Yannis Schumann
| Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 Sep 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 2025-09-30 12:03 -0400 (Tue, 30 Sep 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" | 4843 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 164/2337 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-09-29 21:38:25 -0400 (Mon, 29 Sep 2025) |
| EndedAt: 2025-09-29 21:40:37 -0400 (Mon, 29 Sep 2025) |
| EllapsedTime: 132.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 29.792 2.118 24.715
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-09-29 21:39:41.411185 INFO::Formatting Data.
2025-09-29 21:39:41.412735 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:41.426077 INFO::Removing potential empty rows and columns
2025-09-29 21:39:41.83919 INFO::Found 0 missing values.
2025-09-29 21:39:41.844763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:41.845742 INFO::Done
2025-09-29 21:39:41.846582 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:41.864065 INFO::Starting hierarchical adjustment
2025-09-29 21:39:41.865432 INFO::Found 3 batches.
2025-09-29 21:39:41.866295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:41.867955 INFO::Using default BPPARAM
2025-09-29 21:39:41.868766 INFO::Processing subtree level 1
2025-09-29 21:39:42.051493 INFO::Adjusting the last 1 batches sequentially
2025-09-29 21:39:42.06092 INFO::Done
2025-09-29 21:39:42.061859 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:42.069288 INFO::ASW Batch was -0.108298081050685 prior to batch effect correction and is now -0.108298081050685 .
2025-09-29 21:39:42.070953 INFO::Total function execution time is 0.660464763641357 s and adjustment time is 0.195772886276245 s ( 29.64 )
2025-09-29 21:39:42.092277 INFO::Formatting Data.
2025-09-29 21:39:42.09339 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:42.094802 INFO::Removing potential empty rows and columns
2025-09-29 21:39:42.096461 INFO::Found 0 missing values.
2025-09-29 21:39:42.097841 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.
2025-09-29 21:39:42.114724 INFO::Formatting Data.
2025-09-29 21:39:42.115882 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:42.117265 INFO::Removing potential empty rows and columns
2025-09-29 21:39:42.118866 INFO::Found 0 missing values.
2025-09-29 21:39:42.120235 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.
2025-09-29 21:39:42.144667 INFO::Formatting Data.
2025-09-29 21:39:42.145759 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:42.147068 INFO::Removing potential empty rows and columns
2025-09-29 21:39:42.148586 INFO::Found 0 missing values.
2025-09-29 21:39:42.149897 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.
2025-09-29 21:39:42.156499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:42.157316 INFO::Done
2025-09-29 21:39:42.158087 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:42.161012 INFO::Starting hierarchical adjustment
2025-09-29 21:39:42.162053 INFO::Found 2 batches.
2025-09-29 21:39:42.162867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:42.163817 INFO::Using default BPPARAM
2025-09-29 21:39:42.164678 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:42.166196 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-29 21:39:42.2015 INFO::Done
2025-09-29 21:39:42.202507 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:42.205554 INFO::ASW Batch was 0.0538826613729386 prior to batch effect correction and is now -0.120808086691632 .
2025-09-29 21:39:42.206689 INFO::Total function execution time is 0.0620827674865723 s and adjustment time is 0.0396201610565186 s ( 63.82 )
2025-09-29 21:39:42.210912 INFO::Formatting Data.
2025-09-29 21:39:42.211835 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:42.225873 INFO::Formatting Data.
2025-09-29 21:39:42.226986 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:42.228364 INFO::Removing potential empty rows and columns
2025-09-29 21:39:42.229926 INFO::Found 0 missing values.
2025-09-29 21:39:42.234507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:42.235338 INFO::Done
2025-09-29 21:39:42.236153 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:42.239335 INFO::Starting hierarchical adjustment
2025-09-29 21:39:42.2404 INFO::Found 2 batches.
2025-09-29 21:39:42.241237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:42.242183 INFO::Using default BPPARAM
2025-09-29 21:39:42.243023 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:42.244497 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-29 21:39:42.306562 INFO::Done
2025-09-29 21:39:42.307498 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:42.310294 INFO::ASW Batch was -0.00734888184006645 prior to batch effect correction and is now -0.122003271772067 .
