Yannis Schumann
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:03 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 2025-10-24 21:31:37 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 21:33:10 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 92.1 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 24.469 1.32 17.908
* 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")
2025-10-24 21:32:29.625245 INFO::Formatting Data.
2025-10-24 21:32:29.626619 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:29.639189 INFO::Removing potential empty rows and columns
2025-10-24 21:32:29.905309 INFO::Found 0 missing values.
2025-10-24 21:32:29.909242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:29.909912 INFO::Done
2025-10-24 21:32:29.910545 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:29.922367 INFO::Starting hierarchical adjustment
2025-10-24 21:32:29.923261 INFO::Found 3 batches.
2025-10-24 21:32:29.923842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:29.925017 INFO::Using default BPPARAM
2025-10-24 21:32:29.925705 INFO::Processing subtree level 1
2025-10-24 21:32:30.031664 INFO::Adjusting the last 1 batches sequentially
2025-10-24 21:32:30.033461 INFO::Done
2025-10-24 21:32:30.034151 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:30.03671 INFO::ASW Batch was -0.067761570545867 prior to batch effect correction and is now -0.067761570545867 .
2025-10-24 21:32:30.037837 INFO::Total function execution time is 0.413276195526123 s and adjustment time is 0.110396385192871 s ( 26.71 )
2025-10-24 21:32:30.05171 INFO::Formatting Data.
2025-10-24 21:32:30.052618 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:30.053585 INFO::Removing potential empty rows and columns
2025-10-24 21:32:30.054731 INFO::Found 0 missing values.
2025-10-24 21:32:30.055712 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-24 21:32:30.066958 INFO::Formatting Data.
2025-10-24 21:32:30.067736 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:30.068655 INFO::Removing potential empty rows and columns
2025-10-24 21:32:30.069735 INFO::Found 0 missing values.
2025-10-24 21:32:30.070662 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-24 21:32:30.086755 INFO::Formatting Data.
2025-10-24 21:32:30.087533 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:30.088439 INFO::Removing potential empty rows and columns
2025-10-24 21:32:30.089513 INFO::Found 0 missing values.
2025-10-24 21:32:30.090483 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-24 21:32:30.09566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:30.096294 INFO::Done
2025-10-24 21:32:30.09687 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:30.099015 INFO::Starting hierarchical adjustment
2025-10-24 21:32:30.099796 INFO::Found 2 batches.
2025-10-24 21:32:30.100395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:30.101043 INFO::Using default BPPARAM
2025-10-24 21:32:30.101603 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:30.102574 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-24 21:32:30.125512 INFO::Done
2025-10-24 21:32:30.126264 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:30.128408 INFO::ASW Batch was -0.0667241720582335 prior to batch effect correction and is now -0.102267175376035 .
2025-10-24 21:32:30.129285 INFO::Total function execution time is 0.0425639152526855 s and adjustment time is 0.0258760452270508 s ( 60.79 )
2025-10-24 21:32:30.132275 INFO::Formatting Data.
2025-10-24 21:32:30.13293 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:30.141788 INFO::Formatting Data.
2025-10-24 21:32:30.142524 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:30.143434 INFO::Removing potential empty rows and columns
2025-10-24 21:32:30.144511 INFO::Found 0 missing values.
2025-10-24 21:32:30.147464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:30.148008 INFO::Done
2025-10-24 21:32:30.14857 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:30.150742 INFO::Starting hierarchical adjustment
2025-10-24 21:32:30.151485 INFO::Found 2 batches.
2025-10-24 21:32:30.152019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:30.152664 INFO::Using default BPPARAM
2025-10-24 21:32:30.153243 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:30.154196 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:30.191947 INFO::Done
2025-10-24 21:32:30.192605 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:30.194454 INFO::ASW Batch was 0.0862703530018891 prior to batch effect correction and is now -0.101568118882513 .
