Yannis Schumann
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:11 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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: 2025-03-18 05:26:07 -0000 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 05:27:21 -0000 (Tue, 18 Mar 2025) |
| EllapsedTime: 74.1 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 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* 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 27.472 1.47 19.884
* 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-4.4.3/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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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")
2025-03-18 05:27:06.023738 INFO::Formatting Data.
2025-03-18 05:27:06.025985 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:06.042953 INFO::Removing potential empty rows and columns
2025-03-18 05:27:06.407254 INFO::Found 0 missing values.
2025-03-18 05:27:06.411752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:06.412575 INFO::Done
2025-03-18 05:27:06.413297 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:06.427495 INFO::Starting hierarchical adjustment
2025-03-18 05:27:06.428577 INFO::Found 3 batches.
2025-03-18 05:27:06.429317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:06.430761 INFO::Using default BPPARAM
2025-03-18 05:27:06.431478 INFO::Processing subtree level 1
2025-03-18 05:27:06.555895 INFO::Adjusting the last 1 batches sequentially
2025-03-18 05:27:06.558385 INFO::Done
2025-03-18 05:27:06.559346 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:06.563036 INFO::ASW Batch was -0.0664586837997947 prior to batch effect correction and is now -0.0664586837997947 .
2025-03-18 05:27:06.564684 INFO::Total function execution time is 0.542036533355713 s and adjustment time is 0.129995107650757 s ( 23.98 )
2025-03-18 05:27:06.5839 INFO::Formatting Data.
2025-03-18 05:27:06.584895 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:06.586147 INFO::Removing potential empty rows and columns
2025-03-18 05:27:06.587609 INFO::Found 0 missing values.
2025-03-18 05:27:06.588886 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-18 05:27:06.603824 INFO::Formatting Data.
2025-03-18 05:27:06.60503 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:06.606305 INFO::Removing potential empty rows and columns
2025-03-18 05:27:06.607734 INFO::Found 0 missing values.
2025-03-18 05:27:06.60902 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-18 05:27:06.631397 INFO::Formatting Data.
2025-03-18 05:27:06.632358 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:06.633582 INFO::Removing potential empty rows and columns
2025-03-18 05:27:06.635005 INFO::Found 0 missing values.
2025-03-18 05:27:06.636267 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-18 05:27:06.642908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:06.643768 INFO::Done
2025-03-18 05:27:06.644471 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:06.647254 INFO::Starting hierarchical adjustment
2025-03-18 05:27:06.648288 INFO::Found 2 batches.
2025-03-18 05:27:06.649072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:06.649993 INFO::Using default BPPARAM
2025-03-18 05:27:06.650733 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:06.652065 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:06.682527 INFO::Done
2025-03-18 05:27:06.683434 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:06.68629 INFO::ASW Batch was -0.0172831117057458 prior to batch effect correction and is now -0.0897748999595872 .
2025-03-18 05:27:06.687457 INFO::Total function execution time is 0.0561201572418213 s and adjustment time is 0.0344099998474121 s ( 61.31 )
2025-03-18 05:27:06.691258 INFO::Formatting Data.
2025-03-18 05:27:06.692202 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:06.704921 INFO::Formatting Data.
2025-03-18 05:27:06.70603 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:06.707422 INFO::Removing potential empty rows and columns
2025-03-18 05:27:06.709064 INFO::Found 0 missing values.
2025-03-18 05:27:06.713646 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:06.714553 INFO::Done
2025-03-18 05:27:06.715322 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:06.718174 INFO::Starting hierarchical adjustment
2025-03-18 05:27:06.719278 INFO::Found 2 batches.
2025-03-18 05:27:06.720046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:06.720983 INFO::Using default BPPARAM
2025-03-18 05:27:06.721832 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:06.723206 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:06.743231 INFO::Done
2025-03-18 05:27:06.744095 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:06.746758 INFO::ASW Batch was -0.0199353215145944 prior to batch effect correction and is now -0.115428270334416 .