2025-09-29 21:39:42.311371 INFO::Total function execution time is 0.0855703353881836 s and adjustment time is 0.0663754940032959 s ( 77.57 )
2025-09-29 21:39:42.312847 INFO::Formatting Data.
2025-09-29 21:39:42.313696 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:42.314887 INFO::Removing potential empty rows and columns
2025-09-29 21:39:42.316355 INFO::Found 0 missing values.
2025-09-29 21:39:42.320211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:42.320951 INFO::Done
2025-09-29 21:39:42.321686 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:42.324436 INFO::Starting hierarchical adjustment
2025-09-29 21:39:42.325407 INFO::Found 2 batches.
2025-09-29 21:39:42.326208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:42.327152 INFO::Using default BPPARAM
2025-09-29 21:39:42.327914 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:42.329186 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-29 21:39:42.351256 INFO::Done
2025-09-29 21:39:42.352168 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:42.35494 INFO::ASW Batch was -0.00734888184006645 prior to batch effect correction and is now -0.122003271772067 .
2025-09-29 21:39:42.356021 INFO::Total function execution time is 0.0431621074676514 s and adjustment time is 0.0260112285614014 s ( 60.26 )
2025-09-29 21:39:47.116505 INFO::Formatting Data.
2025-09-29 21:39:47.11756 INFO::Recognized SummarizedExperiment
2025-09-29 21:39:47.118208 INFO::Typecasting input to dataframe.
2025-09-29 21:39:47.177485 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:47.179412 INFO::Removing potential empty rows and columns
2025-09-29 21:39:47.18573 INFO::Found 0 missing values.
2025-09-29 21:39:47.197763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:47.198797 INFO::Done
2025-09-29 21:39:47.199682 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:47.205723 INFO::Starting hierarchical adjustment
2025-09-29 21:39:47.206864 INFO::Found 2 batches.
2025-09-29 21:39:47.207851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:47.209474 INFO::Using default BPPARAM
2025-09-29 21:39:47.21028 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:47.211805 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-29 21:39:47.305751 INFO::Done
2025-09-29 21:39:47.306804 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:47.31245 INFO::ASW Batch was -0.00378530477571093 prior to batch effect correction and is now -0.089744287140399 .
2025-09-29 21:39:47.313729 INFO::Total function execution time is 0.197558879852295 s and adjustment time is 0.0991308689117432 s ( 50.18 )
2025-09-29 21:39:47.343062 INFO::Formatting Data.
2025-09-29 21:39:47.344174 INFO::Recognized SummarizedExperiment
2025-09-29 21:39:47.34505 INFO::Typecasting input to dataframe.
2025-09-29 21:39:47.359655 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:47.361449 INFO::Removing potential empty rows and columns
2025-09-29 21:39:47.367564 INFO::Found 0 missing values.
2025-09-29 21:39:47.379731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:47.380746 INFO::Done
2025-09-29 21:39:47.381575 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:47.387266 INFO::Starting hierarchical adjustment
2025-09-29 21:39:47.38836 INFO::Found 2 batches.
2025-09-29 21:39:47.389173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:47.390075 INFO::Using default BPPARAM
2025-09-29 21:39:47.390884 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:47.392371 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-29 21:39:47.434479 INFO::Done
2025-09-29 21:39:47.435551 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:47.441174 INFO::ASW Batch was 0.0135048587596876 prior to batch effect correction and is now 0.0135048587596876 .
2025-09-29 21:39:47.442455 INFO::Total function execution time is 0.0993690490722656 s and adjustment time is 0.0463128089904785 s ( 46.61 )
2025-09-29 21:39:47.470309 INFO::Formatting Data.
2025-09-29 21:39:47.471444 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:47.472809 INFO::Removing potential empty rows and columns
2025-09-29 21:39:47.474398 INFO::Found 0 missing values.