2025-10-24 21:32:30.195194 INFO::Total function execution time is 0.0534498691558838 s and adjustment time is 0.0406103134155273 s ( 75.98 )
2025-10-24 21:32:30.196169 INFO::Formatting Data.
2025-10-24 21:32:30.196735 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:30.197527 INFO::Removing potential empty rows and columns
2025-10-24 21:32:30.198478 INFO::Found 0 missing values.
2025-10-24 21:32:30.201054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:30.20156 INFO::Done
2025-10-24 21:32:30.202034 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:30.203843 INFO::Starting hierarchical adjustment
2025-10-24 21:32:30.204508 INFO::Found 2 batches.
2025-10-24 21:32:30.204993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:30.205554 INFO::Using default BPPARAM
2025-10-24 21:32:30.206034 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:30.206856 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:30.220359 INFO::Done
2025-10-24 21:32:30.220945 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:30.222762 INFO::ASW Batch was 0.0862703530018891 prior to batch effect correction and is now -0.101568118882513 .
2025-10-24 21:32:30.22349 INFO::Total function execution time is 0.0273280143737793 s and adjustment time is 0.0159831047058105 s ( 58.49 )
2025-10-24 21:32:33.125006 INFO::Formatting Data.
2025-10-24 21:32:33.125786 INFO::Recognized SummarizedExperiment
2025-10-24 21:32:33.126277 INFO::Typecasting input to dataframe.
2025-10-24 21:32:33.158093 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:33.159471 INFO::Removing potential empty rows and columns
2025-10-24 21:32:33.163356 INFO::Found 0 missing values.
2025-10-24 21:32:33.170744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:33.171457 INFO::Done
2025-10-24 21:32:33.172019 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:33.17588 INFO::Starting hierarchical adjustment
2025-10-24 21:32:33.176644 INFO::Found 2 batches.
2025-10-24 21:32:33.177187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:33.178327 INFO::Using default BPPARAM
2025-10-24 21:32:33.17893 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:33.179972 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-24 21:32:33.240874 INFO::Done
2025-10-24 21:32:33.241641 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:33.245507 INFO::ASW Batch was 0.0260015396303286 prior to batch effect correction and is now -0.0961412948225362 .
2025-10-24 21:32:33.24644 INFO::Total function execution time is 0.121739625930786 s and adjustment time is 0.0643384456634521 s ( 52.85 )
2025-10-24 21:32:33.26668 INFO::Formatting Data.
2025-10-24 21:32:33.267571 INFO::Recognized SummarizedExperiment
2025-10-24 21:32:33.268149 INFO::Typecasting input to dataframe.
2025-10-24 21:32:33.278053 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:33.279284 INFO::Removing potential empty rows and columns
2025-10-24 21:32:33.283339 INFO::Found 0 missing values.
2025-10-24 21:32:33.290703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:33.291358 INFO::Done
2025-10-24 21:32:33.2919 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:33.295671 INFO::Starting hierarchical adjustment
2025-10-24 21:32:33.296444 INFO::Found 2 batches.
2025-10-24 21:32:33.296983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:33.297641 INFO::Using default BPPARAM
2025-10-24 21:32:33.298182 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:33.299224 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-24 21:32:33.325778 INFO::Done
2025-10-24 21:32:33.326609 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:33.330732 INFO::ASW Batch was 0.0208546848233001 prior to batch effect correction and is now 0.0208546848233001 .
2025-10-24 21:32:33.331718 INFO::Total function execution time is 0.0650253295898438 s and adjustment time is 0.0294365882873535 s ( 45.27 )
2025-10-24 21:32:33.35239 INFO::Formatting Data.
2025-10-24 21:32:33.353433 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:33.354494 INFO::Removing potential empty rows and columns
2025-10-24 21:32:33.355646 INFO::Found 0 missing values.