2025-03-18 05:27:06.747878 INFO::Total function execution time is 0.0430536270141602 s and adjustment time is 0.024169921875 s ( 56.14 )
2025-03-18 05:27:06.749464 INFO::Formatting Data.
2025-03-18 05:27:06.750407 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:06.751654 INFO::Removing potential empty rows and columns
2025-03-18 05:27:06.753205 INFO::Found 0 missing values.
2025-03-18 05:27:06.757526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:06.758377 INFO::Done
2025-03-18 05:27:06.75909 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:06.761807 INFO::Starting hierarchical adjustment
2025-03-18 05:27:06.762838 INFO::Found 2 batches.
2025-03-18 05:27:06.763558 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:06.764373 INFO::Using default BPPARAM
2025-03-18 05:27:06.765144 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:06.766438 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:06.78653 INFO::Done
2025-03-18 05:27:06.787379 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:06.790086 INFO::ASW Batch was -0.0199353215145944 prior to batch effect correction and is now -0.115428270334416 .
2025-03-18 05:27:06.7912 INFO::Total function execution time is 0.041792631149292 s and adjustment time is 0.0238924026489258 s ( 57.17 )
2025-03-18 05:27:10.635187 INFO::Formatting Data.
2025-03-18 05:27:10.636217 INFO::Recognized SummarizedExperiment
2025-03-18 05:27:10.636876 INFO::Typecasting input to dataframe.
2025-03-18 05:27:10.677931 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:10.679436 INFO::Removing potential empty rows and columns
2025-03-18 05:27:10.684161 INFO::Found 0 missing values.
2025-03-18 05:27:10.693462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:10.694334 INFO::Done
2025-03-18 05:27:10.69501 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:10.699676 INFO::Starting hierarchical adjustment
2025-03-18 05:27:10.700696 INFO::Found 2 batches.
2025-03-18 05:27:10.701404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:10.702778 INFO::Using default BPPARAM
2025-03-18 05:27:10.703545 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:10.70479 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:10.777844 INFO::Done
2025-03-18 05:27:10.778663 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:10.782993 INFO::ASW Batch was -0.00103452599151859 prior to batch effect correction and is now -0.0965655042661047 .
2025-03-18 05:27:10.784109 INFO::Total function execution time is 0.14951491355896 s and adjustment time is 0.0773370265960693 s ( 51.73 )
2025-03-18 05:27:10.807293 INFO::Formatting Data.
2025-03-18 05:27:10.808154 INFO::Recognized SummarizedExperiment
2025-03-18 05:27:10.808851 INFO::Typecasting input to dataframe.
2025-03-18 05:27:10.821413 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:10.822871 INFO::Removing potential empty rows and columns
2025-03-18 05:27:10.827851 INFO::Found 0 missing values.
2025-03-18 05:27:10.837419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:10.838295 INFO::Done
2025-03-18 05:27:10.838991 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:10.843579 INFO::Starting hierarchical adjustment
2025-03-18 05:27:10.844609 INFO::Found 2 batches.
2025-03-18 05:27:10.845358 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:10.846178 INFO::Using default BPPARAM
2025-03-18 05:27:10.846878 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:10.848172 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:10.88138 INFO::Done
2025-03-18 05:27:10.882255 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:10.886757 INFO::ASW Batch was -0.0241063119147062 prior to batch effect correction and is now -0.0241063119147062 .
2025-03-18 05:27:10.88811 INFO::Total function execution time is 0.0807788372039795 s and adjustment time is 0.0369629859924316 s ( 45.76 )
2025-03-18 05:27:10.912017 INFO::Formatting Data.
2025-03-18 05:27:10.912951 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:10.914103 INFO::Removing potential empty rows and columns
2025-03-18 05:27:10.915418 INFO::Found 0 missing values.
2025-03-18 05:27:10.919494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:10.920309 INFO::Done
2025-03-18 05:27:10.921021 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:10.923547 INFO::Starting hierarchical adjustment
2025-03-18 05:27:10.924513 INFO::Found 3 batches.
