Yannis Schumann
| Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-07 12:06 -0400 (Tue, 07 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
| 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 164/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2025-10-06 18:23:18 -0400 (Mon, 06 Oct 2025) |
| EndedAt: 2025-10-06 18:23:49 -0400 (Mon, 06 Oct 2025) |
| EllapsedTime: 31.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* 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 9.774 0.389 7.349
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
2025-10-06 18:23:41.984179 INFO::Formatting Data.
2025-10-06 18:23:41.98581 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:41.990212 INFO::Removing potential empty rows and columns
2025-10-06 18:23:42.09505 INFO::Found 0 missing values.
2025-10-06 18:23:42.096499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:42.096761 INFO::Done
2025-10-06 18:23:42.09698 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:42.103627 INFO::Starting hierarchical adjustment
2025-10-06 18:23:42.103986 INFO::Found 3 batches.
2025-10-06 18:23:42.104195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:42.104667 INFO::Using default BPPARAM
2025-10-06 18:23:42.104861 INFO::Processing subtree level 1
2025-10-06 18:23:42.150958 INFO::Adjusting the last 1 batches sequentially
2025-10-06 18:23:42.15217 INFO::Done
2025-10-06 18:23:42.152403 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:42.153515 INFO::ASW Batch was -0.0486702900050013 prior to batch effect correction and is now -0.0486702900050013 .
2025-10-06 18:23:42.153952 INFO::Total function execution time is 0.170257806777954 s and adjustment time is 0.0482709407806396 s ( 28.35 )
2025-10-06 18:23:42.160415 INFO::Formatting Data.
2025-10-06 18:23:42.160683 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:42.160996 INFO::Removing potential empty rows and columns
2025-10-06 18:23:42.161405 INFO::Found 0 missing values.
2025-10-06 18:23:42.161721 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.
2025-10-06 18:23:42.165869 INFO::Formatting Data.
2025-10-06 18:23:42.166114 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:42.166399 INFO::Removing potential empty rows and columns
2025-10-06 18:23:42.167103 INFO::Found 0 missing values.
2025-10-06 18:23:42.167381 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.
2025-10-06 18:23:42.17359 INFO::Formatting Data.
2025-10-06 18:23:42.173848 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:42.17415 INFO::Removing potential empty rows and columns
2025-10-06 18:23:42.174519 INFO::Found 0 missing values.
2025-10-06 18:23:42.174836 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.
2025-10-06 18:23:42.176434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:42.176636 INFO::Done
2025-10-06 18:23:42.176826 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:42.17762 INFO::Starting hierarchical adjustment
2025-10-06 18:23:42.177845 INFO::Found 2 batches.
2025-10-06 18:23:42.178017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:42.17827 INFO::Using default BPPARAM
2025-10-06 18:23:42.178443 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:42.178738 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-06 18:23:42.189582 INFO::Done
2025-10-06 18:23:42.189887 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:42.190691 INFO::ASW Batch was 0.0557066392694725 prior to batch effect correction and is now -0.0916601083316 .
2025-10-06 18:23:42.190999 INFO::Total function execution time is 0.0174329280853271 s and adjustment time is 0.0117461681365967 s ( 67.38 )
2025-10-06 18:23:42.192158 INFO::Formatting Data.
2025-10-06 18:23:42.192361 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:42.195623 INFO::Formatting Data.
2025-10-06 18:23:42.195864 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:42.196164 INFO::Removing potential empty rows and columns
2025-10-06 18:23:42.196546 INFO::Found 0 missing values.
2025-10-06 18:23:42.197506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:42.197687 INFO::Done
2025-10-06 18:23:42.197866 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:42.198754 INFO::Starting hierarchical adjustment
2025-10-06 18:23:42.198978 INFO::Found 2 batches.
2025-10-06 18:23:42.199155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:42.199379 INFO::Using default BPPARAM
2025-10-06 18:23:42.199551 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:42.199853 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:42.219506 INFO::Done
2025-10-06 18:23:42.219749 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:42.220446 INFO::ASW Batch was -0.0727338226358102 prior to batch effect correction and is now -0.09229843107098 .
2025-10-06 18:23:42.22072 INFO::Total function execution time is 0.0251169204711914 s and adjustment time is 0.0205550193786621 s ( 81.84 )
2025-10-06 18:23:42.221067 INFO::Formatting Data.
