Yannis Schumann
| Snapshot Date: 2025-01-19 12:27 -0500 (Sun, 19 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-20 12:16 -0500 (Mon, 20 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| 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 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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: 1.2.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-01-19 18:50:16 -0500 (Sun, 19 Jan 2025) |
| EndedAt: 2025-01-19 18:51:43 -0500 (Sun, 19 Jan 2025) |
| EllapsedTime: 86.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.864 1.807 18.373
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-01-19 18:51:07.825737 INFO::Formatting Data.
2025-01-19 18:51:07.82697 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:07.837351 INFO::Removing potential empty rows and columns
2025-01-19 18:51:08.070624 INFO::Found 0 missing values.
2025-01-19 18:51:08.073961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:08.074592 INFO::Done
2025-01-19 18:51:08.075115 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:08.086417 INFO::Starting hierarchical adjustment
2025-01-19 18:51:08.087256 INFO::Found 3 batches.
2025-01-19 18:51:08.087772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:08.088864 INFO::Using default BPPARAM
2025-01-19 18:51:08.089376 INFO::Processing subtree level 1
2025-01-19 18:51:08.182218 INFO::Adjusting the last 1 batches sequentially
2025-01-19 18:51:08.184002 INFO::Done
2025-01-19 18:51:08.184664 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:08.187128 INFO::ASW Batch was -0.0140841069798107 prior to batch effect correction and is now -0.0140841069798107 .
2025-01-19 18:51:08.188167 INFO::Total function execution time is 0.363065481185913 s and adjustment time is 0.0969078540802002 s ( 26.69 )
2025-01-19 18:51:08.201494 INFO::Formatting Data.
2025-01-19 18:51:08.202238 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:08.203108 INFO::Removing potential empty rows and columns
2025-01-19 18:51:08.204177 INFO::Found 0 missing values.
2025-01-19 18:51:08.205076 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.
2025-01-19 18:51:08.21551 INFO::Formatting Data.
2025-01-19 18:51:08.216179 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:08.216991 INFO::Removing potential empty rows and columns
2025-01-19 18:51:08.217973 INFO::Found 0 missing values.
2025-01-19 18:51:08.218844 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.
2025-01-19 18:51:08.234013 INFO::Formatting Data.
2025-01-19 18:51:08.234682 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:08.235487 INFO::Removing potential empty rows and columns
2025-01-19 18:51:08.236456 INFO::Found 0 missing values.
2025-01-19 18:51:08.237319 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.
2025-01-19 18:51:08.241637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:08.242151 INFO::Done
2025-01-19 18:51:08.242675 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:08.244599 INFO::Starting hierarchical adjustment
2025-01-19 18:51:08.245281 INFO::Found 2 batches.
2025-01-19 18:51:08.24577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:08.246371 INFO::Using default BPPARAM
2025-01-19 18:51:08.246874 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:08.247727 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:08.268715 INFO::Done
2025-01-19 18:51:08.26938 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:08.271306 INFO::ASW Batch was -0.0441917532695355 prior to batch effect correction and is now -0.12749147541531 .
2025-01-19 18:51:08.272053 INFO::Total function execution time is 0.0380973815917969 s and adjustment time is 0.0235419273376465 s ( 61.79 )
2025-01-19 18:51:08.27465 INFO::Formatting Data.
2025-01-19 18:51:08.275249 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:08.283698 INFO::Formatting Data.
2025-01-19 18:51:08.284376 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:08.285229 INFO::Removing potential empty rows and columns
2025-01-19 18:51:08.286231 INFO::Found 0 missing values.
2025-01-19 18:51:08.289057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:08.289629 INFO::Done
2025-01-19 18:51:08.290116 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:08.292104 INFO::Starting hierarchical adjustment
2025-01-19 18:51:08.292773 INFO::Found 2 batches.
