Yannis Schumann
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 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 2025-04-02 19:35 -0400 (Wed, 02 Apr 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" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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: 2025-04-01 04:08:50 -0000 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 04:10:26 -0000 (Tue, 01 Apr 2025) |
| EllapsedTime: 96.2 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 26.97 1.316 22.966
* 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")
2025-04-01 04:10:05.019156 INFO::Formatting Data.
2025-04-01 04:10:05.020866 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:05.037712 INFO::Removing potential empty rows and columns
2025-04-01 04:10:05.745634 INFO::Found 0 missing values.
2025-04-01 04:10:05.750226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:05.751008 INFO::Done
2025-04-01 04:10:05.751721 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:05.765711 INFO::Starting hierarchical adjustment
2025-04-01 04:10:05.766877 INFO::Found 3 batches.
2025-04-01 04:10:05.767597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:05.769035 INFO::Using default BPPARAM
2025-04-01 04:10:05.769761 INFO::Processing subtree level 1
2025-04-01 04:10:05.888736 INFO::Adjusting the last 1 batches sequentially
2025-04-01 04:10:05.899203 INFO::Done
2025-04-01 04:10:05.899994 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:05.90758 INFO::ASW Batch was -0.0771390397250429 prior to batch effect correction and is now -0.0771390397250429 .
2025-04-01 04:10:05.913277 INFO::Total function execution time is 0.890839815139771 s and adjustment time is 0.132558345794678 s ( 14.88 )
2025-04-01 04:10:05.935137 INFO::Formatting Data.
2025-04-01 04:10:05.936088 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:05.937228 INFO::Removing potential empty rows and columns
2025-04-01 04:10:05.938726 INFO::Found 0 missing values.
2025-04-01 04:10:05.939887 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.
2025-04-01 04:10:05.954133 INFO::Formatting Data.
2025-04-01 04:10:05.955307 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:05.95644 INFO::Removing potential empty rows and columns
2025-04-01 04:10:05.957822 INFO::Found 0 missing values.
2025-04-01 04:10:05.95902 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.
2025-04-01 04:10:05.98023 INFO::Formatting Data.
2025-04-01 04:10:05.981138 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:05.982222 INFO::Removing potential empty rows and columns
2025-04-01 04:10:05.983587 INFO::Found 0 missing values.
2025-04-01 04:10:05.984724 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.
2025-04-01 04:10:05.990858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:05.991624 INFO::Done
2025-04-01 04:10:05.992297 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:05.99484 INFO::Starting hierarchical adjustment
2025-04-01 04:10:05.995782 INFO::Found 2 batches.
2025-04-01 04:10:05.996485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:05.997367 INFO::Using default BPPARAM
2025-04-01 04:10:05.998079 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:05.999354 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:06.027864 INFO::Done
2025-04-01 04:10:06.028724 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:06.031361 INFO::ASW Batch was -0.0460702379723358 prior to batch effect correction and is now -0.119111670968073 .
2025-04-01 04:10:06.032406 INFO::Total function execution time is 0.0522294044494629 s and adjustment time is 0.0322368144989014 s ( 61.72 )
2025-04-01 04:10:06.035981 INFO::Formatting Data.
2025-04-01 04:10:06.036865 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:06.048923 INFO::Formatting Data.
2025-04-01 04:10:06.049883 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:06.051126 INFO::Removing potential empty rows and columns
2025-04-01 04:10:06.052538 INFO::Found 0 missing values.
2025-04-01 04:10:06.056534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:06.057326 INFO::Done
2025-04-01 04:10:06.058024 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:06.060681 INFO::Starting hierarchical adjustment
2025-04-01 04:10:06.061714 INFO::Found 2 batches.
2025-04-01 04:10:06.062438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:06.063328 INFO::Using default BPPARAM
2025-04-01 04:10:06.06407 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:06.065366 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:06.08504 INFO::Done
2025-04-01 04:10:06.085899 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:06.088554 INFO::ASW Batch was -0.0324032998231085 prior to batch effect correction and is now -0.106638809336914 .
