Yannis Schumann
| Snapshot Date: 2026-05-13 13:45 -0400 (Wed, 13 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-14 11:32 -0400 (Thu, 14 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4893 |
| 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 174/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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: 1.9.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz |
| StartedAt: 2026-05-13 21:37:42 -0400 (Wed, 13 May 2026) |
| EndedAt: 2026-05-13 21:39:13 -0400 (Wed, 13 May 2026) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-14 01:37:42 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 24.188 1.305 17.303
* 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-3.24-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.9.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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")
2026-05-13 21:38:34.284517 INFO::Formatting Data.
2026-05-13 21:38:34.286045 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:34.298305 INFO::Removing potential empty rows and columns
2026-05-13 21:38:34.546239 INFO::Found 0 missing values.
2026-05-13 21:38:34.549718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:34.550413 INFO::Done
2026-05-13 21:38:34.550997 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:34.563338 INFO::Starting hierarchical adjustment
2026-05-13 21:38:34.564229 INFO::Found 3 batches.
2026-05-13 21:38:34.564841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:34.565967 INFO::Using default BPPARAM
2026-05-13 21:38:34.566556 INFO::Processing subtree level 1
2026-05-13 21:38:34.665724 INFO::Adjusting the last 1 batches sequentially
2026-05-13 21:38:34.667505 INFO::Done
2026-05-13 21:38:34.66821 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:34.67068 INFO::ASW Batch was -0.0772040347541721 prior to batch effect correction and is now -0.0772040347541721 .
2026-05-13 21:38:34.671762 INFO::Total function execution time is 0.388158798217773 s and adjustment time is 0.10343074798584 s ( 26.65 )
2026-05-13 21:38:34.68591 INFO::Formatting Data.
2026-05-13 21:38:34.686723 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:34.687651 INFO::Removing potential empty rows and columns
2026-05-13 21:38:34.688755 INFO::Found 0 missing values.
2026-05-13 21:38:34.68977 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.
2026-05-13 21:38:34.708947 INFO::Formatting Data.
2026-05-13 21:38:34.710156 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:34.711267 INFO::Removing potential empty rows and columns
2026-05-13 21:38:34.712567 INFO::Found 0 missing values.
2026-05-13 21:38:34.713693 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.
2026-05-13 21:38:34.731283 INFO::Formatting Data.
2026-05-13 21:38:34.732104 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:34.733004 INFO::Removing potential empty rows and columns
2026-05-13 21:38:34.73404 INFO::Found 0 missing values.
2026-05-13 21:38:34.734967 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.
2026-05-13 21:38:34.739351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:34.739944 INFO::Done
2026-05-13 21:38:34.740511 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:34.742906 INFO::Starting hierarchical adjustment
2026-05-13 21:38:34.743652 INFO::Found 2 batches.
2026-05-13 21:38:34.744208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:34.744954 INFO::Using default BPPARAM
2026-05-13 21:38:34.745553 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:34.746549 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-13 21:38:34.769648 INFO::Done
2026-05-13 21:38:34.770396 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:34.77243 INFO::ASW Batch was 0.00722230816764104 prior to batch effect correction and is now -0.122873758512311 .
2026-05-13 21:38:34.773242 INFO::Total function execution time is 0.0420148372650146 s and adjustment time is 0.0261099338531494 s ( 62.14 )
2026-05-13 21:38:34.776144 INFO::Formatting Data.
2026-05-13 21:38:34.776819 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:34.785636 INFO::Formatting Data.
2026-05-13 21:38:34.78642 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:34.787345 INFO::Removing potential empty rows and columns
2026-05-13 21:38:34.788479 INFO::Found 0 missing values.
2026-05-13 21:38:34.791453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:34.792039 INFO::Done
2026-05-13 21:38:34.792617 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:34.794726 INFO::Starting hierarchical adjustment
2026-05-13 21:38:34.795477 INFO::Found 2 batches.