2025-01-19 18:51:08.293293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:08.293868 INFO::Using default BPPARAM
2025-01-19 18:51:08.294407 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:08.295488 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:08.309865 INFO::Done
2025-01-19 18:51:08.310451 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:08.312338 INFO::ASW Batch was 0.0676584664672881 prior to batch effect correction and is now -0.11399827741415 .
2025-01-19 18:51:08.313085 INFO::Total function execution time is 0.0294311046600342 s and adjustment time is 0.0172100067138672 s ( 58.48 )
2025-01-19 18:51:08.314092 INFO::Formatting Data.
2025-01-19 18:51:08.314651 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:08.315455 INFO::Removing potential empty rows and columns
2025-01-19 18:51:08.316408 INFO::Found 0 missing values.
2025-01-19 18:51:08.319156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:08.319639 INFO::Done
2025-01-19 18:51:08.320125 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:08.322008 INFO::Starting hierarchical adjustment
2025-01-19 18:51:08.322649 INFO::Found 2 batches.
2025-01-19 18:51:08.323142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:08.323689 INFO::Using default BPPARAM
2025-01-19 18:51:08.324179 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:08.325004 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:08.339522 INFO::Done
2025-01-19 18:51:08.340162 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:08.342067 INFO::ASW Batch was 0.0676584664672881 prior to batch effect correction and is now -0.11399827741415 .
2025-01-19 18:51:08.342816 INFO::Total function execution time is 0.0287113189697266 s and adjustment time is 0.0169992446899414 s ( 59.21 )
2025-01-19 18:51:10.320384 INFO::Formatting Data.
2025-01-19 18:51:10.321051 INFO::Recognized SummarizedExperiment
2025-01-19 18:51:10.32152 INFO::Typecasting input to dataframe.
2025-01-19 18:51:10.350302 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:10.351427 INFO::Removing potential empty rows and columns
2025-01-19 18:51:10.35442 INFO::Found 0 missing values.
2025-01-19 18:51:10.359942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:10.360486 INFO::Done
2025-01-19 18:51:10.360928 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:10.363838 INFO::Starting hierarchical adjustment
2025-01-19 18:51:10.364464 INFO::Found 2 batches.
2025-01-19 18:51:10.364915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:10.36588 INFO::Using default BPPARAM
2025-01-19 18:51:10.366325 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:10.367147 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:10.412284 INFO::Done
2025-01-19 18:51:10.412947 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:10.415932 INFO::ASW Batch was -0.00750509658050562 prior to batch effect correction and is now -0.0945467605635573 .
2025-01-19 18:51:10.416683 INFO::Total function execution time is 0.0965933799743652 s and adjustment time is 0.0479204654693604 s ( 49.61 )
2025-01-19 18:51:10.431775 INFO::Formatting Data.
2025-01-19 18:51:10.43238 INFO::Recognized SummarizedExperiment
2025-01-19 18:51:10.432817 INFO::Typecasting input to dataframe.
2025-01-19 18:51:10.440513 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:10.441479 INFO::Removing potential empty rows and columns
2025-01-19 18:51:10.444379 INFO::Found 0 missing values.
2025-01-19 18:51:10.450124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:10.450629 INFO::Done
2025-01-19 18:51:10.451071 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:10.453971 INFO::Starting hierarchical adjustment
2025-01-19 18:51:10.454563 INFO::Found 2 batches.
2025-01-19 18:51:10.455008 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:10.455486 INFO::Using default BPPARAM
2025-01-19 18:51:10.455915 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:10.456718 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:10.476773 INFO::Done
2025-01-19 18:51:10.477368 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:10.480286 INFO::ASW Batch was 0.00586165041117202 prior to batch effect correction and is now 0.00586165041117202 .
2025-01-19 18:51:10.481002 INFO::Total function execution time is 0.0492191314697266 s and adjustment time is 0.0223174095153809 s ( 45.34 )
2025-01-19 18:51:10.496267 INFO::Formatting Data.
