Yannis Schumann
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:08 -0400 (Mon, 10 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" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-03-07 00:19:20 -0500 (Fri, 07 Mar 2025) |
| EndedAt: 2025-03-07 00:21:43 -0500 (Fri, 07 Mar 2025) |
| EllapsedTime: 143.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 43.899 2.585 34.438
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-03-07 00:21:04.827422 INFO::Formatting Data.
2025-03-07 00:21:04.833946 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:04.866345 INFO::Removing potential empty rows and columns
2025-03-07 00:21:05.576744 INFO::Found 0 missing values.
2025-03-07 00:21:05.587987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:05.58966 INFO::Done
2025-03-07 00:21:05.590932 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:05.618712 INFO::Starting hierarchical adjustment
2025-03-07 00:21:05.620691 INFO::Found 3 batches.
2025-03-07 00:21:05.622073 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:05.624935 INFO::Using default BPPARAM
2025-03-07 00:21:05.626492 INFO::Processing subtree level 1
2025-03-07 00:21:05.916398 INFO::Adjusting the last 1 batches sequentially
2025-03-07 00:21:05.923042 INFO::Done
2025-03-07 00:21:05.926443 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:05.934847 INFO::ASW Batch was -0.109990590753486 prior to batch effect correction and is now -0.109990590753486 .
2025-03-07 00:21:05.937571 INFO::Total function execution time is 1.1113920211792 s and adjustment time is 0.302180767059326 s ( 27.19 )
2025-03-07 00:21:05.974813 INFO::Formatting Data.
2025-03-07 00:21:05.976525 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:05.978742 INFO::Removing potential empty rows and columns
2025-03-07 00:21:05.981926 INFO::Found 0 missing values.
2025-03-07 00:21:05.984385 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.
2025-03-07 00:21:06.016548 INFO::Formatting Data.
2025-03-07 00:21:06.018427 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:06.020882 INFO::Removing potential empty rows and columns
2025-03-07 00:21:06.024629 INFO::Found 0 missing values.
2025-03-07 00:21:06.02716 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.
2025-03-07 00:21:06.074029 INFO::Formatting Data.
2025-03-07 00:21:06.075602 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:06.078118 INFO::Removing potential empty rows and columns
2025-03-07 00:21:06.081181 INFO::Found 0 missing values.
2025-03-07 00:21:06.08355 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.
2025-03-07 00:21:06.098105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:06.101229 INFO::Done
2025-03-07 00:21:06.102624 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:06.107984 INFO::Starting hierarchical adjustment
2025-03-07 00:21:06.111079 INFO::Found 2 batches.
2025-03-07 00:21:06.112661 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:06.11442 INFO::Using default BPPARAM
2025-03-07 00:21:06.1158 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:06.118082 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:06.187623 INFO::Done
2025-03-07 00:21:06.189006 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:06.193732 INFO::ASW Batch was -0.0775753670681905 prior to batch effect correction and is now -0.125923055743492 .
2025-03-07 00:21:06.19574 INFO::Total function execution time is 0.121741056442261 s and adjustment time is 0.0781369209289551 s ( 64.18 )
2025-03-07 00:21:06.202121 INFO::Formatting Data.
2025-03-07 00:21:06.203796 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:06.224476 INFO::Formatting Data.
2025-03-07 00:21:06.226155 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:06.228343 INFO::Removing potential empty rows and columns
2025-03-07 00:21:06.231036 INFO::Found 0 missing values.
2025-03-07 00:21:06.239105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:06.24059 INFO::Done
2025-03-07 00:21:06.24186 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:06.246759 INFO::Starting hierarchical adjustment
2025-03-07 00:21:06.24865 INFO::Found 2 batches.
2025-03-07 00:21:06.249961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:06.251623 INFO::Using default BPPARAM
2025-03-07 00:21:06.253173 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:06.255764 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:06.295547 INFO::Done
2025-03-07 00:21:06.297036 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:06.303746 INFO::ASW Batch was -0.0168881814440889 prior to batch effect correction and is now -0.114422893602158 .
