Yannis Schumann
| Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-23 12:11 -0500 (Thu, 23 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-01-21 04:45:07 -0000 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 04:46:22 -0000 (Tue, 21 Jan 2025) |
| EllapsedTime: 75.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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 28.168 1.262 20.391
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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")
2025-01-21 04:46:06.98549 INFO::Formatting Data.
2025-01-21 04:46:06.987427 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:07.00504 INFO::Removing potential empty rows and columns
2025-01-21 04:46:07.621325 INFO::Found 0 missing values.
2025-01-21 04:46:07.626056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:07.627027 INFO::Done
2025-01-21 04:46:07.627816 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:07.643961 INFO::Starting hierarchical adjustment
2025-01-21 04:46:07.645222 INFO::Found 3 batches.
2025-01-21 04:46:07.646036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:07.647698 INFO::Using default BPPARAM
2025-01-21 04:46:07.648557 INFO::Processing subtree level 1
2025-01-21 04:46:07.777494 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:46:07.779875 INFO::Done
2025-01-21 04:46:07.780802 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:07.784278 INFO::ASW Batch was -0.113501495857503 prior to batch effect correction and is now -0.113501495857503 .
2025-01-21 04:46:07.785828 INFO::Total function execution time is 0.801324844360352 s and adjustment time is 0.134888887405396 s ( 16.83 )
2025-01-21 04:46:07.806227 INFO::Formatting Data.
2025-01-21 04:46:07.807317 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:07.808565 INFO::Removing potential empty rows and columns
2025-01-21 04:46:07.810275 INFO::Found 0 missing values.
2025-01-21 04:46:07.811655 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.
2025-01-21 04:46:07.82719 INFO::Formatting Data.
2025-01-21 04:46:07.828185 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:07.829471 INFO::Removing potential empty rows and columns
2025-01-21 04:46:07.830981 INFO::Found 0 missing values.
2025-01-21 04:46:07.832289 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.
2025-01-21 04:46:07.855589 INFO::Formatting Data.
2025-01-21 04:46:07.85659 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:07.857851 INFO::Removing potential empty rows and columns
2025-01-21 04:46:07.859382 INFO::Found 0 missing values.
2025-01-21 04:46:07.860635 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.
2025-01-21 04:46:07.867072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:07.867975 INFO::Done
2025-01-21 04:46:07.868701 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:07.871464 INFO::Starting hierarchical adjustment
2025-01-21 04:46:07.872517 INFO::Found 2 batches.
2025-01-21 04:46:07.873343 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:07.874254 INFO::Using default BPPARAM
2025-01-21 04:46:07.875084 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:07.876465 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:07.907806 INFO::Done
2025-01-21 04:46:07.908705 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:07.911726 INFO::ASW Batch was 0.0333039145256449 prior to batch effect correction and is now -0.113968911706911 .
2025-01-21 04:46:07.913028 INFO::Total function execution time is 0.0574557781219482 s and adjustment time is 0.0354659557342529 s ( 61.73 )
2025-01-21 04:46:07.917104 INFO::Formatting Data.
2025-01-21 04:46:07.918161 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:07.930974 INFO::Formatting Data.
2025-01-21 04:46:07.931983 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:07.933299 INFO::Removing potential empty rows and columns
2025-01-21 04:46:07.934867 INFO::Found 0 missing values.
2025-01-21 04:46:07.939354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:07.940277 INFO::Done
2025-01-21 04:46:07.941056 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:07.943992 INFO::Starting hierarchical adjustment
2025-01-21 04:46:07.945213 INFO::Found 2 batches.
2025-01-21 04:46:07.946011 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:07.947029 INFO::Using default BPPARAM
2025-01-21 04:46:07.947811 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:07.949171 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:07.971844 INFO::Done
2025-01-21 04:46:07.972815 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:07.975794 INFO::ASW Batch was -0.026675968945515 prior to batch effect correction and is now -0.118001245288819 .