2025-10-06 18:23:42.221258 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:42.221532 INFO::Removing potential empty rows and columns
2025-10-06 18:23:42.221857 INFO::Found 0 missing values.
2025-10-06 18:23:42.222701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:42.222876 INFO::Done
2025-10-06 18:23:42.223039 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:42.223675 INFO::Starting hierarchical adjustment
2025-10-06 18:23:42.223895 INFO::Found 2 batches.
2025-10-06 18:23:42.224054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:42.224239 INFO::Using default BPPARAM
2025-10-06 18:23:42.224391 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:42.224641 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:42.230024 INFO::Done
2025-10-06 18:23:42.230275 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:42.230985 INFO::ASW Batch was -0.0727338226358102 prior to batch effect correction and is now -0.09229843107098 .
2025-10-06 18:23:42.231243 INFO::Total function execution time is 0.0101711750030518 s and adjustment time is 0.00615906715393066 s ( 60.55 )
2025-10-06 18:23:43.400599 INFO::Formatting Data.
2025-10-06 18:23:43.400879 INFO::Recognized SummarizedExperiment
2025-10-06 18:23:43.401045 INFO::Typecasting input to dataframe.
2025-10-06 18:23:43.413208 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:43.413646 INFO::Removing potential empty rows and columns
2025-10-06 18:23:43.41481 INFO::Found 0 missing values.
2025-10-06 18:23:43.416921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:43.417107 INFO::Done
2025-10-06 18:23:43.417261 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:43.418466 INFO::Starting hierarchical adjustment
2025-10-06 18:23:43.418683 INFO::Found 2 batches.
2025-10-06 18:23:43.418834 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:43.419155 INFO::Using default BPPARAM
2025-10-06 18:23:43.419306 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:43.419588 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-06 18:23:43.436698 INFO::Done
2025-10-06 18:23:43.43694 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:43.438157 INFO::ASW Batch was -0.0123707957302516 prior to batch effect correction and is now -0.0855583281905165 .
2025-10-06 18:23:43.43842 INFO::Total function execution time is 0.03792405128479 s and adjustment time is 0.0180468559265137 s ( 47.59 )
2025-10-06 18:23:43.44467 INFO::Formatting Data.
2025-10-06 18:23:43.444916 INFO::Recognized SummarizedExperiment
2025-10-06 18:23:43.445093 INFO::Typecasting input to dataframe.
2025-10-06 18:23:43.448036 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:43.448399 INFO::Removing potential empty rows and columns
2025-10-06 18:23:43.449529 INFO::Found 0 missing values.
2025-10-06 18:23:43.451604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:43.451773 INFO::Done
2025-10-06 18:23:43.451925 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:43.453108 INFO::Starting hierarchical adjustment
2025-10-06 18:23:43.453324 INFO::Found 2 batches.
2025-10-06 18:23:43.453473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:43.453649 INFO::Using default BPPARAM
2025-10-06 18:23:43.453789 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:43.454061 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-06 18:23:43.461823 INFO::Done
2025-10-06 18:23:43.462049 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:43.463223 INFO::ASW Batch was -0.00453849922535581 prior to batch effect correction and is now -0.00453849922535581 .
2025-10-06 18:23:43.463476 INFO::Total function execution time is 0.0188100337982178 s and adjustment time is 0.00853395462036133 s ( 45.37 )
2025-10-06 18:23:43.469839 INFO::Formatting Data.
2025-10-06 18:23:43.470061 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:43.470326 INFO::Removing potential empty rows and columns
2025-10-06 18:23:43.470619 INFO::Found 0 missing values.
2025-10-06 18:23:43.471432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:43.471595 INFO::Done
2025-10-06 18:23:43.471744 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:43.472341 INFO::Starting hierarchical adjustment
2025-10-06 18:23:43.47255 INFO::Found 3 batches.
2025-10-06 18:23:43.472694 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:43.47287 INFO::Using default BPPARAM
2025-10-06 18:23:43.47301 INFO::Processing subtree level 1
2025-10-06 18:23:43.535588 INFO::Adjusting the last 1 batches sequentially
2025-10-06 18:23:43.536953 INFO::Done
2025-10-06 18:23:43.537351 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:43.539047 INFO::ASW Batch was -0.0807374530620353 prior to batch effect correction and is now -0.141763951091989 .