2025-04-01 04:10:06.08965 INFO::Total function execution time is 0.04081130027771 s and adjustment time is 0.0235207080841064 s ( 57.63 )
2025-04-01 04:10:06.091075 INFO::Formatting Data.
2025-04-01 04:10:06.091855 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:06.093017 INFO::Removing potential empty rows and columns
2025-04-01 04:10:06.094437 INFO::Found 0 missing values.
2025-04-01 04:10:06.098468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:06.099305 INFO::Done
2025-04-01 04:10:06.100015 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:06.102663 INFO::Starting hierarchical adjustment
2025-04-01 04:10:06.103633 INFO::Found 2 batches.
2025-04-01 04:10:06.10433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:06.10524 INFO::Using default BPPARAM
2025-04-01 04:10:06.105939 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:06.107192 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:06.127014 INFO::Done
2025-04-01 04:10:06.127878 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:06.130518 INFO::ASW Batch was -0.0324032998231085 prior to batch effect correction and is now -0.106638809336914 .
2025-04-01 04:10:06.131636 INFO::Total function execution time is 0.0405614376068115 s and adjustment time is 0.0235569477081299 s ( 58.08 )
2025-04-01 04:10:10.639975 INFO::Formatting Data.
2025-04-01 04:10:10.640876 INFO::Recognized SummarizedExperiment
2025-04-01 04:10:10.64156 INFO::Typecasting input to dataframe.
2025-04-01 04:10:10.684292 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:10.685848 INFO::Removing potential empty rows and columns
2025-04-01 04:10:10.690651 INFO::Found 0 missing values.
2025-04-01 04:10:10.699985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:10.700875 INFO::Done
2025-04-01 04:10:10.701594 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:10.706191 INFO::Starting hierarchical adjustment
2025-04-01 04:10:10.707342 INFO::Found 2 batches.
2025-04-01 04:10:10.7081 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:10.7095 INFO::Using default BPPARAM
2025-04-01 04:10:10.710222 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:10.711596 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:10.785632 INFO::Done
2025-04-01 04:10:10.786489 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:10.791123 INFO::ASW Batch was -0.0183934015217276 prior to batch effect correction and is now -0.0908525539802201 .
2025-04-01 04:10:10.792335 INFO::Total function execution time is 0.152741193771362 s and adjustment time is 0.0785036087036133 s ( 51.4 )
2025-04-01 04:10:10.816206 INFO::Formatting Data.
2025-04-01 04:10:10.817155 INFO::Recognized SummarizedExperiment
2025-04-01 04:10:10.817878 INFO::Typecasting input to dataframe.
2025-04-01 04:10:10.830671 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:10.832295 INFO::Removing potential empty rows and columns
2025-04-01 04:10:10.837594 INFO::Found 0 missing values.
2025-04-01 04:10:10.848086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:10.849042 INFO::Done
2025-04-01 04:10:10.849856 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:10.854875 INFO::Starting hierarchical adjustment
2025-04-01 04:10:10.856037 INFO::Found 2 batches.
2025-04-01 04:10:10.856875 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:10.857757 INFO::Using default BPPARAM
2025-04-01 04:10:10.858516 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:10.85995 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:10.895334 INFO::Done
2025-04-01 04:10:10.896268 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:10.901387 INFO::ASW Batch was -0.0155308852569189 prior to batch effect correction and is now -0.0155308852569189 .
2025-04-01 04:10:10.902703 INFO::Total function execution time is 0.0863733291625977 s and adjustment time is 0.0395190715789795 s ( 45.75 )
2025-04-01 04:10:10.928672 INFO::Formatting Data.
2025-04-01 04:10:10.929709 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:10.931006 INFO::Removing potential empty rows and columns
2025-04-01 04:10:10.932472 INFO::Found 0 missing values.
