14 18:58:26.819257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:26.820046 INFO::Done
2025-02-14 18:58:26.820794 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:26.822918 INFO::Starting hierarchical adjustment
2025-02-14 18:58:26.823567 INFO::Found 3 batches.
2025-02-14 18:58:26.824164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:26.825001 INFO::Using default BPPARAM
2025-02-14 18:58:26.825695 INFO::Processing subtree level 1
2025-02-14 18:58:27.224093 INFO::Adjusting the last 1 batches sequentially
2025-02-14 18:58:27.228344 INFO::Done
2025-02-14 18:58:27.229157 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:27.23367 INFO::ASW Batch was -0.0410334492770959 prior to batch effect correction and is now -0.181706691903878 .
2025-02-14 18:58:27.235346 INFO::Total function execution time is 0.42306113243103 s and adjustment time is 0.404863119125366 s ( 95.7 )
2025-02-14 18:58:27.496857 INFO::Skipping initial DF formatting
2025-02-14 18:58:27.497679 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:27.50216 INFO::Starting hierarchical adjustment
2025-02-14 18:58:27.503058 INFO::Found 5 batches.
2025-02-14 18:58:27.503577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:27.50417 INFO::Using default BPPARAM
2025-02-14 18:58:27.504655 INFO::Processing subtree level 1
2025-02-14 18:58:27.745923 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:27.75949 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:27.798014 INFO::Done
2025-02-14 18:58:27.799228 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:27.806211 INFO::ASW Batch was 0.484358667381183 prior to batch effect correction and is now 0.484358667381183 .
2025-02-14 18:58:27.806938 INFO::ASW Label was 0.37443462592591 prior to batch effect correction and is now 0.37443462592591 .
2025-02-14 18:58:27.808039 INFO::Total function execution time is 0.311293125152588 s and adjustment time is 0.295037984848022 s ( 94.78 )
2025-02-14 18:58:27.836027 INFO::Formatting Data.
2025-02-14 18:58:27.836854 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:27.838033 INFO::Removing potential empty rows and columns
2025-02-14 18:58:27.839561 INFO::Found 0 missing values.
2025-02-14 18:58:27.845248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:27.846069 INFO::Done
2025-02-14 18:58:27.846914 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:27.850446 INFO::Starting hierarchical adjustment
2025-02-14 18:58:27.851203 INFO::Found 5 batches.
2025-02-14 18:58:27.85188 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:27.852592 INFO::Using default BPPARAM
2025-02-14 18:58:27.853234 INFO::Processing subtree level 1
2025-02-14 18:58:28.057202 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:28.066454 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:28.094576 INFO::Done
2025-02-14 18:58:28.095646 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:28.100467 INFO::ASW Batch was 0.250442592359419 prior to batch effect correction and is now 0.00711841506452666 .
2025-02-14 18:58:28.101415 INFO::ASW Label was 0.576355384023008 prior to batch effect correction and is now 0.707279198068705 .
2025-02-14 18:58:28.102673 INFO::Total function execution time is 0.266648054122925 s and adjustment time is 0.243201017379761 s ( 91.21 )
2025-02-14 18:58:28.103967 INFO::Formatting Data.
2025-02-14 18:58:28.104868 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:28.106624 INFO::Removing potential empty rows and columns
2025-02-14 18:58:28.108133 INFO::Found 0 missing values.
2025-02-14 18:58:28.114194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:28.115099 INFO::Done
2025-02-14 18:58:28.115929 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:28.120208 INFO::Starting hierarchical adjustment
2025-02-14 18:58:28.121096 INFO::Found 5 batches.
2025-02-14 18:58:28.121594 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:28.122178 INFO::Using default BPPARAM
2025-02-14 18:58:28.122678 INFO::Processing subtree level 1
2025-02-14 18:58:28.316889 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:28.328112 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:28.35959 INFO::Done
2025-02-14 18:58:28.360757 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:28.366057 INFO::ASW Batch was 0.250442592359419 prior to batch effect correction and is now 0.00711841506452666 .