2025-10-06 18:23:43.540377 INFO::Total function execution time is 0.0703630447387695 s and adjustment time is 0.0644450187683105 s ( 91.59 )
2025-10-06 18:23:43.547978 INFO::Skipping initial DF formatting
2025-10-06 18:23:43.548217 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:43.54962 INFO::Starting hierarchical adjustment
2025-10-06 18:23:43.549885 INFO::Found 5 batches.
2025-10-06 18:23:43.550379 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:43.550599 INFO::Using default BPPARAM
2025-10-06 18:23:43.550762 INFO::Processing subtree level 1
2025-10-06 18:23:43.663983 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:43.668894 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-06 18:23:43.677834 INFO::Done
2025-10-06 18:23:43.678608 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:43.682004 INFO::ASW Batch was 0.529687197059579 prior to batch effect correction and is now 0.529687197059579 .
2025-10-06 18:23:43.682267 INFO::ASW Label was 0.378489905355188 prior to batch effect correction and is now 0.378489905355188 .
2025-10-06 18:23:43.683094 INFO::Total function execution time is 0.135117053985596 s and adjustment time is 0.128005981445312 s ( 94.74 )
2025-10-06 18:23:43.74505 INFO::Formatting Data.
2025-10-06 18:23:43.74566 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:43.746171 INFO::Removing potential empty rows and columns
2025-10-06 18:23:43.746582 INFO::Found 0 missing values.
2025-10-06 18:23:43.748137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:43.748322 INFO::Done
2025-10-06 18:23:43.748488 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:43.749607 INFO::Starting hierarchical adjustment
2025-10-06 18:23:43.749868 INFO::Found 5 batches.
2025-10-06 18:23:43.750058 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:43.750355 INFO::Using default BPPARAM
2025-10-06 18:23:43.750566 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:43.832489 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:43.835373 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:43.849469 INFO::Done
2025-10-06 18:23:43.850101 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:43.852455 INFO::ASW Batch was 0.547117765185509 prior to batch effect correction and is now 0.0490220743829419 .
2025-10-06 18:23:43.852781 INFO::ASW Label was 0.27680028788464 prior to batch effect correction and is now 0.668260190116172 .
2025-10-06 18:23:43.853459 INFO::Total function execution time is 0.108368158340454 s and adjustment time is 0.0996448993682861 s ( 91.95 )
2025-10-06 18:23:43.853978 INFO::Formatting Data.
2025-10-06 18:23:43.854259 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:43.854669 INFO::Removing potential empty rows and columns
2025-10-06 18:23:43.855227 INFO::Found 0 missing values.
2025-10-06 18:23:43.857766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:43.858198 INFO::Done
2025-10-06 18:23:43.858509 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:43.859936 INFO::Starting hierarchical adjustment
2025-10-06 18:23:43.860497 INFO::Found 5 batches.
2025-10-06 18:23:43.860789 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:43.861202 INFO::Using default BPPARAM
2025-10-06 18:23:43.86167 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:43.94234 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:43.944472 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:43.953548 INFO::Done
2025-10-06 18:23:43.954025 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:43.955558 INFO::ASW Batch was 0.547117765185509 prior to batch effect correction and is now 0.0490220743829419 .
2025-10-06 18:23:43.955775 INFO::ASW Label was 0.27680028788464 prior to batch effect correction and is now 0.668260190116172 .
2025-10-06 18:23:43.956301 INFO::Total function execution time is 0.102340221405029 s and adjustment time is 0.0933279991149902 s ( 91.19 )
2025-10-06 18:23:43.961826 INFO::Formatting Data.
2025-10-06 18:23:43.962064 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:43.962379 INFO::Removing potential empty rows and columns
2025-10-06 18:23:43.962751 INFO::Found 0 missing values.
2025-10-06 18:23:43.964076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:43.964266 INFO::Done
2025-10-06 18:23:43.964456 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:43.965623 INFO::Starting hierarchical adjustment
2025-10-06 18:23:43.965898 INFO::Found 5 batches.