2025-01-19 18:51:10.496949 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:10.497681 INFO::Removing potential empty rows and columns
2025-01-19 18:51:10.498528 INFO::Found 0 missing values.
2025-01-19 18:51:10.500919 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:10.501354 INFO::Done
2025-01-19 18:51:10.501762 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:10.503437 INFO::Starting hierarchical adjustment
2025-01-19 18:51:10.504048 INFO::Found 3 batches.
2025-01-19 18:51:10.504496 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:10.504985 INFO::Using default BPPARAM
2025-01-19 18:51:10.5054 INFO::Processing subtree level 1
2025-01-19 18:51:10.650748 INFO::Adjusting the last 1 batches sequentially
2025-01-19 18:51:10.652819 INFO::Done
2025-01-19 18:51:10.653629 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:10.656463 INFO::ASW Batch was -0.101500884700806 prior to batch effect correction and is now -0.161874495409491 .
2025-01-19 18:51:10.657565 INFO::Total function execution time is 0.161280870437622 s and adjustment time is 0.148799896240234 s ( 92.26 )
2025-01-19 18:51:10.67211 INFO::Skipping initial DF formatting
2025-01-19 18:51:10.672743 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:10.676436 INFO::Starting hierarchical adjustment
2025-01-19 18:51:10.67714 INFO::Found 5 batches.
2025-01-19 18:51:10.677653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:10.678236 INFO::Using default BPPARAM
2025-01-19 18:51:10.678718 INFO::Processing subtree level 1
2025-01-19 18:51:10.805986 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:10.80758 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:10.826048 INFO::Done
2025-01-19 18:51:10.826688 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:10.830498 INFO::ASW Batch was 0.559723025045438 prior to batch effect correction and is now 0.559723025045438 .
2025-01-19 18:51:10.831067 INFO::ASW Label was 0.328981946690733 prior to batch effect correction and is now 0.328981946690733 .
2025-01-19 18:51:10.831828 INFO::Total function execution time is 0.159776449203491 s and adjustment time is 0.149034976959229 s ( 93.28 )
2025-01-19 18:51:10.847443 INFO::Formatting Data.
2025-01-19 18:51:10.848129 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:10.848939 INFO::Removing potential empty rows and columns
2025-01-19 18:51:10.849847 INFO::Found 0 missing values.
2025-01-19 18:51:10.85344 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:10.85394 INFO::Done
2025-01-19 18:51:10.854392 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:10.857051 INFO::Starting hierarchical adjustment
2025-01-19 18:51:10.857685 INFO::Found 5 batches.
2025-01-19 18:51:10.858167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:10.858695 INFO::Using default BPPARAM
2025-01-19 18:51:10.859181 INFO::Processing subtree level 1
2025-01-19 18:51:10.968509 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:10.970036 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:10.984777 INFO::Done
2025-01-19 18:51:10.985426 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:10.988414 INFO::ASW Batch was 0.350406178271061 prior to batch effect correction and is now -0.0866246966388827 .
2025-01-19 18:51:10.988979 INFO::ASW Label was 0.173184064563283 prior to batch effect correction and is now 0.83433136613157 .
2025-01-19 18:51:10.989753 INFO::Total function execution time is 0.142346858978271 s and adjustment time is 0.127203941345215 s ( 89.36 )
2025-01-19 18:51:10.990561 INFO::Formatting Data.
2025-01-19 18:51:10.991179 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:10.992014 INFO::Removing potential empty rows and columns
2025-01-19 18:51:10.992955 INFO::Found 0 missing values.
2025-01-19 18:51:10.996827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:10.99733 INFO::Done
2025-01-19 18:51:10.997811 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.000649 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.001348 INFO::Found 5 batches.
2025-01-19 18:51:11.001841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.002415 INFO::Using default BPPARAM
2025-01-19 18:51:11.002946 INFO::Processing subtree level 1
2025-01-19 18:51:11.113796 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:11.115299 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:11.129904 INFO::Done
2025-01-19 18:51:11.130549 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:11.133503 INFO::ASW Batch was 0.350406178271061 prior to batch effect correction and is now -0.0866246966388827 .