2025-04-01 04:10:10.937052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:10.937909 INFO::Done
2025-04-01 04:10:10.938713 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:10.941536 INFO::Starting hierarchical adjustment
2025-04-01 04:10:10.942808 INFO::Found 3 batches.
2025-04-01 04:10:10.943628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:10.944492 INFO::Using default BPPARAM
2025-04-01 04:10:10.945321 INFO::Processing subtree level 1
2025-04-01 04:10:11.242394 INFO::Adjusting the last 1 batches sequentially
2025-04-01 04:10:11.248898 INFO::Done
2025-04-01 04:10:11.249895 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:11.257416 INFO::ASW Batch was -0.109226376163355 prior to batch effect correction and is now -0.156223570215728 .
2025-04-01 04:10:11.258781 INFO::Total function execution time is 0.330089092254639 s and adjustment time is 0.302383184432983 s ( 91.61 )
2025-04-01 04:10:11.294619 INFO::Skipping initial DF formatting
2025-04-01 04:10:11.295512 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:11.300873 INFO::Starting hierarchical adjustment
2025-04-01 04:10:11.302032 INFO::Found 5 batches.
2025-04-01 04:10:11.302876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:11.303785 INFO::Using default BPPARAM
2025-04-01 04:10:11.304551 INFO::Processing subtree level 1
2025-04-01 04:10:11.476486 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:11.482746 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:11.512953 INFO::Done
2025-04-01 04:10:11.51386 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:11.519654 INFO::ASW Batch was 0.522680231485757 prior to batch effect correction and is now 0.522680231485757 .
2025-04-01 04:10:11.520534 INFO::ASW Label was 0.337005029342272 prior to batch effect correction and is now 0.337005029342272 .
2025-04-01 04:10:11.521707 INFO::Total function execution time is 0.227161645889282 s and adjustment time is 0.211139917373657 s ( 92.95 )
2025-04-01 04:10:11.54646 INFO::Formatting Data.
2025-04-01 04:10:11.547568 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:11.548933 INFO::Removing potential empty rows and columns
2025-04-01 04:10:11.550444 INFO::Found 0 missing values.
2025-04-01 04:10:11.556823 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:11.557736 INFO::Done
2025-04-01 04:10:11.558532 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:11.562821 INFO::Starting hierarchical adjustment
2025-04-01 04:10:11.564013 INFO::Found 5 batches.
2025-04-01 04:10:11.564855 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:11.565756 INFO::Using default BPPARAM
2025-04-01 04:10:11.566518 INFO::Processing subtree level 1
2025-04-01 04:10:11.765353 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:11.767702 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:11.816314 INFO::Done
2025-04-01 04:10:11.821562 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:11.827651 INFO::ASW Batch was 0.432627619304379 prior to batch effect correction and is now -0.106620185256663 .
2025-04-01 04:10:11.828661 INFO::ASW Label was 0.377170453210333 prior to batch effect correction and is now 0.819571570224608 .
2025-04-01 04:10:11.829959 INFO::Total function execution time is 0.283554792404175 s and adjustment time is 0.252519845962524 s ( 89.06 )
2025-04-01 04:10:11.831303 INFO::Formatting Data.
2025-04-01 04:10:11.832306 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:11.8337 INFO::Removing potential empty rows and columns
2025-04-01 04:10:11.835322 INFO::Found 0 missing values.
2025-04-01 04:10:11.842015 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:11.84301 INFO::Done
2025-04-01 04:10:11.84383 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:11.848402 INFO::Starting hierarchical adjustment
2025-04-01 04:10:11.84979 INFO::Found 5 batches.
2025-04-01 04:10:11.850763 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:11.851842 INFO::Using default BPPARAM
2025-04-01 04:10:11.852813 INFO::Processing subtree level 1
2025-04-01 04:10:12.031609 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:12.04184 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:12.086284 INFO::Done
2025-04-01 04:10:12.087272 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:12.095681 INFO::ASW Batch was 0.432627619304379 prior to batch effect correction and is now -0.106620185256663 .
