Yannis Schumann
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 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 2025-10-24 12:06 -0400 (Fri, 24 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" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 166/2359 | 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 12.7.6 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: 2025-10-23 18:42:20 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 18:42:52 -0400 (Thu, 23 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 9.682 0.451 6.951
* 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")
2025-10-23 18:42:44.439755 INFO::Formatting Data.
2025-10-23 18:42:44.441343 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:44.445958 INFO::Removing potential empty rows and columns
2025-10-23 18:42:44.554302 INFO::Found 0 missing values.
2025-10-23 18:42:44.572968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:44.573246 INFO::Done
2025-10-23 18:42:44.573435 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:44.578722 INFO::Starting hierarchical adjustment
2025-10-23 18:42:44.579024 INFO::Found 3 batches.
2025-10-23 18:42:44.579211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:44.579656 INFO::Using default BPPARAM
2025-10-23 18:42:44.579825 INFO::Processing subtree level 1
2025-10-23 18:42:44.633709 INFO::Adjusting the last 1 batches sequentially
2025-10-23 18:42:44.634827 INFO::Done
2025-10-23 18:42:44.636825 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:44.638484 INFO::ASW Batch was -0.0367954048333883 prior to batch effect correction and is now -0.0367954048333883 .
2025-10-23 18:42:44.639188 INFO::Total function execution time is 0.200001001358032 s and adjustment time is 0.0558719635009766 s ( 27.94 )
2025-10-23 18:42:44.646096 INFO::Formatting Data.
2025-10-23 18:42:44.646344 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:44.646696 INFO::Removing potential empty rows and columns
2025-10-23 18:42:44.647085 INFO::Found 0 missing values.
2025-10-23 18:42:44.647384 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.
2025-10-23 18:42:44.651509 INFO::Formatting Data.
2025-10-23 18:42:44.65176 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:44.652061 INFO::Removing potential empty rows and columns
2025-10-23 18:42:44.652401 INFO::Found 0 missing values.
2025-10-23 18:42:44.652689 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.
2025-10-23 18:42:44.658638 INFO::Formatting Data.
2025-10-23 18:42:44.658888 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:44.659648 INFO::Removing potential empty rows and columns
2025-10-23 18:42:44.659974 INFO::Found 0 missing values.
2025-10-23 18:42:44.66029 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.
2025-10-23 18:42:44.66174 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:44.661949 INFO::Done
2025-10-23 18:42:44.662142 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:44.66286 INFO::Starting hierarchical adjustment
2025-10-23 18:42:44.663086 INFO::Found 2 batches.
2025-10-23 18:42:44.663258 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:44.663881 INFO::Using default BPPARAM
2025-10-23 18:42:44.664058 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:44.664369 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 18:42:44.675157 INFO::Done
2025-10-23 18:42:44.67543 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:44.676199 INFO::ASW Batch was -0.0180982747707807 prior to batch effect correction and is now -0.091704401953826 .
2025-10-23 18:42:44.676474 INFO::Total function execution time is 0.0178399085998535 s and adjustment time is 0.0120940208435059 s ( 67.79 )
2025-10-23 18:42:44.677575 INFO::Formatting Data.
2025-10-23 18:42:44.677781 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:44.680904 INFO::Formatting Data.
2025-10-23 18:42:44.681126 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:44.681389 INFO::Removing potential empty rows and columns
2025-10-23 18:42:44.681751 INFO::Found 0 missing values.
2025-10-23 18:42:44.682635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:44.682813 INFO::Done
2025-10-23 18:42:44.682983 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:44.683749 INFO::Starting hierarchical adjustment
2025-10-23 18:42:44.683961 INFO::Found 2 batches.
2025-10-23 18:42:44.684133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:44.68433 INFO::Using default BPPARAM
2025-10-23 18:42:44.684519 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:44.684804 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 18:42:44.705573 INFO::Done
2025-10-23 18:42:44.705803 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:44.706428 INFO::ASW Batch was -0.0305015338621889 prior to batch effect correction and is now -0.100001582635457 .
2025-10-23 18:42:44.706694 INFO::Total function execution time is 0.0257790088653564 s and adjustment time is 0.021651029586792 s ( 83.99 )
2025-10-23 18:42:44.707011 INFO::Formatting Data.