2025-01-19 18:51:11.134064 INFO::ASW Label was 0.173184064563283 prior to batch effect correction and is now 0.83433136613157 .
2025-01-19 18:51:11.134837 INFO::Total function execution time is 0.144266843795776 s and adjustment time is 0.128679513931274 s ( 89.2 )
2025-01-19 18:51:11.147633 INFO::Formatting Data.
2025-01-19 18:51:11.14836 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:11.149244 INFO::Removing potential empty rows and columns
2025-01-19 18:51:11.150216 INFO::Found 0 missing values.
2025-01-19 18:51:11.154183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:11.154692 INFO::Done
2025-01-19 18:51:11.155206 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.157975 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.158649 INFO::Found 5 batches.
2025-01-19 18:51:11.159158 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.159746 INFO::Using default BPPARAM
2025-01-19 18:51:11.160244 INFO::Processing subtree level 1
2025-01-19 18:51:11.321258 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:11.322792 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:11.33778 INFO::Done
2025-01-19 18:51:11.338505 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:11.341605 INFO::ASW Batch was 0.281412233408164 prior to batch effect correction and is now 0.00725437838367921 .
2025-01-19 18:51:11.342188 INFO::ASW Label was 0.501799633697616 prior to batch effect correction and is now 0.778776196237632 .
2025-01-19 18:51:11.342972 INFO::Total function execution time is 0.195403814315796 s and adjustment time is 0.179237127304077 s ( 91.73 )
2025-01-19 18:51:11.343765 INFO::Formatting Data.
2025-01-19 18:51:11.344367 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:11.345237 INFO::Removing potential empty rows and columns
2025-01-19 18:51:11.346186 INFO::Found 0 missing values.
2025-01-19 18:51:11.350229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:11.367719 INFO::Done
2025-01-19 18:51:11.368919 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.37175 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.372426 INFO::Found 5 batches.
2025-01-19 18:51:11.372921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.373456 INFO::Using default BPPARAM
2025-01-19 18:51:11.373935 INFO::Processing subtree level 1
2025-01-19 18:51:11.497336 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:11.499102 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:11.514662 INFO::Done
2025-01-19 18:51:11.515322 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:11.518505 INFO::ASW Batch was 0.281412233408164 prior to batch effect correction and is now 0.00725437838367921 .
2025-01-19 18:51:11.519089 INFO::ASW Label was 0.501799633697616 prior to batch effect correction and is now 0.778776196237632 .
2025-01-19 18:51:11.519849 INFO::Total function execution time is 0.17607855796814 s and adjustment time is 0.142361402511597 s ( 80.85 )
2025-01-19 18:51:11.533014 INFO::Formatting Data.
2025-01-19 18:51:11.533685 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:11.534539 INFO::Removing potential empty rows and columns
2025-01-19 18:51:11.535612 INFO::Found 0 missing values.
2025-01-19 18:51:11.538372 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:11.538882 INFO::Done
2025-01-19 18:51:11.539355 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.542235 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.542904 INFO::Found 2 batches.
2025-01-19 18:51:11.543396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.543968 INFO::Using default BPPARAM
2025-01-19 18:51:11.544538 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:11.545402 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:11.559648 INFO::Done
2025-01-19 18:51:11.560236 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:11.56308 INFO::ASW Batch was 0.571664238801364 prior to batch effect correction and is now -0.0336089106700677 .
2025-01-19 18:51:11.563613 INFO::ASW Label was 0.415154860791407 prior to batch effect correction and is now 0.876799429260889 .
2025-01-19 18:51:11.564363 INFO::Total function execution time is 0.0314047336578369 s and adjustment time is 0.016871452331543 s ( 53.72 )
2025-01-19 18:51:11.565094 INFO::Formatting Data.