2025-04-01 04:10:12.09659 INFO::ASW Label was 0.377170453210333 prior to batch effect correction and is now 0.819571570224608 .
2025-04-01 04:10:12.101941 INFO::Total function execution time is 0.270633697509766 s and adjustment time is 0.236753463745117 s ( 87.48 )
2025-04-01 04:10:12.141219 INFO::Formatting Data.
2025-04-01 04:10:12.142269 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:12.143485 INFO::Removing potential empty rows and columns
2025-04-01 04:10:12.148926 INFO::Found 0 missing values.
2025-04-01 04:10:12.159151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:12.160013 INFO::Done
2025-04-01 04:10:12.164765 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:12.172951 INFO::Starting hierarchical adjustment
2025-04-01 04:10:12.174119 INFO::Found 5 batches.
2025-04-01 04:10:12.174912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:12.175762 INFO::Using default BPPARAM
2025-04-01 04:10:12.176663 INFO::Processing subtree level 1
2025-04-01 04:10:12.416942 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:12.419123 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:12.44413 INFO::Done
2025-04-01 04:10:12.4451 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:12.449413 INFO::ASW Batch was 0.598308838380254 prior to batch effect correction and is now -0.0883556928570753 .
2025-04-01 04:10:12.450352 INFO::ASW Label was 0.203377444846938 prior to batch effect correction and is now 0.816769372442221 .
2025-04-01 04:10:12.451584 INFO::Total function execution time is 0.310420513153076 s and adjustment time is 0.270218849182129 s ( 87.05 )
2025-04-01 04:10:12.452807 INFO::Formatting Data.
2025-04-01 04:10:12.45369 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:12.454945 INFO::Removing potential empty rows and columns
2025-04-01 04:10:12.456311 INFO::Found 0 missing values.
2025-04-01 04:10:12.462311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:12.463243 INFO::Done
2025-04-01 04:10:12.46396 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:12.470913 INFO::Starting hierarchical adjustment
2025-04-01 04:10:12.471969 INFO::Found 5 batches.
2025-04-01 04:10:12.472698 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:12.473603 INFO::Using default BPPARAM
2025-04-01 04:10:12.47435 INFO::Processing subtree level 1
2025-04-01 04:10:12.673206 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:12.675305 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:12.720982 INFO::Done
2025-04-01 04:10:12.721902 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:12.72619 INFO::ASW Batch was 0.598308838380254 prior to batch effect correction and is now -0.0883556928570753 .
2025-04-01 04:10:12.726994 INFO::ASW Label was 0.203377444846938 prior to batch effect correction and is now 0.816769372442221 .
2025-04-01 04:10:12.728096 INFO::Total function execution time is 0.275302886962891 s and adjustment time is 0.249177932739258 s ( 90.51 )
2025-04-01 04:10:12.746154 INFO::Formatting Data.
2025-04-01 04:10:12.747162 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:12.74835 INFO::Removing potential empty rows and columns
2025-04-01 04:10:12.749762 INFO::Found 0 missing values.
2025-04-01 04:10:12.753599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:12.754346 INFO::Done
2025-04-01 04:10:12.755086 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:12.758924 INFO::Starting hierarchical adjustment
2025-04-01 04:10:12.759917 INFO::Found 2 batches.
2025-04-01 04:10:12.760633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:12.761512 INFO::Using default BPPARAM
2025-04-01 04:10:12.762228 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:12.763462 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:12.782767 INFO::Done
2025-04-01 04:10:12.783611 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:12.787391 INFO::ASW Batch was 0.532507764848834 prior to batch effect correction and is now -0.0335316922553621 .
2025-04-01 04:10:12.788167 INFO::ASW Label was 0.468792634261879 prior to batch effect correction and is now 0.893964062447012 .
2025-04-01 04:10:12.789227 INFO::Total function execution time is 0.0431709289550781 s and adjustment time is 0.0230457782745361 s ( 53.38 )
2025-04-01 04:10:12.79025 INFO::Formatting Data.