2025-02-14 18:58:28.367001 INFO::ASW Label was 0.576355384023008 prior to batch effect correction and is now 0.707279198068705 .
2025-02-14 18:58:28.367906 INFO::Total function execution time is 0.26403021812439 s and adjustment time is 0.238604068756104 s ( 90.37 )
2025-02-14 18:58:28.388159 INFO::Formatting Data.
2025-02-14 18:58:28.388983 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:28.389969 INFO::Removing potential empty rows and columns
2025-02-14 18:58:28.391441 INFO::Found 0 missing values.
2025-02-14 18:58:28.396687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:28.397586 INFO::Done
2025-02-14 18:58:28.398282 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:28.402037 INFO::Starting hierarchical adjustment
2025-02-14 18:58:28.402877 INFO::Found 5 batches.
2025-02-14 18:58:28.403433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:28.40439 INFO::Using default BPPARAM
2025-02-14 18:58:28.40513 INFO::Processing subtree level 1
2025-02-14 18:58:28.588963 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:28.606242 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:28.634185 INFO::Done
2025-02-14 18:58:28.635561 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:28.640465 INFO::ASW Batch was 0.488004765315091 prior to batch effect correction and is now -0.021481856235116 .
2025-02-14 18:58:28.641465 INFO::ASW Label was 0.302472994108337 prior to batch effect correction and is now 0.813996909774992 .
2025-02-14 18:58:28.642645 INFO::Total function execution time is 0.254637002944946 s and adjustment time is 0.231425046920776 s ( 90.88 )
2025-02-14 18:58:28.643503 INFO::Formatting Data.
2025-02-14 18:58:28.644113 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:28.645006 INFO::Removing potential empty rows and columns
2025-02-14 18:58:28.646446 INFO::Found 0 missing values.
2025-02-14 18:58:28.650483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:28.651066 INFO::Done
2025-02-14 18:58:28.651684 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:28.656927 INFO::Starting hierarchical adjustment
2025-02-14 18:58:28.6587 INFO::Found 5 batches.
2025-02-14 18:58:28.659558 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:28.660479 INFO::Using default BPPARAM
2025-02-14 18:58:28.661251 INFO::Processing subtree level 1
2025-02-14 18:58:28.829708 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:28.849022 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:28.886708 INFO::Done
2025-02-14 18:58:28.887628 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:28.891226 INFO::ASW Batch was 0.488004765315091 prior to batch effect correction and is now -0.021481856235116 .
2025-02-14 18:58:28.892514 INFO::ASW Label was 0.302472994108337 prior to batch effect correction and is now 0.813996909774992 .
2025-02-14 18:58:28.893974 INFO::Total function execution time is 0.25012993812561 s and adjustment time is 0.228239059448242 s ( 91.25 )
2025-02-14 18:58:28.91491 INFO::Formatting Data.
2025-02-14 18:58:28.915692 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:28.916907 INFO::Removing potential empty rows and columns
2025-02-14 18:58:28.918201 INFO::Found 0 missing values.
2025-02-14 18:58:28.920934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:28.921464 INFO::Done
2025-02-14 18:58:28.921956 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:28.924573 INFO::Starting hierarchical adjustment
2025-02-14 18:58:28.925242 INFO::Found 2 batches.
2025-02-14 18:58:28.925748 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:28.926481 INFO::Using default BPPARAM
2025-02-14 18:58:28.927233 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:28.928133 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:28.946242 INFO::Done
2025-02-14 18:58:28.946928 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:28.951 INFO::ASW Batch was 0.419989367609757 prior to batch effect correction and is now 0.0123084004132802 .
2025-02-14 18:58:28.951655 INFO::ASW Label was 0.500984904779566 prior to batch effect correction and is now 0.86143959272313 .
2025-02-14 18:58:28.952438 INFO::Total function execution time is 0.0376219749450684 s and adjustment time is 0.0210821628570557 s ( 56.04 )
2025-02-14 18:58:28.953165 INFO::Formatting Data.
2025-02-14 18:58:28.953903 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:28.955228 INFO::Removing potential empty rows and columns
2025-02-14 18:58:28.956675 INFO::Found 0 missing values.