2025-09-29 21:39:47.479034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:47.479879 INFO::Done
2025-09-29 21:39:47.480688 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:47.483648 INFO::Starting hierarchical adjustment
2025-09-29 21:39:47.484708 INFO::Found 3 batches.
2025-09-29 21:39:47.489592 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:47.490594 INFO::Using default BPPARAM
2025-09-29 21:39:47.491363 INFO::Processing subtree level 1
2025-09-29 21:39:47.723207 INFO::Adjusting the last 1 batches sequentially
2025-09-29 21:39:47.729367 INFO::Done
2025-09-29 21:39:47.730293 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:47.736357 INFO::ASW Batch was -0.0799999585369194 prior to batch effect correction and is now -0.156415282444864 .
2025-09-29 21:39:47.737613 INFO::Total function execution time is 0.267375707626343 s and adjustment time is 0.244835615158081 s ( 91.57 )
2025-09-29 21:39:47.774698 INFO::Skipping initial DF formatting
2025-09-29 21:39:47.775622 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:47.780507 INFO::Starting hierarchical adjustment
2025-09-29 21:39:47.781503 INFO::Found 5 batches.
2025-09-29 21:39:47.782196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:47.78295 INFO::Using default BPPARAM
2025-09-29 21:39:47.783587 INFO::Processing subtree level 1
2025-09-29 21:39:48.227906 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:48.233788 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-29 21:39:48.300068 INFO::Done
2025-09-29 21:39:48.301358 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:48.318106 INFO::ASW Batch was 0.47223030069187 prior to batch effect correction and is now 0.47223030069187 .
2025-09-29 21:39:48.322407 INFO::ASW Label was 0.38611113592296 prior to batch effect correction and is now 0.38611113592296 .
2025-09-29 21:39:48.328188 INFO::Total function execution time is 0.549399614334106 s and adjustment time is 0.518652200698853 s ( 94.4 )
2025-09-29 21:39:48.463326 INFO::Formatting Data.
2025-09-29 21:39:48.464376 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:48.468694 INFO::Removing potential empty rows and columns
2025-09-29 21:39:48.469953 INFO::Found 0 missing values.
2025-09-29 21:39:48.479112 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:48.479837 INFO::Done
2025-09-29 21:39:48.480561 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:48.487054 INFO::Starting hierarchical adjustment
2025-09-29 21:39:48.488017 INFO::Found 5 batches.
2025-09-29 21:39:48.488719 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:48.489594 INFO::Using default BPPARAM
2025-09-29 21:39:48.4903 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.
2025-09-29 21:39:48.702351 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:48.704526 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-29 21:39:48.72647 INFO::Done
2025-09-29 21:39:48.731045 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:48.739656 INFO::ASW Batch was 0.274401529001778 prior to batch effect correction and is now -0.0801969391312434 .
2025-09-29 21:39:48.740557 INFO::ASW Label was 0.396486379216824 prior to batch effect correction and is now 0.838742085172992 .
2025-09-29 21:39:48.741644 INFO::Total function execution time is 0.278450727462769 s and adjustment time is 0.238600969314575 s ( 85.69 )
2025-09-29 21:39:48.742763 INFO::Formatting Data.
2025-09-29 21:39:48.743673 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:48.744876 INFO::Removing potential empty rows and columns
2025-09-29 21:39:48.746258 INFO::Found 0 missing values.
2025-09-29 21:39:48.751777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:48.7525 INFO::Done
2025-09-29 21:39:48.753187 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:48.757006 INFO::Starting hierarchical adjustment
2025-09-29 21:39:48.757932 INFO::Found 5 batches.
2025-09-29 21:39:48.758582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:48.759378 INFO::Using default BPPARAM
2025-09-29 21:39:48.76004 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.
2025-09-29 21:39:48.934351 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:48.936259 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-29 21:39:48.955769 INFO::Done
2025-09-29 21:39:48.956672 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:48.960737 INFO::ASW Batch was 0.274401529001778 prior to batch effect correction and is now -0.0801969391312434 .