2025-04-01 04:10:12.791108 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:12.792233 INFO::Removing potential empty rows and columns
2025-04-01 04:10:12.79357 INFO::Found 0 missing values.
2025-04-01 04:10:12.797351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:12.798078 INFO::Done
2025-04-01 04:10:12.798811 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:12.802718 INFO::Starting hierarchical adjustment
2025-04-01 04:10:12.803697 INFO::Found 2 batches.
2025-04-01 04:10:12.804412 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:12.805248 INFO::Using default BPPARAM
2025-04-01 04:10:12.805974 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:12.807226 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:12.82648 INFO::Done
2025-04-01 04:10:12.827363 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:12.83113 INFO::ASW Batch was 0.532507764848834 prior to batch effect correction and is now -0.0335316922553621 .
2025-04-01 04:10:12.831884 INFO::ASW Label was 0.468792634261879 prior to batch effect correction and is now 0.893964062447012 .
2025-04-01 04:10:12.832904 INFO::Total function execution time is 0.0426316261291504 s and adjustment time is 0.0229732990264893 s ( 53.89 )
2025-04-01 04:10:12.847516 INFO::Formatting Data.
2025-04-01 04:10:12.848421 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:12.849558 INFO::Removing potential empty rows and columns
2025-04-01 04:10:12.850766 INFO::Found 0 missing values.
2025-04-01 04:10:12.853624 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:12.854313 INFO::Done
2025-04-01 04:10:12.855034 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:12.85746 INFO::Starting hierarchical adjustment
2025-04-01 04:10:12.858375 INFO::Found 2 batches.
2025-04-01 04:10:12.859114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:12.8599 INFO::Using default BPPARAM
2025-04-01 04:10:12.860592 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:12.861765 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:12.902805 INFO::Done
2025-04-01 04:10:12.903641 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:12.906102 INFO::ASW Batch was -0.0987473154221303 prior to batch effect correction and is now -0.122426626086084 .
2025-04-01 04:10:12.90715 INFO::Total function execution time is 0.0596978664398193 s and adjustment time is 0.0446093082427979 s ( 74.73 )
2025-04-01 04:10:12.922493 INFO::Formatting Data.
2025-04-01 04:10:12.923452 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:12.924544 INFO::Removing potential empty rows and columns
2025-04-01 04:10:12.92587 INFO::Found 0 missing values.
2025-04-01 04:10:12.927337 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.
2025-04-01 04:10:12.933645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:12.934399 INFO::Done
2025-04-01 04:10:12.935147 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:12.938923 INFO::Starting hierarchical adjustment
2025-04-01 04:10:12.939874 INFO::Found 2 batches.
2025-04-01 04:10:12.940586 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:12.941421 INFO::Using default BPPARAM
2025-04-01 04:10:12.942132 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:12.943432 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:12.967227 INFO::Done
2025-04-01 04:10:12.968059 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:12.971786 INFO::ASW Batch was 0.612774293393134 prior to batch effect correction and is now 0.0973472214538874 .
2025-04-01 04:10:12.972533 INFO::ASW Label was 0.479028012751219 prior to batch effect correction and is now 0.849708123599073 .
2025-04-01 04:10:12.973573 INFO::Total function execution time is 0.0511627197265625 s and adjustment time is 0.0275311470031738 s ( 53.81 )
2025-04-01 04:10:12.974557 INFO::Formatting Data.
2025-04-01 04:10:12.97539 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:12.976581 INFO::Removing potential empty rows and columns
2025-04-01 04:10:12.977901 INFO::Found 0 missing values.
2025-04-01 04:10:12.979098 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.
2025-04-01 04:10:12.985315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:12.98609 INFO::Done
2025-04-01 04:10:12.986811 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:12.990562 INFO::Starting hierarchical adjustment
2025-04-01 04:10:12.991537 INFO::Found 2 batches.