2025-02-14 18:58:28.960226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:28.960963 INFO::Done
2025-02-14 18:58:28.961758 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:28.965254 INFO::Starting hierarchical adjustment
2025-02-14 18:58:28.966336 INFO::Found 2 batches.
2025-02-14 18:58:28.967116 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:28.968015 INFO::Using default BPPARAM
2025-02-14 18:58:28.968853 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:28.970767 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:28.989716 INFO::Done
2025-02-14 18:58:28.990736 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:28.995433 INFO::ASW Batch was 0.419989367609757 prior to batch effect correction and is now 0.0123084004132802 .
2025-02-14 18:58:28.99642 INFO::ASW Label was 0.500984904779566 prior to batch effect correction and is now 0.86143959272313 .
2025-02-14 18:58:28.997619 INFO::Total function execution time is 0.0443730354309082 s and adjustment time is 0.0235509872436523 s ( 53.07 )
2025-02-14 18:58:29.013765 INFO::Formatting Data.
2025-02-14 18:58:29.014537 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:29.01541 INFO::Removing potential empty rows and columns
2025-02-14 18:58:29.016266 INFO::Found 0 missing values.
2025-02-14 18:58:29.018146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:29.018636 INFO::Done
2025-02-14 18:58:29.019186 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:29.021342 INFO::Starting hierarchical adjustment
2025-02-14 18:58:29.022002 INFO::Found 2 batches.
2025-02-14 18:58:29.022489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:29.023031 INFO::Using default BPPARAM
2025-02-14 18:58:29.023504 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:29.025265 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:29.066812 INFO::Done
2025-02-14 18:58:29.06785 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:29.07055 INFO::ASW Batch was -0.138459758206415 prior to batch effect correction and is now -0.172954590162834 .
2025-02-14 18:58:29.0714 INFO::Total function execution time is 0.0577101707458496 s and adjustment time is 0.044849157333374 s ( 77.71 )
2025-02-14 18:58:29.090804 INFO::Formatting Data.
2025-02-14 18:58:29.091819 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:29.092712 INFO::Removing potential empty rows and columns
2025-02-14 18:58:29.094006 INFO::Found 0 missing values.
2025-02-14 18:58:29.096096 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.
2025-02-14 18:58:29.101424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:29.102464 INFO::Done
2025-02-14 18:58:29.103408 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:29.107129 INFO::Starting hierarchical adjustment
2025-02-14 18:58:29.108214 INFO::Found 2 batches.
2025-02-14 18:58:29.108753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:29.1093 INFO::Using default BPPARAM
2025-02-14 18:58:29.10978 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:29.111037 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:29.130076 INFO::Done
2025-02-14 18:58:29.131135 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:29.1344 INFO::ASW Batch was 0.366480677174859 prior to batch effect correction and is now -0.0245314319367675 .
2025-02-14 18:58:29.135022 INFO::ASW Label was 0.690424390286474 prior to batch effect correction and is now 0.954299539332578 .
2025-02-14 18:58:29.136227 INFO::Total function execution time is 0.0455000400543213 s and adjustment time is 0.022089958190918 s ( 48.55 )
2025-02-14 18:58:29.137264 INFO::Formatting Data.
2025-02-14 18:58:29.13806 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:29.139311 INFO::Removing potential empty rows and columns
2025-02-14 18:58:29.140515 INFO::Found 0 missing values.
2025-02-14 18:58:29.141978 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.
2025-02-14 18:58:29.146248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:29.146876 INFO::Done
2025-02-14 18:58:29.147454 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:29.151595 INFO::Starting hierarchical adjustment
2025-02-14 18:58:29.15269 INFO::Found 2 batches.
2025-02-14 18:58:29.15362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:29.154621 INFO::Using default BPPARAM
2025-02-14 18:58:29.15542 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:29.156916 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:29.177128 INFO::Done
2025-02-14 18:58:29.177895 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:29.18162 INFO::ASW Batch was 0.366480677174859 prior to batch effect correction and is now -0.0245314319367675 .