2025-10-24 21:32:33.358912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:33.359498 INFO::Done
2025-10-24 21:32:33.360018 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:33.362313 INFO::Starting hierarchical adjustment
2025-10-24 21:32:33.363046 INFO::Found 3 batches.
2025-10-24 21:32:33.363591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:33.364228 INFO::Using default BPPARAM
2025-10-24 21:32:33.364755 INFO::Processing subtree level 1
2025-10-24 21:32:33.518479 INFO::Adjusting the last 1 batches sequentially
2025-10-24 21:32:33.520639 INFO::Done
2025-10-24 21:32:33.521397 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:33.524286 INFO::ASW Batch was -0.0887633048625299 prior to batch effect correction and is now -0.176765233611369 .
2025-10-24 21:32:33.525283 INFO::Total function execution time is 0.172960519790649 s and adjustment time is 0.157726287841797 s ( 91.19 )
2025-10-24 21:32:33.541002 INFO::Skipping initial DF formatting
2025-10-24 21:32:33.541876 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:33.546209 INFO::Starting hierarchical adjustment
2025-10-24 21:32:33.547039 INFO::Found 5 batches.
2025-10-24 21:32:33.547627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:33.548295 INFO::Using default BPPARAM
2025-10-24 21:32:33.548847 INFO::Processing subtree level 1
2025-10-24 21:32:33.796952 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:33.798856 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-24 21:32:33.819388 INFO::Done
2025-10-24 21:32:33.820327 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:33.884171 INFO::ASW Batch was 0.532646651215512 prior to batch effect correction and is now 0.532646651215512 .
2025-10-24 21:32:33.885191 INFO::ASW Label was 0.346699933273609 prior to batch effect correction and is now 0.346699933273609 .
2025-10-24 21:32:33.886154 INFO::Total function execution time is 0.345288515090942 s and adjustment time is 0.272459030151367 s ( 78.91 )
2025-10-24 21:32:33.907425 INFO::Formatting Data.
2025-10-24 21:32:33.90848 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:33.909638 INFO::Removing potential empty rows and columns
2025-10-24 21:32:33.910849 INFO::Found 0 missing values.
2025-10-24 21:32:33.915431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:33.916051 INFO::Done
2025-10-24 21:32:33.916637 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:33.920327 INFO::Starting hierarchical adjustment
2025-10-24 21:32:33.921156 INFO::Found 5 batches.
2025-10-24 21:32:33.921718 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:33.922415 INFO::Using default BPPARAM
2025-10-24 21:32:33.922955 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.068864 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.070805 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.091084 INFO::Done
2025-10-24 21:32:34.092026 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.096112 INFO::ASW Batch was 0.605879957142191 prior to batch effect correction and is now -0.0685888647925943 .
2025-10-24 21:32:34.096838 INFO::ASW Label was 0.194014560852387 prior to batch effect correction and is now 0.812781542283258 .
2025-10-24 21:32:34.09778 INFO::Total function execution time is 0.190546751022339 s and adjustment time is 0.170061588287354 s ( 89.25 )
2025-10-24 21:32:34.098875 INFO::Formatting Data.
2025-10-24 21:32:34.099703 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:34.100832 INFO::Removing potential empty rows and columns
2025-10-24 21:32:34.102158 INFO::Found 0 missing values.
2025-10-24 21:32:34.107051 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:34.107656 INFO::Done
2025-10-24 21:32:34.108272 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:34.112153 INFO::Starting hierarchical adjustment
2025-10-24 21:32:34.112945 INFO::Found 5 batches.
2025-10-24 21:32:34.122187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:34.123085 INFO::Using default BPPARAM
2025-10-24 21:32:34.123728 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.257279 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.258997 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.276106 INFO::Done
2025-10-24 21:32:34.276874 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.280557 INFO::ASW Batch was 0.605879957142191 prior to batch effect correction and is now -0.0685888647925943 .
2025-10-24 21:32:34.281232 INFO::ASW Label was 0.194014560852387 prior to batch effect correction and is now 0.812781542283258 .