2025-10-06 18:23:43.96608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:43.966318 INFO::Using default BPPARAM
2025-10-06 18:23:43.966613 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:44.033196 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:44.034975 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:44.043429 INFO::Done
2025-10-06 18:23:44.043819 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.045515 INFO::ASW Batch was 0.336704128267287 prior to batch effect correction and is now -0.0379568111205113 .
2025-10-06 18:23:44.045743 INFO::ASW Label was 0.482942813526484 prior to batch effect correction and is now 0.747793381333429 .
2025-10-06 18:23:44.046165 INFO::Total function execution time is 0.0843379497528076 s and adjustment time is 0.0775949954986572 s ( 92 )
2025-10-06 18:23:44.046465 INFO::Formatting Data.
2025-10-06 18:23:44.04665 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.046944 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.04728 INFO::Found 0 missing values.
2025-10-06 18:23:44.048564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.048735 INFO::Done
2025-10-06 18:23:44.048894 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.049864 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.050108 INFO::Found 5 batches.
2025-10-06 18:23:44.050284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.050505 INFO::Using default BPPARAM
2025-10-06 18:23:44.05076 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:44.109736 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:44.11208 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:44.12137 INFO::Done
2025-10-06 18:23:44.121767 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.12377 INFO::ASW Batch was 0.336704128267287 prior to batch effect correction and is now -0.0379568111205113 .
2025-10-06 18:23:44.124004 INFO::ASW Label was 0.482942813526484 prior to batch effect correction and is now 0.747793381333429 .
2025-10-06 18:23:44.124675 INFO::Total function execution time is 0.078179121017456 s and adjustment time is 0.0713019371032715 s ( 91.2 )
2025-10-06 18:23:44.131315 INFO::Formatting Data.
2025-10-06 18:23:44.131563 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.131864 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.132213 INFO::Found 0 missing values.
2025-10-06 18:23:44.133111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.133319 INFO::Done
2025-10-06 18:23:44.133485 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.134444 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.134692 INFO::Found 2 batches.
2025-10-06 18:23:44.134864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.135087 INFO::Using default BPPARAM
2025-10-06 18:23:44.135268 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:44.135549 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:44.140677 INFO::Done
2025-10-06 18:23:44.1409 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.141829 INFO::ASW Batch was 0.785677612639931 prior to batch effect correction and is now -0.0171385137512683 .
2025-10-06 18:23:44.142007 INFO::ASW Label was 0.220746738352456 prior to batch effect correction and is now 0.782788622718473 .
2025-10-06 18:23:44.142257 INFO::Total function execution time is 0.0109608173370361 s and adjustment time is 0.00603103637695312 s ( 55.02 )
2025-10-06 18:23:44.142503 INFO::Formatting Data.
2025-10-06 18:23:44.142682 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.142942 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.143267 INFO::Found 0 missing values.
2025-10-06 18:23:44.144309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.144585 INFO::Done
2025-10-06 18:23:44.144785 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.145872 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.146114 INFO::Found 2 batches.
2025-10-06 18:23:44.146289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.146484 INFO::Using default BPPARAM
2025-10-06 18:23:44.146642 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:44.146913 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-06 18:23:44.151992 INFO::Done
2025-10-06 18:23:44.152215 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.153144 INFO::ASW Batch was 0.785677612639931 prior to batch effect correction and is now -0.0171385137512683 .
2025-10-06 18:23:44.153337 INFO::ASW Label was 0.220746738352456 prior to batch effect correction and is now 0.782788622718473 .
2025-10-06 18:23:44.153596 INFO::Total function execution time is 0.011085033416748 s and adjustment time is 0.00592803955078125 s ( 53.48 )
2025-10-06 18:23:44.158355 INFO::Formatting Data.
2025-10-06 18:23:44.158613 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.158893 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.159182 INFO::Found 0 missing values.
2025-10-06 18:23:44.159824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.159984 INFO::Done
2025-10-06 18:23:44.160143 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.160713 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.160945 INFO::Found 2 batches.
2025-10-06 18:23:44.161101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.161281 INFO::Using default BPPARAM
2025-10-06 18:23:44.161428 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:44.161693 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-06 18:23:44.172831 INFO::Done
2025-10-06 18:23:44.173077 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.173732 INFO::ASW Batch was -0.0445226221385381 prior to batch effect correction and is now -0.0771506910032147 .