2025-01-19 18:51:11.565675 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:11.566503 INFO::Removing potential empty rows and columns
2025-01-19 18:51:11.567453 INFO::Found 0 missing values.
2025-01-19 18:51:11.570059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:11.570601 INFO::Done
2025-01-19 18:51:11.571103 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.573842 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.574505 INFO::Found 2 batches.
2025-01-19 18:51:11.575003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.57559 INFO::Using default BPPARAM
2025-01-19 18:51:11.576101 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:11.576939 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:11.590729 INFO::Done
2025-01-19 18:51:11.591322 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:11.594119 INFO::ASW Batch was 0.571664238801364 prior to batch effect correction and is now -0.0336089106700677 .
2025-01-19 18:51:11.594652 INFO::ASW Label was 0.415154860791407 prior to batch effect correction and is now 0.876799429260889 .
2025-01-19 18:51:11.595377 INFO::Total function execution time is 0.030282735824585 s and adjustment time is 0.016359806060791 s ( 54.02 )
2025-01-19 18:51:11.606538 INFO::Formatting Data.
2025-01-19 18:51:11.607311 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:11.608176 INFO::Removing potential empty rows and columns
2025-01-19 18:51:11.609089 INFO::Found 0 missing values.
2025-01-19 18:51:11.611278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:11.611768 INFO::Done
2025-01-19 18:51:11.61227 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.614206 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.614894 INFO::Found 2 batches.
2025-01-19 18:51:11.615386 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.615931 INFO::Using default BPPARAM
2025-01-19 18:51:11.616395 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:11.617219 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:11.647459 INFO::Done
2025-01-19 18:51:11.648135 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:11.650506 INFO::ASW Batch was 0.238237453666122 prior to batch effect correction and is now -0.12357027593314 .
2025-01-19 18:51:11.651368 INFO::Total function execution time is 0.0449209213256836 s and adjustment time is 0.0327033996582031 s ( 72.8 )
2025-01-19 18:51:11.663061 INFO::Formatting Data.
2025-01-19 18:51:11.663749 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:11.66465 INFO::Removing potential empty rows and columns
2025-01-19 18:51:11.665685 INFO::Found 0 missing values.
2025-01-19 18:51:11.66684 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.
2025-01-19 18:51:11.671183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:11.671706 INFO::Done
2025-01-19 18:51:11.672181 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.675086 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.675771 INFO::Found 2 batches.
2025-01-19 18:51:11.676264 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.676797 INFO::Using default BPPARAM
2025-01-19 18:51:11.677271 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:11.678173 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:11.69552 INFO::Done
2025-01-19 18:51:11.696259 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:11.699283 INFO::ASW Batch was 0.613177001805621 prior to batch effect correction and is now 0.17157483653527 .
2025-01-19 18:51:11.699881 INFO::ASW Label was 0.406219563672593 prior to batch effect correction and is now 0.684151988216948 .
2025-01-19 18:51:11.70065 INFO::Total function execution time is 0.037639856338501 s and adjustment time is 0.0198616981506348 s ( 52.77 )
2025-01-19 18:51:11.701493 INFO::Formatting Data.
2025-01-19 18:51:11.702167 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:11.703172 INFO::Removing potential empty rows and columns
2025-01-19 18:51:11.704147 INFO::Found 0 missing values.
2025-01-19 18:51:11.704997 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.
2025-01-19 18:51:11.709281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:11.709781 INFO::Done
2025-01-19 18:51:11.710266 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.71309 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.713774 INFO::Found 2 batches.
2025-01-19 18:51:11.714286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.714846 INFO::Using default BPPARAM
2025-01-19 18:51:11.71532 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:11.716163 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:11.731666 INFO::Done
2025-01-19 18:51:11.732278 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:11.735072 INFO::ASW Batch was 0.613177001805621 prior to batch effect correction and is now 0.17157483653527 .