2025-03-07 00:21:06.30582 INFO::Total function execution time is 0.0814011096954346 s and adjustment time is 0.0472679138183594 s ( 58.07 )
2025-03-07 00:21:06.30847 INFO::Formatting Data.
2025-03-07 00:21:06.310158 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:06.312508 INFO::Removing potential empty rows and columns
2025-03-07 00:21:06.315458 INFO::Found 0 missing values.
2025-03-07 00:21:06.323657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:06.325158 INFO::Done
2025-03-07 00:21:06.326499 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:06.331596 INFO::Starting hierarchical adjustment
2025-03-07 00:21:06.333543 INFO::Found 2 batches.
2025-03-07 00:21:06.334941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:06.336577 INFO::Using default BPPARAM
2025-03-07 00:21:06.33802 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:06.340487 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:06.384193 INFO::Done
2025-03-07 00:21:06.385626 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:06.390703 INFO::ASW Batch was -0.0168881814440889 prior to batch effect correction and is now -0.114422893602158 .
2025-03-07 00:21:06.393134 INFO::Total function execution time is 0.0846889019012451 s and adjustment time is 0.0510730743408203 s ( 60.31 )
2025-03-07 00:21:13.040096 INFO::Formatting Data.
2025-03-07 00:21:13.041761 INFO::Recognized SummarizedExperiment
2025-03-07 00:21:13.043098 INFO::Typecasting input to dataframe.
2025-03-07 00:21:13.122663 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:13.125053 INFO::Removing potential empty rows and columns
2025-03-07 00:21:13.13566 INFO::Found 0 missing values.
2025-03-07 00:21:13.157256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:13.158588 INFO::Done
2025-03-07 00:21:13.159729 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:13.16971 INFO::Starting hierarchical adjustment
2025-03-07 00:21:13.171444 INFO::Found 2 batches.
2025-03-07 00:21:13.175596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:13.178751 INFO::Using default BPPARAM
2025-03-07 00:21:13.180082 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:13.182254 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:13.329636 INFO::Done
2025-03-07 00:21:13.33132 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:13.339901 INFO::ASW Batch was -0.00512528010741516 prior to batch effect correction and is now -0.0877620293857291 .
2025-03-07 00:21:13.342099 INFO::Total function execution time is 0.302686929702759 s and adjustment time is 0.158536911010742 s ( 52.38 )
2025-03-07 00:21:13.393841 INFO::Formatting Data.
2025-03-07 00:21:13.39559 INFO::Recognized SummarizedExperiment
2025-03-07 00:21:13.397193 INFO::Typecasting input to dataframe.
2025-03-07 00:21:13.426474 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:13.429615 INFO::Removing potential empty rows and columns
2025-03-07 00:21:13.441532 INFO::Found 0 missing values.
2025-03-07 00:21:13.47126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:13.472911 INFO::Done
2025-03-07 00:21:13.474265 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:13.4842 INFO::Starting hierarchical adjustment
2025-03-07 00:21:13.485924 INFO::Found 2 batches.
2025-03-07 00:21:13.487207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:13.488622 INFO::Using default BPPARAM
2025-03-07 00:21:13.489865 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:13.494439 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:13.582681 INFO::Done
2025-03-07 00:21:13.584209 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:13.593425 INFO::ASW Batch was 0.028037644086634 prior to batch effect correction and is now 0.028037644086634 .
2025-03-07 00:21:13.595696 INFO::Total function execution time is 0.201748847961426 s and adjustment time is 0.0960910320281982 s ( 47.63 )
2025-03-07 00:21:13.651488 INFO::Formatting Data.
2025-03-07 00:21:13.655183 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:13.657785 INFO::Removing potential empty rows and columns
2025-03-07 00:21:13.660581 INFO::Found 0 missing values.
2025-03-07 00:21:13.669812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:13.671391 INFO::Done
2025-03-07 00:21:13.672855 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:13.678598 INFO::Starting hierarchical adjustment
2025-03-07 00:21:13.680502 INFO::Found 3 batches.