2025-09-29 21:39:48.961536 INFO::ASW Label was 0.396486379216824 prior to batch effect correction and is now 0.838742085172992 .
2025-09-29 21:39:48.962555 INFO::Total function execution time is 0.219804763793945 s and adjustment time is 0.198020458221436 s ( 90.09 )
2025-09-29 21:39:48.978754 INFO::Formatting Data.
2025-09-29 21:39:48.979761 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:48.980833 INFO::Removing potential empty rows and columns
2025-09-29 21:39:48.98189 INFO::Found 0 missing values.
2025-09-29 21:39:48.98658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:48.987251 INFO::Done
2025-09-29 21:39:48.989989 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:48.99774 INFO::Starting hierarchical adjustment
2025-09-29 21:39:48.998608 INFO::Found 5 batches.
2025-09-29 21:39:48.999213 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:48.999906 INFO::Using default BPPARAM
2025-09-29 21:39:49.004616 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.
2025-09-29 21:39:49.237281 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:49.239208 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-29 21:39:49.280833 INFO::Done
2025-09-29 21:39:49.285915 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:49.293918 INFO::ASW Batch was 0.594316921524198 prior to batch effect correction and is now -0.0488771286437579 .
2025-09-29 21:39:49.294762 INFO::ASW Label was 0.242177185644983 prior to batch effect correction and is now 0.73257952766306 .
2025-09-29 21:39:49.295795 INFO::Total function execution time is 0.317119121551514 s and adjustment time is 0.282357692718506 s ( 89.04 )
2025-09-29 21:39:49.296837 INFO::Formatting Data.
2025-09-29 21:39:49.301614 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:49.302707 INFO::Removing potential empty rows and columns
2025-09-29 21:39:49.303919 INFO::Found 0 missing values.
2025-09-29 21:39:49.312796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:49.313466 INFO::Done
2025-09-29 21:39:49.314044 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:49.324672 INFO::Starting hierarchical adjustment
2025-09-29 21:39:49.325554 INFO::Found 5 batches.
2025-09-29 21:39:49.326197 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:49.326941 INFO::Using default BPPARAM
2025-09-29 21:39:49.327591 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.
2025-09-29 21:39:49.632629 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:49.634933 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-29 21:39:49.683721 INFO::Done
2025-09-29 21:39:49.684749 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:49.69357 INFO::ASW Batch was 0.594316921524198 prior to batch effect correction and is now -0.0488771286437579 .
2025-09-29 21:39:49.698901 INFO::ASW Label was 0.242177185644983 prior to batch effect correction and is now 0.73257952766306 .
2025-09-29 21:39:49.700319 INFO::Total function execution time is 0.403435707092285 s and adjustment time is 0.358264446258545 s ( 88.8 )
2025-09-29 21:39:49.718259 INFO::Formatting Data.
2025-09-29 21:39:49.719371 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:49.720611 INFO::Removing potential empty rows and columns
2025-09-29 21:39:49.721957 INFO::Found 0 missing values.
2025-09-29 21:39:49.725675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:49.726419 INFO::Done
2025-09-29 21:39:49.727085 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:49.731211 INFO::Starting hierarchical adjustment
2025-09-29 21:39:49.732217 INFO::Found 2 batches.
2025-09-29 21:39:49.732897 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:49.733697 INFO::Using default BPPARAM
2025-09-29 21:39:49.734361 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:49.735571 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-29 21:39:49.763472 INFO::Done
2025-09-29 21:39:49.764439 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:49.768801 INFO::ASW Batch was 0.682752176871625 prior to batch effect correction and is now -0.0264327699520382 .
2025-09-29 21:39:49.773959 INFO::ASW Label was 0.349653119788028 prior to batch effect correction and is now 0.901401645785372 .
2025-09-29 21:39:49.775423 INFO::Total function execution time is 0.057382345199585 s and adjustment time is 0.0314128398895264 s ( 54.74 )
2025-09-29 21:39:49.776393 INFO::Formatting Data.