2025-10-06 18:23:44.174014 INFO::Total function execution time is 0.0156769752502441 s and adjustment time is 0.0119249820709229 s ( 76.07 )
2025-10-06 18:23:44.17901 INFO::Formatting Data.
2025-10-06 18:23:44.179254 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.179536 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.17994 INFO::Found 0 missing values.
2025-10-06 18:23:44.180409 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.
2025-10-06 18:23:44.182016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.182228 INFO::Done
2025-10-06 18:23:44.182393 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.183371 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.183575 INFO::Found 2 batches.
2025-10-06 18:23:44.183744 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.183934 INFO::Using default BPPARAM
2025-10-06 18:23:44.184103 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:44.184384 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-06 18:23:44.19013 INFO::Done
2025-10-06 18:23:44.190368 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.191294 INFO::ASW Batch was 0.494238659549157 prior to batch effect correction and is now -0.0274863852696011 .
2025-10-06 18:23:44.191494 INFO::ASW Label was 0.600806602818644 prior to batch effect correction and is now 0.94906561703075 .
2025-10-06 18:23:44.191766 INFO::Total function execution time is 0.0127799510955811 s and adjustment time is 0.00659394264221191 s ( 51.6 )
2025-10-06 18:23:44.192028 INFO::Formatting Data.
2025-10-06 18:23:44.192208 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.192497 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.192814 INFO::Found 0 missing values.
2025-10-06 18:23:44.193096 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.
2025-10-06 18:23:44.194493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.194675 INFO::Done
2025-10-06 18:23:44.194828 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.195706 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.195925 INFO::Found 2 batches.
2025-10-06 18:23:44.196088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.19628 INFO::Using default BPPARAM
2025-10-06 18:23:44.196433 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:44.196688 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-06 18:23:44.203162 INFO::Done
2025-10-06 18:23:44.203453 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.204533 INFO::ASW Batch was 0.494238659549157 prior to batch effect correction and is now -0.0274863852696011 .
2025-10-06 18:23:44.204732 INFO::ASW Label was 0.600806602818644 prior to batch effect correction and is now 0.94906561703075 .
2025-10-06 18:23:44.204984 INFO::Total function execution time is 0.0129489898681641 s and adjustment time is 0.0072629451751709 s ( 56.09 )
2025-10-06 18:23:44.274936 INFO::Formatting Data.
2025-10-06 18:23:44.275251 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.275566 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.275907 INFO::Found 0 missing values.
2025-10-06 18:23:44.277249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.277564 INFO::Done
2025-10-06 18:23:44.277827 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.278772 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.27907 INFO::Found 3 batches.
2025-10-06 18:23:44.279257 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.279496 INFO::Using default BPPARAM
2025-10-06 18:23:44.279678 INFO::Processing subtree level 1
2025-10-06 18:23:44.328427 INFO::Adjusting the last 1 batches sequentially
2025-10-06 18:23:44.330559 INFO::Done
2025-10-06 18:23:44.331012 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.333989 INFO::ASW Batch was -0.0253806843082988 prior to batch effect correction and is now -0.0253806843082988 .
2025-10-06 18:23:44.335104 INFO::Total function execution time is 0.0600950717926025 s and adjustment time is 0.0515439510345459 s ( 85.77 )
2025-10-06 18:23:44.33588 INFO::Formatting Data.
2025-10-06 18:23:44.336248 INFO::Typecasting input to dataframe.
2025-10-06 18:23:44.336546 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.33692 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.337395 INFO::Found 0 missing values.
2025-10-06 18:23:44.338371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.33855 INFO::Done
2025-10-06 18:23:44.338714 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.339398 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.339644 INFO::Found 3 batches.
2025-10-06 18:23:44.339935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.340173 INFO::Using default BPPARAM
2025-10-06 18:23:44.340346 INFO::Processing subtree level 1
2025-10-06 18:23:44.388277 INFO::Adjusting the last 1 batches sequentially
2025-10-06 18:23:44.390752 INFO::Done
2025-10-06 18:23:44.391436 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.395184 INFO::ASW Batch was -0.0253806843082988 prior to batch effect correction and is now -0.0253806843082988 .
2025-10-06 18:23:44.396302 INFO::Total function execution time is 0.0603759288787842 s and adjustment time is 0.0511360168457031 s ( 84.7 )
2025-10-06 18:23:44.403193 INFO::Formatting Data.