2025-01-21 04:46:07.977047 INFO::Total function execution time is 0.046119213104248 s and adjustment time is 0.0268392562866211 s ( 58.2 )
2025-01-21 04:46:07.978668 INFO::Formatting Data.
2025-01-21 04:46:07.979574 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:07.980865 INFO::Removing potential empty rows and columns
2025-01-21 04:46:07.982397 INFO::Found 0 missing values.
2025-01-21 04:46:07.986867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:07.987791 INFO::Done
2025-01-21 04:46:07.988529 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:07.991575 INFO::Starting hierarchical adjustment
2025-01-21 04:46:07.992735 INFO::Found 2 batches.
2025-01-21 04:46:07.993586 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:07.994433 INFO::Using default BPPARAM
2025-01-21 04:46:07.995195 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:07.996545 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:08.018546 INFO::Done
2025-01-21 04:46:08.019445 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:08.022316 INFO::ASW Batch was -0.026675968945515 prior to batch effect correction and is now -0.118001245288819 .
2025-01-21 04:46:08.023567 INFO::Total function execution time is 0.0449581146240234 s and adjustment time is 0.0259864330291748 s ( 57.8 )
2025-01-21 04:46:11.002226 INFO::Formatting Data.
2025-01-21 04:46:11.003141 INFO::Recognized SummarizedExperiment
2025-01-21 04:46:11.003779 INFO::Typecasting input to dataframe.
2025-01-21 04:46:11.045846 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:11.047377 INFO::Removing potential empty rows and columns
2025-01-21 04:46:11.052054 INFO::Found 0 missing values.
2025-01-21 04:46:11.061131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:11.061935 INFO::Done
2025-01-21 04:46:11.062604 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:11.067084 INFO::Starting hierarchical adjustment
2025-01-21 04:46:11.068038 INFO::Found 2 batches.
2025-01-21 04:46:11.068683 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:11.070055 INFO::Using default BPPARAM
2025-01-21 04:46:11.07074 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:11.07194 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:11.141928 INFO::Done
2025-01-21 04:46:11.14274 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:11.146892 INFO::ASW Batch was 0.0190533449757841 prior to batch effect correction and is now -0.0995369590987486 .
2025-01-21 04:46:11.147938 INFO::Total function execution time is 0.146162509918213 s and adjustment time is 0.0740623474121094 s ( 50.67 )
2025-01-21 04:46:11.170798 INFO::Formatting Data.
2025-01-21 04:46:11.171651 INFO::Recognized SummarizedExperiment
2025-01-21 04:46:11.172309 INFO::Typecasting input to dataframe.
2025-01-21 04:46:11.184157 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:11.185584 INFO::Removing potential empty rows and columns
2025-01-21 04:46:11.189849 INFO::Found 0 missing values.
2025-01-21 04:46:11.198685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:11.199509 INFO::Done
2025-01-21 04:46:11.200178 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:11.204517 INFO::Starting hierarchical adjustment
2025-01-21 04:46:11.20557 INFO::Found 2 batches.
2025-01-21 04:46:11.206251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:11.207033 INFO::Using default BPPARAM
2025-01-21 04:46:11.207701 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:11.209 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:11.240908 INFO::Done
2025-01-21 04:46:11.241757 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:11.246036 INFO::ASW Batch was -0.00167801754585018 prior to batch effect correction and is now -0.00167801754585018 .
2025-01-21 04:46:11.247183 INFO::Total function execution time is 0.0763587951660156 s and adjustment time is 0.0354986190795898 s ( 46.49 )
2025-01-21 04:46:11.270562 INFO::Formatting Data.
2025-01-21 04:46:11.271479 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:11.272552 INFO::Removing potential empty rows and columns
2025-01-21 04:46:11.273833 INFO::Found 0 missing values.
2025-01-21 04:46:11.277648 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:11.278404 INFO::Done
2025-01-21 04:46:11.279096 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:11.281536 INFO::Starting hierarchical adjustment
2025-01-21 04:46:11.282444 INFO::Found 3 batches.