2025-09-29 21:39:49.777105 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:49.781496 INFO::Removing potential empty rows and columns
2025-09-29 21:39:49.786306 INFO::Found 0 missing values.
2025-09-29 21:39:49.789573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:49.79024 INFO::Done
2025-09-29 21:39:49.790854 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:49.797001 INFO::Starting hierarchical adjustment
2025-09-29 21:39:49.797917 INFO::Found 2 batches.
2025-09-29 21:39:49.79856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:49.799267 INFO::Using default BPPARAM
2025-09-29 21:39:49.799856 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:49.800919 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-29 21:39:49.826869 INFO::Done
2025-09-29 21:39:49.827706 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:49.831042 INFO::ASW Batch was 0.682752176871625 prior to batch effect correction and is now -0.0264327699520382 .
2025-09-29 21:39:49.831731 INFO::ASW Label was 0.349653119788028 prior to batch effect correction and is now 0.901401645785372 .
2025-09-29 21:39:49.832643 INFO::Total function execution time is 0.056279182434082 s and adjustment time is 0.0291080474853516 s ( 51.72 )
2025-09-29 21:39:49.851548 INFO::Formatting Data.
2025-09-29 21:39:49.852499 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:49.853512 INFO::Removing potential empty rows and columns
2025-09-29 21:39:49.858647 INFO::Found 0 missing values.
2025-09-29 21:39:49.861156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:49.861785 INFO::Done
2025-09-29 21:39:49.866464 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:49.868735 INFO::Starting hierarchical adjustment
2025-09-29 21:39:49.872993 INFO::Found 2 batches.
2025-09-29 21:39:49.873801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:49.874497 INFO::Using default BPPARAM
2025-09-29 21:39:49.875093 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:49.880205 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-29 21:39:49.933489 INFO::Done
2025-09-29 21:39:49.934323 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:49.936544 INFO::ASW Batch was -0.0755396964388674 prior to batch effect correction and is now -0.100787470803462 .
2025-09-29 21:39:49.937505 INFO::Total function execution time is 0.0860676765441895 s and adjustment time is 0.0606498718261719 s ( 70.47 )
2025-09-29 21:39:49.950982 INFO::Formatting Data.
2025-09-29 21:39:49.951895 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:49.952895 INFO::Removing potential empty rows and columns
2025-09-29 21:39:49.954004 INFO::Found 0 missing values.
2025-09-29 21:39:49.955097 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.
2025-09-29 21:39:49.960358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:49.960978 INFO::Done
2025-09-29 21:39:49.961535 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:49.964658 INFO::Starting hierarchical adjustment
2025-09-29 21:39:49.965465 INFO::Found 2 batches.
2025-09-29 21:39:49.966069 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:49.966781 INFO::Using default BPPARAM
2025-09-29 21:39:49.967392 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:49.968475 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-29 21:39:49.986955 INFO::Done
2025-09-29 21:39:49.987746 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:49.991009 INFO::ASW Batch was 0.670014796644516 prior to batch effect correction and is now -0.027131374514619 .
2025-09-29 21:39:49.991688 INFO::ASW Label was 0.391190454138841 prior to batch effect correction and is now 0.865578820615755 .
2025-09-29 21:39:49.992572 INFO::Total function execution time is 0.0416998863220215 s and adjustment time is 0.0216269493103027 s ( 51.86 )
2025-09-29 21:39:49.993464 INFO::Formatting Data.
2025-09-29 21:39:49.994183 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:49.995219 INFO::Removing potential empty rows and columns
2025-09-29 21:39:49.996314 INFO::Found 0 missing values.
2025-09-29 21:39:49.997333 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.
2025-09-29 21:39:50.002368 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:50.002974 INFO::Done
2025-09-29 21:39:50.003579 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:50.006783 INFO::Starting hierarchical adjustment
2025-09-29 21:39:50.007589 INFO::Found 2 batches.