2025-10-23 18:42:44.707197 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:44.70746 INFO::Removing potential empty rows and columns
2025-10-23 18:42:44.707762 INFO::Found 0 missing values.
2025-10-23 18:42:44.708563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:44.708722 INFO::Done
2025-10-23 18:42:44.708865 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:44.709392 INFO::Starting hierarchical adjustment
2025-10-23 18:42:44.709597 INFO::Found 2 batches.
2025-10-23 18:42:44.709747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:44.709919 INFO::Using default BPPARAM
2025-10-23 18:42:44.710059 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:44.710288 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 18:42:44.715225 INFO::Done
2025-10-23 18:42:44.715415 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:44.716005 INFO::ASW Batch was -0.0305015338621889 prior to batch effect correction and is now -0.100001582635457 .
2025-10-23 18:42:44.716515 INFO::Total function execution time is 0.00948786735534668 s and adjustment time is 0.00565791130065918 s ( 59.63 )
2025-10-23 18:42:45.840345 INFO::Formatting Data.
2025-10-23 18:42:45.840619 INFO::Recognized SummarizedExperiment
2025-10-23 18:42:45.840777 INFO::Typecasting input to dataframe.
2025-10-23 18:42:45.85067 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:45.851074 INFO::Removing potential empty rows and columns
2025-10-23 18:42:45.852226 INFO::Found 0 missing values.
2025-10-23 18:42:45.854358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:45.854554 INFO::Done
2025-10-23 18:42:45.854705 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:45.855877 INFO::Starting hierarchical adjustment
2025-10-23 18:42:45.856129 INFO::Found 2 batches.
2025-10-23 18:42:45.856275 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:45.856606 INFO::Using default BPPARAM
2025-10-23 18:42:45.85675 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:45.857032 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 18:42:45.874148 INFO::Done
2025-10-23 18:42:45.87438 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:45.875536 INFO::ASW Batch was 0.0159509961561719 prior to batch effect correction and is now -0.0939924204553632 .
2025-10-23 18:42:45.875788 INFO::Total function execution time is 0.0355398654937744 s and adjustment time is 0.0180501937866211 s ( 50.79 )
2025-10-23 18:42:45.881741 INFO::Formatting Data.
2025-10-23 18:42:45.881959 INFO::Recognized SummarizedExperiment
2025-10-23 18:42:45.882117 INFO::Typecasting input to dataframe.
2025-10-23 18:42:45.885069 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:45.885428 INFO::Removing potential empty rows and columns
2025-10-23 18:42:45.886577 INFO::Found 0 missing values.
2025-10-23 18:42:45.888634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:45.888805 INFO::Done
2025-10-23 18:42:45.888961 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:45.890115 INFO::Starting hierarchical adjustment
2025-10-23 18:42:45.890318 INFO::Found 2 batches.
2025-10-23 18:42:45.890463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:45.890636 INFO::Using default BPPARAM
2025-10-23 18:42:45.890776 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:45.891055 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 18:42:45.898716 INFO::Done
2025-10-23 18:42:45.898927 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:45.900062 INFO::ASW Batch was -0.0119390942647627 prior to batch effect correction and is now -0.0119390942647627 .
2025-10-23 18:42:45.900311 INFO::Total function execution time is 0.0185670852661133 s and adjustment time is 0.00843596458435059 s ( 45.44 )
2025-10-23 18:42:45.906482 INFO::Formatting Data.
2025-10-23 18:42:45.906695 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:45.906953 INFO::Removing potential empty rows and columns
2025-10-23 18:42:45.907243 INFO::Found 0 missing values.
2025-10-23 18:42:45.908043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:45.908199 INFO::Done
2025-10-23 18:42:45.908341 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:45.908918 INFO::Starting hierarchical adjustment
2025-10-23 18:42:45.909106 INFO::Found 3 batches.
2025-10-23 18:42:45.909249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:45.909421 INFO::Using default BPPARAM
2025-10-23 18:42:45.909588 INFO::Processing subtree level 1
2025-10-23 18:42:45.971926 INFO::Adjusting the last 1 batches sequentially
2025-10-23 18:42:45.973022 INFO::Done
2025-10-23 18:42:45.973255 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:45.975471 INFO::ASW Batch was -0.00691085199536833 prior to batch effect correction and is now -0.144128795662277 .