2026-05-13 21:38:34.796058 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:34.796723 INFO::Using default BPPARAM
2026-05-13 21:38:34.797292 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:34.798285 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-13 21:38:34.81537 INFO::Done
2026-05-13 21:38:34.816238 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:34.818495 INFO::ASW Batch was -0.0858866132128968 prior to batch effect correction and is now -0.111385649040251 .
2026-05-13 21:38:34.81941 INFO::Total function execution time is 0.0337767601013184 s and adjustment time is 0.0200159549713135 s ( 59.26 )
2026-05-13 21:38:34.820687 INFO::Formatting Data.
2026-05-13 21:38:34.82142 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:34.82246 INFO::Removing potential empty rows and columns
2026-05-13 21:38:34.823637 INFO::Found 0 missing values.
2026-05-13 21:38:34.826844 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:34.827467 INFO::Done
2026-05-13 21:38:34.828053 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:34.830387 INFO::Starting hierarchical adjustment
2026-05-13 21:38:34.831228 INFO::Found 2 batches.
2026-05-13 21:38:34.831868 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:34.832571 INFO::Using default BPPARAM
2026-05-13 21:38:34.8332 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:34.834229 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-13 21:38:34.84971 INFO::Done
2026-05-13 21:38:34.850451 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:34.852505 INFO::ASW Batch was -0.0858866132128968 prior to batch effect correction and is now -0.111385649040251 .
2026-05-13 21:38:34.853311 INFO::Total function execution time is 0.0326452255249023 s and adjustment time is 0.0186333656311035 s ( 57.08 )
2026-05-13 21:38:38.130185 INFO::Formatting Data.
2026-05-13 21:38:38.130985 INFO::Recognized SummarizedExperiment
2026-05-13 21:38:38.131554 INFO::Typecasting input to dataframe.
2026-05-13 21:38:38.161366 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:38.162582 INFO::Removing potential empty rows and columns
2026-05-13 21:38:38.165863 INFO::Found 0 missing values.
2026-05-13 21:38:38.172144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:38.172732 INFO::Done
2026-05-13 21:38:38.173247 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:38.176531 INFO::Starting hierarchical adjustment
2026-05-13 21:38:38.177207 INFO::Found 2 batches.
2026-05-13 21:38:38.177743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:38.178774 INFO::Using default BPPARAM
2026-05-13 21:38:38.179288 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:38.180233 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-13 21:38:38.229798 INFO::Done
2026-05-13 21:38:38.230583 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:38.23387 INFO::ASW Batch was 0.0169793354344357 prior to batch effect correction and is now -0.0889523010387489 .
2026-05-13 21:38:38.23469 INFO::Total function execution time is 0.104781866073608 s and adjustment time is 0.0526962280273438 s ( 50.29 )
2026-05-13 21:38:38.251994 INFO::Formatting Data.
2026-05-13 21:38:38.25274 INFO::Recognized SummarizedExperiment
2026-05-13 21:38:38.253261 INFO::Typecasting input to dataframe.
2026-05-13 21:38:38.261599 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:38.262686 INFO::Removing potential empty rows and columns
2026-05-13 21:38:38.265918 INFO::Found 0 missing values.
2026-05-13 21:38:38.272119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:38.272677 INFO::Done
2026-05-13 21:38:38.273175 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:38.276431 INFO::Starting hierarchical adjustment
2026-05-13 21:38:38.277105 INFO::Found 2 batches.
2026-05-13 21:38:38.277629 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:38.278212 INFO::Using default BPPARAM
2026-05-13 21:38:38.278735 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:38.279651 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-13 21:38:38.303574 INFO::Done
2026-05-13 21:38:38.304363 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:38.307996 INFO::ASW Batch was -0.00346427087665087 prior to batch effect correction and is now -0.00346427087665087 .
2026-05-13 21:38:38.308883 INFO::Total function execution time is 0.0568537712097168 s and adjustment time is 0.0265524387359619 s ( 46.7 )
2026-05-13 21:38:38.32785 INFO::Formatting Data.