2025-03-07 00:21:13.681965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:13.683559 INFO::Using default BPPARAM
2025-03-07 00:21:13.684974 INFO::Processing subtree level 1
2025-03-07 00:21:14.056028 INFO::Adjusting the last 1 batches sequentially
2025-03-07 00:21:14.066271 INFO::Done
2025-03-07 00:21:14.068574 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:14.081943 INFO::ASW Batch was -0.0805826667994339 prior to batch effect correction and is now -0.149074654056637 .
2025-03-07 00:21:14.084931 INFO::Total function execution time is 0.433454036712646 s and adjustment time is 0.386184215545654 s ( 89.09 )
2025-03-07 00:21:14.129746 INFO::Skipping initial DF formatting
2025-03-07 00:21:14.132106 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:14.142415 INFO::Starting hierarchical adjustment
2025-03-07 00:21:14.144331 INFO::Found 5 batches.
2025-03-07 00:21:14.145689 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:14.147753 INFO::Using default BPPARAM
2025-03-07 00:21:14.149161 INFO::Processing subtree level 1
2025-03-07 00:21:14.458758 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:14.471408 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:14.542591 INFO::Done
2025-03-07 00:21:14.545108 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:14.558039 INFO::ASW Batch was 0.479159643977616 prior to batch effect correction and is now 0.479159643977616 .
2025-03-07 00:21:14.559549 INFO::ASW Label was 0.411045416688517 prior to batch effect correction and is now 0.411045416688517 .
2025-03-07 00:21:14.561964 INFO::Total function execution time is 0.432217121124268 s and adjustment time is 0.398646831512451 s ( 92.23 )
2025-03-07 00:21:14.620219 INFO::Formatting Data.
2025-03-07 00:21:14.621955 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:14.624135 INFO::Removing potential empty rows and columns
2025-03-07 00:21:14.626631 INFO::Found 0 missing values.
2025-03-07 00:21:14.637363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:14.63869 INFO::Done
2025-03-07 00:21:14.640116 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:14.648999 INFO::Starting hierarchical adjustment
2025-03-07 00:21:14.650934 INFO::Found 5 batches.
2025-03-07 00:21:14.652212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:14.655177 INFO::Using default BPPARAM
2025-03-07 00:21:14.656604 INFO::Processing subtree level 1
2025-03-07 00:21:14.923386 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:14.932624 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:14.991857 INFO::Done
2025-03-07 00:21:14.994755 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:15.003829 INFO::ASW Batch was 0.322758365273864 prior to batch effect correction and is now -0.0439224708037657 .
2025-03-07 00:21:15.005461 INFO::ASW Label was 0.289166690436056 prior to batch effect correction and is now 0.788395772624901 .
2025-03-07 00:21:15.007681 INFO::Total function execution time is 0.387468099594116 s and adjustment time is 0.341275930404663 s ( 88.08 )
2025-03-07 00:21:15.010479 INFO::Formatting Data.
2025-03-07 00:21:15.01222 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:15.014448 INFO::Removing potential empty rows and columns
2025-03-07 00:21:15.017118 INFO::Found 0 missing values.
2025-03-07 00:21:15.028492 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:15.03109 INFO::Done
2025-03-07 00:21:15.032559 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:15.040994 INFO::Starting hierarchical adjustment
2025-03-07 00:21:15.042982 INFO::Found 5 batches.
2025-03-07 00:21:15.044715 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:15.047465 INFO::Using default BPPARAM
2025-03-07 00:21:15.048967 INFO::Processing subtree level 1
2025-03-07 00:21:15.301878 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:15.312703 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:15.370996 INFO::Done
2025-03-07 00:21:15.373553 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:15.381076 INFO::ASW Batch was 0.322758365273864 prior to batch effect correction and is now -0.0439224708037657 .
2025-03-07 00:21:15.38254 INFO::ASW Label was 0.289166690436056 prior to batch effect correction and is now 0.788395772624901 .
2025-03-07 00:21:15.384614 INFO::Total function execution time is 0.374128103256226 s and adjustment time is 0.328402042388916 s ( 87.78 )
2025-03-07 00:21:15.429442 INFO::Formatting Data.