2025-09-29 21:39:50.008202 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:50.008882 INFO::Using default BPPARAM
2025-09-29 21:39:50.009447 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:50.010345 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-29 21:39:50.028912 INFO::Done
2025-09-29 21:39:50.029676 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:50.033009 INFO::ASW Batch was 0.670014796644516 prior to batch effect correction and is now -0.027131374514619 .
2025-09-29 21:39:50.033712 INFO::ASW Label was 0.391190454138841 prior to batch effect correction and is now 0.865578820615755 .
2025-09-29 21:39:50.034637 INFO::Total function execution time is 0.0411834716796875 s and adjustment time is 0.0214729309082031 s ( 52.14 )
2025-09-29 21:39:50.285057 INFO::Formatting Data.
2025-09-29 21:39:50.286325 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:50.287441 INFO::Removing potential empty rows and columns
2025-09-29 21:39:50.288737 INFO::Found 0 missing values.
2025-09-29 21:39:50.292387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:50.293023 INFO::Done
2025-09-29 21:39:50.293656 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:50.296359 INFO::Starting hierarchical adjustment
2025-09-29 21:39:50.297187 INFO::Found 3 batches.
2025-09-29 21:39:50.2978 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:50.298589 INFO::Using default BPPARAM
2025-09-29 21:39:50.2992 INFO::Processing subtree level 1
2025-09-29 21:39:50.428321 INFO::Adjusting the last 1 batches sequentially
2025-09-29 21:39:50.434381 INFO::Done
2025-09-29 21:39:50.435245 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:50.438097 INFO::ASW Batch was -0.01468101477035 prior to batch effect correction and is now -0.01468101477035 .
2025-09-29 21:39:50.439239 INFO::Total function execution time is 0.154608964920044 s and adjustment time is 0.13733983039856 s ( 88.83 )
2025-09-29 21:39:50.440439 INFO::Formatting Data.
2025-09-29 21:39:50.441225 INFO::Typecasting input to dataframe.
2025-09-29 21:39:50.442137 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:50.443223 INFO::Removing potential empty rows and columns
2025-09-29 21:39:50.444489 INFO::Found 0 missing values.
2025-09-29 21:39:50.448086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:50.448736 INFO::Done
2025-09-29 21:39:50.449372 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:50.451719 INFO::Starting hierarchical adjustment
2025-09-29 21:39:50.452566 INFO::Found 3 batches.
2025-09-29 21:39:50.453189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:50.453913 INFO::Using default BPPARAM
2025-09-29 21:39:50.454557 INFO::Processing subtree level 1
2025-09-29 21:39:50.56413 INFO::Adjusting the last 1 batches sequentially
2025-09-29 21:39:50.566197 INFO::Done
2025-09-29 21:39:50.566949 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:50.56973 INFO::ASW Batch was -0.01468101477035 prior to batch effect correction and is now -0.01468101477035 .
2025-09-29 21:39:50.570814 INFO::Total function execution time is 0.130365610122681 s and adjustment time is 0.113775014877319 s ( 87.27 )
2025-09-29 21:39:50.585782 INFO::Formatting Data.
2025-09-29 21:39:50.586711 INFO::Typecasting input to dataframe.
2025-09-29 21:39:50.587734 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:50.588814 INFO::Removing potential empty rows and columns
2025-09-29 21:39:50.59006 INFO::Found 0 missing values.
2025-09-29 21:39:50.593598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:50.594248 INFO::Done
2025-09-29 21:39:50.594846 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:50.597168 INFO::Starting hierarchical adjustment
2025-09-29 21:39:50.597991 INFO::Found 3 batches.
2025-09-29 21:39:50.598629 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:50.599354 INFO::Using default BPPARAM
2025-09-29 21:39:50.599977 INFO::Processing subtree level 1
2025-09-29 21:39:50.707999 INFO::Adjusting the last 1 batches sequentially
2025-09-29 21:39:50.710233 INFO::Done
2025-09-29 21:39:50.710996 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:50.71396 INFO::ASW Batch was -0.15604495095071 prior to batch effect correction and is now -0.15604495095071 .