2025-03-18 05:27:10.925237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:10.926043 INFO::Using default BPPARAM
2025-03-18 05:27:10.926742 INFO::Processing subtree level 1
2025-03-18 05:27:11.097758 INFO::Adjusting the last 1 batches sequentially
2025-03-18 05:27:11.100151 INFO::Done
2025-03-18 05:27:11.100983 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:11.104465 INFO::ASW Batch was -0.0371328959898638 prior to batch effect correction and is now -0.155485005970588 .
2025-03-18 05:27:11.105867 INFO::Total function execution time is 0.193799495697021 s and adjustment time is 0.175817966461182 s ( 90.72 )
2025-03-18 05:27:11.124903 INFO::Skipping initial DF formatting
2025-03-18 05:27:11.125837 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:11.131108 INFO::Starting hierarchical adjustment
2025-03-18 05:27:11.132197 INFO::Found 5 batches.
2025-03-18 05:27:11.132939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:11.133865 INFO::Using default BPPARAM
2025-03-18 05:27:11.134575 INFO::Processing subtree level 1
2025-03-18 05:27:11.283522 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:11.285551 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:11.311905 INFO::Done
2025-03-18 05:27:11.312763 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:11.318351 INFO::ASW Batch was 0.465399393848378 prior to batch effect correction and is now 0.465399393848378 .
2025-03-18 05:27:11.319212 INFO::ASW Label was 0.403566222712741 prior to batch effect correction and is now 0.403566222712741 .
2025-03-18 05:27:11.320338 INFO::Total function execution time is 0.195505857467651 s and adjustment time is 0.179903030395508 s ( 92.02 )
2025-03-18 05:27:11.343792 INFO::Formatting Data.
2025-03-18 05:27:11.344712 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:11.345899 INFO::Removing potential empty rows and columns
2025-03-18 05:27:11.347221 INFO::Found 0 missing values.
2025-03-18 05:27:11.352946 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:11.353821 INFO::Done
2025-03-18 05:27:11.354539 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:11.358374 INFO::Starting hierarchical adjustment
2025-03-18 05:27:11.359427 INFO::Found 5 batches.
2025-03-18 05:27:11.36017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:11.361006 INFO::Using default BPPARAM
2025-03-18 05:27:11.36176 INFO::Processing subtree level 1
2025-03-18 05:27:11.484168 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:11.486266 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:11.508187 INFO::Done
2025-03-18 05:27:11.509105 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:11.513406 INFO::ASW Batch was 0.20240636668414 prior to batch effect correction and is now -0.0887774702059679 .
2025-03-18 05:27:11.514344 INFO::ASW Label was 0.562909629968523 prior to batch effect correction and is now 0.902427299785304 .
2025-03-18 05:27:11.515476 INFO::Total function execution time is 0.171723604202271 s and adjustment time is 0.148959636688232 s ( 86.74 )
2025-03-18 05:27:11.516648 INFO::Formatting Data.
2025-03-18 05:27:11.517591 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:11.518913 INFO::Removing potential empty rows and columns
2025-03-18 05:27:11.520346 INFO::Found 0 missing values.
2025-03-18 05:27:11.526582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:11.527473 INFO::Done
2025-03-18 05:27:11.528246 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:11.532404 INFO::Starting hierarchical adjustment
2025-03-18 05:27:11.533538 INFO::Found 5 batches.
2025-03-18 05:27:11.534383 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:11.535285 INFO::Using default BPPARAM
2025-03-18 05:27:11.536061 INFO::Processing subtree level 1
2025-03-18 05:27:11.661844 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:11.663972 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:11.685525 INFO::Done
2025-03-18 05:27:11.686512 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:11.691052 INFO::ASW Batch was 0.20240636668414 prior to batch effect correction and is now -0.0887774702059679 .
2025-03-18 05:27:11.691957 INFO::ASW Label was 0.562909629968523 prior to batch effect correction and is now 0.902427299785304 .
2025-03-18 05:27:11.693152 INFO::Total function execution time is 0.176492214202881 s and adjustment time is 0.152194261550903 s ( 86.23 )
2025-03-18 05:27:11.712318 INFO::Formatting Data.