2026-05-13 21:38:38.328686 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:38.329623 INFO::Removing potential empty rows and columns
2026-05-13 21:38:38.330706 INFO::Found 0 missing values.
2026-05-13 21:38:38.333777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:38.334349 INFO::Done
2026-05-13 21:38:38.33492 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:38.337037 INFO::Starting hierarchical adjustment
2026-05-13 21:38:38.33778 INFO::Found 3 batches.
2026-05-13 21:38:38.338335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:38.338998 INFO::Using default BPPARAM
2026-05-13 21:38:38.339578 INFO::Processing subtree level 1
2026-05-13 21:38:38.477157 INFO::Adjusting the last 1 batches sequentially
2026-05-13 21:38:38.479145 INFO::Done
2026-05-13 21:38:38.479905 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:38.482605 INFO::ASW Batch was 0.0521272410142156 prior to batch effect correction and is now -0.182403907057346 .
2026-05-13 21:38:38.483617 INFO::Total function execution time is 0.155782222747803 s and adjustment time is 0.141489505767822 s ( 90.83 )
2026-05-13 21:38:38.498479 INFO::Skipping initial DF formatting
2026-05-13 21:38:38.499213 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:38.503629 INFO::Starting hierarchical adjustment
2026-05-13 21:38:38.504478 INFO::Found 5 batches.
2026-05-13 21:38:38.505072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:38.50576 INFO::Using default BPPARAM
2026-05-13 21:38:38.506341 INFO::Processing subtree level 1
2026-05-13 21:38:38.632735 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:38.634859 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-13 21:38:38.656642 INFO::Done
2026-05-13 21:38:38.657604 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:38.662421 INFO::ASW Batch was 0.482845425852896 prior to batch effect correction and is now 0.482845425852896 .
2026-05-13 21:38:38.663126 INFO::ASW Label was 0.393320693961399 prior to batch effect correction and is now 0.393320693961399 .
2026-05-13 21:38:38.664127 INFO::Total function execution time is 0.165699481964111 s and adjustment time is 0.152271747589111 s ( 91.9 )
2026-05-13 21:38:38.684838 INFO::Formatting Data.
2026-05-13 21:38:38.68593 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:38.687058 INFO::Removing potential empty rows and columns
2026-05-13 21:38:38.688269 INFO::Found 0 missing values.
2026-05-13 21:38:38.693267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:38.693965 INFO::Done
2026-05-13 21:38:38.694624 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:38.698165 INFO::Starting hierarchical adjustment
2026-05-13 21:38:38.699044 INFO::Found 5 batches.
2026-05-13 21:38:38.699696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:38.700446 INFO::Using default BPPARAM
2026-05-13 21:38:38.70108 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.
2026-05-13 21:38:38.816929 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:38.818952 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-13 21:38:38.837025 INFO::Done
2026-05-13 21:38:38.837955 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:38.841773 INFO::ASW Batch was 0.346469395166714 prior to batch effect correction and is now -0.050157735605625 .
2026-05-13 21:38:38.842493 INFO::ASW Label was 0.442884493085756 prior to batch effect correction and is now 0.792498814659317 .
2026-05-13 21:38:38.843427 INFO::Total function execution time is 0.158742189407349 s and adjustment time is 0.138102054595947 s ( 87 )
2026-05-13 21:38:38.844392 INFO::Formatting Data.
2026-05-13 21:38:38.845085 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:38.846084 INFO::Removing potential empty rows and columns
2026-05-13 21:38:38.847188 INFO::Found 0 missing values.
2026-05-13 21:38:38.851655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:38.852254 INFO::Done
2026-05-13 21:38:38.852825 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:38.856108 INFO::Starting hierarchical adjustment
2026-05-13 21:38:38.856874 INFO::Found 5 batches.
2026-05-13 21:38:38.857453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:38.858129 INFO::Using default BPPARAM
2026-05-13 21:38:38.858708 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.
2026-05-13 21:38:38.979263 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:38.981246 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-13 21:38:38.998321 INFO::Done
2026-05-13 21:38:38.999174 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.002849 INFO::ASW Batch was 0.346469395166714 prior to batch effect correction and is now -0.050157735605625 .
2026-05-13 21:38:39.003544 INFO::ASW Label was 0.442884493085756 prior to batch effect correction and is now 0.792498814659317 .
2026-05-13 21:38:39.004449 INFO::Total function execution time is 0.160070419311523 s and adjustment time is 0.141558170318604 s ( 88.43 )
2026-05-13 21:38:39.019192 INFO::Formatting Data.
2026-05-13 21:38:39.020044 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.02102 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.022086 INFO::Found 0 missing values.
2026-05-13 21:38:39.02633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.026977 INFO::Done
2026-05-13 21:38:39.027562 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.030833 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.031597 INFO::Found 5 batches.
2026-05-13 21:38:39.032179 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.032863 INFO::Using default BPPARAM
2026-05-13 21:38:39.033446 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.
2026-05-13 21:38:39.148016 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:39.150119 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-13 21:38:39.167585 INFO::Done
2026-05-13 21:38:39.168478 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.17215 INFO::ASW Batch was 0.410755464062298 prior to batch effect correction and is now -0.0528645410757098 .
2026-05-13 21:38:39.172838 INFO::ASW Label was 0.398469849263017 prior to batch effect correction and is now 0.799396789109959 .
2026-05-13 21:38:39.173769 INFO::Total function execution time is 0.154608249664307 s and adjustment time is 0.13607382774353 s ( 88.01 )
2026-05-13 21:38:39.174695 INFO::Formatting Data.
2026-05-13 21:38:39.175404 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.176399 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.177504 INFO::Found 0 missing values.
2026-05-13 21:38:39.182184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.183142 INFO::Done
2026-05-13 21:38:39.183816 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.187124 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.187901 INFO::Found 5 batches.
2026-05-13 21:38:39.188496 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.189165 INFO::Using default BPPARAM
2026-05-13 21:38:39.189747 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.
2026-05-13 21:38:39.308361 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:39.310276 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-13 21:38:39.326703 INFO::Done
2026-05-13 21:38:39.327479 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.330891 INFO::ASW Batch was 0.410755464062298 prior to batch effect correction and is now -0.0528645410757098 .
2026-05-13 21:38:39.331562 INFO::ASW Label was 0.398469849263017 prior to batch effect correction and is now 0.799396789109959 .
2026-05-13 21:38:39.332432 INFO::Total function execution time is 0.157730340957642 s and adjustment time is 0.138934135437012 s ( 88.08 )
2026-05-13 21:38:39.346668 INFO::Formatting Data.
2026-05-13 21:38:39.347509 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.348508 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.349613 INFO::Found 0 missing values.
2026-05-13 21:38:39.352489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.35313 INFO::Done
2026-05-13 21:38:39.353711 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.356818 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.357591 INFO::Found 2 batches.
2026-05-13 21:38:39.358167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.358859 INFO::Using default BPPARAM
2026-05-13 21:38:39.359441 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:39.360429 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-13 21:38:39.375533 INFO::Done
2026-05-13 21:38:39.376315 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.379673 INFO::ASW Batch was 0.634673393421064 prior to batch effect correction and is now -0.0339450792724468 .
2026-05-13 21:38:39.380344 INFO::ASW Label was 0.425736957281995 prior to batch effect correction and is now 0.902565502216806 .
2026-05-13 21:38:39.381246 INFO::Total function execution time is 0.0346500873565674 s and adjustment time is 0.0181019306182861 s ( 52.24 )
2026-05-13 21:38:39.382137 INFO::Formatting Data.
2026-05-13 21:38:39.382904 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.383887 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.384996 INFO::Found 0 missing values.
2026-05-13 21:38:39.388049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.388673 INFO::Done
2026-05-13 21:38:39.389248 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.392235 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.392981 INFO::Found 2 batches.
2026-05-13 21:38:39.393598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.394235 INFO::Using default BPPARAM
2026-05-13 21:38:39.394803 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:39.395759 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-13 21:38:39.410951 INFO::Done
2026-05-13 21:38:39.411726 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.414779 INFO::ASW Batch was 0.634673393421064 prior to batch effect correction and is now -0.0339450792724468 .
2026-05-13 21:38:39.415434 INFO::ASW Label was 0.425736957281995 prior to batch effect correction and is now 0.902565502216806 .
2026-05-13 21:38:39.416252 INFO::Total function execution time is 0.03413987159729 s and adjustment time is 0.0180840492248535 s ( 52.97 )
2026-05-13 21:38:39.42818 INFO::Formatting Data.
2026-05-13 21:38:39.429094 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.430077 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.431078 INFO::Found 0 missing values.
2026-05-13 21:38:39.433355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.433942 INFO::Done
2026-05-13 21:38:39.434504 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.436472 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.437212 INFO::Found 2 batches.
2026-05-13 21:38:39.437786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.438443 INFO::Using default BPPARAM
2026-05-13 21:38:39.439014 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:39.439955 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-13 21:38:39.472872 INFO::Done
2026-05-13 21:38:39.473678 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.47575 INFO::ASW Batch was -0.14485151649966 prior to batch effect correction and is now -0.160689166022113 .
2026-05-13 21:38:39.476631 INFO::Total function execution time is 0.0485274791717529 s and adjustment time is 0.0357661247253418 s ( 73.7 )
2026-05-13 21:38:39.489006 INFO::Formatting Data.
2026-05-13 21:38:39.489838 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.490766 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.491828 INFO::Found 0 missing values.
2026-05-13 21:38:39.493017 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.
2026-05-13 21:38:39.497742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.498322 INFO::Done
2026-05-13 21:38:39.49889 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.5019 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.50265 INFO::Found 2 batches.
2026-05-13 21:38:39.503205 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.503865 INFO::Using default BPPARAM
2026-05-13 21:38:39.504429 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:39.505384 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-13 21:38:39.522303 INFO::Done
2026-05-13 21:38:39.523072 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.526066 INFO::ASW Batch was 0.433442409105366 prior to batch effect correction and is now 0.0584955664748853 .
2026-05-13 21:38:39.526694 INFO::ASW Label was 0.64789042873895 prior to batch effect correction and is now 0.895733240864479 .
2026-05-13 21:38:39.527494 INFO::Total function execution time is 0.0385563373565674 s and adjustment time is 0.0197646617889404 s ( 51.26 )
2026-05-13 21:38:39.528319 INFO::Formatting Data.
2026-05-13 21:38:39.528978 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.529942 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.530959 INFO::Found 0 missing values.
2026-05-13 21:38:39.531915 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.
2026-05-13 21:38:39.536628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.537227 INFO::Done
2026-05-13 21:38:39.537806 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.540839 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.541582 INFO::Found 2 batches.
2026-05-13 21:38:39.542146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.542812 INFO::Using default BPPARAM
2026-05-13 21:38:39.543369 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:39.54433 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-13 21:38:39.561638 INFO::Done
2026-05-13 21:38:39.562434 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.565508 INFO::ASW Batch was 0.433442409105366 prior to batch effect correction and is now 0.0584955664748853 .
2026-05-13 21:38:39.566126 INFO::ASW Label was 0.64789042873895 prior to batch effect correction and is now 0.895733240864479 .
2026-05-13 21:38:39.566964 INFO::Total function execution time is 0.0386605262756348 s and adjustment time is 0.0201795101165771 s ( 52.2 )
2026-05-13 21:38:39.778769 INFO::Formatting Data.
2026-05-13 21:38:39.779627 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.780598 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.781709 INFO::Found 0 missing values.
2026-05-13 21:38:39.785074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.785692 INFO::Done
2026-05-13 21:38:39.786246 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.788415 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.789177 INFO::Found 3 batches.
2026-05-13 21:38:39.789757 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.790414 INFO::Using default BPPARAM
2026-05-13 21:38:39.790979 INFO::Processing subtree level 1
2026-05-13 21:38:39.884001 INFO::Adjusting the last 1 batches sequentially
2026-05-13 21:38:39.887218 INFO::Done
2026-05-13 21:38:39.888432 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:39.892601 INFO::ASW Batch was -0.0298849487166563 prior to batch effect correction and is now -0.0298849487166563 .
2026-05-13 21:38:39.894216 INFO::Total function execution time is 0.115360260009766 s and adjustment time is 0.0980937480926514 s ( 85.03 )
2026-05-13 21:38:39.895942 INFO::Formatting Data.
2026-05-13 21:38:39.896985 INFO::Typecasting input to dataframe.
2026-05-13 21:38:39.898246 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:39.899816 INFO::Removing potential empty rows and columns
2026-05-13 21:38:39.90163 INFO::Found 0 missing values.
2026-05-13 21:38:39.907079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:39.908089 INFO::Done
2026-05-13 21:38:39.90902 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:39.912485 INFO::Starting hierarchical adjustment
2026-05-13 21:38:39.913643 INFO::Found 3 batches.
2026-05-13 21:38:39.9145 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:39.915525 INFO::Using default BPPARAM
2026-05-13 21:38:39.916431 INFO::Processing subtree level 1
2026-05-13 21:38:40.033822 INFO::Adjusting the last 1 batches sequentially
2026-05-13 21:38:40.035996 INFO::Done
2026-05-13 21:38:40.036782 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:40.039707 INFO::ASW Batch was -0.0298849487166563 prior to batch effect correction and is now -0.0298849487166563 .
2026-05-13 21:38:40.040795 INFO::Total function execution time is 0.144925117492676 s and adjustment time is 0.12260103225708 s ( 84.6 )
2026-05-13 21:38:40.05559 INFO::Formatting Data.
2026-05-13 21:38:40.056597 INFO::Typecasting input to dataframe.
2026-05-13 21:38:40.057559 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:40.058589 INFO::Removing potential empty rows and columns
2026-05-13 21:38:40.059772 INFO::Found 0 missing values.
2026-05-13 21:38:40.062926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:40.063535 INFO::Done
2026-05-13 21:38:40.06409 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:40.066214 INFO::Starting hierarchical adjustment
2026-05-13 21:38:40.06697 INFO::Found 3 batches.
2026-05-13 21:38:40.067546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:40.068225 INFO::Using default BPPARAM
2026-05-13 21:38:40.068803 INFO::Processing subtree level 1
2026-05-13 21:38:40.160215 INFO::Adjusting the last 1 batches sequentially
2026-05-13 21:38:40.163303 INFO::Done
2026-05-13 21:38:40.164578 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:40.169044 INFO::ASW Batch was -0.0129839773870768 prior to batch effect correction and is now -0.0129839773870768 .
2026-05-13 21:38:40.170705 INFO::Total function execution time is 0.11505913734436 s and adjustment time is 0.0963807106018066 s ( 83.77 )
2026-05-13 21:38:40.402327 INFO::Formatting Data.
2026-05-13 21:38:40.403324 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:40.404583 INFO::Removing potential empty rows and columns
2026-05-13 21:38:40.407621 INFO::Found 1000 missing values.
2026-05-13 21:38:40.42824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:40.429225 INFO::Done
2026-05-13 21:38:40.429872 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:40.43576 INFO::Starting hierarchical adjustment
2026-05-13 21:38:40.436635 INFO::Found 10 batches.
2026-05-13 21:38:40.437225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:40.437925 INFO::Using default BPPARAM
2026-05-13 21:38:40.438537 INFO::Processing subtree level 1
2026-05-13 21:38:40.585917 INFO::Processing subtree level 2
2026-05-13 21:38:40.735619 INFO::Adjusting the last 1 batches sequentially
2026-05-13 21:38:40.737844 INFO::Done
2026-05-13 21:38:40.738642 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:40.744571 INFO::ASW Batch was 0.509830862157167 prior to batch effect correction and is now 0.509830862157167 .
2026-05-13 21:38:40.745264 INFO::ASW Label was 0.297851848327709 prior to batch effect correction and is now 0.297851848327709 .
2026-05-13 21:38:40.746282 INFO::Total function execution time is 0.34404444694519 s and adjustment time is 0.301361799240112 s ( 87.59 )
2026-05-13 21:38:40.747242 INFO::Formatting Data.
2026-05-13 21:38:40.747952 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:40.749312 INFO::Removing potential empty rows and columns
2026-05-13 21:38:40.752326 INFO::Found 1000 missing values.
2026-05-13 21:38:40.772617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:40.773523 INFO::Done
2026-05-13 21:38:40.774165 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:40.779974 INFO::Starting hierarchical adjustment
2026-05-13 21:38:40.780785 INFO::Found 10 batches.
2026-05-13 21:38:42.068668 INFO::Set up parallel execution backend with 2 workers
2026-05-13 21:38:42.082687 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-13 21:38:43.398204 INFO::Adjusting the last 2 batches sequentially
2026-05-13 21:38:43.401386 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-13 21:38:43.418229 INFO::Done
2026-05-13 21:38:43.418982 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:43.423823 INFO::ASW Batch was 0.509830862157167 prior to batch effect correction and is now 0.509830862157167 .
2026-05-13 21:38:43.42446 INFO::ASW Label was 0.297851848327709 prior to batch effect correction and is now 0.297851848327709 .
2026-05-13 21:38:43.425249 INFO::Total function execution time is 2.67805957794189 s and adjustment time is 2.63757467269897 s ( 98.49 )
2026-05-13 21:38:43.587965 INFO::Formatting Data.
2026-05-13 21:38:43.589015 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:43.590108 INFO::Removing potential empty rows and columns
2026-05-13 21:38:43.591301 INFO::Found 0 missing values.
2026-05-13 21:38:43.595304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:43.595919 INFO::Done
2026-05-13 21:38:43.596499 INFO::Acquiring quality metrics before batch effect correction.
2026-05-13 21:38:43.59954 INFO::Starting hierarchical adjustment
2026-05-13 21:38:43.600296 INFO::Found 3 batches.
2026-05-13 21:38:43.600893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-13 21:38:43.60162 INFO::Using default BPPARAM
2026-05-13 21:38:43.602221 INFO::Processing subtree level 1
2026-05-13 21:38:43.740546 INFO::Adjusting the last 1 batches sequentially
2026-05-13 21:38:43.742765 INFO::Done
2026-05-13 21:38:43.743526 INFO::Acquiring quality metrics after batch effect correction.
2026-05-13 21:38:43.74722 INFO::ASW Batch was 0.158823122592504 prior to batch effect correction and is now -0.153835746215337 .
2026-05-13 21:38:43.747926 INFO::ASW Label was -0.214767766233 prior to batch effect correction and is now -0.0865255443002977 .
2026-05-13 21:38:43.74896 INFO::Total function execution time is 0.161096096038818 s and adjustment time is 0.142589569091797 s ( 88.51 )
2026-05-13 21:38:43.905714 INFO::Formatting Data.
2026-05-13 21:38:43.906801 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:43.907961 INFO::Removing potential empty rows and columns
2026-05-13 21:38:43.909245 INFO::Found 2 missing values.
2026-05-13 21:38:43.912564 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:43.913178 INFO::Done
2026-05-13 21:38:43.943863 INFO::Found NA in Reference column
2026-05-13 21:38:43.954341 INFO::Require at least two references per batch.