2025-03-07 00:21:15.431166 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:15.433269 INFO::Removing potential empty rows and columns
2025-03-07 00:21:15.43741 INFO::Found 0 missing values.
2025-03-07 00:21:15.449996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:15.451523 INFO::Done
2025-03-07 00:21:15.452827 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:15.461401 INFO::Starting hierarchical adjustment
2025-03-07 00:21:15.464056 INFO::Found 5 batches.
2025-03-07 00:21:15.465564 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:15.467156 INFO::Using default BPPARAM
2025-03-07 00:21:15.468478 INFO::Processing subtree level 1
2025-03-07 00:21:15.742052 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:15.751654 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:15.811029 INFO::Done
2025-03-07 00:21:15.813629 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:15.823796 INFO::ASW Batch was 0.212257641818626 prior to batch effect correction and is now -0.111082356150537 .
2025-03-07 00:21:15.825965 INFO::ASW Label was 0.470849923652421 prior to batch effect correction and is now 0.876948893447594 .
2025-03-07 00:21:15.828048 INFO::Total function execution time is 0.398633003234863 s and adjustment time is 0.348075151443481 s ( 87.32 )
2025-03-07 00:21:15.8337 INFO::Formatting Data.
2025-03-07 00:21:15.835435 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:15.837588 INFO::Removing potential empty rows and columns
2025-03-07 00:21:15.840822 INFO::Found 0 missing values.
2025-03-07 00:21:15.853669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:15.855087 INFO::Done
2025-03-07 00:21:15.856373 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:15.863545 INFO::Starting hierarchical adjustment
2025-03-07 00:21:15.866177 INFO::Found 5 batches.
2025-03-07 00:21:15.867695 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:15.869813 INFO::Using default BPPARAM
2025-03-07 00:21:15.871331 INFO::Processing subtree level 1
2025-03-07 00:21:16.129179 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:16.140109 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:16.198914 INFO::Done
2025-03-07 00:21:16.203571 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:16.215658 INFO::ASW Batch was 0.212257641818626 prior to batch effect correction and is now -0.111082356150537 .
2025-03-07 00:21:16.217376 INFO::ASW Label was 0.470849923652421 prior to batch effect correction and is now 0.876948893447594 .
2025-03-07 00:21:16.221871 INFO::Total function execution time is 0.385844945907593 s and adjustment time is 0.333779096603394 s ( 86.51 )
2025-03-07 00:21:16.26127 INFO::Formatting Data.
2025-03-07 00:21:16.262937 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:16.26511 INFO::Removing potential empty rows and columns
2025-03-07 00:21:16.267724 INFO::Found 0 missing values.
2025-03-07 00:21:16.274885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:16.277181 INFO::Done
2025-03-07 00:21:16.278541 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:16.285443 INFO::Starting hierarchical adjustment
2025-03-07 00:21:16.289956 INFO::Found 2 batches.
2025-03-07 00:21:16.291427 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:16.293433 INFO::Using default BPPARAM
2025-03-07 00:21:16.294701 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:16.296876 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:16.342539 INFO::Done
2025-03-07 00:21:16.344011 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:16.352579 INFO::ASW Batch was 0.244906087687007 prior to batch effect correction and is now 0.105809788028952 .
2025-03-07 00:21:16.354139 INFO::ASW Label was 0.816800364445539 prior to batch effect correction and is now 0.871330286498631 .
2025-03-07 00:21:16.356199 INFO::Total function execution time is 0.0949859619140625 s and adjustment time is 0.0549359321594238 s ( 57.84 )
2025-03-07 00:21:16.358923 INFO::Formatting Data.
2025-03-07 00:21:16.360643 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:16.362746 INFO::Removing potential empty rows and columns
2025-03-07 00:21:16.365383 INFO::Found 0 missing values.
2025-03-07 00:21:16.372695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:16.374093 INFO::Done
2025-03-07 00:21:16.375342 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:16.385284 INFO::Starting hierarchical adjustment
2025-03-07 00:21:16.389255 INFO::Found 2 batches.