2025-04-01 04:10:12.992247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:12.993069 INFO::Using default BPPARAM
2025-04-01 04:10:12.993775 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:12.99505 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:13.01666 INFO::Done
2025-04-01 04:10:13.017529 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:13.021318 INFO::ASW Batch was 0.612774293393134 prior to batch effect correction and is now 0.0973472214538874 .
2025-04-01 04:10:13.022047 INFO::ASW Label was 0.479028012751219 prior to batch effect correction and is now 0.849708123599073 .
2025-04-01 04:10:13.023098 INFO::Total function execution time is 0.0485284328460693 s and adjustment time is 0.0253157615661621 s ( 52.17 )
2025-04-01 04:10:13.385508 INFO::Formatting Data.
2025-04-01 04:10:13.386467 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:13.387654 INFO::Removing potential empty rows and columns
2025-04-01 04:10:13.389074 INFO::Found 0 missing values.
2025-04-01 04:10:13.393388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:13.394139 INFO::Done
2025-04-01 04:10:13.394901 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:13.397576 INFO::Starting hierarchical adjustment
2025-04-01 04:10:13.398528 INFO::Found 3 batches.
2025-04-01 04:10:13.399263 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:13.40007 INFO::Using default BPPARAM
2025-04-01 04:10:13.40079 INFO::Processing subtree level 1
2025-04-01 04:10:13.52295 INFO::Adjusting the last 1 batches sequentially
2025-04-01 04:10:13.533576 INFO::Done
2025-04-01 04:10:13.534547 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:13.542175 INFO::ASW Batch was -0.025123539140612 prior to batch effect correction and is now -0.025123539140612 .
2025-04-01 04:10:13.543629 INFO::Total function execution time is 0.158117771148682 s and adjustment time is 0.135191917419434 s ( 85.5 )
2025-04-01 04:10:13.549278 INFO::Formatting Data.
2025-04-01 04:10:13.550357 INFO::Typecasting input to dataframe.
2025-04-01 04:10:13.551661 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:13.557196 INFO::Removing potential empty rows and columns
2025-04-01 04:10:13.55905 INFO::Found 0 missing values.
2025-04-01 04:10:13.567901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:13.57284 INFO::Done
2025-04-01 04:10:13.573807 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:13.576672 INFO::Starting hierarchical adjustment
2025-04-01 04:10:13.578919 INFO::Found 3 batches.
2025-04-01 04:10:13.579686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:13.580587 INFO::Using default BPPARAM
2025-04-01 04:10:13.581377 INFO::Processing subtree level 1
2025-04-01 04:10:13.702904 INFO::Adjusting the last 1 batches sequentially
2025-04-01 04:10:13.713535 INFO::Done
2025-04-01 04:10:13.714521 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:13.722149 INFO::ASW Batch was -0.025123539140612 prior to batch effect correction and is now -0.025123539140612 .
2025-04-01 04:10:13.723626 INFO::Total function execution time is 0.174382448196411 s and adjustment time is 0.134860038757324 s ( 77.34 )
2025-04-01 04:10:13.760549 INFO::Formatting Data.
2025-04-01 04:10:13.761569 INFO::Typecasting input to dataframe.
2025-04-01 04:10:13.762749 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:13.764015 INFO::Removing potential empty rows and columns
2025-04-01 04:10:13.765586 INFO::Found 0 missing values.
2025-04-01 04:10:13.77025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:13.771123 INFO::Done
2025-04-01 04:10:13.77186 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:13.774663 INFO::Starting hierarchical adjustment
2025-04-01 04:10:13.775724 INFO::Found 3 batches.
2025-04-01 04:10:13.77648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:13.777383 INFO::Using default BPPARAM
2025-04-01 04:10:13.778142 INFO::Processing subtree level 1
2025-04-01 04:10:13.89905 INFO::Adjusting the last 1 batches sequentially
2025-04-01 04:10:13.910123 INFO::Done
2025-04-01 04:10:13.911158 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:13.918789 INFO::ASW Batch was -0.0543758111235227 prior to batch effect correction and is now -0.0543758111235227 .