2025-10-23 18:42:45.976123 INFO::Total function execution time is 0.0696132183074951 s and adjustment time is 0.0639419555664062 s ( 91.85 )
2025-10-23 18:42:45.982678 INFO::Skipping initial DF formatting
2025-10-23 18:42:45.9829 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:45.984223 INFO::Starting hierarchical adjustment
2025-10-23 18:42:45.984473 INFO::Found 5 batches.
2025-10-23 18:42:45.984654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:45.985006 INFO::Using default BPPARAM
2025-10-23 18:42:45.985168 INFO::Processing subtree level 1
2025-10-23 18:42:46.105183 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.10807 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 18:42:46.117549 INFO::Done
2025-10-23 18:42:46.11798 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.120261 INFO::ASW Batch was 0.580376772584934 prior to batch effect correction and is now 0.580376772584934 .
2025-10-23 18:42:46.120599 INFO::ASW Label was 0.32432303647067 prior to batch effect correction and is now 0.32432303647067 .
2025-10-23 18:42:46.121264 INFO::Total function execution time is 0.138537168502808 s and adjustment time is 0.13311505317688 s ( 96.09 )
2025-10-23 18:42:46.160476 INFO::Formatting Data.
2025-10-23 18:42:46.160817 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.16117 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.161841 INFO::Found 0 missing values.
2025-10-23 18:42:46.163143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.163328 INFO::Done
2025-10-23 18:42:46.163506 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.164547 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.164772 INFO::Found 5 batches.
2025-10-23 18:42:46.16493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.165136 INFO::Using default BPPARAM
2025-10-23 18:42:46.165339 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.
2025-10-23 18:42:46.236128 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.238205 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 18:42:46.251791 INFO::Done
2025-10-23 18:42:46.252422 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.255379 INFO::ASW Batch was 0.366608755264894 prior to batch effect correction and is now -0.0546410122168563 .
2025-10-23 18:42:46.255733 INFO::ASW Label was 0.470987598438045 prior to batch effect correction and is now 0.806132864172166 .
2025-10-23 18:42:46.256216 INFO::Total function execution time is 0.0957210063934326 s and adjustment time is 0.0868852138519287 s ( 90.77 )
2025-10-23 18:42:46.256756 INFO::Formatting Data.
2025-10-23 18:42:46.257042 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.25749 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.258134 INFO::Found 0 missing values.
2025-10-23 18:42:46.260881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.261218 INFO::Done
2025-10-23 18:42:46.261456 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.26284 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.263357 INFO::Found 5 batches.
2025-10-23 18:42:46.263551 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.26384 INFO::Using default BPPARAM
2025-10-23 18:42:46.26417 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.
2025-10-23 18:42:46.316036 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.318138 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 18:42:46.327284 INFO::Done
2025-10-23 18:42:46.327752 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.329501 INFO::ASW Batch was 0.366608755264894 prior to batch effect correction and is now -0.0546410122168563 .
2025-10-23 18:42:46.329723 INFO::ASW Label was 0.470987598438045 prior to batch effect correction and is now 0.806132864172166 .
2025-10-23 18:42:46.330157 INFO::Total function execution time is 0.0733850002288818 s and adjustment time is 0.0641510486602783 s ( 87.42 )
2025-10-23 18:42:46.336685 INFO::Formatting Data.
2025-10-23 18:42:46.336947 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.337256 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.337591 INFO::Found 0 missing values.
2025-10-23 18:42:46.338856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.339065 INFO::Done
2025-10-23 18:42:46.339311 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.340541 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.340888 INFO::Found 5 batches.
2025-10-23 18:42:46.341099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.341333 INFO::Using default BPPARAM
2025-10-23 18:42:46.341532 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.
2025-10-23 18:42:46.405925 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.407687 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 18:42:46.416317 INFO::Done
2025-10-23 18:42:46.416714 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.418445 INFO::ASW Batch was 0.152854252376951 prior to batch effect correction and is now -0.104904030085146 .
2025-10-23 18:42:46.418678 INFO::ASW Label was 0.554270004009578 prior to batch effect correction and is now 0.822631297484438 .