2025-03-07 00:21:16.390715 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:16.392366 INFO::Using default BPPARAM
2025-03-07 00:21:16.393845 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:16.396263 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:16.440683 INFO::Done
2025-03-07 00:21:16.442014 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:16.449843 INFO::ASW Batch was 0.244906087687007 prior to batch effect correction and is now 0.105809788028952 .
2025-03-07 00:21:16.451303 INFO::ASW Label was 0.816800364445539 prior to batch effect correction and is now 0.871330286498631 .
2025-03-07 00:21:16.453142 INFO::Total function execution time is 0.0943210124969482 s and adjustment time is 0.0518589019775391 s ( 54.98 )
2025-03-07 00:21:16.485727 INFO::Formatting Data.
2025-03-07 00:21:16.488079 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:16.490289 INFO::Removing potential empty rows and columns
2025-03-07 00:21:16.49227 INFO::Found 0 missing values.
2025-03-07 00:21:16.497003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:16.500924 INFO::Done
2025-03-07 00:21:16.502349 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:16.508523 INFO::Starting hierarchical adjustment
2025-03-07 00:21:16.510776 INFO::Found 2 batches.
2025-03-07 00:21:16.512886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:16.514531 INFO::Using default BPPARAM
2025-03-07 00:21:16.51585 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:16.518263 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:16.616173 INFO::Done
2025-03-07 00:21:16.617672 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:16.622297 INFO::ASW Batch was -0.134285835867335 prior to batch effect correction and is now -0.13543997670151 .
2025-03-07 00:21:16.625132 INFO::Total function execution time is 0.139482975006104 s and adjustment time is 0.105753898620605 s ( 75.82 )
2025-03-07 00:21:16.663294 INFO::Formatting Data.
2025-03-07 00:21:16.66509 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:16.667078 INFO::Removing potential empty rows and columns
2025-03-07 00:21:16.671865 INFO::Found 0 missing values.
2025-03-07 00:21:16.674378 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.
2025-03-07 00:21:16.690486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:16.691894 INFO::Done
2025-03-07 00:21:16.693099 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:16.701806 INFO::Starting hierarchical adjustment
2025-03-07 00:21:16.704291 INFO::Found 2 batches.
2025-03-07 00:21:16.705748 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:16.708678 INFO::Using default BPPARAM
2025-03-07 00:21:16.710195 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:16.712744 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:16.765889 INFO::Done
2025-03-07 00:21:16.768303 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:16.775844 INFO::ASW Batch was 0.781123485333422 prior to batch effect correction and is now 0.0340707655072224 .
2025-03-07 00:21:16.778388 INFO::ASW Label was 0.26906468078185 prior to batch effect correction and is now 0.836016224591941 .
2025-03-07 00:21:16.781131 INFO::Total function execution time is 0.117942094802856 s and adjustment time is 0.0625758171081543 s ( 53.06 )
2025-03-07 00:21:16.783247 INFO::Formatting Data.
2025-03-07 00:21:16.784894 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:16.787143 INFO::Removing potential empty rows and columns
2025-03-07 00:21:16.790471 INFO::Found 0 missing values.
2025-03-07 00:21:16.792991 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.
2025-03-07 00:21:16.808224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:16.810408 INFO::Done
2025-03-07 00:21:16.811956 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:16.821424 INFO::Starting hierarchical adjustment
2025-03-07 00:21:16.823413 INFO::Found 2 batches.
2025-03-07 00:21:16.824743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:16.82627 INFO::Using default BPPARAM
2025-03-07 00:21:16.827739 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:16.83024 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:16.882256 INFO::Done
2025-03-07 00:21:16.883748 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:16.892994 INFO::ASW Batch was 0.781123485333422 prior to batch effect correction and is now 0.0340707655072224 .
2025-03-07 00:21:16.894453 INFO::ASW Label was 0.26906468078185 prior to batch effect correction and is now 0.836016224591941 .
2025-03-07 00:21:16.896547 INFO::Total function execution time is 0.113425970077515 s and adjustment time is 0.0592391490936279 s ( 52.23 )
2025-03-07 00:21:17.545123 INFO::Formatting Data.