2025-04-01 04:10:13.920245 INFO::Total function execution time is 0.159741163253784 s and adjustment time is 0.134519338607788 s ( 84.21 )
2025-04-01 04:10:14.169889 INFO::Formatting Data.
2025-04-01 04:10:14.171 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:14.172661 INFO::Removing potential empty rows and columns
2025-04-01 04:10:14.177347 INFO::Found 1000 missing values.
2025-04-01 04:10:14.209964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:14.210917 INFO::Done
2025-04-01 04:10:14.211724 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:14.227977 INFO::Starting hierarchical adjustment
2025-04-01 04:10:14.233309 INFO::Found 10 batches.
2025-04-01 04:10:14.234209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:14.235328 INFO::Using default BPPARAM
2025-04-01 04:10:14.236122 INFO::Processing subtree level 1
2025-04-01 04:10:14.604658 INFO::Processing subtree level 2
2025-04-01 04:10:14.93827 INFO::Adjusting the last 1 batches sequentially
2025-04-01 04:10:14.945231 INFO::Done
2025-04-01 04:10:14.946294 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:14.963262 INFO::ASW Batch was 0.47361741275691 prior to batch effect correction and is now 0.47361741275691 .
2025-04-01 04:10:14.964374 INFO::ASW Label was 0.335797079272075 prior to batch effect correction and is now 0.335797079272075 .
2025-04-01 04:10:14.970029 INFO::Total function execution time is 0.800127267837524 s and adjustment time is 0.712226629257202 s ( 89.01 )
2025-04-01 04:10:14.971442 INFO::Formatting Data.
2025-04-01 04:10:14.97249 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:14.97867 INFO::Removing potential empty rows and columns
2025-04-01 04:10:14.987556 INFO::Found 1000 missing values.
2025-04-01 04:10:15.025314 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:15.026306 INFO::Done
2025-04-01 04:10:15.027209 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:15.035217 INFO::Starting hierarchical adjustment
2025-04-01 04:10:15.036456 INFO::Found 10 batches.
2025-04-01 04:10:16.073658 INFO::Set up parallel execution backend with 2 workers
2025-04-01 04:10:16.076015 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-04-01 04:10:17.856313 INFO::Adjusting the last 2 batches sequentially
2025-04-01 04:10:17.859401 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-01 04:10:17.884377 INFO::Done
2025-04-01 04:10:17.8853 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:17.892238 INFO::ASW Batch was 0.47361741275691 prior to batch effect correction and is now 0.47361741275691 .
2025-04-01 04:10:17.893162 INFO::ASW Label was 0.335797079272075 prior to batch effect correction and is now 0.335797079272075 .
2025-04-01 04:10:17.894325 INFO::Total function execution time is 2.92292952537537 s and adjustment time is 2.84817433357239 s ( 97.44 )
2025-04-01 04:10:18.114694 INFO::Formatting Data.
2025-04-01 04:10:18.115869 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.117273 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.118984 INFO::Found 0 missing values.
2025-04-01 04:10:18.124966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.125851 INFO::Done
2025-04-01 04:10:18.126696 INFO::Acquiring quality metrics before batch effect correction.
2025-04-01 04:10:18.130818 INFO::Starting hierarchical adjustment
2025-04-01 04:10:18.131961 INFO::Found 3 batches.
2025-04-01 04:10:18.132806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-01 04:10:18.133726 INFO::Using default BPPARAM
2025-04-01 04:10:18.134535 INFO::Processing subtree level 1
2025-04-01 04:10:18.308888 INFO::Adjusting the last 1 batches sequentially
2025-04-01 04:10:18.311435 INFO::Done
2025-04-01 04:10:18.312397 INFO::Acquiring quality metrics after batch effect correction.
2025-04-01 04:10:18.325591 INFO::ASW Batch was 0.227798083568419 prior to batch effect correction and is now -0.163662832932225 .
2025-04-01 04:10:18.326665 INFO::ASW Label was -0.208480820428985 prior to batch effect correction and is now -0.127317788688227 .