2025-10-23 18:42:46.419034 INFO::Total function execution time is 0.0823380947113037 s and adjustment time is 0.0755069255828857 s ( 91.7 )
2025-10-23 18:42:46.419359 INFO::Formatting Data.
2025-10-23 18:42:46.419567 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.419995 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.420392 INFO::Found 0 missing values.
2025-10-23 18:42:46.421745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.421951 INFO::Done
2025-10-23 18:42:46.422122 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.423171 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.423414 INFO::Found 5 batches.
2025-10-23 18:42:46.423617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.423883 INFO::Using default BPPARAM
2025-10-23 18:42:46.424065 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.
2025-10-23 18:42:46.485561 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.487585 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 18:42:46.499646 INFO::Done
2025-10-23 18:42:46.500101 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.502549 INFO::ASW Batch was 0.152854252376951 prior to batch effect correction and is now -0.104904030085146 .
2025-10-23 18:42:46.50304 INFO::ASW Label was 0.554270004009578 prior to batch effect correction and is now 0.822631297484438 .
2025-10-23 18:42:46.503826 INFO::Total function execution time is 0.084414005279541 s and adjustment time is 0.0762720108032227 s ( 90.35 )
2025-10-23 18:42:46.511503 INFO::Formatting Data.
2025-10-23 18:42:46.511955 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.512319 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.512756 INFO::Found 0 missing values.
2025-10-23 18:42:46.513815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.51401 INFO::Done
2025-10-23 18:42:46.514203 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.515307 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.515588 INFO::Found 2 batches.
2025-10-23 18:42:46.51579 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.516038 INFO::Using default BPPARAM
2025-10-23 18:42:46.516217 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.516538 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 18:42:46.522575 INFO::Done
2025-10-23 18:42:46.522848 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.524028 INFO::ASW Batch was 0.398317118655883 prior to batch effect correction and is now -0.0379811509710446 .
2025-10-23 18:42:46.524247 INFO::ASW Label was 0.696023850166523 prior to batch effect correction and is now 0.965509658284836 .
2025-10-23 18:42:46.524556 INFO::Total function execution time is 0.0130851268768311 s and adjustment time is 0.00704288482666016 s ( 53.82 )
2025-10-23 18:42:46.524869 INFO::Formatting Data.
2025-10-23 18:42:46.525074 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.525365 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.525689 INFO::Found 0 missing values.
2025-10-23 18:42:46.526642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.526827 INFO::Done
2025-10-23 18:42:46.527009 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.528051 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.528299 INFO::Found 2 batches.
2025-10-23 18:42:46.52847 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.528707 INFO::Using default BPPARAM
2025-10-23 18:42:46.528913 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.52925 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-23 18:42:46.535002 INFO::Done
2025-10-23 18:42:46.535243 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.536326 INFO::ASW Batch was 0.398317118655883 prior to batch effect correction and is now -0.0379811509710446 .
2025-10-23 18:42:46.536525 INFO::ASW Label was 0.696023850166523 prior to batch effect correction and is now 0.965509658284836 .
2025-10-23 18:42:46.536948 INFO::Total function execution time is 0.0119218826293945 s and adjustment time is 0.00673699378967285 s ( 56.51 )
2025-10-23 18:42:46.54183 INFO::Formatting Data.
2025-10-23 18:42:46.542084 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.542405 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.542714 INFO::Found 0 missing values.
2025-10-23 18:42:46.54344 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.543625 INFO::Done
2025-10-23 18:42:46.543858 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.544517 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.544783 INFO::Found 2 batches.
2025-10-23 18:42:46.54498 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.54519 INFO::Using default BPPARAM
2025-10-23 18:42:46.545375 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.545714 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 18:42:46.559123 INFO::Done
2025-10-23 18:42:46.559386 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.560137 INFO::ASW Batch was -0.0896407218166808 prior to batch effect correction and is now -0.160412928999487 .
2025-10-23 18:42:46.56044 INFO::Total function execution time is 0.0186569690704346 s and adjustment time is 0.01438307762146 s ( 77.09 )
2025-10-23 18:42:46.565444 INFO::Formatting Data.