2025-02-14 18:58:29.182568 INFO::ASW Label was 0.690424390286474 prior to batch effect correction and is now 0.954299539332578 .
2025-02-14 18:58:29.183742 INFO::Total function execution time is 0.04646897315979 s and adjustment time is 0.024528980255127 s ( 52.79 )
2025-02-14 18:58:29.462662 INFO::Formatting Data.
2025-02-14 18:58:29.463788 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:29.465189 INFO::Removing potential empty rows and columns
2025-02-14 18:58:29.466751 INFO::Found 0 missing values.
2025-02-14 18:58:29.470736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:29.471555 INFO::Done
2025-02-14 18:58:29.472426 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:29.474263 INFO::Starting hierarchical adjustment
2025-02-14 18:58:29.474896 INFO::Found 3 batches.
2025-02-14 18:58:29.475377 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:29.476068 INFO::Using default BPPARAM
2025-02-14 18:58:29.476862 INFO::Processing subtree level 1
2025-02-14 18:58:29.603829 INFO::Adjusting the last 1 batches sequentially
2025-02-14 18:58:29.616354 INFO::Done
2025-02-14 18:58:29.618346 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:29.62759 INFO::ASW Batch was -0.0380000521982403 prior to batch effect correction and is now -0.0380000521982403 .
2025-02-14 18:58:29.629903 INFO::Total function execution time is 0.16713809967041 s and adjustment time is 0.141524791717529 s ( 84.68 )
2025-02-14 18:58:29.63204 INFO::Formatting Data.
2025-02-14 18:58:29.633997 INFO::Typecasting input to dataframe.
2025-02-14 18:58:29.635059 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:29.636539 INFO::Removing potential empty rows and columns
2025-02-14 18:58:29.638552 INFO::Found 0 missing values.
2025-02-14 18:58:29.64278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:29.644527 INFO::Done
2025-02-14 18:58:29.645137 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:29.647638 INFO::Starting hierarchical adjustment
2025-02-14 18:58:29.648571 INFO::Found 3 batches.
2025-02-14 18:58:29.649358 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:29.65064 INFO::Using default BPPARAM
2025-02-14 18:58:29.651173 INFO::Processing subtree level 1
2025-02-14 18:58:29.777335 INFO::Adjusting the last 1 batches sequentially
2025-02-14 18:58:29.818419 INFO::Done
2025-02-14 18:58:29.823152 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:29.839852 INFO::ASW Batch was -0.0380000521982403 prior to batch effect correction and is now -0.0380000521982403 .
2025-02-14 18:58:29.843975 INFO::Total function execution time is 0.210945844650269 s and adjustment time is 0.170078039169312 s ( 80.63 )
2025-02-14 18:58:29.872011 INFO::Formatting Data.
2025-02-14 18:58:29.872847 INFO::Typecasting input to dataframe.
2025-02-14 18:58:29.874326 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:29.875607 INFO::Removing potential empty rows and columns
2025-02-14 18:58:29.878508 INFO::Found 0 missing values.
2025-02-14 18:58:29.882922 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:29.883906 INFO::Done
2025-02-14 18:58:29.884799 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:29.886712 INFO::Starting hierarchical adjustment
2025-02-14 18:58:29.887651 INFO::Found 3 batches.
2025-02-14 18:58:29.888371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:29.889495 INFO::Using default BPPARAM
2025-02-14 18:58:29.890013 INFO::Processing subtree level 1
2025-02-14 18:58:30.006762 INFO::Adjusting the last 1 batches sequentially
2025-02-14 18:58:30.018807 INFO::Done
2025-02-14 18:58:30.02059 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:30.030339 INFO::ASW Batch was -0.0329490273783295 prior to batch effect correction and is now -0.0329490273783295 .
2025-02-14 18:58:30.032504 INFO::Total function execution time is 0.159925222396851 s and adjustment time is 0.131271123886108 s ( 82.08 )
2025-02-14 18:58:30.307985 INFO::Formatting Data.
2025-02-14 18:58:30.309636 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:30.312126 INFO::Removing potential empty rows and columns
2025-02-14 18:58:30.316727 INFO::Found 1000 missing values.