2025-03-07 00:21:17.546837 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:17.548945 INFO::Removing potential empty rows and columns
2025-03-07 00:21:17.555213 INFO::Found 0 missing values.
2025-03-07 00:21:17.563899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:17.565402 INFO::Done
2025-03-07 00:21:17.566767 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:17.571635 INFO::Starting hierarchical adjustment
2025-03-07 00:21:17.573504 INFO::Found 3 batches.
2025-03-07 00:21:17.57623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:17.577861 INFO::Using default BPPARAM
2025-03-07 00:21:17.579184 INFO::Processing subtree level 1
2025-03-07 00:21:17.813546 INFO::Adjusting the last 1 batches sequentially
2025-03-07 00:21:17.824726 INFO::Done
2025-03-07 00:21:17.828371 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:17.840821 INFO::ASW Batch was -0.028436784171205 prior to batch effect correction and is now -0.028436784171205 .
2025-03-07 00:21:17.846234 INFO::Total function execution time is 0.300889015197754 s and adjustment time is 0.25157618522644 s ( 83.61 )
2025-03-07 00:21:17.8501 INFO::Formatting Data.
2025-03-07 00:21:17.852351 INFO::Typecasting input to dataframe.
2025-03-07 00:21:17.855506 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:17.858286 INFO::Removing potential empty rows and columns
2025-03-07 00:21:17.86119 INFO::Found 0 missing values.
2025-03-07 00:21:17.869505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:17.870983 INFO::Done
2025-03-07 00:21:17.872298 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:17.877765 INFO::Starting hierarchical adjustment
2025-03-07 00:21:17.879715 INFO::Found 3 batches.
2025-03-07 00:21:17.88108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:17.884633 INFO::Using default BPPARAM
2025-03-07 00:21:17.886046 INFO::Processing subtree level 1
2025-03-07 00:21:18.124098 INFO::Adjusting the last 1 batches sequentially
2025-03-07 00:21:18.134527 INFO::Done
2025-03-07 00:21:18.137397 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:18.149155 INFO::ASW Batch was -0.028436784171205 prior to batch effect correction and is now -0.028436784171205 .
2025-03-07 00:21:18.153955 INFO::Total function execution time is 0.303832054138184 s and adjustment time is 0.255201101303101 s ( 83.99 )
2025-03-07 00:21:18.200578 INFO::Formatting Data.
2025-03-07 00:21:18.208458 INFO::Typecasting input to dataframe.
2025-03-07 00:21:18.210711 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:18.213389 INFO::Removing potential empty rows and columns
2025-03-07 00:21:18.216003 INFO::Found 0 missing values.
2025-03-07 00:21:18.226302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:18.227808 INFO::Done
2025-03-07 00:21:18.229148 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:18.235688 INFO::Starting hierarchical adjustment
2025-03-07 00:21:18.23757 INFO::Found 3 batches.
2025-03-07 00:21:18.238998 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:18.241178 INFO::Using default BPPARAM
2025-03-07 00:21:18.242616 INFO::Processing subtree level 1
2025-03-07 00:21:18.743338 INFO::Adjusting the last 1 batches sequentially
2025-03-07 00:21:18.749187 INFO::Done
2025-03-07 00:21:18.750764 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:18.79575 INFO::ASW Batch was -0.148274820236129 prior to batch effect correction and is now -0.148274820236129 .
2025-03-07 00:21:18.804507 INFO::Total function execution time is 0.601977825164795 s and adjustment time is 0.511950016021729 s ( 85.04 )
2025-03-07 00:21:19.444888 INFO::Formatting Data.
2025-03-07 00:21:19.44677 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:19.45033 INFO::Removing potential empty rows and columns
2025-03-07 00:21:19.458448 INFO::Found 1000 missing values.
2025-03-07 00:21:19.537195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:19.538867 INFO::Done
2025-03-07 00:21:19.540385 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:19.557371 INFO::Starting hierarchical adjustment
2025-03-07 00:21:19.56008 INFO::Found 10 batches.