2025-01-21 04:46:11.283129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:11.283869 INFO::Using default BPPARAM
2025-01-21 04:46:11.284521 INFO::Processing subtree level 1
2025-01-21 04:46:11.476922 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:46:11.479493 INFO::Done
2025-01-21 04:46:11.480407 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:11.484004 INFO::ASW Batch was 0.0121793896593961 prior to batch effect correction and is now -0.1580937820925 .
2025-01-21 04:46:11.485483 INFO::Total function execution time is 0.214947938919067 s and adjustment time is 0.19718599319458 s ( 91.74 )
2025-01-21 04:46:11.507342 INFO::Skipping initial DF formatting
2025-01-21 04:46:11.508297 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:11.51385 INFO::Starting hierarchical adjustment
2025-01-21 04:46:11.515025 INFO::Found 5 batches.
2025-01-21 04:46:11.51582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:11.516736 INFO::Using default BPPARAM
2025-01-21 04:46:11.517552 INFO::Processing subtree level 1
2025-01-21 04:46:11.707436 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:11.709928 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:11.741476 INFO::Done
2025-01-21 04:46:11.742432 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:11.748547 INFO::ASW Batch was 0.601398970087556 prior to batch effect correction and is now 0.601398970087556 .
2025-01-21 04:46:11.7495 INFO::ASW Label was 0.399262628393963 prior to batch effect correction and is now 0.399262628393964 .
2025-01-21 04:46:11.750766 INFO::Total function execution time is 0.243473529815674 s and adjustment time is 0.226625680923462 s ( 93.08 )
2025-01-21 04:46:11.777409 INFO::Formatting Data.
2025-01-21 04:46:11.778429 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:11.779707 INFO::Removing potential empty rows and columns
2025-01-21 04:46:11.781132 INFO::Found 0 missing values.
2025-01-21 04:46:11.787325 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:11.788201 INFO::Done
2025-01-21 04:46:11.789009 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:11.793086 INFO::Starting hierarchical adjustment
2025-01-21 04:46:11.794172 INFO::Found 5 batches.
2025-01-21 04:46:11.794943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:11.795804 INFO::Using default BPPARAM
2025-01-21 04:46:11.796556 INFO::Processing subtree level 1
2025-01-21 04:46:11.953283 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:11.955462 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:11.979767 INFO::Done
2025-01-21 04:46:11.980718 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:11.985323 INFO::ASW Batch was 0.690516873061101 prior to batch effect correction and is now -0.0928338910449836 .
2025-01-21 04:46:11.986275 INFO::ASW Label was 0.133324482320521 prior to batch effect correction and is now 0.815069646544227 .
2025-01-21 04:46:11.987513 INFO::Total function execution time is 0.210167169570923 s and adjustment time is 0.185800075531006 s ( 88.41 )
2025-01-21 04:46:11.988723 INFO::Formatting Data.
2025-01-21 04:46:11.989637 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:11.990918 INFO::Removing potential empty rows and columns
2025-01-21 04:46:11.992333 INFO::Found 0 missing values.
2025-01-21 04:46:11.998736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:11.999621 INFO::Done
2025-01-21 04:46:12.000359 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:12.004733 INFO::Starting hierarchical adjustment
2025-01-21 04:46:12.005884 INFO::Found 5 batches.
2025-01-21 04:46:12.006653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:12.007574 INFO::Using default BPPARAM
2025-01-21 04:46:12.008325 INFO::Processing subtree level 1
2025-01-21 04:46:12.167096 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:12.169601 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:12.202204 INFO::Done
2025-01-21 04:46:12.203553 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:12.20898 INFO::ASW Batch was 0.690516873061101 prior to batch effect correction and is now -0.0928338910449836 .
2025-01-21 04:46:12.210013 INFO::ASW Label was 0.133324482320521 prior to batch effect correction and is now 0.815069646544227 .