2025-03-18 05:27:11.71338 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:11.714716 INFO::Removing potential empty rows and columns
2025-03-18 05:27:11.716169 INFO::Found 0 missing values.
2025-03-18 05:27:11.722393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:11.723286 INFO::Done
2025-03-18 05:27:11.724068 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:11.728229 INFO::Starting hierarchical adjustment
2025-03-18 05:27:11.729396 INFO::Found 5 batches.
2025-03-18 05:27:11.730226 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:11.731092 INFO::Using default BPPARAM
2025-03-18 05:27:11.731866 INFO::Processing subtree level 1
2025-03-18 05:27:11.863897 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:11.866109 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:11.890643 INFO::Done
2025-03-18 05:27:11.89157 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:11.896094 INFO::ASW Batch was 0.267836738676224 prior to batch effect correction and is now -0.0931516932620287 .
2025-03-18 05:27:11.897027 INFO::ASW Label was 0.47037913883527 prior to batch effect correction and is now 0.836463540750629 .
2025-03-18 05:27:11.898221 INFO::Total function execution time is 0.185961008071899 s and adjustment time is 0.161454916000366 s ( 86.82 )
2025-03-18 05:27:11.899395 INFO::Formatting Data.
2025-03-18 05:27:11.900264 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:11.901547 INFO::Removing potential empty rows and columns
2025-03-18 05:27:11.903003 INFO::Found 0 missing values.
2025-03-18 05:27:11.908967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:11.909915 INFO::Done
2025-03-18 05:27:11.910656 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:11.914706 INFO::Starting hierarchical adjustment
2025-03-18 05:27:11.915833 INFO::Found 5 batches.
2025-03-18 05:27:11.916612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:11.917528 INFO::Using default BPPARAM
2025-03-18 05:27:11.918346 INFO::Processing subtree level 1
2025-03-18 05:27:12.050162 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:12.052442 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:12.075725 INFO::Done
2025-03-18 05:27:12.076785 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:12.081939 INFO::ASW Batch was 0.267836738676224 prior to batch effect correction and is now -0.0931516932620287 .
2025-03-18 05:27:12.082935 INFO::ASW Label was 0.47037913883527 prior to batch effect correction and is now 0.836463540750629 .
2025-03-18 05:27:12.084287 INFO::Total function execution time is 0.184840679168701 s and adjustment time is 0.160075426101685 s ( 86.6 )
2025-03-18 05:27:12.104914 INFO::Formatting Data.
2025-03-18 05:27:12.106131 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:12.107582 INFO::Removing potential empty rows and columns
2025-03-18 05:27:12.109037 INFO::Found 0 missing values.
2025-03-18 05:27:12.112899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:12.11374 INFO::Done
2025-03-18 05:27:12.114478 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:12.118363 INFO::Starting hierarchical adjustment
2025-03-18 05:27:12.119389 INFO::Found 2 batches.
2025-03-18 05:27:12.120127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:12.120995 INFO::Using default BPPARAM
2025-03-18 05:27:12.121764 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:12.123023 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:12.142403 INFO::Done
2025-03-18 05:27:12.143252 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:12.147116 INFO::ASW Batch was 0.606655570767208 prior to batch effect correction and is now -0.0367652043290113 .
2025-03-18 05:27:12.147984 INFO::ASW Label was 0.451517865174118 prior to batch effect correction and is now 0.944217228653794 .
2025-03-18 05:27:12.149045 INFO::Total function execution time is 0.0442485809326172 s and adjustment time is 0.0231983661651611 s ( 52.43 )
2025-03-18 05:27:12.150085 INFO::Formatting Data.
2025-03-18 05:27:12.150896 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:12.152067 INFO::Removing potential empty rows and columns
2025-03-18 05:27:12.153455 INFO::Found 0 missing values.
2025-03-18 05:27:12.157356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:12.158217 INFO::Done
2025-03-18 05:27:12.158914 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:12.162805 INFO::Starting hierarchical adjustment
2025-03-18 05:27:12.163862 INFO::Found 2 batches.