2025-10-24 21:32:34.282111 INFO::Total function execution time is 0.18326735496521 s and adjustment time is 0.16332221031189 s ( 89.12 )
2025-10-24 21:32:34.296249 INFO::Formatting Data.
2025-10-24 21:32:34.297055 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:34.298015 INFO::Removing potential empty rows and columns
2025-10-24 21:32:34.299151 INFO::Found 0 missing values.
2025-10-24 21:32:34.303586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:34.304186 INFO::Done
2025-10-24 21:32:34.304724 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:34.308321 INFO::Starting hierarchical adjustment
2025-10-24 21:32:34.309072 INFO::Found 5 batches.
2025-10-24 21:32:34.309634 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:34.310308 INFO::Using default BPPARAM
2025-10-24 21:32:34.310851 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.443464 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.445341 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.462847 INFO::Done
2025-10-24 21:32:34.463685 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.467535 INFO::ASW Batch was 0.418184482129436 prior to batch effect correction and is now -0.0695016154029988 .
2025-10-24 21:32:34.468227 INFO::ASW Label was 0.294034494638502 prior to batch effect correction and is now 0.794114938425633 .
2025-10-24 21:32:34.469098 INFO::Total function execution time is 0.17293643951416 s and adjustment time is 0.153879880905151 s ( 88.98 )
2025-10-24 21:32:34.470007 INFO::Formatting Data.
2025-10-24 21:32:34.470667 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:34.471613 INFO::Removing potential empty rows and columns
2025-10-24 21:32:34.472675 INFO::Found 0 missing values.
2025-10-24 21:32:34.477041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:34.477639 INFO::Done
2025-10-24 21:32:34.47819 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:34.481482 INFO::Starting hierarchical adjustment
2025-10-24 21:32:34.482275 INFO::Found 5 batches.
2025-10-24 21:32:34.482859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:34.48352 INFO::Using default BPPARAM
2025-10-24 21:32:34.484075 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.637581 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.639417 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.659477 INFO::Done
2025-10-24 21:32:34.660427 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.664 INFO::ASW Batch was 0.418184482129436 prior to batch effect correction and is now -0.0695016154029988 .
2025-10-24 21:32:34.664707 INFO::ASW Label was 0.294034494638502 prior to batch effect correction and is now 0.794114938425633 .
2025-10-24 21:32:34.665656 INFO::Total function execution time is 0.195647478103638 s and adjustment time is 0.17729377746582 s ( 90.62 )
2025-10-24 21:32:34.680473 INFO::Formatting Data.
2025-10-24 21:32:34.681341 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:34.682398 INFO::Removing potential empty rows and columns
2025-10-24 21:32:34.683524 INFO::Found 0 missing values.
2025-10-24 21:32:34.686434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:34.687023 INFO::Done
2025-10-24 21:32:34.687598 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:34.690796 INFO::Starting hierarchical adjustment
2025-10-24 21:32:34.691568 INFO::Found 2 batches.
2025-10-24 21:32:34.69215 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:34.692828 INFO::Using default BPPARAM
2025-10-24 21:32:34.693423 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.694425 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.71051 INFO::Done
2025-10-24 21:32:34.711279 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.714443 INFO::ASW Batch was 0.40758652919719 prior to batch effect correction and is now 5.08380238067131e-06 .
2025-10-24 21:32:34.715079 INFO::ASW Label was 0.659251455937933 prior to batch effect correction and is now 0.915849671670248 .
2025-10-24 21:32:34.715922 INFO::Total function execution time is 0.035531759262085 s and adjustment time is 0.0190742015838623 s ( 53.68 )
2025-10-24 21:32:34.716757 INFO::Formatting Data.
2025-10-24 21:32:34.71743 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:34.718365 INFO::Removing potential empty rows and columns
2025-10-24 21:32:34.719408 INFO::Found 0 missing values.