2025-01-21 04:46:12.211434 INFO::Total function execution time is 0.222628116607666 s and adjustment time is 0.196426391601562 s ( 88.23 )
2025-01-21 04:46:12.23408 INFO::Formatting Data.
2025-01-21 04:46:12.235386 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:12.237091 INFO::Removing potential empty rows and columns
2025-01-21 04:46:12.239034 INFO::Found 0 missing values.
2025-01-21 04:46:12.246776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:12.247828 INFO::Done
2025-01-21 04:46:12.248898 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:12.254048 INFO::Starting hierarchical adjustment
2025-01-21 04:46:12.255595 INFO::Found 5 batches.
2025-01-21 04:46:12.256633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:12.257901 INFO::Using default BPPARAM
2025-01-21 04:46:12.258934 INFO::Processing subtree level 1
2025-01-21 04:46:12.481189 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:12.483377 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:12.510689 INFO::Done
2025-01-21 04:46:12.511657 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:12.516325 INFO::ASW Batch was 0.55072189993765 prior to batch effect correction and is now -0.099164345437465 .
2025-01-21 04:46:12.517382 INFO::ASW Label was 0.264387881399814 prior to batch effect correction and is now 0.678000223635994 .
2025-01-21 04:46:12.518698 INFO::Total function execution time is 0.284691572189331 s and adjustment time is 0.255509853363037 s ( 89.75 )
2025-01-21 04:46:12.519966 INFO::Formatting Data.
2025-01-21 04:46:12.52095 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:12.522316 INFO::Removing potential empty rows and columns
2025-01-21 04:46:12.523843 INFO::Found 0 missing values.
2025-01-21 04:46:12.530567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:12.571913 INFO::Done
2025-01-21 04:46:12.572794 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:12.577234 INFO::Starting hierarchical adjustment
2025-01-21 04:46:12.578417 INFO::Found 5 batches.
2025-01-21 04:46:12.579237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:12.580131 INFO::Using default BPPARAM
2025-01-21 04:46:12.580979 INFO::Processing subtree level 1
2025-01-21 04:46:12.759943 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:12.770812 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:12.798489 INFO::Done
2025-01-21 04:46:12.799542 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:12.804899 INFO::ASW Batch was 0.55072189993765 prior to batch effect correction and is now -0.099164345437465 .
2025-01-21 04:46:12.805764 INFO::ASW Label was 0.264387881399814 prior to batch effect correction and is now 0.678000223635994 .
2025-01-21 04:46:12.807015 INFO::Total function execution time is 0.287030935287476 s and adjustment time is 0.22024393081665 s ( 76.73 )
2025-01-21 04:46:12.829046 INFO::Formatting Data.
2025-01-21 04:46:12.830118 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:12.831538 INFO::Removing potential empty rows and columns
2025-01-21 04:46:12.833328 INFO::Found 0 missing values.
2025-01-21 04:46:12.837972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:12.838892 INFO::Done
2025-01-21 04:46:12.839647 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:12.844153 INFO::Starting hierarchical adjustment
2025-01-21 04:46:12.845236 INFO::Found 2 batches.
2025-01-21 04:46:12.84602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:12.846936 INFO::Using default BPPARAM
2025-01-21 04:46:12.84778 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:12.849151 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:12.872809 INFO::Done
2025-01-21 04:46:12.873752 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:12.878334 INFO::ASW Batch was 0.452996116689572 prior to batch effect correction and is now 0.15047611459367 .
2025-01-21 04:46:12.879205 INFO::ASW Label was 0.674947116780632 prior to batch effect correction and is now 0.819512522571924 .
2025-01-21 04:46:12.880434 INFO::Total function execution time is 0.0515363216400146 s and adjustment time is 0.027724027633667 s ( 53.8 )
2025-01-21 04:46:12.881621 INFO::Formatting Data.