2025-09-29 21:39:50.715064 INFO::Total function execution time is 0.129338026046753 s and adjustment time is 0.112366199493408 s ( 86.88 )
2025-09-29 21:39:50.88586 INFO::Formatting Data.
2025-09-29 21:39:50.886801 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:50.888123 INFO::Removing potential empty rows and columns
2025-09-29 21:39:50.891671 INFO::Found 1000 missing values.
2025-09-29 21:39:50.914386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:50.915214 INFO::Done
2025-09-29 21:39:50.915842 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:50.922313 INFO::Starting hierarchical adjustment
2025-09-29 21:39:50.923178 INFO::Found 10 batches.
2025-09-29 21:39:50.923804 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:50.924529 INFO::Using default BPPARAM
2025-09-29 21:39:50.925166 INFO::Processing subtree level 1
2025-09-29 21:39:51.124398 INFO::Processing subtree level 2
2025-09-29 21:39:51.339034 INFO::Adjusting the last 1 batches sequentially
2025-09-29 21:39:51.341662 INFO::Done
2025-09-29 21:39:51.342577 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:51.350851 INFO::ASW Batch was 0.47139478186395 prior to batch effect correction and is now 0.47139478186395 .
2025-09-29 21:39:51.351778 INFO::ASW Label was 0.371753725283577 prior to batch effect correction and is now 0.371753725283577 .
2025-09-29 21:39:51.353131 INFO::Total function execution time is 0.467241525650024 s and adjustment time is 0.418632030487061 s ( 89.6 )
2025-09-29 21:39:51.354419 INFO::Formatting Data.
2025-09-29 21:39:51.355384 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:51.357205 INFO::Removing potential empty rows and columns
2025-09-29 21:39:51.361646 INFO::Found 1000 missing values.
2025-09-29 21:39:51.392905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:51.393982 INFO::Done
2025-09-29 21:39:51.394919 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:51.40359 INFO::Starting hierarchical adjustment
2025-09-29 21:39:51.404784 INFO::Found 10 batches.
2025-09-29 21:39:52.604101 INFO::Set up parallel execution backend with 2 workers
2025-09-29 21:39:52.606227 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-29 21:39:53.93385 INFO::Adjusting the last 2 batches sequentially
2025-09-29 21:39:53.935891 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-29 21:39:53.955505 INFO::Done
2025-09-29 21:39:53.956164 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:53.96147 INFO::ASW Batch was 0.47139478186395 prior to batch effect correction and is now 0.47139478186395 .
2025-09-29 21:39:53.962065 INFO::ASW Label was 0.371753725283577 prior to batch effect correction and is now 0.371753725283577 .
2025-09-29 21:39:53.962877 INFO::Total function execution time is 2.60856914520264 s and adjustment time is 2.55099821090698 s ( 97.79 )
2025-09-29 21:39:54.165205 INFO::Formatting Data.
2025-09-29 21:39:54.16604 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.167062 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.168284 INFO::Found 0 missing values.
2025-09-29 21:39:54.176498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.177098 INFO::Done
2025-09-29 21:39:54.17769 INFO::Acquiring quality metrics before batch effect correction.
2025-09-29 21:39:54.184764 INFO::Starting hierarchical adjustment
2025-09-29 21:39:54.189641 INFO::Found 3 batches.
2025-09-29 21:39:54.190254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-29 21:39:54.190946 INFO::Using default BPPARAM
2025-09-29 21:39:54.191534 INFO::Processing subtree level 1
2025-09-29 21:39:54.352695 INFO::Adjusting the last 1 batches sequentially
2025-09-29 21:39:54.355053 INFO::Done
2025-09-29 21:39:54.360149 INFO::Acquiring quality metrics after batch effect correction.
2025-09-29 21:39:54.368494 INFO::ASW Batch was 0.152707823695379 prior to batch effect correction and is now -0.168075469068446 .
2025-09-29 21:39:54.373598 INFO::ASW Label was -0.151001586225918 prior to batch effect correction and is now 0.0580402545866566 .