2025-01-19 18:51:11.735593 INFO::ASW Label was 0.406219563672593 prior to batch effect correction and is now 0.684151988216948 .
2025-01-19 18:51:11.73633 INFO::Total function execution time is 0.0348570346832275 s and adjustment time is 0.0180275440216064 s ( 51.72 )
2025-01-19 18:51:11.924389 INFO::Formatting Data.
2025-01-19 18:51:11.925125 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:11.925946 INFO::Removing potential empty rows and columns
2025-01-19 18:51:11.926888 INFO::Found 0 missing values.
2025-01-19 18:51:11.929613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:11.930116 INFO::Done
2025-01-19 18:51:11.930574 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:11.932406 INFO::Starting hierarchical adjustment
2025-01-19 18:51:11.933049 INFO::Found 3 batches.
2025-01-19 18:51:11.933523 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:11.934089 INFO::Using default BPPARAM
2025-01-19 18:51:11.934566 INFO::Processing subtree level 1
2025-01-19 18:51:12.058686 INFO::Adjusting the last 1 batches sequentially
2025-01-19 18:51:12.060485 INFO::Done
2025-01-19 18:51:12.061117 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:12.063397 INFO::ASW Batch was -0.0964308687019499 prior to batch effect correction and is now -0.0964308687019499 .
2025-01-19 18:51:12.064306 INFO::Total function execution time is 0.139957189559937 s and adjustment time is 0.127541303634644 s ( 91.13 )
2025-01-19 18:51:12.065273 INFO::Formatting Data.
2025-01-19 18:51:12.065911 INFO::Typecasting input to dataframe.
2025-01-19 18:51:12.066608 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:12.067476 INFO::Removing potential empty rows and columns
2025-01-19 18:51:12.068502 INFO::Found 0 missing values.
2025-01-19 18:51:12.071395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:12.071925 INFO::Done
2025-01-19 18:51:12.072417 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:12.074404 INFO::Starting hierarchical adjustment
2025-01-19 18:51:12.07511 INFO::Found 3 batches.
2025-01-19 18:51:12.075656 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:12.076258 INFO::Using default BPPARAM
2025-01-19 18:51:12.07673 INFO::Processing subtree level 1
2025-01-19 18:51:12.201887 INFO::Adjusting the last 1 batches sequentially
2025-01-19 18:51:12.203561 INFO::Done
2025-01-19 18:51:12.204167 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:12.206415 INFO::ASW Batch was -0.0964308687019499 prior to batch effect correction and is now -0.0964308687019499 .
2025-01-19 18:51:12.207278 INFO::Total function execution time is 0.142004251480103 s and adjustment time is 0.128582239151001 s ( 90.55 )
2025-01-19 18:51:12.219275 INFO::Formatting Data.
2025-01-19 18:51:12.219988 INFO::Typecasting input to dataframe.
2025-01-19 18:51:12.220778 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:12.221658 INFO::Removing potential empty rows and columns
2025-01-19 18:51:12.222694 INFO::Found 0 missing values.
2025-01-19 18:51:12.225554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:12.226069 INFO::Done
2025-01-19 18:51:12.226553 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:12.228487 INFO::Starting hierarchical adjustment
2025-01-19 18:51:12.229164 INFO::Found 3 batches.
2025-01-19 18:51:12.229653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:12.230233 INFO::Using default BPPARAM
2025-01-19 18:51:12.230725 INFO::Processing subtree level 1
2025-01-19 18:51:12.349967 INFO::Adjusting the last 1 batches sequentially
2025-01-19 18:51:12.353516 INFO::Done
2025-01-19 18:51:12.35414 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:12.356428 INFO::ASW Batch was 0.0140387092233943 prior to batch effect correction and is now 0.0140387092233943 .
2025-01-19 18:51:12.357268 INFO::Total function execution time is 0.138055086135864 s and adjustment time is 0.124457359313965 s ( 90.15 )
2025-01-19 18:51:12.503878 INFO::Formatting Data.