2025-01-21 04:46:12.88253 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:12.883855 INFO::Removing potential empty rows and columns
2025-01-21 04:46:12.885495 INFO::Found 0 missing values.
2025-01-21 04:46:12.889877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:12.89088 INFO::Done
2025-01-21 04:46:12.891615 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:12.895949 INFO::Starting hierarchical adjustment
2025-01-21 04:46:12.897062 INFO::Found 2 batches.
2025-01-21 04:46:12.897851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:12.898936 INFO::Using default BPPARAM
2025-01-21 04:46:12.899721 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:12.901095 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:12.924194 INFO::Done
2025-01-21 04:46:12.925204 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:12.929596 INFO::ASW Batch was 0.452996116689572 prior to batch effect correction and is now 0.15047611459367 .
2025-01-21 04:46:12.930414 INFO::ASW Label was 0.674947116780632 prior to batch effect correction and is now 0.819512522571924 .
2025-01-21 04:46:12.931572 INFO::Total function execution time is 0.0499541759490967 s and adjustment time is 0.027360200881958 s ( 54.77 )
2025-01-21 04:46:12.956217 INFO::Formatting Data.
2025-01-21 04:46:12.957525 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:12.959055 INFO::Removing potential empty rows and columns
2025-01-21 04:46:12.960479 INFO::Found 0 missing values.
2025-01-21 04:46:12.964014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:12.964809 INFO::Done
2025-01-21 04:46:12.96574 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:12.968891 INFO::Starting hierarchical adjustment
2025-01-21 04:46:12.96998 INFO::Found 2 batches.
2025-01-21 04:46:12.970799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:12.97171 INFO::Using default BPPARAM
2025-01-21 04:46:12.972474 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:12.973882 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:13.024672 INFO::Done
2025-01-21 04:46:13.025686 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:13.028939 INFO::ASW Batch was -0.003148450152126 prior to batch effect correction and is now -0.103758183399249 .
2025-01-21 04:46:13.030147 INFO::Total function execution time is 0.0741012096405029 s and adjustment time is 0.0548756122589111 s ( 74.05 )
2025-01-21 04:46:13.049636 INFO::Formatting Data.
2025-01-21 04:46:13.050795 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:13.052159 INFO::Removing potential empty rows and columns
2025-01-21 04:46:13.053747 INFO::Found 0 missing values.
2025-01-21 04:46:13.055474 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.
2025-01-21 04:46:13.062831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:13.064056 INFO::Done
2025-01-21 04:46:13.064972 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:13.069454 INFO::Starting hierarchical adjustment
2025-01-21 04:46:13.070593 INFO::Found 2 batches.
2025-01-21 04:46:13.07136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:13.072244 INFO::Using default BPPARAM
2025-01-21 04:46:13.073036 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:13.074692 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:13.102388 INFO::Done
2025-01-21 04:46:13.103464 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:13.108007 INFO::ASW Batch was 0.649366698380759 prior to batch effect correction and is now 0.278608768025518 .
2025-01-21 04:46:13.108977 INFO::ASW Label was 0.473645652255506 prior to batch effect correction and is now 0.698246790859888 .
2025-01-21 04:46:13.110144 INFO::Total function execution time is 0.0605897903442383 s and adjustment time is 0.0320010185241699 s ( 52.82 )
2025-01-21 04:46:13.111524 INFO::Formatting Data.
2025-01-21 04:46:13.11259 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:13.114236 INFO::Removing potential empty rows and columns
2025-01-21 04:46:13.115744 INFO::Found 0 missing values.
2025-01-21 04:46:13.117136 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.
2025-01-21 04:46:13.124277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:13.125119 INFO::Done
2025-01-21 04:46:13.12587 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:13.130014 INFO::Starting hierarchical adjustment
2025-01-21 04:46:13.131052 INFO::Found 2 batches.