2025-03-07 00:21:19.561525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:19.563166 INFO::Using default BPPARAM
2025-03-07 00:21:19.564797 INFO::Processing subtree level 1
2025-03-07 00:21:19.983551 INFO::Processing subtree level 2
2025-03-07 00:21:20.552039 INFO::Adjusting the last 1 batches sequentially
2025-03-07 00:21:20.568216 INFO::Done
2025-03-07 00:21:20.57283 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:20.598682 INFO::ASW Batch was 0.521040676458718 prior to batch effect correction and is now 0.521040676458718 .
2025-03-07 00:21:20.600991 INFO::ASW Label was 0.311361543586978 prior to batch effect correction and is now 0.311361543586978 .
2025-03-07 00:21:20.604024 INFO::Total function execution time is 1.15916395187378 s and adjustment time is 1.00859999656677 s ( 87.01 )
2025-03-07 00:21:20.606714 INFO::Formatting Data.
2025-03-07 00:21:20.609074 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:20.613266 INFO::Removing potential empty rows and columns
2025-03-07 00:21:20.621584 INFO::Found 1000 missing values.
2025-03-07 00:21:20.688208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:20.690402 INFO::Done
2025-03-07 00:21:20.691793 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:20.705911 INFO::Starting hierarchical adjustment
2025-03-07 00:21:20.707883 INFO::Found 10 batches.
2025-03-07 00:21:22.189261 INFO::Set up parallel execution backend with 2 workers
2025-03-07 00:21:22.190592 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-07 00:21:24.16884 INFO::Adjusting the last 2 batches sequentially
2025-03-07 00:21:24.171934 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-07 00:21:24.224888 INFO::Done
2025-03-07 00:21:24.226208 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:24.237937 INFO::ASW Batch was 0.521040676458718 prior to batch effect correction and is now 0.521040676458718 .
2025-03-07 00:21:24.239976 INFO::ASW Label was 0.311361543586978 prior to batch effect correction and is now 0.311361543586978 .
2025-03-07 00:21:24.241563 INFO::Total function execution time is 3.6350200176239 s and adjustment time is 3.51741909980774 s ( 96.76 )
2025-03-07 00:21:24.660821 INFO::Formatting Data.
2025-03-07 00:21:24.662444 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:24.665196 INFO::Removing potential empty rows and columns
2025-03-07 00:21:24.66815 INFO::Found 0 missing values.
2025-03-07 00:21:24.680871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:24.684855 INFO::Done
2025-03-07 00:21:24.68618 INFO::Acquiring quality metrics before batch effect correction.
2025-03-07 00:21:24.692586 INFO::Starting hierarchical adjustment
2025-03-07 00:21:24.697264 INFO::Found 3 batches.
2025-03-07 00:21:24.699039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-07 00:21:24.700575 INFO::Using default BPPARAM
2025-03-07 00:21:24.701902 INFO::Processing subtree level 1
2025-03-07 00:21:25.003243 INFO::Adjusting the last 1 batches sequentially
2025-03-07 00:21:25.016321 INFO::Done
2025-03-07 00:21:25.018448 INFO::Acquiring quality metrics after batch effect correction.
2025-03-07 00:21:25.035351 INFO::ASW Batch was 0.0913072741441223 prior to batch effect correction and is now -0.172153479957182 .
2025-03-07 00:21:25.038928 INFO::ASW Label was -0.116621860140647 prior to batch effect correction and is now 0.0735528464119141 .
2025-03-07 00:21:25.043055 INFO::Total function execution time is 0.382213830947876 s and adjustment time is 0.319468975067139 s ( 83.58 )
2025-03-07 00:21:25.432028 INFO::Formatting Data.
2025-03-07 00:21:25.433771 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:25.439206 INFO::Removing potential empty rows and columns
2025-03-07 00:21:25.442119 INFO::Found 2 missing values.
2025-03-07 00:21:25.452067 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:25.453508 INFO::Done
2025-03-07 00:21:25.545264 INFO::Found NA in Reference column
2025-03-07 00:21:25.574944 INFO::Require at least two references per batch.