2025-10-24 21:32:34.722232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:34.722814 INFO::Done
2025-10-24 21:32:34.723378 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:34.726461 INFO::Starting hierarchical adjustment
2025-10-24 21:32:34.727209 INFO::Found 2 batches.
2025-10-24 21:32:34.727756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:34.728403 INFO::Using default BPPARAM
2025-10-24 21:32:34.728948 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.729886 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-24 21:32:34.745361 INFO::Done
2025-10-24 21:32:34.746078 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.749227 INFO::ASW Batch was 0.40758652919719 prior to batch effect correction and is now 5.08380238067131e-06 .
2025-10-24 21:32:34.749863 INFO::ASW Label was 0.659251455937933 prior to batch effect correction and is now 0.915849671670248 .
2025-10-24 21:32:34.750707 INFO::Total function execution time is 0.0339608192443848 s and adjustment time is 0.018298864364624 s ( 53.88 )
2025-10-24 21:32:34.762364 INFO::Formatting Data.
2025-10-24 21:32:34.763137 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:34.764093 INFO::Removing potential empty rows and columns
2025-10-24 21:32:34.765096 INFO::Found 0 missing values.
2025-10-24 21:32:34.76734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:34.767898 INFO::Done
2025-10-24 21:32:34.768442 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:34.77046 INFO::Starting hierarchical adjustment
2025-10-24 21:32:34.771197 INFO::Found 2 batches.
2025-10-24 21:32:34.771748 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:34.772382 INFO::Using default BPPARAM
2025-10-24 21:32:34.772921 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.773867 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-24 21:32:34.807147 INFO::Done
2025-10-24 21:32:34.80787 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.809918 INFO::ASW Batch was 0.263575452124641 prior to batch effect correction and is now -0.0751823427196971 .
2025-10-24 21:32:34.810775 INFO::Total function execution time is 0.0485799312591553 s and adjustment time is 0.0360727310180664 s ( 74.25 )
2025-10-24 21:32:34.822859 INFO::Formatting Data.
2025-10-24 21:32:34.823649 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:34.824589 INFO::Removing potential empty rows and columns
2025-10-24 21:32:34.825649 INFO::Found 0 missing values.
2025-10-24 21:32:34.826838 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-24 21:32:34.831603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:34.832238 INFO::Done
2025-10-24 21:32:34.832778 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:34.835921 INFO::Starting hierarchical adjustment
2025-10-24 21:32:34.836685 INFO::Found 2 batches.
2025-10-24 21:32:34.837244 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:34.837875 INFO::Using default BPPARAM
2025-10-24 21:32:34.838451 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.839464 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-24 21:32:34.856737 INFO::Done
2025-10-24 21:32:34.857457 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.86053 INFO::ASW Batch was 0.898208534393814 prior to batch effect correction and is now 0.00711358702418994 .
2025-10-24 21:32:34.861168 INFO::ASW Label was 0.0923646125298756 prior to batch effect correction and is now 0.755328525738234 .
2025-10-24 21:32:34.861964 INFO::Total function execution time is 0.0391769409179688 s and adjustment time is 0.0201783180236816 s ( 51.51 )
2025-10-24 21:32:34.8628 INFO::Formatting Data.
2025-10-24 21:32:34.863456 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:34.86442 INFO::Removing potential empty rows and columns
2025-10-24 21:32:34.865473 INFO::Found 0 missing values.
2025-10-24 21:32:34.866447 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-24 21:32:34.871098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:34.871674 INFO::Done
2025-10-24 21:32:34.872229 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:34.875276 INFO::Starting hierarchical adjustment
2025-10-24 21:32:34.875992 INFO::Found 2 batches.
2025-10-24 21:32:34.876562 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:34.87721 INFO::Using default BPPARAM
2025-10-24 21:32:34.877761 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:34.878724 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-24 21:32:34.895544 INFO::Done
2025-10-24 21:32:34.896241 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:34.899286 INFO::ASW Batch was 0.898208534393814 prior to batch effect correction and is now 0.00711358702418994 .
2025-10-24 21:32:34.899895 INFO::ASW Label was 0.0923646125298756 prior to batch effect correction and is now 0.755328525738234 .
2025-10-24 21:32:34.900733 INFO::Total function execution time is 0.0379331111907959 s and adjustment time is 0.01969313621521 s ( 51.92 )
2025-10-24 21:32:35.114359 INFO::Formatting Data.
2025-10-24 21:32:35.115215 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:35.116153 INFO::Removing potential empty rows and columns
2025-10-24 21:32:35.117246 INFO::Found 0 missing values.
2025-10-24 21:32:35.12043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:35.121003 INFO::Done
2025-10-24 21:32:35.12156 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:35.12372 INFO::Starting hierarchical adjustment
2025-10-24 21:32:35.12447 INFO::Found 3 batches.
2025-10-24 21:32:35.12504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:35.125679 INFO::Using default BPPARAM
2025-10-24 21:32:35.126375 INFO::Processing subtree level 1
2025-10-24 21:32:35.215837 INFO::Adjusting the last 1 batches sequentially
2025-10-24 21:32:35.21771 INFO::Done
2025-10-24 21:32:35.218373 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:35.220994 INFO::ASW Batch was -0.0229965851705852 prior to batch effect correction and is now -0.0229965851705852 .
2025-10-24 21:32:35.221967 INFO::Total function execution time is 0.107712030410767 s and adjustment time is 0.0933859348297119 s ( 86.7 )
2025-10-24 21:32:35.223084 INFO::Formatting Data.
2025-10-24 21:32:35.223769 INFO::Typecasting input to dataframe.
2025-10-24 21:32:35.224551 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:35.225498 INFO::Removing potential empty rows and columns
2025-10-24 21:32:35.226643 INFO::Found 0 missing values.
2025-10-24 21:32:35.229849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:35.230429 INFO::Done
2025-10-24 21:32:35.230977 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:35.23302 INFO::Starting hierarchical adjustment
2025-10-24 21:32:35.233763 INFO::Found 3 batches.
2025-10-24 21:32:35.234316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:35.234951 INFO::Using default BPPARAM
2025-10-24 21:32:35.235558 INFO::Processing subtree level 1
2025-10-24 21:32:35.320487 INFO::Adjusting the last 1 batches sequentially
2025-10-24 21:32:35.322279 INFO::Done
2025-10-24 21:32:35.322939 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:35.325479 INFO::ASW Batch was -0.0229965851705852 prior to batch effect correction and is now -0.0229965851705852 .
2025-10-24 21:32:35.326472 INFO::Total function execution time is 0.103355407714844 s and adjustment time is 0.0886440277099609 s ( 85.77 )
2025-10-24 21:32:35.339419 INFO::Formatting Data.
2025-10-24 21:32:35.340234 INFO::Typecasting input to dataframe.
2025-10-24 21:32:35.341085 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:35.342091 INFO::Removing potential empty rows and columns
2025-10-24 21:32:35.343187 INFO::Found 0 missing values.
2025-10-24 21:32:35.346245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:35.346807 INFO::Done
2025-10-24 21:32:35.347368 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:35.349493 INFO::Starting hierarchical adjustment
2025-10-24 21:32:35.350241 INFO::Found 3 batches.
2025-10-24 21:32:35.350782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:35.351448 INFO::Using default BPPARAM
2025-10-24 21:32:35.351993 INFO::Processing subtree level 1
2025-10-24 21:32:35.443154 INFO::Adjusting the last 1 batches sequentially
2025-10-24 21:32:35.445017 INFO::Done
2025-10-24 21:32:35.445694 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:35.448439 INFO::ASW Batch was 0.011292178202215 prior to batch effect correction and is now 0.011292178202215 .
2025-10-24 21:32:35.449455 INFO::Total function execution time is 0.110069513320923 s and adjustment time is 0.0949296951293945 s ( 86.25 )
2025-10-24 21:32:35.591095 INFO::Formatting Data.
2025-10-24 21:32:35.592077 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:35.593276 INFO::Removing potential empty rows and columns
2025-10-24 21:32:35.596082 INFO::Found 1000 missing values.
2025-10-24 21:32:35.615429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:35.616243 INFO::Done
2025-10-24 21:32:35.616827 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:35.622644 INFO::Starting hierarchical adjustment
2025-10-24 21:32:35.623487 INFO::Found 10 batches.
2025-10-24 21:32:35.624056 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:35.624708 INFO::Using default BPPARAM
2025-10-24 21:32:35.625289 INFO::Processing subtree level 1
2025-10-24 21:32:35.761852 INFO::Processing subtree level 2
2025-10-24 21:32:35.91802 INFO::Adjusting the last 1 batches sequentially
2025-10-24 21:32:35.921216 INFO::Done
2025-10-24 21:32:35.922051 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:35.928419 INFO::ASW Batch was 0.445499071729545 prior to batch effect correction and is now 0.445499071729545 .
2025-10-24 21:32:35.929193 INFO::ASW Label was 0.393480491187386 prior to batch effect correction and is now 0.393480491187386 .
2025-10-24 21:32:35.930254 INFO::Total function execution time is 0.339232921600342 s and adjustment time is 0.29784369468689 s ( 87.8 )
2025-10-24 21:32:35.931225 INFO::Formatting Data.
2025-10-24 21:32:35.931917 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:35.933308 INFO::Removing potential empty rows and columns
2025-10-24 21:32:35.936302 INFO::Found 1000 missing values.
2025-10-24 21:32:35.955909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:35.956811 INFO::Done
2025-10-24 21:32:35.957419 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:35.96333 INFO::Starting hierarchical adjustment
2025-10-24 21:32:35.964195 INFO::Found 10 batches.
2025-10-24 21:32:37.523095 INFO::Set up parallel execution backend with 2 workers
2025-10-24 21:32:37.526425 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-24 21:32:39.082689 INFO::Adjusting the last 2 batches sequentially
2025-10-24 21:32:39.084814 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-24 21:32:39.102721 INFO::Done
2025-10-24 21:32:39.103524 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:39.108659 INFO::ASW Batch was 0.445499071729545 prior to batch effect correction and is now 0.445499071729545 .
2025-10-24 21:32:39.109382 INFO::ASW Label was 0.393480491187386 prior to batch effect correction and is now 0.393480491187386 .
2025-10-24 21:32:39.110225 INFO::Total function execution time is 3.17902398109436 s and adjustment time is 3.13866949081421 s ( 98.73 )
2025-10-24 21:32:39.269533 INFO::Formatting Data.
2025-10-24 21:32:39.270489 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.271531 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.272697 INFO::Found 0 missing values.
2025-10-24 21:32:39.276531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.277153 INFO::Done
2025-10-24 21:32:39.277687 INFO::Acquiring quality metrics before batch effect correction.
2025-10-24 21:32:39.280702 INFO::Starting hierarchical adjustment
2025-10-24 21:32:39.281526 INFO::Found 3 batches.
2025-10-24 21:32:39.28207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-24 21:32:39.282697 INFO::Using default BPPARAM
2025-10-24 21:32:39.28324 INFO::Processing subtree level 1
2025-10-24 21:32:39.405802 INFO::Adjusting the last 1 batches sequentially
2025-10-24 21:32:39.407624 INFO::Done
2025-10-24 21:32:39.408334 INFO::Acquiring quality metrics after batch effect correction.
2025-10-24 21:32:39.411827 INFO::ASW Batch was 0.119204576728352 prior to batch effect correction and is now -0.130700549428114 .