2025-03-18 05:27:12.164579 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:12.165393 INFO::Using default BPPARAM
2025-03-18 05:27:12.166144 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:12.167433 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:12.187065 INFO::Done
2025-03-18 05:27:12.187946 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:12.191835 INFO::ASW Batch was 0.606655570767208 prior to batch effect correction and is now -0.0367652043290113 .
2025-03-18 05:27:12.192681 INFO::ASW Label was 0.451517865174118 prior to batch effect correction and is now 0.944217228653794 .
2025-03-18 05:27:12.193787 INFO::Total function execution time is 0.0436654090881348 s and adjustment time is 0.0233855247497559 s ( 53.56 )
2025-03-18 05:27:12.2086 INFO::Formatting Data.
2025-03-18 05:27:12.209707 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:12.21082 INFO::Removing potential empty rows and columns
2025-03-18 05:27:12.211949 INFO::Found 0 missing values.
2025-03-18 05:27:12.214814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:12.215584 INFO::Done
2025-03-18 05:27:12.216272 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:12.218803 INFO::Starting hierarchical adjustment
2025-03-18 05:27:12.219779 INFO::Found 2 batches.
2025-03-18 05:27:12.22048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:12.22459 INFO::Using default BPPARAM
2025-03-18 05:27:12.225494 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:12.226989 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:12.271262 INFO::Done
2025-03-18 05:27:12.272113 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:12.27478 INFO::ASW Batch was -0.0262482000121585 prior to batch effect correction and is now -0.105757846377747 .
2025-03-18 05:27:12.275888 INFO::Total function execution time is 0.0673413276672363 s and adjustment time is 0.0516693592071533 s ( 76.73 )
2025-03-18 05:27:12.292421 INFO::Formatting Data.
2025-03-18 05:27:12.2934 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:12.294721 INFO::Removing potential empty rows and columns
2025-03-18 05:27:12.296059 INFO::Found 0 missing values.
2025-03-18 05:27:12.297647 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-18 05:27:12.303746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:12.304571 INFO::Done
2025-03-18 05:27:12.305315 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:12.309125 INFO::Starting hierarchical adjustment
2025-03-18 05:27:12.310168 INFO::Found 2 batches.
2025-03-18 05:27:12.310877 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:12.311685 INFO::Using default BPPARAM
2025-03-18 05:27:12.312368 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:12.313694 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:12.335639 INFO::Done
2025-03-18 05:27:12.336486 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:12.340264 INFO::ASW Batch was 0.637318368891837 prior to batch effect correction and is now 0.00374275789425666 .
2025-03-18 05:27:12.341087 INFO::ASW Label was 0.483686685341819 prior to batch effect correction and is now 0.918341861706808 .
2025-03-18 05:27:12.342158 INFO::Total function execution time is 0.0498020648956299 s and adjustment time is 0.0256483554840088 s ( 51.5 )
2025-03-18 05:27:12.343163 INFO::Formatting Data.
2025-03-18 05:27:12.343949 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:12.345224 INFO::Removing potential empty rows and columns
2025-03-18 05:27:12.34663 INFO::Found 0 missing values.
2025-03-18 05:27:12.347872 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-18 05:27:12.354424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:12.355294 INFO::Done
2025-03-18 05:27:12.356305 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:12.360332 INFO::Starting hierarchical adjustment
2025-03-18 05:27:12.36148 INFO::Found 2 batches.
2025-03-18 05:27:12.362254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:12.363069 INFO::Using default BPPARAM
2025-03-18 05:27:12.363798 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:12.365165 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:12.387375 INFO::Done
2025-03-18 05:27:12.388253 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:12.392154 INFO::ASW Batch was 0.637318368891837 prior to batch effect correction and is now 0.00374275789425666 .
2025-03-18 05:27:12.393054 INFO::ASW Label was 0.483686685341819 prior to batch effect correction and is now 0.918341861706808 .