2025-10-23 18:42:46.565729 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.566029 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.566364 INFO::Found 0 missing values.
2025-10-23 18:42:46.566833 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.
2025-10-23 18:42:46.568401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.568584 INFO::Done
2025-10-23 18:42:46.568763 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.569801 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.570048 INFO::Found 2 batches.
2025-10-23 18:42:46.570211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.570404 INFO::Using default BPPARAM
2025-10-23 18:42:46.570564 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.570835 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 18:42:46.576716 INFO::Done
2025-10-23 18:42:46.576937 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.577922 INFO::ASW Batch was 0.750245394308302 prior to batch effect correction and is now 0.0716299678049876 .
2025-10-23 18:42:46.578129 INFO::ASW Label was 0.302596893218716 prior to batch effect correction and is now 0.829198223046009 .
2025-10-23 18:42:46.578367 INFO::Total function execution time is 0.0129499435424805 s and adjustment time is 0.00670981407165527 s ( 51.81 )
2025-10-23 18:42:46.578601 INFO::Formatting Data.
2025-10-23 18:42:46.578822 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.579133 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.579442 INFO::Found 0 missing values.
2025-10-23 18:42:46.579744 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.
2025-10-23 18:42:46.58117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.581332 INFO::Done
2025-10-23 18:42:46.581484 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.582379 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.582611 INFO::Found 2 batches.
2025-10-23 18:42:46.582785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.582968 INFO::Using default BPPARAM
2025-10-23 18:42:46.583143 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:46.58343 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 18:42:46.58912 INFO::Done
2025-10-23 18:42:46.589345 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.590282 INFO::ASW Batch was 0.750245394308302 prior to batch effect correction and is now 0.0716299678049876 .
2025-10-23 18:42:46.590485 INFO::ASW Label was 0.302596893218716 prior to batch effect correction and is now 0.829198223046009 .
2025-10-23 18:42:46.590751 INFO::Total function execution time is 0.0121331214904785 s and adjustment time is 0.00654411315917969 s ( 53.94 )
2025-10-23 18:42:46.658638 INFO::Formatting Data.
2025-10-23 18:42:46.65892 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.659257 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.6596 INFO::Found 0 missing values.
2025-10-23 18:42:46.660494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.660684 INFO::Done
2025-10-23 18:42:46.660836 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.661535 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.661744 INFO::Found 3 batches.
2025-10-23 18:42:46.661895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.662082 INFO::Using default BPPARAM
2025-10-23 18:42:46.662238 INFO::Processing subtree level 1
2025-10-23 18:42:46.708919 INFO::Adjusting the last 1 batches sequentially
2025-10-23 18:42:46.710456 INFO::Done
2025-10-23 18:42:46.711651 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.715939 INFO::ASW Batch was -0.0411777178179597 prior to batch effect correction and is now -0.0411777178179597 .
2025-10-23 18:42:46.717442 INFO::Total function execution time is 0.0583410263061523 s and adjustment time is 0.0487439632415771 s ( 83.55 )
2025-10-23 18:42:46.717955 INFO::Formatting Data.
2025-10-23 18:42:46.718319 INFO::Typecasting input to dataframe.
2025-10-23 18:42:46.718625 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.719234 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.719931 INFO::Found 0 missing values.
2025-10-23 18:42:46.721081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.721276 INFO::Done
2025-10-23 18:42:46.721483 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.722296 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.72255 INFO::Found 3 batches.
2025-10-23 18:42:46.722741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.723195 INFO::Using default BPPARAM
2025-10-23 18:42:46.7234 INFO::Processing subtree level 1
2025-10-23 18:42:46.766786 INFO::Adjusting the last 1 batches sequentially
2025-10-23 18:42:46.768332 INFO::Done
2025-10-23 18:42:46.768797 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.770632 INFO::ASW Batch was -0.0411777178179597 prior to batch effect correction and is now -0.0411777178179597 .
2025-10-23 18:42:46.771342 INFO::Total function execution time is 0.0532040596008301 s and adjustment time is 0.0458431243896484 s ( 86.16 )
2025-10-23 18:42:46.77838 INFO::Formatting Data.
2025-10-23 18:42:46.778648 INFO::Typecasting input to dataframe.