2025-01-19 18:51:12.504634 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:12.505728 INFO::Removing potential empty rows and columns
2025-01-19 18:51:12.50844 INFO::Found 1000 missing values.
2025-01-19 18:51:12.526496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:12.52721 INFO::Done
2025-01-19 18:51:12.527713 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:12.532969 INFO::Starting hierarchical adjustment
2025-01-19 18:51:12.533737 INFO::Found 10 batches.
2025-01-19 18:51:12.534307 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:12.534858 INFO::Using default BPPARAM
2025-01-19 18:51:12.53534 INFO::Processing subtree level 1
2025-01-19 18:51:12.696532 INFO::Processing subtree level 2
2025-01-19 18:51:12.878494 INFO::Adjusting the last 1 batches sequentially
2025-01-19 18:51:12.880639 INFO::Done
2025-01-19 18:51:12.881293 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:12.886655 INFO::ASW Batch was 0.462979943324226 prior to batch effect correction and is now 0.462979943324226 .
2025-01-19 18:51:12.887257 INFO::ASW Label was 0.35352855512605 prior to batch effect correction and is now 0.35352855512605 .
2025-01-19 18:51:12.888133 INFO::Total function execution time is 0.384310483932495 s and adjustment time is 0.347037315368652 s ( 90.3 )
2025-01-19 18:51:12.888963 INFO::Formatting Data.
2025-01-19 18:51:12.889585 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:12.890928 INFO::Removing potential empty rows and columns
2025-01-19 18:51:12.893868 INFO::Found 1000 missing values.
2025-01-19 18:51:12.912552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:12.913288 INFO::Done
2025-01-19 18:51:12.913819 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:12.919191 INFO::Starting hierarchical adjustment
2025-01-19 18:51:12.919964 INFO::Found 10 batches.
2025-01-19 18:51:13.78626 INFO::Set up parallel execution backend with 2 workers
2025-01-19 18:51:13.787678 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-19 18:51:14.851906 INFO::Adjusting the last 2 batches sequentially
2025-01-19 18:51:14.853313 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-19 18:51:14.868388 INFO::Done
2025-01-19 18:51:14.868953 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:14.873186 INFO::ASW Batch was 0.462979943324226 prior to batch effect correction and is now 0.462979943324226 .
2025-01-19 18:51:14.873668 INFO::ASW Label was 0.35352855512605 prior to batch effect correction and is now 0.35352855512605 .
2025-01-19 18:51:14.874324 INFO::Total function execution time is 1.98541331291199 s and adjustment time is 1.94859933853149 s ( 98.15 )
2025-01-19 18:51:15.005415 INFO::Formatting Data.
2025-01-19 18:51:15.006088 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.006921 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.007883 INFO::Found 0 missing values.
2025-01-19 18:51:15.011222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.011699 INFO::Done
2025-01-19 18:51:15.01216 INFO::Acquiring quality metrics before batch effect correction.
2025-01-19 18:51:15.014588 INFO::Starting hierarchical adjustment
2025-01-19 18:51:15.01521 INFO::Found 3 batches.
2025-01-19 18:51:15.015728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-19 18:51:15.016281 INFO::Using default BPPARAM
2025-01-19 18:51:15.016757 INFO::Processing subtree level 1
2025-01-19 18:51:15.111689 INFO::Adjusting the last 1 batches sequentially
2025-01-19 18:51:15.113364 INFO::Done
2025-01-19 18:51:15.113945 INFO::Acquiring quality metrics after batch effect correction.
2025-01-19 18:51:15.116852 INFO::ASW Batch was 0.115159129728247 prior to batch effect correction and is now -0.14870967270095 .
2025-01-19 18:51:15.117388 INFO::ASW Label was -0.160596373938662 prior to batch effect correction and is now 0.0582707811882201 .
