Yannis Schumann
| Snapshot Date: 2025-08-18 13:45 -0400 (Mon, 18 Aug 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 2025-08-19 12:07 -0400 (Tue, 19 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
| 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 162/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-08-19 05:11:00 -0000 (Tue, 19 Aug 2025) |
| EndedAt: 2025-08-19 05:12:18 -0000 (Tue, 19 Aug 2025) |
| EllapsedTime: 78.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 27.078 1.402 19.793
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-08-19 05:12:02.003445 INFO::Formatting Data.
2025-08-19 05:12:02.005319 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:02.022781 INFO::Removing potential empty rows and columns
2025-08-19 05:12:02.406848 INFO::Found 0 missing values.
2025-08-19 05:12:02.411929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:02.412877 INFO::Done
2025-08-19 05:12:02.413687 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:02.429338 INFO::Starting hierarchical adjustment
2025-08-19 05:12:02.430528 INFO::Found 3 batches.
2025-08-19 05:12:02.431365 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:02.433031 INFO::Using default BPPARAM
2025-08-19 05:12:02.434034 INFO::Processing subtree level 1
2025-08-19 05:12:02.558986 INFO::Adjusting the last 1 batches sequentially
2025-08-19 05:12:02.561627 INFO::Done
2025-08-19 05:12:02.562634 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:02.566496 INFO::ASW Batch was -0.025107568278942 prior to batch effect correction and is now -0.025107568278942 .
2025-08-19 05:12:02.56825 INFO::Total function execution time is 0.565566539764404 s and adjustment time is 0.131346940994263 s ( 23.22 )
2025-08-19 05:12:02.589248 INFO::Formatting Data.
2025-08-19 05:12:02.590303 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:02.591652 INFO::Removing potential empty rows and columns
2025-08-19 05:12:02.593322 INFO::Found 0 missing values.
2025-08-19 05:12:02.594715 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.
2025-08-19 05:12:02.610422 INFO::Formatting Data.
2025-08-19 05:12:02.61151 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:02.612855 INFO::Removing potential empty rows and columns
2025-08-19 05:12:02.614437 INFO::Found 0 missing values.
2025-08-19 05:12:02.615827 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.
2025-08-19 05:12:02.638909 INFO::Formatting Data.
2025-08-19 05:12:02.639997 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:02.641331 INFO::Removing potential empty rows and columns
2025-08-19 05:12:02.642873 INFO::Found 0 missing values.
2025-08-19 05:12:02.644272 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.
2025-08-19 05:12:02.650988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:02.651932 INFO::Done
2025-08-19 05:12:02.652769 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:02.655702 INFO::Starting hierarchical adjustment
2025-08-19 05:12:02.656824 INFO::Found 2 batches.
2025-08-19 05:12:02.657637 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:02.658568 INFO::Using default BPPARAM
2025-08-19 05:12:02.659343 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:02.660919 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 05:12:02.702885 INFO::Done
2025-08-19 05:12:02.704049 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:02.707484 INFO::ASW Batch was -0.0605828429977958 prior to batch effect correction and is now -0.110378004624196 .
2025-08-19 05:12:02.708893 INFO::Total function execution time is 0.0699658393859863 s and adjustment time is 0.0462343692779541 s ( 66.08 )
2025-08-19 05:12:02.713496 INFO::Formatting Data.
2025-08-19 05:12:02.71462 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:02.728034 INFO::Formatting Data.
2025-08-19 05:12:02.729196 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:02.730608 INFO::Removing potential empty rows and columns
2025-08-19 05:12:02.732365 INFO::Found 0 missing values.
2025-08-19 05:12:02.737155 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:02.738149 INFO::Done
2025-08-19 05:12:02.739025 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:02.742469 INFO::Starting hierarchical adjustment
2025-08-19 05:12:02.743745 INFO::Found 2 batches.
2025-08-19 05:12:02.744647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:02.745697 INFO::Using default BPPARAM
2025-08-19 05:12:02.746575 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:02.748091 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 05:12:02.818586 INFO::Done
2025-08-19 05:12:02.819552 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:02.822489 INFO::ASW Batch was 0.190598671629079 prior to batch effect correction and is now -0.120770689596134 .
2025-08-19 05:12:02.823773 INFO::Total function execution time is 0.0957872867584229 s and adjustment time is 0.0751168727874756 s ( 78.42 )
2025-08-19 05:12:02.82541 INFO::Formatting Data.
2025-08-19 05:12:02.826359 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:02.82772 INFO::Removing potential empty rows and columns
2025-08-19 05:12:02.829384 INFO::Found 0 missing values.
2025-08-19 05:12:02.833932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:02.834853 INFO::Done
2025-08-19 05:12:02.835748 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:02.838748 INFO::Starting hierarchical adjustment
2025-08-19 05:12:02.83996 INFO::Found 2 batches.
2025-08-19 05:12:02.840811 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:02.841729 INFO::Using default BPPARAM
2025-08-19 05:12:02.842518 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:02.84394 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 05:12:02.866523 INFO::Done
2025-08-19 05:12:02.867457 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:02.870346 INFO::ASW Batch was 0.190598671629079 prior to batch effect correction and is now -0.120770689596134 .
2025-08-19 05:12:02.871576 INFO::Total function execution time is 0.0461058616638184 s and adjustment time is 0.0267853736877441 s ( 58.1 )
2025-08-19 05:12:06.77995 INFO::Formatting Data.
2025-08-19 05:12:06.780896 INFO::Recognized SummarizedExperiment
2025-08-19 05:12:06.781605 INFO::Typecasting input to dataframe.
2025-08-19 05:12:06.824171 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:06.82583 INFO::Removing potential empty rows and columns
2025-08-19 05:12:06.83111 INFO::Found 0 missing values.
2025-08-19 05:12:06.841703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:06.842657 INFO::Done
2025-08-19 05:12:06.843487 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:06.848544 INFO::Starting hierarchical adjustment
2025-08-19 05:12:06.849734 INFO::Found 2 batches.
2025-08-19 05:12:06.850558 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:06.852046 INFO::Using default BPPARAM
2025-08-19 05:12:06.852914 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:06.854357 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 05:12:06.9374 INFO::Done
2025-08-19 05:12:06.938419 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:06.94362 INFO::ASW Batch was 0.0093600852968379 prior to batch effect correction and is now -0.0891152453251906 .
2025-08-19 05:12:06.944944 INFO::Total function execution time is 0.165381193161011 s and adjustment time is 0.0878849029541016 s ( 53.14 )
2025-08-19 05:12:06.972462 INFO::Formatting Data.
2025-08-19 05:12:06.973493 INFO::Recognized SummarizedExperiment
2025-08-19 05:12:06.974273 INFO::Typecasting input to dataframe.
2025-08-19 05:12:06.987585 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:06.989218 INFO::Removing potential empty rows and columns
2025-08-19 05:12:06.994415 INFO::Found 0 missing values.
2025-08-19 05:12:07.005208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:07.006152 INFO::Done
2025-08-19 05:12:07.006959 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:07.012132 INFO::Starting hierarchical adjustment
2025-08-19 05:12:07.013364 INFO::Found 2 batches.
2025-08-19 05:12:07.014184 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:07.015082 INFO::Using default BPPARAM
2025-08-19 05:12:07.015921 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:07.017405 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 05:12:07.053478 INFO::Done
2025-08-19 05:12:07.054477 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:07.059725 INFO::ASW Batch was 0.000855775721363648 prior to batch effect correction and is now 0.000855775721363648 .
2025-08-19 05:12:07.061092 INFO::Total function execution time is 0.088554859161377 s and adjustment time is 0.0403439998626709 s ( 45.56 )
2025-08-19 05:12:07.089083 INFO::Formatting Data.
2025-08-19 05:12:07.090216 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:07.091598 INFO::Removing potential empty rows and columns
2025-08-19 05:12:07.093256 INFO::Found 0 missing values.
2025-08-19 05:12:07.098049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:07.099039 INFO::Done
2025-08-19 05:12:07.099967 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:07.103065 INFO::Starting hierarchical adjustment
2025-08-19 05:12:07.104317 INFO::Found 3 batches.
2025-08-19 05:12:07.105244 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:07.106192 INFO::Using default BPPARAM
2025-08-19 05:12:07.107057 INFO::Processing subtree level 1
2025-08-19 05:12:07.277617 INFO::Adjusting the last 1 batches sequentially
2025-08-19 05:12:07.280214 INFO::Done
2025-08-19 05:12:07.281254 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:07.285024 INFO::ASW Batch was -0.0727878686079648 prior to batch effect correction and is now -0.180946825058837 .
2025-08-19 05:12:07.286471 INFO::Total function execution time is 0.197410583496094 s and adjustment time is 0.17613959312439 s ( 89.22 )
2025-08-19 05:12:07.307308 INFO::Skipping initial DF formatting
2025-08-19 05:12:07.308392 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:07.314614 INFO::Starting hierarchical adjustment
2025-08-19 05:12:07.316128 INFO::Found 5 batches.
2025-08-19 05:12:07.317161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:07.318202 INFO::Using default BPPARAM
2025-08-19 05:12:07.31911 INFO::Processing subtree level 1
2025-08-19 05:12:07.586833 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:07.589497 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 05:12:07.618489 INFO::Done
2025-08-19 05:12:07.619485 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:07.62575 INFO::ASW Batch was 0.531305077567926 prior to batch effect correction and is now 0.531305077567926 .
2025-08-19 05:12:07.626687 INFO::ASW Label was 0.322899589131647 prior to batch effect correction and is now 0.322899589131647 .
2025-08-19 05:12:07.628032 INFO::Total function execution time is 0.320772886276245 s and adjustment time is 0.302676439285278 s ( 94.36 )
2025-08-19 05:12:07.728666 INFO::Formatting Data.
2025-08-19 05:12:07.729822 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:07.731141 INFO::Removing potential empty rows and columns
2025-08-19 05:12:07.732734 INFO::Found 0 missing values.
2025-08-19 05:12:07.739163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:07.740142 INFO::Done
2025-08-19 05:12:07.741038 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:07.745397 INFO::Starting hierarchical adjustment
2025-08-19 05:12:07.746767 INFO::Found 5 batches.
2025-08-19 05:12:07.747758 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:07.74877 INFO::Using default BPPARAM
2025-08-19 05:12:07.749583 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.
2025-08-19 05:12:07.914441 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:07.916801 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 05:12:07.942367 INFO::Done
2025-08-19 05:12:07.943366 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:07.948317 INFO::ASW Batch was 0.287482726085681 prior to batch effect correction and is now -0.100270767178701 .
2025-08-19 05:12:07.9493 INFO::ASW Label was 0.381151341164256 prior to batch effect correction and is now 0.906199097266966 .
2025-08-19 05:12:07.950508 INFO::Total function execution time is 0.221895694732666 s and adjustment time is 0.195868730545044 s ( 88.27 )
2025-08-19 05:12:07.951719 INFO::Formatting Data.
2025-08-19 05:12:07.952646 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:07.954122 INFO::Removing potential empty rows and columns
2025-08-19 05:12:07.955813 INFO::Found 0 missing values.
2025-08-19 05:12:07.962639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:07.963584 INFO::Done
2025-08-19 05:12:07.964388 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:07.968846 INFO::Starting hierarchical adjustment
2025-08-19 05:12:07.970069 INFO::Found 5 batches.
2025-08-19 05:12:07.970866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:07.971883 INFO::Using default BPPARAM
2025-08-19 05:12:07.972722 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.
2025-08-19 05:12:08.126677 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:08.129019 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 05:12:08.165569 INFO::Done
2025-08-19 05:12:08.167186 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:08.174304 INFO::ASW Batch was 0.287482726085681 prior to batch effect correction and is now -0.100270767178701 .
2025-08-19 05:12:08.17552 INFO::ASW Label was 0.381151341164256 prior to batch effect correction and is now 0.906199097266966 .
2025-08-19 05:12:08.177092 INFO::Total function execution time is 0.22520899772644 s and adjustment time is 0.195588827133179 s ( 86.85 )
2025-08-19 05:12:08.204129 INFO::Formatting Data.
2025-08-19 05:12:08.205498 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:08.207224 INFO::Removing potential empty rows and columns
2025-08-19 05:12:08.209349 INFO::Found 0 missing values.
2025-08-19 05:12:08.217721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:08.219075 INFO::Done
2025-08-19 05:12:08.220353 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:08.22631 INFO::Starting hierarchical adjustment
2025-08-19 05:12:08.227899 INFO::Found 5 batches.
2025-08-19 05:12:08.229043 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:08.230392 INFO::Using default BPPARAM
2025-08-19 05:12:08.231488 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.
2025-08-19 05:12:08.410905 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:08.413306 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 05:12:08.437963 INFO::Done
2025-08-19 05:12:08.43902 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:08.444159 INFO::ASW Batch was 0.395131785309263 prior to batch effect correction and is now -0.0597382529625613 .
2025-08-19 05:12:08.445277 INFO::ASW Label was 0.383474241442492 prior to batch effect correction and is now 0.737035615121634 .
2025-08-19 05:12:08.446564 INFO::Total function execution time is 0.242547988891602 s and adjustment time is 0.210414409637451 s ( 86.75 )
2025-08-19 05:12:08.447882 INFO::Formatting Data.
2025-08-19 05:12:08.448897 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:08.450261 INFO::Removing potential empty rows and columns
2025-08-19 05:12:08.451913 INFO::Found 0 missing values.
2025-08-19 05:12:08.458375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:08.459347 INFO::Done
2025-08-19 05:12:08.460289 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:08.464781 INFO::Starting hierarchical adjustment
2025-08-19 05:12:08.466079 INFO::Found 5 batches.
2025-08-19 05:12:08.466964 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:08.468021 INFO::Using default BPPARAM
2025-08-19 05:12:08.469009 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.
2025-08-19 05:12:08.633713 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:08.636312 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 05:12:08.66231 INFO::Done
2025-08-19 05:12:08.663466 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:08.669042 INFO::ASW Batch was 0.395131785309263 prior to batch effect correction and is now -0.0597382529625613 .
2025-08-19 05:12:08.670142 INFO::ASW Label was 0.383474241442492 prior to batch effect correction and is now 0.737035615121634 .
2025-08-19 05:12:08.671499 INFO::Total function execution time is 0.223573923110962 s and adjustment time is 0.196424245834351 s ( 87.86 )
2025-08-19 05:12:08.691649 INFO::Formatting Data.
2025-08-19 05:12:08.692737 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:08.694126 INFO::Removing potential empty rows and columns
2025-08-19 05:12:08.695716 INFO::Found 0 missing values.
2025-08-19 05:12:08.700096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:08.701086 INFO::Done
2025-08-19 05:12:08.701923 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:08.706395 INFO::Starting hierarchical adjustment
2025-08-19 05:12:08.707672 INFO::Found 2 batches.
2025-08-19 05:12:08.708542 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:08.709541 INFO::Using default BPPARAM
2025-08-19 05:12:08.710387 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:08.71185 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 05:12:08.734103 INFO::Done
2025-08-19 05:12:08.73507 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:08.739499 INFO::ASW Batch was 0.499458552691342 prior to batch effect correction and is now -0.0365369424818299 .
2025-08-19 05:12:08.740466 INFO::ASW Label was 0.597621373598375 prior to batch effect correction and is now 0.948004573366474 .
2025-08-19 05:12:08.741634 INFO::Total function execution time is 0.0500917434692383 s and adjustment time is 0.0267138481140137 s ( 53.33 )
2025-08-19 05:12:08.742796 INFO::Formatting Data.
2025-08-19 05:12:08.74377 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:08.745088 INFO::Removing potential empty rows and columns
2025-08-19 05:12:08.746605 INFO::Found 0 missing values.
2025-08-19 05:12:08.750843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:08.751807 INFO::Done
2025-08-19 05:12:08.75262 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:08.756974 INFO::Starting hierarchical adjustment
2025-08-19 05:12:08.758127 INFO::Found 2 batches.
2025-08-19 05:12:08.758949 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:08.759895 INFO::Using default BPPARAM
2025-08-19 05:12:08.760706 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:08.762143 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 05:12:08.784066 INFO::Done
2025-08-19 05:12:08.785089 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:08.789472 INFO::ASW Batch was 0.499458552691342 prior to batch effect correction and is now -0.0365369424818299 .
2025-08-19 05:12:08.790448 INFO::ASW Label was 0.597621373598375 prior to batch effect correction and is now 0.948004573366474 .
2025-08-19 05:12:08.791658 INFO::Total function execution time is 0.048835277557373 s and adjustment time is 0.0261363983154297 s ( 53.52 )
2025-08-19 05:12:08.808698 INFO::Formatting Data.
2025-08-19 05:12:08.809822 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:08.811122 INFO::Removing potential empty rows and columns
2025-08-19 05:12:08.812537 INFO::Found 0 missing values.
2025-08-19 05:12:08.815934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:08.816865 INFO::Done
2025-08-19 05:12:08.81771 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:08.820583 INFO::Starting hierarchical adjustment
2025-08-19 05:12:08.821724 INFO::Found 2 batches.
2025-08-19 05:12:08.822539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:08.823518 INFO::Using default BPPARAM
2025-08-19 05:12:08.824367 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:08.825843 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 05:12:08.874188 INFO::Done
2025-08-19 05:12:08.875173 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:08.878105 INFO::ASW Batch was -0.0497798606534643 prior to batch effect correction and is now -0.116787280372236 .
2025-08-19 05:12:08.879463 INFO::Total function execution time is 0.070798397064209 s and adjustment time is 0.0526659488677979 s ( 74.39 )
2025-08-19 05:12:08.897312 INFO::Formatting Data.
2025-08-19 05:12:08.898389 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:08.899726 INFO::Removing potential empty rows and columns
2025-08-19 05:12:08.901304 INFO::Found 0 missing values.
2025-08-19 05:12:08.903095 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.
2025-08-19 05:12:08.910439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:08.91139 INFO::Done
2025-08-19 05:12:08.912259 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:08.916685 INFO::Starting hierarchical adjustment
2025-08-19 05:12:08.917931 INFO::Found 2 batches.
2025-08-19 05:12:08.918752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:08.919685 INFO::Using default BPPARAM
2025-08-19 05:12:08.920478 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:08.92196 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 05:12:08.947026 INFO::Done
2025-08-19 05:12:08.948096 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:08.952518 INFO::ASW Batch was 0.511294302722264 prior to batch effect correction and is now 0.0177266312948307 .
2025-08-19 05:12:08.953511 INFO::ASW Label was 0.324097434007028 prior to batch effect correction and is now 0.872558245155342 .
2025-08-19 05:12:08.954667 INFO::Total function execution time is 0.057426929473877 s and adjustment time is 0.0292999744415283 s ( 51.02 )
2025-08-19 05:12:08.955848 INFO::Formatting Data.
2025-08-19 05:12:08.956794 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:08.958182 INFO::Removing potential empty rows and columns
2025-08-19 05:12:08.959694 INFO::Found 0 missing values.
2025-08-19 05:12:08.961065 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.
2025-08-19 05:12:08.968087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:08.969074 INFO::Done
2025-08-19 05:12:08.969864 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:08.98115 INFO::Starting hierarchical adjustment
2025-08-19 05:12:08.982632 INFO::Found 2 batches.
2025-08-19 05:12:08.983632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:08.984656 INFO::Using default BPPARAM
2025-08-19 05:12:08.985605 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:08.987309 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 05:12:09.014605 INFO::Done
2025-08-19 05:12:09.015727 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:09.020497 INFO::ASW Batch was 0.511294302722264 prior to batch effect correction and is now 0.0177266312948307 .
2025-08-19 05:12:09.02155 INFO::ASW Label was 0.324097434007028 prior to batch effect correction and is now 0.872558245155342 .
2025-08-19 05:12:09.022833 INFO::Total function execution time is 0.0669572353363037 s and adjustment time is 0.03226637840271 s ( 48.19 )
2025-08-19 05:12:09.340045 INFO::Formatting Data.
2025-08-19 05:12:09.341064 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:09.342319 INFO::Removing potential empty rows and columns
2025-08-19 05:12:09.343879 INFO::Found 0 missing values.
2025-08-19 05:12:09.34835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:09.349279 INFO::Done
2025-08-19 05:12:09.350196 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:09.353058 INFO::Starting hierarchical adjustment
2025-08-19 05:12:09.354136 INFO::Found 3 batches.
2025-08-19 05:12:09.354884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:09.355795 INFO::Using default BPPARAM
2025-08-19 05:12:09.356561 INFO::Processing subtree level 1
2025-08-19 05:12:09.464078 INFO::Adjusting the last 1 batches sequentially
2025-08-19 05:12:09.466527 INFO::Done
2025-08-19 05:12:09.467507 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:09.471048 INFO::ASW Batch was -0.0195406962569708 prior to batch effect correction and is now -0.0195406962569708 .
2025-08-19 05:12:09.472494 INFO::Total function execution time is 0.132456541061401 s and adjustment time is 0.112595081329346 s ( 85.01 )
2025-08-19 05:12:09.474094 INFO::Formatting Data.
2025-08-19 05:12:09.47508 INFO::Typecasting input to dataframe.
2025-08-19 05:12:09.476248 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:09.4776 INFO::Removing potential empty rows and columns
2025-08-19 05:12:09.479336 INFO::Found 0 missing values.
2025-08-19 05:12:09.48407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:09.485029 INFO::Done
2025-08-19 05:12:09.485857 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:09.488805 INFO::Starting hierarchical adjustment
2025-08-19 05:12:09.489912 INFO::Found 3 batches.
2025-08-19 05:12:09.490705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:09.491677 INFO::Using default BPPARAM
2025-08-19 05:12:09.492497 INFO::Processing subtree level 1
2025-08-19 05:12:09.59778 INFO::Adjusting the last 1 batches sequentially
2025-08-19 05:12:09.600174 INFO::Done
2025-08-19 05:12:09.601173 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:09.604776 INFO::ASW Batch was -0.0195406962569708 prior to batch effect correction and is now -0.0195406962569708 .
2025-08-19 05:12:09.606309 INFO::Total function execution time is 0.132166147232056 s and adjustment time is 0.110464334487915 s ( 83.58 )
2025-08-19 05:12:09.625071 INFO::Formatting Data.
2025-08-19 05:12:09.626106 INFO::Typecasting input to dataframe.
2025-08-19 05:12:09.627296 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:09.628602 INFO::Removing potential empty rows and columns
2025-08-19 05:12:09.630157 INFO::Found 0 missing values.
2025-08-19 05:12:09.634472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:09.635346 INFO::Done
2025-08-19 05:12:09.636168 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:09.639014 INFO::Starting hierarchical adjustment
2025-08-19 05:12:09.640131 INFO::Found 3 batches.
2025-08-19 05:12:09.64095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:09.64184 INFO::Using default BPPARAM
2025-08-19 05:12:09.64267 INFO::Processing subtree level 1
2025-08-19 05:12:09.749477 INFO::Adjusting the last 1 batches sequentially
2025-08-19 05:12:09.752074 INFO::Done
2025-08-19 05:12:09.7531 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:09.756881 INFO::ASW Batch was -0.0493701385519876 prior to batch effect correction and is now -0.0493701385519876 .
2025-08-19 05:12:09.758356 INFO::Total function execution time is 0.133289575576782 s and adjustment time is 0.112131834030151 s ( 84.13 )
2025-08-19 05:12:09.944675 INFO::Formatting Data.
2025-08-19 05:12:09.945841 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:09.947625 INFO::Removing potential empty rows and columns
2025-08-19 05:12:09.952008 INFO::Found 1000 missing values.
2025-08-19 05:12:09.981805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:09.982785 INFO::Done
2025-08-19 05:12:09.983653 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:09.991658 INFO::Starting hierarchical adjustment
2025-08-19 05:12:09.992941 INFO::Found 10 batches.
2025-08-19 05:12:09.99382 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:09.994777 INFO::Using default BPPARAM
2025-08-19 05:12:09.995656 INFO::Processing subtree level 1
2025-08-19 05:12:10.159376 INFO::Processing subtree level 2
2025-08-19 05:12:10.344419 INFO::Adjusting the last 1 batches sequentially
2025-08-19 05:12:10.347322 INFO::Done
2025-08-19 05:12:10.348335 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:10.356661 INFO::ASW Batch was 0.46235483530568 prior to batch effect correction and is now 0.46235483530568 .
2025-08-19 05:12:10.357745 INFO::ASW Label was 0.362084957839059 prior to batch effect correction and is now 0.362084957839059 .
2025-08-19 05:12:10.359146 INFO::Total function execution time is 0.414495229721069 s and adjustment time is 0.354660749435425 s ( 85.56 )
2025-08-19 05:12:10.360484 INFO::Formatting Data.
2025-08-19 05:12:10.361544 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:10.363431 INFO::Removing potential empty rows and columns
2025-08-19 05:12:10.36774 INFO::Found 1000 missing values.
2025-08-19 05:12:10.399761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:10.400884 INFO::Done
2025-08-19 05:12:10.401761 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:10.410026 INFO::Starting hierarchical adjustment
2025-08-19 05:12:10.411282 INFO::Found 10 batches.
2025-08-19 05:12:11.598005 INFO::Set up parallel execution backend with 2 workers
2025-08-19 05:12:11.600628 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-19 05:12:13.004848 INFO::Adjusting the last 2 batches sequentially
2025-08-19 05:12:13.007139 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 05:12:13.033418 INFO::Done
2025-08-19 05:12:13.034452 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:13.041507 INFO::ASW Batch was 0.46235483530568 prior to batch effect correction and is now 0.46235483530568 .
2025-08-19 05:12:13.042416 INFO::ASW Label was 0.362084957839059 prior to batch effect correction and is now 0.362084957839059 .
2025-08-19 05:12:13.043539 INFO::Total function execution time is 2.68303942680359 s and adjustment time is 2.62238645553589 s ( 97.74 )
2025-08-19 05:12:13.238487 INFO::Formatting Data.
2025-08-19 05:12:13.239634 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:13.240999 INFO::Removing potential empty rows and columns
2025-08-19 05:12:13.242648 INFO::Found 0 missing values.
2025-08-19 05:12:13.248515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:13.249465 INFO::Done
2025-08-19 05:12:13.250252 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 05:12:13.25434 INFO::Starting hierarchical adjustment
2025-08-19 05:12:13.255555 INFO::Found 3 batches.
2025-08-19 05:12:13.256341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 05:12:13.257277 INFO::Using default BPPARAM
2025-08-19 05:12:13.258068 INFO::Processing subtree level 1
2025-08-19 05:12:13.397676 INFO::Adjusting the last 1 batches sequentially
2025-08-19 05:12:13.400455 INFO::Done
2025-08-19 05:12:13.401585 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 05:12:13.406858 INFO::ASW Batch was 0.226027455947959 prior to batch effect correction and is now -0.146770264002335 .
2025-08-19 05:12:13.407997 INFO::ASW Label was -0.195519312116101 prior to batch effect correction and is now -0.0867317799630278 .
2025-08-19 05:12:13.409544 INFO::Total function execution time is 0.171120166778564 s and adjustment time is 0.145124197006226 s ( 84.81 )
2025-08-19 05:12:13.610367 INFO::Formatting Data.
2025-08-19 05:12:13.611588 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:13.612993 INFO::Removing potential empty rows and columns
2025-08-19 05:12:13.614665 INFO::Found 2 missing values.
2025-08-19 05:12:13.619457 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:13.62043 INFO::Done
2025-08-19 05:12:13.665753 INFO::Found NA in Reference column
2025-08-19 05:12:13.681278 INFO::Require at least two references per batch.