2025-10-23 18:42:46.778946 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.779265 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.779836 INFO::Found 0 missing values.
2025-10-23 18:42:46.780763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.780955 INFO::Done
2025-10-23 18:42:46.78112 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.781799 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.782011 INFO::Found 3 batches.
2025-10-23 18:42:46.782163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.782381 INFO::Using default BPPARAM
2025-10-23 18:42:46.782543 INFO::Processing subtree level 1
2025-10-23 18:42:46.820472 INFO::Adjusting the last 1 batches sequentially
2025-10-23 18:42:46.822008 INFO::Done
2025-10-23 18:42:46.822307 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:46.824064 INFO::ASW Batch was -0.0343893375065974 prior to batch effect correction and is now -0.0343893375065974 .
2025-10-23 18:42:46.824663 INFO::Total function execution time is 0.0462551116943359 s and adjustment time is 0.0400328636169434 s ( 86.55 )
2025-10-23 18:42:46.898883 INFO::Formatting Data.
2025-10-23 18:42:46.899135 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:46.899495 INFO::Removing potential empty rows and columns
2025-10-23 18:42:46.900444 INFO::Found 1000 missing values.
2025-10-23 18:42:46.906101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:46.906342 INFO::Done
2025-10-23 18:42:46.906518 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:46.908558 INFO::Starting hierarchical adjustment
2025-10-23 18:42:46.908844 INFO::Found 10 batches.
2025-10-23 18:42:46.909007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:46.909349 INFO::Using default BPPARAM
2025-10-23 18:42:46.909506 INFO::Processing subtree level 1
2025-10-23 18:42:46.963462 INFO::Processing subtree level 2
2025-10-23 18:42:47.025615 INFO::Adjusting the last 1 batches sequentially
2025-10-23 18:42:47.027681 INFO::Done
2025-10-23 18:42:47.02795 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:47.0309 INFO::ASW Batch was 0.487521810868579 prior to batch effect correction and is now 0.487521810868579 .
2025-10-23 18:42:47.031139 INFO::ASW Label was 0.345223939196733 prior to batch effect correction and is now 0.345223939196733 .
2025-10-23 18:42:47.031712 INFO::Total function execution time is 0.13281512260437 s and adjustment time is 0.118885040283203 s ( 89.51 )
2025-10-23 18:42:47.03206 INFO::Formatting Data.
2025-10-23 18:42:47.032249 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:47.03266 INFO::Removing potential empty rows and columns
2025-10-23 18:42:47.033647 INFO::Found 1000 missing values.
2025-10-23 18:42:47.03935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:47.039701 INFO::Done
2025-10-23 18:42:47.040103 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:47.042091 INFO::Starting hierarchical adjustment
2025-10-23 18:42:47.043137 INFO::Found 10 batches.
2025-10-23 18:42:47.453923 INFO::Set up parallel execution backend with 2 workers
2025-10-23 18:42:47.454248 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-23 18:42:47.957762 INFO::Adjusting the last 2 batches sequentially
2025-10-23 18:42:47.958371 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-23 18:42:47.964192 INFO::Done
2025-10-23 18:42:47.964425 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:47.96641 INFO::ASW Batch was 0.487521810868579 prior to batch effect correction and is now 0.487521810868579 .
2025-10-23 18:42:47.966585 INFO::ASW Label was 0.345223939196733 prior to batch effect correction and is now 0.345223939196733 .
2025-10-23 18:42:47.966832 INFO::Total function execution time is 0.934777975082397 s and adjustment time is 0.921453952789307 s ( 98.57 )
2025-10-23 18:42:48.024866 INFO::Formatting Data.
2025-10-23 18:42:48.025164 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.02551 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.025975 INFO::Found 0 missing values.
2025-10-23 18:42:48.027408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.02761 INFO::Done
2025-10-23 18:42:48.027799 INFO::Acquiring quality metrics before batch effect correction.
2025-10-23 18:42:48.028816 INFO::Starting hierarchical adjustment
2025-10-23 18:42:48.029101 INFO::Found 3 batches.
2025-10-23 18:42:48.029284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-23 18:42:48.029541 INFO::Using default BPPARAM
2025-10-23 18:42:48.029736 INFO::Processing subtree level 1
2025-10-23 18:42:48.084044 INFO::Adjusting the last 1 batches sequentially
2025-10-23 18:42:48.085651 INFO::Done
2025-10-23 18:42:48.086005 INFO::Acquiring quality metrics after batch effect correction.