2025-01-19 18:51:15.118213 INFO::Total function execution time is 0.1128249168396 s and adjustment time is 0.0982553958892822 s ( 87.09 )
2025-01-19 18:51:15.221355 INFO::Formatting Data.
2025-01-19 18:51:15.222084 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.222884 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.223798 INFO::Found 2 missing values.
2025-01-19 18:51:15.226357 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.226828 INFO::Done
2025-01-19 18:51:15.253711 INFO::Found NA in Reference column
2025-01-19 18:51:15.26761 INFO::Require at least two references per batch.
2025-01-19 18:51:15.297567 INFO::Formatting Data.
2025-01-19 18:51:15.298561 INFO::Recognized SummarizedExperiment
2025-01-19 18:51:15.299347 INFO::Typecasting input to dataframe.
2025-01-19 18:51:15.313607 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.315341 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.320664 INFO::Found 0 missing values.
2025-01-19 18:51:15.331045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.33607 INFO::Done
2025-01-19 18:51:15.387884 INFO::Formatting Data.
2025-01-19 18:51:15.388892 INFO::Recognized SummarizedExperiment
2025-01-19 18:51:15.389647 INFO::Typecasting input to dataframe.
2025-01-19 18:51:15.433005 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.434735 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.440085 INFO::Found 0 missing values.
2025-01-19 18:51:15.456819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.457763 INFO::Done
2025-01-19 18:51:15.474174 INFO::Formatting Data.
2025-01-19 18:51:15.474844 INFO::Recognized SummarizedExperiment
2025-01-19 18:51:15.475315 INFO::Typecasting input to dataframe.
2025-01-19 18:51:15.491262 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.492209 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.4932 INFO::Found 0 missing values.
2025-01-19 18:51:15.494047 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.
2025-01-19 18:51:15.498155 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.498647 INFO::Done
2025-01-19 18:51:15.508079 INFO::Formatting Data.
2025-01-19 18:51:15.508756 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.509569 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.51049 INFO::Found 0 missing values.
2025-01-19 18:51:15.513636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.514185 INFO::Done
2025-01-19 18:51:15.530251 INFO::Formatting Data.
2025-01-19 18:51:15.531134 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.532064 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.533052 INFO::Found 0 missing values.
2025-01-19 18:51:15.535776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.536295 INFO::Done
2025-01-19 18:51:15.563635 INFO::Formatting Data.
2025-01-19 18:51:15.564393 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.565506 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.566667 INFO::Found 1 missing values.
2025-01-19 18:51:15.569304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.569782 INFO::Done
2025-01-19 18:51:15.586828 INFO::Formatting Data.
2025-01-19 18:51:15.58755 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.588345 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.589258 INFO::Found 2 missing values.
2025-01-19 18:51:15.590127 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.
2025-01-19 18:51:15.592306 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.592784 INFO::Done
2025-01-19 18:51:15.602104 INFO::Formatting Data.
2025-01-19 18:51:15.602746 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.603545 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.604426 INFO::Found 2 missing values.
2025-01-19 18:51:15.605971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.606437 INFO::Done
2025-01-19 18:51:15.616151 INFO::Formatting Data.
2025-01-19 18:51:15.616796 INFO::Typecasting input to dataframe.
2025-01-19 18:51:15.617606 INFO::Replacing NaNs with NAs.
2025-01-19 18:51:15.61852 INFO::Removing potential empty rows and columns
2025-01-19 18:51:15.61948 INFO::Found 0 missing values.
2025-01-19 18:51:15.622348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-19 18:51:15.622825 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.177 3.165 19.098
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.864 | 1.807 | 18.373 | |
| compute_asw | 0.027 | 0.000 | 0.026 | |
| count_existing | 0.015 | 0.000 | 0.015 | |
| generate_data_covariables | 0.013 | 0.001 | 0.013 | |
| generate_dataset | 0.011 | 0.002 | 0.012 | |