2025-01-21 04:46:13.131811 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:13.132677 INFO::Using default BPPARAM
2025-01-21 04:46:13.13354 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:13.134909 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:13.161056 INFO::Done
2025-01-21 04:46:13.161999 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:13.166431 INFO::ASW Batch was 0.649366698380759 prior to batch effect correction and is now 0.278608768025518 .
2025-01-21 04:46:13.167303 INFO::ASW Label was 0.473645652255506 prior to batch effect correction and is now 0.698246790859888 .
2025-01-21 04:46:13.16851 INFO::Total function execution time is 0.0570213794708252 s and adjustment time is 0.0301711559295654 s ( 52.91 )
2025-01-21 04:46:13.505863 INFO::Formatting Data.
2025-01-21 04:46:13.507042 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:13.508484 INFO::Removing potential empty rows and columns
2025-01-21 04:46:13.510186 INFO::Found 0 missing values.
2025-01-21 04:46:13.515398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:13.516372 INFO::Done
2025-01-21 04:46:13.517403 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:13.520472 INFO::Starting hierarchical adjustment
2025-01-21 04:46:13.521671 INFO::Found 3 batches.
2025-01-21 04:46:13.522533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:13.523433 INFO::Using default BPPARAM
2025-01-21 04:46:13.524208 INFO::Processing subtree level 1
2025-01-21 04:46:13.681437 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:46:13.683912 INFO::Done
2025-01-21 04:46:13.684944 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:13.688639 INFO::ASW Batch was -0.0699434048696476 prior to batch effect correction and is now -0.0699434048696476 .
2025-01-21 04:46:13.690151 INFO::Total function execution time is 0.184318065643311 s and adjustment time is 0.162465572357178 s ( 88.14 )
2025-01-21 04:46:13.691792 INFO::Formatting Data.
2025-01-21 04:46:13.692877 INFO::Typecasting input to dataframe.
2025-01-21 04:46:13.694093 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:13.695601 INFO::Removing potential empty rows and columns
2025-01-21 04:46:13.697421 INFO::Found 0 missing values.
2025-01-21 04:46:13.702659 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:13.703619 INFO::Done
2025-01-21 04:46:13.704485 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:13.707722 INFO::Starting hierarchical adjustment
2025-01-21 04:46:13.709012 INFO::Found 3 batches.
2025-01-21 04:46:13.709902 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:13.710978 INFO::Using default BPPARAM
2025-01-21 04:46:13.711872 INFO::Processing subtree level 1
2025-01-21 04:46:13.881459 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:46:13.884103 INFO::Done
2025-01-21 04:46:13.885204 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:13.88926 INFO::ASW Batch was -0.0699434048696476 prior to batch effect correction and is now -0.0699434048696476 .
2025-01-21 04:46:13.891006 INFO::Total function execution time is 0.19915246963501 s and adjustment time is 0.175330877304077 s ( 88.04 )
2025-01-21 04:46:13.912621 INFO::Formatting Data.
2025-01-21 04:46:13.913884 INFO::Typecasting input to dataframe.
2025-01-21 04:46:13.915427 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:13.917024 INFO::Removing potential empty rows and columns
2025-01-21 04:46:13.918958 INFO::Found 0 missing values.
2025-01-21 04:46:13.924378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:13.925422 INFO::Done
2025-01-21 04:46:13.926353 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:13.929641 INFO::Starting hierarchical adjustment
2025-01-21 04:46:13.930961 INFO::Found 3 batches.
2025-01-21 04:46:13.932065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:13.933152 INFO::Using default BPPARAM
2025-01-21 04:46:13.934067 INFO::Processing subtree level 1
2025-01-21 04:46:14.117354 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:46:14.120006 INFO::Done
2025-01-21 04:46:14.121069 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:14.125027 INFO::ASW Batch was -0.0873762841716653 prior to batch effect correction and is now -0.0873762841716653 .
2025-01-21 04:46:14.126848 INFO::Total function execution time is 0.214125394821167 s and adjustment time is 0.189306020736694 s ( 88.41 )
2025-01-21 04:46:14.350386 INFO::Formatting Data.