2025-03-18 05:27:12.394159 INFO::Total function execution time is 0.0509941577911377 s and adjustment time is 0.0261082649230957 s ( 51.2 )
2025-03-18 05:27:12.788439 INFO::Formatting Data.
2025-03-18 05:27:12.789664 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:12.791006 INFO::Removing potential empty rows and columns
2025-03-18 05:27:12.792629 INFO::Found 0 missing values.
2025-03-18 05:27:12.797691 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:12.798624 INFO::Done
2025-03-18 05:27:12.799414 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:12.802956 INFO::Starting hierarchical adjustment
2025-03-18 05:27:12.804083 INFO::Found 3 batches.
2025-03-18 05:27:12.804904 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:12.805871 INFO::Using default BPPARAM
2025-03-18 05:27:12.806656 INFO::Processing subtree level 1
2025-03-18 05:27:12.936344 INFO::Adjusting the last 1 batches sequentially
2025-03-18 05:27:12.938847 INFO::Done
2025-03-18 05:27:12.939737 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:12.943269 INFO::ASW Batch was -0.110113430928434 prior to batch effect correction and is now -0.110113430928434 .
2025-03-18 05:27:12.94472 INFO::Total function execution time is 0.156270265579224 s and adjustment time is 0.135000944137573 s ( 86.39 )
2025-03-18 05:27:12.946379 INFO::Formatting Data.
2025-03-18 05:27:12.947427 INFO::Typecasting input to dataframe.
2025-03-18 05:27:12.948793 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:12.950289 INFO::Removing potential empty rows and columns
2025-03-18 05:27:12.951993 INFO::Found 0 missing values.
2025-03-18 05:27:12.956646 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:12.957505 INFO::Done
2025-03-18 05:27:12.958307 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:12.961153 INFO::Starting hierarchical adjustment
2025-03-18 05:27:12.962246 INFO::Found 3 batches.
2025-03-18 05:27:12.963004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:12.963931 INFO::Using default BPPARAM
2025-03-18 05:27:12.964734 INFO::Processing subtree level 1
2025-03-18 05:27:13.091115 INFO::Adjusting the last 1 batches sequentially
2025-03-18 05:27:13.093753 INFO::Done
2025-03-18 05:27:13.094738 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:13.098517 INFO::ASW Batch was -0.110113430928434 prior to batch effect correction and is now -0.110113430928434 .
2025-03-18 05:27:13.100027 INFO::Total function execution time is 0.153605699539185 s and adjustment time is 0.131673574447632 s ( 85.72 )
2025-03-18 05:27:13.120295 INFO::Formatting Data.
2025-03-18 05:27:13.121481 INFO::Typecasting input to dataframe.
2025-03-18 05:27:13.122856 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:13.124305 INFO::Removing potential empty rows and columns
2025-03-18 05:27:13.126145 INFO::Found 0 missing values.
2025-03-18 05:27:13.131487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:13.132464 INFO::Done
2025-03-18 05:27:13.133313 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:13.136349 INFO::Starting hierarchical adjustment
2025-03-18 05:27:13.137633 INFO::Found 3 batches.
2025-03-18 05:27:13.138477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:13.139423 INFO::Using default BPPARAM
2025-03-18 05:27:13.14023 INFO::Processing subtree level 1
2025-03-18 05:27:13.265061 INFO::Adjusting the last 1 batches sequentially
2025-03-18 05:27:13.26807 INFO::Done
2025-03-18 05:27:13.268943 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:13.272391 INFO::ASW Batch was -0.116115996399966 prior to batch effect correction and is now -0.116115996399966 .
2025-03-18 05:27:13.277586 INFO::Total function execution time is 0.157329797744751 s and adjustment time is 0.130662679672241 s ( 83.05 )
2025-03-18 05:27:13.479776 INFO::Formatting Data.
2025-03-18 05:27:13.480934 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:13.482717 INFO::Removing potential empty rows and columns
2025-03-18 05:27:13.487367 INFO::Found 1000 missing values.