2025-04-01 04:10:18.328058 INFO::Total function execution time is 0.213420391082764 s and adjustment time is 0.179683446884155 s ( 84.19 )
2025-04-01 04:10:18.538931 INFO::Formatting Data.
2025-04-01 04:10:18.539973 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.54135 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.543163 INFO::Found 2 missing values.
2025-04-01 04:10:18.547713 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.548557 INFO::Done
2025-04-01 04:10:18.591467 INFO::Found NA in Reference column
2025-04-01 04:10:18.605727 INFO::Require at least two references per batch.
2025-04-01 04:10:18.635347 INFO::Formatting Data.
2025-04-01 04:10:18.636302 INFO::Recognized SummarizedExperiment
2025-04-01 04:10:18.637087 INFO::Typecasting input to dataframe.
2025-04-01 04:10:18.65063 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.652214 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.657413 INFO::Found 0 missing values.
2025-04-01 04:10:18.670463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.671352 INFO::Done
2025-04-01 04:10:18.694452 INFO::Formatting Data.
2025-04-01 04:10:18.695399 INFO::Recognized SummarizedExperiment
2025-04-01 04:10:18.696111 INFO::Typecasting input to dataframe.
2025-04-01 04:10:18.721761 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.723453 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.728808 INFO::Found 0 missing values.
2025-04-01 04:10:18.746402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.747377 INFO::Done
2025-04-01 04:10:18.769746 INFO::Formatting Data.
2025-04-01 04:10:18.770717 INFO::Recognized SummarizedExperiment
2025-04-01 04:10:18.771499 INFO::Typecasting input to dataframe.
2025-04-01 04:10:18.796449 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.797861 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.799467 INFO::Found 0 missing values.
2025-04-01 04:10:18.800855 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.
2025-04-01 04:10:18.807934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.808831 INFO::Done
2025-04-01 04:10:18.824009 INFO::Formatting Data.
2025-04-01 04:10:18.825046 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.826338 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.827901 INFO::Found 0 missing values.
2025-04-01 04:10:18.832778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.833689 INFO::Done
2025-04-01 04:10:18.85129 INFO::Formatting Data.
2025-04-01 04:10:18.852384 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.853684 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.855203 INFO::Found 0 missing values.
2025-04-01 04:10:18.859763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.860612 INFO::Done
2025-04-01 04:10:18.904208 INFO::Formatting Data.
2025-04-01 04:10:18.905271 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.906791 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.908666 INFO::Found 1 missing values.
2025-04-01 04:10:18.912381 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.913203 INFO::Done
2025-04-01 04:10:18.940093 INFO::Formatting Data.
2025-04-01 04:10:18.941214 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.942446 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.943872 INFO::Found 2 missing values.
2025-04-01 04:10:18.945166 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.
2025-04-01 04:10:18.948604 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.949411 INFO::Done
2025-04-01 04:10:18.964074 INFO::Formatting Data.
2025-04-01 04:10:18.965152 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.966371 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.967735 INFO::Found 2 missing values.
2025-04-01 04:10:18.970032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.970841 INFO::Done
2025-04-01 04:10:18.985929 INFO::Formatting Data.
2025-04-01 04:10:18.986938 INFO::Typecasting input to dataframe.
2025-04-01 04:10:18.98803 INFO::Replacing NaNs with NAs.
2025-04-01 04:10:18.989212 INFO::Removing potential empty rows and columns
2025-04-01 04:10:18.990689 INFO::Found 0 missing values.
2025-04-01 04:10:18.994983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-01 04:10:18.995771 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.159 3.891 29.715
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.970 | 1.316 | 22.966 | |
| compute_asw | 0.032 | 0.000 | 0.032 | |
| count_existing | 0.016 | 0.000 | 0.016 | |
| generate_data_covariables | 0.006 | 0.008 | 0.015 | |
| generate_dataset | 0.013 | 0.000 | 0.014 | |