2025-01-21 04:46:14.351722 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:14.353672 INFO::Removing potential empty rows and columns
2025-01-21 04:46:14.358881 INFO::Found 1000 missing values.
2025-01-21 04:46:14.390889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:14.391832 INFO::Done
2025-01-21 04:46:14.392685 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:14.400791 INFO::Starting hierarchical adjustment
2025-01-21 04:46:14.40218 INFO::Found 10 batches.
2025-01-21 04:46:14.403061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:14.403955 INFO::Using default BPPARAM
2025-01-21 04:46:14.404736 INFO::Processing subtree level 1
2025-01-21 04:46:14.620842 INFO::Processing subtree level 2
2025-01-21 04:46:14.857922 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:46:14.860699 INFO::Done
2025-01-21 04:46:14.861723 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:14.870205 INFO::ASW Batch was 0.57215179166174 prior to batch effect correction and is now 0.57215179166174 .
2025-01-21 04:46:14.87132 INFO::ASW Label was 0.267452299671273 prior to batch effect correction and is now 0.267452299671273 .
2025-01-21 04:46:14.872698 INFO::Total function execution time is 0.522356510162354 s and adjustment time is 0.458837747573853 s ( 87.84 )
2025-01-21 04:46:14.874042 INFO::Formatting Data.
2025-01-21 04:46:14.875113 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:14.877212 INFO::Removing potential empty rows and columns
2025-01-21 04:46:14.882452 INFO::Found 1000 missing values.
2025-01-21 04:46:14.91493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:14.915911 INFO::Done
2025-01-21 04:46:14.916769 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:14.924822 INFO::Starting hierarchical adjustment
2025-01-21 04:46:14.926086 INFO::Found 10 batches.
2025-01-21 04:46:16.086789 INFO::Set up parallel execution backend with 2 workers
2025-01-21 04:46:16.088616 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-21 04:46:17.357803 INFO::Adjusting the last 2 batches sequentially
2025-01-21 04:46:17.359555 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-21 04:46:17.383003 INFO::Done
2025-01-21 04:46:17.383853 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:17.390343 INFO::ASW Batch was 0.57215179166174 prior to batch effect correction and is now 0.57215179166174 .
2025-01-21 04:46:17.391181 INFO::ASW Label was 0.267452299671273 prior to batch effect correction and is now 0.267452299671273 .
2025-01-21 04:46:17.392152 INFO::Total function execution time is 2.51817774772644 s and adjustment time is 2.45717716217041 s ( 97.58 )
2025-01-21 04:46:17.585459 INFO::Formatting Data.
2025-01-21 04:46:17.586568 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:17.58789 INFO::Removing potential empty rows and columns
2025-01-21 04:46:17.58948 INFO::Found 0 missing values.
2025-01-21 04:46:17.595269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:17.596146 INFO::Done
2025-01-21 04:46:17.59689 INFO::Acquiring quality metrics before batch effect correction.
2025-01-21 04:46:17.600727 INFO::Starting hierarchical adjustment
2025-01-21 04:46:17.601869 INFO::Found 3 batches.
2025-01-21 04:46:17.602779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-21 04:46:17.603628 INFO::Using default BPPARAM
2025-01-21 04:46:17.604384 INFO::Processing subtree level 1
2025-01-21 04:46:17.741548 INFO::Adjusting the last 1 batches sequentially
2025-01-21 04:46:17.743864 INFO::Done
2025-01-21 04:46:17.74467 INFO::Acquiring quality metrics after batch effect correction.
2025-01-21 04:46:17.749209 INFO::ASW Batch was 0.160394936977412 prior to batch effect correction and is now -0.136202963823268 .
2025-01-21 04:46:17.750165 INFO::ASW Label was -0.182838982800987 prior to batch effect correction and is now 0.0434816507165827 .