2025-10-24 21:32:39.412525 INFO::ASW Label was -0.14789767227635 prior to batch effect correction and is now 0.0578062385254642 .
2025-10-24 21:32:39.413473 INFO::Total function execution time is 0.144017219543457 s and adjustment time is 0.126268625259399 s ( 87.68 )
2025-10-24 21:32:39.547461 INFO::Formatting Data.
2025-10-24 21:32:39.548458 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.549406 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.550513 INFO::Found 2 missing values.
2025-10-24 21:32:39.553397 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.553943 INFO::Done
2025-10-24 21:32:39.580678 INFO::Found NA in Reference column
2025-10-24 21:32:39.590017 INFO::Require at least two references per batch.
2025-10-24 21:32:39.610567 INFO::Formatting Data.
2025-10-24 21:32:39.611345 INFO::Recognized SummarizedExperiment
2025-10-24 21:32:39.611881 INFO::Typecasting input to dataframe.
2025-10-24 21:32:39.621429 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.622633 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.625972 INFO::Found 0 missing values.
2025-10-24 21:32:39.632394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.633024 INFO::Done
2025-10-24 21:32:39.647942 INFO::Formatting Data.
2025-10-24 21:32:39.648715 INFO::Recognized SummarizedExperiment
2025-10-24 21:32:39.649268 INFO::Typecasting input to dataframe.
2025-10-24 21:32:39.666185 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.667398 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.670734 INFO::Found 0 missing values.
2025-10-24 21:32:39.681026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.681724 INFO::Done
2025-10-24 21:32:39.697462 INFO::Formatting Data.
2025-10-24 21:32:39.698284 INFO::Recognized SummarizedExperiment
2025-10-24 21:32:39.698822 INFO::Typecasting input to dataframe.
2025-10-24 21:32:39.716583 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.717661 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.718754 INFO::Found 0 missing values.
2025-10-24 21:32:39.719696 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-24 21:32:39.724082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.724677 INFO::Done
2025-10-24 21:32:39.734391 INFO::Formatting Data.
2025-10-24 21:32:39.735286 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.73623 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.737263 INFO::Found 0 missing values.
2025-10-24 21:32:39.740098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.740664 INFO::Done
2025-10-24 21:32:39.751484 INFO::Formatting Data.
2025-10-24 21:32:39.752282 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.753201 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.754244 INFO::Found 0 missing values.
2025-10-24 21:32:39.757164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.757697 INFO::Done
2025-10-24 21:32:39.789269 INFO::Formatting Data.
2025-10-24 21:32:39.790337 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.791569 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.7929 INFO::Found 1 missing values.
2025-10-24 21:32:39.795824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.796494 INFO::Done
2025-10-24 21:32:39.818264 INFO::Formatting Data.
2025-10-24 21:32:39.819184 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.820129 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.821217 INFO::Found 2 missing values.
2025-10-24 21:32:39.82226 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-10-24 21:32:39.824754 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.825347 INFO::Done
2025-10-24 21:32:39.836351 INFO::Formatting Data.
2025-10-24 21:32:39.837253 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.838374 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.839442 INFO::Found 2 missing values.
2025-10-24 21:32:39.841223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.841814 INFO::Done
2025-10-24 21:32:39.853702 INFO::Formatting Data.
2025-10-24 21:32:39.854716 INFO::Typecasting input to dataframe.
2025-10-24 21:32:39.855701 INFO::Replacing NaNs with NAs.
2025-10-24 21:32:39.856699 INFO::Removing potential empty rows and columns
2025-10-24 21:32:39.857882 INFO::Found 0 missing values.
2025-10-24 21:32:39.860974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-24 21:32:39.861545 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.402 4.372 21.303
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.469 | 1.320 | 17.908 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.002 | 0.014 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.010 | 0.003 | 0.012 | |