2025-03-18 05:27:13.518706 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:13.519655 INFO::Done
2025-03-18 05:27:13.520457 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:13.528408 INFO::Starting hierarchical adjustment
2025-03-18 05:27:13.529631 INFO::Found 10 batches.
2025-03-18 05:27:13.530452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:13.531353 INFO::Using default BPPARAM
2025-03-18 05:27:13.532127 INFO::Processing subtree level 1
2025-03-18 05:27:13.726394 INFO::Processing subtree level 2
2025-03-18 05:27:13.944213 INFO::Adjusting the last 1 batches sequentially
2025-03-18 05:27:13.946961 INFO::Done
2025-03-18 05:27:13.947898 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:13.956142 INFO::ASW Batch was 0.512353736408433 prior to batch effect correction and is now 0.512353736408433 .
2025-03-18 05:27:13.957166 INFO::ASW Label was 0.323021221433449 prior to batch effect correction and is now 0.323021221433449 .
2025-03-18 05:27:13.958507 INFO::Total function execution time is 0.478780746459961 s and adjustment time is 0.417598009109497 s ( 87.22 )
2025-03-18 05:27:13.959753 INFO::Formatting Data.
2025-03-18 05:27:13.9607 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:13.962611 INFO::Removing potential empty rows and columns
2025-03-18 05:27:13.967145 INFO::Found 1000 missing values.
2025-03-18 05:27:13.997139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:13.998133 INFO::Done
2025-03-18 05:27:13.998908 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:14.006509 INFO::Starting hierarchical adjustment
2025-03-18 05:27:14.00767 INFO::Found 10 batches.
2025-03-18 05:27:15.01356 INFO::Set up parallel execution backend with 2 workers
2025-03-18 05:27:15.015652 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-18 05:27:16.226525 INFO::Adjusting the last 2 batches sequentially
2025-03-18 05:27:16.229569 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 05:27:16.254141 INFO::Done
2025-03-18 05:27:16.25502 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:16.261727 INFO::ASW Batch was 0.512353736408433 prior to batch effect correction and is now 0.512353736408433 .
2025-03-18 05:27:16.262594 INFO::ASW Label was 0.323021221433449 prior to batch effect correction and is now 0.323021221433449 .
2025-03-18 05:27:16.263643 INFO::Total function execution time is 2.30393767356873 s and adjustment time is 2.2466938495636 s ( 97.52 )
2025-03-18 05:27:16.447082 INFO::Formatting Data.
2025-03-18 05:27:16.448157 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:16.449427 INFO::Removing potential empty rows and columns
2025-03-18 05:27:16.450983 INFO::Found 0 missing values.
2025-03-18 05:27:16.456542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:16.457423 INFO::Done
2025-03-18 05:27:16.458185 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 05:27:16.462009 INFO::Starting hierarchical adjustment
2025-03-18 05:27:16.463068 INFO::Found 3 batches.
2025-03-18 05:27:16.463778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 05:27:16.4646 INFO::Using default BPPARAM
2025-03-18 05:27:16.465354 INFO::Processing subtree level 1
2025-03-18 05:27:16.594663 INFO::Adjusting the last 1 batches sequentially
2025-03-18 05:27:16.596986 INFO::Done
2025-03-18 05:27:16.597829 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 05:27:16.60214 INFO::ASW Batch was 0.201765660468334 prior to batch effect correction and is now -0.1317239002919 .
2025-03-18 05:27:16.603041 INFO::ASW Label was -0.194315038247059 prior to batch effect correction and is now -0.0165933467182099 .
2025-03-18 05:27:16.604297 INFO::Total function execution time is 0.157242298126221 s and adjustment time is 0.134125232696533 s ( 85.3 )
2025-03-18 05:27:16.798406 INFO::Formatting Data.
2025-03-18 05:27:16.800511 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:16.801964 INFO::Removing potential empty rows and columns
2025-03-18 05:27:16.803698 INFO::Found 2 missing values.
2025-03-18 05:27:16.808257 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:16.809147 INFO::Done
2025-03-18 05:27:16.849117 INFO::Found NA in Reference column
2025-03-18 05:27:16.863063 INFO::Require at least two references per batch.