2025-02-14 18:58:30.343761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:30.345236 INFO::Done
2025-02-14 18:58:30.346072 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:30.354198 INFO::Starting hierarchical adjustment
2025-02-14 18:58:30.355398 INFO::Found 10 batches.
2025-02-14 18:58:30.356238 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:30.357907 INFO::Using default BPPARAM
2025-02-14 18:58:30.359533 INFO::Processing subtree level 1
2025-02-14 18:58:30.528718 INFO::Processing subtree level 2
2025-02-14 18:58:30.729515 INFO::Adjusting the last 1 batches sequentially
2025-02-14 18:58:30.75292 INFO::Done
2025-02-14 18:58:30.754733 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:30.768821 INFO::ASW Batch was 0.525327868780272 prior to batch effect correction and is now 0.525327868780272 .
2025-02-14 18:58:30.770462 INFO::ASW Label was 0.308367882483639 prior to batch effect correction and is now 0.308367882483639 .
2025-02-14 18:58:30.77303 INFO::Total function execution time is 0.464608907699585 s and adjustment time is 0.397738933563232 s ( 85.61 )
2025-02-14 18:58:30.775084 INFO::Formatting Data.
2025-02-14 18:58:30.776791 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:30.77867 INFO::Removing potential empty rows and columns
2025-02-14 18:58:30.78537 INFO::Found 1000 missing values.
2025-02-14 18:58:30.81261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:30.814507 INFO::Done
2025-02-14 18:58:30.815578 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:30.822315 INFO::Starting hierarchical adjustment
2025-02-14 18:58:30.823234 INFO::Found 10 batches.
2025-02-14 18:58:31.909274 INFO::Set up parallel execution backend with 2 workers
2025-02-14 18:58:31.910072 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-14 18:58:33.191594 INFO::Adjusting the last 2 batches sequentially
2025-02-14 18:58:33.192776 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 18:58:33.210518 INFO::Done
2025-02-14 18:58:33.21144 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:33.218022 INFO::ASW Batch was 0.525327868780272 prior to batch effect correction and is now 0.525327868780272 .
2025-02-14 18:58:33.218964 INFO::ASW Label was 0.308367882483639 prior to batch effect correction and is now 0.308367882483639 .
2025-02-14 18:58:33.220034 INFO::Total function execution time is 2.44505500793457 s and adjustment time is 2.38745284080505 s ( 97.64 )
2025-02-14 18:58:33.47182 INFO::Formatting Data.
2025-02-14 18:58:33.473045 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:33.47445 INFO::Removing potential empty rows and columns
2025-02-14 18:58:33.476218 INFO::Found 0 missing values.
2025-02-14 18:58:33.479697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:33.480299 INFO::Done
2025-02-14 18:58:33.480801 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 18:58:33.484302 INFO::Starting hierarchical adjustment
2025-02-14 18:58:33.485378 INFO::Found 3 batches.
2025-02-14 18:58:33.486173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 18:58:33.487075 INFO::Using default BPPARAM
2025-02-14 18:58:33.487847 INFO::Processing subtree level 1
2025-02-14 18:58:33.658806 INFO::Adjusting the last 1 batches sequentially
2025-02-14 18:58:33.679557 INFO::Done
2025-02-14 18:58:33.68502 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 18:58:33.695953 INFO::ASW Batch was 0.177404727821991 prior to batch effect correction and is now -0.160794623269721 .
2025-02-14 18:58:33.697855 INFO::ASW Label was -0.125110648447521 prior to batch effect correction and is now -0.002938568803878 .
2025-02-14 18:58:33.700234 INFO::Total function execution time is 0.227726936340332 s and adjustment time is 0.194368839263916 s ( 85.35 )
2025-02-14 18:58:33.882325 INFO::Formatting Data.
2025-02-14 18:58:33.883165 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:33.884074 INFO::Removing potential empty rows and columns
2025-02-14 18:58:33.885067 INFO::Found 2 missing values.