2026-05-13 21:38:43.977408 INFO::Formatting Data.
2026-05-13 21:38:43.978358 INFO::Recognized SummarizedExperiment
2026-05-13 21:38:43.979496 INFO::Typecasting input to dataframe.
2026-05-13 21:38:43.990155 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:43.991513 INFO::Removing potential empty rows and columns
2026-05-13 21:38:43.995483 INFO::Found 0 missing values.
2026-05-13 21:38:44.003204 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.003896 INFO::Done
2026-05-13 21:38:44.021406 INFO::Formatting Data.
2026-05-13 21:38:44.022275 INFO::Recognized SummarizedExperiment
2026-05-13 21:38:44.022868 INFO::Typecasting input to dataframe.
2026-05-13 21:38:44.042574 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:44.044106 INFO::Removing potential empty rows and columns
2026-05-13 21:38:44.048334 INFO::Found 0 missing values.
2026-05-13 21:38:44.06076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.061578 INFO::Done
2026-05-13 21:38:44.078684 INFO::Formatting Data.
2026-05-13 21:38:44.079617 INFO::Recognized SummarizedExperiment
2026-05-13 21:38:44.080246 INFO::Typecasting input to dataframe.
2026-05-13 21:38:44.098633 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:44.099844 INFO::Removing potential empty rows and columns
2026-05-13 21:38:44.101086 INFO::Found 0 missing values.
2026-05-13 21:38:44.102097 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.
2026-05-13 21:38:44.10678 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.107389 INFO::Done
2026-05-13 21:38:44.118569 INFO::Formatting Data.
2026-05-13 21:38:44.119647 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:44.120694 INFO::Removing potential empty rows and columns
2026-05-13 21:38:44.121814 INFO::Found 0 missing values.
2026-05-13 21:38:44.12493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.125539 INFO::Done
2026-05-13 21:38:44.138236 INFO::Formatting Data.
2026-05-13 21:38:44.139138 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:44.140108 INFO::Removing potential empty rows and columns
2026-05-13 21:38:44.141283 INFO::Found 0 missing values.
2026-05-13 21:38:44.144468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.145052 INFO::Done
2026-05-13 21:38:44.177698 INFO::Formatting Data.
2026-05-13 21:38:44.178691 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:44.179866 INFO::Removing potential empty rows and columns
2026-05-13 21:38:44.181182 INFO::Found 1 missing values.
2026-05-13 21:38:44.184016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.184626 INFO::Done
2026-05-13 21:38:44.205656 INFO::Formatting Data.
2026-05-13 21:38:44.206597 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:44.207639 INFO::Removing potential empty rows and columns
2026-05-13 21:38:44.208737 INFO::Found 2 missing values.
2026-05-13 21:38:44.209764 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.
2026-05-13 21:38:44.212292 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.212987 INFO::Done
2026-05-13 21:38:44.223816 INFO::Formatting Data.
2026-05-13 21:38:44.224632 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:44.225562 INFO::Removing potential empty rows and columns
2026-05-13 21:38:44.226522 INFO::Found 2 missing values.
2026-05-13 21:38:44.228183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.228728 INFO::Done
2026-05-13 21:38:44.239748 INFO::Formatting Data.
2026-05-13 21:38:44.240679 INFO::Typecasting input to dataframe.
2026-05-13 21:38:44.241579 INFO::Replacing NaNs with NAs.
2026-05-13 21:38:44.242514 INFO::Removing potential empty rows and columns
2026-05-13 21:38:44.24361 INFO::Found 0 missing values.
2026-05-13 21:38:44.24656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-13 21:38:44.24711 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.014 4.045 21.658
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.188 | 1.305 | 17.303 | |
| compute_asw | 0.023 | 0.001 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.013 | |
| generate_data_covariables | 0.013 | 0.000 | 0.012 | |
| generate_dataset | 0.010 | 0.001 | 0.012 | |