2025-03-18 05:27:16.897169 INFO::Formatting Data.
2025-03-18 05:27:16.898176 INFO::Recognized SummarizedExperiment
2025-03-18 05:27:16.898915 INFO::Typecasting input to dataframe.
2025-03-18 05:27:16.916831 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:16.918479 INFO::Removing potential empty rows and columns
2025-03-18 05:27:16.923755 INFO::Found 0 missing values.
2025-03-18 05:27:16.934608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:16.935611 INFO::Done
2025-03-18 05:27:16.958493 INFO::Formatting Data.
2025-03-18 05:27:16.959581 INFO::Recognized SummarizedExperiment
2025-03-18 05:27:16.960716 INFO::Typecasting input to dataframe.
2025-03-18 05:27:16.987567 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:16.98918 INFO::Removing potential empty rows and columns
2025-03-18 05:27:16.994427 INFO::Found 0 missing values.
2025-03-18 05:27:17.011552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:17.012466 INFO::Done
2025-03-18 05:27:17.034192 INFO::Formatting Data.
2025-03-18 05:27:17.035161 INFO::Recognized SummarizedExperiment
2025-03-18 05:27:17.035904 INFO::Typecasting input to dataframe.
2025-03-18 05:27:17.060718 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:17.06217 INFO::Removing potential empty rows and columns
2025-03-18 05:27:17.063684 INFO::Found 0 missing values.
2025-03-18 05:27:17.065034 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-18 05:27:17.071546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:17.072416 INFO::Done
2025-03-18 05:27:17.086099 INFO::Formatting Data.
2025-03-18 05:27:17.087078 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:17.088177 INFO::Removing potential empty rows and columns
2025-03-18 05:27:17.089536 INFO::Found 0 missing values.
2025-03-18 05:27:17.093906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:17.094772 INFO::Done
2025-03-18 05:27:17.11059 INFO::Formatting Data.
2025-03-18 05:27:17.111587 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:17.112694 INFO::Removing potential empty rows and columns
2025-03-18 05:27:17.114107 INFO::Found 0 missing values.
2025-03-18 05:27:17.118242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:17.119016 INFO::Done
2025-03-18 05:27:17.160365 INFO::Formatting Data.
2025-03-18 05:27:17.161387 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:17.162846 INFO::Removing potential empty rows and columns
2025-03-18 05:27:17.164635 INFO::Found 1 missing values.
2025-03-18 05:27:17.168248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:17.169054 INFO::Done
2025-03-18 05:27:17.205043 INFO::Formatting Data.
2025-03-18 05:27:17.206451 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:17.207734 INFO::Removing potential empty rows and columns
2025-03-18 05:27:17.209318 INFO::Found 2 missing values.
2025-03-18 05:27:17.210683 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-18 05:27:17.214303 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:17.215127 INFO::Done
2025-03-18 05:27:17.229877 INFO::Formatting Data.
2025-03-18 05:27:17.231011 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:17.23222 INFO::Removing potential empty rows and columns
2025-03-18 05:27:17.233547 INFO::Found 2 missing values.
2025-03-18 05:27:17.235796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:17.236545 INFO::Done
2025-03-18 05:27:17.252167 INFO::Formatting Data.
2025-03-18 05:27:17.253242 INFO::Typecasting input to dataframe.
2025-03-18 05:27:17.254381 INFO::Replacing NaNs with NAs.
2025-03-18 05:27:17.255531 INFO::Removing potential empty rows and columns
2025-03-18 05:27:17.257109 INFO::Found 0 missing values.
2025-03-18 05:27:17.261859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 05:27:17.262829 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.357 4.258 24.262
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.472 | 1.470 | 19.884 | |
| compute_asw | 0.033 | 0.000 | 0.033 | |
| count_existing | 0.015 | 0.003 | 0.018 | |
| generate_data_covariables | 0.007 | 0.008 | 0.015 | |
| generate_dataset | 0.014 | 0.001 | 0.014 | |