2025-09-29 21:39:54.374895 INFO::Total function execution time is 0.209697008132935 s and adjustment time is 0.16552734375 s ( 78.94 )
2025-09-29 21:39:54.570673 INFO::Formatting Data.
2025-09-29 21:39:54.571869 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.573084 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.57459 INFO::Found 2 missing values.
2025-09-29 21:39:54.578709 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.579469 INFO::Done
2025-09-29 21:39:54.617008 INFO::Found NA in Reference column
2025-09-29 21:39:54.630114 INFO::Require at least two references per batch.
2025-09-29 21:39:54.660047 INFO::Formatting Data.
2025-09-29 21:39:54.661036 INFO::Recognized SummarizedExperiment
2025-09-29 21:39:54.66183 INFO::Typecasting input to dataframe.
2025-09-29 21:39:54.676659 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.678313 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.684013 INFO::Found 0 missing values.
2025-09-29 21:39:54.694646 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.695459 INFO::Done
2025-09-29 21:39:54.718757 INFO::Formatting Data.
2025-09-29 21:39:54.719765 INFO::Recognized SummarizedExperiment
2025-09-29 21:39:54.720608 INFO::Typecasting input to dataframe.
2025-09-29 21:39:54.746465 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.748177 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.753839 INFO::Found 0 missing values.
2025-09-29 21:39:54.771064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.771958 INFO::Done
2025-09-29 21:39:54.795764 INFO::Formatting Data.
2025-09-29 21:39:54.796716 INFO::Recognized SummarizedExperiment
2025-09-29 21:39:54.797511 INFO::Typecasting input to dataframe.
2025-09-29 21:39:54.821555 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.822917 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.824421 INFO::Found 0 missing values.
2025-09-29 21:39:54.825726 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.
2025-09-29 21:39:54.832251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.833024 INFO::Done
2025-09-29 21:39:54.847156 INFO::Formatting Data.
2025-09-29 21:39:54.848129 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.849298 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.850686 INFO::Found 0 missing values.
2025-09-29 21:39:54.854854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.855592 INFO::Done
2025-09-29 21:39:54.870573 INFO::Formatting Data.
2025-09-29 21:39:54.871543 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.872725 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.874112 INFO::Found 0 missing values.
2025-09-29 21:39:54.87842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.879169 INFO::Done
2025-09-29 21:39:54.920639 INFO::Formatting Data.
2025-09-29 21:39:54.921772 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.923271 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.925004 INFO::Found 1 missing values.
2025-09-29 21:39:54.928971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.929752 INFO::Done
2025-09-29 21:39:54.956495 INFO::Formatting Data.
2025-09-29 21:39:54.957664 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.958889 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.960305 INFO::Found 2 missing values.
2025-09-29 21:39:54.961604 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.
2025-09-29 21:39:54.964919 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.965719 INFO::Done
2025-09-29 21:39:54.979104 INFO::Formatting Data.
2025-09-29 21:39:54.980083 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:54.98131 INFO::Removing potential empty rows and columns
2025-09-29 21:39:54.982572 INFO::Found 2 missing values.
2025-09-29 21:39:54.98479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:54.985536 INFO::Done
2025-09-29 21:39:54.999898 INFO::Formatting Data.
2025-09-29 21:39:55.000913 INFO::Typecasting input to dataframe.
2025-09-29 21:39:55.00209 INFO::Replacing NaNs with NAs.
2025-09-29 21:39:55.00331 INFO::Removing potential empty rows and columns
2025-09-29 21:39:55.004762 INFO::Found 0 missing values.
2025-09-29 21:39:55.008974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-29 21:39:55.009723 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.571 4.841 30.130
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.792 | 2.118 | 24.715 | |
| compute_asw | 0.038 | 0.002 | 0.040 | |
| count_existing | 0.020 | 0.003 | 0.023 | |
| generate_data_covariables | 0.020 | 0.001 | 0.020 | |
| generate_dataset | 0.019 | 0.001 | 0.020 | |