2025-02-14 18:58:33.888992 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:33.889991 INFO::Done
2025-02-14 18:58:33.932914 INFO::Found NA in Reference column
2025-02-14 18:58:33.948807 INFO::Require at least two references per batch.
2025-02-14 18:58:33.978182 INFO::Formatting Data.
2025-02-14 18:58:33.979268 INFO::Recognized SummarizedExperiment
2025-02-14 18:58:33.98016 INFO::Typecasting input to dataframe.
2025-02-14 18:58:33.990545 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:33.99207 INFO::Removing potential empty rows and columns
2025-02-14 18:58:33.996944 INFO::Found 0 missing values.
2025-02-14 18:58:34.003763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.00475 INFO::Done
2025-02-14 18:58:34.022017 INFO::Formatting Data.
2025-02-14 18:58:34.022816 INFO::Recognized SummarizedExperiment
2025-02-14 18:58:34.023358 INFO::Typecasting input to dataframe.
2025-02-14 18:58:34.046148 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:34.04742 INFO::Removing potential empty rows and columns
2025-02-14 18:58:34.050869 INFO::Found 0 missing values.
2025-02-14 18:58:34.061362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.062031 INFO::Done
2025-02-14 18:58:34.077678 INFO::Formatting Data.
2025-02-14 18:58:34.078699 INFO::Recognized SummarizedExperiment
2025-02-14 18:58:34.080232 INFO::Typecasting input to dataframe.
2025-02-14 18:58:34.100173 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:34.101725 INFO::Removing potential empty rows and columns
2025-02-14 18:58:34.103313 INFO::Found 0 missing values.
2025-02-14 18:58:34.104618 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.
2025-02-14 18:58:34.1106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.111536 INFO::Done
2025-02-14 18:58:34.125414 INFO::Formatting Data.
2025-02-14 18:58:34.126291 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:34.127706 INFO::Removing potential empty rows and columns
2025-02-14 18:58:34.129247 INFO::Found 0 missing values.
2025-02-14 18:58:34.132347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.132889 INFO::Done
2025-02-14 18:58:34.147106 INFO::Formatting Data.
2025-02-14 18:58:34.147923 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:34.14879 INFO::Removing potential empty rows and columns
2025-02-14 18:58:34.150059 INFO::Found 0 missing values.
2025-02-14 18:58:34.154489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.155446 INFO::Done
2025-02-14 18:58:34.204046 INFO::Formatting Data.
2025-02-14 18:58:34.205293 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:34.206934 INFO::Removing potential empty rows and columns
2025-02-14 18:58:34.208705 INFO::Found 1 missing values.
2025-02-14 18:58:34.211999 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.212623 INFO::Done
2025-02-14 18:58:34.242185 INFO::Formatting Data.
2025-02-14 18:58:34.243383 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:34.244359 INFO::Removing potential empty rows and columns
2025-02-14 18:58:34.245619 INFO::Found 2 missing values.
2025-02-14 18:58:34.247098 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.
2025-02-14 18:58:34.249412 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.25021 INFO::Done
2025-02-14 18:58:34.266847 INFO::Formatting Data.
2025-02-14 18:58:34.268026 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:34.268978 INFO::Removing potential empty rows and columns
2025-02-14 18:58:34.269884 INFO::Found 2 missing values.
2025-02-14 18:58:34.271607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.272387 INFO::Done
2025-02-14 18:58:34.290372 INFO::Formatting Data.
2025-02-14 18:58:34.291519 INFO::Typecasting input to dataframe.
2025-02-14 18:58:34.292679 INFO::Replacing NaNs with NAs.
2025-02-14 18:58:34.293529 INFO::Removing potential empty rows and columns
2025-02-14 18:58:34.29472 INFO::Found 0 missing values.
2025-02-14 18:58:34.298398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 18:58:34.29914 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.393 4.397 25.193
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.587 | 1.416 | 18.514 | |
| compute_asw | 0.026 | 0.002 | 0.028 | |
| count_existing | 0.016 | 0.001 | 0.017 | |
| generate_data_covariables | 0.016 | 0.001 | 0.017 | |
| generate_dataset | 0.014 | 0.001 | 0.016 | |