2025-10-06 18:23:44.403698 INFO::Typecasting input to dataframe.
2025-10-06 18:23:44.403976 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.404281 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.404684 INFO::Found 0 missing values.
2025-10-06 18:23:44.405613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.405809 INFO::Done
2025-10-06 18:23:44.405971 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.406601 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.406828 INFO::Found 3 batches.
2025-10-06 18:23:44.406983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.407202 INFO::Using default BPPARAM
2025-10-06 18:23:44.407349 INFO::Processing subtree level 1
2025-10-06 18:23:44.449289 INFO::Adjusting the last 1 batches sequentially
2025-10-06 18:23:44.452016 INFO::Done
2025-10-06 18:23:44.452493 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.455465 INFO::ASW Batch was -0.05491720595638 prior to batch effect correction and is now -0.05491720595638 .
2025-10-06 18:23:44.456589 INFO::Total function execution time is 0.0533609390258789 s and adjustment time is 0.0452339649200439 s ( 84.77 )
2025-10-06 18:23:44.522534 INFO::Formatting Data.
2025-10-06 18:23:44.522794 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.523171 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.524086 INFO::Found 1000 missing values.
2025-10-06 18:23:44.529732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.529941 INFO::Done
2025-10-06 18:23:44.530108 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.532044 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.532295 INFO::Found 10 batches.
2025-10-06 18:23:44.532455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:44.532684 INFO::Using default BPPARAM
2025-10-06 18:23:44.532851 INFO::Processing subtree level 1
2025-10-06 18:23:44.583182 INFO::Processing subtree level 2
2025-10-06 18:23:44.640645 INFO::Adjusting the last 1 batches sequentially
2025-10-06 18:23:44.644942 INFO::Done
2025-10-06 18:23:44.645402 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:44.649789 INFO::ASW Batch was 0.482231943983498 prior to batch effect correction and is now 0.482231943983498 .
2025-10-06 18:23:44.650015 INFO::ASW Label was 0.342718572462589 prior to batch effect correction and is now 0.342718572462589 .
2025-10-06 18:23:44.651036 INFO::Total function execution time is 0.128298997879028 s and adjustment time is 0.112689018249512 s ( 87.83 )
2025-10-06 18:23:44.651428 INFO::Formatting Data.
2025-10-06 18:23:44.651894 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:44.652399 INFO::Removing potential empty rows and columns
2025-10-06 18:23:44.653288 INFO::Found 1000 missing values.
2025-10-06 18:23:44.658974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:44.65921 INFO::Done
2025-10-06 18:23:44.659392 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:44.661427 INFO::Starting hierarchical adjustment
2025-10-06 18:23:44.661681 INFO::Found 10 batches.
2025-10-06 18:23:45.105789 INFO::Set up parallel execution backend with 2 workers
2025-10-06 18:23:45.106094 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-06 18:23:45.624118 INFO::Adjusting the last 2 batches sequentially
2025-10-06 18:23:45.624733 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-06 18:23:45.630257 INFO::Done
2025-10-06 18:23:45.630464 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:45.632322 INFO::ASW Batch was 0.482231943983498 prior to batch effect correction and is now 0.482231943983498 .
2025-10-06 18:23:45.632496 INFO::ASW Label was 0.342718572462589 prior to batch effect correction and is now 0.342718572462589 .
2025-10-06 18:23:45.632729 INFO::Total function execution time is 0.981310129165649 s and adjustment time is 0.968625783920288 s ( 98.71 )
2025-10-06 18:23:45.703741 INFO::Formatting Data.
2025-10-06 18:23:45.704078 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.704449 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.704908 INFO::Found 0 missing values.
2025-10-06 18:23:45.706257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.706454 INFO::Done
2025-10-06 18:23:45.706642 INFO::Acquiring quality metrics before batch effect correction.
2025-10-06 18:23:45.707673 INFO::Starting hierarchical adjustment
2025-10-06 18:23:45.707906 INFO::Found 3 batches.