2025-03-07 00:21:25.63845 INFO::Formatting Data.
2025-03-07 00:21:25.640249 INFO::Recognized SummarizedExperiment
2025-03-07 00:21:25.641867 INFO::Typecasting input to dataframe.
2025-03-07 00:21:25.677506 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:25.680342 INFO::Removing potential empty rows and columns
2025-03-07 00:21:25.696562 INFO::Found 0 missing values.
2025-03-07 00:21:25.740726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:25.742313 INFO::Done
2025-03-07 00:21:25.809319 INFO::Formatting Data.
2025-03-07 00:21:25.810761 INFO::Recognized SummarizedExperiment
2025-03-07 00:21:25.81209 INFO::Typecasting input to dataframe.
2025-03-07 00:21:25.886491 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:25.889087 INFO::Removing potential empty rows and columns
2025-03-07 00:21:25.900509 INFO::Found 0 missing values.
2025-03-07 00:21:25.94719 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:25.949357 INFO::Done
2025-03-07 00:21:26.000757 INFO::Formatting Data.
2025-03-07 00:21:26.004602 INFO::Recognized SummarizedExperiment
2025-03-07 00:21:26.006126 INFO::Typecasting input to dataframe.
2025-03-07 00:21:26.072308 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:26.07469 INFO::Removing potential empty rows and columns
2025-03-07 00:21:26.078216 INFO::Found 0 missing values.
2025-03-07 00:21:26.082852 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.
2025-03-07 00:21:26.098834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:26.100111 INFO::Done
2025-03-07 00:21:26.139976 INFO::Formatting Data.
2025-03-07 00:21:26.141706 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:26.146802 INFO::Removing potential empty rows and columns
2025-03-07 00:21:26.14958 INFO::Found 0 missing values.
2025-03-07 00:21:26.160588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:26.162431 INFO::Done
2025-03-07 00:21:26.195945 INFO::Formatting Data.
2025-03-07 00:21:26.197591 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:26.201228 INFO::Removing potential empty rows and columns
2025-03-07 00:21:26.204374 INFO::Found 0 missing values.
2025-03-07 00:21:26.212387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:26.213752 INFO::Done
2025-03-07 00:21:26.307209 INFO::Formatting Data.
2025-03-07 00:21:26.308934 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:26.311472 INFO::Removing potential empty rows and columns
2025-03-07 00:21:26.314665 INFO::Found 1 missing values.
2025-03-07 00:21:26.327712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:26.329087 INFO::Done
2025-03-07 00:21:26.390218 INFO::Formatting Data.
2025-03-07 00:21:26.392024 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:26.393976 INFO::Removing potential empty rows and columns
2025-03-07 00:21:26.396385 INFO::Found 2 missing values.
2025-03-07 00:21:26.3989 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.
2025-03-07 00:21:26.406401 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:26.407893 INFO::Done
2025-03-07 00:21:26.440616 INFO::Formatting Data.
2025-03-07 00:21:26.442191 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:26.444173 INFO::Removing potential empty rows and columns
2025-03-07 00:21:26.446412 INFO::Found 2 missing values.
2025-03-07 00:21:26.452131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:26.453574 INFO::Done
2025-03-07 00:21:26.492953 INFO::Formatting Data.
2025-03-07 00:21:26.495172 INFO::Typecasting input to dataframe.
2025-03-07 00:21:26.497269 INFO::Replacing NaNs with NAs.
2025-03-07 00:21:26.499534 INFO::Removing potential empty rows and columns
2025-03-07 00:21:26.503372 INFO::Found 0 missing values.
2025-03-07 00:21:26.512199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-07 00:21:26.514459 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.105 6.786 44.861
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.899 | 2.585 | 34.438 | |
| compute_asw | 0.056 | 0.001 | 0.062 | |
| count_existing | 0.030 | 0.003 | 0.034 | |
| generate_data_covariables | 0.026 | 0.002 | 0.030 | |
| generate_dataset | 0.025 | 0.001 | 0.030 | |