2025-10-23 18:42:48.088412 INFO::ASW Batch was 0.192245741122668 prior to batch effect correction and is now -0.170062830795724 .
2025-10-23 18:42:48.088908 INFO::ASW Label was -0.178244527476472 prior to batch effect correction and is now 0.0595872714556216 .
2025-10-23 18:42:48.089593 INFO::Total function execution time is 0.0647242069244385 s and adjustment time is 0.056610107421875 s ( 87.46 )
2025-10-23 18:42:48.141235 INFO::Formatting Data.
2025-10-23 18:42:48.141636 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.142054 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.142612 INFO::Found 2 missing values.
2025-10-23 18:42:48.143804 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.144009 INFO::Done
2025-10-23 18:42:48.155959 INFO::Found NA in Reference column
2025-10-23 18:42:48.160174 INFO::Require at least two references per batch.
2025-10-23 18:42:48.170071 INFO::Formatting Data.
2025-10-23 18:42:48.170381 INFO::Recognized SummarizedExperiment
2025-10-23 18:42:48.170583 INFO::Typecasting input to dataframe.
2025-10-23 18:42:48.175972 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.176392 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.177705 INFO::Found 0 missing values.
2025-10-23 18:42:48.180193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.180378 INFO::Done
2025-10-23 18:42:48.186132 INFO::Formatting Data.
2025-10-23 18:42:48.186356 INFO::Recognized SummarizedExperiment
2025-10-23 18:42:48.186529 INFO::Typecasting input to dataframe.
2025-10-23 18:42:48.192256 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.192659 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.193934 INFO::Found 0 missing values.
2025-10-23 18:42:48.197928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.198116 INFO::Done
2025-10-23 18:42:48.203887 INFO::Formatting Data.
2025-10-23 18:42:48.204126 INFO::Recognized SummarizedExperiment
2025-10-23 18:42:48.204306 INFO::Typecasting input to dataframe.
2025-10-23 18:42:48.209831 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.21017 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.210534 INFO::Found 0 missing values.
2025-10-23 18:42:48.210847 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.
2025-10-23 18:42:48.212238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.212417 INFO::Done
2025-10-23 18:42:48.21632 INFO::Formatting Data.
2025-10-23 18:42:48.21655 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.216825 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.21714 INFO::Found 0 missing values.
2025-10-23 18:42:48.218011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.21824 INFO::Done
2025-10-23 18:42:48.22235 INFO::Formatting Data.
2025-10-23 18:42:48.222578 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.222861 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.223176 INFO::Found 0 missing values.
2025-10-23 18:42:48.224071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.224251 INFO::Done
2025-10-23 18:42:48.236049 INFO::Formatting Data.
2025-10-23 18:42:48.236367 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.236753 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.23721 INFO::Found 1 missing values.
2025-10-23 18:42:48.238177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.238403 INFO::Done
2025-10-23 18:42:48.24588 INFO::Formatting Data.
2025-10-23 18:42:48.246142 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.246474 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.246782 INFO::Found 2 missing values.
2025-10-23 18:42:48.247075 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.
2025-10-23 18:42:48.247861 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.248042 INFO::Done
2025-10-23 18:42:48.252054 INFO::Formatting Data.
2025-10-23 18:42:48.252321 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.252607 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.25298 INFO::Found 2 missing values.
2025-10-23 18:42:48.253532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.253714 INFO::Done
2025-10-23 18:42:48.258063 INFO::Formatting Data.
2025-10-23 18:42:48.258332 INFO::Typecasting input to dataframe.
2025-10-23 18:42:48.2586 INFO::Replacing NaNs with NAs.
2025-10-23 18:42:48.25885 INFO::Removing potential empty rows and columns
2025-10-23 18:42:48.259209 INFO::Found 0 missing values.
2025-10-23 18:42:48.260101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-23 18:42:48.260261 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.602 1.626 8.474
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.682 | 0.451 | 6.951 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.004 | 0.001 | 0.005 | |
| generate_data_covariables | 0.004 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |