Yannis Schumann
| Snapshot Date: 2025-04-22 13:40 -0400 (Tue, 22 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_21 |
| git_last_commit: dedce04 |
| git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-24 13:02 -0400 (Thu, 24 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.4.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.4.0.tar.gz |
| StartedAt: 2025-04-22 23:50:13 -0400 (Tue, 22 Apr 2025) |
| EndedAt: 2025-04-22 23:52:29 -0400 (Tue, 22 Apr 2025) |
| EllapsedTime: 136.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.4.0'
* 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 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 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 8.8 0.53 17.8
* 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: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'BERT' ... ** this is package 'BERT' version '1.4.0' ** 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 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2025-04-22 23:51:18.044094 INFO::Formatting Data.
2025-04-22 23:51:18.046219 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:18.055128 INFO::Removing potential empty rows and columns
2025-04-22 23:51:18.271859 INFO::Found 0 missing values.
2025-04-22 23:51:18.276593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:18.277976 INFO::Done
2025-04-22 23:51:18.27917 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:18.294919 INFO::Starting hierarchical adjustment
2025-04-22 23:51:18.296023 INFO::Found 3 batches.
2025-04-22 23:51:18.29676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:18.29803 INFO::Using default BPPARAM
2025-04-22 23:51:18.298809 INFO::Processing subtree level 1
2025-04-22 23:51:20.990864 INFO::Adjusting the last 1 batches sequentially
2025-04-22 23:51:20.993023 INFO::Done
2025-04-22 23:51:20.994271 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:20.997647 INFO::ASW Batch was -0.0538055931321397 prior to batch effect correction and is now -0.0538055931321397 .
2025-04-22 23:51:20.999452 INFO::Total function execution time is 2.95567893981934 s and adjustment time is 2.69714379310608 s ( 91.25 )
2025-04-22 23:51:21.023311 INFO::Formatting Data.
2025-04-22 23:51:21.024373 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:21.025505 INFO::Removing potential empty rows and columns
2025-04-22 23:51:21.026654 INFO::Found 0 missing values.
2025-04-22 23:51:21.027789 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.
2025-04-22 23:51:21.036146 INFO::Formatting Data.
2025-04-22 23:51:21.037023 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:21.038008 INFO::Removing potential empty rows and columns
2025-04-22 23:51:21.039094 INFO::Found 0 missing values.
2025-04-22 23:51:21.040158 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.
2025-04-22 23:51:21.05696 INFO::Formatting Data.
2025-04-22 23:51:21.058462 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:21.060103 INFO::Removing potential empty rows and columns
2025-04-22 23:51:21.061866 INFO::Found 0 missing values.
2025-04-22 23:51:21.063535 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.
2025-04-22 23:51:21.069205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:21.07047 INFO::Done
2025-04-22 23:51:21.071604 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:21.074593 INFO::Starting hierarchical adjustment
2025-04-22 23:51:21.07593 INFO::Found 2 batches.
2025-04-22 23:51:21.077118 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:21.078358 INFO::Using default BPPARAM
2025-04-22 23:51:21.079475 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:21.081119 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:21.104798 INFO::Done
2025-04-22 23:51:21.106116 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:21.109172 INFO::ASW Batch was 0.005826873187862 prior to batch effect correction and is now -0.0967902900193413 .
2025-04-22 23:51:21.110613 INFO::Total function execution time is 0.0537397861480713 s and adjustment time is 0.0290288925170898 s ( 54.02 )
2025-04-22 23:51:21.114535 INFO::Formatting Data.
2025-04-22 23:51:21.115802 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:21.126008 INFO::Formatting Data.
2025-04-22 23:51:21.127336 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:21.128914 INFO::Removing potential empty rows and columns
2025-04-22 23:51:21.130554 INFO::Found 0 missing values.
2025-04-22 23:51:21.134224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:21.135356 INFO::Done
2025-04-22 23:51:21.136471 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:21.139526 INFO::Starting hierarchical adjustment
2025-04-22 23:51:21.140942 INFO::Found 2 batches.
2025-04-22 23:51:21.142063 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:21.143332 INFO::Using default BPPARAM
2025-04-22 23:51:21.144537 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:21.146262 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:21.164692 INFO::Done
2025-04-22 23:51:21.166061 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:21.169248 INFO::ASW Batch was -0.00157121818683525 prior to batch effect correction and is now -0.0975514487929383 .
2025-04-22 23:51:21.170709 INFO::Total function execution time is 0.0447390079498291 s and adjustment time is 0.0239169597625732 s ( 53.46 )
2025-04-22 23:51:21.172519 INFO::Formatting Data.
2025-04-22 23:51:21.17372 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:21.175324 INFO::Removing potential empty rows and columns
2025-04-22 23:51:21.177069 INFO::Found 0 missing values.
2025-04-22 23:51:21.180838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:21.181997 INFO::Done
2025-04-22 23:51:21.18312 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:21.18609 INFO::Starting hierarchical adjustment
2025-04-22 23:51:21.187391 INFO::Found 2 batches.
2025-04-22 23:51:21.188502 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:21.189685 INFO::Using default BPPARAM
2025-04-22 23:51:21.19082 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:21.192458 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:21.210609 INFO::Done
2025-04-22 23:51:21.211909 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:21.214972 INFO::ASW Batch was -0.00157121818683525 prior to batch effect correction and is now -0.0975514487929383 .
2025-04-22 23:51:21.21644 INFO::Total function execution time is 0.0439040660858154 s and adjustment time is 0.0233728885650635 s ( 53.24 )
2025-04-22 23:51:23.773576 INFO::Formatting Data.
2025-04-22 23:51:23.775047 INFO::Recognized SummarizedExperiment
2025-04-22 23:51:23.77632 INFO::Typecasting input to dataframe.
2025-04-22 23:51:23.821213 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:23.823441 INFO::Removing potential empty rows and columns
2025-04-22 23:51:23.827866 INFO::Found 0 missing values.
2025-04-22 23:51:23.833276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:23.834181 INFO::Done
2025-04-22 23:51:23.834929 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:23.838644 INFO::Starting hierarchical adjustment
2025-04-22 23:51:23.839559 INFO::Found 2 batches.
2025-04-22 23:51:23.840283 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:23.841556 INFO::Using default BPPARAM
2025-04-22 23:51:23.842327 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:23.843536 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:24.671638 INFO::Done
2025-04-22 23:51:24.672936 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:24.678516 INFO::ASW Batch was 0.00361196947356828 prior to batch effect correction and is now -0.0890348816208923 .
2025-04-22 23:51:24.680126 INFO::Total function execution time is 0.906934976577759 s and adjustment time is 0.832162141799927 s ( 91.76 )
2025-04-22 23:51:24.708105 INFO::Formatting Data.
2025-04-22 23:51:24.709467 INFO::Recognized SummarizedExperiment
2025-04-22 23:51:24.710627 INFO::Typecasting input to dataframe.
2025-04-22 23:51:24.722996 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:24.72501 INFO::Removing potential empty rows and columns
2025-04-22 23:51:24.729606 INFO::Found 0 missing values.
2025-04-22 23:51:24.738435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:24.739813 INFO::Done
2025-04-22 23:51:24.740995 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:24.746607 INFO::Starting hierarchical adjustment
2025-04-22 23:51:24.748046 INFO::Found 2 batches.
2025-04-22 23:51:24.749212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:24.750517 INFO::Using default BPPARAM
2025-04-22 23:51:24.751806 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:24.753859 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:24.791715 INFO::Done
2025-04-22 23:51:24.793148 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:24.79921 INFO::ASW Batch was -0.0189477881584458 prior to batch effect correction and is now -0.0189477881584458 .
2025-04-22 23:51:24.80089 INFO::Total function execution time is 0.0927460193634033 s and adjustment time is 0.0438120365142822 s ( 47.24 )
2025-04-22 23:51:24.83361 INFO::Formatting Data.
2025-04-22 23:51:24.835199 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:24.83696 INFO::Removing potential empty rows and columns
2025-04-22 23:51:24.838815 INFO::Found 0 missing values.
2025-04-22 23:51:24.843239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:24.844506 INFO::Done
2025-04-22 23:51:24.845703 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:24.848923 INFO::Starting hierarchical adjustment
2025-04-22 23:51:24.850331 INFO::Found 3 batches.
2025-04-22 23:51:24.851509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:24.852796 INFO::Using default BPPARAM
2025-04-22 23:51:24.853976 INFO::Processing subtree level 1
2025-04-22 23:51:35.313073 INFO::Adjusting the last 1 batches sequentially
2025-04-22 23:51:35.315061 INFO::Done
2025-04-22 23:51:35.315921 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:35.318137 INFO::ASW Batch was 0.0524645819543977 prior to batch effect correction and is now -0.119072286675774 .
2025-04-22 23:51:35.319091 INFO::Total function execution time is 10.4857099056244 s and adjustment time is 10.464940071106 s ( 99.8 )
2025-04-22 23:51:35.336713 INFO::Skipping initial DF formatting
2025-04-22 23:51:35.337648 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:35.341989 INFO::Starting hierarchical adjustment
2025-04-22 23:51:35.342992 INFO::Found 5 batches.
2025-04-22 23:51:35.343792 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:35.344611 INFO::Using default BPPARAM
2025-04-22 23:51:35.345502 INFO::Processing subtree level 1
2025-04-22 23:51:38.244349 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:38.246495 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:38.270905 INFO::Done
2025-04-22 23:51:38.272223 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:38.279092 INFO::ASW Batch was 0.543059948122446 prior to batch effect correction and is now 0.543059948122446 .
2025-04-22 23:51:38.280487 INFO::ASW Label was 0.392452886162609 prior to batch effect correction and is now 0.392452886162609 .
2025-04-22 23:51:38.282051 INFO::Total function execution time is 2.94533705711365 s and adjustment time is 2.92799997329712 s ( 99.41 )
2025-04-22 23:51:38.310885 INFO::Formatting Data.
2025-04-22 23:51:38.312342 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:38.313995 INFO::Removing potential empty rows and columns
2025-04-22 23:51:38.315767 INFO::Found 0 missing values.
2025-04-22 23:51:38.321406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:38.322701 INFO::Done
2025-04-22 23:51:38.323918 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:38.328694 INFO::Starting hierarchical adjustment
2025-04-22 23:51:38.330188 INFO::Found 5 batches.
2025-04-22 23:51:38.331383 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:38.33265 INFO::Using default BPPARAM
2025-04-22 23:51:38.333829 INFO::Processing subtree level 1
2025-04-22 23:51:41.311261 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:41.313263 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:41.33042 INFO::Done
2025-04-22 23:51:41.331671 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:41.335971 INFO::ASW Batch was 0.579627525299412 prior to batch effect correction and is now -0.0578586473762236 .
2025-04-22 23:51:41.337093 INFO::ASW Label was 0.275144542025092 prior to batch effect correction and is now 0.711223569905961 .
2025-04-22 23:51:41.338439 INFO::Total function execution time is 3.02767205238342 s and adjustment time is 3.00041699409485 s ( 99.1 )
2025-04-22 23:51:41.339823 INFO::Formatting Data.
2025-04-22 23:51:41.340931 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:41.34235 INFO::Removing potential empty rows and columns
2025-04-22 23:51:41.343944 INFO::Found 0 missing values.
2025-04-22 23:51:41.34964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:41.350752 INFO::Done
2025-04-22 23:51:41.351778 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:41.355946 INFO::Starting hierarchical adjustment
2025-04-22 23:51:41.357199 INFO::Found 5 batches.
2025-04-22 23:51:41.358207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:41.359318 INFO::Using default BPPARAM
2025-04-22 23:51:41.36033 INFO::Processing subtree level 1
2025-04-22 23:51:44.475918 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:44.477811 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:44.49572 INFO::Done
2025-04-22 23:51:44.496608 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:44.500136 INFO::ASW Batch was 0.579627525299412 prior to batch effect correction and is now -0.0578586473762236 .
2025-04-22 23:51:44.500945 INFO::ASW Label was 0.275144542025092 prior to batch effect correction and is now 0.711223569905961 .
2025-04-22 23:51:44.501978 INFO::Total function execution time is 3.16221404075623 s and adjustment time is 3.13870191574097 s ( 99.26 )
2025-04-22 23:51:44.524053 INFO::Formatting Data.
2025-04-22 23:51:44.525132 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:44.526254 INFO::Removing potential empty rows and columns
2025-04-22 23:51:44.527334 INFO::Found 0 missing values.
2025-04-22 23:51:44.530714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:44.531454 INFO::Done
2025-04-22 23:51:44.532169 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:44.535202 INFO::Starting hierarchical adjustment
2025-04-22 23:51:44.536097 INFO::Found 5 batches.
2025-04-22 23:51:44.536817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:44.537594 INFO::Using default BPPARAM
2025-04-22 23:51:44.538414 INFO::Processing subtree level 1
2025-04-22 23:51:47.602094 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:47.604167 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:47.623017 INFO::Done
2025-04-22 23:51:47.624247 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:47.628084 INFO::ASW Batch was 0.440124207333082 prior to batch effect correction and is now -0.0853241550548214 .
2025-04-22 23:51:47.629 INFO::ASW Label was 0.364121013539474 prior to batch effect correction and is now 0.77090211336185 .
2025-04-22 23:51:47.630017 INFO::Total function execution time is 3.10603904724121 s and adjustment time is 3.08698081970215 s ( 99.39 )
2025-04-22 23:51:47.631015 INFO::Formatting Data.
2025-04-22 23:51:47.631813 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:47.632922 INFO::Removing potential empty rows and columns
2025-04-22 23:51:47.634031 INFO::Found 0 missing values.
2025-04-22 23:51:47.637582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:47.63833 INFO::Done
2025-04-22 23:51:47.639035 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:47.642174 INFO::Starting hierarchical adjustment
2025-04-22 23:51:47.643217 INFO::Found 5 batches.
2025-04-22 23:51:47.64392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:47.644749 INFO::Using default BPPARAM
2025-04-22 23:51:47.645502 INFO::Processing subtree level 1
2025-04-22 23:51:50.624632 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:50.626668 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:50.643044 INFO::Done
2025-04-22 23:51:50.644309 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:50.648498 INFO::ASW Batch was 0.440124207333082 prior to batch effect correction and is now -0.0853241550548214 .
2025-04-22 23:51:50.649655 INFO::ASW Label was 0.364121013539474 prior to batch effect correction and is now 0.77090211336185 .
2025-04-22 23:51:50.651015 INFO::Total function execution time is 3.01996779441833 s and adjustment time is 2.99991106987 s ( 99.34 )
2025-04-22 23:51:50.672572 INFO::Formatting Data.
2025-04-22 23:51:50.673976 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:50.675544 INFO::Removing potential empty rows and columns
2025-04-22 23:51:50.677166 INFO::Found 0 missing values.
2025-04-22 23:51:50.680575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:50.681701 INFO::Done
2025-04-22 23:51:50.682785 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:50.686922 INFO::Starting hierarchical adjustment
2025-04-22 23:51:50.688302 INFO::Found 2 batches.
2025-04-22 23:51:50.689407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:50.690573 INFO::Using default BPPARAM
2025-04-22 23:51:50.691655 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:50.693251 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:50.709894 INFO::Done
2025-04-22 23:51:50.711181 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:50.715482 INFO::ASW Batch was 0.730930857564186 prior to batch effect correction and is now 0.0154501831542088 .
2025-04-22 23:51:50.716704 INFO::ASW Label was 0.320743159358945 prior to batch effect correction and is now 0.865165121505566 .
2025-04-22 23:51:50.718099 INFO::Total function execution time is 0.0456161499023438 s and adjustment time is 0.0217618942260742 s ( 47.71 )
2025-04-22 23:51:50.719534 INFO::Formatting Data.
2025-04-22 23:51:50.720744 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:50.722276 INFO::Removing potential empty rows and columns
2025-04-22 23:51:50.723868 INFO::Found 0 missing values.
2025-04-22 23:51:50.727335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:50.728448 INFO::Done
2025-04-22 23:51:50.729539 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:50.733825 INFO::Starting hierarchical adjustment
2025-04-22 23:51:50.735219 INFO::Found 2 batches.
2025-04-22 23:51:50.736345 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:50.737586 INFO::Using default BPPARAM
2025-04-22 23:51:50.738704 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:50.740413 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:50.760333 INFO::Done
2025-04-22 23:51:50.761727 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:50.766695 INFO::ASW Batch was 0.730930857564186 prior to batch effect correction and is now 0.0154501831542088 .
2025-04-22 23:51:50.768049 INFO::ASW Label was 0.320743159358945 prior to batch effect correction and is now 0.865165121505566 .
2025-04-22 23:51:50.769658 INFO::Total function execution time is 0.0500888824462891 s and adjustment time is 0.0252740383148193 s ( 50.46 )
2025-04-22 23:51:50.792486 INFO::Formatting Data.
2025-04-22 23:51:50.794004 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:50.795683 INFO::Removing potential empty rows and columns
2025-04-22 23:51:50.797354 INFO::Found 0 missing values.
2025-04-22 23:51:50.800687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:50.801874 INFO::Done
2025-04-22 23:51:50.803033 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:50.806106 INFO::Starting hierarchical adjustment
2025-04-22 23:51:50.807506 INFO::Found 2 batches.
2025-04-22 23:51:50.808653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:50.809918 INFO::Using default BPPARAM
2025-04-22 23:51:50.811084 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:50.812859 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:50.85519 INFO::Done
2025-04-22 23:51:50.856599 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:50.85996 INFO::ASW Batch was -0.0073708625391092 prior to batch effect correction and is now -0.124323775877093 .
2025-04-22 23:51:50.86154 INFO::Total function execution time is 0.0691359043121338 s and adjustment time is 0.0478429794311523 s ( 69.2 )
2025-04-22 23:51:50.885385 INFO::Formatting Data.
2025-04-22 23:51:50.886885 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:50.888651 INFO::Removing potential empty rows and columns
2025-04-22 23:51:50.890532 INFO::Found 0 missing values.
2025-04-22 23:51:50.892554 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.
2025-04-22 23:51:50.899384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:50.900779 INFO::Done
2025-04-22 23:51:50.902033 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:50.907006 INFO::Starting hierarchical adjustment
2025-04-22 23:51:50.908618 INFO::Found 2 batches.
2025-04-22 23:51:50.909889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:50.911249 INFO::Using default BPPARAM
2025-04-22 23:51:50.912478 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:50.914337 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:50.938108 INFO::Done
2025-04-22 23:51:50.939616 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:50.944713 INFO::ASW Batch was 0.448704168615993 prior to batch effect correction and is now 0.0548673322759516 .
2025-04-22 23:51:50.946064 INFO::ASW Label was 0.621957463417494 prior to batch effect correction and is now 0.891429768505057 .
2025-04-22 23:51:50.94767 INFO::Total function execution time is 0.0623910427093506 s and adjustment time is 0.0297110080718994 s ( 47.62 )
2025-04-22 23:51:50.949177 INFO::Formatting Data.
2025-04-22 23:51:50.950508 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:50.95234 INFO::Removing potential empty rows and columns
2025-04-22 23:51:50.954234 INFO::Found 0 missing values.
2025-04-22 23:51:50.956024 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.
2025-04-22 23:51:50.963104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:50.964472 INFO::Done
2025-04-22 23:51:50.965768 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:50.970884 INFO::Starting hierarchical adjustment
2025-04-22 23:51:50.972458 INFO::Found 2 batches.
2025-04-22 23:51:50.973699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:50.975022 INFO::Using default BPPARAM
2025-04-22 23:51:50.976277 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:51:50.978188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:51:51.002494 INFO::Done
2025-04-22 23:51:51.003932 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:51.008984 INFO::ASW Batch was 0.448704168615993 prior to batch effect correction and is now 0.0548673322759516 .
2025-04-22 23:51:51.010294 INFO::ASW Label was 0.621957463417494 prior to batch effect correction and is now 0.891429768505057 .
2025-04-22 23:51:51.011848 INFO::Total function execution time is 0.0626530647277832 s and adjustment time is 0.0302801132202148 s ( 48.33 )
2025-04-22 23:51:51.24826 INFO::Formatting Data.
2025-04-22 23:51:51.249333 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:51.250545 INFO::Removing potential empty rows and columns
2025-04-22 23:51:51.251938 INFO::Found 0 missing values.
2025-04-22 23:51:51.255349 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:51.256213 INFO::Done
2025-04-22 23:51:51.257068 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:51.259675 INFO::Starting hierarchical adjustment
2025-04-22 23:51:51.260767 INFO::Found 3 batches.
2025-04-22 23:51:51.261609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:51.262593 INFO::Using default BPPARAM
2025-04-22 23:51:51.263443 INFO::Processing subtree level 1
2025-04-22 23:51:54.061653 INFO::Adjusting the last 1 batches sequentially
2025-04-22 23:51:54.06381 INFO::Done
2025-04-22 23:51:54.065077 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:54.068108 INFO::ASW Batch was -0.0688339391019803 prior to batch effect correction and is now -0.0688339391019803 .
2025-04-22 23:51:54.069575 INFO::Total function execution time is 2.82134413719177 s and adjustment time is 2.80320596694946 s ( 99.36 )
2025-04-22 23:51:54.071178 INFO::Formatting Data.
2025-04-22 23:51:54.072365 INFO::Typecasting input to dataframe.
2025-04-22 23:51:54.073709 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:54.0752 INFO::Removing potential empty rows and columns
2025-04-22 23:51:54.076799 INFO::Found 0 missing values.
2025-04-22 23:51:54.080698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:54.081414 INFO::Done
2025-04-22 23:51:54.082089 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:54.08414 INFO::Starting hierarchical adjustment
2025-04-22 23:51:54.084983 INFO::Found 3 batches.
2025-04-22 23:51:54.085666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:54.086415 INFO::Using default BPPARAM
2025-04-22 23:51:54.087099 INFO::Processing subtree level 1
2025-04-22 23:51:56.821528 INFO::Adjusting the last 1 batches sequentially
2025-04-22 23:51:56.822975 INFO::Done
2025-04-22 23:51:56.823748 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:56.82572 INFO::ASW Batch was -0.0688339391019803 prior to batch effect correction and is now -0.0688339391019803 .
2025-04-22 23:51:56.826642 INFO::Total function execution time is 2.75555300712585 s and adjustment time is 2.73811292648315 s ( 99.37 )
2025-04-22 23:51:56.841819 INFO::Formatting Data.
2025-04-22 23:51:56.842769 INFO::Typecasting input to dataframe.
2025-04-22 23:51:56.843783 INFO::Replacing NaNs with NAs.
2025-04-22 23:51:56.844817 INFO::Removing potential empty rows and columns
2025-04-22 23:51:56.845945 INFO::Found 0 missing values.
2025-04-22 23:51:56.848641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:51:56.849349 INFO::Done
2025-04-22 23:51:56.850065 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:51:56.852073 INFO::Starting hierarchical adjustment
2025-04-22 23:51:56.853009 INFO::Found 3 batches.
2025-04-22 23:51:56.853714 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:51:56.854642 INFO::Using default BPPARAM
2025-04-22 23:51:56.855493 INFO::Processing subtree level 1
2025-04-22 23:51:59.525583 INFO::Adjusting the last 1 batches sequentially
2025-04-22 23:51:59.527762 INFO::Done
2025-04-22 23:51:59.52899 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:51:59.532119 INFO::ASW Batch was -0.12121815256761 prior to batch effect correction and is now -0.12121815256761 .
2025-04-22 23:51:59.533545 INFO::Total function execution time is 2.69174098968506 s and adjustment time is 2.67484283447266 s ( 99.37 )
2025-04-22 23:52:02.398438 INFO::Formatting Data.
2025-04-22 23:52:02.399981 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:02.401846 INFO::Removing potential empty rows and columns
2025-04-22 23:52:02.405712 INFO::Found 1000 missing values.
2025-04-22 23:52:02.429066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:02.430496 INFO::Done
2025-04-22 23:52:02.431763 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:52:02.441683 INFO::Starting hierarchical adjustment
2025-04-22 23:52:02.443328 INFO::Found 10 batches.
2025-04-22 23:52:02.444661 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:52:02.44597 INFO::Using default BPPARAM
2025-04-22 23:52:02.447185 INFO::Processing subtree level 1
2025-04-22 23:52:05.275162 INFO::Processing subtree level 2
2025-04-22 23:52:08.181968 INFO::Adjusting the last 1 batches sequentially
2025-04-22 23:52:08.184367 INFO::Done
2025-04-22 23:52:08.185658 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:52:08.194879 INFO::ASW Batch was 0.484139421427101 prior to batch effect correction and is now 0.484139421427101 .
2025-04-22 23:52:08.196258 INFO::ASW Label was 0.35990638775598 prior to batch effect correction and is now 0.35990638775598 .
2025-04-22 23:52:08.198018 INFO::Total function execution time is 5.79966688156128 s and adjustment time is 5.74129796028137 s ( 98.99 )
2025-04-22 23:52:08.1995 INFO::Formatting Data.
2025-04-22 23:52:08.200753 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:08.202561 INFO::Removing potential empty rows and columns
2025-04-22 23:52:08.206019 INFO::Found 1000 missing values.
2025-04-22 23:52:08.228036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:08.229409 INFO::Done
2025-04-22 23:52:08.230644 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:52:08.240227 INFO::Starting hierarchical adjustment
2025-04-22 23:52:08.241799 INFO::Found 10 batches.
2025-04-22 23:52:09.028747 INFO::Set up parallel execution backend with 2 workers
2025-04-22 23:52:09.030233 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-04-22 23:52:12.123366 INFO::Adjusting the last 2 batches sequentially
2025-04-22 23:52:12.125541 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-22 23:52:12.149831 INFO::Done
2025-04-22 23:52:12.151275 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:52:12.161069 INFO::ASW Batch was 0.484139421427101 prior to batch effect correction and is now 0.484139421427101 .
2025-04-22 23:52:12.162425 INFO::ASW Label was 0.35990638775598 prior to batch effect correction and is now 0.35990638775598 .
2025-04-22 23:52:12.163999 INFO::Total function execution time is 3.96448493003845 s and adjustment time is 3.90821599960327 s ( 98.58 )
2025-04-22 23:52:15.170982 INFO::Formatting Data.
2025-04-22 23:52:15.17212 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:15.173865 INFO::Removing potential empty rows and columns
2025-04-22 23:52:15.175733 INFO::Found 0 missing values.
2025-04-22 23:52:15.181074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:15.18233 INFO::Done
2025-04-22 23:52:15.183566 INFO::Acquiring quality metrics before batch effect correction.
2025-04-22 23:52:15.187976 INFO::Starting hierarchical adjustment
2025-04-22 23:52:15.189442 INFO::Found 3 batches.
2025-04-22 23:52:15.190659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-22 23:52:15.191972 INFO::Using default BPPARAM
2025-04-22 23:52:15.193196 INFO::Processing subtree level 1
2025-04-22 23:52:18.347563 INFO::Adjusting the last 1 batches sequentially
2025-04-22 23:52:18.34972 INFO::Done
2025-04-22 23:52:18.350969 INFO::Acquiring quality metrics after batch effect correction.
2025-04-22 23:52:18.355045 INFO::ASW Batch was 0.18309605257961 prior to batch effect correction and is now -0.156859054292221 .
2025-04-22 23:52:18.356303 INFO::ASW Label was -0.176434463933799 prior to batch effect correction and is now 0.125418893829632 .
2025-04-22 23:52:18.35781 INFO::Total function execution time is 3.1868908405304 s and adjustment time is 3.16048502922058 s ( 99.17 )
2025-04-22 23:52:18.545792 INFO::Formatting Data.
2025-04-22 23:52:18.546813 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.547892 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.549032 INFO::Found 2 missing values.
2025-04-22 23:52:18.551525 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.552259 INFO::Done
2025-04-22 23:52:18.593432 INFO::Found NA in Reference column
2025-04-22 23:52:18.607093 INFO::Require at least two references per batch.
2025-04-22 23:52:18.630448 INFO::Formatting Data.
2025-04-22 23:52:18.631382 INFO::Recognized SummarizedExperiment
2025-04-22 23:52:18.63211 INFO::Typecasting input to dataframe.
2025-04-22 23:52:18.639825 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.64111 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.64381 INFO::Found 0 missing values.
2025-04-22 23:52:18.648772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.649588 INFO::Done
2025-04-22 23:52:18.663913 INFO::Formatting Data.
2025-04-22 23:52:18.66482 INFO::Recognized SummarizedExperiment
2025-04-22 23:52:18.665532 INFO::Typecasting input to dataframe.
2025-04-22 23:52:18.681407 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.682729 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.685503 INFO::Found 0 missing values.
2025-04-22 23:52:18.693068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.693901 INFO::Done
2025-04-22 23:52:18.708363 INFO::Formatting Data.
2025-04-22 23:52:18.709302 INFO::Recognized SummarizedExperiment
2025-04-22 23:52:18.710471 INFO::Typecasting input to dataframe.
2025-04-22 23:52:18.724849 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.726028 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.727199 INFO::Found 0 missing values.
2025-04-22 23:52:18.728773 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.
2025-04-22 23:52:18.732909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.733653 INFO::Done
2025-04-22 23:52:18.748482 INFO::Formatting Data.
2025-04-22 23:52:18.749475 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.750517 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.751629 INFO::Found 0 missing values.
2025-04-22 23:52:18.754215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.754934 INFO::Done
2025-04-22 23:52:18.771512 INFO::Formatting Data.
2025-04-22 23:52:18.772506 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.773565 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.774713 INFO::Found 0 missing values.
2025-04-22 23:52:18.777341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.778074 INFO::Done
2025-04-22 23:52:18.822934 INFO::Formatting Data.
2025-04-22 23:52:18.823936 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.825094 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.826281 INFO::Found 1 missing values.
2025-04-22 23:52:18.828618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.829345 INFO::Done
2025-04-22 23:52:18.854213 INFO::Formatting Data.
2025-04-22 23:52:18.855197 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.856221 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.857274 INFO::Found 2 missing values.
2025-04-22 23:52:18.85835 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.
2025-04-22 23:52:18.86043 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.861146 INFO::Done
2025-04-22 23:52:18.874978 INFO::Formatting Data.
2025-04-22 23:52:18.875946 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.876997 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.87806 INFO::Found 2 missing values.
2025-04-22 23:52:18.879684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.8804 INFO::Done
2025-04-22 23:52:18.894926 INFO::Formatting Data.
2025-04-22 23:52:18.89588 INFO::Typecasting input to dataframe.
2025-04-22 23:52:18.89686 INFO::Replacing NaNs with NAs.
2025-04-22 23:52:18.897868 INFO::Removing potential empty rows and columns
2025-04-22 23:52:18.898944 INFO::Found 0 missing values.
2025-04-22 23:52:18.901488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-22 23:52:18.902209 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
29.26 1.68 75.71
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.80 | 0.53 | 17.80 | |
| compute_asw | 0.01 | 0.00 | 0.01 | |
| count_existing | 0.01 | 0.00 | 0.02 | |
| generate_data_covariables | 0.04 | 0.00 | 0.03 | |
| generate_dataset | 0.01 | 0.00 | 0.02 | |