2025-10-06 18:23:45.708077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-06 18:23:45.708305 INFO::Using default BPPARAM
2025-10-06 18:23:45.708481 INFO::Processing subtree level 1
2025-10-06 18:23:45.762832 INFO::Adjusting the last 1 batches sequentially
2025-10-06 18:23:45.764126 INFO::Done
2025-10-06 18:23:45.764403 INFO::Acquiring quality metrics after batch effect correction.
2025-10-06 18:23:45.766136 INFO::ASW Batch was 0.205756280437749 prior to batch effect correction and is now -0.173598585705579 .
2025-10-06 18:23:45.766436 INFO::ASW Label was -0.141408840514888 prior to batch effect correction and is now 0.0391750596518366 .
2025-10-06 18:23:45.766955 INFO::Total function execution time is 0.0632178783416748 s and adjustment time is 0.0562629699707031 s ( 89 )
2025-10-06 18:23:45.82515 INFO::Formatting Data.
2025-10-06 18:23:45.825495 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.825811 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.826208 INFO::Found 2 missing values.
2025-10-06 18:23:45.827141 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.827323 INFO::Done
2025-10-06 18:23:45.837662 INFO::Found NA in Reference column
2025-10-06 18:23:45.841337 INFO::Require at least two references per batch.
2025-10-06 18:23:45.849939 INFO::Formatting Data.
2025-10-06 18:23:45.850224 INFO::Recognized SummarizedExperiment
2025-10-06 18:23:45.850408 INFO::Typecasting input to dataframe.
2025-10-06 18:23:45.854745 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.855157 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.856488 INFO::Found 0 missing values.
2025-10-06 18:23:45.858963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.859173 INFO::Done
2025-10-06 18:23:45.864867 INFO::Formatting Data.
2025-10-06 18:23:45.865081 INFO::Recognized SummarizedExperiment
2025-10-06 18:23:45.865241 INFO::Typecasting input to dataframe.
2025-10-06 18:23:45.87093 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.871324 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.872591 INFO::Found 0 missing values.
2025-10-06 18:23:45.876438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.876632 INFO::Done
2025-10-06 18:23:45.882429 INFO::Formatting Data.
2025-10-06 18:23:45.882669 INFO::Recognized SummarizedExperiment
2025-10-06 18:23:45.882846 INFO::Typecasting input to dataframe.
2025-10-06 18:23:45.888204 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.888536 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.888896 INFO::Found 0 missing values.
2025-10-06 18:23:45.889207 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.
2025-10-06 18:23:45.890618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.890836 INFO::Done
2025-10-06 18:23:45.894825 INFO::Formatting Data.
2025-10-06 18:23:45.895074 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.895365 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.895703 INFO::Found 0 missing values.
2025-10-06 18:23:45.896597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.896818 INFO::Done
2025-10-06 18:23:45.901329 INFO::Formatting Data.
2025-10-06 18:23:45.901583 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.901853 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.902201 INFO::Found 0 missing values.
2025-10-06 18:23:45.903098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.903286 INFO::Done
2025-10-06 18:23:45.915139 INFO::Formatting Data.
2025-10-06 18:23:45.91545 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.915809 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.916245 INFO::Found 1 missing values.
2025-10-06 18:23:45.917151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.91736 INFO::Done
2025-10-06 18:23:45.92529 INFO::Formatting Data.
2025-10-06 18:23:45.925563 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.925852 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.926181 INFO::Found 2 missing values.
2025-10-06 18:23:45.92648 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.
2025-10-06 18:23:45.927275 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.927467 INFO::Done
2025-10-06 18:23:45.931579 INFO::Formatting Data.
2025-10-06 18:23:45.931828 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.932118 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.932483 INFO::Found 2 missing values.
2025-10-06 18:23:45.933017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.933201 INFO::Done
2025-10-06 18:23:45.937413 INFO::Formatting Data.
2025-10-06 18:23:45.93767 INFO::Typecasting input to dataframe.
2025-10-06 18:23:45.93795 INFO::Replacing NaNs with NAs.
2025-10-06 18:23:45.938194 INFO::Removing potential empty rows and columns
2025-10-06 18:23:45.93856 INFO::Found 0 missing values.
2025-10-06 18:23:45.939498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-06 18:23:45.939681 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.679 1.637 8.501
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.774 | 0.389 | 7.349 | |
| compute_asw | 0.01 | 0.00 | 0.01 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.005 | 0.000 | 0.004 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |