Yannis Schumann
| Snapshot Date: 2025-09-15 13:45 -0400 (Mon, 15 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 2025-09-16 12:03 -0400 (Tue, 16 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" | 4726 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4545 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4529 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4554 |
| 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 163/2330 | 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: 2025-09-15 21:10:48 -0400 (Mon, 15 Sep 2025) |
| EndedAt: 2025-09-15 21:12:40 -0400 (Mon, 15 Sep 2025) |
| EllapsedTime: 112.1 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 25.641 1.709 19.333
* 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")
2025-09-15 21:11:46.444245 INFO::Formatting Data.
2025-09-15 21:11:46.445678 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:46.458871 INFO::Removing potential empty rows and columns
2025-09-15 21:11:46.765826 INFO::Found 0 missing values.
2025-09-15 21:11:46.769686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:46.770412 INFO::Done
2025-09-15 21:11:46.77104 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:46.783962 INFO::Starting hierarchical adjustment
2025-09-15 21:11:46.784973 INFO::Found 3 batches.
2025-09-15 21:11:46.785608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:46.786922 INFO::Using default BPPARAM
2025-09-15 21:11:46.78758 INFO::Processing subtree level 1
2025-09-15 21:11:46.948461 INFO::Adjusting the last 1 batches sequentially
2025-09-15 21:11:46.953573 INFO::Done
2025-09-15 21:11:46.954378 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:46.960284 INFO::ASW Batch was -0.0603507362917522 prior to batch effect correction and is now -0.0603507362917522 .
2025-09-15 21:11:46.961557 INFO::Total function execution time is 0.518060445785522 s and adjustment time is 0.16880202293396 s ( 32.58 )
2025-09-15 21:11:46.980438 INFO::Formatting Data.
2025-09-15 21:11:46.981309 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:46.982382 INFO::Removing potential empty rows and columns
2025-09-15 21:11:46.983633 INFO::Found 0 missing values.
2025-09-15 21:11:46.984683 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.
2025-09-15 21:11:46.996902 INFO::Formatting Data.
2025-09-15 21:11:46.997738 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:46.998732 INFO::Removing potential empty rows and columns
2025-09-15 21:11:46.999926 INFO::Found 0 missing values.
2025-09-15 21:11:47.000951 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.
2025-09-15 21:11:47.018925 INFO::Formatting Data.
2025-09-15 21:11:47.01979 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:47.020764 INFO::Removing potential empty rows and columns
2025-09-15 21:11:47.021781 INFO::Found 0 missing values.
2025-09-15 21:11:47.022828 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.
2025-09-15 21:11:47.027853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:47.028482 INFO::Done
2025-09-15 21:11:47.029075 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:47.031367 INFO::Starting hierarchical adjustment
2025-09-15 21:11:47.032177 INFO::Found 2 batches.
2025-09-15 21:11:47.032784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:47.0335 INFO::Using default BPPARAM
2025-09-15 21:11:47.034106 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:47.035213 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-15 21:11:47.060819 INFO::Done
2025-09-15 21:11:47.061635 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:47.064037 INFO::ASW Batch was -0.02275034543205 prior to batch effect correction and is now -0.0893758614663935 .
2025-09-15 21:11:47.064961 INFO::Total function execution time is 0.0461061000823975 s and adjustment time is 0.0287539958953857 s ( 62.36 )
2025-09-15 21:11:47.068077 INFO::Formatting Data.
2025-09-15 21:11:47.068826 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:47.079298 INFO::Formatting Data.
2025-09-15 21:11:47.080157 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:47.081192 INFO::Removing potential empty rows and columns
2025-09-15 21:11:47.082395 INFO::Found 0 missing values.
2025-09-15 21:11:47.085813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:47.086451 INFO::Done
2025-09-15 21:11:47.087058 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:47.089489 INFO::Starting hierarchical adjustment
2025-09-15 21:11:47.090318 INFO::Found 2 batches.
2025-09-15 21:11:47.090947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:47.091673 INFO::Using default BPPARAM
2025-09-15 21:11:47.092292 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:47.093424 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-15 21:11:47.137223 INFO::Done
2025-09-15 21:11:47.137983 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:47.140194 INFO::ASW Batch was 0.0144523575913247 prior to batch effect correction and is now -0.121024389488169 .
2025-09-15 21:11:47.141087 INFO::Total function execution time is 0.0618476867675781 s and adjustment time is 0.0470407009124756 s ( 76.06 )
2025-09-15 21:11:47.142257 INFO::Formatting Data.
2025-09-15 21:11:47.142952 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:47.143888 INFO::Removing potential empty rows and columns
2025-09-15 21:11:47.145045 INFO::Found 0 missing values.
2025-09-15 21:11:47.148143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:47.148741 INFO::Done
2025-09-15 21:11:47.149306 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:47.151501 INFO::Starting hierarchical adjustment
2025-09-15 21:11:47.152291 INFO::Found 2 batches.
2025-09-15 21:11:47.152877 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:47.153527 INFO::Using default BPPARAM
2025-09-15 21:11:47.154099 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:47.155094 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-15 21:11:47.171706 INFO::Done
2025-09-15 21:11:47.172451 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:47.174639 INFO::ASW Batch was 0.0144523575913247 prior to batch effect correction and is now -0.121024389488169 .
2025-09-15 21:11:47.175509 INFO::Total function execution time is 0.0332663059234619 s and adjustment time is 0.0195503234863281 s ( 58.77 )
2025-09-15 21:11:51.037708 INFO::Formatting Data.
2025-09-15 21:11:51.038735 INFO::Recognized SummarizedExperiment
2025-09-15 21:11:51.039486 INFO::Typecasting input to dataframe.
2025-09-15 21:11:51.085123 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:51.086989 INFO::Removing potential empty rows and columns
2025-09-15 21:11:51.093458 INFO::Found 0 missing values.
2025-09-15 21:11:51.105723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:51.106743 INFO::Done
2025-09-15 21:11:51.107613 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:51.113219 INFO::Starting hierarchical adjustment
2025-09-15 21:11:51.114326 INFO::Found 2 batches.
2025-09-15 21:11:51.11514 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:51.116734 INFO::Using default BPPARAM
2025-09-15 21:11:51.11753 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:51.119024 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-15 21:11:51.209529 INFO::Done
2025-09-15 21:11:51.210807 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:51.216445 INFO::ASW Batch was 0.00993658538077165 prior to batch effect correction and is now -0.0905669898665644 .
2025-09-15 21:11:51.217681 INFO::Total function execution time is 0.180358409881592 s and adjustment time is 0.0954082012176514 s ( 52.9 )
2025-09-15 21:11:51.246024 INFO::Formatting Data.
2025-09-15 21:11:51.247075 INFO::Recognized SummarizedExperiment
2025-09-15 21:11:51.247913 INFO::Typecasting input to dataframe.
2025-09-15 21:11:51.262694 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:51.264407 INFO::Removing potential empty rows and columns
2025-09-15 21:11:51.270557 INFO::Found 0 missing values.
2025-09-15 21:11:51.282393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:51.283403 INFO::Done
2025-09-15 21:11:51.284257 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:51.290091 INFO::Starting hierarchical adjustment
2025-09-15 21:11:51.291214 INFO::Found 2 batches.
2025-09-15 21:11:51.292029 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:51.292927 INFO::Using default BPPARAM
2025-09-15 21:11:51.293727 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:51.295447 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-15 21:11:51.338434 INFO::Done
2025-09-15 21:11:51.339492 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:51.345404 INFO::ASW Batch was -0.00056075789905534 prior to batch effect correction and is now -0.00056075789905534 .
2025-09-15 21:11:51.346671 INFO::Total function execution time is 0.100613594055176 s and adjustment time is 0.047407865524292 s ( 47.12 )
2025-09-15 21:11:51.374169 INFO::Formatting Data.
2025-09-15 21:11:51.375299 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:51.376657 INFO::Removing potential empty rows and columns
2025-09-15 21:11:51.378207 INFO::Found 0 missing values.
2025-09-15 21:11:51.383002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:51.383837 INFO::Done
2025-09-15 21:11:51.384629 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:51.387562 INFO::Starting hierarchical adjustment
2025-09-15 21:11:51.388598 INFO::Found 3 batches.
2025-09-15 21:11:51.38939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:51.390292 INFO::Using default BPPARAM
2025-09-15 21:11:51.391086 INFO::Processing subtree level 1
2025-09-15 21:11:51.580709 INFO::Adjusting the last 1 batches sequentially
2025-09-15 21:11:51.586804 INFO::Done
2025-09-15 21:11:51.587682 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:51.592832 INFO::ASW Batch was -0.00769101936111117 prior to batch effect correction and is now -0.191090350468666 .
2025-09-15 21:11:51.594068 INFO::Total function execution time is 0.219952583312988 s and adjustment time is 0.19438624382019 s ( 88.38 )
2025-09-15 21:11:51.621261 INFO::Skipping initial DF formatting
2025-09-15 21:11:51.622129 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:51.626892 INFO::Starting hierarchical adjustment
2025-09-15 21:11:51.62783 INFO::Found 5 batches.
2025-09-15 21:11:51.628475 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:51.62924 INFO::Using default BPPARAM
2025-09-15 21:11:51.629877 INFO::Processing subtree level 1
2025-09-15 21:11:51.931349 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:51.940373 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-15 21:11:51.965216 INFO::Done
2025-09-15 21:11:51.966172 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:51.971789 INFO::ASW Batch was 0.531025185590492 prior to batch effect correction and is now 0.531025185590492 .
2025-09-15 21:11:51.972549 INFO::ASW Label was 0.361219116809602 prior to batch effect correction and is now 0.361219116809602 .
2025-09-15 21:11:51.973566 INFO::Total function execution time is 0.352379322052002 s and adjustment time is 0.337551355361938 s ( 95.79 )
2025-09-15 21:11:52.044953 INFO::Formatting Data.
2025-09-15 21:11:52.045834 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:52.046847 INFO::Removing potential empty rows and columns
2025-09-15 21:11:52.04801 INFO::Found 0 missing values.
2025-09-15 21:11:52.05254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:52.053168 INFO::Done
2025-09-15 21:11:52.053772 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:52.057176 INFO::Starting hierarchical adjustment
2025-09-15 21:11:52.058038 INFO::Found 5 batches.
2025-09-15 21:11:52.058635 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:52.059344 INFO::Using default BPPARAM
2025-09-15 21:11:52.059941 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.
2025-09-15 21:11:52.287395 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:52.289339 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-15 21:11:52.311011 INFO::Done
2025-09-15 21:11:52.312066 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:52.316458 INFO::ASW Batch was 0.241487868158922 prior to batch effect correction and is now -0.0707062083819423 .
2025-09-15 21:11:52.317369 INFO::ASW Label was 0.335614377457384 prior to batch effect correction and is now 0.853276618193427 .
2025-09-15 21:11:52.318572 INFO::Total function execution time is 0.273625612258911 s and adjustment time is 0.253080606460571 s ( 92.49 )
2025-09-15 21:11:52.319803 INFO::Formatting Data.
2025-09-15 21:11:52.320619 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:52.321754 INFO::Removing potential empty rows and columns
2025-09-15 21:11:52.323164 INFO::Found 0 missing values.
2025-09-15 21:11:52.328955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:52.329636 INFO::Done
2025-09-15 21:11:52.330373 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:52.334568 INFO::Starting hierarchical adjustment
2025-09-15 21:11:52.33543 INFO::Found 5 batches.
2025-09-15 21:11:52.336055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:52.33679 INFO::Using default BPPARAM
2025-09-15 21:11:52.337463 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.
2025-09-15 21:11:52.582343 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:52.588624 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-15 21:11:52.630209 INFO::Done
2025-09-15 21:11:52.631211 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:52.635728 INFO::ASW Batch was 0.241487868158922 prior to batch effect correction and is now -0.0707062083819423 .
2025-09-15 21:11:52.63655 INFO::ASW Label was 0.335614377457384 prior to batch effect correction and is now 0.853276618193427 .
2025-09-15 21:11:52.637669 INFO::Total function execution time is 0.31786060333252 s and adjustment time is 0.294913291931152 s ( 92.78 )
2025-09-15 21:11:52.656282 INFO::Formatting Data.
2025-09-15 21:11:52.657339 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:52.658628 INFO::Removing potential empty rows and columns
2025-09-15 21:11:52.660051 INFO::Found 0 missing values.
2025-09-15 21:11:52.665989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:52.666732 INFO::Done
2025-09-15 21:11:52.667457 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:52.671589 INFO::Starting hierarchical adjustment
2025-09-15 21:11:52.67265 INFO::Found 5 batches.
2025-09-15 21:11:52.673392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:52.674281 INFO::Using default BPPARAM
2025-09-15 21:11:52.675028 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.
2025-09-15 21:11:52.904908 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:52.907182 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-15 21:11:52.952931 INFO::Done
2025-09-15 21:11:52.953891 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:52.962388 INFO::ASW Batch was 0.119749334001878 prior to batch effect correction and is now -0.0832508035273393 .
2025-09-15 21:11:52.967364 INFO::ASW Label was 0.47143021569679 prior to batch effect correction and is now 0.895456968409063 .
2025-09-15 21:11:52.968516 INFO::Total function execution time is 0.312305450439453 s and adjustment time is 0.280436277389526 s ( 89.8 )
2025-09-15 21:11:52.973662 INFO::Formatting Data.
2025-09-15 21:11:52.975413 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:52.976695 INFO::Removing potential empty rows and columns
2025-09-15 21:11:52.982133 INFO::Found 0 missing values.
2025-09-15 21:11:52.991444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:52.99627 INFO::Done
2025-09-15 21:11:52.996981 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:53.001002 INFO::Starting hierarchical adjustment
2025-09-15 21:11:53.001933 INFO::Found 5 batches.
2025-09-15 21:11:53.002587 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:53.003352 INFO::Using default BPPARAM
2025-09-15 21:11:53.003991 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.
2025-09-15 21:11:53.217781 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:53.2203 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-15 21:11:53.265038 INFO::Done
2025-09-15 21:11:53.266007 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:53.270504 INFO::ASW Batch was 0.119749334001878 prior to batch effect correction and is now -0.0832508035273393 .
2025-09-15 21:11:53.271313 INFO::ASW Label was 0.47143021569679 prior to batch effect correction and is now 0.895456968409063 .
2025-09-15 21:11:53.272457 INFO::Total function execution time is 0.298780202865601 s and adjustment time is 0.263247013092041 s ( 88.11 )
2025-09-15 21:11:53.289902 INFO::Formatting Data.
2025-09-15 21:11:53.290949 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:53.292122 INFO::Removing potential empty rows and columns
2025-09-15 21:11:53.293637 INFO::Found 0 missing values.
2025-09-15 21:11:53.297587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:53.298273 INFO::Done
2025-09-15 21:11:53.298922 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:53.303334 INFO::Starting hierarchical adjustment
2025-09-15 21:11:53.304221 INFO::Found 2 batches.
2025-09-15 21:11:53.304885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:53.305623 INFO::Using default BPPARAM
2025-09-15 21:11:53.306274 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:53.307575 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-15 21:11:53.329787 INFO::Done
2025-09-15 21:11:53.330879 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:53.33469 INFO::ASW Batch was 0.440243804284804 prior to batch effect correction and is now 0.0702411031674084 .
2025-09-15 21:11:53.335644 INFO::ASW Label was 0.635321686801105 prior to batch effect correction and is now 0.889602922625277 .
2025-09-15 21:11:53.336911 INFO::Total function execution time is 0.0470926761627197 s and adjustment time is 0.0256636142730713 s ( 54.5 )
2025-09-15 21:11:53.338098 INFO::Formatting Data.
2025-09-15 21:11:53.338874 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:53.339957 INFO::Removing potential empty rows and columns
2025-09-15 21:11:53.341201 INFO::Found 0 missing values.
2025-09-15 21:11:53.345502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:53.346369 INFO::Done
2025-09-15 21:11:53.347185 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:53.351218 INFO::Starting hierarchical adjustment
2025-09-15 21:11:53.352097 INFO::Found 2 batches.
2025-09-15 21:11:53.352746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:53.353687 INFO::Using default BPPARAM
2025-09-15 21:11:53.354522 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:53.355966 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-15 21:11:53.376922 INFO::Done
2025-09-15 21:11:53.37799 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:53.381843 INFO::ASW Batch was 0.440243804284804 prior to batch effect correction and is now 0.0702411031674084 .
2025-09-15 21:11:53.38278 INFO::ASW Label was 0.635321686801105 prior to batch effect correction and is now 0.889602922625277 .
2025-09-15 21:11:53.384028 INFO::Total function execution time is 0.0459074974060059 s and adjustment time is 0.0249314308166504 s ( 54.31 )
2025-09-15 21:11:53.399616 INFO::Formatting Data.
2025-09-15 21:11:53.400817 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:53.402208 INFO::Removing potential empty rows and columns
2025-09-15 21:11:53.403632 INFO::Found 0 missing values.
2025-09-15 21:11:53.406495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:53.407167 INFO::Done
2025-09-15 21:11:53.407797 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:53.410202 INFO::Starting hierarchical adjustment
2025-09-15 21:11:53.411168 INFO::Found 2 batches.
2025-09-15 21:11:53.411985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:53.412929 INFO::Using default BPPARAM
2025-09-15 21:11:53.413768 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:53.41489 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-15 21:11:53.478238 INFO::Done
2025-09-15 21:11:53.479389 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:53.490733 INFO::ASW Batch was 0.10074367289835 prior to batch effect correction and is now -0.113494149137357 .
2025-09-15 21:11:53.492183 INFO::Total function execution time is 0.0926609039306641 s and adjustment time is 0.0672304630279541 s ( 72.56 )
2025-09-15 21:11:53.511057 INFO::Formatting Data.
2025-09-15 21:11:53.512256 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:53.513658 INFO::Removing potential empty rows and columns
2025-09-15 21:11:53.515258 INFO::Found 0 missing values.
2025-09-15 21:11:53.518434 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.
2025-09-15 21:11:53.526966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:53.527814 INFO::Done
2025-09-15 21:11:53.528418 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:53.531982 INFO::Starting hierarchical adjustment
2025-09-15 21:11:53.532826 INFO::Found 2 batches.
2025-09-15 21:11:53.533433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:53.53413 INFO::Using default BPPARAM
2025-09-15 21:11:53.534708 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:53.535778 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-15 21:11:53.555243 INFO::Done
2025-09-15 21:11:53.556047 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:53.559334 INFO::ASW Batch was 0.464510088708519 prior to batch effect correction and is now 0.0111075982202014 .
2025-09-15 21:11:53.560034 INFO::ASW Label was 0.615329526197961 prior to batch effect correction and is now 0.915136158618278 .
2025-09-15 21:11:53.56093 INFO::Total function execution time is 0.0500955581665039 s and adjustment time is 0.0225753784179688 s ( 45.06 )
2025-09-15 21:11:53.56188 INFO::Formatting Data.
2025-09-15 21:11:53.562574 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:53.563614 INFO::Removing potential empty rows and columns
2025-09-15 21:11:53.564756 INFO::Found 0 missing values.
2025-09-15 21:11:53.565789 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.
2025-09-15 21:11:53.570896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:53.571509 INFO::Done
2025-09-15 21:11:53.572096 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:53.575341 INFO::Starting hierarchical adjustment
2025-09-15 21:11:53.576148 INFO::Found 2 batches.
2025-09-15 21:11:53.57674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:53.577433 INFO::Using default BPPARAM
2025-09-15 21:11:53.578027 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:53.579062 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-15 21:11:53.597509 INFO::Done
2025-09-15 21:11:53.598286 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:53.601515 INFO::ASW Batch was 0.464510088708519 prior to batch effect correction and is now 0.0111075982202014 .
2025-09-15 21:11:53.602192 INFO::ASW Label was 0.615329526197961 prior to batch effect correction and is now 0.915136158618278 .
2025-09-15 21:11:53.603085 INFO::Total function execution time is 0.0412533283233643 s and adjustment time is 0.0215048789978027 s ( 52.13 )
2025-09-15 21:11:53.83404 INFO::Formatting Data.
2025-09-15 21:11:53.835038 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:53.836066 INFO::Removing potential empty rows and columns
2025-09-15 21:11:53.837263 INFO::Found 0 missing values.
2025-09-15 21:11:53.840777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:53.841407 INFO::Done
2025-09-15 21:11:53.842008 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:53.84432 INFO::Starting hierarchical adjustment
2025-09-15 21:11:53.84515 INFO::Found 3 batches.
2025-09-15 21:11:53.845766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:53.846458 INFO::Using default BPPARAM
2025-09-15 21:11:53.84707 INFO::Processing subtree level 1
2025-09-15 21:11:53.992607 INFO::Adjusting the last 1 batches sequentially
2025-09-15 21:11:53.998143 INFO::Done
2025-09-15 21:11:53.999159 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:54.009781 INFO::ASW Batch was -0.0905129171750426 prior to batch effect correction and is now -0.0905129171750426 .
2025-09-15 21:11:54.011227 INFO::Total function execution time is 0.17717981338501 s and adjustment time is 0.153113842010498 s ( 86.42 )
2025-09-15 21:11:54.01688 INFO::Formatting Data.
2025-09-15 21:11:54.017983 INFO::Typecasting input to dataframe.
2025-09-15 21:11:54.019177 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:54.020555 INFO::Removing potential empty rows and columns
2025-09-15 21:11:54.026267 INFO::Found 0 missing values.
2025-09-15 21:11:54.035157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:54.0361 INFO::Done
2025-09-15 21:11:54.036935 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:54.044161 INFO::Starting hierarchical adjustment
2025-09-15 21:11:54.047703 INFO::Found 3 batches.
2025-09-15 21:11:54.048602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:54.049565 INFO::Using default BPPARAM
2025-09-15 21:11:54.050406 INFO::Processing subtree level 1
2025-09-15 21:11:54.188068 INFO::Adjusting the last 1 batches sequentially
2025-09-15 21:11:54.194656 INFO::Done
2025-09-15 21:11:54.195707 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:54.202382 INFO::ASW Batch was -0.0905129171750426 prior to batch effect correction and is now -0.0905129171750426 .
2025-09-15 21:11:54.206905 INFO::Total function execution time is 0.190991401672363 s and adjustment time is 0.147204160690308 s ( 77.07 )
2025-09-15 21:11:54.240803 INFO::Formatting Data.
2025-09-15 21:11:54.241784 INFO::Typecasting input to dataframe.
2025-09-15 21:11:54.242772 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:54.243834 INFO::Removing potential empty rows and columns
2025-09-15 21:11:54.245111 INFO::Found 0 missing values.
2025-09-15 21:11:54.248665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:54.24931 INFO::Done
2025-09-15 21:11:54.249918 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:54.252243 INFO::Starting hierarchical adjustment
2025-09-15 21:11:54.253082 INFO::Found 3 batches.
2025-09-15 21:11:54.253697 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:54.254409 INFO::Using default BPPARAM
2025-09-15 21:11:54.255059 INFO::Processing subtree level 1
2025-09-15 21:11:54.415496 INFO::Adjusting the last 1 batches sequentially
2025-09-15 21:11:54.422044 INFO::Done
2025-09-15 21:11:54.423054 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:54.429681 INFO::ASW Batch was -0.024280401308184 prior to batch effect correction and is now -0.024280401308184 .
2025-09-15 21:11:54.431124 INFO::Total function execution time is 0.190335750579834 s and adjustment time is 0.169070243835449 s ( 88.83 )
2025-09-15 21:11:54.698034 INFO::Formatting Data.
2025-09-15 21:11:54.699001 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:54.700333 INFO::Removing potential empty rows and columns
2025-09-15 21:11:54.703669 INFO::Found 1000 missing values.
2025-09-15 21:11:54.72688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:54.727736 INFO::Done
2025-09-15 21:11:54.728369 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:54.734883 INFO::Starting hierarchical adjustment
2025-09-15 21:11:54.735839 INFO::Found 10 batches.
2025-09-15 21:11:54.73646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:54.737192 INFO::Using default BPPARAM
2025-09-15 21:11:54.737812 INFO::Processing subtree level 1
2025-09-15 21:11:55.00422 INFO::Processing subtree level 2
2025-09-15 21:11:55.360337 INFO::Adjusting the last 1 batches sequentially
2025-09-15 21:11:55.367447 INFO::Done
2025-09-15 21:11:55.372643 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:55.385768 INFO::ASW Batch was 0.482554474758896 prior to batch effect correction and is now 0.482554474758896 .
2025-09-15 21:11:55.386909 INFO::ASW Label was 0.347283462768115 prior to batch effect correction and is now 0.347283462768115 .
2025-09-15 21:11:55.388376 INFO::Total function execution time is 0.690408945083618 s and adjustment time is 0.63175368309021 s ( 91.5 )
2025-09-15 21:11:55.38978 INFO::Formatting Data.
2025-09-15 21:11:55.390805 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:55.392777 INFO::Removing potential empty rows and columns
2025-09-15 21:11:55.397367 INFO::Found 1000 missing values.
2025-09-15 21:11:55.429581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:55.430823 INFO::Done
2025-09-15 21:11:55.431752 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:55.440577 INFO::Starting hierarchical adjustment
2025-09-15 21:11:55.441848 INFO::Found 10 batches.
2025-09-15 21:11:56.620003 INFO::Set up parallel execution backend with 2 workers
2025-09-15 21:11:56.622181 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-15 21:11:57.948167 INFO::Adjusting the last 2 batches sequentially
2025-09-15 21:11:57.950099 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-15 21:11:58.004573 INFO::Done
2025-09-15 21:11:58.009643 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:58.016788 INFO::ASW Batch was 0.482554474758896 prior to batch effect correction and is now 0.482554474758896 .
2025-09-15 21:11:58.017627 INFO::ASW Label was 0.347283462768115 prior to batch effect correction and is now 0.347283462768115 .
2025-09-15 21:11:58.018709 INFO::Total function execution time is 2.62902283668518 s and adjustment time is 2.56299471855164 s ( 97.49 )
2025-09-15 21:11:58.217994 INFO::Formatting Data.
2025-09-15 21:11:58.219088 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:58.220423 INFO::Removing potential empty rows and columns
2025-09-15 21:11:58.221968 INFO::Found 0 missing values.
2025-09-15 21:11:58.227291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:58.228042 INFO::Done
2025-09-15 21:11:58.228774 INFO::Acquiring quality metrics before batch effect correction.
2025-09-15 21:11:58.232572 INFO::Starting hierarchical adjustment
2025-09-15 21:11:58.233525 INFO::Found 3 batches.
2025-09-15 21:11:58.234251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-15 21:11:58.235113 INFO::Using default BPPARAM
2025-09-15 21:11:58.235854 INFO::Processing subtree level 1
2025-09-15 21:11:58.386376 INFO::Adjusting the last 1 batches sequentially
2025-09-15 21:11:58.392252 INFO::Done
2025-09-15 21:11:58.3933 INFO::Acquiring quality metrics after batch effect correction.
2025-09-15 21:11:58.397783 INFO::ASW Batch was 0.189953235964528 prior to batch effect correction and is now -0.137805239151167 .
2025-09-15 21:11:58.398622 INFO::ASW Label was -0.187555475140694 prior to batch effect correction and is now -0.0660288417054087 .
2025-09-15 21:11:58.39991 INFO::Total function execution time is 0.181961297988892 s and adjustment time is 0.158861637115479 s ( 87.31 )
2025-09-15 21:11:58.676538 INFO::Formatting Data.
2025-09-15 21:11:58.677481 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:58.682543 INFO::Removing potential empty rows and columns
2025-09-15 21:11:58.683779 INFO::Found 2 missing values.
2025-09-15 21:11:58.687099 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:58.687709 INFO::Done
2025-09-15 21:11:58.741574 INFO::Found NA in Reference column
2025-09-15 21:11:58.766326 INFO::Require at least two references per batch.
2025-09-15 21:11:58.818408 INFO::Formatting Data.
2025-09-15 21:11:58.823652 INFO::Recognized SummarizedExperiment
2025-09-15 21:11:58.824564 INFO::Typecasting input to dataframe.
2025-09-15 21:11:58.867291 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:58.869277 INFO::Removing potential empty rows and columns
2025-09-15 21:11:58.874669 INFO::Found 0 missing values.
2025-09-15 21:11:58.885689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:58.886697 INFO::Done
2025-09-15 21:11:58.926955 INFO::Formatting Data.
2025-09-15 21:11:58.927924 INFO::Recognized SummarizedExperiment
2025-09-15 21:11:58.928561 INFO::Typecasting input to dataframe.
2025-09-15 21:11:58.975056 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:58.976587 INFO::Removing potential empty rows and columns
2025-09-15 21:11:58.984042 INFO::Found 0 missing values.
2025-09-15 21:11:59.000529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:59.001342 INFO::Done
2025-09-15 21:11:59.027381 INFO::Formatting Data.
2025-09-15 21:11:59.028243 INFO::Recognized SummarizedExperiment
2025-09-15 21:11:59.028862 INFO::Typecasting input to dataframe.
2025-09-15 21:11:59.069879 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:59.071115 INFO::Removing potential empty rows and columns
2025-09-15 21:11:59.072379 INFO::Found 0 missing values.
2025-09-15 21:11:59.073434 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.
2025-09-15 21:11:59.078515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:59.079142 INFO::Done
2025-09-15 21:11:59.093986 INFO::Formatting Data.
2025-09-15 21:11:59.094794 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:59.095742 INFO::Removing potential empty rows and columns
2025-09-15 21:11:59.102637 INFO::Found 0 missing values.
2025-09-15 21:11:59.109995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:59.110599 INFO::Done
2025-09-15 21:11:59.133549 INFO::Formatting Data.
2025-09-15 21:11:59.134448 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:59.139439 INFO::Removing potential empty rows and columns
2025-09-15 21:11:59.140676 INFO::Found 0 missing values.
2025-09-15 21:11:59.148078 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:59.1487 INFO::Done
2025-09-15 21:11:59.223132 INFO::Formatting Data.
2025-09-15 21:11:59.228148 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:59.229426 INFO::Removing potential empty rows and columns
2025-09-15 21:11:59.230819 INFO::Found 1 missing values.
2025-09-15 21:11:59.237756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:59.238387 INFO::Done
2025-09-15 21:11:59.292991 INFO::Formatting Data.
2025-09-15 21:11:59.293952 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:59.294927 INFO::Removing potential empty rows and columns
2025-09-15 21:11:59.301027 INFO::Found 2 missing values.
2025-09-15 21:11:59.302202 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.
2025-09-15 21:11:59.307528 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:59.30825 INFO::Done
2025-09-15 21:11:59.332776 INFO::Formatting Data.
2025-09-15 21:11:59.333682 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:59.334666 INFO::Removing potential empty rows and columns
2025-09-15 21:11:59.33848 INFO::Found 2 missing values.
2025-09-15 21:11:59.340409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:59.341032 INFO::Done
2025-09-15 21:11:59.358881 INFO::Formatting Data.
2025-09-15 21:11:59.359894 INFO::Typecasting input to dataframe.
2025-09-15 21:11:59.36104 INFO::Replacing NaNs with NAs.
2025-09-15 21:11:59.362248 INFO::Removing potential empty rows and columns
2025-09-15 21:11:59.363664 INFO::Found 0 missing values.
2025-09-15 21:11:59.36803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-15 21:11:59.368784 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.680 4.787 29.097
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.641 | 1.709 | 19.333 | |
| compute_asw | 0.038 | 0.000 | 0.039 | |
| count_existing | 0.021 | 0.001 | 0.022 | |
| generate_data_covariables | 0.019 | 0.001 | 0.020 | |
| generate_dataset | 0.018 | 0.001 | 0.018 | |