2025-08-19 05:12:13.714542 INFO::Formatting Data.
2025-08-19 05:12:13.715647 INFO::Recognized SummarizedExperiment
2025-08-19 05:12:13.716486 INFO::Typecasting input to dataframe.
2025-08-19 05:12:13.731575 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:13.73321 INFO::Removing potential empty rows and columns
2025-08-19 05:12:13.746069 INFO::Found 0 missing values.
2025-08-19 05:12:13.7583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:13.759239 INFO::Done
2025-08-19 05:12:13.785338 INFO::Formatting Data.
2025-08-19 05:12:13.78632 INFO::Recognized SummarizedExperiment
2025-08-19 05:12:13.787092 INFO::Typecasting input to dataframe.
2025-08-19 05:12:13.814544 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:13.816222 INFO::Removing potential empty rows and columns
2025-08-19 05:12:13.821783 INFO::Found 0 missing values.
2025-08-19 05:12:13.83951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:13.840434 INFO::Done
2025-08-19 05:12:13.863699 INFO::Formatting Data.
2025-08-19 05:12:13.86468 INFO::Recognized SummarizedExperiment
2025-08-19 05:12:13.865491 INFO::Typecasting input to dataframe.
2025-08-19 05:12:13.890781 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:13.892195 INFO::Removing potential empty rows and columns
2025-08-19 05:12:13.893763 INFO::Found 0 missing values.
2025-08-19 05:12:13.895075 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.
2025-08-19 05:12:13.902006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:13.902915 INFO::Done
2025-08-19 05:12:13.918015 INFO::Formatting Data.
2025-08-19 05:12:13.919072 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:13.92036 INFO::Removing potential empty rows and columns
2025-08-19 05:12:13.921891 INFO::Found 0 missing values.
2025-08-19 05:12:13.926403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:13.92733 INFO::Done
2025-08-19 05:12:13.945337 INFO::Formatting Data.
2025-08-19 05:12:13.946406 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:13.947706 INFO::Removing potential empty rows and columns
2025-08-19 05:12:13.949186 INFO::Found 0 missing values.
2025-08-19 05:12:13.953732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:13.954608 INFO::Done
2025-08-19 05:12:14.001232 INFO::Formatting Data.
2025-08-19 05:12:14.002392 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:14.003977 INFO::Removing potential empty rows and columns
2025-08-19 05:12:14.005794 INFO::Found 1 missing values.
2025-08-19 05:12:14.010032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:14.011078 INFO::Done
2025-08-19 05:12:14.040446 INFO::Formatting Data.
2025-08-19 05:12:14.041583 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:14.04287 INFO::Removing potential empty rows and columns
2025-08-19 05:12:14.044293 INFO::Found 2 missing values.
2025-08-19 05:12:14.045667 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.
2025-08-19 05:12:14.049252 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:14.050159 INFO::Done
2025-08-19 05:12:14.065569 INFO::Formatting Data.
2025-08-19 05:12:14.066666 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:14.067976 INFO::Removing potential empty rows and columns
2025-08-19 05:12:14.069438 INFO::Found 2 missing values.
2025-08-19 05:12:14.071929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:14.072794 INFO::Done
2025-08-19 05:12:14.088885 INFO::Formatting Data.
2025-08-19 05:12:14.08997 INFO::Typecasting input to dataframe.
2025-08-19 05:12:14.091125 INFO::Replacing NaNs with NAs.
2025-08-19 05:12:14.092385 INFO::Removing potential empty rows and columns
2025-08-19 05:12:14.093996 INFO::Found 0 missing values.
2025-08-19 05:12:14.098732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 05:12:14.099696 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.355 4.461 25.315
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.078 | 1.402 | 19.793 | |
| compute_asw | 0.031 | 0.004 | 0.035 | |
| count_existing | 0.017 | 0.000 | 0.017 | |
| generate_data_covariables | 0.016 | 0.000 | 0.015 | |
| generate_dataset | 0.014 | 0.000 | 0.014 | |