2025-01-21 04:46:17.751483 INFO::Total function execution time is 0.166061639785767 s and adjustment time is 0.142230033874512 s ( 85.65 )
2025-01-21 04:46:17.921257 INFO::Formatting Data.
2025-01-21 04:46:17.922291 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:17.923546 INFO::Removing potential empty rows and columns
2025-01-21 04:46:17.925075 INFO::Found 2 missing values.
2025-01-21 04:46:17.929485 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:17.930341 INFO::Done
2025-01-21 04:46:17.97196 INFO::Found NA in Reference column
2025-01-21 04:46:17.986239 INFO::Require at least two references per batch.
2025-01-21 04:46:18.016279 INFO::Formatting Data.
2025-01-21 04:46:18.017266 INFO::Recognized SummarizedExperiment
2025-01-21 04:46:18.017997 INFO::Typecasting input to dataframe.
2025-01-21 04:46:18.032604 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.034259 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.039735 INFO::Found 0 missing values.
2025-01-21 04:46:18.050348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.051253 INFO::Done
2025-01-21 04:46:18.07335 INFO::Formatting Data.
2025-01-21 04:46:18.074311 INFO::Recognized SummarizedExperiment
2025-01-21 04:46:18.075044 INFO::Typecasting input to dataframe.
2025-01-21 04:46:18.101082 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.102803 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.108355 INFO::Found 0 missing values.
2025-01-21 04:46:18.12623 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.127207 INFO::Done
2025-01-21 04:46:18.149431 INFO::Formatting Data.
2025-01-21 04:46:18.150361 INFO::Recognized SummarizedExperiment
2025-01-21 04:46:18.151099 INFO::Typecasting input to dataframe.
2025-01-21 04:46:18.176251 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.177607 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.179105 INFO::Found 0 missing values.
2025-01-21 04:46:18.180313 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.
2025-01-21 04:46:18.186875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.187711 INFO::Done
2025-01-21 04:46:18.202348 INFO::Formatting Data.
2025-01-21 04:46:18.203392 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.204583 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.206039 INFO::Found 0 missing values.
2025-01-21 04:46:18.211092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.211972 INFO::Done
2025-01-21 04:46:18.228087 INFO::Formatting Data.
2025-01-21 04:46:18.229187 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.230367 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.231791 INFO::Found 0 missing values.
2025-01-21 04:46:18.235994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.236834 INFO::Done
2025-01-21 04:46:18.277658 INFO::Formatting Data.
2025-01-21 04:46:18.278682 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.280254 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.281982 INFO::Found 1 missing values.
2025-01-21 04:46:18.286016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.286813 INFO::Done
2025-01-21 04:46:18.312932 INFO::Formatting Data.
2025-01-21 04:46:18.313941 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.315144 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.316451 INFO::Found 2 missing values.
2025-01-21 04:46:18.317682 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.
2025-01-21 04:46:18.320955 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.321717 INFO::Done
2025-01-21 04:46:18.337142 INFO::Formatting Data.
2025-01-21 04:46:18.338205 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.339553 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.341037 INFO::Found 2 missing values.
2025-01-21 04:46:18.343629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.3445 INFO::Done
2025-01-21 04:46:18.361214 INFO::Formatting Data.
2025-01-21 04:46:18.3623 INFO::Typecasting input to dataframe.
2025-01-21 04:46:18.363616 INFO::Replacing NaNs with NAs.
2025-01-21 04:46:18.365108 INFO::Removing potential empty rows and columns
2025-01-21 04:46:18.366833 INFO::Found 0 missing values.
2025-01-21 04:46:18.371827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-21 04:46:18.37281 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.742 4.493 24.830
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.168 | 1.262 | 20.391 | |
| compute_asw | 0.032 | 0.000 | 0.032 | |
| count_existing | 0.016 | 0.000 | 0.016 | |
| generate_data_covariables | 0.014 | 0.000 | 0.015 | |
| generate_dataset | 0.014 | 0.000 | 0.014 | |